From 1a6be557010bcf55d1c6d2e38ab1f8b5efe7303b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:01 +0200 Subject: [PATCH 0001/1394] gnu: jc: Update to 1.19.0. * gnu/packages/admin.scm (jc): Update to 1.19.0. [arguments]: Add a new 'hack-time-zone phase. --- gnu/packages/admin.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index d22753c64fe..af75dee6975 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4541,7 +4541,7 @@ supplied by the user when logging in.") (define-public jc (package (name "jc") - (version "1.13.4") + (version "1.19.0") (source (origin ;; The PyPI tarball lacks the test suite. @@ -4551,8 +4551,16 @@ supplied by the user when logging in.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0rwvyyrdnw43pixp8h51rncq2inc9pbbj1j2191y5si00pjw34zr")))) + (base32 "021zk0y8kb6v3qf3hwfg8qjzzmrca039nz3fjywiy2njmbhr8hyi")))) (build-system python-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + ;; XXX Guix's America/Los_Angeles time zone is somehow broken. + (add-before 'check 'hack-time-zone + (lambda _ + (substitute* (find-files "tests" "^test.*\\.py$") + (("America/Los_Angeles") "PST8PDT"))))))) (propagated-inputs (list python-pygments python-ruamel.yaml python-xmltodict)) (home-page "https://github.com/kellyjonbrazil/jc") From c5d68c6d12e691bceba60bc9537ea499bb50273d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Erik=20=C5=A0abi=C4=8D?= Date: Sat, 21 May 2022 12:01:17 +0200 Subject: [PATCH 0002/1394] gnu: emacs-list-utils: Update to 0.4.6-1.0dec8c0. * gnu/packages/emacs-xyz.scm (emacs-list-utils): Update to 0.4.6-1.0dec8c0. [arguments]: Remove the upstreamed 'patch-require-cl phase. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/emacs-xyz.scm | 46 +++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 25 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 173071102ea..977debae518 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -18731,31 +18731,27 @@ and @code{erc-send-modify-hook} to download and show images.") (license license:gpl3+))) (define-public emacs-list-utils - (package - (name "emacs-list-utils") - (version "0.4.6") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/rolandwalker/list-utils") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "07hbz2md52ccy95gv4d5n6szrfmpfqf3w4kwqdg2cf54c7kgf7hw")))) - (build-system emacs-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-require-cl - (lambda _ - (substitute* "list-utils.el" - (("\\(require 'cl\\)") "(require 'cl-lib)")) - #t))))) - (home-page "https://github.com/rolandwalker/list-utils") - (synopsis "List-manipulation utility functions") - (description "This package provides a list manipulation library for Emacs.") - (license license:gpl3+))) + ;; Use a git snapshot until upstream fixes the build with emacs 28.1. + ;; See . + (let ((commit "0dec8c02962d2591766739e37c5714ba21133093") (revision "1")) + (package + (name "emacs-list-utils") + (version (git-version "0.4.6" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rolandwalker/list-utils") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "11nm8649a131bn2kwj4fxkiijdx2d4f1byx7a985zlb3bzdwnaw8")))) + (build-system emacs-build-system) + (home-page "https://github.com/rolandwalker/list-utils") + (synopsis "List-manipulation utility functions") + (description + "This package provides a list manipulation library for Emacs.") + (license license:gpl3+)))) (define-public emacs-parsec (package From 6e184232daf27a39a5978f72260c12c582aaf138 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:01 +0200 Subject: [PATCH 0003/1394] gnu: python-astroquery: Update to 0.4.6. * gnu/packages/astronomy.scm (python-astroquery): Update to 0.4.6. --- gnu/packages/astronomy.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index c209b1538f7..336c5440a93 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 John Darrington -;;; Copyright © 2018–2021 Tobias Geerinckx-Rice +;;; Copyright © 2018–2022 Tobias Geerinckx-Rice ;;; Copyright © 2018, 2019, 2020, 2021, 2022 Efraim Flashner ;;; Copyright © 2019 by Amar Singh ;;; Copyright © 2020 R Veera Kumar @@ -748,13 +748,13 @@ astronomy and astrophysics.") (define-public python-astroquery (package (name "python-astroquery") - (version "0.4.5") + (version "0.4.6") (source (origin (method url-fetch) (uri (pypi-uri "astroquery" version)) (sha256 - (base32 "06xy0qzqmps6z5vwfkh5fkhr151p7g94r2j0mvp1rc8zns22y010")))) + (base32 "1vhkzsqlgn3ji5by2rdf2gwklhbyzvpzb1iglalhqjkkrdaaaz1h")))) (build-system python-build-system) (arguments `(#:phases From 0a468697dd76b9d05016e3d36726086aa8bc0bc1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:01 +0200 Subject: [PATCH 0004/1394] gnu: python-fitsio: Update to 1.1.7. * gnu/packages/astronomy.scm (python-fitsio): Update to 1.1.7. [arguments]: Don't explicitly return #t from phases. --- gnu/packages/astronomy.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 336c5440a93..4e58e65c2ef 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -107,21 +107,20 @@ in FITS files.") (define-public python-fitsio (package (name "python-fitsio") - (version "1.1.5") + (version "1.1.7") (source (origin (method url-fetch) (uri (pypi-uri "fitsio" version)) (sha256 - (base32 "1llql2i6xr9lkdl81jx5nvz80kspamvira90546y32ldy551hq1l")) + (base32 "0q8siijys9kmjnqvyipjgh6hkhf4fwvr1swhsf4if211i9b0m1xy")) (modules '((guix build utils))) (snippet ;; Remove the bundled cfitsio `(begin (delete-file-recursively "cfitsio3490") (substitute* "MANIFEST.in" - (("recursive-include cfitsio3490.*$\n") "")) - #t)))) + (("recursive-include cfitsio3490.*$\n") "")))))) (build-system python-build-system) (arguments `(#:phases From 33da08497753ea47e0c3e2117d7f5522ea3aabde Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:01 +0200 Subject: [PATCH 0005/1394] gnu: python-jplephem: Update to 2.17. * gnu/packages/astronomy.scm (python-jplephem): Update to 2.17. --- gnu/packages/astronomy.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 4e58e65c2ef..cd0949b04f6 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1365,13 +1365,13 @@ Moon position, etc.") (define-public python-jplephem (package (name "python-jplephem") - (version "2.16") + (version "2.17") (source (origin (method url-fetch) (uri (pypi-uri "jplephem" version)) (sha256 - (base32 "1xvivnsywjaf5lxn3kyg2jhhq393gcwkjrl634m8dn52ypidrcdb")))) + (base32 "09xaibxnwbzzs3x9g3ibqa2la17z3r6in93321glh02dbibfbip1")))) (build-system python-build-system) (arguments `(#:phases From b4caea953aaf1d79166b9ebb8e0badc6c4877f90 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:01 +0200 Subject: [PATCH 0006/1394] gnu: python-aiounittest: Update to 1.4.1. * gnu/packages/check.scm (python-aiounittest): Update to 1.4.1. --- gnu/packages/check.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 8c161a4a4f7..8df5d874765 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -16,7 +16,7 @@ ;;; Copyright © 2016 Troy Sankey ;;; Copyright © 2016 Lukas Gradl ;;; Copyright © 2016 Hartmut Goebel -;;; Copyright © 2016–2021 Tobias Geerinckx-Rice +;;; Copyright © 2016–2022 Tobias Geerinckx-Rice ;;; Copyright © 2017 Julien Lepiller ;;; Copyright © 2017 Thomas Danckaert ;;; Copyright © 2017, 2018 Arun Isaac @@ -3314,7 +3314,7 @@ system. The code under test requires no modification to work with pyfakefs.") (define-public python-aiounittest (package (name "python-aiounittest") - (version "1.4.0") + (version "1.4.1") ;; Pypi package lacks tests. (source (origin (method git-fetch) @@ -3324,7 +3324,7 @@ system. The code under test requires no modification to work with pyfakefs.") (file-name (git-file-name name version)) (sha256 (base32 - "0hql5mw62lclrpblbh7xvinwjfcdcfvhhlvl7xlq2hi9isjq1c8r")))) + "10x7ds09b9415r92f7g9714gxixvvq3bm5mnh29ml9aba8blcb0n")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases From 00b6a808b7bf2f5d5d3b6b299ee0d14ff0f09057 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:06 +0200 Subject: [PATCH 0007/1394] gnu: guile-xcb: Always use the input Guile's effective version. * gnu/packages/guile-wm.scm (guile-xcb)[arguments]: Replace hard-coded version number with that of the "guile" input. --- gnu/packages/guile-wm.scm | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/gnu/packages/guile-wm.scm b/gnu/packages/guile-wm.scm index 911cda89685..63a5b2ce225 100644 --- a/gnu/packages/guile-wm.scm +++ b/gnu/packages/guile-wm.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2017, 2019 Ricardo Wurmus ;;; Copyright © 2017 Nikita ;;; Copyright © 2019 Pierre-Moana Levesque +;;; Copyright © 2022 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,7 +31,8 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) - #:use-module (guix build-system gnu)) + #:use-module (guix build-system gnu) + #:use-module (guix utils)) (define-public guile-xcb (let ((commit "db7d5a393cc37a56f66541b3f33938b40c6f35b3") @@ -48,16 +50,17 @@ (base32 "16w4vgzbmnwih4bgfn8rw85ryfvzhc6hyly6bic9sd7hhc82rcnd")))) (build-system gnu-build-system) - (arguments '(;; Parallel builds fail. - #:parallel-build? #f - #:configure-flags (list (string-append - "--with-guile-site-dir=" - (assoc-ref %outputs "out") - "/share/guile/site/2.2") - (string-append - "--with-guile-site-ccache-dir=" - (assoc-ref %outputs "out") - "/lib/guile/2.2/site-ccache")))) + (arguments + `( ;; Parallel builds fail. + #:parallel-build? #f + #:configure-flags + (let ((out (assoc-ref %outputs "out")) + (effective ,(version-major+minor + (package-version (this-package-input "guile"))))) + (list (string-append "--with-guile-site-dir=" out + "/share/guile/site/" effective) + (string-append "--with-guile-site-ccache-dir=" out + "/lib/guile/" effective "/site-ccache"))))) (native-inputs (list guile-2.2 pkg-config texinfo)) (inputs `(("guile" ,guile-2.2) ("xcb" ,xcb-proto))) From 53762a1bfd49ac6434befd1d0bea02e833c64319 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:03 +0200 Subject: [PATCH 0008/1394] gnu: guile-xcb: Remove input labels. * gnu/packages/guile-wm.scm (guile-xcb)[inputs]: Remove input labels. --- gnu/packages/guile-wm.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/guile-wm.scm b/gnu/packages/guile-wm.scm index 63a5b2ce225..fd7a722a287 100644 --- a/gnu/packages/guile-wm.scm +++ b/gnu/packages/guile-wm.scm @@ -62,8 +62,7 @@ (string-append "--with-guile-site-ccache-dir=" out "/lib/guile/" effective "/site-ccache"))))) (native-inputs (list guile-2.2 pkg-config texinfo)) - (inputs `(("guile" ,guile-2.2) - ("xcb" ,xcb-proto))) + (inputs (list guile-2.2 xcb-proto)) (home-page "https://github.com/mwitmer/guile-xcb") (synopsis "XCB bindings for Guile") (description From 83a760dd58fe975fc32b94161ae076a726e8b9a0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:03 +0200 Subject: [PATCH 0009/1394] gnu: guile-wm: Always use the input Guile's effective version. * gnu/packages/guile-wm.scm (guile-wm)[arguments]: Replace hard-coded version number with that of the "guile" input. --- gnu/packages/guile-wm.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/gnu/packages/guile-wm.scm b/gnu/packages/guile-wm.scm index fd7a722a287..2487f89f979 100644 --- a/gnu/packages/guile-wm.scm +++ b/gnu/packages/guile-wm.scm @@ -95,14 +95,17 @@ dependencies.") (ice-9 popen)) ;; The '.scm' files go to $(datadir), so set that to the ;; standard value. - #:configure-flags (list (string-append "--datadir=" - (assoc-ref %outputs "out") - "/share/guile/site/2.2")) + #:configure-flags + (let ((out (assoc-ref %outputs "out")) + (effective ,(version-major+minor + (package-version (this-package-input "guile"))))) + (list (string-append "--datadir=" out + "/share/guile/site/" effective))) #:phases (modify-phases %standard-phases (add-before 'configure 'set-module-directory (lambda* (#:key outputs #:allow-other-keys) - ;; Install .scm files to $out/share/guile/site/2.2. + ;; Install .scm files to $out/share/guile/site/x.y. (let ((out (assoc-ref outputs "out")) (effective (read-line (open-pipe* OPEN_READ From 9744b3b244f8f95d8b8254d2cbae69e09cdbb714 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:00 +0200 Subject: [PATCH 0010/1394] gnu: guile-wm: Remove trailing #t from phases. * gnu/packages/guile-wm.scm (guile-wm)[arguments]: Don't explicitly return #t. --- gnu/packages/guile-wm.scm | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/gnu/packages/guile-wm.scm b/gnu/packages/guile-wm.scm index 2487f89f979..ff885506fa3 100644 --- a/gnu/packages/guile-wm.scm +++ b/gnu/packages/guile-wm.scm @@ -115,8 +115,7 @@ dependencies.") (("^wmdir = .*$") (string-append "wmdir = " out "/share/guile/site/" - effective "\n")))) - #t)) + effective "\n")))))) (add-after 'install 'set-load-path (lambda* (#:key inputs outputs #:allow-other-keys) ;; Put Guile-XCB's and Guile-WM's modules in the @@ -136,8 +135,7 @@ dependencies.") (,mods ,(string-append xcb "/share/guile/site/" effective))) `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,gos ,(string-append xcb "/lib/guile/" - effective "/site-ccache"))))) - #t)) + effective "/site-ccache"))))))) (add-after 'install 'install-go-files (lambda* (#:key outputs inputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -158,8 +156,7 @@ dependencies.") (go (string-append object-dir base ".go"))) (invoke "guild" "compile" "-L" module-dir file "-o" go))) - (find-files module-dir "\\.scm$")) - #t))) + (find-files module-dir "\\.scm$"))))) (add-after 'install 'install-xsession (lambda* (#:key outputs #:allow-other-keys) ;; add a .desktop file to xsessions @@ -175,8 +172,7 @@ dependencies.") Comment=~a~@ Exec=~a/bin/guile-wm~@ Type=Application~%" - ,name ,synopsis %output)))) - #t))))) + ,name ,synopsis %output))))))))) (native-inputs (list guile-2.2 guile-xcb pkg-config texinfo)) (inputs (list guile-2.2 guile-xcb)) (home-page "https://github.com/mwitmer/guile-wm/releases") From bdb60a8e7919e835d555bd17e87edcd4fd73d368 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:02 +0200 Subject: [PATCH 0011/1394] gnu: libcbor: Update to 0.9.0. * gnu/packages/compression.scm (libcbor): Update to 0.9.0. --- gnu/packages/compression.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 449d3e34bbb..26c4ff43780 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -2715,7 +2715,7 @@ can append files to the end of such compressed archives.") (define-public libcbor (package (name "libcbor") - (version "0.8.0") + (version "0.9.0") (source (origin (method git-fetch) @@ -2723,7 +2723,7 @@ can append files to the end of such compressed archives.") (url "https://github.com/PJK/libcbor") (commit (string-append "v" version)))) (file-name (git-file-name name version)) - (sha256 (base32 "01dv4vxcmbvpphqy16vqiwh25wx11x630js5wfnx7cryarsh9ld7")))) + (sha256 (base32 "1n9fx5i81wr9j18bhz74wclfkwqf1k3piq6lzngvkmq04krzi7ss")))) (build-system cmake-build-system) (arguments '(#:configure-flags From 03216987c992a081b071641cfa45a283e7682bb5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:00 +0200 Subject: [PATCH 0012/1394] gnu: libcbor: Mark up description. * gnu/packages/compression.scm (libcbor)[description]: Use @acronym{}. --- gnu/packages/compression.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 26c4ff43780..a70c6c42161 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -2737,8 +2737,8 @@ can append files to the end of such compressed archives.") (string-append "-DCMAKE_INSTALL_RPATH=" lib))))) (synopsis "The C library for parsing and generating CBOR") (description - "The Concise Binary Object Representation (CBOR) is a data format whose -design goals include the possibility of extremely small code size, fairly + "@acronym{CBOR, The Concise Binary Object Representation} is a data format +whose design goals include the possibility of extremely small code size, fairly small message size, and extensibility without the need for version negotiation. These design goals make it different from earlier binary serializations such as ASN.1 and MessagePack.") From 97e7fbe9580b663b828dd2fe7bc7e9cb4fd31f86 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:02 +0200 Subject: [PATCH 0013/1394] gnu: lxc: Update to 4.0.12. * gnu/packages/virtualization.scm (lxc): Update to 4.0.12. --- gnu/packages/virtualization.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 750b08f6510..60dc0e75889 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -1096,7 +1096,7 @@ all common programming languages. Vala bindings are also provided.") (define-public lxc (package (name "lxc") - (version "4.0.11") + (version "4.0.12") (source (origin (method url-fetch) (uri (string-append @@ -1104,7 +1104,7 @@ all common programming languages. Vala bindings are also provided.") version ".tar.gz")) (sha256 (base32 - "0b7hv4n8b3lndhr0jf9j1gkbzxm8897a1myjsfgwzad9gkhq395g")))) + "1vyk2j5w9gfyh23w3ar09cycyws16mxh3clbb33yhqzwcs1jy96v")))) (build-system gnu-build-system) (native-inputs (list pkg-config docbook2x)) From 0b535a400fcc36fdae964e79d0ddf499057368b8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:01 +0200 Subject: [PATCH 0014/1394] gnu: jumpapp: Update to 1.2. * gnu/packages/xdisorg.scm (jumpapp): Update to 1.2. [arguments]: Don't explicitly return #t from phases. --- gnu/packages/xdisorg.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 08f4780fc27..e5a98edb355 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -2961,7 +2961,7 @@ This package is the fork of hsetroot by Hyriand.") (define-public jumpapp (package (name "jumpapp") - (version "1.1") + (version "1.2") (source (origin (method git-fetch) @@ -2970,7 +2970,7 @@ This package is the fork of hsetroot by Hyriand.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1jrk4mm42sz6ca2gkb6w3dad53d4im4shpgsq8s4vr6xpl3b43ry")))) + (base32 "05shgw4agkhgk5vbvc05s12q7m0djc0m4qrd328hmis37bxp9j7n")))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -2981,8 +2981,7 @@ This package is the fork of hsetroot by Hyriand.") (let ((out (assoc-ref outputs "out"))) (substitute* "Makefile" (("PREFIX =.*") - (string-append "PREFIX = " out "\n"))) - #true)))))) + (string-append "PREFIX = " out "\n"))))))))) (propagated-inputs (list wmctrl xdotool xprop)) (native-inputs From 6068b83b82475566acd4162467bcf54270f338f9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:02 +0200 Subject: [PATCH 0015/1394] gnu: java-jdom: Update to 2.0.6.1 [fixes CVE-2021-33813]. * gnu/packages/xml.scm (java-jdom): Update to 2.0.6.1. --- gnu/packages/xml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 11b0a4ef54e..ecc19a7eb84 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -2238,7 +2238,7 @@ implements @code{XMLStreamWriter} and @code{XMLStreamReader} and supports (define-public java-jdom2 (package (name "java-jdom") - (version "2.0.6") + (version "2.0.6.1") (source (origin (method git-fetch) (uri (git-reference @@ -2247,7 +2247,7 @@ implements @code{XMLStreamWriter} and @code{XMLStreamReader} and supports (file-name (git-file-name name version)) (sha256 (base32 - "14vv1kxrsdvwi4cz3rx6r48w5y6fvk9cymil8qhvxwp56xxrgxiq")))) + "1r4pwl0z7hm45v9l2wbq3fjmqi13zmwzbrggyqizrwv31kghhx56")))) (build-system ant-build-system) (arguments `(#:build-target "package" From d37c7f7ad4134cc15d1558eb6c0bc4c59a0db1af Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Fri, 27 May 2022 00:12:37 +0200 Subject: [PATCH 0016/1394] gnu: emacs-deferred: Fix wrong number of arguments. * gnu/packages/patches/emacs-deferred-fix-number-of-arguments.patch: New file. * gnu/packages/emacs-xyz.scm (emacs-deferred)[patches]: Use it here. * gnu/local.mk (dist_patch_DATA): Add it here. --- gnu/local.mk | 1 + gnu/packages/emacs-xyz.scm | 4 +- ...acs-deferred-fix-number-of-arguments.patch | 58 +++++++++++++++++++ 3 files changed, 62 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/emacs-deferred-fix-number-of-arguments.patch diff --git a/gnu/local.mk b/gnu/local.mk index a4250248cad..bc82c5ba9f2 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1023,6 +1023,7 @@ dist_patch_DATA = \ %D%/packages/patches/elm-offline-package-registry.patch \ %D%/packages/patches/elm-reactor-static-files.patch \ %D%/packages/patches/elogind-revert-polkit-detection.patch \ + %D%/packages/patches/emacs-deferred-fix-number-of-arguments.patch \ %D%/packages/patches/emacs-exec-path.patch \ %D%/packages/patches/emacs-ess-fix-obsolete-function-alias.patch \ %D%/packages/patches/emacs-git-email-missing-parens.patch \ diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 977debae518..f7fb6aac35d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6552,7 +6552,9 @@ framework for Emacs Lisp to be used with @code{ert}.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0xy9zb6wwkgwhcxdnslqk52bq3z24chgk6prqi4ks0qcf2bwyh5h")))) + (base32 "0xy9zb6wwkgwhcxdnslqk52bq3z24chgk6prqi4ks0qcf2bwyh5h")) + (patches + (search-patches "emacs-deferred-fix-number-of-arguments.patch")))) (build-system emacs-build-system) (arguments `(#:phases diff --git a/gnu/packages/patches/emacs-deferred-fix-number-of-arguments.patch b/gnu/packages/patches/emacs-deferred-fix-number-of-arguments.patch new file mode 100644 index 00000000000..fdb444c29b3 --- /dev/null +++ b/gnu/packages/patches/emacs-deferred-fix-number-of-arguments.patch @@ -0,0 +1,58 @@ +From 226734f06196d31971d8ca2026a9ce432d5227d0 Mon Sep 17 00:00:00 2001 +From: r0man +Date: Thu, 26 May 2022 10:42:25 +0200 +Subject: [PATCH] Fix wrong-number-of-arguments error + +With Emacs 28 I'm seeing the following error when running the tests. + +``` +deferred error : (wrong-number-of-arguments # 4) +``` + +I believe this is because the `start-process-shell-command` function +is called with the command arguments as &rest parameters. This is the +function signature of `start-process-shell-command`, and it only takes +3 arguments, the name, buffer, and command. The command argument can +be a shell string like "ls -l" for example. + +``` +(defun start-process-shell-command (name buffer command) ...) +``` + +The `start-process` function on the other hand has &rest parameters +and can be called with a list of arguments. + +``` +(defun start-process (name buffer program &rest program-args) ...) +``` + +This PR fixes the issue by concatenating the command and it's argument +before calling out to `deferred:process-buffer-gen`, which is used in +both cases, when calling `start-process-shell-command`, and when +calling `start-process`. +--- + deferred.el | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/deferred.el b/deferred.el +index 041c90b..3092ac0 100644 +--- a/deferred.el ++++ b/deferred.el +@@ -754,7 +754,7 @@ object. The process name and buffer name of the argument of the + `start-process-shell-command' are generated by this function automatically. + The next deferred object receives stdout and stderr string from + the command process." +- (deferred:process-gen 'start-process-shell-command command args)) ++ (deferred:process-gen 'start-process-shell-command (string-join (cons command args) " ") nil)) + + (defun deferred:process-buffer (command &rest args) + "A deferred wrapper of `start-process'. Return a deferred +@@ -770,7 +770,7 @@ object. The process name and buffer name of the argument of the + `start-process-shell-command' are generated by this function automatically. + The next deferred object receives stdout and stderr buffer from + the command process." +- (deferred:process-buffer-gen 'start-process-shell-command command args)) ++ (deferred:process-buffer-gen 'start-process-shell-command (string-join (cons command args) " ") nil)) + + (defun deferred:process-gen (f command args) + "[internal]" From 8ff87f24a73626c13da258b09dee24a962fc5972 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:00 +0200 Subject: [PATCH 0017/1394] gnu: jo: Update to 1.6. * gnu/packages/web.scm (jo): Update to 1.6. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index ffcb709e820..58b3ee6117f 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6256,14 +6256,14 @@ inspired by Ruby's @code{fakeweb}.") (define-public jo (package (name "jo") - (version "1.4") + (version "1.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/jpmens/jo/releases/download/" version "/jo-" version ".tar.gz")) (sha256 - (base32 "18jna9xlpxci3cak3z85c448zv2zr41baclgym3hk433p0p4vii4")))) + (base32 "18fizi0368jgajrmy13xpdiks76jwch8lhx1d1sagmd63cpmj5gb")))) (build-system gnu-build-system) (home-page "https://github.com/jpmens/jo") (synopsis "Output JSON from a shell") From 38bf6c7d0cb588e8d4546db7d2e0bae2ec25183d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:03 +0200 Subject: [PATCH 0018/1394] gnu: obs-websocket: Update to 4.9.1. * gnu/packages/video.scm (obs-websocket): Update to 4.9.1. [arguments]: Update CMakeLists.txt permissions substitution. Don't explicitly return #t from phases. --- gnu/packages/video.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 61f8bd924d4..022c615f49f 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -3499,7 +3499,7 @@ OBS audio sources.") (define-public obs-websocket (package (name "obs-websocket") - (version "4.9.0") + (version "4.9.1") (source (origin (method git-fetch) @@ -3509,7 +3509,7 @@ OBS audio sources.") (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 "1r47861ma1s3998clahbnbc216wcf706b1ps514k5p28h511l5w0")))) + (base32 "0giwhm0rbc578qng4invqqma935zzjlf05msz1gx986aqk654s7k")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no tests @@ -3519,10 +3519,10 @@ OBS audio sources.") (lambda* _ (substitute* "CMakeLists.txt" ;; Remove lines that set writeable permissions on outputs. + (("PERMISSIONS [^)]*") "") (("set\\(CMAKE_INSTALL_DEFAULT_DIRECTORY_PERMISSIONS") "") - (("OWNER_READ.*\\)") "") - (("PERMISSIONS") ")")) - #t))))) + ;; Ug^WClever hack to comment out the next line, which is ‘)’. + (("(OWNER|GROUP|WORLD)_READ .*") "#"))))))) (inputs (list obs qtbase-5)) (home-page "https://github.com/Palakis/obs-websocket") From 57be6ba0f3e185bb33e6791a7312f33d080cbb9e Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Fri, 27 May 2022 13:57:20 +0100 Subject: [PATCH 0019/1394] gnu: python-protobuf-3.6: Add missing input. This was removed from python-protobuf in 5f8491ea95d7ba88801aa28b6d2b98f30b033186. * gnu/packages/protobuf.scm (python-protobuf-3.6)[inputs]: Add python-six. --- gnu/packages/protobuf.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm index e525a55fc63..d6cc03faf38 100644 --- a/gnu/packages/protobuf.scm +++ b/gnu/packages/protobuf.scm @@ -300,7 +300,10 @@ structured data.") (uri (pypi-uri "protobuf" version)) (sha256 (base32 - "04bqb12smlckzmgkj6vgmpbr3cby0n6726cmz33bqr7kn1vb728l")))))) + "04bqb12smlckzmgkj6vgmpbr3cby0n6726cmz33bqr7kn1vb728l")))) + (inputs + (cons python-six + (package-inputs python-protobuf))))) (define-public python-proto-plus (package From 9bb71eaac0f8665d2e77dc05deae63ed804adfb7 Mon Sep 17 00:00:00 2001 From: Jack Hill Date: Thu, 26 May 2022 22:04:03 -0400 Subject: [PATCH 0020/1394] gnu: nginx-rtmp-module: Use #:configure-flags from nginx. * gnu/packages/web.scm (nginx-rtmp-module)[arguments]: Simplify copying of arguments from nginx and augment #:configure-flags from nginx rather than overwriting. Signed-off-by: Christopher Baines --- gnu/packages/web.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 58b3ee6117f..d4032a96e28 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -793,11 +793,10 @@ programming language."))) ,@(package-inputs nginx))) (arguments (substitute-keyword-arguments - `(#:make-flags '("modules") - #:modules ((guix build utils) - (guix build gnu-build-system)) - ,@(package-arguments nginx) - #:configure-flags '("--add-dynamic-module=.")) + `(#:make-flags '("modules") ;Only build this module not all of nginx. + ,@(package-arguments nginx)) + ((#:configure-flags flags) + #~(cons "--add-dynamic-module=." #$flags)) ((#:phases phases) #~(modify-phases #$phases (add-after 'unpack 'unpack-nginx-sources From 0e953f3332cc862b08ecb2342bdac9976dd6d08c Mon Sep 17 00:00:00 2001 From: Jack Hill Date: Thu, 26 May 2022 22:04:04 -0400 Subject: [PATCH 0021/1394] gnu: nginx-rtmp-module: Use gexps in phases. * gnu/packages/web.scm (nginx-rtmp-module)[#:phases]: Use gexps and remove trailing #t. Signed-off-by: Christopher Baines --- gnu/packages/web.scm | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index d4032a96e28..4723d218d40 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -800,24 +800,22 @@ programming language."))) ((#:phases phases) #~(modify-phases #$phases (add-after 'unpack 'unpack-nginx-sources - (lambda* (#:key inputs native-inputs #:allow-other-keys) + (lambda _ (begin ;; The nginx source code is part of the module’s source. (format #t "decompressing nginx source code~%") - (invoke "tar" "xvf" (assoc-ref inputs "nginx-sources") + (invoke "tar" "xvf" #$(this-package-input "nginx-sources") ;; This package's LICENSE file would be ;; overwritten with the one from nginx when ;; unpacking the nginx source, so rename the nginx ;; one when unpacking. "--transform=s,/LICENSE$,/LICENSE.nginx," - "--strip-components=1") - #t))) + "--strip-components=1")))) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((modules-dir (string-append (assoc-ref outputs "out") + (lambda _ + (let ((modules-dir (string-append #$output "/etc/nginx/modules"))) - (install-file "objs/ngx_rtmp_module.so" modules-dir) - #t))) + (install-file "objs/ngx_rtmp_module.so" modules-dir)))) (delete 'fix-root-dirs) (delete 'install-man-page))))) (home-page "https://github.com/arut/nginx-rtmp-module") From 704426cd46de2f953372f0383afedeb4fd6fa4e4 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 26 May 2022 22:23:49 -0400 Subject: [PATCH 0022/1394] gnu: linux-libre: Update to 5.17.11. * gnu/packages/linux.scm (linux-libre-5.17-version): Update to 5.17.11. (linux-libre-5.17-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 18bd229dcf0..3bba7a90f4b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -348,7 +348,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-5.17-version "5.17.9") +(define-public linux-libre-5.17-version "5.17.11") (define-public linux-libre-5.17-gnu-revision "gnu") (define deblob-scripts-5.17 (linux-libre-deblob-scripts @@ -358,7 +358,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1zd4ds6ha4a2acqnalp234r2m9rz9p30qmy1aqri78i06aw7flwn"))) (define-public linux-libre-5.17-pristine-source (let ((version linux-libre-5.17-version) - (hash (base32 "0y2rmn86z3cvgv71b6sjjyafnlbanlib1kjpjjqzjbgg86y2890p"))) + (hash (base32 "0c8vz02lbfm0zkgsr1gvdp8bzxz255dk863pnakw6d77z9bfc22p"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.17))) From bccf17f615f6d718b02279244a7cc22d00109d34 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 26 May 2022 22:24:08 -0400 Subject: [PATCH 0023/1394] gnu: linux-libre 5.15: Update to 5.15.43. * gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.43. (linux-libre-5.15-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 3bba7a90f4b..b0e8f957545 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -366,7 +366,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.15-version "5.15.41") +(define-public linux-libre-5.15-version "5.15.43") (define-public linux-libre-5.15-gnu-revision "gnu") (define deblob-scripts-5.15 (linux-libre-deblob-scripts @@ -376,7 +376,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0gs92qbpvirwd02rpwwnja7771z2azbiy9ppy9ynpr14lxmzxnnh"))) (define-public linux-libre-5.15-pristine-source (let ((version linux-libre-5.15-version) - (hash (base32 "07jrsr54rvhry3g401h58r1773zinq49dbrkb9v1p6q27gyb2z1w"))) + (hash (base32 "04hwaykdjdqhcdk1pr6p4kkyw6h3z6ig4qpsra2klxsqklx92jq6"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.15))) From aad9cc6f259df6a95de3d278cf79287e7c530169 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 26 May 2022 22:24:28 -0400 Subject: [PATCH 0024/1394] gnu: linux-libre 5.10: Update to 5.10.118. * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.118. (linux-libre-5.10-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b0e8f957545..c8f5f6420da 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -381,7 +381,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.15))) -(define-public linux-libre-5.10-version "5.10.117") +(define-public linux-libre-5.10-version "5.10.118") (define-public linux-libre-5.10-gnu-revision "gnu1") (define deblob-scripts-5.10 (linux-libre-deblob-scripts @@ -391,7 +391,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1xyhz0dyrkg2avz382ly3dzpa5v89x49gfzx80c1drpwsk7jg6gp"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "1iyw3nmsga2binmrhfnzsf1pvn2bs21a8jw6vm89k26z5h8zfgkh"))) + (hash (base32 "0jqbzvgbvaldwwarvg27mcv2kfcgmfw72zpy4h4sp5d1hzqj1q65"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) From dcbe1b789b92b9db317e8bebc1ce1f9e09549284 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 26 May 2022 22:24:40 -0400 Subject: [PATCH 0025/1394] gnu: linux-libre 5.4: Update to 5.4.196. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.196. (linux-libre-5.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index c8f5f6420da..9d4c85e1d4e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -396,7 +396,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.195") +(define-public linux-libre-5.4-version "5.4.196") (define-public linux-libre-5.4-gnu-revision "gnu1") (define deblob-scripts-5.4 (linux-libre-deblob-scripts @@ -406,7 +406,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "05i286d98fm2pdf9724x1dsmfcm7gsd7yyyvxqlpisyj1kx14hda"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "078380qhds2jwfmrchna6p27wpfb74pvnj4xiyc5k38gysfmnbzj"))) + (hash (base32 "1x5irgki792f21hm5146xary0260cl9r475kvw8vm9w32vyx18ig"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) From 1244e9facd48009488dc5a0265254fea054a0b29 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 26 May 2022 22:24:56 -0400 Subject: [PATCH 0026/1394] gnu: linux-libre 4.19: Update to 4.19.245. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.245. (linux-libre-4.19-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 9d4c85e1d4e..78f5325acf1 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -411,7 +411,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.4))) -(define-public linux-libre-4.19-version "4.19.244") +(define-public linux-libre-4.19-version "4.19.245") (define-public linux-libre-4.19-gnu-revision "gnu1") (define deblob-scripts-4.19 (linux-libre-deblob-scripts @@ -421,7 +421,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1dnjgx1nmawm9gm0yf15nl80nmg7hy7q2vl3jxjbwj6hlrfv5dmx"))) (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "1g9562v6ny196rw2n3kj43nrz65qa7imwnmfasvj6x8fm8bdhz79"))) + (hash (base32 "1s58qci6xhmss12glzkqk41kp60pqmzh4d84kyz4m4nf4xhdvzcr"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) From be03c5e0aae2483903cc0d5ef65103943a7380b5 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 26 May 2022 22:25:13 -0400 Subject: [PATCH 0027/1394] gnu: linux-libre 4.14: Update to 4.14.281. * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.281. (linux-libre-4.14-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 78f5325acf1..9a2b4b54d0b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -426,7 +426,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.19))) -(define-public linux-libre-4.14-version "4.14.280") +(define-public linux-libre-4.14-version "4.14.281") (define-public linux-libre-4.14-gnu-revision "gnu1") (define deblob-scripts-4.14 (linux-libre-deblob-scripts @@ -436,7 +436,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1dnjgx1nmawm9gm0yf15nl80nmg7hy7q2vl3jxjbwj6hlrfv5dmx"))) (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "01jr0f7mq919s7xxvv8sc1mg6isc1ggij33l2s0n6jvykm23ghrr"))) + (hash (base32 "0pivb1m2cwqnlm8bhd4ccnlq9pwp2r5lmn77gp91k6vbjv3gkqis"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) From 6e9d99f97f15347f44df0518faa5e3b8b9d5184e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 26 May 2022 22:25:28 -0400 Subject: [PATCH 0028/1394] gnu: linux-libre 4.9: Update to 4.9.316. * gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.316. (linux-libre-4.9-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 9a2b4b54d0b..2af32fc88f4 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -441,7 +441,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.14))) -(define-public linux-libre-4.9-version "4.9.315") +(define-public linux-libre-4.9-version "4.9.316") (define-public linux-libre-4.9-gnu-revision "gnu1") (define deblob-scripts-4.9 (linux-libre-deblob-scripts @@ -451,7 +451,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "14jyn2yrbm6ayp0bszs4f9jy3p1qkrj5p5gf5c42spr67aa2lv2v"))) (define-public linux-libre-4.9-pristine-source (let ((version linux-libre-4.9-version) - (hash (base32 "1171p90s00jxg1clyz8kp81ilmdzygg131mxysr6lpkaisahkjg6"))) + (hash (base32 "05yd7djm6dcxv3vaylhmj3p0yml421azv8qabmhv4ric1f99idjp"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.9))) From 36fde042af0f420ee3a385062612b2a2c2f2f7c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 27 May 2022 23:07:56 +0200 Subject: [PATCH 0029/1394] gnu: python-peachpy: Update to 913d74c. Fixes . Reported by Sebastian Gibb . * gnu/packages/python-xyz.scm (python-peachpy): Update to 913d74c. --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 44eeb0d7fe7..1c783d2dcb6 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -29614,9 +29614,9 @@ and BMI2).") (define-public python-peachpy ;; There is no tag in this repo. - (let ((commit "906d578266dc7188bf61e4cdbc9f8ea7d69edec0") + (let ((commit "913d74c35a6b1d330e90bfc055208ce5b06b35a0") (version "0.2.0") ;from 'peachpy/__init__.py' - (revision "1")) + (revision "2")) (package (name "python-peachpy") (version (git-version version revision commit)) @@ -29627,7 +29627,7 @@ and BMI2).") (file-name (git-file-name name version)) (sha256 (base32 - "1yy62k3cjr6556nbp651w6v4hzl7kz4y75wy2dfqgndgbnixskx2")) + "1wnqxspxsacw4556q0b9fbw11nhrkgn6gs8g43jdnpa35f3z9kb6")) (patches (search-patches "python-peachpy-determinism.patch")))) (build-system python-build-system) (arguments From 5ae78c523a0a07edc9b920976c7cbd4ee04bb5c4 Mon Sep 17 00:00:00 2001 From: Benjamin Slade Date: Sat, 21 May 2022 14:22:22 -0600 Subject: [PATCH 0030/1394] gnu: yad: Update to 12.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gtk.scm (yad): Update to 12.0. Signed-off-by: Ludovic Courtès --- gnu/packages/gtk.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 96297535cef..af695d118b9 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -30,6 +30,7 @@ ;;; Copyright © 2021 Maxime Devos ;;; Copyright © 2021 Wamm K. D. ;;; Copyright © 2022 Zhu Zihao +;;; Copyright © 2022 Benjamin Slade ;;; ;;; This file is part of GNU Guix. ;;; @@ -2546,7 +2547,7 @@ independent of your desktop environment, and supports global key bindings.") (define-public yad (package (name "yad") - (version "5.0") + (version "12.0") (source (origin (method git-fetch) @@ -2555,7 +2556,7 @@ independent of your desktop environment, and supports global key bindings.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "07rd61hvilsxxrj7lf8c9k0a8glj07s48m7ya8d45030r90g3lvc")))) + (base32 "1nbbw4vwlxjlp83d35w54952b6rrn8qlr3d053lisqwl0hfcm7if")))) (build-system glib-or-gtk-build-system) (arguments `(#:configure-flags From 4f122abfe0732e40f9422cc90c6c067d2825cf0a Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Sat, 21 May 2022 23:27:59 +0300 Subject: [PATCH 0031/1394] gnu: Add python-catalogue. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-xyz.scm (python-catalogue): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1c783d2dcb6..32bdd1b6514 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -31742,3 +31742,29 @@ when the object is garbage collected.") "Simple but high performance Cython hash table mapping pre-randomized keys to void* values.") (license license:expat))) + +(define-public python-catalogue + (package + (name "python-catalogue") + (version "2.0.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "catalogue" version)) + (sha256 + (base32 + "0srdxiil2xys8q1gpc1nvzhvis3a33d8a7amk2i1rlpbg6p36pak")))) + (build-system python-build-system) + (native-inputs (list python-pytest)) + (inputs (list python python-zipp python-typing-extensions python-mypy)) + (home-page "https://github.com/explosion/catalogue") + (synopsis "Lightweight function registries for your library") + (description + "\"catalogue\" is a tiny, zero-dependencies library that +makes it easy to add function (or object) registries to your code. Function +registries are helpful when you have objects that need to be both easily +serializable and fully customizable. Instead of passing a function into your +object, you pass in an identifier name, which the object can use to lookup the +function from the registry. This makes the object easy to serialize, because the +name is a simple string. If you instead saved the function, you'd have to use +Pickle for serialization, which has many drawbacks.") + (license license:expat))) From 3a5540a12c68298908c5dd76eb6ec9768c6b541d Mon Sep 17 00:00:00 2001 From: Niklas Eklund Date: Sat, 21 May 2022 23:25:45 +0200 Subject: [PATCH 0032/1394] gnu: emacs-detached: Update to 0.7. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-detached): Update to 0.7. (emacs-dtache): Define as a deprecated alias. I have both renamed the package dtache -> detached as well as moving the development from gitlab to sourcehut. This patch reflects those changes, as well as updating to the latest release of the package. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 39 ++++++++++++++++++++------------------ 1 file changed, 21 insertions(+), 18 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f7fb6aac35d..ed1b005d6ef 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -24348,49 +24348,52 @@ indentation and a command to plot the file.") according to their use.") (license license:gpl3+)))) -(define-public emacs-dtache +(define-public emacs-detached (package - (name "emacs-dtache") - (version "0.5") + (name "emacs-detached") + (version "0.7") (source (origin (method git-fetch) (uri (git-reference - (url "https://gitlab.com/niklaseklund/dtache") + (url "https://git.sr.ht/~niklaseklund/detached.el") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "05gm5l533y8xr00w3c3i4fbhzhib6i7q2bbnpkm08w1n8a08iaj5")))) + "160h60vrpxslw6y290ndc065cc75dab58aq7kjqash94vkifnii2")))) (arguments (list #:tests? #t #:test-command #~(list "ert-runner") #:phases #~(modify-phases %standard-phases - (add-before 'install 'install-dtache-env + (add-before 'install 'install-detached-env (lambda _ - (install-file "dtache-env" (string-append #$output "/bin")))) + (install-file "detached-env" (string-append #$output "/bin")))) (add-after 'unpack 'configure (lambda* (#:key inputs #:allow-other-keys) - (make-file-writable "dtache.el") - (emacs-substitute-variables "dtache.el" - ("dtache-env" - (string-append #$output "/bin/dtache-env")) - ("dtache-dtach-program" + (make-file-writable "detached.el") + (emacs-substitute-variables "detached.el" + ("detached-env" + (string-append #$output "/bin/detached-env")) + ("detached-dtach-program" (search-input-file inputs "/bin/dtach")) - ("dtache-shell-program" + ("detached-shell-program" (search-input-file inputs "/bin/bash")))))))) (build-system emacs-build-system) (native-inputs (list emacs-ert-runner)) (inputs (list dtach)) - (home-page "https://gitlab.com/niklaseklund/dtache") - (synopsis "Run and interact with detached shell commands") + (home-page "https://git.sr.ht/~niklaseklund/detached.el") + (synopsis "A package to launch, and manage, detached processes") (description - "The dtache package allows users to run shell commands -detached from Emacs. These commands are launched in sessions, using the -program dtach.") + "The detached package allows users to run processes +detached from Emacs. It provides integration with multiple built-in modes, as +well as providing an interface to attach and interact with the processes.") (license license:gpl3+))) +(define-public emacs-dtache + (deprecated-package "emacs-dtache" emacs-detached)) + (define-public emacs-dtrt-indent (package (name "emacs-dtrt-indent") From eefff9fb7463a6ff9559921641365928ab1a6519 Mon Sep 17 00:00:00 2001 From: jgart Date: Sat, 21 May 2022 17:54:16 -0500 Subject: [PATCH 0033/1394] gnu: emacs-evil-org: Update to 0d10ff7. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-evil-org): Update to 0d10ff7. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ed1b005d6ef..9a4edbcc22e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -21551,10 +21551,11 @@ provide an incremental search that moves all fake cursors in sync.") (license license:expat)))) (define-public emacs-evil-org - (let ((commit "9d4be14118bf27094a30dbff349b815f098aacbf")) + (let ((commit "0d10ff7bb9a3a93d25cd91018b17f0a052b335f3") + (revision "2")) (package (name "emacs-evil-org") - (version (git-version "1.0.2" "1" commit)) + (version (git-version "1.0.3" revision commit)) (source (origin (method git-fetch) @@ -21564,7 +21565,7 @@ provide an incremental search that moves all fake cursors in sync.") (file-name (git-file-name name version)) (sha256 (base32 - "1fxxfkinb0gq4p5b686r7z4jrkv98zfgh5z889zkjacncv8ibswn")))) + "15g47xgpswzc8lz7qdbbzfcq1n9m4474qa2jkg43l8d5ali8qa7z")))) (build-system emacs-build-system) (propagated-inputs (list emacs-evil)) (home-page From 6caac30e444ef9d0ca7e303ff72be1139453e833 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Sun, 22 May 2022 09:34:05 +0300 Subject: [PATCH 0034/1394] gnu: Add python-wasabi. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-xyz.scm (python-wasabi): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/python-xyz.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 32bdd1b6514..c010d87a014 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -31768,3 +31768,22 @@ function from the registry. This makes the object easy to serialize, because th name is a simple string. If you instead saved the function, you'd have to use Pickle for serialization, which has many drawbacks.") (license license:expat))) + +(define-public python-wasabi + (package + (name "python-wasabi") + (version "0.9.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "wasabi" version)) + (sha256 + (base32 + "1kwqfalq7qxs9f7xb2m055g01qpbznyzxl7sjnzjdvvhkczg39md")))) + (build-system python-build-system) + (native-inputs (list python-pytest)) + (home-page "https://github.com/ines/wasabi") + (synopsis "Console printing and formatting toolkit") + (description + "This package provides a lightweight console printing and formatting +toolkit for Python.") + (license license:expat))) From 5bfb7ebe5dd3011d766a98cb9875399fb836c4b1 Mon Sep 17 00:00:00 2001 From: Pradana AUMARS Date: Sun, 22 May 2022 15:45:04 +0200 Subject: [PATCH 0035/1394] gnu: Add python-srt. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-xyz (python-srt): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/python-xyz.scm | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c010d87a014..04726c7828e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -107,7 +107,7 @@ ;;; Copyright © 2021 Petr Hodina ;;; Copyright © 2021 Simon Streit ;;; Copyright © 2021 Daniel Meißner -;;; Copyright © 2021 Pradana Aumars +;;; Copyright © 2021, 2022 Pradana Aumars ;;; Copyright © 2021, 2022 Felix Gruber ;;; Copyright © 2021 Sébastien Lerique ;;; Copyright © 2021 Raphaël Mélotte @@ -31787,3 +31787,21 @@ Pickle for serialization, which has many drawbacks.") "This package provides a lightweight console printing and formatting toolkit for Python.") (license license:expat))) + +(define-public python-srt + (package + (name "python-srt") + (version "3.5.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "srt" version)) + (sha256 + (base32 + "0l24710spxarijmv3h7iicvx0lv6m3d4xg77nd9kyv8jwifav93s")))) + (build-system python-build-system) + (home-page "https://github.com/cdown/srt") + (synopsis "SRT parsing library") + (description + "This package provides a Python library for parsing, modifying, and +composing subtitles in the SRT file format.") + (license license:expat))) From d4158ea63ad6d112c3e95b3dde99608d7bd99148 Mon Sep 17 00:00:00 2001 From: "yarl-baudig@mailoo.org" Date: Sun, 22 May 2022 15:54:42 +0200 Subject: [PATCH 0036/1394] substitute: Check for --help or --version options early. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Running `guix archive --authorize` sets /etc/guix/acl to 600 via with-atomic-file-output via mkstemp!. Then running `guix substitute --help/--version` fails on "permission denied". While "guix substitute" is an internal tool, the options --help and --version exist and you should be able to run those from the command line. * guix/scripts/substitute.scm (guix-substitute): Earlier check for --help or --version. Signed-off-by: Ludovic Courtès --- guix/scripts/substitute.scm | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm index 908a8334a8f..c5f5d23b476 100755 --- a/guix/scripts/substitute.scm +++ b/guix/scripts/substitute.scm @@ -704,6 +704,14 @@ default value." (category internal) (synopsis "implement the build daemon's substituter protocol") + (match args + ((or ("-V") ("--version")) + (show-version-and-exit "guix substitute")) + ((or ("-h") ("--help") ()) + (show-help) + (exit 0)) + (_ #t)) + (define print-build-trace? (match (or (find-daemon-option "untrusted-print-extended-build-trace") (find-daemon-option "print-extended-build-trace")) @@ -775,10 +783,6 @@ default value." #:print-build-trace? print-build-trace?) (loop)))))) - ((or ("-V") ("--version")) - (show-version-and-exit "guix substitute")) - ((or ("-h") ("--help")) - (show-help)) (opts (leave (G_ "~a: unrecognized options~%") opts)))))) From cfc6bcee4c31c3826657a0bab426142800c9bec3 Mon Sep 17 00:00:00 2001 From: "Wamm K. D" Date: Thu, 19 May 2022 01:05:22 -0500 Subject: [PATCH 0037/1394] gnu: Add python-gatt. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-xyz.scm (python-gatt): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/python-xyz.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 04726c7828e..fe1896efca5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -31805,3 +31805,36 @@ toolkit for Python.") "This package provides a Python library for parsing, modifying, and composing subtitles in the SRT file format.") (license license:expat))) + +(define-public python-gatt + (package + (name "python-gatt") + (version "0.2.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "gatt" version)) + (sha256 + (base32 + "0fjf066jixk30fr8xwfalwfnhqpr56yv0cccyypnx2qp9bi9svb2")))) + (propagated-inputs (list python-dbus python-pygobject)) + (build-system python-build-system) + (home-page "https://github.com/getsenic/gatt-python") + (synopsis "Bluetooth GATT SDK for Python") + (description "The Bluetooth @acronym{GATT, Generic ATTribute Profile} +@acronym{SDK, Software Development Kit} for Python helps you implement and +communicate with any Bluetooth Low Energy device that has a GATT +profile. It supports: + +@itemize @bullet +@item Discovering nearby Bluetooth Low Energy devices +@item Connecting and disconnecting devices +@item Implementing your custom GATT profile +@item Accessing all GATT services +@item Accessing all GATT characteristics +@item Reading characteristic values +@item Writing characteristic values +@item Subscribing for characteristic value change notifications +@end itemize + +Currently, Linux is the only platform supported by this library.") + (license license:expat))) From 83f444de56957ff6a6fa76605c73a57ea76c6e3c Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Fri, 27 May 2022 14:43:31 -0700 Subject: [PATCH 0038/1394] gnu: diffoscope: Update to 214. * gnu/packages/diffoscope.scm (diffoscope): Update to 214. [arguments]: Remove 'xb-tool-external-tool phase. --- gnu/packages/diffoscope.scm | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index bd091fedfc3..16e3b2a481c 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -74,7 +74,7 @@ (define-public diffoscope (package (name "diffoscope") - (version "213") + (version "214") (source (origin (method git-fetch) @@ -83,7 +83,7 @@ (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "075zrraj7pibwgi731pa506pkq5i06mpilqa03w3dd548b1jc9py")) + (base32 "05vzvs8yn963wzxmnqifj0zsa9scxcq3iqrq9msm0vqznb1xgp7q")) (patches (search-patches "diffoscope-fix-llvm-test.patch")))) (build-system python-build-system) @@ -111,13 +111,6 @@ (string-append "['" (which "stat") "',")) (("\\['getfacl',") (string-append "['" (which "getfacl") "',"))))) - (add-after 'unpack 'xb-tool-external-tool - ;; Fixed upstream, remove this phase when updating to - ;; diffoscope 213 - (lambda _ - (substitute* "diffoscope/external_tools.py" - ((".debian.: .libxmlb-dev.") - "\"debian\": \"libxmlb-dev\", \"guix\": \"libxmlb\"")))) (add-after 'build 'build-man-page (lambda* (#:key (make-flags '()) #:allow-other-keys) (apply invoke "make" "-C" "doc" make-flags))) From 0bb6504ba6072dfca342a1410b34fd50814f629f Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Sun, 22 May 2022 17:43:42 +0800 Subject: [PATCH 0039/1394] gnu: emacs-magit: Use G-expressions. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-magit)[arguments]: Use G-expressions. <#:phases>: Use search-input-file to find perl for ‘patch-exec-paths’. Signed-off-by: Liliana Marie Prikler --- gnu/packages/emacs-xyz.scm | 91 +++++++++++++++++++------------------- 1 file changed, 46 insertions(+), 45 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9a4edbcc22e..30f1f9bcae1 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -891,51 +891,52 @@ libgit2 bindings for Emacs, intended to boost the performance of Magit.") (base32 "0cxyvp2aav27znc7mf6c83q5pddpdniaqkrxn1r8dbgr540qmnpn")))) (build-system emacs-build-system) (arguments - `(#:emacs ,emacs-no-x ;module support is required - #:tests? #t - #:test-command '("make" "test") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'build-info-manual - (lambda _ - (invoke "make" "info") - ;; Copy info files to the lisp directory, which acts as - ;; the root of the project for the emacs-build-system. - (for-each (lambda (f) - (install-file f "lisp")) - (find-files "Documentation" "\\.info$")) - (chdir "lisp"))) - (add-after 'build-info-manual 'set-magit-version - (lambda _ - (make-file-writable "magit.el") - (emacs-substitute-variables "magit.el" - ("magit-version" ,version)))) - (add-after 'set-magit-version 'patch-exec-paths - (lambda* (#:key inputs #:allow-other-keys) - (let ((perl (assoc-ref inputs "perl"))) - (make-file-writable "magit-sequence.el") - (emacs-substitute-variables "magit-sequence.el" - ("magit-perl-executable" (string-append perl "/bin/perl")))))) - (add-before 'check 'configure-git - (lambda _ - ;; Otherwise some tests fail with error "unable to auto-detect - ;; email address". - (setenv "HOME" (getcwd)) - (invoke "git" "config" "--global" "user.name" "toto") - (invoke "git" "config" "--global" "user.email" - "toto@toto.com"))) - (add-after 'configure-git 'disable-tramp-test - (lambda _ - ;; There is an issue causing TRAMP to fail in the build - ;; environment. Setting the tramp-remote-shell parameter of - ;; the sudo-method to the file name of the shell didn't help. - (chdir "..") - (substitute* "t/magit-tests.el" - (("^\\(ert-deftest magit-toplevel:tramp.*" all) - (string-append all " (skip-unless nil)"))))) - (add-before 'install 'enter-lisp-directory - (lambda _ - (chdir "lisp")))))) + (list + #:emacs emacs-no-x ;module support is required + #:tests? #t + #:test-command #~(list "make" "test") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'build-info-manual + (lambda _ + (invoke "make" "info") + ;; Copy info files to the lisp directory, which acts as + ;; the root of the project for the emacs-build-system. + (for-each (lambda (f) + (install-file f "lisp")) + (find-files "Documentation" "\\.info$")) + (chdir "lisp"))) + (add-after 'build-info-manual 'set-magit-version + (lambda _ + (make-file-writable "magit.el") + (emacs-substitute-variables "magit.el" + ("magit-version" #$version)))) + (add-after 'set-magit-version 'patch-exec-paths + (lambda* (#:key inputs #:allow-other-keys) + (make-file-writable "magit-sequence.el") + (emacs-substitute-variables "magit-sequence.el" + ("magit-perl-executable" + (search-input-file inputs "/bin/perl"))))) + (add-before 'check 'configure-git + (lambda _ + ;; Otherwise some tests fail with error "unable to auto-detect + ;; email address". + (setenv "HOME" (getcwd)) + (invoke "git" "config" "--global" "user.name" "toto") + (invoke "git" "config" "--global" "user.email" + "toto@toto.com"))) + (add-after 'configure-git 'disable-tramp-test + (lambda _ + ;; There is an issue causing TRAMP to fail in the build + ;; environment. Setting the tramp-remote-shell parameter of + ;; the sudo-method to the file name of the shell didn't help. + (chdir "..") + (substitute* "t/magit-tests.el" + (("^\\(ert-deftest magit-toplevel:tramp.*" all) + (string-append all " (skip-unless nil)"))))) + (add-before 'install 'enter-lisp-directory + (lambda _ + (chdir "lisp")))))) (native-inputs (list texinfo)) (inputs From 9368341092815a142f123b4df2254ddd61879668 Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Sat, 28 May 2022 10:10:31 +0800 Subject: [PATCH 0040/1394] gnu: emacs-magit: Drop the libgit backend. The libgit backend currently provides next to no features, but demands extra maintenance overhead. It is in fact not a usable backend; thus let's not use it. * gnu/packages/emacs-xyz.scm (emacs-magit)[arguments] <#:emacs>: Drop argument. <#:exclude>: Add sources related to emacs-libgit. [inputs]: Remove emacs-libgit. Signed-off-by: Liliana Marie Prikler --- gnu/packages/emacs-xyz.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 30f1f9bcae1..665c69a20ce 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -892,9 +892,11 @@ libgit2 bindings for Emacs, intended to boost the performance of Magit.") (build-system emacs-build-system) (arguments (list - #:emacs emacs-no-x ;module support is required #:tests? #t #:test-command #~(list "make" "test") + #:exclude #~(cons* "magit-libgit.el" + "magit-libgit-pkg.el" + %default-exclude) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'build-info-manual @@ -942,7 +944,7 @@ libgit2 bindings for Emacs, intended to boost the performance of Magit.") (inputs (list git perl)) (propagated-inputs - (list emacs-dash emacs-libgit emacs-transient emacs-with-editor)) + (list emacs-dash emacs-transient emacs-with-editor)) (home-page "https://magit.vc/") (synopsis "Emacs interface for the Git version control system") (description From 2a97acbe3db5d160f97914550ece0d03b44168d4 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 28 May 2022 08:49:41 +0200 Subject: [PATCH 0041/1394] gnu: emacs-magit: Use directory excursions rather than wild chdir. * gnu/packages/emacs-xyz.scm (emacs-magit)[#:phases] : Don't chdir. : Use full file names. : Drop phase. : Wrap in directory excursions. --- gnu/packages/emacs-xyz.scm | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 665c69a20ce..31822dc6414 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -906,17 +906,16 @@ libgit2 bindings for Emacs, intended to boost the performance of Magit.") ;; the root of the project for the emacs-build-system. (for-each (lambda (f) (install-file f "lisp")) - (find-files "Documentation" "\\.info$")) - (chdir "lisp"))) + (find-files "Documentation" "\\.info$")))) (add-after 'build-info-manual 'set-magit-version (lambda _ - (make-file-writable "magit.el") - (emacs-substitute-variables "magit.el" + (make-file-writable "lisp/magit.el") + (emacs-substitute-variables "lisp/magit.el" ("magit-version" #$version)))) (add-after 'set-magit-version 'patch-exec-paths (lambda* (#:key inputs #:allow-other-keys) - (make-file-writable "magit-sequence.el") - (emacs-substitute-variables "magit-sequence.el" + (make-file-writable "lisp/magit-sequence.el") + (emacs-substitute-variables "lisp/magit-sequence.el" ("magit-perl-executable" (search-input-file inputs "/bin/perl"))))) (add-before 'check 'configure-git @@ -932,13 +931,17 @@ libgit2 bindings for Emacs, intended to boost the performance of Magit.") ;; There is an issue causing TRAMP to fail in the build ;; environment. Setting the tramp-remote-shell parameter of ;; the sudo-method to the file name of the shell didn't help. - (chdir "..") (substitute* "t/magit-tests.el" (("^\\(ert-deftest magit-toplevel:tramp.*" all) (string-append all " (skip-unless nil)"))))) - (add-before 'install 'enter-lisp-directory - (lambda _ - (chdir "lisp")))))) + (replace 'expand-load-path + (lambda args + (with-directory-excursion "lisp" + (apply (assoc-ref %standard-phases 'expand-load-path) args)))) + (replace 'install + (lambda args + (with-directory-excursion "lisp" + (apply (assoc-ref %standard-phases 'install) args))))))) (native-inputs (list texinfo)) (inputs From 092ec158f73b0f4a4817517149e4cb49b2d8e490 Mon Sep 17 00:00:00 2001 From: Remco van 't Veer Date: Sat, 28 May 2022 10:57:18 +0200 Subject: [PATCH 0042/1394] gnu: Add quodlibet. * gnu/packages/music.scm (quodlibet): New variable. Signed-off-by: Liliana Marie Prikler --- gnu/packages/music.scm | 83 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 83 insertions(+) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index b224a145d55..80b490b35f9 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -45,6 +45,7 @@ ;;; Copyright © 2021 Xinglu Chen ;;; Copyright © 2021 Thomas Albers Raviola ;;; Copyright © 2022 Sughosha +;;; Copyright © 2022 Remco van 't Veer ;;; ;;; This file is part of GNU Guix. ;;; @@ -153,6 +154,7 @@ #:use-module (gnu packages protobuf) #:use-module (gnu packages pulseaudio) ;libsndfile #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-web) @@ -6878,3 +6880,84 @@ choice.") streaming audio server.") (home-page "https://musikcube.com/") (license license:bsd-3))) + +(define-public quodlibet + (package + (name "quodlibet") + (version "4.5.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/quodlibet/quodlibet") + (commit (string-append "release-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1i5k93k3bfp7hpcwkbr865mbj9jam3jv2a5k1bazcyp4f5vdrb0v")))) + (build-system python-build-system) + (arguments + (list + #:modules '((guix build python-build-system) + ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:) + (guix build utils)) + #:imported-modules `((guix build python-build-system) + ,@%glib-or-gtk-build-system-modules) + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + (setenv "HOME" (getcwd)))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (if tests? + (invoke "xvfb-run" "pytest" + ;; needs network + "--ignore=tests/test_browsers_iradio.py" + ;; broken upstream + "--disable-warnings" + "--ignore=tests/quality") + (format #t "test suite not run~%")))) + (add-after 'install 'glib-or-gtk-wrap ; ensure icons loaded + (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)) + (add-after 'install 'wrap-gi-typelib ; GObject Introspection + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (gi-typelib-path (getenv "GI_TYPELIB_PATH"))) + (for-each (lambda (prog) + (wrap-program (string-append out "/bin/" prog) + `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path)))) + '("exfalso" "quodlibet")))))))) + (native-inputs (list xvfb-run gettext-minimal)) + (inputs + (list adwaita-icon-theme + gtk+ + glib + gsettings-desktop-schemas + gst-plugins-bad + gst-plugins-base + gst-plugins-good + gst-plugins-ugly + gstreamer + gtk+ + hicolor-icon-theme + librsvg + libsoup-minimal-2 + python + python-cheetah + python-dbus + python-feedparser + python-gst + python-iniconfig + python-mutagen + python-pycairo + python-pygobject + python-pytest + python-sgmllib3k + python-toml)) + (home-page "https://github.com/quodlibet/quodlibet") + (synopsis "Music manager and player") + (description "Quod Libet provides several ways to browse and view your +local music library, along with flexible search capabilities. It includes +a tag editor, which can also be invoked as a standalone program, and further +supports streaming audio and feeds (such as podcasts).") + (license license:gpl2+))) From cc0401a9de1aa89fd8c150141b51e6b0f053a606 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 28 May 2022 17:26:12 +0200 Subject: [PATCH 0043/1394] gnu: quodlibet: Fix inputs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/music.scm (quodlibet)[inputs]: Add bash-minimal for ‘wrap-program’. Remove extraneous gtk+. --- gnu/packages/music.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 80b490b35f9..9011f262a47 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -6930,7 +6930,7 @@ streaming audio server.") (native-inputs (list xvfb-run gettext-minimal)) (inputs (list adwaita-icon-theme - gtk+ + bash-minimal glib gsettings-desktop-schemas gst-plugins-bad From 4a53069b382f2b489ad197ede4d2c4cd2c7c8c16 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 27 May 2022 14:41:29 +0300 Subject: [PATCH 0044/1394] gnu: clang-from-llvm: Fix build on some architectures. * gnu/packages/llvm.scm (clang-from-llvm)[arguments]: Adjust custom 'symlink-cfi_ignorelist phase to only symlink when the file exists. --- gnu/packages/llvm.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index c93c1db7fef..aedf039ff41 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2017 Roel Janssen ;;; Copyright © 2018–2022 Marius Bakke ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice -;;; Copyright © 2018, 2021 Efraim Flashner +;;; Copyright © 2018, 2021, 2022 Efraim Flashner ;;; Copyright © 2018 Tim Gesthuizen ;;; Copyright © 2018 Pierre Neidhardt ;;; Copyright © 2019 Rutger Helling @@ -353,8 +353,11 @@ given PATCHES. When TOOLS-EXTRA is given, it must point to the (mkdir-p lib-share) ;; Symlink the ignorelist to where Clang expects ;; to find it. - (symlink cfi-ignorelist - (string-append lib-share "/" file-name)))))) + ;; Not all architectures support CFI. + ;; see: compiler-rt/cmake/config-ix.cmake + (when (file-exists? cfi-ignorelist) + (symlink cfi-ignorelist + (string-append lib-share "/" file-name))))))) '()) (add-after 'install 'install-clean-up-/share/clang (lambda* (#:key outputs #:allow-other-keys) From 39227724e8edccc8aa6e62be8920bf3c0c4579b0 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 27 May 2022 18:28:44 +0300 Subject: [PATCH 0045/1394] gnu: mesa: Build with llvm on armhf-linux. * gnu/packages/gl.scm (mesa)[inputs]: Add llvm for all architectures. [native-inputs]: Add glslang for all architectures. [arguments]: Adjust configure-flags to give armhf-linux its own gallium-drivers and enable llvm support. Rewrite portions that no longer depend on specific architectures to enable flags. Adjust custom 'disable-failing-test phase to skip a test on armhf-linux. --- gnu/packages/gl.scm | 44 +++++++++++++++++--------------------------- 1 file changed, 17 insertions(+), 27 deletions(-) diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm index f4313b41516..d3ee7aed93b 100644 --- a/gnu/packages/gl.scm +++ b/gnu/packages/gl.scm @@ -294,25 +294,15 @@ also known as DXTn or DXTC) for Mesa.") ("libxml2" ,libxml2) ("libxrandr" ,libxrandr) ("libxvmc" ,libxvmc) - ,@(match (%current-system) - ((or "x86_64-linux" "i686-linux" "powerpc64le-linux" "aarch64-linux" - "powerpc-linux" "riscv64-linux") - ;; Note: update the 'clang' input of mesa-opencl when bumping this. - `(("llvm" ,llvm-11))) - (_ - `())) + ;; Note: update the 'clang' input of mesa-opencl when bumping this. + ("llvm" ,llvm-11) ("wayland" ,wayland) ("wayland-protocols" ,wayland-protocols))) (native-inputs `(("bison" ,bison) ("flex" ,flex) ("gettext" ,gettext-minimal) - ,@(match (%current-system) - ((or "x86_64-linux" "i686-linux" "powerpc64le-linux" "aarch64-linux" - "powerpc-linux" "riscv64-linux") - `(("glslang" ,glslang))) - (_ - `())) + ("glslang" ,glslang) ("pkg-config" ,pkg-config) ("python" ,python-wrapper) ("python-libxml2", python-libxml2) ;for OpenGL ES 1.1 and 2.0 support @@ -322,9 +312,12 @@ also known as DXTn or DXTC) for Mesa.") (arguments `(#:configure-flags '(,@(match (%current-system) - ((or "armhf-linux" "aarch64-linux") + ("aarch64-linux" ;; TODO: Fix svga driver for non-Intel architectures. '("-Dgallium-drivers=etnaviv,freedreno,kmsro,lima,nouveau,panfrost,r300,r600,swrast,tegra,v3d,vc4,virgl")) + ("armhf-linux" + ;; Freedreno FTBFS when built on a 64-bit machine. + '("-Dgallium-drivers=etnaviv,kmsro,lima,nouveau,panfrost,r300,r600,swrast,tegra,v3d,vc4,virgl")) ((or "powerpc64le-linux" "powerpc-linux" "riscv64-linux") '("-Dgallium-drivers=nouveau,r300,r600,radeonsi,swrast,virgl")) (_ @@ -356,13 +349,8 @@ also known as DXTn or DXTC) for Mesa.") (_ '("-Dvulkan-drivers=auto"))) - ;; Enable the Vulkan overlay layer on architectures using llvm. - ,@(match (%current-system) - ((or "x86_64-linux" "i686-linux" "powerpc64le-linux" "aarch64-linux" - "powerpc-linux" "riscv64-linux") - '("-Dvulkan-layers=device-select,overlay")) - (_ - '())) + ;; Enable the Vulkan overlay layer on all architectures. + "-Dvulkan-layers=device-select,overlay" ;; Also enable the tests. "-Dbuild-tests=true" @@ -371,13 +359,11 @@ also known as DXTn or DXTC) for Mesa.") ;; from the default dri drivers ,@(match (%current-system) ((or "x86_64-linux" "i686-linux") - '("-Ddri-drivers=i915,i965,nouveau,r200,r100" - "-Dllvm=enabled")) ; default is x86/x86_64 only - ((or "powerpc64le-linux" "aarch64-linux" "powerpc-linux" "riscv64-linux") - '("-Ddri-drivers=nouveau,r200,r100" - "-Dllvm=enabled")) + '("-Ddri-drivers=i915,i965,nouveau,r200,r100")) (_ - '("-Ddri-drivers=nouveau,r200,r100")))) + '("-Ddri-drivers=nouveau,r200,r100"))) + + "-Dllvm=enabled") ; default is x86/x86_64 only ;; XXX: 'debugoptimized' causes LTO link failures on some drivers. The ;; documentation recommends using 'release' for performance anyway. @@ -435,6 +421,10 @@ also known as DXTn or DXTC) for Mesa.") ;; The simplest way to skip it is to run a different test instead. `((substitute* "src/freedreno/ir3/meson.build" (("disasm\\.c'") "delay.c',\n link_args: ld_args_build_id")))) + ("armhf-linux" + ;; Disable some of the llvmpipe tests. + `((substitute* "src/gallium/drivers/llvmpipe/meson.build" + (("'lp_test_arit', ") "")))) (_ '((display "No tests to disable on this architecture.\n")))))) (add-before 'configure 'fix-dlopen-libnames From 81803c5eaae4ac6d48415a47b5d92de7a9e18b1a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 28 May 2022 22:18:40 +0300 Subject: [PATCH 0046/1394] gnu: wget2: Update to 2.0.1. * gnu/packages/wget.scm (wget2): Update to 2.0.1. [arguments]: Remove trailing #t from phases. --- gnu/packages/wget.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index 9d23ecdaef7..f5b7a5b91f0 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2012 Nikita Karetnikov ;;; Copyright © 2014, 2015, 2017, 2018 Ludovic Courtès -;;; Copyright © 2016, 2017, 2019, 2020, 2021 Efraim Flashner +;;; Copyright © 2016, 2017, 2019-2022 Efraim Flashner ;;; Copyright © 2017 Rutger Helling ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen @@ -135,14 +135,14 @@ online pastebin services.") (define-public wget2 (package (name "wget2") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/wget/wget2-" version ".tar.gz")) (sha256 (base32 - "0i0m4k6w9smsr2m5mj05zvl1fb110izyl2qqrk0yqlxnmfhgpqjg")))) + "1caxhkwk08z3npzw8x2qhkmjc224cfw1aphvbv8bidbvd41zmdqb")))) (build-system gnu-build-system) (arguments `(#:phases @@ -152,8 +152,7 @@ online pastebin services.") (substitute* "tests/Makefile.in" (("test-gpg-verify-no-file\\$\\(EXEEXT)") "") (("test-gpg-valid\\$\\(EXEEXT)") "") - (("test-gpg-styles\\$\\(EXEEXT)") "")) - #t))) + (("test-gpg-styles\\$\\(EXEEXT)") ""))))) #:configure-flags '("--enable-static=no"))) (inputs (list bzip2 From 0542905a2c5cb4f645399e19c2a4924dc757057e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 28 May 2022 22:19:56 +0300 Subject: [PATCH 0047/1394] gnu: wget2: Reindent package. * gnu/packages/wget.scm (wget2): Reindent package with 'guix style'. --- gnu/packages/wget.scm | 76 +++++++++++++++++++++---------------------- 1 file changed, 37 insertions(+), 39 deletions(-) diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index f5b7a5b91f0..7c8c961dfb3 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -134,42 +134,40 @@ online pastebin services.") (define-public wget2 (package - (name "wget2") - (version "2.0.1") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://gnu/wget/wget2-" version ".tar.gz")) - (sha256 - (base32 - "1caxhkwk08z3npzw8x2qhkmjc224cfw1aphvbv8bidbvd41zmdqb")))) - (build-system gnu-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'skip-network-tests - (lambda _ - (substitute* "tests/Makefile.in" - (("test-gpg-verify-no-file\\$\\(EXEEXT)") "") - (("test-gpg-valid\\$\\(EXEEXT)") "") - (("test-gpg-styles\\$\\(EXEEXT)") ""))))) - #:configure-flags '("--enable-static=no"))) - (inputs - (list bzip2 - gnutls/dane - gpgme - libidn2 - libmicrohttpd - libpsl - pcre2 - zlib)) - ;; TODO: Add libbrotlidec, libnghttp2. - (native-inputs - (list pkg-config)) - (home-page "https://gitlab.com/gnuwget/wget2") - (synopsis "Successor of GNU Wget") - (description "GNU Wget2 is the successor of GNU Wget, a file and recursive -website downloader. Designed and written from scratch it wraps around libwget, -that provides the basic functions needed by a web client.") - (properties '((ftp-directory . "/gnu/wget"))) - (license (list license:gpl3+ license:lgpl3+)))) + (name "wget2") + (version "2.0.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnu/wget/wget2-" version ".tar.gz")) + (sha256 + (base32 + "1caxhkwk08z3npzw8x2qhkmjc224cfw1aphvbv8bidbvd41zmdqb")))) + (build-system gnu-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'skip-network-tests + (lambda _ + (substitute* "tests/Makefile.in" + (("test-gpg-verify-no-file\\$\\(EXEEXT)") "") + (("test-gpg-valid\\$\\(EXEEXT)") "") + (("test-gpg-styles\\$\\(EXEEXT)") ""))))) + #:configure-flags + '("--enable-static=no"))) + (inputs (list bzip2 + gnutls/dane + gpgme + libidn2 + libmicrohttpd + libpsl + pcre2 + zlib)) + ;; TODO: Add libbrotlidec, libnghttp2. + (native-inputs (list pkg-config)) + (home-page "https://gitlab.com/gnuwget/wget2") + (synopsis "Successor of GNU Wget") + (description + "GNU Wget2 is the successor of GNU Wget, a file and recursive website +downloader. Designed and written from scratch it wraps around libwget, that +provides the basic functions needed by a web client.") + (properties '((ftp-directory . "/gnu/wget"))) + (license (list license:gpl3+ license:lgpl3+)))) From 43e82253c1a0c5608bb97815778ffc19ad4c85b8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 25 May 2022 07:33:02 +0200 Subject: [PATCH 0048/1394] gnu: r-with-tests: Update to 4.2.0. * gnu/packages/statistics.scm (r-with-tests): Update to 4.2.0. [arguments]: Add phase 'patch-tests; add phase 'set-home. --- gnu/packages/statistics.scm | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index aad329400fb..67f169661f8 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -203,7 +203,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.1.3") + (version "4.2.0") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -211,7 +211,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "1mpy4sar1amx5ai9rqr9s0nw8p65iqfrqbm5n9h402b17hrmpzqm")))) + "123l17sv3smh5cz0vrjxjj8jf81bb860kah6iww9bl3skdqvgsiq")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -237,6 +237,16 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (("uname") uname-bin)) (substitute* "src/unix/sys-std.c" (("rm -Rf ") (string-append rm-bin " -Rf ")))))) + (add-after 'unpack 'patch-tests + (lambda _ + ;; This is needed because R is run during the check phase and + ;; /bin/sh doesn't exist in the build container. + (substitute* "src/unix/sys-unix.c" + (("\"/bin/sh\"") + (string-append "\"" (which "sh") "\""))) + ;; This test fails because line numbers are off by two. + (substitute* "tests/reg-packages.R" + (("8 <= print" m) (string-append "## " m))))) (add-after 'unpack 'build-reproducibly (lambda _ ;; The documentation contains time stamps to demonstrate @@ -315,6 +325,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ (setenv "TZDIR" (search-input-directory inputs "share/zoneinfo")))) + (add-before 'check 'set-home + ;; Some tests require that HOME be set. + (lambda _ (setenv "HOME" "/tmp"))) (add-after 'build 'make-info (lambda _ (invoke "make" "info"))) (add-after 'build 'install-info From ac12a57b7836dfbb8539fb27f570632c94c7cc12 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:02 +0200 Subject: [PATCH 0049/1394] gnu: r-activepathways: Update to 1.1.0. * gnu/packages/bioconductor.scm (r-activepathways): Update to 1.1.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4baa80dcb13..7c7bf84aea0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12317,14 +12317,14 @@ using whole genome sequencing data.") (define-public r-activepathways (package (name "r-activepathways") - (version "1.0.4") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "ActivePathways" version)) (sha256 (base32 - "1prhwx0nnwy2q62l2r0z31mhk4mq6xdr6mjihdlwpwgwq4rfi60y")))) + "0zbrgz91mlik7j8j11wsdswqqqfsijj8jkgd5fx1ar3mc6rqsmbg")))) (properties `((upstream-name . "ActivePathways"))) (build-system r-build-system) From 3ceaa41e67b20cfb0f2a1ec772fe01bbb1651c53 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:08 +0200 Subject: [PATCH 0050/1394] gnu: r-wgcna: Update to 1.71. * gnu/packages/bioconductor.scm (r-wgcna): Update to 1.71. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c7bf84aea0..ba6a015595f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13567,14 +13567,14 @@ S4Vectors package itself.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.70-3") + (version "1.71") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r")))) + "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs From 3360f14b080e6718785c73844abfc02c40f6a965 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:08 +0200 Subject: [PATCH 0051/1394] gnu: r-ldheatmap: Update to 1.0-6. * gnu/packages/bioconductor.scm (r-ldheatmap): Update to 1.0-6. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ba6a015595f..87f8543cf22 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14832,14 +14832,14 @@ defining LD blocks.") (define-public r-ldheatmap (package (name "r-ldheatmap") - (version "1.0-4") + (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "LDheatmap" version)) (sha256 (base32 - "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7")))) + "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc")))) (properties `((upstream-name . "LDheatmap"))) (build-system r-build-system) (propagated-inputs From 32a3b09c51a8c3f4075dbf1215b7b5efa3f3ea2a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:09 +0200 Subject: [PATCH 0052/1394] gnu: r-abn: Update to 2.7-1. * gnu/packages/bioconductor.scm (r-abn): Update to 2.7-1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 87f8543cf22..bf371a970a5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14858,14 +14858,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "2.7-0") + (version "2.7-1") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "13i2f4lw1rzj89bp31sn03prq1bqj7bsxwdr8z2ql02yqks9phg0")))) + "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr")))) (build-system r-build-system) (inputs (list gsl)) From d4e4cf21b8502d098e42943cb67a44cc2b9da21a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:09 +0200 Subject: [PATCH 0053/1394] gnu: r-datawizard: Update to 0.4.1. * gnu/packages/cran.scm (r-datawizard): Update to 0.4.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0fdcfb3cb93..c2a2abf903d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -255,14 +255,14 @@ etc.") (define-public r-datawizard (package (name "r-datawizard") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 - "1j26xv1zm7qwp80gy6vlysq3zxdj9r8ivi54b1d6s0ckqkww6gja")))) + "09lyh1awm2rplfzgwbdw4iy76mbaqwjd4hwlrsgvxj9pwdnjs4cx")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs From a075d93dfc647e046fcb643c93bd781d12bb4cf9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:09 +0200 Subject: [PATCH 0054/1394] gnu: r-v8: Update to 4.2.0. * gnu/packages/cran.scm (r-v8): Update to 4.2.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c2a2abf903d..8bdc0c07746 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -655,14 +655,14 @@ similar rank-based tests for equal probability distributions due to Neuhauser (define-public r-v8 (package (name "r-v8") - (version "4.1.0") + (version "4.2.0") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 - "15ylzcxlhkba99cccw5rvhwhg9i4zcax2fhmr03w8g4fdhbd3n89")))) + "0hs7ajjw6y3q7mp7z00a9712y4cn6wgcnk5dbjbzlc6cfk4zsqkc")))) (properties `((upstream-name . "V8"))) (build-system r-build-system) (arguments From fbac14dd2821a4300cf50a0310a3b4cde383467e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:09 +0200 Subject: [PATCH 0055/1394] gnu: r-zoo: Update to 1.8-10. * gnu/packages/cran.scm (r-zoo): Update to 1.8-10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8bdc0c07746..c2ae265a3c8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -787,13 +787,13 @@ known as Dynamic Linear Models.") (define-public r-zoo (package (name "r-zoo") - (version "1.8-9") + (version "1.8-10") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 - "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp")))) + "0izd66dywq6qd62hdp64apncainrrb9mgmm19wf6a8jc03c858n9")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) From 9d83753c402dba21e1cbfa9c95438019bbd9b381 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:10 +0200 Subject: [PATCH 0056/1394] gnu: r-scales: Update to 1.2.0. * gnu/packages/cran.scm (r-scales): Update to 1.2.0. [propagated-inputs]: Add r-rlang. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c2ae265a3c8..3cddebc2809 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1175,13 +1175,13 @@ available as companion packages.") (define-public r-scales (package (name "r-scales") - (version "1.1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "scales" version)) (sha256 - (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0")))) + (base32 "1pq2rrix6a5gsi8xw38viiydp1bsxxmcmyy7dv9q8gkb1qj50p8q")))) (build-system r-build-system) (propagated-inputs (list r-farver @@ -1189,6 +1189,7 @@ available as companion packages.") r-lifecycle r-munsell r-rcolorbrewer + r-rlang r-r6 r-viridislite)) (home-page "https://github.com/hadley/scales") From 819d200a0b254023e96096cf008790e1e182acdf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:10 +0200 Subject: [PATCH 0057/1394] gnu: r-polychrome: Update to 1.5.1. * gnu/packages/cran.scm (r-polychrome): Update to 1.5.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3cddebc2809..7bc7f73695e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1319,13 +1319,13 @@ with default R plot functions.") (define-public r-polychrome (package (name "r-polychrome") - (version "1.3.1") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "Polychrome" version)) (sha256 - (base32 "044vbylgbqf0ccv4r15nmbw1vz0j95g67i6blw73hvbvbm6w5x4d")))) + (base32 "0hyi02m2jpdhk1ky6ihz6dv5pwqwjwk4csjim2qr8ywx8midmrvg")))) (properties `((upstream-name . "Polychrome"))) (build-system r-build-system) (propagated-inputs From fd8062128b2a9d9d4aa7845f403453856870b21e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:10 +0200 Subject: [PATCH 0058/1394] gnu: r-mboost: Update to 2.9-7. * gnu/packages/cran.scm (r-mboost): Update to 2.9-7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7bc7f73695e..b1c72ab7738 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1471,13 +1471,13 @@ objects.") (define-public r-mboost (package (name "r-mboost") - (version "2.9-6") + (version "2.9-7") (source (origin (method url-fetch) (uri (cran-uri "mboost" version)) (sha256 (base32 - "1gvcq1y9prpgxw5kxa20l31p384gksfx0pn7gf29jbl3cknqiyix")))) + "01ln0vxbbx1fq77q17sx61si82lhfibbchsnf2yw9032cn8wnhh2")))) (build-system r-build-system) (propagated-inputs (list r-lattice From d4241d5af6e3f8365892083cc520798f8452cff7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:11 +0200 Subject: [PATCH 0059/1394] gnu: r-shadowtext: Update to 0.1.2. * gnu/packages/cran.scm (r-shadowtext): Update to 0.1.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b1c72ab7738..ff2779ec1ad 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1500,13 +1500,13 @@ high-dimensional data.") (define-public r-shadowtext (package (name "r-shadowtext") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "shadowtext" version)) (sha256 (base32 - "01h0w3b02r8snjkx5sxkf2x8xm4gd0r8jm27xqz9cv6hgqfmh1pb")))) + "0zdfidrcnmxmfhngv86ppxrjmpmz9kl78l4yfah2lc5vgmrlwg15")))) (properties `((upstream-name . "shadowtext"))) (build-system r-build-system) (propagated-inputs From 5128750299c541d8f689d9e792c544ceb82ee4ce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:11 +0200 Subject: [PATCH 0060/1394] gnu: r-astsa: Update to 1.15. * gnu/packages/cran.scm (r-astsa): Update to 1.15. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ff2779ec1ad..0de3b724c5b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1597,13 +1597,13 @@ read a protected key.") (define-public r-astsa (package (name "r-astsa") - (version "1.14") + (version "1.15") (source (origin (method url-fetch) (uri (cran-uri "astsa" version)) (sha256 - (base32 "09zx2q419p0b1c336ybh4i62v5dvn3sp39dxn5kwlrqchjj7f5z6")))) + (base32 "0mllsq0xdqkviyvs77lq565r1vznsj1qp9cnlj5p48k9v76d7arp")))) (properties `((upstream-name . "astsa"))) (build-system r-build-system) (home-page "https://github.com/nickpoison/astsa/") From 20739d83a7ade2d7b43a36055f002b66f7b69153 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:11 +0200 Subject: [PATCH 0061/1394] gnu: r-vegan: Update to 2.6-2. * gnu/packages/cran.scm (r-vegan): Update to 2.6-2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0de3b724c5b..1e27efb3b65 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1620,14 +1620,14 @@ Analysis Approach Using R. Chapman-Hall, 2019, (define-public r-vegan (package (name "r-vegan") - (version "2.5-7") + (version "2.6-2") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6")))) + "0nf0ny6jzfy135xiygzzkr0y55y8g27hrbk8c869plarr48d2xxb")))) (build-system r-build-system) (native-inputs (list r-knitr ; needed for vignettes From 33756c6ed5a4479555c93a16f4bf97c08be2d35c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:11 +0200 Subject: [PATCH 0062/1394] gnu: r-fastghquad: Update to 1.0.1. * gnu/packages/cran.scm (r-fastghquad): Update to 1.0.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1e27efb3b65..7aa421c5d56 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2273,14 +2273,14 @@ data structures in C++.") (define-public r-fastghquad (package (name "r-fastghquad") - (version "1.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "fastGHQuad" version)) (sha256 (base32 - "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj")))) + "1zj7nsbnx4g253m3dpz9vi3zk3jxwrixwjw1ks6n4shpb4dlkp2w")))) (properties `((upstream-name . "fastGHQuad"))) (build-system r-build-system) (propagated-inputs From 1baffaf49104307d7ef4798a4875fb856f26fbb3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:12 +0200 Subject: [PATCH 0063/1394] gnu: r-rstpm2: Update to 1.5.6. * gnu/packages/cran.scm (r-rstpm2): Update to 1.5.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7aa421c5d56..2438c5abfc5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2295,14 +2295,14 @@ rules and utility functions for adaptive GH quadrature.") (define-public r-rstpm2 (package (name "r-rstpm2") - (version "1.5.2") + (version "1.5.6") (source (origin (method url-fetch) (uri (cran-uri "rstpm2" version)) (sha256 (base32 - "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4")))) + "17mhzfxh761vl64ar6pynpj3k2jkhjgbacxsjhkrfkbmy3aiv0d1")))) (properties `((upstream-name . "rstpm2"))) (build-system r-build-system) (propagated-inputs From dea8ee293e400c8e6f4894c7d8a8857342a7c6ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:12 +0200 Subject: [PATCH 0064/1394] gnu: r-shinyfiles: Update to 0.9.2. * gnu/packages/cran.scm (r-shinyfiles): Update to 0.9.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2438c5abfc5..d6a607a7197 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2788,13 +2788,13 @@ application framework for R, making it easy to create attractive dashboards.") (define-public r-shinyfiles (package (name "r-shinyfiles") - (version "0.9.1") + (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 - (base32 "0f8dfdiar376lx0979ccyghgx5rhr08v5z3z60asrrjsxlq4cs85")))) + (base32 "1l4a4v9ivxkj2vx6xw4z3pk7a8px23icppcgvgpybibq2j74pglg")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs From 3a389207b5c54552486fc80ee901b089da7aaaf1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:12 +0200 Subject: [PATCH 0065/1394] gnu: r-haven: Update to 2.5.0. * gnu/packages/cran.scm (r-haven): Update to 2.5.0. [propagated-inputs]: Add r-cli and r-lifecycle. --- gnu/packages/cran.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d6a607a7197..0aab68d0fa4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3425,14 +3425,14 @@ including functions for geolocation and routing.") (define-public r-haven (package (name "r-haven") - (version "2.4.3") + (version "2.5.0") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 - "0pr9jcdk1r9pi9iz0xm1g5yy5qyjk5r7hh9467abx4kpwx3hzdwm")) + "1x5g6kjrzcyarbjz91f4aaspx7rb50qs6a9y29mzr3mjq4dk305m")) (modules '((guix build utils))) (snippet ;; unvendor readstat @@ -3451,9 +3451,11 @@ including functions for geolocation and routing.") (native-inputs (list r-knitr)) (propagated-inputs - (list r-cpp11 + (list r-cli + r-cpp11 r-forcats r-hms + r-lifecycle r-rlang r-readr r-tibble From 30fc048229e537998fb1c1c3838db248f0d10258 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:12 +0200 Subject: [PATCH 0066/1394] gnu: r-ps: Update to 1.7.0. * gnu/packages/cran.scm (r-ps): Update to 1.7.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0aab68d0fa4..e7d6a6cd01e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3716,13 +3716,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.6.0") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9")))) + (base32 "1qaj9gyz7q09aadlnj5al53k2pa4axmzjsbndf5r0b51qqrcy842")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") From 9c33d6688db7165285f8aae0a72cf80c4861d023 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:13 +0200 Subject: [PATCH 0067/1394] gnu: r-rcppxptrutils: Update to 0.1.2. * gnu/packages/cran.scm (r-rcppxptrutils): Update to 0.1.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e7d6a6cd01e..f7c859c8698 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3875,13 +3875,13 @@ with @code{Rcpp}.") (define-public r-rcppxptrutils (package (name "r-rcppxptrutils") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "RcppXPtrUtils" version)) (sha256 - (base32 "0jh64c46gp99d2nsih14vx34pamc8i7gkmiy2nj94rx3sxq62yh5")))) + (base32 "0hm57nf4dzgsmg4hjj6wikwjx93fgfwkmybw6ly4b58wi6qwml1l")))) (properties `((upstream-name . "RcppXPtrUtils"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) From c02dbd5c801dc88c77b6e5f292abf74901a026e3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:13 +0200 Subject: [PATCH 0068/1394] gnu: r-circlize: Update to 0.4.15. * gnu/packages/cran.scm (r-circlize): Update to 0.4.15. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f7c859c8698..f5fff4410b9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4020,14 +4020,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.14") + (version "0.4.15") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "0b0yqjmbj1s1jg7y6cgyawadlfv0i6xrls8a4qy9qs7hz8zrpvb1")))) + "1iswb7dy08as3pbzxvhx5qlsbnwvp79nwg8m158nfz7y2d9xa0nn")))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-globaloptions r-shape)) From 51bc6378393ba82352a33580b6e59115f6ad0d5b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:13 +0200 Subject: [PATCH 0069/1394] gnu: r-ff: Update to 4.0.7. * gnu/packages/cran.scm (r-ff): Update to 4.0.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f5fff4410b9..81358abcfe0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4172,14 +4172,14 @@ any subsequent lookup as it keeps the hash table in memory.") (define-public r-ff (package (name "r-ff") - (version "4.0.5") + (version "4.0.7") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 - "0dsh6llfdz04w94xr3yl2b4vkk9g3rwhvfnxcd025v2424krxfls")))) + "1yl3ipzz9bjkfy9bbna7xz5n7iz4lchnw5l7agww7by764yk6iqa")))) (build-system r-build-system) (propagated-inputs (list r-bit)) (home-page "http://ff.r-forge.r-project.org/") From 20cbdd3d2d6707b613c756234619d8ed1e90aaca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:14 +0200 Subject: [PATCH 0070/1394] gnu: r-reshape: Update to 0.8.9. * gnu/packages/cran.scm (r-reshape): Update to 0.8.9. [propagated-inputs]: Remove r-rcpp. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 81358abcfe0..64ae523ddaf 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4254,17 +4254,17 @@ curve to a data matrix in arbitrary dimensions.") (define-public r-reshape (package (name "r-reshape") - (version "0.8.8") + (version "0.8.9") (source (origin (method url-fetch) (uri (cran-uri "reshape" version)) (sha256 (base32 - "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad")))) + "0j203qmc076x5lp6q2xi4dq4xdb73jmsa42rpxp1c37knnrph4br")))) (build-system r-build-system) (propagated-inputs - (list r-plyr r-rcpp)) + (list r-plyr)) (home-page "http://had.co.nz/reshape") (synopsis "Flexibly reshape data") (description From 9879432da2fd15dea06771acf0406f7683bbf4e9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:14 +0200 Subject: [PATCH 0071/1394] gnu: r-restrserve: Update to 1.1.1. * gnu/packages/cran.scm (r-restrserve): Update to 1.1.1. [propagated-inputs]: Add r-digest. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 64ae523ddaf..9d3319d112d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4275,16 +4275,17 @@ curve to a data matrix in arbitrary dimensions.") (define-public r-restrserve (package (name "r-restrserve") - (version "1.0.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "RestRserve" version)) (sha256 - (base32 "0qb1x13n2sm0lg52x3289jsln3gw9rawfs1z2372pvr9ydpjsfqb")))) + (base32 "1ydsdgy6mxl0zqk7xqf4v6if5nf2qv7k48q340fhaqyjk2gd60p7")))) (build-system r-build-system) (propagated-inputs (list r-checkmate + r-digest r-jsonlite r-mime r-r6 From 8fa3e9f5137fd6af8694fd3907631c983168f7c1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:14 +0200 Subject: [PATCH 0072/1394] gnu: r-sp: Update to 1.4-7. * gnu/packages/cran.scm (r-sp): Update to 1.4-7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9d3319d112d..438c41f92ce 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4388,13 +4388,13 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.4-6") + (version "1.4-7") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 - (base32 "09m2ddbrbs2aqnq5si42ipa0g1vbd0pxg4zbcx59is2047pv7sws")))) + (base32 "1bdi06n5zkjnnyh0rallf04s0vlcx9rg9p5q7s6vfqvkf19nk501")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) From 69d208b4ded874a299f6d6160897354cd346aa65 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:14 +0200 Subject: [PATCH 0073/1394] gnu: r-rmtstat: Update to 0.3.1. * gnu/packages/cran.scm (r-rmtstat): Update to 0.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 438c41f92ce..56836c9feb4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4432,14 +4432,14 @@ a variety of different samplers.") (define-public r-rmtstat (package (name "r-rmtstat") - (version "0.3") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "RMTstat" version)) (sha256 (base32 - "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1")))) + "1r1a2sdqv64m9cpm2pz6r8abf7l810126ayd8iq3gx86c7bjfj5v")))) (properties `((upstream-name . "RMTstat"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/RMTstat") From 3651780fc2cfe440a0cc2ec1f0c1e15929ccf622 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:15 +0200 Subject: [PATCH 0074/1394] gnu: r-extremes: Update to 2.1-2. * gnu/packages/cran.scm (r-extremes): Update to 2.1-2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 56836c9feb4..9c293e3d541 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4593,14 +4593,14 @@ spreadsheet software.") (define-public r-extremes (package (name "r-extremes") - (version "2.1-1") + (version "2.1-2") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 - "00ps7yggp89sx1j0w6c8dk0la3k95rwjv1iz7rdfqy7i46xjf6as")))) + "19q560prq02h3bwk01jb68693qb5bhsv8wiqhia7v5knm34qv8x7")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs From e5eec206ae16f5296f1b755296360e3b99fc1136 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:15 +0200 Subject: [PATCH 0075/1394] gnu: r-bbmle: Update to 1.0.25. * gnu/packages/cran.scm (r-bbmle): Update to 1.0.25. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9c293e3d541..29ef76ed557 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4740,14 +4740,14 @@ matrices, a special case of sparse matrices.") (define-public r-bbmle (package (name "r-bbmle") - (version "1.0.24") + (version "1.0.25") (source (origin (method url-fetch) (uri (cran-uri "bbmle" version)) (sha256 (base32 - "1bck8rmink4wsk8pcbnj4d60svxymp29pxbzwj8p9gzsg42c1v81")))) + "0mdj21q7k0fp4cj7la14vmcjmp49zqm57g7r6zrwmxpv0acwda46")))) (build-system r-build-system) (propagated-inputs (list r-bdsmatrix From 99206a360fdd04e4c8a0cc718bc98530faf7410b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:15 +0200 Subject: [PATCH 0076/1394] gnu: r-energy: Update to 1.7-10. * gnu/packages/cran.scm (r-energy): Update to 1.7-10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 29ef76ed557..1b0747637f9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4876,14 +4876,14 @@ data). Weighted versions of MLE, MME and QME are available.") (define-public r-energy (package (name "r-energy") - (version "1.7-9") + (version "1.7-10") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 - "1ndssfi0hbnsm5jwrns7m63ppxm221hd6gk0b0wa1a7mk7ny1l38")))) + "19xyw5bkyzfk22gly2ca2nsznqnrhaq4a77727kr1k26bj3y8gal")))) (build-system r-build-system) (propagated-inputs (list r-boot r-gsl r-rcpp)) From f8f43d685e99a32416ec8eb95fb232596a12746b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:15 +0200 Subject: [PATCH 0077/1394] gnu: r-geometry: Update to 0.4.6. * gnu/packages/cran.scm (r-geometry): Update to 0.4.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1b0747637f9..0500315ecfc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5242,14 +5242,14 @@ Optimization problems by using the simplex algorithm.") (define-public r-geometry (package (name "r-geometry") - (version "0.4.5") + (version "0.4.6") (source (origin (method url-fetch) (uri (cran-uri "geometry" version)) (sha256 (base32 - "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg")))) + "1n7m0djqlhrv01l98r76grkki6cv4k4q2z6c7fksqgq4r2l6a14i")))) (build-system r-build-system) (propagated-inputs (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress)) From a03033dde1df0a623a1165623c24dbf3dedd1246 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:16 +0200 Subject: [PATCH 0078/1394] gnu: r-psych: Update to 2.2.5. * gnu/packages/cran.scm (r-psych): Update to 2.2.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0500315ecfc..0fedb50600d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5378,14 +5378,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "2.2.3") + (version "2.2.5") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "0fi7gcaxcb1mdyfpgjm03sxz3qgp1s0hnrgx8pyswni5skb903pn")))) + "08f3byqwabgkqcxwpjbsxdcjkdg012iraqinw0fzskfl1srzkhyw")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mnormt r-nlme)) From 63993ae9e004104be523d525765624d0bb0cba90 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:16 +0200 Subject: [PATCH 0079/1394] gnu: r-broom: Update to 0.8.0. * gnu/packages/cran.scm (r-broom): Update to 0.8.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0fedb50600d..c9fa25a9c04 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5431,14 +5431,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.7.12") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1nbv4a4s8548h2q226xmhyp42higayh95yvllh1rcs264lmw3yh4")))) + "16grzja9hz5mqpfzbp1r6zif1gp7swfadkm52340si9h8ifhk8b6")))) (build-system r-build-system) (propagated-inputs (list r-backports From 2ccb1881d4fbd734c401b23ea95898621b1ce72a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:16 +0200 Subject: [PATCH 0080/1394] gnu: r-pdist: Update to 1.2.1. * gnu/packages/cran.scm (r-pdist): Update to 1.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c9fa25a9c04..d712fd0f253 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5515,14 +5515,14 @@ models.") (define-public r-pdist (package (name "r-pdist") - (version "1.2") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "pdist" version)) (sha256 (base32 - "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd")))) + "0bvg8si81hs79v39d7svv4zbv2p0sk2r6m9vamibvkh9qvl4x406")))) (build-system r-build-system) (home-page "https://github.com/jeffwong/pdist") (synopsis "Partitioned distance function") From 83b90cc4a1baaf29362815fd63d835e469c9dae0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:17 +0200 Subject: [PATCH 0081/1394] gnu: r-hardyweinberg: Update to 1.7.5. * gnu/packages/cran.scm (r-hardyweinberg): Update to 1.7.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d712fd0f253..157f8781eb9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5884,14 +5884,14 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.7.4") + (version "1.7.5") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "11y3zg8aqxk5xdzsv7i3bgqkky6a0wgf2n8saa3a4adq75k328ib")))) + "0b3szw090dsc3bkas2kvx787ww2i6zzg2qmdyivmqc8amx5arn6g")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs From 7bf051be755d9647293a7c03e8a6a48052eaf942 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:17 +0200 Subject: [PATCH 0082/1394] gnu: r-venndiagram: Update to 1.7.3. * gnu/packages/cran.scm (r-venndiagram): Update to 1.7.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 157f8781eb9..913f9f2c8db 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5936,13 +5936,13 @@ and density estimation") (define-public r-venndiagram (package (name "r-venndiagram") - (version "1.7.1") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "VennDiagram" version)) (sha256 (base32 - "0yw54j9as0vf8ypnq4a3sl2w0lajri6s979f4y11hjzpgmr1m16b")))) + "0ilcxcp8qskmb5cp7fyb7i0qizg42lrx0ny8ws3if90kfrglghp7")))) (properties `((upstream-name . "VennDiagram"))) (build-system r-build-system) (propagated-inputs From c95a8f8488a4378cf1c5d8095e18b4bd81845ba2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:17 +0200 Subject: [PATCH 0083/1394] gnu: r-cli: Update to 3.3.0. * gnu/packages/cran.scm (r-cli): Update to 3.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 913f9f2c8db..93944e47187 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6270,14 +6270,14 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "3.2.0") + (version "3.3.0") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "0qp8k1afrn6ppwi6d9n05fjgj02196qcsppji3q37ph99msinnnd")))) + "0qqd4mscv8ndjbji7knprdlv2hhyk35gazagvapbjzq1p6yfpaf3")))) (build-system r-build-system) (propagated-inputs (list r-glue)) From 8defafa74212e92c18c60f3e246cc04ed3559637 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:17 +0200 Subject: [PATCH 0084/1394] gnu: r-webshot: Update to 0.5.3. * gnu/packages/cran.scm (r-webshot): Update to 0.5.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 93944e47187..2e81b02de41 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6419,14 +6419,14 @@ of merit, ordering functions, and enhanced versions of @code{pairs} and (define-public r-webshot (package (name "r-webshot") - (version "0.5.2") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 - "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi")))) + "1h6v94zwq0ypgi4vf8xlhp5k13j7f9061hx908177i68c6zg5i5p")))) (build-system r-build-system) (propagated-inputs (list r-callr r-jsonlite r-magrittr)) From 9bce612543ddf983e81fe4092b848cb243ee7d33 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:18 +0200 Subject: [PATCH 0085/1394] gnu: r-xfun: Update to 0.31. * gnu/packages/cran.scm (r-xfun): Update to 0.31. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2e81b02de41..5cc74210d54 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6474,13 +6474,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.30") + (version "0.31") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "1vn0cbskyrk8ww9yx75jni9s684yv4cvbj643lvg0lg00briry7b")))) + (base32 "0dgjkrlwl6rxmvdn6s1xrbiaa53hkfx2s7rqrbrc7c6shbkg6sfi")))) (build-system r-build-system) ;; knitr itself depends on xfun #; From c0d953640393650a2481f242921951186f723a67 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:18 +0200 Subject: [PATCH 0086/1394] gnu: r-vctrs: Update to 0.4.1. * gnu/packages/cran.scm (r-vctrs): Update to 0.4.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5cc74210d54..9abe6965f23 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6561,14 +6561,14 @@ estimated from a given sample.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "0bslr22jnnwxx45s1a19az6saqf2svi8vkjf64pnpc6rma4ygpl9")))) + "1pb0wjpwix29q8d8p3wi72a9mp9mif7369pk31w238cs00g8hxln")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-rlang)) From fb302963e48426ff62baee6a5cfe5d6ac7b4e1bf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:18 +0200 Subject: [PATCH 0087/1394] gnu: r-uuid: Update to 1.1-0. * gnu/packages/cran.scm (r-uuid): Update to 1.1-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9abe6965f23..7f70a4abd5c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6648,14 +6648,14 @@ packages that work with genomic data.") (define-public r-uuid (package (name "r-uuid") - (version "1.0-4") + (version "1.1-0") (source (origin (method url-fetch) (uri (cran-uri "uuid" version)) (sha256 (base32 - "08j3ylf49l9qslhlcxvix3mqw6hh8kxainnklv0qmwmwj6q6i5i8")))) + "0bzlc2knmr338h4ykx8v8c2a1inizxafj8rh13kwii68gpp50nz7")))) (build-system r-build-system) (home-page "https://www.rforge.net/uuid") (synopsis "Tools for generating and handling of UUIDs") From 29e58b927803530c9352da44b74245f126ec6d9a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:18 +0200 Subject: [PATCH 0088/1394] gnu: r-tinytex: Update to 0.39. * gnu/packages/cran.scm (r-tinytex): Update to 0.39. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7f70a4abd5c..54e4aaea0c1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6667,14 +6667,14 @@ packages that work with genomic data.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.38") + (version "0.39") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "11hww4x4q44xg559gplmjc6hmzmap0w249nnzyw5dy2ys30bbhga")))) + "1v95pjxdq0ma90jji5yqh8ihlcf35cmrqx9v0z649zh0q9vrnbpj")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) From 4b71cb93038526d9f8a6f6f01a6093262e83b538 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:19 +0200 Subject: [PATCH 0089/1394] gnu: r-network: Update to 1.17.2. * gnu/packages/cran.scm (r-network): Update to 1.17.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 54e4aaea0c1..4f32aeeecaa 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6726,14 +6726,14 @@ features: (define-public r-network (package (name "r-network") - (version "1.17.1") + (version "1.17.2") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 - "19q563v5xfkbmr0ws9nhqx4wrxkf9jsck51rqc8mm2gq2h03lg7w")))) + "1xrhzbci7ls4h05skdlirxl49jsvmylrqivz2kd6i33wh2ca324m")))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-statnet-common r-tibble)) From 20e8098845a3cd09f984c221984771bf116ae7fa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:19 +0200 Subject: [PATCH 0090/1394] gnu: r-statnet-common: Update to 4.6.0. * gnu/packages/cran.scm (r-statnet-common): Update to 4.6.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4f32aeeecaa..f956a22daac 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6795,14 +6795,14 @@ vectors.") (define-public r-statnet-common (package (name "r-statnet-common") - (version "4.5.0") + (version "4.6.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 - "0bw8dwnv568i60xrj6d7gv0hnna1x7rvqaayy5i0827khvdj7nrw")))) + "07djgc6qbxahiy5v15lfayxbj4188lxsb8xcs7hnbm2hic953bfx")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) From 336d2a712c7637b91a00f3d80d09824c802d99e1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:19 +0200 Subject: [PATCH 0091/1394] gnu: r-quantmod: Update to 0.4.20. * gnu/packages/cran.scm (r-quantmod): Update to 0.4.20. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f956a22daac..a8182b6a5f7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7212,14 +7212,14 @@ Fisher's method), and Sidak correction.") (define-public r-quantmod (package (name "r-quantmod") - (version "0.4.18") + (version "0.4.20") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 - "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a")))) + "154fqhw46kc7r08zsj5fsg97hg93phsli3z14xwmz22xb50xymzp")))) (build-system r-build-system) (propagated-inputs (list r-curl r-ttr r-xts r-zoo)) From ea5ade6de09b2bff2729ec0c78423c98b3b0a282 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:19 +0200 Subject: [PATCH 0092/1394] gnu: r-tseries: Update to 0.10-51. * gnu/packages/cran.scm (r-tseries): Update to 0.10-51. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a8182b6a5f7..599b64121f5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7233,14 +7233,14 @@ financial trading strategies.") (define-public r-tseries (package (name "r-tseries") - (version "0.10-50") + (version "0.10-51") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 - "16654v691jqpgiisz442h9znlxgj96c9gvhk3pgmm48bfsxs6iqw")))) + "0zr09ikaz96djcvnjbr8ah6waqzjy06f4yd4isshlwc391q20px5")))) (build-system r-build-system) (propagated-inputs (list r-quadprog r-quantmod r-zoo)) From 91c053804d53c4122375ebcf7509ccd12cbf5fe4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:20 +0200 Subject: [PATCH 0093/1394] gnu: r-import: Update to 1.3.0. * gnu/packages/cran.scm (r-import): Update to 1.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 599b64121f5..581754b4d1e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7679,14 +7679,14 @@ Memorial-Sloan-Kettering Cancer Center (MSKCC).") (define-public r-import (package (name "r-import") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "import" version)) (sha256 (base32 - "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37")))) + "19g4jnfg9pkvvsncw62yc15xlb97hfbdqxivpjd9jqi36i6mdjrg")))) (build-system r-build-system) (native-inputs (list r-knitr)) From d10b32c7eddf47f05654803e2961298cc07b1c0e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:20 +0200 Subject: [PATCH 0094/1394] gnu: r-shinyace: Update to 0.4.2. * gnu/packages/cran.scm (r-shinyace): Update to 0.4.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 581754b4d1e..008c0d3935c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7705,14 +7705,14 @@ files.") (define-public r-shinyace (package (name "r-shinyace") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 - "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn")))) + "12mqvdh6rxsr61pc3pzla95r5f4l7xagjs2rcdr7c2lbqyxpx6aa")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs From b2a592537fff7e2c933545a6fe5bb5a1ee6e0d98 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:20 +0200 Subject: [PATCH 0095/1394] gnu: r-radiant-data: Update to 1.4.2. * gnu/packages/cran.scm (r-radiant-data): Update to 1.4.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 008c0d3935c..c830a64f7d3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7796,14 +7796,14 @@ systems.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "12x4nz5n6yz1a67ji79pwvznp9flmn50hpp9y9sfhixir7dvwy27")) + "0c5c99q13pwv6k0b07x3r2bxmh0h2w15h02xb1pincgs61qwi15k")) (modules '((guix build utils))) (snippet '(begin From da073f7f8429779d0e9e9b069a94827f7d132a10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:21 +0200 Subject: [PATCH 0096/1394] gnu: r-algdesign: Update to 1.2.1. * gnu/packages/cran.scm (r-algdesign): Update to 1.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c830a64f7d3..4da2cc5bcc7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7857,13 +7857,13 @@ the application.") (define-public r-algdesign (package (name "r-algdesign") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "AlgDesign" version)) (sha256 - (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz")))) + (base32 "01cx63wqr6yvgl5ml1lj6gh9p1sn42b6qcnsppcw7mvba9n652ar")))) (properties `((upstream-name . "AlgDesign"))) (build-system r-build-system) (home-page "https://github.com/jvbraun/AlgDesign") From 24dd8530221b5cd9c5c6d29bb35ec9b3dd66a3a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:21 +0200 Subject: [PATCH 0097/1394] gnu: r-fnn: Update to 1.1.3.1. * gnu/packages/cran.scm (r-fnn): Update to 1.1.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4da2cc5bcc7..df71bdaa40b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8063,14 +8063,14 @@ multivariate plot methods.") (define-public r-fnn (package (name "r-fnn") - (version "1.1.3") + (version "1.1.3.1") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 - "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny")))) + "0nmynpiy3d2dnd5ngjf4m79jy02byhk43gj0xny9a6j8243f5c2j")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") From 64c6f89671cb5bd94e9e72915fd671d27e5adf70 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:21 +0200 Subject: [PATCH 0098/1394] gnu: r-abc: Update to 2.2.1. * gnu/packages/cran.scm (r-abc): Update to 2.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index df71bdaa40b..bc89e2990e8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8287,14 +8287,14 @@ goodness-of-fit.") (define-public r-abc (package (name "r-abc") - (version "2.1") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "abc" version)) (sha256 (base32 - "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb")))) + "16753lyzk2dfwgdjfyanwacqw3bvrwby52inq4709804labs6lnv")))) (build-system r-build-system) (propagated-inputs (list r-abc-data r-locfit r-mass r-nnet r-quantreg)) From 02c4b86cf3f36395751845674c037a746f7e2069 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:21 +0200 Subject: [PATCH 0099/1394] gnu: r-maptools: Update to 1.1-4. * gnu/packages/cran.scm (r-maptools): Update to 1.1-4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bc89e2990e8..89015eebbb4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8393,14 +8393,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "1.1-3") + (version "1.1-4") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "0ixvh4qbdjjl19ghgbb2r26yksya977q1yzs4yn5wshwm0763xph")))) + "1jgx8iiirj8qhrmh19mkisa35jcql7352dmc7lvwi5vxg3wjbvpk")))) (build-system r-build-system) (propagated-inputs (list r-foreign r-lattice r-sp)) From ad26dda85197a47e3cf966f4e96aae6fcfd4f35e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:22 +0200 Subject: [PATCH 0100/1394] gnu: r-renv: Update to 0.15.5. * gnu/packages/cran.scm (r-renv): Update to 0.15.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 89015eebbb4..53a8fd95b48 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8835,14 +8835,14 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "0.15.4") + (version "0.15.5") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "0byfs4cydhyqzdrxjv7sa6i30xc7qhnx0qw9d8wwwlzdkv235flf")))) + "0bjq3ms5dg155clya62m462m93g90sxfxm7b4cqhqbx8vakskwdl")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs From 7e9031c41dc7a8e2c762ebb6117b461c8a95e2a8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:22 +0200 Subject: [PATCH 0101/1394] gnu: r-reticulate: Update to 1.25. * gnu/packages/cran.scm (r-reticulate): Update to 1.25. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 53a8fd95b48..e59578d60b0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8952,14 +8952,14 @@ always locate the files relative to your project root.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.24") + (version "1.25") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "1k0nv43fa9lx44pamxpprnvvmsp15adn5z6hg9siyq0n94hca65r")))) + "0b1szzsqyc8wcfpkn5517bb1ds064vs2hky71my3p74kfngay991")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs From 87439c8a9a6dd45e23cb1a97887ef140fa54dc9a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:22 +0200 Subject: [PATCH 0102/1394] gnu: r-nbclust: Update to 3.0.1. * gnu/packages/cran.scm (r-nbclust): Update to 3.0.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e59578d60b0..4c98629b596 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9352,14 +9352,14 @@ that account for the effects of ANSI text formatting control sequences.") (define-public r-nbclust (package (name "r-nbclust") - (version "3.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "NbClust" version)) (sha256 (base32 - "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c")))) + "0k5hr4zgx4gp1n62xchgz2zvyl35ba2cnczhhvj8rfbg2n4hx6qs")))) (properties `((upstream-name . "NbClust"))) (build-system r-build-system) (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package") From 45e709aba990c144b872fca9fc32942e8f026573 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:22 +0200 Subject: [PATCH 0103/1394] gnu: r-rjags: Update to 4-13. * gnu/packages/cran.scm (r-rjags): Update to 4-13. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4c98629b596..191570c6fdd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9526,14 +9526,14 @@ functions.") (define-public r-rjags (package (name "r-rjags") - (version "4-12") + (version "4-13") (source (origin (method url-fetch) (uri (cran-uri "rjags" version)) (sha256 (base32 - "041y4zfr50y96g0kl857jcba0a3gpdpk8qfn9fj8zxzbz71k87xr")))) + "0cibz6xhmh86fh7ynmdgpmlchizi57pi6dpslgc2if17a56c6p7q")))) (build-system r-build-system) (propagated-inputs (list r-coda)) From 054842979e1351d13df0809f996bf8c46680e0ec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:22 +0200 Subject: [PATCH 0104/1394] gnu: r-insight: Update to 0.17.1. * gnu/packages/cran.scm (r-insight): Update to 0.17.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 191570c6fdd..3667ce777fc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9816,14 +9816,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.17.0") + (version "0.17.1") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "1rxcy8nyg3y50czm3y1x2pibivywcb1bjmvpyqlzg4yy2j84v69p")))) + "0dffrsimgijdqsgvr9cad4g4w97d5ssjl3l0fm5ssly9l115ag35")))) (build-system r-build-system) (native-inputs (list r-knitr)) From 65a0fa0dd3af714d82b02fcdb52bbed09b6fffdb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:23 +0200 Subject: [PATCH 0105/1394] gnu: r-argparse: Update to 2.1.5. * gnu/packages/cran.scm (r-argparse): Update to 2.1.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3667ce777fc..7a68506b4a1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10101,14 +10101,14 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "2.1.3") + (version "2.1.5") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "0vm6nrzl6rsq2qw3km3i4s92kq9phs3cbxzv3i8hlyld9ajk3nmf")))) + "13b5halfxc7nr57vkz3qmkkcpw1hr4xdk1mjh2cq8cvpnjz15qc3")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs From 5ac39e473847b50c3f01e3edc7063feddbf5b8d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:23 +0200 Subject: [PATCH 0106/1394] gnu: r-doby: Update to 4.6.13. * gnu/packages/cran.scm (r-doby): Update to 4.6.13. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7a68506b4a1..b3d33d43d93 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10195,14 +10195,14 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.12") + (version "4.6.13") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "1m60ya4cdickqsj0dc90bv4n47df6qg6n82fikxrkl4yhg7yyn1i")))) + "0qnfcw4rg5kd1mll3rq6vchz3lgdqfif9469p8x6ixsgrxxpivbz")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs From 2bdc02ca09145e839512046198118861649fd5db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:23 +0200 Subject: [PATCH 0107/1394] gnu: r-cmplot: Update to 4.1.0. * gnu/packages/cran.scm (r-cmplot): Update to 4.1.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b3d33d43d93..e4bf183dce3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10506,14 +10506,14 @@ from the @code{stats} package (plus some extra parameters).") (define-public r-cmplot (package (name "r-cmplot") - (version "4.0.0") + (version "4.1.0") (source (origin (method url-fetch) (uri (cran-uri "CMplot" version)) (sha256 (base32 - "0xyh75y0c84nnkrv6c8xrvla54w51phgdwn8a69799f2r87z7c81")))) + "1h09prpiw7l32mr7jarp8ddrddg1431nfn4kw3bznfnv0sr78zfg")))) (properties `((upstream-name . "CMplot"))) (build-system r-build-system) (home-page "https://github.com/YinLiLin/CMplot") From 256e1f2358e7ffe74575f350627dec27a499690e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:23 +0200 Subject: [PATCH 0108/1394] gnu: r-drtmle: Update to 1.1.1. * gnu/packages/cran.scm (r-drtmle): Update to 1.1.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e4bf183dce3..b4c6ce6fb44 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10836,14 +10836,14 @@ a library of prediction algorithms to be used in the super learner.") (define-public r-drtmle (package (name "r-drtmle") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "drtmle" version)) (sha256 (base32 - "08a6k0nrg6mqdslwjc71583x52vnax87nbfalk98zczwvrrdwvxa")))) + "12vplpz9bg5444jy29mbdr70hqby073vb3iw76v2csrwy3ws3f21")))) (properties `((upstream-name . "drtmle"))) (build-system r-build-system) (propagated-inputs From c00b0070bfbdf607c1025c77513f3eaa8eed7f3e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:24 +0200 Subject: [PATCH 0109/1394] gnu: r-dofuture: Update to 0.12.2. * gnu/packages/cran.scm (r-dofuture): Update to 0.12.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b4c6ce6fb44..17190ec6cc6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10861,14 +10861,14 @@ both to consistency and asymptotic normality.") (define-public r-dofuture (package (name "r-dofuture") - (version "0.12.1") + (version "0.12.2") (source (origin (method url-fetch) (uri (cran-uri "doFuture" version)) (sha256 (base32 - "0fhk32ih9cbwxw3mvkddqjv0dsaw9xk8qjdslfcabvmixhnh3s6m")))) + "0w07pmzpsfq4kvfc745s1i9b6dfn1df1wrfi4s9ys4ir3g2s8nk1")))) (properties `((upstream-name . "doFuture"))) (build-system r-build-system) (arguments From bf192c0bef90e8dd137c7e97c2ddada0e927743b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:24 +0200 Subject: [PATCH 0110/1394] gnu: r-labelled: Update to 2.9.1. * gnu/packages/cran.scm (r-labelled): Update to 2.9.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 17190ec6cc6..80c687f7c2f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10972,14 +10972,14 @@ subsequence} (LCS) using a dynamic programming algorithm.") (define-public r-labelled (package (name "r-labelled") - (version "2.9.0") + (version "2.9.1") (source (origin (method url-fetch) (uri (cran-uri "labelled" version)) (sha256 (base32 - "0ffnhlr239nqcwb35m4hll21abnnhpmyy5wlxnyahrg0kqb0xb1n")))) + "0h7scbyzh7kr51gds222rkhld2b3k36s86hj8rrzpwv4bwj0pccy")))) (properties `((upstream-name . "labelled"))) (build-system r-build-system) (propagated-inputs From f230bab5d99748f5362bf61454fb251e465730e2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:24 +0200 Subject: [PATCH 0111/1394] gnu: r-svdialogs: Update to 1.1.0. * gnu/packages/cran.scm (r-svdialogs): Update to 1.1.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 80c687f7c2f..5be3d97ce1b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11166,13 +11166,13 @@ calls to the particular toolkits in use in function of the context.") (define-public r-svdialogs (package (name "r-svdialogs") - (version "1.0.3") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "svDialogs" version)) (sha256 - (base32 "0j00xjvkwv992ir48czhvyj29rb9vpd243vbyyj2binn0q0qa431")))) + (base32 "0z3a5glsi0ab43mdk2yvslxyzg12nbqqqc35jvgzj475mpkbgjif")))) (properties `((upstream-name . "svDialogs"))) (build-system r-build-system) (inputs From 80730da84e6ed492ad8d76f9138ad803d1511552 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:24 +0200 Subject: [PATCH 0112/1394] gnu: r-furrr: Update to 0.3.0. * gnu/packages/cran.scm (r-furrr): Update to 0.3.0. [propagated-inputs]: Remove r-ellipsis. --- gnu/packages/cran.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5be3d97ce1b..da7cb840582 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11259,18 +11259,17 @@ genotypes as \"graphical genotypes\".") (define-public r-furrr (package (name "r-furrr") - (version "0.2.3") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "furrr" version)) (sha256 (base32 - "001p2yhznrpnrjvdcmf2h3wpgdnw01wnqgid7wbq8bhavhi3888a")))) + "117xj66l14r08macwghgyibzm282ljv1afpa133h952gc70irs9z")))) (build-system r-build-system) (propagated-inputs - (list r-ellipsis - r-future + (list r-future r-globals r-lifecycle r-purrr From 0d606a229ef884d82db2989f7251e3c08343da6b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:25 +0200 Subject: [PATCH 0113/1394] gnu: r-th-data: Update to 1.1-1. * gnu/packages/cran.scm (r-th-data): Update to 1.1-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index da7cb840582..c188f8598a7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12028,14 +12028,14 @@ cross-sectional, time series, clustered, panel, and longitudinal data.") (define-public r-th-data (package (name "r-th-data") - (version "1.1-0") + (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "TH.data" version)) (sha256 (base32 - "0ghihfpk5d8gsdlzf6phw7dwwz3adx64pxk82vlmlqx53ljpxcr1")))) + "0ynxacnz002bjsp2ybql7rdqw4zd14af8r7w44nwbx22n4bapwzd")))) (properties `((upstream-name . "TH.data"))) (build-system r-build-system) (propagated-inputs From 847c134325d46cde14259d3716a66352d972378b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:25 +0200 Subject: [PATCH 0114/1394] gnu: r-multcomp: Update to 1.4-19. * gnu/packages/cran.scm (r-multcomp): Update to 1.4-19. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c188f8598a7..8cd49cfff75 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12052,14 +12052,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-18") + (version "1.4-19") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "01i8gjppyxl3xph1dw0kags8qbb7r06j91kk3lkqn5gzrxjmwyhh")))) + "0mz5wdqrqpp2gqijfpp9rgfbq8yvxki4is8fbbc4qwdwryqp6d7h")))) (build-system r-build-system) (propagated-inputs (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data)) From b56c3b790c9452ac0c57abe684e086e0e3b1d23c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:25 +0200 Subject: [PATCH 0115/1394] gnu: r-emmeans: Update to 1.7.4-1. * gnu/packages/cran.scm (r-emmeans): Update to 1.7.4-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8cd49cfff75..92ed530c6e0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12097,14 +12097,14 @@ the differences were not significantly different.") (define-public r-emmeans (package (name "r-emmeans") - (version "1.7.3") + (version "1.7.4-1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "0kbbin3zfxqkm5awq4331fv7y2kfpdhkwrqh91prl7qpf8kscin6")))) + "08g7ifqhwqa00hc850nwx03dp7isz0281ig6kvixc4xdahmkm8zp")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv r-xtable)) From 142ce27e7ac83ea19c960f4977a6b3eed6d375dc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:25 +0200 Subject: [PATCH 0116/1394] gnu: r-tmb: Update to 1.9.0. * gnu/packages/cran.scm (r-tmb): Update to 1.9.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 92ed530c6e0..6aca05a5b4c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12226,14 +12226,14 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.8.1") + (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "1hzvvx1g5nkmiqwzihj8nir48k7idbw1jvb14ldjk9rsikgpywdl")))) + "1mr5vwamw6ag1fhd83jyy6015296908qwshwq0fcphhiv60x579c")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs From 50f2249e1937c7e8235f311d140c795e8e8cb9af Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:26 +0200 Subject: [PATCH 0117/1394] gnu: r-bayestestr: Update to 0.12.1. * gnu/packages/cran.scm (r-bayestestr): Update to 0.12.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6aca05a5b4c..9f9e49ff5e6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12329,14 +12329,14 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.11.5") + (version "0.12.1") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "0lz8mzacxgmll576p88654mrvlk4pzvhwwghvn5pm7zxisgx0kq0")))) + "1fbkpagc5zznrafy7h68nhx43a1yg4v7242pbqjkd0h2481c101z")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs From 1a4f4cc6f5f09bb9bdd314fc7b8cc1bd47fe8b3c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:26 +0200 Subject: [PATCH 0118/1394] gnu: r-effectsize: Update to 0.7.0. * gnu/packages/cran.scm (r-effectsize): Update to 0.7.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9f9e49ff5e6..bfc6c8a3607 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12410,14 +12410,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.6.0.1") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "1rhpbhyrv0avinm6dz6v2qw4xxdl9m1wknq1dv2flfxgcz0k9qiz")))) + "07dbj7n9vwjkb7xrdj224lzc3ppr3jjdgyyilkj7gpkvgjgfrqhz")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs From d90ccca7a47404bbb6df86b20873a2d9ce240cfc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:26 +0200 Subject: [PATCH 0119/1394] gnu: r-usethis: Update to 2.1.6. * gnu/packages/cran.scm (r-usethis): Update to 2.1.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bfc6c8a3607..317ea7c07f5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12699,14 +12699,14 @@ User credentials are shared with command line git through the (define-public r-usethis (package (name "r-usethis") - (version "2.1.5") + (version "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 - "0lph2rxv7nq3h022gp8d50wbq5lwicnx85d2l5dx876wxhb9wlvx")))) + "0638dzl4nm4c36990sf2biy74hjr2fzlqzfb98fsqrbhaw3ngp1i")))) (build-system r-build-system) (propagated-inputs (list r-cli From 41261ba3c8d86628b956119abffae4abe1290201 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:26 +0200 Subject: [PATCH 0120/1394] gnu: r-summarytools: Update to 1.0.1. * gnu/packages/cran.scm (r-summarytools): Update to 1.0.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 317ea7c07f5..ed430b838e2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12887,14 +12887,14 @@ ways.") (define-public r-summarytools (package (name "r-summarytools") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 - "04qcysfywljnqkcz2b7kzpy0xv3ykkvvb14vnda63z1wvmadyhkn")))) + "0gr95cd1ja8di6s0xghk6w7nj3bh3z4g7j7ixdy7f88q681aixgx")))) (build-system r-build-system) (propagated-inputs (list r-base64enc From c64d37aa2d311f5e4766707f55a9aa56ed3f9fd3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:27 +0200 Subject: [PATCH 0121/1394] gnu: r-afex: Update to 1.1-1. * gnu/packages/cran.scm (r-afex): Update to 1.1-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ed430b838e2..cf1f4d411a6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13058,14 +13058,14 @@ analysing multivariate abundance data in community ecology.") (define-public r-afex (package (name "r-afex") - (version "1.1-0") + (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "afex" version)) (sha256 (base32 - "0h8zqv82dqll19l3p89a2csvgnx8ayb2bajq7b35a8svhj427zax")))) + "09q426s2zmzxx5ilxy0x5mflpb38pl075ss1s8xvpswkn6cia0b6")))) (build-system r-build-system) ;; This is needed for the vignette builder (arguments From b4ad23fd8d435aaed04c44221df40a44e2c29bd2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:27 +0200 Subject: [PATCH 0122/1394] gnu: r-biocmanager: Update to 1.30.18. * gnu/packages/cran.scm (r-biocmanager): Update to 1.30.18. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cf1f4d411a6..75d942c77a0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13349,13 +13349,13 @@ netCDF files.") (define-public r-biocmanager (package (name "r-biocmanager") - (version "1.30.16") + (version "1.30.18") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 - (base32 "0m9qxwqajg8lp0z06blbpgk3zw0z73aly1cvmjk6mvwja6jm99vm")))) + (base32 "0dawbd546rznllpw5wq282r0viga4cck398d4s1inkk18mmi4qzp")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (native-inputs From 9f4b3bfec549f33a02b0661c6d7b005bfabc10b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:27 +0200 Subject: [PATCH 0123/1394] gnu: r-rgl: Update to 0.108.3.2. * gnu/packages/cran.scm (r-rgl): Update to 0.108.3.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 75d942c77a0..b88f88c7ca2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13370,14 +13370,14 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "0.108.3") + (version "0.108.3.2") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "0fqkx079z9y5b1gdg6qfz2wpw2j8q3ddflfkd9wwrkyacas6xyc9")))) + "0r9wzhjzl346i37ngs6hqzmizhi53kzqz582lv822v6yxang6fh3")))) (build-system r-build-system) (native-inputs (list pkg-config r-knitr)) From 3db089a2920a8a794c74eee8f586be9fbcc890bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:28 +0200 Subject: [PATCH 0124/1394] gnu: r-ks: Update to 1.13.5. * gnu/packages/cran.scm (r-ks): Update to 1.13.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b88f88c7ca2..1a45641bce2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13451,13 +13451,13 @@ isosurfaces.") (define-public r-ks (package (name "r-ks") - (version "1.13.4") + (version "1.13.5") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 - (base32 "15sm1ys7sk0gn7hr1vik4xrn4jdf837knwk7j8h32lr29w9mh917")))) + (base32 "05bqrjkbx2kn5aax0hy3xd6pf7nxka9bm1sp8ll1cc2gf1nx1i6i")))) (build-system r-build-system) (propagated-inputs (list r-fnn From e1048c8ef5be7949890fc426aa05cf3769f6f3c5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:28 +0200 Subject: [PATCH 0125/1394] gnu: r-circular: Update to 0.4-95. * gnu/packages/cran.scm (r-circular): Update to 0.4-95. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1a45641bce2..c5e25864f13 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13536,14 +13536,14 @@ University Press, 2007.") (define-public r-circular (package (name "r-circular") - (version "0.4-94") + (version "0.4-95") (source (origin (method url-fetch) (uri (cran-uri "circular" version)) (sha256 (base32 - "0wanbd6n7g1avvyc7pm0lnkwg868dix2byiz4wm6vmxzm0y47fmr")))) + "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8")))) (build-system r-build-system) (propagated-inputs (list r-boot r-mvtnorm)) From 9d96f5c9c5f0a5201469c0b0f514a4f9a992230a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:28 +0200 Subject: [PATCH 0126/1394] gnu: r-activity: Update to 1.3.2. * gnu/packages/cran.scm (r-activity): Update to 1.3.2. [propagated-inputs]: Remove r-circular. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c5e25864f13..b8df25bd9fc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13560,17 +13560,17 @@ Scientific.") (define-public r-activity (package (name "r-activity") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "activity" version)) (sha256 (base32 - "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5")))) + "11n6wmqz7p3428rr615f92m61a5gb908xpn4l8q484h61bwg38c3")))) (build-system r-build-system) (propagated-inputs - (list r-circular r-insol r-pbapply)) + (list r-insol r-pbapply)) (home-page "https://cran.r-project.org/web/packages/activity/") (synopsis "Animal activity statistics") (description From 11e13a213de9ed755eb84548fd18318bc1370291 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:29 +0200 Subject: [PATCH 0127/1394] gnu: r-ouch: Update to 2.18. * gnu/packages/cran.scm (r-ouch): Update to 2.18. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b8df25bd9fc..78b99131cc9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13584,14 +13584,14 @@ circular variables).") (define-public r-ouch (package (name "r-ouch") - (version "2.17") + (version "2.18") (source (origin (method url-fetch) (uri (cran-uri "ouch" version)) (sha256 (base32 - "1a7r24j59xz3lxa5wc694j6b80j8m5l86zd1sw9pvs66l8gd98kf")))) + "119s9llpjy0b4q830xig2xr66fq6izp6mr2k4k79ggmf3gxww8as")))) (build-system r-build-system) (propagated-inputs (list r-subplex)) (home-page "https://kingaa.github.io/ouch/") From 13dc616316dfe8ba25528e292fabfe6153c8842d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:29 +0200 Subject: [PATCH 0128/1394] gnu: r-admisc: Update to 0.27. * gnu/packages/cran.scm (r-admisc): Update to 0.27. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 78b99131cc9..fef8dfaa890 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13688,13 +13688,13 @@ Anderson-Darling Distribution\".") (define-public r-admisc (package (name "r-admisc") - (version "0.26") + (version "0.27") (source (origin (method url-fetch) (uri (cran-uri "admisc" version)) (sha256 - (base32 "19zkwyp8gvq8f74midmwld4azx44sbqxqx9mgs726i6dhnls6821")))) + (base32 "07hfrhv3pcldsffnyfzpa1q3x32gxr1386r8fik1nhql2w46mm13")))) (properties `((upstream-name . "admisc"))) (build-system r-build-system) (home-page "https://github.com/dusadrian/admisc") From d408f8df2a0ea84f05332c350f0439233b186b8c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:29 +0200 Subject: [PATCH 0129/1394] gnu: r-colorramps: Update to 2.3.1. * gnu/packages/cran.scm (r-colorramps): Update to 2.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fef8dfaa890..e4eda56429d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13909,14 +13909,14 @@ over-plotting in scatter plots with text.") (define-public r-colorramps (package (name "r-colorramps") - (version "2.3") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "colorRamps" version)) (sha256 (base32 - "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z")))) + "12jnkj50yh2hc5l7j56lrrrmn58akrj9dwj98vzf42iq4h42kwb1")))) (properties `((upstream-name . "colorRamps"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/colorRamps") From 9683a3bfa6a65c473d7c85cdecbcd6f9ff9fd2ce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:29 +0200 Subject: [PATCH 0130/1394] gnu: r-rspectra: Update to 0.16-1. * gnu/packages/cran.scm (r-rspectra): Update to 0.16-1. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e4eda56429d..f528e0901e0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14167,18 +14167,20 @@ definiteness of a matrix.") (define-public r-rspectra (package (name "r-rspectra") - (version "0.16-0") + (version "0.16-1") (source (origin (method url-fetch) (uri (cran-uri "RSpectra" version)) (sha256 (base32 - "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda")))) + "16ij84wgpsmqmnxqiii8dgihy3bfxazry9znmckhwzba7m0d79fb")))) (properties `((upstream-name . "RSpectra"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcppeigen)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/yixuan/RSpectra") (synopsis "Solvers for large-scale Eigenvalue and SVD problems") (description From ad798636b81481f6b5409462bfb82df2425942ea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:30 +0200 Subject: [PATCH 0131/1394] gnu: r-flare: Update to 1.7.0.1. * gnu/packages/cran.scm (r-flare): Update to 1.7.0.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f528e0901e0..c47464c5a6a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14216,14 +14216,14 @@ diagnostics for controlling type-1 errors are also provided.") (define-public r-flare (package (name "r-flare") - (version "1.7.0") + (version "1.7.0.1") (source (origin (method url-fetch) (uri (cran-uri "flare" version)) (sha256 (base32 - "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251")))) + "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5")))) (build-system r-build-system) (propagated-inputs (list r-igraph r-lattice r-mass r-matrix)) From 0396e479f7f6223b2be021462d43974bd7a7b0dc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:30 +0200 Subject: [PATCH 0132/1394] gnu: r-rnexml: Update to 2.4.7. * gnu/packages/cran.scm (r-rnexml): Update to 2.4.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c47464c5a6a..108a8eac691 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14357,13 +14357,13 @@ methods, incorporating one or more trees and trait data.") (define-public r-rnexml (package (name "r-rnexml") - (version "2.4.6") + (version "2.4.7") (source (origin (method url-fetch) (uri (cran-uri "RNeXML" version)) (sha256 (base32 - "0k56brcg80mvx35hgc5gj8arwba4k7q0075g38qp0qgq9d1b87cs")))) + "1zp6pijsc73jx8cmxb1hng36nvaf5wnhldnzlqhmba9kv9niscfb")))) (build-system r-build-system) (propagated-inputs (list r-ape From 75a2d8e31806f67adae7dc208680e4904957b804 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:30 +0200 Subject: [PATCH 0133/1394] gnu: r-assertive-properties: Update to 0.0-5. * gnu/packages/cran.scm (r-assertive-properties): Update to 0.0-5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 108a8eac691..276838a464b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14907,14 +14907,14 @@ want to include run-time testing features in their own packages.") (define-public r-assertive-properties (package (name "r-assertive-properties") - (version "0.0-4") + (version "0.0-5") (source (origin (method url-fetch) (uri (cran-uri "assertive.properties" version)) (sha256 (base32 - "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw")))) + "1pgljbwwbvbl4kc5c8mcv0qbzq3k6fzi29k88811yml263sm92dn")))) (properties `((upstream-name . "assertive.properties"))) (build-system r-build-system) From 2ce26f27a481af301002e2133cb6c69c62425d3b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:30 +0200 Subject: [PATCH 0134/1394] gnu: r-spatialextremes: Update to 2.1-0. * gnu/packages/cran.scm (r-spatialextremes): Update to 2.1-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 276838a464b..7d8f3694931 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15368,14 +15368,14 @@ covariance functions for large data sets.") (define-public r-spatialextremes (package (name "r-spatialextremes") - (version "2.0-9") + (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "SpatialExtremes" version)) (sha256 (base32 - "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y")))) + "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3")))) (properties `((upstream-name . "SpatialExtremes"))) (build-system r-build-system) From 2b1400d659432db4dc560364c7f692016e7fbdb1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:31 +0200 Subject: [PATCH 0135/1394] gnu: r-epi: Update to 2.46. * gnu/packages/cran.scm (r-epi): Update to 2.46. [propagated-inputs]: Remove r-purrr; add r-magrittr. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7d8f3694931..3ce5452f4f4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15644,14 +15644,14 @@ model with finite state space using the Aalen-Johansen estimator.") (define-public r-epi (package (name "r-epi") - (version "2.44") + (version "2.46") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 - "1wcxr1f7irgfdwzz4vf67114yhxrhxxxnhy4hfaww0zy91vzxx10")))) + "0s3ij0rya4wd7k97kc4s3pwj1d1ypaxl1s7zqr6sa07hp4a8fzz0")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs @@ -15659,12 +15659,12 @@ model with finite state space using the Aalen-Johansen estimator.") r-data-table r-dplyr r-etm + r-magrittr r-mass r-matrix r-mgcv r-numderiv r-plyr - r-purrr r-survival r-zoo)) (home-page "https://BendixCarstensen.com/Epi/") From ec5682eaf40355bf2b7f331243dcb4850baa0b2b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:31 +0200 Subject: [PATCH 0136/1394] gnu: r-globals: Update to 0.15.0. * gnu/packages/cran.scm (r-globals): Update to 0.15.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3ce5452f4f4..3ceff82e93a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15801,14 +15801,14 @@ subsetting.") (define-public r-globals (package (name "r-globals") - (version "0.14.0") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "globals" version)) (sha256 (base32 - "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90")))) + "15llx4233ihj4w815k7inc17530w9ja0mi29n1i0s2sr42j8jdpq")))) (build-system r-build-system) (propagated-inputs (list r-codetools)) From 26cf8fd7a550de8ae6e5f1bcc2107903874087ac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:31 +0200 Subject: [PATCH 0137/1394] gnu: r-parallelly: Update to 1.31.1. * gnu/packages/cran.scm (r-parallelly): Update to 1.31.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3ceff82e93a..f3b5b8455e0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15825,14 +15825,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.31.0") + (version "1.31.1") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "0kjwxgxnlpjbxpr1dyzk3nyx9fwa6vwqr22bvsxz56xwxnirzdxx")))) + "1nhp66psk3m79is5qm4ppxkj7bdy46jr2h2pir22ia9ghhyzris0")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") From 3be0661b5fe7041abc9385865004a14e7cb6de28 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:31 +0200 Subject: [PATCH 0138/1394] gnu: r-future: Update to 1.26.1. * gnu/packages/cran.scm (r-future): Update to 1.26.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f3b5b8455e0..086a58abe10 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15853,14 +15853,14 @@ port-forwarding to your local computer.") (define-public r-future (package (name "r-future") - (version "1.24.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "0xmj17fq9paww796490bmakv6pcvrzk15i8mzhxk1mp9l0mj32vv")))) + "1mchjdvvwgs8v0iv8z5m6gav3xzvnq11h8qrc7lfnrb2x3d0np53")))) (build-system r-build-system) (arguments `(#:phases From 1906d197b8015491310c89acf2943708ba9347d6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:32 +0200 Subject: [PATCH 0139/1394] gnu: r-future-apply: Update to 1.9.0. * gnu/packages/cran.scm (r-future-apply): Update to 1.9.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 086a58abe10..646ed52256e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15888,14 +15888,14 @@ the local machine to, say, distributed processing on a remote compute cluster.") (define-public r-future-apply (package (name "r-future-apply") - (version "1.8.1") + (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 - "1ix61bfbk43pwnjb0wk8lkfgdsy5zi8svk74gar5nrl90b5w6nqd")))) + "1xb7qj8izjwmy4aa92p5f4cdbhgp220hrly3b5879f9hrv2w2rk1")))) (properties `((upstream-name . "future.apply"))) (build-system r-build-system) (arguments From d8a7ea0073ecb7ac5e0f73132584eab91c6c972f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:32 +0200 Subject: [PATCH 0140/1394] gnu: r-shinybs: Update to 0.61.1. * gnu/packages/cran.scm (r-shinybs): Update to 0.61.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 646ed52256e..0e696dbf424 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16071,14 +16071,14 @@ several common set, element and attribute related tasks.") (define-public r-shinybs (package (name "r-shinybs") - (version "0.61") + (version "0.61.1") (source (origin (method url-fetch) (uri (cran-uri "shinyBS" version)) (sha256 (base32 - "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji")))) + "0h51685a9qll4agayldjyryi60ih969219ibg071slv0613p5v8a")))) (properties `((upstream-name . "shinyBS"))) (build-system r-build-system) ;; The tests spawn Shiny browser apps. They cannot be run From a3613ed76d6813fa9102704faa645894c2c6de3f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:32 +0200 Subject: [PATCH 0141/1394] gnu: r-minpack-lm: Update to 1.2-2. * gnu/packages/cran.scm (r-minpack-lm): Update to 1.2-2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0e696dbf424..c5853f2faeb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16509,14 +16509,14 @@ marginal histograms/boxplots/density plots to ggplot2 scatterplots.") (define-public r-minpack-lm (package (name "r-minpack-lm") - (version "1.2-1") + (version "1.2-2") (source (origin (method url-fetch) (uri (cran-uri "minpack.lm" version)) (sha256 (base32 - "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql")))) + "11yz6hk2r33571d16kq01cb1x6sgdzi6jmksqlrm8mr84l95c2f7")))) (properties `((upstream-name . "minpack.lm"))) (build-system r-build-system) (native-inputs (list gfortran)) From d4bfec54d7429c2f55d91c27ad6effac1a6f6493 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:32 +0200 Subject: [PATCH 0142/1394] gnu: r-moments: Update to 0.14.1. * gnu/packages/cran.scm (r-moments): Update to 0.14.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c5853f2faeb..2148028d874 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16533,14 +16533,14 @@ for lower and upper parameter bounds. The implementation can be used via (define-public r-moments (package (name "r-moments") - (version "0.14") + (version "0.14.1") (source (origin (method url-fetch) (uri (cran-uri "moments" version)) (sha256 (base32 - "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra")))) + "0r6qf3i1rzh2822bx1p0h8mh91gsbgg6asl2rzh2l4ys094bilif")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/moments") (synopsis "Moments, cumulants, skewness, kurtosis and related tests") From 4c16cb44031f6aa9121816d8a9e127bd185c86c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:33 +0200 Subject: [PATCH 0143/1394] gnu: r-penalized: Update to 0.9-52. * gnu/packages/cran.scm (r-penalized): Update to 0.9-52. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2148028d874..2c427b5ab5b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16644,14 +16644,14 @@ obtain confidence intervals associated with AIC and BIC.") (define-public r-penalized (package (name "r-penalized") - (version "0.9-51") + (version "0.9-52") (source (origin (method url-fetch) (uri (cran-uri "penalized" version)) (sha256 (base32 - "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a")))) + "08badmgygppbqzay20qijyww028yw6s8dyd8ijcp8g4r9rn8xqyq")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-survival)) From 74ee51895a30befc45df1f5889c5d906e7777c91 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:33 +0200 Subject: [PATCH 0144/1394] gnu: r-gmodels: Update to 2.18.1.1. * gnu/packages/cran.scm (r-gmodels): Update to 2.18.1.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2c427b5ab5b..60009f04164 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16862,14 +16862,14 @@ network.") (define-public r-gmodels (package (name "r-gmodels") - (version "2.18.1") + (version "2.18.1.1") (source (origin (method url-fetch) (uri (cran-uri "gmodels" version)) (sha256 (base32 - "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2")))) + "158y7yh4maawn9vki8cq4sil48xib2bbpl6qgj5gvlkw3c14hzfs")))) (build-system r-build-system) (propagated-inputs (list r-gdata r-mass)) From 085029e733f53ce6f1991db89262b48bbc35d814 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:33 +0200 Subject: [PATCH 0145/1394] gnu: r-seqinr: Update to 4.2-16. * gnu/packages/cran.scm (r-seqinr): Update to 4.2-16. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 60009f04164..63daa983cee 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17217,14 +17217,14 @@ barplots or heatmaps.") (define-public r-seqinr (package (name "r-seqinr") - (version "4.2-8") + (version "4.2-16") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 - "1xz9spln6s9mcwpgcv1m4jymn4gnl1bb6vh90bphqcn0vvlk8jsq")))) + "0cj07b7km5mla63qhbkxg1mnqq6vh79lsyyfpnbm29gw68w2bwy4")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-segmented)) From 0ab5079af915605b5a1361fadb1e21d1f36c68ce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:33 +0200 Subject: [PATCH 0146/1394] gnu: r-spdep: Update to 1.2-4. * gnu/packages/cran.scm (r-spdep): Update to 1.2-4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 63daa983cee..e6cb311d6b8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17477,13 +17477,13 @@ datum transformations.") (define-public r-spdep (package (name "r-spdep") - (version "1.2-3") + (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 - "0qd7qjblx49gp07pcf4qb2f93ab3p126pa77g6mq4z3jaa510hak")) + "0xx6k3rsvsz1hwj0ny8aqfi9ca54x38f8pz8sfya5cggaspxbx59")) (snippet '(for-each delete-file '("inst/doc/CO69.html" "inst/doc/CO69.R" From ae53d4e29c6abc696993b047f5db0c9fc55b4697 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:34 +0200 Subject: [PATCH 0147/1394] gnu: r-adegenet: Update to 2.1.6. * gnu/packages/cran.scm (r-adegenet): Update to 2.1.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e6cb311d6b8..fcec4d741ce 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17519,14 +17519,14 @@ spanning tree.") (define-public r-adegenet (package (name "r-adegenet") - (version "2.1.5") + (version "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "adegenet" version)) (sha256 (base32 - "1wjp31634n6z6wglf4z3ydrhhn5jmpwwckmp3n2b0v5f3p2fivp4")))) + "0sx25p7bgz0h9mc3jsdnnjhvmb7sy8nb3r0z923vhk336d4xw8vq")))) (build-system r-build-system) (propagated-inputs (list r-ade4 From 6957585a41c9170b2287f7244ab9443abda198fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:34 +0200 Subject: [PATCH 0148/1394] gnu: r-polspline: Update to 1.1.20. * gnu/packages/cran.scm (r-polspline): Update to 1.1.20. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fcec4d741ce..f22729af6af 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17656,13 +17656,13 @@ either PDF/EPS files.") (define-public r-polspline (package (name "r-polspline") - (version "1.1.19") + (version "1.1.20") (source (origin (method url-fetch) (uri (cran-uri "polspline" version)) (sha256 - (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm")))) + (base32 "1dd1jwiaglkkhajzvqfkd1x5r3wzjlk5ww0yxzmns0s1kr74i4k9")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/polspline/") From adfb8261c914f53e9d624d385a40bac1c6c9f0e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:34 +0200 Subject: [PATCH 0149/1394] gnu: r-rms: Update to 6.3-0. * gnu/packages/cran.scm (r-rms): Update to 6.3-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f22729af6af..8202b315cd6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17676,13 +17676,13 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "6.2-0") + (version "6.3-0") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 "1di4xvsx0rwkr77nfqiysbg4qf699199xqil70i39d4zwfzqrm8h")))) + (base32 "1yfk800q4mgmrjkh0hqjkiv907sr1bi1jaigrj8l6pmg1mkynhbc")))) (build-system r-build-system) (propagated-inputs (list r-cluster From bad61525232d51518b689d5707c434c889438a64 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:35 +0200 Subject: [PATCH 0150/1394] gnu: r-bookdown: Update to 0.26. * gnu/packages/cran.scm (r-bookdown): Update to 0.26. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8202b315cd6..5fd189336dc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17922,13 +17922,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.25") + (version "0.26") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0v5nlm3lbm0h5cvd9j2211yqk68rkm416aq8qp6r8klj69xm1bri")))) + "11din9h2sgzvg44627xc5is4psbq2b34km5sbiaprskjrf474866")))) (build-system r-build-system) (propagated-inputs (list r-htmltools @@ -17943,7 +17943,7 @@ SELECT or UPDATE queries to an end-point.") ;; input to knitr. #; (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rstudio/bookdown") (synopsis "Authoring books and technical documents with R markdown") (description "This package provides output formats and utilities for From 1d58744415cb8cd3ae4fce03b4459a4824618ef4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:35 +0200 Subject: [PATCH 0151/1394] gnu: r-hierfstat: Update to 0.5-11. * gnu/packages/cran.scm (r-hierfstat): Update to 0.5-11. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5fd189336dc..ba364c827ff 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17998,14 +17998,14 @@ and a QP solver.") (define-public r-hierfstat (package (name "r-hierfstat") - (version "0.5-10") + (version "0.5-11") (source (origin (method url-fetch) (uri (cran-uri "hierfstat" version)) (sha256 (base32 - "1p4vlna185sa3b5xjbysiqxcj9aa5s7dmxy41hg79vlqdivf874r")))) + "0nyb5091lr8ma9vydbssyx9503601rynlrbldv98mmrmh74h6v41")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-adegenet r-gaston r-gtools)) From a124a6904692c07623489ee1f495059dd7650734 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:35 +0200 Subject: [PATCH 0152/1394] gnu: r-hapassoc: Update to 1.2-9. * gnu/packages/cran.scm (r-hapassoc): Update to 1.2-9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ba364c827ff..ee125851cc1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18024,14 +18024,14 @@ variance components, using the likelihood-ratio statistics G.") (define-public r-hapassoc (package (name "r-hapassoc") - (version "1.2-8") + (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "hapassoc" version)) (sha256 (base32 - "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s")))) + "09ijc4sbw743z74fzklmvig11ndkycg6j86k4214wfsj1yj6j9x6")))) (build-system r-build-system) (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html") (synopsis "Inference of trait associations with SNP haplotypes") From b6b8f8c39593403b7abc6ee3446d173a3accefe9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:35 +0200 Subject: [PATCH 0153/1394] gnu: r-r2html: Update to 2.3.3. * gnu/packages/cran.scm (r-r2html): Update to 2.3.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ee125851cc1..163fa9d1e8c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18066,14 +18066,14 @@ handle missing genotypes at some SNPs.") (define-public r-r2html (package (name "r-r2html") - (version "2.3.2") + (version "2.3.3") (source (origin (method url-fetch) (uri (cran-uri "R2HTML" version)) (sha256 (base32 - "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9")))) + "12qg9rp1j26h2f48dfg5k9jds26ycacv3f3ymk686ks43hd1hzja")))) (properties `((upstream-name . "R2HTML"))) (build-system r-build-system) (home-page "https://github.com/nalimilan/R2HTML") From 62ba432c08bab5bf2495a9f54154289ca76db8ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:36 +0200 Subject: [PATCH 0154/1394] gnu: r-extrafont: Update to 0.18. * gnu/packages/cran.scm (r-extrafont): Update to 0.18. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 163fa9d1e8c..622604d6cbe 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18229,14 +18229,14 @@ interaction search in high-dimensional data.") (define-public r-extrafont (package (name "r-extrafont") - (version "0.17") + (version "0.18") (source (origin (method url-fetch) (uri (cran-uri "extrafont" version)) (sha256 (base32 - "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g")))) + "0mx810mld67vb1w3wkl4fhpjmkq32lgpq5x1c0a9rf8li5wskrj4")))) (build-system r-build-system) (propagated-inputs (list r-extrafontdb r-rttf2pt1)) From d66e52f2d95afec9bb76667ee95b44a730cb5a44 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:36 +0200 Subject: [PATCH 0155/1394] gnu: r-aplot: Update to 0.1.4. * gnu/packages/cran.scm (r-aplot): Update to 0.1.4. [propagated-inputs]: Remove r-yulab-utils. --- gnu/packages/cran.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 622604d6cbe..c5d4c24293d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19243,14 +19243,14 @@ external dependencies. This package has is implemented purely in R.") (define-public r-aplot (package (name "r-aplot") - (version "0.1.3") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "aplot" version)) (sha256 (base32 - "10cqa35bh4lhpnybaalp3d69k392b25ba16dgbngqz0vikzp4czk")))) + "1b4jjj05a602dgn6yr1bsmbzlzkj6wf6af3k3w63g3mkqv0xzsfd")))) (properties `((upstream-name . "aplot"))) (build-system r-build-system) (propagated-inputs @@ -19258,8 +19258,7 @@ external dependencies. This package has is implemented purely in R.") r-ggplot2 r-ggplotify r-magrittr - r-patchwork - r-yulab-utils)) + r-patchwork)) (home-page "https://github.com/YuLab-SMU/aplot") (synopsis "Decorate a ggplot with associated information") (description From ee8c5112c9c2362be5f64a3d4d71901027ad50fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:36 +0200 Subject: [PATCH 0156/1394] gnu: r-arrow: Update to 8.0.0. * gnu/packages/cran.scm (r-arrow): Update to 8.0.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c5d4c24293d..90cd03e3061 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19318,14 +19318,14 @@ colored by the number of neighboring points. This is useful to visualize the (define-public r-arrow (package (name "r-arrow") - (version "7.0.0") + (version "8.0.0") (source (origin (method url-fetch) (uri (cran-uri "arrow" version)) (sha256 (base32 - "1s9h2aw6iig45nz2rfk13qbp0qydx6cc4r6qs58f9cm9vgwsg76l")))) + "1b85vc5ld7nibqgsdkl5kbzc0rm5jh5lqfdrssvrrcxpd26a16kc")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs From 3aa01ca69f39350e6c9a8eb3c5ef99aba963aa46 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:36 +0200 Subject: [PATCH 0157/1394] gnu: r-mlapi: Update to 0.1.1. * gnu/packages/cran.scm (r-mlapi): Update to 0.1.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 90cd03e3061..a24ad873530 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19379,14 +19379,14 @@ regular expressions from human readable expressions") (define-public r-mlapi (package (name "r-mlapi") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "mlapi" version)) (sha256 (base32 - "023vk5bp8cjcq88sapkl87kdxr92bay1dyxl6xirnyj699pyj51k")))) + "1qyiii6x9b89i4pd4yi2zd23aabpmnpj18gqi5va0zy0l8r7kknr")))) (properties `((upstream-name . "mlapi"))) (build-system r-build-system) (propagated-inputs From 7131132ae58cacec13d32ac7ece2417124d23c29 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:37 +0200 Subject: [PATCH 0158/1394] gnu: r-text2vec: Update to 0.6.1. * gnu/packages/cran.scm (r-text2vec): Update to 0.6.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a24ad873530..1f059e7e2b1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19465,14 +19465,14 @@ Row} (CSR) format.") (define-public r-text2vec (package (name "r-text2vec") - (version "0.6") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "text2vec" version)) (sha256 (base32 - "0r75cv77x2zm1z66s95hic71dpbqmybz39n48q6mz7gfd3m7312y")))) + "0bisr31051hnshw26rp9r4bm8ksr977dl9k1d3fb1x79pq5aa2pi")))) (properties `((upstream-name . "text2vec"))) (build-system r-build-system) (propagated-inputs From f93554e5cc6ddb52cd7be1d58329fcebfa9ae32e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:37 +0200 Subject: [PATCH 0159/1394] gnu: r-mcmcpack: Update to 1.6-3. * gnu/packages/cran.scm (r-mcmcpack): Update to 1.6-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1f059e7e2b1..deae0191afe 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19501,14 +19501,14 @@ multicore machines.") (define-public r-mcmcpack (package (name "r-mcmcpack") - (version "1.6-2") + (version "1.6-3") (source (origin (method url-fetch) (uri (cran-uri "MCMCpack" version)) (sha256 (base32 - "18nyncvgb75q8flndni99ldr7ynqhillphkj7ydsmfv5w8b0zvqp")))) + "1cwdjn43b9hxpxf9mnas583myhk6r2258mh57f0zsc8bd4hbl56b")))) (properties `((upstream-name . "MCMCpack"))) (build-system r-build-system) (propagated-inputs From b9f2b030e414be8ba3fef49654836650896794e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:37 +0200 Subject: [PATCH 0160/1394] gnu: r-pbmcapply: Update to 1.5.1. * gnu/packages/cran.scm (r-pbmcapply): Update to 1.5.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index deae0191afe..3b55f26a89d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19701,14 +19701,14 @@ the functions can also be applied to other types of categorical data.") (define-public r-pbmcapply (package (name "r-pbmcapply") - (version "1.5.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "pbmcapply" version)) (sha256 (base32 - "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz")))) + "1p8jf7c4k45482w72sr0jw4jkz787krrxai3sl6jz5l4lda2iz3z")))) (build-system r-build-system) (home-page "https://github.com/kvnkuang/pbmcapply") (synopsis "Track the progress of apply procedures with a progress bar") From 1655a725966eea4e76bf2b9659bae8e181a09720 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:37 +0200 Subject: [PATCH 0161/1394] gnu: r-dalex: Update to 2.4.1. * gnu/packages/cran.scm (r-dalex): Update to 2.4.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3b55f26a89d..e423d7a1d97 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19961,14 +19961,14 @@ been used in the call to @code{aov}.") (define-public r-dalex (package (name "r-dalex") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "1s7r7k5ihdbj69r27vbcs3ghra9s4yqw7cyh2rkm2ry901zq3114")))) + "0mcdd2bd8zlsz7x174g87dp8vy4wc06w58dyr27f6lgv9shzya8j")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs From 9abfef11fdaa697fd9fa2e3ea0350d8037c2827b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:38 +0200 Subject: [PATCH 0162/1394] gnu: r-xgboost: Update to 1.6.0.1. * gnu/packages/cran.scm (r-xgboost): Update to 1.6.0.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e423d7a1d97..7bf2a0a0a04 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20132,14 +20132,14 @@ the current document.") (define-public r-xgboost (package (name "r-xgboost") - (version "1.5.2.1") + (version "1.6.0.1") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 - "13mi3rmpxhgm4qbm4xcqml9n5d1xyai2k1mi52i8x60jd5m8s319")))) + "1gafjv6vcpny03lqw8s68xszalsylniavaqwsbzh46vyk4h9mscs")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-matrix)) From 6f73001e39865cf569b03a80ba8b5900aa298f3d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:38 +0200 Subject: [PATCH 0163/1394] gnu: r-leiden: Update to 0.4.2. * gnu/packages/cran.scm (r-leiden): Update to 0.4.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7bf2a0a0a04..15ba55954c6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20345,14 +20345,14 @@ computed using the L1 (Manhattan, taxicab) metric.") (define-public r-leiden (package (name "r-leiden") - (version "0.3.9") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 - "03gaxpcab3a1av5lk8r5ll1s858gvyx5ndknci1sia96w1v44xc1")))) + "1gg24afwbz818041bhmswmdqgxv35zp5h1i1102p58aaiis8dkna")))) (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs From 018becea7ed9a72e5c0707624fb0094670c372dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:38 +0200 Subject: [PATCH 0164/1394] gnu: r-parameters: Update to 0.18.0. * gnu/packages/cran.scm (r-parameters): Update to 0.18.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 15ba55954c6..774ede3469d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20722,14 +20722,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.17.0") + (version "0.18.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "0wrhs3rhr62441cghg4nsrlp6r41nf7x5nclzz71v5c0rfn8jh79")))) + "0r6bj29frhqyv75cviw0p8kns6h8z10n7g7khyk0hzq2fqjsjrwh")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs From 51ddbf136837aafb91dd60ebd0da106c33ad53b1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:38 +0200 Subject: [PATCH 0165/1394] gnu: r-rgdal: Update to 1.5-32. * gnu/packages/cran.scm (r-rgdal): Update to 1.5-32. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 774ede3469d..ad201f8dff6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20750,13 +20750,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.5-30") + (version "1.5-32") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "1f4zshgkaifbfcgq61vqb7jw5w2cc128d98rq2465r8696q2p0s9")))) + (base32 "1vbkyhw8nd7dw1r53qisphav31x6zvpbzilvnlvbjbj9hzhs90s5")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs From a87f437b91f04d051e5c5eb5f51e7add2e13f9a8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:39 +0200 Subject: [PATCH 0166/1394] gnu: r-desolve: Update to 1.32. * gnu/packages/cran.scm (r-desolve): Update to 1.32. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ad201f8dff6..7d9c2f13c62 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20881,13 +20881,13 @@ programming problems.") (define-public r-desolve (package (name "r-desolve") - (version "1.31") + (version "1.32") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 "06gsh514msqdmri78969snhgh22d2bzmnkqfgh0s74aprfd93m8r")))) + (base32 "1bfr4w760nr7mjhpmf32z39swr6isnn1665cld2d1pdgx8b0yrvl")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs From 4416578f91b3a27bec5025fe830af2b116385aad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:39 +0200 Subject: [PATCH 0167/1394] gnu: r-subplex: Update to 1.8. * gnu/packages/cran.scm (r-subplex): Update to 1.8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7d9c2f13c62..8d6ebe6733a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20957,14 +20957,14 @@ porting.") (define-public r-subplex (package (name "r-subplex") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "subplex" version)) (sha256 (base32 - "11zqzydbj6ivgvlw1gv1r2yxra7misbc622g575p2vckhjjg9v6m")))) + "19g5bd39gmcn27xdsklkzxg99x1r5v5q8zcw1iwry31qj24ivhrv")))) (build-system r-build-system) (native-inputs (list gfortran)) From 78f653116aa92d5f1ad48d8df3df05d4aedf97f0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:39 +0200 Subject: [PATCH 0168/1394] gnu: r-reldist: Update to 1.7-1. * gnu/packages/cran.scm (r-reldist): Update to 1.7-1. [propagated-inputs]: Remove r-hmisc. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8d6ebe6733a..e00705b28b5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21565,18 +21565,18 @@ elicitation options based on Kass and Vaidyanathan (1992) (define-public r-reldist (package (name "r-reldist") - (version "1.7-0") + (version "1.7-1") (source (origin (method url-fetch) (uri (cran-uri "reldist" version)) (sha256 (base32 - "0i04d6w3r6fzm4bykz6lnnh6dngmd61v5wlpli70r3fzdzhi7fji")))) + "17kbqqapqmckghv7jizibmicv3bzbycfr3mz4xg3yjp3c2bap4r6")))) (properties `((upstream-name . "reldist"))) (build-system r-build-system) (propagated-inputs - (list r-densestbayes r-hmisc r-mgcv)) + (list r-densestbayes r-mgcv)) (home-page "http://www.stat.ucla.edu/~handcock/RelDist") (synopsis "Relative distribution methods") (description From d26d9d82eb350296efa528f648130d6ef45cdc26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:40 +0200 Subject: [PATCH 0169/1394] gnu: r-mda: Update to 0.5-3. * gnu/packages/cran.scm (r-mda): Update to 0.5-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e00705b28b5..9434a1fa58b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21737,14 +21737,14 @@ data.") (define-public r-mda (package (name "r-mda") - (version "0.5-2") + (version "0.5-3") (source (origin (method url-fetch) (uri (cran-uri "mda" version)) (sha256 (base32 - "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl")))) + "0qw4scc2w7jmnxssj5w2mdxb9rrl4dscqn54gplzm1gk2yf419mx")))) (properties `((upstream-name . "mda"))) (build-system r-build-system) (propagated-inputs (list r-class)) From 45b991e7e126b4964c7eba4165e31d7af98bdb7c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:40 +0200 Subject: [PATCH 0170/1394] gnu: r-randtoolbox: Update to 2.0.0. * gnu/packages/cran.scm (r-randtoolbox): Update to 2.0.0. [native-inputs]: Remove gfortran. --- gnu/packages/cran.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9434a1fa58b..2ae1474a2ff 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21906,20 +21906,18 @@ and prints vectorized images.") (define-public r-randtoolbox (package (name "r-randtoolbox") - (version "1.31.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "randtoolbox" version)) (sha256 (base32 - "1b9vjzqg014hxp1vfb62m01d7xim5vmpbyxzlbll49bqas0jx69h")))) + "005x2igljc6vm0nsmkld9aqjqz1ccwapc8z3aw5c3ivh4n2bghf9")))) (properties `((upstream-name . "randtoolbox"))) (build-system r-build-system) (propagated-inputs (list r-rngwell)) - (native-inputs - (list gfortran)) (home-page "https://cran.r-project.org/web/packages/randtoolbox/") (synopsis "Toolbox for pseudo and quasi random number generation") (description From b788f97e2651b6a0f17727b723361cd30b69fed9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:40 +0200 Subject: [PATCH 0171/1394] gnu: r-gamlss: Update to 5.4-3. * gnu/packages/cran.scm (r-gamlss): Update to 5.4-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2ae1474a2ff..0d90675dd19 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22064,14 +22064,14 @@ models.") (define-public r-gamlss (package (name "r-gamlss") - (version "5.4-1") + (version "5.4-3") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 - "0fp9bmgykpqd950bk58dk423iy5r1fm3dy2gw0cwwmgivpq2lx0q")))) + "0xih19zqgpjl5qv5j38ana6x29y84shn2jfl2lk4kaw3q7yx86b6")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs From 61052b3f1ef354d59a6108c8777e4a2e09f2f4b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:41 +0200 Subject: [PATCH 0172/1394] gnu: r-alabama: Update to 2022.4-1. * gnu/packages/cran.scm (r-alabama): Update to 2022.4-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0d90675dd19..e832107a9e9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22776,14 +22776,14 @@ R\" (ISBN 978-1-119-15272-9.)") (define-public r-alabama (package (name "r-alabama") - (version "2015.3-1") + (version "2022.4-1") (source (origin (method url-fetch) (uri (cran-uri "alabama" version)) (sha256 (base32 - "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036")))) + "0v6kl6ndm8wvp9xzya3x4gj5kh03qgx13x5vyzn410wsndcjiim8")))) (properties `((upstream-name . "alabama"))) (build-system r-build-system) (propagated-inputs (list r-numderiv)) From c6178da3d3edf6a892f5eabd75d3e8c8016622a3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:41 +0200 Subject: [PATCH 0173/1394] gnu: r-fda: Update to 6.0.3. * gnu/packages/cran.scm (r-fda): Update to 6.0.3. [propagated-inputs]: Remove r-matrix. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e832107a9e9..4c8704d1334 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23014,18 +23014,20 @@ variable observed over time.") (define-public r-fda (package (name "r-fda") - (version "5.5.1") + (version "6.0.3") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 - "0fm2vswc8fdi2p1axby0hjwh8m6lc1zrdikrpiamilr6w9m2zanw")))) + "1lvp4i4hqz650k27sa5flbdlkalihc79xy9128hfhr16h6wi8n10")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs - (list r-desolve r-fds r-matrix)) + (list r-desolve r-fds)) + (native-inputs + (list r-knitr)) (home-page "https://www.functionaldata.org") (synopsis "Functional data analysis") (description From d3713d1aecd8fd6af7f0201a3b49b40d79482e94 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:41 +0200 Subject: [PATCH 0174/1394] gnu: r-caret: Update to 6.0-92. * gnu/packages/cran.scm (r-caret): Update to 6.0-92. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4c8704d1334..365a4afccf7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23379,14 +23379,14 @@ it may be seen by an animal with less acute vision.") (define-public r-caret (package (name "r-caret") - (version "6.0-91") + (version "6.0-92") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 - "1kbx51cf71z2x19a0jflwnhx5jd9wk9q9203kzdxlqw5izdjvmdz")))) + "048mp325ndfl83a8p4dkd1b6zh5bws4gg9kxka5ss8qsj8m4m08x")))) (build-system r-build-system) (propagated-inputs (list r-e1071 From 5b9f8d7972049ce9c03fe7139065fd53a3ad475f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:42 +0200 Subject: [PATCH 0175/1394] gnu: r-lim: Update to 1.4.7. * gnu/packages/cran.scm (r-lim): Update to 1.4.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 365a4afccf7..fbf823534f3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24010,14 +24010,14 @@ Francesca Mazzia (2012).") (define-public r-lim (package (name "r-lim") - (version "1.4.6") + (version "1.4.7") (source (origin (method url-fetch) (uri (cran-uri "LIM" version)) (sha256 (base32 - "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8")))) + "0d9bgyd0mnag8wds993dsvlbpkhyakydlzwc3nghxzv2n8504hjj")))) (properties `((upstream-name . "LIM"))) (build-system r-build-system) (propagated-inputs From 0352dfa55306ae75c34cae8e66c031c5633237e5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:42 +0200 Subject: [PATCH 0176/1394] gnu: r-rsvg: Update to 2.3.1. * gnu/packages/cran.scm (r-rsvg): Update to 2.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fbf823534f3..9ef8e7eb16d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24057,14 +24057,14 @@ automatically show a loader when the output is (re)calculating.") (define-public r-rsvg (package (name "r-rsvg") - (version "2.2.0") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "rsvg" version)) (sha256 (base32 - "05mvi1ijnxayyj1f4p8nb56pncmm7x0sbq0d87asv7c7kw765n1a")))) + "096w4d1gvfc65d4jg7ykp23k9f7cf7f8zvzfhvhd7qkfsbjpxqkj")))) (properties `((upstream-name . "rsvg"))) (build-system r-build-system) (inputs From 6530b566b9bb253a800dfb9c56c025e4149ff5ec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:42 +0200 Subject: [PATCH 0177/1394] gnu: r-matrixextra: Update to 0.1.10. * gnu/packages/cran.scm (r-matrixextra): Update to 0.1.10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9ef8e7eb16d..0507b7c419d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24788,13 +24788,13 @@ actuarial models such as pension mathematics.") (define-public r-matrixextra (package (name "r-matrixextra") - (version "0.1.9-1") + (version "0.1.10") (source (origin (method url-fetch) (uri (cran-uri "MatrixExtra" version)) (sha256 - (base32 "098apgqlncgxspa8mi4bx2nk5fbk3880whqiwkvydsfsqrbv1sj0")))) + (base32 "00f6sgw6p2709gs3df68yr59nvsr429pk9xql71id3kachjzh618")))) (properties `((upstream-name . "MatrixExtra"))) (build-system r-build-system) (propagated-inputs From bd273a6b17ad2aa1e94bd596a7d4c0a2b28e4cf1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:43 +0200 Subject: [PATCH 0178/1394] gnu: r-semtools: Update to 0.5-6. * gnu/packages/cran.scm (r-semtools): Update to 0.5-6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0507b7c419d..112f0b7333d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24856,14 +24856,14 @@ least squares.") (define-public r-semtools (package (name "r-semtools") - (version "0.5-5") + (version "0.5-6") (source (origin (method url-fetch) (uri (cran-uri "semTools" version)) (sha256 (base32 - "1dpsn43ifvfy5v8w2fqdy54yclmy0d3qlzix67lflr2r7isq7y6x")))) + "1wnakz76c4mgkwvx3iycmvgrzqys860jg9zpkba0ln5c08ycw8pm")))) (properties `((upstream-name . "semTools"))) (build-system r-build-system) (propagated-inputs From ad9c851588784279c31b47a03be259c3adcebcfe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:43 +0200 Subject: [PATCH 0179/1394] gnu: r-rockchalk: Update to 1.8.152. * gnu/packages/cran.scm (r-rockchalk): Update to 1.8.152. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 112f0b7333d..64ad6e444c8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25030,14 +25030,14 @@ importation and recoding.") (define-public r-rockchalk (package (name "r-rockchalk") - (version "1.8.151") + (version "1.8.152") (source (origin (method url-fetch) (uri (cran-uri "rockchalk" version)) (sha256 (base32 - "17mfaxn3gj0vac5wdmsjj2z2668cszbpvan7hnxp7ic9bvsm1w2y")))) + "1d15jlgcy35pvaicaddd4zrhwm5ajb9yc3jk6dyxm99gc5wcn6h3")))) (properties `((upstream-name . "rockchalk"))) (build-system r-build-system) (propagated-inputs From 10ec759fb4406bb337bfb9a7f05a35610fa83aec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:43 +0200 Subject: [PATCH 0180/1394] gnu: r-lisreltor: Update to 0.1.5. * gnu/packages/cran.scm (r-lisreltor): Update to 0.1.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 64ad6e444c8..486168bccc7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25057,14 +25057,14 @@ fairly comprehensive overview.") (define-public r-lisreltor (package (name "r-lisreltor") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "lisrelToR" version)) (sha256 (base32 - "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5")))) + "0i51v0x87277ly0kggdd594w6q4zq62b4n7xs9r25j08bzs82nfk")))) (properties `((upstream-name . "lisrelToR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=lisrelToR") From 64a8d5df5a14d42d8532cc756b6f392926c4638d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:44 +0200 Subject: [PATCH 0181/1394] gnu: r-bdgraph: Update to 2.67. * gnu/packages/cran.scm (r-bdgraph): Update to 2.67. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 486168bccc7..166b91bc92c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25077,18 +25077,20 @@ output in R.") (define-public r-bdgraph (package (name "r-bdgraph") - (version "2.65") + (version "2.67") (source (origin (method url-fetch) (uri (cran-uri "BDgraph" version)) (sha256 (base32 - "0rg3wi9xwsbj90gb60p3vzkfrf76hwh47nc6fwv6c21yzd3s7vm4")))) + "0s2j4462zlgyjnqvvvxg4lynhmwwnjaw1cr1chzmagfvaj94qhhz")))) (properties `((upstream-name . "BDgraph"))) (build-system r-build-system) (propagated-inputs (list r-igraph)) + (native-inputs + (list r-knitr)) (home-page "https://www.uva.nl/profile/a.mohammadi") (synopsis "Bayesian structure learning in graphical models") (description From 91bb9baa95b7e22b1d5416d591f5b85444f82464 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:44 +0200 Subject: [PATCH 0182/1394] gnu: r-cdm: Update to 8.1-12. * gnu/packages/cran.scm (r-cdm): Update to 8.1-12. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 166b91bc92c..d6649e005f1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25205,14 +25205,14 @@ translated to input syntax for the R packages @code{sem} and @code{lavaan}.") (define-public r-cdm (package (name "r-cdm") - (version "7.6-11") + (version "8.1-12") (source (origin (method url-fetch) (uri (cran-uri "CDM" version)) (sha256 (base32 - "0k3arkzz7nzswjcsr7fdmpfs94ilg8l265dyn49555fw3673cgqj")))) + "1cnk19k09cj81ic43rwbvcalvczfca4ncdyy8r1gyc8fzf2glb0i")))) (properties `((upstream-name . "CDM"))) (build-system r-build-system) (propagated-inputs From d690341eeeecf7bbc0618eb22253de065ed0e64a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:44 +0200 Subject: [PATCH 0183/1394] gnu: r-tam: Update to 4.0-16. * gnu/packages/cran.scm (r-tam): Update to 4.0-16. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d6649e005f1..82f99a07d49 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25236,14 +25236,14 @@ well as Ravand and Robitzsch (2015).") (define-public r-tam (package (name "r-tam") - (version "3.7-16") + (version "4.0-16") (source (origin (method url-fetch) (uri (cran-uri "TAM" version)) (sha256 (base32 - "1969xm1f7s183h0xnd4g1bxhjp80rl7kad29zwcig0fmw6bs2mpd")))) + "00ww277hsyci5rph4gb155h0y95dmjhqgn9amz6g8zbrjb2748dw")))) (properties `((upstream-name . "TAM"))) (build-system r-build-system) (propagated-inputs From 984542a9cd4ab4578fc6171683a4a29105b848fa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:45 +0200 Subject: [PATCH 0184/1394] gnu: r-irtoys: Update to 0.2.2. * gnu/packages/cran.scm (r-irtoys): Update to 0.2.2. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 82f99a07d49..8d4d065da80 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25293,18 +25293,20 @@ elimination, and a simulation module for various binary data matrices.") (define-public r-irtoys (package (name "r-irtoys") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "irtoys" version)) (sha256 (base32 - "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q")))) + "1qshz6czykgf53mq6xiswzv5xsjwrkrinpfkf1yavql4v08hs82b")))) (properties `((upstream-name . "irtoys"))) (build-system r-build-system) (propagated-inputs (list r-ltm r-sm)) + (native-inputs + (list r-knitr)) (home-page "https://cran.r-project.org/package=irtoys") (synopsis "Collection of functions related to Item Response Theory (IRT)") (description From 35fb1a91f558708bbd9881ae74e7d5d385e6d397 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:45 +0200 Subject: [PATCH 0185/1394] gnu: r-packrat: Update to 0.8.0. * gnu/packages/cran.scm (r-packrat): Update to 0.8.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8d4d065da80..545cec25543 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25362,14 +25362,14 @@ interesting features. iheatmapr uses the plotly library for interactivity.") (define-public r-packrat (package (name "r-packrat") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "packrat" version)) (sha256 (base32 - "1hnwhdgqljqs3m7c4rjlyndyc0k85jpa4rbfymxkm3zjg3yy3g78")))) + "1vs4i19x6jdwl3jnanp127k4hk80h1mj56cjn07w1gkl542vj99h")))) (properties `((upstream-name . "packrat"))) (build-system r-build-system) (home-page "https://github.com/rstudio/packrat/") From 56a48826ef86198b27bb39762242054a421e0f2b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:45 +0200 Subject: [PATCH 0186/1394] gnu: r-optimx: Update to 2022-4.30. * gnu/packages/cran.scm (r-optimx): Update to 2022-4.30. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 545cec25543..e90ee5529d6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26520,14 +26520,14 @@ estimation.") (define-public r-optimx (package (name "r-optimx") - (version "2021-10.12") + (version "2022-4.30") (source (origin (method url-fetch) (uri (cran-uri "optimx" version)) (sha256 (base32 - "0hvrpfya767vp3anmb8ih516v4zz1sv4h193rn93kyjydf2lqf1r")))) + "045ls1vl1392ihwln6mngz0zg2w93ym1m607vfrg8v1949x8isgb")))) (properties `((upstream-name . "optimx"))) (build-system r-build-system) (propagated-inputs (list r-numderiv)) From b93b7211d269045318260a18e5d21cb9cd5400bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:45 +0200 Subject: [PATCH 0187/1394] gnu: r-projpred: Update to 2.1.2. * gnu/packages/cran.scm (r-projpred): Update to 2.1.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e90ee5529d6..d4c0b255ae3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26548,14 +26548,14 @@ here.") (define-public r-projpred (package (name "r-projpred") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "projpred" version)) (sha256 (base32 - "170pskvcsyk22xl4q8mklx8nw29miqzb42wajcab7bki8ap1ix46")))) + "1c6gnmknd3vb0fb5h6gd372dk27nzif90b4c1snql49wacg6b2m8")))) (properties `((upstream-name . "projpred"))) (build-system r-build-system) (propagated-inputs From b69e363ada86d9f29c2e035316070bc52750abef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:46 +0200 Subject: [PATCH 0188/1394] gnu: r-brms: Update to 2.17.0. * gnu/packages/cran.scm (r-brms): Update to 2.17.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d4c0b255ae3..3809062bc41 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26669,14 +26669,14 @@ inference diagnostics. (define-public r-brms (package (name "r-brms") - (version "2.16.3") + (version "2.17.0") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "1q93z4cf3iy4rs6pgvph6z7hc8q05iwif76hcg8p4kr6nl82nc38")))) + "0wff5rld4kgkk2nbllvm1h4c596igzgd0q7nx1cabgl11fja7r94")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs From f06c37d446556f1bffb2a837ce8371e07bbe9056 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:46 +0200 Subject: [PATCH 0189/1394] gnu: r-scrypt: Update to 0.1.4. * gnu/packages/cran.scm (r-scrypt): Update to 0.1.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3809062bc41..0deb81f545a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26778,14 +26778,14 @@ pies on a map.") (define-public r-scrypt (package (name "r-scrypt") - (version "0.1.3") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "scrypt" version)) (sha256 (base32 - "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm")))) + "12q9d4m7flbvlgssvjh1ga4jswkmqjfshf6pna6qk6v087gmzdsj")))) (properties `((upstream-name . "scrypt"))) (build-system r-build-system) (propagated-inputs From ba2da161bcfa38913e4bc399faaad83f08145388 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:46 +0200 Subject: [PATCH 0190/1394] gnu: r-iml: Update to 0.11.0. * gnu/packages/cran.scm (r-iml): Update to 0.11.0. [propagated-inputs]: Remove r-keras. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0deb81f545a..72aaafb7b8e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27261,14 +27261,14 @@ simple interface for all functions.") (define-public r-iml (package (name "r-iml") - (version "0.10.1") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "iml" version)) (sha256 (base32 - "1wz6xqhvqkzj723nw7qrlwb1171wvvpxhv3pa8cq7vcbkiflq37r")))) + "1za7bjnp07i20vyb6vxz2ya5cr8g4p076w61n8m38wnz04lz5yz5")))) (properties `((upstream-name . "iml"))) (build-system r-build-system) (propagated-inputs @@ -27278,7 +27278,6 @@ simple interface for all functions.") r-future r-future-apply r-ggplot2 - r-keras r-metrics r-prediction r-r6)) From e6b216b04ad3266bc1e0b34e5f8da40786593a93 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:46 +0200 Subject: [PATCH 0191/1394] gnu: r-spatstat-utils: Update to 2.3-1. * gnu/packages/cran.scm (r-spatstat-utils): Update to 2.3-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 72aaafb7b8e..8a2c2f6b72e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27348,14 +27348,14 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-utils (package (name "r-spatstat-utils") - (version "2.3-0") + (version "2.3-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 - "06nvn2ffyrskhzaavsy6lmdp0m8askkrp1fnwrhjsj01lbjnq2az")))) + "08pybliv4r3v4rcazmlfr4a07sjfhrkmksdmhhq9k185vw4474av")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) From b7cec63ed8fb48c09df7f23a2dd67dd75a7a1601 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:47 +0200 Subject: [PATCH 0192/1394] gnu: r-spatstat-sparse: Update to 2.1-1. * gnu/packages/cran.scm (r-spatstat-sparse): Update to 2.1-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8a2c2f6b72e..91e4e83aaaa 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27369,14 +27369,14 @@ which may also be useful for other purposes.") (define-public r-spatstat-sparse (package (name "r-spatstat-sparse") - (version "2.1-0") + (version "2.1-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.sparse" version)) (sha256 (base32 - "148fxbxss569w73xaqpzwpz9rfjdgznh2ngf06gvm33631222680")))) + "00vkvv5pnm82gn7vqnzrrp68y46gbkhdq0hbwqx7nxjvf5lssdcs")))) (properties `((upstream-name . "spatstat.sparse"))) (build-system r-build-system) From 5e5aaa62af69166dcaf301834825d74579188dcd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:47 +0200 Subject: [PATCH 0193/1394] gnu: r-spatstat-data: Update to 2.2-0. * gnu/packages/cran.scm (r-spatstat-data): Update to 2.2-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 91e4e83aaaa..1ba6052d2ad 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27393,14 +27393,14 @@ matrix calculations that are common in statistics, such as quadratic forms.") (define-public r-spatstat-data (package (name "r-spatstat-data") - (version "2.1-4") + (version "2.2-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 - "0bq9randa3lgkh2q932iss5cxazq743q6p8asiqqf0yi32b003jq")))) + "1rf36zy29h9qabpv19hx84gjdiay7i9y9777d2zn17ahyss3p56k")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs From bdd4773a00d8fdc1303ceb1eb0779b697bd56e85 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:47 +0200 Subject: [PATCH 0194/1394] gnu: r-spatstat-core: Update to 2.4-4. * gnu/packages/cran.scm (r-spatstat-core): Update to 2.4-4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1ba6052d2ad..2a4ccd3d9aa 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27438,14 +27438,14 @@ for the geometry of linear networks.") (define-public r-spatstat-core (package (name "r-spatstat-core") - (version "2.4-2") + (version "2.4-4") (source (origin (method url-fetch) (uri (cran-uri "spatstat.core" version)) (sha256 (base32 - "0bhdxyw212yf9y9nsvbz4yy08ka3wr3hkjqpag0ys2s1p22c51b9")))) + "0fyi8y1z919nzn47kaviln7gflhcp5qdi3gfvf7nwkdix3pkk373")))) (properties `((upstream-name . "spatstat.core"))) (build-system r-build-system) (propagated-inputs From d0fdab7c8c7a6bb81073ee28005190f2ba237ff5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:48 +0200 Subject: [PATCH 0195/1394] gnu: r-exactranktests: Update to 0.8-35. * gnu/packages/cran.scm (r-exactranktests): Update to 0.8-35. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2a4ccd3d9aa..b0cbaf50709 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28025,14 +28025,14 @@ the @code{survival} package.") (define-public r-exactranktests (package (name "r-exactranktests") - (version "0.8-34") + (version "0.8-35") (source (origin (method url-fetch) (uri (cran-uri "exactRankTests" version)) (sha256 (base32 - "1i4mwz61mjlh1ai3dww2pjkicx9ww8c4mljnr8xlawh91479lva9")))) + "1qv9i57chhz8xiv0j8r47rbigyqs72fa7ssz99inyc0s8gzskd3y")))) (properties `((upstream-name . "exactRankTests"))) (build-system r-build-system) From 551aa7beabf45c00b8cdf8d4534e63901c87f6ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:48 +0200 Subject: [PATCH 0196/1394] gnu: r-igraph: Update to 1.3.1. * gnu/packages/cran.scm (r-igraph): Update to 1.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b0cbaf50709..e33e4c2c067 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28235,14 +28235,14 @@ model.") (define-public r-igraph (package (name "r-igraph") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "09dzc8lslljvhj2q46075vxcmlgkvq2qs500zdqyy9g8scq6iqbi")))) + "0khl87ncc9hkvx4f1kyzv7w7bg9zbyd1rk20ja3azkhpqjkjnnjh")))) (build-system r-build-system) (native-inputs (list gfortran)) From b7f48e45b1be347a10284eb2171c5bdda6ec0a0a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:48 +0200 Subject: [PATCH 0197/1394] gnu: r-tidypredict: Update to 0.4.9. * gnu/packages/cran.scm (r-tidypredict): Update to 0.4.9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e33e4c2c067..f3a6c3341b2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28693,14 +28693,14 @@ models without involving a test set.") (define-public r-tidypredict (package (name "r-tidypredict") - (version "0.4.8") + (version "0.4.9") (source (origin (method url-fetch) (uri (cran-uri "tidypredict" version)) (sha256 (base32 - "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy")))) + "0x0r36zvny4rqgndx7iqh39yhr53gl4d8wd8wpvdcgg35q6z02z2")))) (properties `((upstream-name . "tidypredict"))) (build-system r-build-system) (propagated-inputs From a1ba5d43149c5d320444a5be6328317056a2b1ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:48 +0200 Subject: [PATCH 0198/1394] gnu: r-tidytext: Update to 0.3.3. * gnu/packages/cran.scm (r-tidytext): Update to 0.3.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f3a6c3341b2..dd7203e116f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28814,14 +28814,14 @@ vignettes in all common formats.") (define-public r-tidytext (package (name "r-tidytext") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "tidytext" version)) (sha256 (base32 - "0as7lscjl6ywk85almmb4f71vxmgkfds46g52ryggkg2isksvq3g")))) + "0kljaxyhhzbcv9jkjdy0wn6gkamh25y2xfb9k11sqhz3lv72nfvm")))) (properties `((upstream-name . "tidytext"))) (build-system r-build-system) (propagated-inputs From 0ce4f34b63455562d05f9d092f52b0a41bb90b52 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:49 +0200 Subject: [PATCH 0199/1394] gnu: r-lsa: Update to 0.73.3. * gnu/packages/cran.scm (r-lsa): Update to 0.73.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dd7203e116f..0542fb834e6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29014,14 +29014,14 @@ data structures of the tidyverse.") (define-public r-lsa (package (name "r-lsa") - (version "0.73.2") + (version "0.73.3") (source (origin (method url-fetch) (uri (cran-uri "lsa" version)) (sha256 (base32 - "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b")))) + "16k1g0kh3yaw7azg76aqf3hn3b6jgqg92xx0syai8l0my9ci2zzh")))) (properties `((upstream-name . "lsa"))) (build-system r-build-system) (propagated-inputs From 11872751c66123e1340a6d51786334406cd90cd1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:49 +0200 Subject: [PATCH 0200/1394] gnu: r-altmeta: Update to 4.0. * gnu/packages/cran.scm (r-altmeta): Update to 4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0542fb834e6..4fd69744502 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29103,14 +29103,14 @@ phylogenetic relatedness) can also be conducted.") (define-public r-altmeta (package (name "r-altmeta") - (version "3.3") + (version "4.0") (source (origin (method url-fetch) (uri (cran-uri "altmeta" version)) (sha256 (base32 - "1xq12hnzxh7kgv2i36xprg4lkvqfmxwz3sq4a1jlq2d5g3narvcm")))) + "17cyiydf4n5j64izj7jph2v43h4x9kfd5b0x6m0ik5ci2aw8xzr5")))) (properties `((upstream-name . "altmeta"))) (build-system r-build-system) (propagated-inputs From a72a43b1c1754119bf5cc3cabf637973aaa587bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:49 +0200 Subject: [PATCH 0201/1394] gnu: r-seuratobject: Update to 4.1.0. * gnu/packages/cran.scm (r-seuratobject): Update to 4.1.0. [propagated-inputs]: Add r-future, r-future-apply, r-progressr, r-rgeos, and r-sp. --- gnu/packages/cran.scm | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4fd69744502..7400fa7888c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29282,18 +29282,26 @@ data to rasters. It speeds up plotting of data with millions of points.") (define-public r-seuratobject (package (name "r-seuratobject") - (version "4.0.4") + (version "4.1.0") (source (origin (method url-fetch) (uri (cran-uri "SeuratObject" version)) (sha256 (base32 - "1308hjbs8br3gp9vwm65awgp6vimwgi2jyl1ryn96l84savn2ljq")))) + "018anas8a9m3kh9jn5370v64d93k64z3iic13a75hp6r7g5hd94w")))) (properties `((upstream-name . "SeuratObject"))) (build-system r-build-system) (propagated-inputs - (list r-matrix r-rcpp r-rcppeigen r-rlang)) + (list r-future + r-future-apply + r-matrix + r-progressr + r-rcpp + r-rcppeigen + r-rgeos + r-rlang + r-sp)) (home-page "https://satijalab.org/seurat") (synopsis "Data structures for single cell data") (description From 2b8ae352f2fecede2ccdc9ef776f2bb31f80a099 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:50 +0200 Subject: [PATCH 0202/1394] gnu: r-seurat: Update to 4.1.1. * gnu/packages/cran.scm (r-seurat): Update to 4.1.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7400fa7888c..25fb66d6d0a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29315,13 +29315,13 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "4.1.0") + (version "4.1.1") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0p9i3fnkqa3vranr7c7ckzp1kq42d7p0gcfi9ml4kr334yd84195")))) + "1klamxk6dj0jgpfwll5frcnj9h8lh8c5fxdn9ky7h8xk35lsj6i0")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs From d5afacea9b81e1d7788004429611cdbc07ac9097 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:50 +0200 Subject: [PATCH 0203/1394] gnu: r-lpme: Update to 1.1.3. * gnu/packages/cran.scm (r-lpme): Update to 1.1.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 25fb66d6d0a..0691873c6c9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29640,14 +29640,14 @@ kernel estimators.") (define-public r-lpme (package (name "r-lpme") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "lpme" version)) (sha256 (base32 - "1b0w5ji8hjayni1sh5id193cmanf6n11p16fijkxln4sv4lks4aw")))) + "1ch11cwjci98m7952p9wdsh9fj5y1mjya6ayq0q4wmbm824qfpzb")))) (properties `((upstream-name . "lpme"))) (build-system r-build-system) (propagated-inputs From 5618adb20f2b7c02d0d3142aaa93be85f6497f33 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:50 +0200 Subject: [PATCH 0204/1394] gnu: r-mlr3pipelines: Update to 0.4.1. * gnu/packages/cran.scm (r-mlr3pipelines): Update to 0.4.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0691873c6c9..85dc66ada8b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29804,13 +29804,13 @@ package also supersedes the package @code{BBmisc}.") (define-public r-mlr3pipelines (package (name "r-mlr3pipelines") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3pipelines" version)) (sha256 (base32 - "0913f67c1r9bi68gxh1prsp0vch21bl6plahnvjrlbq8rrs1sr6p")))) + "1zz55i8c08znxpcs6gp5inaw96c6la9wnsla0972ankvj1hsrcr2")))) (build-system r-build-system) (propagated-inputs (list r-backports From abb1d0ad6a2d3093187a727b7a88b472999a96e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:50 +0200 Subject: [PATCH 0205/1394] gnu: r-paradox: Update to 0.9.0. * gnu/packages/cran.scm (r-paradox): Update to 0.9.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 85dc66ada8b..189d4866146 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29867,13 +29867,13 @@ performing ordinal regression.") (define-public r-paradox (package (name "r-paradox") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "paradox" version)) (sha256 (base32 - "1jfzbpqi1rp3r8hnk37dqwggp48ha5bnilmdz7dwzfdaskssycxa")))) + "0fzq59903fklgj3kblnpzasy13a82s72c1qjsy7d1m0fyj28ahdw")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-mlr3misc r-r6)) From 63691670cd4a3efcf950421346b0ac1b1d30f795 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:51 +0200 Subject: [PATCH 0206/1394] gnu: r-mlr3learners: Update to 0.5.3. * gnu/packages/cran.scm (r-mlr3learners): Update to 0.5.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 189d4866146..114b6b860d1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29925,13 +29925,13 @@ computational operations, add-on packages provide additional functionality.") (define-public r-mlr3learners (package (name "r-mlr3learners") - (version "0.5.2") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "mlr3learners" version)) (sha256 (base32 - "1d9hcrnj622ynrzg0ii0fkhz2n66ip46yln21jq1pwpwkqwqzv35")))) + "088i2piv7sgxsvc7jyr6mq53vqf8yjdlrysgqphsryq6k50i00zd")))) (build-system r-build-system) (propagated-inputs (list r-checkmate From 3dcc98d817b611fe7a25c4189b40643dd8e8b22b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:51 +0200 Subject: [PATCH 0207/1394] gnu: r-bbotk: Update to 0.5.3. * gnu/packages/cran.scm (r-bbotk): Update to 0.5.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 114b6b860d1..9b7da093f5d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29952,14 +29952,14 @@ vector machines, and gradient boosting.") (define-public r-bbotk (package (name "r-bbotk") - (version "0.5.2") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 - "0k1vlh14mfbcgdw2yfhab7shkrqm4d2h6af12mybr9gks26xmw82")))) + "13qj8qysqismv9k9rfw770r7w8jdaw82n71k7sp3wsrlhxjxw734")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs From bb0ac4a0ef905f3ab5653014579c3abdf2f45abe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:51 +0200 Subject: [PATCH 0208/1394] gnu: r-mlr3tuning: Update to 0.13.1. * gnu/packages/cran.scm (r-mlr3tuning): Update to 0.13.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9b7da093f5d..5174d6bf50d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29982,13 +29982,13 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.13.0") + (version "0.13.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "0czlpi8bshn8cjq7pa1cyy7lpv35g4hv2nbyhc59zrcykzfv8afm")))) + "0jfslx6pwk408ydn69grrvsp22jd7gsjmwvss0a1j0zav3q1pvks")))) (build-system r-build-system) (propagated-inputs (list r-bbotk From c484a63b88751a861b0b191884bd8b64f1e42cec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:51 +0200 Subject: [PATCH 0209/1394] gnu: r-pkgdown: Update to 2.0.3. * gnu/packages/cran.scm (r-pkgdown): Update to 2.0.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5174d6bf50d..6e04601a93f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30335,14 +30335,14 @@ in output to the equivalent HTML.") (define-public r-pkgdown (package (name "r-pkgdown") - (version "2.0.2") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 - "11grx7a2rz6b4kwspm7c8crjav677c22hysnp4bkwh5g8kr5nm2h")))) + "0wqga9bcl7wmvkwpkkmf5hx1cl7rjq5ddvqmxhl4p1dczys3adnr")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) (inputs (list pandoc)) From 25a47c61724580760c6624788629ecff7dedf3b0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:51 +0200 Subject: [PATCH 0210/1394] gnu: r-qdapregex: Update to 0.7.5. * gnu/packages/cran.scm (r-qdapregex): Update to 0.7.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6e04601a93f..b594c8e424b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30444,14 +30444,14 @@ visualized at any level of the experiment's design.") (define-public r-qdapregex (package (name "r-qdapregex") - (version "0.7.2") + (version "0.7.5") (source (origin (method url-fetch) (uri (cran-uri "qdapRegex" version)) (sha256 (base32 - "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p")))) + "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb")))) (properties `((upstream-name . "qdapRegex"))) (build-system r-build-system) (propagated-inputs (list r-stringi)) From 1316ceb1243cb627bfbc06bfd9e0d139e9d54397 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:52 +0200 Subject: [PATCH 0211/1394] gnu: r-pdftools: Update to 3.2.1. * gnu/packages/cran.scm (r-pdftools): Update to 3.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b594c8e424b..5dabf89f917 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30790,14 +30790,14 @@ data you need the @code{pdftools} package.") (define-public r-pdftools (package (name "r-pdftools") - (version "3.1.1") + (version "3.2.1") (source (origin (method url-fetch) (uri (cran-uri "pdftools" version)) (sha256 (base32 - "1lflqf2ypdm4w033vyjykmsy8cl34sp42fzkfgfdhvl2d0xjhl96")))) + "1b9ppdndvlf8nl0i3xy1rx4f9j0j8ic6q9n0c4zn3rv6jdy8zqfi")))) (properties `((upstream-name . "pdftools"))) (build-system r-build-system) (inputs (list zlib poppler)) From 28af966caa8e9a64affd5a0e3d8082d4e4b835e9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:52 +0200 Subject: [PATCH 0212/1394] gnu: r-rmisc: Update to 1.5.1. * gnu/packages/cran.scm (r-rmisc): Update to 1.5.1. [propagated-inputs]: Remove r-rcpp. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5dabf89f917..52bdfc5b89b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31491,16 +31491,16 @@ asynchronously from formatting.") (define-public r-rmisc (package (name "r-rmisc") - (version "1.5") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "Rmisc" version)) (sha256 (base32 - "1ijjhfy3v91fspid77rrkc5dkcb2lav37wc3f4k5lwrn24wzy5y8")))) + "1h6jb0xwkyhm9lwm7nj9bhrb5dhrsifvkpqkrd594j1lz74dar8x")))) (build-system r-build-system) (propagated-inputs - (list r-plyr r-rcpp r-lattice)) + (list r-plyr r-lattice)) (home-page "https://cran.r-project.org/web/packages/Rmisc/") (synopsis "Ryan Miscellaneous") (description "The Rmisc library contains functions for data analysis and From 30cb1c00593a8b2f359e5ff1b19ab96a4c21670a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:52 +0200 Subject: [PATCH 0213/1394] gnu: r-opencpu: Update to 2.2.8. * gnu/packages/cran.scm (r-opencpu): Update to 2.2.8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 52bdfc5b89b..7258fcfaf93 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31564,13 +31564,13 @@ reading and writing arbitrary protocol-buffer data in R.") (define-public r-opencpu (package (name "r-opencpu") - (version "2.2.7") + (version "2.2.8") (source (origin (method url-fetch) (uri (cran-uri "opencpu" version)) (sha256 - (base32 "06jpmk95hm39ib5c75xw0mdrdv9x9zz1qil3m8ysb6pp1xx47jz0")))) + (base32 "1h0s7fbifyf4h1296sdk3amij0m6s12wq32mbky7xg4nz8wj29ni")))) (properties `((upstream-name . "opencpu"))) (build-system r-build-system) (inputs From c8baed28c2a5430140622897ff4a2a607ea25bdf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:53 +0200 Subject: [PATCH 0214/1394] gnu: r-exactextractr: Update to 0.8.2. * gnu/packages/cran.scm (r-exactextractr): Update to 0.8.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7258fcfaf93..b3cf5d1c6ae 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31607,14 +31607,14 @@ Apache2.") (define-public r-exactextractr (package (name "r-exactextractr") - (version "0.8.1") + (version "0.8.2") (source (origin (method url-fetch) (uri (cran-uri "exactextractr" version)) (sha256 (base32 - "11s58vc63r9kah815a18ihb0x2nmnjnpngybw3yr2d6715sz89nc")))) + "0x4axrq9iznvajqy07gcfcrvzniz5yj6wabchgksg0fqz0xancnc")))) (properties `((upstream-name . "exactextractr"))) (build-system r-build-system) (inputs (list geos)) From 76ecfcb472c2414b44d97816738632d32a4b7166 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:53 +0200 Subject: [PATCH 0215/1394] gnu: r-stringfish: Update to 0.15.7. * gnu/packages/cran.scm (r-stringfish): Update to 0.15.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b3cf5d1c6ae..e34f91ec837 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31633,14 +31633,14 @@ the @code{raster} package that is suitable for extracting raster values using (define-public r-stringfish (package (name "r-stringfish") - (version "0.15.5") + (version "0.15.7") (source (origin (method url-fetch) (uri (cran-uri "stringfish" version)) (sha256 (base32 - "0ac17wl0fcpmipbvhhg5nyccg055671fnlxvnjd5l3kilx313wlx")))) + "0ddpsi7z0kzqgbq9y646pk9afclq0r7ak22zsdh0i93ni0x71c9l")))) (properties `((upstream-name . "stringfish"))) (build-system r-build-system) (propagated-inputs From 2c3bcdce95303958134b6a2e203d85a61c477aeb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:53 +0200 Subject: [PATCH 0216/1394] gnu: r-tensorflow: Update to 2.9.0. * gnu/packages/cran.scm (r-tensorflow): Update to 2.9.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e34f91ec837..829af1b25cf 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31787,14 +31787,14 @@ Tensorflow graphs.") (define-public r-tensorflow (package (name "r-tensorflow") - (version "2.8.0") + (version "2.9.0") (source (origin (method url-fetch) (uri (cran-uri "tensorflow" version)) (sha256 (base32 - "19ayjvlxmgjais0kx6fj9an1h1i8mh4c9dhah7dj6390p53pgz93")))) + "12c6ndxx4g6fqjakpzp9pgl29ghswhqyr6q9jahpk0cawizh2znj")))) (properties `((upstream-name . "tensorflow"))) (build-system r-build-system) (inputs (list tensorflow)) From 20d8275a2af463c958127b88e35856792f7be981 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:53 +0200 Subject: [PATCH 0217/1394] gnu: r-keras: Update to 2.9.0. * gnu/packages/cran.scm (r-keras): Update to 2.9.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 829af1b25cf..a202b728889 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31818,14 +31818,14 @@ between them.") (define-public r-keras (package (name "r-keras") - (version "2.8.0") + (version "2.9.0") (source (origin (method url-fetch) (uri (cran-uri "keras" version)) (sha256 (base32 - "10zvy4lmhb2sbn0gsm12pf95pxj9bmi8241ap1n6170xsld9phcf")))) + "06513d1fp7cxk4v03xm9lhgj6xmp9dqqvw3lnzwbzjwdkfj948yc")))) (properties `((upstream-name . "keras"))) (build-system r-build-system) (propagated-inputs From 0632b773f00ebfb866d28e338d4e37ee7f9af61c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:54 +0200 Subject: [PATCH 0218/1394] gnu: r-rfigshare: Update to 0.3.8. * gnu/packages/cran.scm (r-rfigshare): Update to 0.3.8. [propagated-inputs]: Remove r-plyr. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a202b728889..47bfda9fbd3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32004,24 +32004,25 @@ with the dynamic plots from @code{dygraphs}.") (define-public r-rfigshare (package (name "r-rfigshare") - (version "0.3.7") + (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "rfigshare" version)) (sha256 (base32 - "1qgzn0mpjy4czy0pnbi395fxxx84arkg8r7rk8aidmd34584gjiq")))) + "10shwl1y9220m7ld5w9fjsjzy5yg8myrz9cz97ps9z2bw7bvka5j")))) (properties `((upstream-name . "rfigshare"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-httpuv r-httr - r-plyr r-rjsonio r-xml r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/ropensci/rfigshare") (synopsis "R Interface to figshare") (description From 97a7dedc41c2d5beb4495731a0ef095fd01873ea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:54 +0200 Subject: [PATCH 0219/1394] gnu: r-zoolog: Update to 1.0.1. * gnu/packages/cran.scm (r-zoolog): Update to 1.0.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 47bfda9fbd3..150ed193272 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32512,14 +32512,14 @@ zoom/navigate any plot when called with any active plot.") (define-public r-zoolog (package (name "r-zoolog") - (version "0.4.1") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "zoolog" version)) (sha256 (base32 - "1wxxxscw4ji4p4599vdw6vcrkqm0g75x1gh13m4758lb51wav9ks")))) + "00fi7czfwr0ll9070w3ijskd0xvilj02gy8wkgqzzrlilij8ah7p")))) (properties `((upstream-name . "zoolog"))) (build-system r-build-system) (propagated-inputs From 7718bdabbdcc4f6959c59e1430ff26218124d8f5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:54 +0200 Subject: [PATCH 0220/1394] gnu: r-mlearning: Update to 1.1.1. * gnu/packages/cran.scm (r-mlearning): Update to 1.1.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 150ed193272..d020af5a5d0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32566,14 +32566,14 @@ large datasets.") (define-public r-mlearning (package (name "r-mlearning") - (version "1.0-0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "mlearning" version)) (sha256 (base32 - "0r8xfaxw83s2r27b8x5qd0k4r5ayxpkafzn9b1a0jvsr87i6520r")))) + "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3")))) (properties `((upstream-name . "mlearning"))) (build-system r-build-system) (propagated-inputs From a9ba9c78ac81747a5a5fba46335a4ca8756ec45d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:54 +0200 Subject: [PATCH 0221/1394] gnu: r-mass: Update to 7.3-57. * gnu/packages/statistics.scm (r-mass): Update to 7.3-57. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 67f169661f8..ecd4986dc99 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -506,14 +506,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-56") + (version "7.3-57") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "11gv5965ba6xr4qsp1945vd39rp0sggzpa103rwj1c5hw0abvnlv")))) + "13asg609szqq8d1a4ybr508qcanr9gvqd439vfras6mw0l0qi2xx")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") From e4178aceb921b568e5803772479e61c584e64201 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:54 +0200 Subject: [PATCH 0222/1394] gnu: r-dichromat: Update to 2.0-0.1. * gnu/packages/statistics.scm (r-dichromat): Update to 2.0-0.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ecd4986dc99..274a32fd67a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -925,13 +925,13 @@ additions (tooltips, bipartite diagram type).") (define-public r-dichromat (package (name "r-dichromat") - (version "2.0-0") + (version "2.0-0.1") (source (origin (method url-fetch) (uri (cran-uri "dichromat" version)) (sha256 - (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i")))) + (base32 "10b0avdar3d1y8x2ya3x5kqxqg0z0mq872hdzvc1nn4amplph1d1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/dichromat") (synopsis "Color schemes for dichromats") From 3bdc46b1f37aa0359a0b4905593c33cb6a5aaf2c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:55 +0200 Subject: [PATCH 0223/1394] gnu: r-ggplot2: Update to 3.3.6. * gnu/packages/statistics.scm (r-ggplot2): Update to 3.3.6. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 274a32fd67a..6c480e6b618 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1228,13 +1228,13 @@ using just two functions: melt and dcast (or acast).") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.3.5") + (version "3.3.6") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "1si46bf9p09qzs208hqffwcb40305p361whmwhc1pwrsmx7jjxdh")))) + (base32 "1aa377jdfajj8ld2fh159y8havlibsr4pjisf6mkzk8g5awlxjxz")))) (build-system r-build-system) (propagated-inputs (list r-digest From f4b673392458f2935f6d991578d7a6fe637b82d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:55 +0200 Subject: [PATCH 0224/1394] gnu: r-knitr: Update to 1.39. * gnu/packages/statistics.scm (r-knitr): Update to 1.39. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6c480e6b618..fb3b088c1b5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1550,13 +1550,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.38") + (version "1.39") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "1bg7nmd2bvfd2gscp4nly4a2c05bpgzq536bmmf93vaf860yhf6i")))) + "0wmcj6xv0bcqzmp5vm8s574rfx366rkgm03lgyppk9ywxgnna6n9")))) (build-system r-build-system) (propagated-inputs (list r-evaluate r-highr r-stringr r-xfun r-yaml)) From 51d6e174eb5a30d55712c58a626a5806b3f5b0f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:55 +0200 Subject: [PATCH 0225/1394] gnu: r-testthat: Update to 3.1.4. * gnu/packages/statistics.scm (r-testthat): Update to 3.1.4. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index fb3b088c1b5..d3aee024b00 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1693,13 +1693,13 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "3.1.3") + (version "3.1.4") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "0c7whxl6zwapqzdplwplvhs73w9blb419h2mdl21pwmqjhzjaq68")))) + "02cwdix7v8zsvcmcl3h5hfi66w1ln9qi60risf5nl62f3c1yqzm4")))) (build-system r-build-system) (propagated-inputs (list r-brio From 3fa3f4c39e14bcac17f66baa574153aa571e1561 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:55 +0200 Subject: [PATCH 0226/1394] gnu: r-tibble: Update to 3.1.7. * gnu/packages/statistics.scm (r-tibble): Update to 3.1.7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d3aee024b00..199d6414151 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1773,14 +1773,14 @@ like tidy evaluation.") (define-public r-tibble (package (name "r-tibble") - (version "3.1.6") + (version "3.1.7") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "14l2i6ri3v5y0h8g0ahc4kz0pdqsp5yabxk2w8wavss6y44xjcsv")))) + "0wn8j7slfqrdl126g536sg1xkrvjd9rlsk0bjqk3b03nyj8hi9g1")))) (build-system r-build-system) (propagated-inputs (list r-ellipsis From e5bc9d8cd8674ba075201b0e2c84c4d26daaf078 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:55 +0200 Subject: [PATCH 0227/1394] gnu: r-dplyr: Update to 1.0.9. * gnu/packages/statistics.scm (r-dplyr): Update to 1.0.9. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 199d6414151..6d2d01256cf 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1803,13 +1803,13 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "1.0.8") + (version "1.0.9") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "0xb04ckp29pva1h2rfahqhmk9gcwp2dbbx3av8ip40v7dnha6siv")))) + "0sxl9yzccsdhlrrwj26lmh9frsijxyfaf7csv8mf7d0q4qqzgqg2")))) (build-system r-build-system) (propagated-inputs (list r-generics From 17e540f66f41f91b9c05f9e5a7ea0ad43c54a0b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:56 +0200 Subject: [PATCH 0228/1394] gnu: r-ade4: Update to 1.7-19. * gnu/packages/statistics.scm (r-ade4): Update to 1.7-19. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6d2d01256cf..7b3b4394e07 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2126,14 +2126,14 @@ chain.") (define-public r-ade4 (package (name "r-ade4") - (version "1.7-18") + (version "1.7-19") (source (origin (method url-fetch) (uri (cran-uri "ade4" version)) (sha256 (base32 - "09f5kh2mwygqpnvf53k0r54k0cvaafxm9x4nm819gwv05k2g9dpc")))) + "1vv5y6badksnpjb3bcphhjdzzh6i2grmwnsalcf2cfpr3y412lf8")))) (build-system r-build-system) (propagated-inputs (list r-mass r-pixmap r-sp)) From 69dc1acefd611542ee06b999428bc3db4457aef5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:56 +0200 Subject: [PATCH 0229/1394] gnu: r-checkmate: Update to 2.1.0. * gnu/packages/statistics.scm (r-checkmate): Update to 2.1.0. [native-inputs]: Add r-knitr. --- gnu/packages/statistics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7b3b4394e07..48c510e388f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2258,17 +2258,19 @@ R version.") (define-public r-checkmate (package (name "r-checkmate") - (version "2.0.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "checkmate" version)) (sha256 (base32 - "193gkifr9spp0x0rwnjq1spdhjkfkh4mv27iklskcj604075phhd")))) + "1ii11lypfz8qwswaiagaxnfq6wqkg3cq4j7k9q40sdd0cd8xv15p")))) (build-system r-build-system) (propagated-inputs (list r-backports)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/mllg/checkmate") (synopsis "Fast and versatile argument checks") (description From cf63da4707dec08f47c753f02512f66fd0a6baa8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:56 +0200 Subject: [PATCH 0230/1394] gnu: r-roxygen2: Update to 7.2.0. * gnu/packages/statistics.scm (r-roxygen2): Update to 7.2.0. [propagated-inputs]: Add r-cli and r-withr. --- gnu/packages/statistics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 48c510e388f..f277a5e079d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2421,16 +2421,17 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "7.1.2") + (version "7.2.0") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "1zf55wywlpy7mk7zfyi3s9fhhg1m9kvafzj46iqw5cbvnlg3ssdk")))) + "12s436jn7aagjpc2lnlrhzwqgsdl8lbbwhkddih6rnxrczawzgrf")))) (build-system r-build-system) (propagated-inputs (list r-brew + r-cli r-commonmark r-cpp11 r-desc @@ -2442,6 +2443,7 @@ tables, autolinks and strikethrough text.") r-rlang r-stringi r-stringr + r-withr r-xml2)) (native-inputs (list r-knitr)) From 2d694eb39bef1f6721c71379a201432d1f0b18ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:56 +0200 Subject: [PATCH 0231/1394] gnu: r-openssl: Update to 2.0.2. * gnu/packages/statistics.scm (r-openssl): Update to 2.0.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f277a5e079d..2ccc032980b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2457,14 +2457,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "2.0.0") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "0jsnzxa72bfxsdai25xyklmmrraaf9yv2nmqmf0bgzrkbzkgsa7b")))) + "1i7il5kkr1yp2xk8zw7max4llga4hfz0cx9sx0v2xnb9pg4ksbc6")))) (build-system r-build-system) (arguments (list From 6f62d6f81162ee8d5ad27c0d6b2e82dc79befc45 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:57 +0200 Subject: [PATCH 0232/1394] gnu: r-httr: Update to 1.4.3. * gnu/packages/statistics.scm (r-httr): Update to 1.4.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2ccc032980b..c0c85c0439f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2499,13 +2499,13 @@ integers.") (define-public r-httr (package (name "r-httr") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "httr" version)) (sha256 (base32 - "1y8y1g1dkgv9jafrk1kj6pzxpw95c0rr9lplblfq2byrs1pfsas6")))) + "0skwi501rzndywn81704d68n1l6lrvqilf91q08cjfhpjvx171ls")))) (build-system r-build-system) (propagated-inputs (list r-curl r-jsonlite r-openssl r-mime r-r6)) From 195779e0480c24a0b741f3d005cd4235288e15ce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:57 +0200 Subject: [PATCH 0233/1394] gnu: r-rcpparmadillo: Update to 0.11.1.1.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.11.1.1.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c0c85c0439f..f820ec35fb4 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2738,13 +2738,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.11.0.0.0") + (version "0.11.1.1.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "13blvrlbw8194a96v38hnllnwvyhdw5x9m0dnkyw3xsi3jrhcxin")))) + "15s8lx3s0g9npwmys509ahrqc786lg2cid21civ3wm219i4gq2zb")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs From 0bf02501385712612494dc1a352f83510b887afd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:57 +0200 Subject: [PATCH 0234/1394] gnu: r-rmarkdown: Update to 2.14. * gnu/packages/statistics.scm (r-rmarkdown): Update to 2.14. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f820ec35fb4..ca390f8898b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2830,13 +2830,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.13") + (version "2.14") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "0i07p3dxxv2s2a4xmyhc3qxmwg86vakniq5jjjclmcq2sahvw5vj")))) + (base32 "081j1hpxcwadn606ch5lq279s66c1b0f0mjvap7yimnrljpigv79")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs From acf09b40b56d905d55eac22b3660059a4bd20cf8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:57 +0200 Subject: [PATCH 0235/1394] gnu: r-rsqlite: Update to 2.2.14. * gnu/packages/statistics.scm (r-rsqlite): Update to 2.2.14. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ca390f8898b..0ea29227306 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2945,13 +2945,13 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "2.2.12") + (version "2.2.14") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "12ka9cp591sc3hn5r6z4skbjzm3nfq338wlpjdmw6rz26mmr2c9s")))) + "0z307d7rx7blh2apc9dbw9vgad2ldbf9vbdjhmwlj0mwbs3nmqra")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs From b2197d6e0704cf77c777888954c4eaea403d9905 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:58 +0200 Subject: [PATCH 0236/1394] gnu: r-segmented: Update to 1.5-0. * gnu/packages/statistics.scm (r-segmented): Update to 1.5-0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0ea29227306..92754f18e5c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3139,14 +3139,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "1.4-1") + (version "1.5-0") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "1aagn2v48ncwxx79h601nlalbgc40fc81nqaw6nbncqkqm0zaxi3")))) + "1d8np6psnmqyq3bxxd17ivp6pq6p8rx5hal4bgz8ckc4d1i9lp6n")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/segmented") From 33c177ee36d9af16c3bafc356b09c7fa098e96c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:58 +0200 Subject: [PATCH 0237/1394] gnu: r-dt: Update to 0.23. * gnu/packages/statistics.scm (r-dt): Update to 0.23. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 92754f18e5c..e30853841f3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3582,13 +3582,13 @@ using the multicore functionality of the parallel package.") "datatables-extensions/Select")))) (package (name "r-dt") - (version "0.22") + (version "0.23") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "16ah0h60ygvj49cs6cxxhdxx68cs6v6m35w5r1j5h8nxz171q61z")) + "0w6wgiwa3zgldp175a3q7zfw853xqc7mfj34n6hja48ln7yf42in")) (modules '((guix build utils))) (snippet '(for-each delete-file From c7563bf578c4d77d057a5b84685adc66ca716534 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:58 +0200 Subject: [PATCH 0238/1394] gnu: r-glmnet: Update to 4.1-4. * gnu/packages/statistics.scm (r-glmnet): Update to 4.1-4. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index e30853841f3..17abd836fa3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3733,13 +3733,13 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "4.1-3") + (version "4.1-4") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 - (base32 "0nij8v44b5dvp1vc843sfkl9ds83n6g687m2p37q1rdn82m3bg34")))) + (base32 "1y80a3b5s24ywhlil3r7b3a0vs9j59d7jkxrqa8zz09x1c5ggc7n")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) From 2af5707049771c7f71c8f3a938effa5d14a61e99 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:58 +0200 Subject: [PATCH 0239/1394] gnu: r-rtsne: Update to 0.16. * gnu/packages/statistics.scm (r-rtsne): Update to 0.16. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 17abd836fa3..44f7d912f59 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3834,14 +3834,14 @@ the way current RNG settings can be changed.") (define-public r-rtsne (package (name "r-rtsne") - (version "0.15") + (version "0.16") (source (origin (method url-fetch) (uri (cran-uri "Rtsne" version)) (sha256 (base32 - "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn")))) + "1mgviwrqwapn8w7rq0sjxca5vi7ylgmm876ijwp22a3chbf5m82j")))) (properties `((upstream-name . "Rtsne"))) (build-system r-build-system) (propagated-inputs From 334a26cb37bd0a1463ee3733ff72dae8d714b22c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:59 +0200 Subject: [PATCH 0240/1394] gnu: r-bigmemory: Update to 4.6.1. * gnu/packages/statistics.scm (r-bigmemory): Update to 4.6.1. [propagated-inputs]: Add r-uuid. [inputs]: Add util-linux:lib. --- gnu/packages/statistics.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 44f7d912f59..ce0b195dcb0 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -68,6 +68,7 @@ #:use-module (gnu packages java) #:use-module (gnu packages javascript) #:use-module (gnu packages libffi) + #:use-module (gnu packages linux) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) @@ -3922,17 +3923,19 @@ message passing.") (define-public r-bigmemory (package (name "r-bigmemory") - (version "4.5.36") + (version "4.6.1") (source (origin (method url-fetch) (uri (cran-uri "bigmemory" version)) (sha256 (base32 - "03pg8mxdc7q0249visjmc8bc3xmwxsfg3i2n6higicj4cfz7zihq")))) + "0hainqkm7cs8gjm42vkpdrr0284smsbwdfackp34yv7dhxy1avmm")))) (build-system r-build-system) (propagated-inputs - (list r-bh r-rcpp r-bigmemory-sri)) + (list r-bh r-bigmemory-sri r-rcpp r-uuid)) + (inputs + (list `(,util-linux "lib"))) ;for -luuid (home-page "http://www.bigmemory.org") (synopsis "Manage large matrices with shared memory or memory-mapped files") (description "This package provides methods to create, store, access, and From e6b17481d9fe890a4ec287c13177a4331539ce2e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:59 +0200 Subject: [PATCH 0241/1394] gnu: r-matrixstats: Update to 0.62.0. * gnu/packages/statistics.scm (r-matrixstats): Update to 0.62.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ce0b195dcb0..30bb8b1df94 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4095,13 +4095,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.61.0") + (version "0.62.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "16pxsba5i51ifbbgvxln2w6nigbwd3290b2ckgzn5bmib7nc1lyv")))) + "1jjfsi5vzx6js7phlnd3v64fd05fg0jyz8iq5pivy36jdmmh3ql5")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (arguments From 417517cd3f20c1f057b0edc6c38d3797b94a5fa9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:59 +0200 Subject: [PATCH 0242/1394] gnu: r-hmisc: Update to 4.7-0. * gnu/packages/statistics.scm (r-hmisc): Update to 4.7-0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 30bb8b1df94..7f2d864d8ce 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4486,13 +4486,13 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "4.6-0") + (version "4.7-0") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 - (base32 "1bd1c8sichyijprfpnqj5g72nmgs9jvi0zyw8v4nsg1kn83fj71c")))) + (base32 "1gc71wg6f17x6nriphs1kk39ix7lpqk32clk1qshqy8wl6f2vv19")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs From a853e9c7c4e4e9691344928a8e639ef1ed87899c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:59 +0200 Subject: [PATCH 0243/1394] gnu: r-gtools: Update to 3.9.2.1. * gnu/packages/statistics.scm (r-gtools): Update to 3.9.2.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7f2d864d8ce..c75af2c410e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4612,14 +4612,14 @@ Zurich, including many that are related to graphics.") (define-public r-gtools (package (name "r-gtools") - (version "3.9.2") + (version "3.9.2.1") (source (origin (method url-fetch) (uri (cran-uri "gtools" version)) (sha256 (base32 - "0lx97yafrms2mjym8rhcq5586z7s1iqgy8qfm4px3xl1yn5qkc83")))) + "0pxg0ang9q26hlwgf53pp1hq6rlarq5rnrrr9dl14f5kgfnynpzc")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/gtools") (synopsis "Various R programming tools") From 9879075a1415505789369f38788a24b474a0b434 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:30:59 +0200 Subject: [PATCH 0244/1394] gnu: r-gdata: Update to 2.18.0.1. * gnu/packages/statistics.scm (r-gdata): Update to 2.18.0.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c75af2c410e..5c0c2101557 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4634,14 +4634,14 @@ tests for whether a value is missing, empty or contains only @code{NA} and (define-public r-gdata (package (name "r-gdata") - (version "2.18.0") + (version "2.18.0.1") (source (origin (method url-fetch) (uri (cran-uri "gdata" version)) (sha256 (base32 - "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b")))) + "1n9jw136kk5ld27qvny7cx2s8l34jdgmzlx40x62mmcqjddksbsy")))) (build-system r-build-system) (inputs (list perl)) From 98e40f2d4643376936ce2874fa55894070cbd817 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:00 +0200 Subject: [PATCH 0245/1394] gnu: r-gplots: Update to 3.1.3. * gnu/packages/statistics.scm (r-gplots): Update to 3.1.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5c0c2101557..e76f3e1e122 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4674,14 +4674,14 @@ including: (define-public r-gplots (package (name "r-gplots") - (version "3.1.1") + (version "3.1.3") (source (origin (method url-fetch) (uri (cran-uri "gplots" version)) (sha256 (base32 - "0f8khaymz383w2ksnk80d4kpnvgmdk37pbycpsnl2vabaz11kbpr")))) + "05k7a8x62qs5g6mps62vb3mwjdnfjzvjb20yws3x0r2j42g3p1cz")))) (build-system r-build-system) (propagated-inputs (list r-catools r-gtools r-kernsmooth)) From d1856b061c18c7ed61a7a367c47ae60d13706b3e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:00 +0200 Subject: [PATCH 0246/1394] gnu: r-lars: Update to 1.3. * gnu/packages/statistics.scm (r-lars): Update to 1.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index e76f3e1e122..f2ea0579c33 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5017,14 +5017,14 @@ mixture models.") (define-public r-lars (package (name "r-lars") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "lars" version)) (sha256 (base32 - "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34")))) + "17al1g0pvfz9frs2kxicqr8dyp7ciz3x87yx2l4lqd53ls6nm7n6")))) (build-system r-build-system) (inputs (list gfortran)) From 917c943fbc53af33e86bb9426031ec5c07114a7c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:00 +0200 Subject: [PATCH 0247/1394] gnu: r-randomforest: Update to 4.7-1.1. * gnu/packages/statistics.scm (r-randomforest): Update to 4.7-1.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f2ea0579c33..c84286abdb6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5064,14 +5064,14 @@ perform @dfn{independent component analysis} (ICA) and projection pursuit.") (define-public r-randomforest (package (name "r-randomforest") - (version "4.7-1") + (version "4.7-1.1") (source (origin (method url-fetch) (uri (cran-uri "randomForest" version)) (sha256 (base32 - "04q6gb917md4yw837cf9vlx1q8ljl06jw7yhykzb6nl47w55jnkq")))) + "1micz9794j7xmj755ln2692rzip8azndflxgdg6xn3j86issi7pm")))) (properties `((upstream-name . "randomForest"))) (build-system r-build-system) (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/") From 347104de8a70130878a346e711fe9859756252fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:00 +0200 Subject: [PATCH 0248/1394] gnu: r-mclust: Update to 5.4.10. * gnu/packages/statistics.scm (r-mclust): Update to 5.4.10. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c84286abdb6..6a1e587ee32 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5150,14 +5150,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "5.4.9") + (version "5.4.10") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "0s4mva0n04f3pl41msmzhlh7pnk0zbmf06n826smxkw6mz327wb5")))) + "0wh6nsbma4b0wsmqm2ynbznl2wlwdly4vg583f6z0zd1qkrvn6ra")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) From f327949d97f0169cdbc85e335e9fde986c28437b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:00 +0200 Subject: [PATCH 0249/1394] gnu: r-pcapp: Update to 2.0-1. * gnu/packages/statistics.scm (r-pcapp): Update to 2.0-1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6a1e587ee32..b2f445e5c17 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5242,14 +5242,14 @@ regression methodology including model selections and multivariate statistics.") (define-public r-pcapp (package (name "r-pcapp") - (version "1.9-74") + (version "2.0-1") (source (origin (method url-fetch) (uri (cran-uri "pcaPP" version)) (sha256 (base32 - "1dlrz5plb8b89vr3j6sn9jwryyhcwflqkiilxkybbr379m1pp0sh")))) + "06hjhr0dzdp5yhd421q9scbv6w6bchicbn2bl7am490ncgrf544n")))) (properties `((upstream-name . "pcaPP"))) (build-system r-build-system) (propagated-inputs From f4721c4a414ef034a56abe5d95178ea6b6559031 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:00 +0200 Subject: [PATCH 0250/1394] gnu: r-rrcov: Update to 1.7-0. * gnu/packages/statistics.scm (r-rrcov): Update to 1.7-0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index b2f445e5c17..aad6669578b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5264,14 +5264,14 @@ analysis} (PCA) by projection pursuit.") (define-public r-rrcov (package (name "r-rrcov") - (version "1.6-2") + (version "1.7-0") (source (origin (method url-fetch) (uri (cran-uri "rrcov" version)) (sha256 (base32 - "18x8y2b9n2plpn4086nkjk9c27p7gb78kbrv5pj9r8fb0idl5rn5")))) + "1z98j9973hl19b70dcwfcf55ifxr2a9v53daaq2sagynh95aik6b")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mvtnorm r-pcapp r-robustbase)) From 8685079a32ca7e7ddc0a00d376be67b4df452399 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:01 +0200 Subject: [PATCH 0251/1394] gnu: r-quantreg: Update to 5.93. * gnu/packages/statistics.scm (r-quantreg): Update to 5.93. [propagated-inputs]: Add r-mass and r-survival. [native-inputs]: Add r-r-rsp. [arguments]: Add phase 'set-HOME. --- gnu/packages/statistics.scm | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index aad6669578b..9167159cdff 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5527,18 +5527,24 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.88") + (version "5.93") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 - (base32 "0grsha18zkiil0qnxc1d7kc3w26i6aaa4av9n9ahdm8yf59yah0r")))) + (base32 "0fg5x6sa8mz2hh9nak0wajh4l6h03x216462vs94rgq0ln24kafl")))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs - (list gfortran)) + (list gfortran + r-r-rsp)) ;for vignettes (propagated-inputs - (list r-matrix r-matrixmodels r-sparsem)) + (list r-mass r-matrix r-matrixmodels r-sparsem r-survival)) (home-page "https://www.r-project.org") (synopsis "Quantile regression") (description From 40daf6db0a3b3757b4f5cfd1f546702cc5d83fa0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:01 +0200 Subject: [PATCH 0252/1394] gnu: r-nloptr: Update to 2.0.3. * gnu/packages/statistics.scm (r-nloptr): Update to 2.0.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9167159cdff..78acaa0d26f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5558,14 +5558,14 @@ expected shortfall risk are also included.") (define-public r-nloptr (package (name "r-nloptr") - (version "2.0.0") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "nloptr" version)) (sha256 (base32 - "16k124ll14p3ygny6i1zd7yza83bv2sk87x922n1bfn9rx4k3jk5")))) + "1mqnjswm0dl6vqc8b2s5k3n1mhanaha3l33vh68dh6zx8q9aq9kv")))) (build-system r-build-system) (native-inputs (list r-knitr ; for building vignettes From 58c5fe19184351e8f198cdc4418257c6a39e8a26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:01 +0200 Subject: [PATCH 0253/1394] gnu: r-car: Update to 3.0-13. * gnu/packages/statistics.scm (r-car): Update to 3.0-13. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 78acaa0d26f..b51cec32209 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5668,13 +5668,13 @@ Companion to Applied Regression, Third Edition, Sage.") (define-public r-car (package (name "r-car") - (version "3.0-12") + (version "3.0-13") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 - (base32 "00kk8l71508f73kyn21is1mx6kjbrzdq3ls94c5ajhiqmvpsd6dq")))) + (base32 "1ss7kvi5hf9s4b6i7y06zl4iip1w1h8ff4zzf529wk18h3dfhnnk")))) (build-system r-build-system) (propagated-inputs (list r-abind From a415f00c5d1de39adbf25a6990faaf3d42de7597 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:01 +0200 Subject: [PATCH 0254/1394] gnu: r-tclust: Update to 1.5-1. * gnu/packages/statistics.scm (r-tclust): Update to 1.5-1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index b51cec32209..0822fb73251 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5818,14 +5818,14 @@ multivariate case.") (define-public r-tclust (package (name "r-tclust") - (version "1.4-2") + (version "1.5-1") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 - "1nb5iky4kc832627jf28lzj19wrvgwg5da6fyl3kyf0npmyx1p4m")))) + "09zk38gih67a8lk72k46mfgv21jpnxh2nzrxc5ypdc2bfwq8nckk")))) (build-system r-build-system) ;; These are all suggested packages, not build dependencies. (propagated-inputs From 217d08960ab1f54babf14d5cf2febf6f1f6b8b23 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:01 +0200 Subject: [PATCH 0255/1394] gnu: r-clubsandwich: Update to 0.5.6. * gnu/packages/statistics.scm (r-clubsandwich): Update to 0.5.6. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0822fb73251..c4155aca730 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -6480,14 +6480,14 @@ mediation and estimating power.") (define-public r-clubsandwich (package (name "r-clubsandwich") - (version "0.5.5") + (version "0.5.6") (source (origin (method url-fetch) (uri (cran-uri "clubSandwich" version)) (sha256 (base32 - "1ifnc2rg5agf7lpilmm27iq0af7ghfhkvwykajhvykgf6h4clvhf")))) + "0mll8q61vnb980dck8ihxcy89z8m7f8i16mqdvr4l2ljywkhpzvd")))) (properties `((upstream-name . "clubSandwich"))) (build-system r-build-system) (propagated-inputs From 7d9ed0b53daf3eb3b8025c7d302148a2b677f0a9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:01 +0200 Subject: [PATCH 0256/1394] gnu: r-logspline: Update to 2.1.17. * gnu/packages/statistics.scm (r-logspline): Update to 2.1.17. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c4155aca730..68b2258a540 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -6629,14 +6629,14 @@ or eta squared effect size.") (define-public r-logspline (package (name "r-logspline") - (version "2.1.16") + (version "2.1.17") (source (origin (method url-fetch) (uri (cran-uri "logspline" version)) (sha256 (base32 - "12hkdi77vkic05p2vhap025xdcg1n53ywm239v18713pihdlj63l")))) + "05c8l22zcvb086909h9vw7icphww703vkcxp2h881y4n1232pdq3")))) (properties `((upstream-name . "logspline"))) (build-system r-build-system) (native-inputs (list gfortran)) From 55a04c5245f10ea7b9385261b81ee00629fc9ddd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:02 +0200 Subject: [PATCH 0257/1394] gnu: r-datasaurus: Update to 0.1.6. * gnu/packages/statistics.scm (r-datasaurus): Update to 0.1.6. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 68b2258a540..c7496987b01 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -6804,14 +6804,14 @@ Michael Lim & Trevor Hastie (2015)") (define-public r-datasaurus (package (name "r-datasaurus") - (version "0.1.4") + (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "datasauRus" version)) (sha256 (base32 - "1w1yhwwrmh95bklacz44wjwynxd8cj3z8b9zvsnzmk18m5a4k0fl")))) + "0vgylf3bab0xcfg08xwvfq9yhxy6w0fxi7wp4kkxfyjb0pw15qxk")))) (properties `((upstream-name . "datasauRus"))) (build-system r-build-system) (native-inputs (list r-knitr)) From 7fadf9bad73851ee2207d24c3ab40e66a8280f8a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:02 +0200 Subject: [PATCH 0258/1394] gnu: r-desctools: Update to 0.99.45. * gnu/packages/statistics.scm (r-desctools): Update to 0.99.45. [propagated-inputs]: Add r-httr and r-readxl. --- gnu/packages/statistics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c7496987b01..fac9189aea1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -6920,13 +6920,13 @@ Calculates confidence intervals for the difference in proportion.") (define-public r-desctools (package (name "r-desctools") - (version "0.99.44") + (version "0.99.45") (source (origin (method url-fetch) (uri (cran-uri "DescTools" version)) (sha256 - (base32 "04wp3sp6sahgq167465y38y13h1ia5a4zqazysacpjxd1if0578j")))) + (base32 "01gbmikpzjmymvb7p76k7wqvfvwznl6v0qa78jy7bi6fzmbp1zld")))) (properties `((upstream-name . "DescTools"))) (build-system r-build-system) (propagated-inputs @@ -6936,9 +6936,11 @@ Calculates confidence intervals for the difference in proportion.") r-exact r-expm r-gld + r-httr r-mass r-mvtnorm r-rcpp + r-readxl r-rstudioapi)) (native-inputs (list gfortran)) (home-page "https://andrisignorell.github.io/DescTools/") From 48328055d832b0a7f2a66cce416c7169f5c2d784 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 08:31:02 +0200 Subject: [PATCH 0259/1394] gnu: r-binom: Update to 1.1-1.1. * gnu/packages/statistics.scm (r-binom): Update to 1.1-1.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index fac9189aea1..a8457657b80 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -7044,13 +7044,13 @@ the presence of variance components/nonparametric terms for models fit with (define-public r-binom (package (name "r-binom") - (version "1.1-1") + (version "1.1-1.1") (source (origin (method url-fetch) (uri (cran-uri "binom" version)) (sha256 - (base32 "0mjj92dqf5q69jxzqya4izb1mly3mkydbnmlm4wb3zqqg82a324c")))) + (base32 "1yxyhsd0savwirlmgnq6973slfakqyfvjm0zz60cmc9v490my8gf")))) (properties `((upstream-name . "binom"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=binom") From 2e2fed31a379ce247e30457b4ee4e820ee9a8cf8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 09:48:15 +0200 Subject: [PATCH 0260/1394] gnu: nlopt: Update to 2.7.1. * gnu/packages/maths.scm (nlopt): Update to 2.7.1. [source]: Fetch from git. [build-system]: Use cmake-build-system. [arguments]: Adjuts 'set-libnlopt-file-name phase. [inputs]: Replace guile-2.0 with guile-3.0; add octave and python. [native-inputs]: Add swig. --- gnu/packages/maths.scm | 43 +++++++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 98e239d5bd9..16faf1ec18a 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2014-2022 Eric Bavier ;;; Copyright © 2014 Federico Beffa ;;; Copyright © 2014 Mathieu Lirzin -;;; Copyright © 2015–2021 Ricardo Wurmus +;;; Copyright © 2015–2022 Ricardo Wurmus ;;; Copyright © 2015 Sou Bunnbu ;;; Copyright © 2015, 2018 Mark H Weaver ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner @@ -152,6 +152,7 @@ #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages sphinx) + #:use-module (gnu packages swig) #:use-module (gnu packages tcl) #:use-module (gnu packages texinfo) #:use-module (gnu packages tex) @@ -1915,34 +1916,34 @@ with the provided training tools.") (define-public nlopt (package (name "nlopt") - (version "2.4.2") + (version "2.7.1") (source (origin - (method url-fetch) - (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/stevengj/nlopt/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0")))) - (build-system gnu-build-system) + (base32 "1xpdza28i8w441fwv6a5f3qk4zi7ys6ws9fx6kr5ny27dfdz6rr1")))) + (build-system cmake-build-system) (arguments - `(;; Shared libraries are not built by default. They are required to - ;; build the Guile, Octave, and Python bindings. - #:configure-flags '("--enable-shared") - - #:phases + `(#:phases (modify-phases %standard-phases (add-before 'configure 'set-libnlopt-file-name (lambda* (#:key outputs #:allow-other-keys) ;; Make sure the Scheme module refers to the library by its - ;; absolute file name (we cannot do that from a snippet - ;; because the expansion of @libdir@ contains - ;; ${exec_prefix}.) + ;; absolute file name. (let ((out (assoc-ref outputs "out"))) - (substitute* "swig/nlopt.scm.in" - (("libnlopt") - (string-append out "/lib/libnlopt"))) - #t)))))) - (inputs (list guile-2.0)) - (native-inputs (list pkg-config)) + (substitute* "src/swig/nlopt-guile.i" + (("\"nlopt_guile\"") + (format #f "~s" + `(format #f "~anlopt_guile" + (if (getenv "NLOPT_UNINSTALLED") + "" + ,(format #f "~a/lib/guile/3.0/extensions/" out)))))) + (setenv "NLOPT_UNINSTALLED" "1"))))))) + (inputs (list guile-3.0 octave python)) + (native-inputs (list pkg-config swig)) (home-page "http://ab-initio.mit.edu/wiki/") (synopsis "Library for nonlinear optimization") (description "NLopt is a library for nonlinear optimization, providing a From 02c8c3ffbdbdf914d8aa59d0161d01e4c4ddcf37 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 09:59:33 +0200 Subject: [PATCH 0261/1394] gnu: r-rcurl: Update to 1.98-1.6. * gnu/packages/statistics.scm (r-rcurl): Update to 1.98-1.6. [source]: Take from CRAN. [arguments]: Remove trailing #T from build phase. [native-inputs]: Add libxml2. [inputs]: Use new input list style. --- gnu/packages/statistics.scm | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a8457657b80..43b9c1b8044 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2976,15 +2976,13 @@ engine (version 3.8.8.2) is included.") (define-public r-rcurl (package (name "r-rcurl") - (version "1.95-0.1.2") + (version "1.98-1.6") (source (origin (method url-fetch) - (uri (string-append "https://www.bioconductor.org/packages/" - "release/extra/src/" - "contrib/RCurl_" version ".tar.gz")) + (uri (cran-uri "RCurl" version)) (sha256 (base32 - "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc")))) + "18nif4phr5vfhri07mnchiym0qfm31ak9nxvb2v9ac84mij6idbc")))) (properties `((upstream-name . "RCurl"))) (build-system r-build-system) (arguments @@ -2997,10 +2995,11 @@ engine (version 3.8.8.2) is included.") (string-append "\ certs = Sys.getenv(\"CURL_CA_BUNDLE\") if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) } -" m))) - #t))))) +" m)))))))) + (native-inputs + (list libxml2)) (inputs - `(("libcurl" ,curl))) + (list curl)) (propagated-inputs (list r-bitops)) (home-page "http://www.omegahat.net/RCurl") From d723619fc30667514fea944256bd55afe5e219f0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 10:34:30 +0200 Subject: [PATCH 0262/1394] gnu: r-biostrings: Patch for R 4.2.0. * gnu/packages/bioconductor.scm (r-biostrings)[arguments]: Add build phase 'patch-for-R-4.2.0. --- gnu/packages/bioconductor.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bf371a970a5..0410ff8a82f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3104,6 +3104,19 @@ objects.") (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + ;; See commit c3340745870a88d1558e093a7f892c1aeac784ef in + ;; https://github.com/Bioconductor/Biostrings/ + (add-after 'unpack 'patch-for-R-4.2.0 + (lambda _ + (substitute* '("src/BitMatrix.c" + "src/RoSeqs_utils.c" + "src/match_pdict_utils.c" + "src/xscat.c") + (("#include .*") + "#define Salloc(n,t) (t*)S_alloc(n, sizeof(t)) /* from old */\n"))))))) (propagated-inputs (list r-biocgenerics r-crayon From 39dab63790686558a1a69e75aa4bd6f1c1ea19c4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:07:12 +0200 Subject: [PATCH 0263/1394] gnu: Add r-dixontest. * gnu/packages/cran.scm (r-dixontest): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d020af5a5d0..ba3aedbdefc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -347,6 +347,29 @@ visualization of their differences.") (description "This package implements Dirichlet regression models.") (license license:gpl2+))) +(define-public r-dixontest + (package + (name "r-dixontest") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "dixonTest" version)) + (sha256 + (base32 "1a3yc30g5rbb0jhm2b0iir5i1dy4jyl67spkhx4yysg4snz131wv")))) + (properties `((upstream-name . "dixonTest"))) + (build-system r-build-system) + (native-inputs (list gfortran)) + (home-page "https://cran.r-project.org/package=dixonTest") + (synopsis "Dixon's ratio test for outlier detection") + (description + "For outlier detection in small and normally distributed samples the ratio +test of Dixon (Q-test) can be used. Density, distribution function, quantile +function and random generation for Dixon's ratio statistics are provided as +wrapper functions. The core applies McBane's Fortran functions that use +Gaussian quadrature for a numerical solution.") + (license license:gpl3))) + (define-public r-emdist (package (name "r-emdist") From 1445f2c508a9b6d2e04dd8ce05a76b7ac7bed970 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:07:25 +0200 Subject: [PATCH 0264/1394] gnu: Add r-rcppml. * gnu/packages/cran.scm (r-rcppml): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ba3aedbdefc..61a1b055b99 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3854,6 +3854,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see @code{citation(\"Rcpp\")} for details on these last two.") (license license:gpl2+))) +(define-public r-rcppml + (package + (name "r-rcppml") + (version "0.3.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppML" version)) + (sha256 + (base32 "1ih8i7i6m221iw227mnl3rvnaw2l53h8fpnc4f8yn9sm10anap1j")))) + (properties `((upstream-name . "RcppML"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-rcpp r-rcppeigen)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/zdebruine/RcppML") + (synopsis "Rcpp machine learning library") + (description + "This package provides fast machine learning algorithms including matrix +factorization and divisive clustering for large sparse and dense matrices.") + (license license:gpl2+))) + (define-public r-rcppthread (package (name "r-rcppthread") From 641f5c599e68f191fc94f458abae727d7f4028cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:18:57 +0200 Subject: [PATCH 0265/1394] gnu: apache-arrow: Update to 8.0.0. * gnu/packages/databases.scm (apache-arrow): Update to 8.0.0. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 2161340ef96..2d72c78233b 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -4207,7 +4207,7 @@ the SQL language using a syntax that reflects the resulting query.") (define-public apache-arrow (package (name "apache-arrow") - (version "7.0.0") + (version "8.0.0") (source (origin (method git-fetch) @@ -4217,7 +4217,7 @@ the SQL language using a syntax that reflects the resulting query.") (file-name (git-file-name name version)) (sha256 (base32 - "19xx6mlddca79q6d3wga574m4y32ixmxx2rmk6j3f22i5c37mjzw")))) + "1gwiflk72pq1krc0sjzabypmh7slfyf7ak71fiypy3xgzw8a777c")))) (build-system cmake-build-system) (arguments `(#:tests? #f From 556ca8ba21ffb37c429b6c060d491136027a6cb5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:20:32 +0200 Subject: [PATCH 0266/1394] guix: Upgrade to Bioconductor 3.15. * guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to 3.15. * guix/import/cran.scm (%bioconductor-version): Same. --- guix/build-system/r.scm | 2 +- guix/import/cran.scm | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm index 2c82390ba6b..620822b8705 100644 --- a/guix/build-system/r.scm +++ b/guix/build-system/r.scm @@ -61,7 +61,7 @@ release corresponding to NAME and VERSION." "/src/contrib/" name "_" version ".tar.gz") ;; TODO: use %bioconductor-version from (guix import cran) - (string-append "https://bioconductor.org/packages/3.14" + (string-append "https://bioconductor.org/packages/3.15" type-url-part "/src/contrib/" name "_" version ".tar.gz")))) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index e848ebc7894..4e1ce7c010f 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -156,9 +156,9 @@ package definition." (define %cran-canonical-url "https://cran.r-project.org/package=") (define %bioconductor-url "https://bioconductor.org/packages/") -;; The latest Bioconductor release is 3.14. Bioconductor packages should be +;; The latest Bioconductor release is 3.15. Bioconductor packages should be ;; updated together. -(define %bioconductor-version "3.14") +(define %bioconductor-version "3.15") (define* (bioconductor-packages-list-url #:optional type) (string-append "https://bioconductor.org/packages/" From 413133e4309a19c4830170271ee58c6cd9f0ff62 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:19:36 +0200 Subject: [PATCH 0267/1394] gnu: Add r-decoupler. * gnu/packages/bioconductor.scm (r-decoupler): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0410ff8a82f..4e06a3c6947 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2167,6 +2167,47 @@ set analyses, and can deal with repeated or longitudinal data.") biological sequences.") (license license:gpl3))) +(define-public r-decoupler + (package + (name "r-decoupler") + (version "2.2.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "decoupleR" version)) + (sha256 + (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m")))) + (properties `((upstream-name . "decoupleR"))) + (build-system r-build-system) + (propagated-inputs + (list r-broom + r-dplyr + r-magrittr + r-matrix + r-purrr + r-rlang + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-withr)) + (native-inputs (list r-knitr)) + (home-page "https://saezlab.github.io/decoupleR/") + (synopsis "Computational methods to infer biological activities from omics data") + (description + "Many methods allow us to extract biological activities from omics data using +information from prior knowledge resources, reducing the dimensionality for +increased statistical power and better interpretability. decoupleR is a +Bioconductor package containing different statistical methods to extract these +signatures within a unified framework. decoupleR allows the user to flexibly +test any method with any resource. It incorporates methods that take into +account the sign and weight of network interactions. decoupleR can be used +with any omic, as long as its features can be linked to a biological process +based on prior knowledge. For example, in transcriptomics gene sets regulated +by a transcription factor, or in phospho-proteomics phosphosites that are +targeted by a kinase.") + (license license:gpl3))) + (define-public r-deepsnv (package (name "r-deepsnv") From 90d165ea864439744772575c1b8d469576d1f419 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:23:09 +0200 Subject: [PATCH 0268/1394] gnu: r-biostrings: Update to 2.64.0. * gnu/packages/bioconductor.scm (r-biostrings): Update to 2.64.0. [arguments]: Remove build phase 'patch-for-R-4.2.0. --- gnu/packages/bioconductor.scm | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4e06a3c6947..0635890a4ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3135,29 +3135,16 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "11qkw863mkfz3mc55v2gmfr4w3xziqfb5pq3hmjqpn8vpw8ax3xq")))) + "1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - ;; See commit c3340745870a88d1558e093a7f892c1aeac784ef in - ;; https://github.com/Bioconductor/Biostrings/ - (add-after 'unpack 'patch-for-R-4.2.0 - (lambda _ - (substitute* '("src/BitMatrix.c" - "src/RoSeqs_utils.c" - "src/match_pdict_utils.c" - "src/xscat.c") - (("#include .*") - "#define Salloc(n,t) (t*)S_alloc(n, sizeof(t)) /* from old */\n"))))))) (propagated-inputs (list r-biocgenerics r-crayon From 67d858b97cc6dc7a10ca38b1e6390192ff3bf765 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:36:49 +0200 Subject: [PATCH 0269/1394] gnu: r-abarray: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-abarray): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0635890a4ff..a426d825de5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1551,13 +1551,13 @@ TCGAbiolinksGUI package.") (define-public r-abarray (package (name "r-abarray") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABarray" version)) (sha256 (base32 - "0yh7jmkwdg3kmm98ii0cxbla3s5bwy84fpg6xcpggsrriwzwfb5k")))) + "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r")))) (properties `((upstream-name . "ABarray"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest)) From 5911a8992bf149363ba518ea6911aae8ddb3b417 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:30 +0200 Subject: [PATCH 0270/1394] gnu: r-absseq: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-absseq): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a426d825de5..1b40b2f5281 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1577,13 +1577,13 @@ into folders according to the analysis settings used.") (define-public r-absseq (package (name "r-absseq") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABSSeq" version)) (sha256 (base32 - "0l2hh6qv4lhw1g1kciw2f3ssj3lw83hqxnkmxzmv7snik3k6i650")))) + "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv")))) (properties `((upstream-name . "ABSSeq"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit)) From 69dc67d9aa41a9310c01abaa575b4edfc2e50f98 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:30 +0200 Subject: [PATCH 0271/1394] gnu: r-adam: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-adam): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b40b2f5281..494a164f0e0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1606,13 +1606,13 @@ ranking by fold-change and visualization.") (define-public r-adam (package (name "r-adam") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 - "18zwci0ab54q7rdwj0n63w0i14lfrb4cccp09bcrq10gl1ki07f5")))) + "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr From 1d3b5f80e75375fc91db4ae0c9ae0d2ac171a7e5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:30 +0200 Subject: [PATCH 0272/1394] gnu: r-adamgui: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-adamgui): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 494a164f0e0..09604239eb8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1641,13 +1641,13 @@ functionally associated genes} (GFAG).") (define-public r-adamgui (package (name "r-adamgui") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAMgui" version)) (sha256 (base32 - "0n06bb9djigha0249lxx84pn9q0xiryxbv25qsc3p2h46iaxi3wq")))) + "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs")))) (properties `((upstream-name . "ADAMgui"))) (build-system r-build-system) (propagated-inputs From 3a29b78fa9161473aff8d076cde247870cea05e9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:30 +0200 Subject: [PATCH 0273/1394] gnu: r-adimpute: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-adimpute): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 09604239eb8..27216b2b522 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1689,13 +1689,13 @@ the @code{GFAGpathUi} function.") (define-public r-adimpute (package (name "r-adimpute") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADImpute" version)) (sha256 (base32 - "1bkq1hd8sqg9r28r70a9vd3gb2nsmg6dybf002d621p88cdfjib2")))) + "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w")))) (properties `((upstream-name . "ADImpute"))) (build-system r-build-system) (propagated-inputs From 3e524e46a043711db22c17352156294e40d7321c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:30 +0200 Subject: [PATCH 0274/1394] gnu: r-adsplit: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-adsplit): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 27216b2b522..4e2ff9ebd66 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1738,13 +1738,13 @@ results from different methods into an ensemble.") (define-public r-adsplit (package (name "r-adsplit") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 - "1b4ck371h3a76m5h0brvlzsyg1g6q5fjrhra5hqv9pwxr330h9r2")))) + "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm")))) (properties `((upstream-name . "adSplit"))) (build-system r-build-system) (propagated-inputs From f4a85d5555c40bdeccb1894fbda5fcd2e2f97a4b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:30 +0200 Subject: [PATCH 0275/1394] gnu: r-affixcan: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-affixcan): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4e2ff9ebd66..b0a4731ae73 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1766,13 +1766,13 @@ the supporting gene set is determined.") (define-public r-affixcan (package (name "r-affixcan") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffiXcan" version)) (sha256 (base32 - "06yn87briv2141jqad934gg5rcd90w5nghrgmbhqnmwafn72gj9d")))) + "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq")))) (properties `((upstream-name . "AffiXcan"))) (build-system r-build-system) (propagated-inputs From 052d0d283adb58c12854bd5fa2259a2f64b89516 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:31 +0200 Subject: [PATCH 0276/1394] gnu: r-affyrnadegradation: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-affyrnadegradation): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b0a4731ae73..b4edb6e3c71 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1794,13 +1794,13 @@ expression values are known.") (define-public r-affyrnadegradation (package (name "r-affyrnadegradation") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyRNADegradation" version)) (sha256 (base32 - "00hzr62xn1i1w4g8krsxhivzwn8hd7hwhkdxyrpz6cs9vgr4x9kd")))) + "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf")))) (properties `((upstream-name . "AffyRNADegradation"))) (build-system r-build-system) (propagated-inputs (list r-affy)) From 6e1d25615130944cdc14fe9498b49aa2ccce069b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:31 +0200 Subject: [PATCH 0277/1394] gnu: r-agdex: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-agdex): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4edb6e3c71..137886f8f4c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1819,13 +1819,13 @@ of samples that are affected by RNA degradation.") (define-public r-agdex (package (name "r-agdex") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AGDEX" version)) (sha256 (base32 - "0y0q4zdybr5hlsi7qy2hf6c2sqr2z2211wz36dz70jkqyr0ggw64")))) + "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9")))) (properties `((upstream-name . "AGDEX"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-gseabase)) From e704ed78b5f34c52afbb7e1a6d3fd3b49eeb66ac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:31 +0200 Subject: [PATCH 0278/1394] gnu: r-aggregatebiovar: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-aggregatebiovar): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 137886f8f4c..2f8cad9128c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1846,13 +1846,13 @@ experiment.") (define-public r-aggregatebiovar (package (name "r-aggregatebiovar") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aggregateBioVar" version)) (sha256 (base32 - "1wbfp1pf62di6pzxsf36lmzk6y9dllz1n4iv3mhpb1x8cvy4hqqk")))) + "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1")))) (properties `((upstream-name . "aggregateBioVar"))) (build-system r-build-system) (propagated-inputs From a5e1a37cdfdb88210b751866fcd317a4b792258f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:31 +0200 Subject: [PATCH 0279/1394] gnu: r-agilp: Update to 3.28.0. * gnu/packages/bioconductor.scm (r-agilp): Update to 3.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2f8cad9128c..64f12d1e05f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1880,13 +1880,13 @@ bulk RNA-seq tools.") (define-public r-agilp (package (name "r-agilp") - (version "3.26.0") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "agilp" version)) (sha256 (base32 - "02cyc2y4v3y16zlrnax2c96b2qfxj6b2j37ps4g2gdqgas08n9xp")))) + "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf")))) (properties `((upstream-name . "agilp"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/agilp") From 5f9a73d6652f6c4c2ac50113a2cdf1f1091635bf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:31 +0200 Subject: [PATCH 0280/1394] gnu: r-adductomicsr: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-adductomicsr): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 64f12d1e05f..294a2d96d0e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1902,13 +1902,13 @@ but which also provides utilities which may be useful for other platforms.") (define-public r-adductomicsr (package (name "r-adductomicsr") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductomicsR" version)) (sha256 (base32 - "0cnvxrk0h3r6jpa4g4qismg6zk5c7rf8lqixg89c24i98gffkbcl")))) + "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys")))) (properties `((upstream-name . "adductomicsR"))) (build-system r-build-system) (propagated-inputs From 75628fc7ce22890344e582b6fd7a648548acb3dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:31 +0200 Subject: [PATCH 0281/1394] gnu: r-aneufinder: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 294a2d96d0e..c0a38585599 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1977,13 +1977,13 @@ objects are used so that other packages could be used as well.") (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0")))) + "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl")))) (build-system r-build-system) (native-inputs (list r-knitr)) From b19400063ef4f3b6f8533a1eab49a3bbc3992cbe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:31 +0200 Subject: [PATCH 0282/1394] gnu: r-biocversion: Update to 3.15.2. * gnu/packages/bioconductor.scm (r-biocversion): Update to 3.15.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c0a38585599..7754e5bce9f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2019,14 +2019,14 @@ sequencing data.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.14.0") + (version "3.15.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0qwzkh2alw7xhjprh719la0lg1q38pmjbipy3s2fy79m4xy8y8ik")))) + "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") From 00d51727e5d7ba89de5ad49a79f235e81130bff9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:32 +0200 Subject: [PATCH 0283/1394] gnu: r-biocgenerics: Update to 0.42.0. * gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7754e5bce9f..dec8c299e4d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2039,13 +2039,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.40.0") + (version "0.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0nr5x4r8f2krnfrxm7wrzgzr7nbljypi985cbwx5hxhn95zmfifh")))) + "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) From 6f0430cdc2a4fd2cb2e0b12984fb7877fd6d6a2f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:32 +0200 Subject: [PATCH 0284/1394] gnu: r-coverageview: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-coverageview): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dec8c299e4d..860417862a3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2059,13 +2059,13 @@ packages.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as")))) + "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors From b0bd7ec471aed0c99e57a80666ee19a8b1cd0b36 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:32 +0200 Subject: [PATCH 0285/1394] gnu: r-cummerbund: Update to 2.38.0. * gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 860417862a3..aa0f4d4fb54 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2086,13 +2086,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql")))) + "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 25847e60fe22f2f82c62d2856b83f6ce882b329d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:32 +0200 Subject: [PATCH 0286/1394] gnu: r-dearseq: Update to 1.8.1. * gnu/packages/bioconductor.scm (r-dearseq): Update to 1.8.1. [propagated-inputs]: Add r-compquadform, r-dplyr, r-magrittr, r-reshape2, r-rlang, r-tibble, and r-viridislite. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aa0f4d4fb54..60c2177a6d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2116,24 +2116,32 @@ used visualizations.") (define-public r-dearseq (package (name "r-dearseq") - (version "1.6.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "07vr27rv3z86ajd62c0ilvfgz9z35qsiwwi5pv4sygbhnnjwh3rc")))) + "1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1")))) (build-system r-build-system) (propagated-inputs - (list r-ggplot2 + (list r-compquadform + r-dplyr + r-ggplot2 r-kernsmooth + r-magrittr r-matrixstats r-patchwork r-pbapply + r-reshape2 + r-rlang r-statmod r-survey - r-kernsmooth)) + r-tibble + r-viridislite)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/borishejblum/dearseq") (synopsis "DEA for RNA-seq data through a robust variance component test") (description From 7149e667c1668274629d7fce9ec34ba58fa25149 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:32 +0200 Subject: [PATCH 0287/1394] gnu: r-decipher: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-decipher): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 60c2177a6d9..aa3ecdb7f76 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2154,13 +2154,13 @@ set analyses, and can deal with repeated or longitudinal data.") (define-public r-decipher (package (name "r-decipher") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm")))) + "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5")))) (build-system r-build-system) (propagated-inputs (list r-biostrings From d15f46c5cf381bc79cd3dcb96c879892b3c6c99d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:32 +0200 Subject: [PATCH 0288/1394] gnu: r-deepsnv: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aa3ecdb7f76..d5dc61ed33e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2219,13 +2219,13 @@ targeted by a kinase.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "1wi6j6yb6i9fs9yszfywqz3w50mhl85dkfmr4w3phwvkf0xkn81w")))) + "0si1x2bi5pff1dicpqg7hv4ziq46vm7lic72724ljsclpz9bfv6q")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs From a2173119ecb14f789f0681175d556a468aabdabc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:33 +0200 Subject: [PATCH 0289/1394] gnu: r-delayedarray: Update to 0.22.0. * gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d5dc61ed33e..2dc17f2451a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2255,13 +2255,13 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.20.0") + (version "0.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "1cm6zh01mvhiq7zrik7q3dmgxinyjz1nyg6rfj93kpkvcb5d4wpj")))) + "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) From cea1b9029a13d7fba12fc8bd7e201133f598d607 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:33 +0200 Subject: [PATCH 0290/1394] gnu: r-derfinderhelper: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-derfinderhelper): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2dc17f2451a..335e2a7d4d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2285,13 +2285,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-derfinderhelper (package (name "r-derfinderhelper") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinderHelper" version)) (sha256 - (base32 "06x0wy2wzpngak1pnrj2p0xzlx1nbcz0hs3p9q5ic6ib2rgwrh35")))) + (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5")))) (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs From 59fff0e2d25346966cc7cfbf8ab16db83ad9df56 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:33 +0200 Subject: [PATCH 0291/1394] gnu: r-drimseq: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-drimseq): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 335e2a7d4d1..dc9bd9e754d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2310,13 +2310,13 @@ calculation in parallel.") (define-public r-drimseq (package (name "r-drimseq") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 - (base32 "0y2jb0hb633id038zmwnfny6h4ai77fdyy02f77vha1z8xg5nl02")))) + (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs From 051b7e63f2ff9a7f9eaa93b47c84f029e1afffa7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:33 +0200 Subject: [PATCH 0292/1394] gnu: r-bluster: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-bluster): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dc9bd9e754d..180277883e4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2345,13 +2345,13 @@ results.") (define-public r-bluster (package (name "r-bluster") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "1j24l12i3aga4qd827sj8b160yvrhlznggb4piddkmhjc0sppbjm")))) + "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs From 48c3389314d17a08c9da0db897e3ddd3c5bbe165 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:33 +0200 Subject: [PATCH 0293/1394] gnu: r-ideoviz: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 180277883e4..f3cf34ffa4f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2375,13 +2375,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g")))) + "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 285b5cb7fa3e30ce6afc14c0b3736c48087d30d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:33 +0200 Subject: [PATCH 0294/1394] gnu: r-iranges: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-iranges): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f3cf34ffa4f..9f067d69854 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2399,13 +2399,13 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-iranges (package (name "r-iranges") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "07zs231wbfwwc1c1165rhp711fbss40p9l8kyjjv9flzpr3hr1pg")))) + "0hfx5n0b4pqrrc1w2dik596803ly8ffnxfs768iy5l5kr8wwyc8k")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) From a15c457c59e49d6630fce53e5fa2004be0722fef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:33 +0200 Subject: [PATCH 0295/1394] gnu: r-isoformswitchanalyzer: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-isoformswitchanalyzer): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f067d69854..710ab6625dc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2427,13 +2427,13 @@ possible.") (define-public r-isoformswitchanalyzer (package (name "r-isoformswitchanalyzer") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) (sha256 - (base32 "14bqf39gw5ab5r9sr3afkig1jbzdvds1bmcvc6bpb45kschx7fwf")))) + (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd")))) (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs From 429e687e69ade4c1d606c7350b9437081ee34d46 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:34 +0200 Subject: [PATCH 0296/1394] gnu: r-affy: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-affy): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 710ab6625dc..fb34ab4b52b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2629,14 +2629,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a")))) + "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7")))) (build-system r-build-system) (propagated-inputs (list r-affyio From 45a6d9c0f455705cea154c7135d13074dd418c4e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:34 +0200 Subject: [PATCH 0297/1394] gnu: r-affycomp: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-affycomp): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fb34ab4b52b..03a2016ab44 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2657,14 +2657,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21")))) + "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) From 83f8f3ae081a4fb24046d52b186031d343c47315 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:34 +0200 Subject: [PATCH 0298/1394] gnu: r-affycompatible: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 03a2016ab44..7199083072b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2678,14 +2678,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "1qlfh1gcwa6akd5dhdqh260yaw1j6dap6a15ghwf74rchi5218sg")))) + "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) From d4af958ae8946054c830de4d5b27056eb3371a6c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:34 +0200 Subject: [PATCH 0299/1394] gnu: r-affycontam: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-affycontam): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7199083072b..4ed20066993 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2704,14 +2704,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "1vw3nxg9jvlw0zg9h70w2ww8l42qpyvgf12hsla9hyyfhj3m6i9f")))) + "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs From fb1fb2b8c234c80e3ba4aeab7a3b0b963d8967e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:34 +0200 Subject: [PATCH 0300/1394] gnu: r-affycoretools: Update to 1.68.1. * gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.68.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4ed20066993..dd438d99347 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2727,14 +2727,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.66.0") + (version "1.68.1") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "1ccyaj129ii9f47r41qsy34y6ck4wna55j8vz3v3hbldddn93f40")))) + "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs From da1e879b9bfb939161949dadca9a3fd0c525a66f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:34 +0200 Subject: [PATCH 0301/1394] gnu: r-affyio: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-affyio): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd438d99347..d8ed5ac0d5a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2769,14 +2769,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm")))) + "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp")))) (build-system r-build-system) (propagated-inputs (list r-zlibbioc)) From b928f25f51c16c9a9055452db8509ca0afe23b19 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:34 +0200 Subject: [PATCH 0302/1394] gnu: r-affxparser: Update to 1.68.1. * gnu/packages/bioconductor.scm (r-affxparser): Update to 1.68.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d8ed5ac0d5a..9591a8237fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2793,14 +2793,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.66.0") + (version "1.68.1") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "1bd0f8ifj6l7dx2m3wpmd0mji2gdf39mzgcjf9lbvvmbqnbxbcal")))) + "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") From 2563aeb416a5027dcfb9083e4cb57bdd741d3853 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:35 +0200 Subject: [PATCH 0303/1394] gnu: r-annotate: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-annotate): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9591a8237fb..70544990948 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2821,14 +2821,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84")))) + "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 0dcb2df4e1d306a084964141fddb1c7598deab98 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:35 +0200 Subject: [PATCH 0304/1394] gnu: r-annotationdbi: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 70544990948..7852ae9a71f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2848,13 +2848,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.56.2") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "01zwq14msbbwzxv8rgpmyr74ymvhq0vnmxkxxwd886iac5vjlgi8")))) + "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) From 3db379730549a5e3958d522e3f88df0e4384c39f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:35 +0200 Subject: [PATCH 0305/1394] gnu: r-annotationfilter: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-annotationfilter): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7852ae9a71f..b79b1bd13b3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2878,13 +2878,13 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "15fp1228yb06jm5cblvhw3qv9mlpbjfggaz2nvi3p46mby1vs64w")))) + "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) From 282985f6c3636c386c06d74dca4f661710fbf183 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:35 +0200 Subject: [PATCH 0306/1394] gnu: r-annotationforge: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b79b1bd13b3..2c02d096976 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2903,14 +2903,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "02wvni5q560idi6677g5f4md73z4qzjl5yycxv5dbvgbl2picisz")))) + "18rcfadxdaggyjj3rj17nbvgddlqs6zlr5jmq9a02kin59czvzz8")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) From 0b2579cbe07482049da1a0ae55a295f92ffd86a5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:35 +0200 Subject: [PATCH 0307/1394] gnu: r-annotationhub: Update to 3.4.0. * gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c02d096976..e68f49fff1f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2935,14 +2935,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.2.2") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "08dk4h07gpi3rk9s80wrbx2ww2chj688qzbwlx8n4dz788lqbfz8")))) + "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs From 043b388f387bcaaa488e77b4e915f04249d93635 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:35 +0200 Subject: [PATCH 0308/1394] gnu: r-aroma-light: Update to 3.26.0. * gnu/packages/bioconductor.scm (r-aroma-light): Update to 3.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e68f49fff1f..765e81efca3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2976,14 +2976,14 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.24.0") + (version "3.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "12qa85hsp8d1xhgn27iymknbhpnp9bd7hsgqxwvp1i8kki06z5hp")))) + "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs From 4d9011c00bd17714609a6ad11448d9099e1b9f94 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:36 +0200 Subject: [PATCH 0309/1394] gnu: r-bamsignals: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 765e81efca3..db3019463b3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3000,14 +3000,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv")))) + "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics From 70b29256f650742393d80ce8f8f6778f5ad9950c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:36 +0200 Subject: [PATCH 0310/1394] gnu: r-biobase: Update to 2.56.0. * gnu/packages/bioconductor.scm (r-biobase): Update to 2.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db3019463b3..aa3438067c6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3030,13 +3030,13 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww")))) + "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) From 48ca8c80267d3610c0d5367fa48b57122aba8acc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:36 +0200 Subject: [PATCH 0311/1394] gnu: r-biomart: Update to 2.52.0. * gnu/packages/bioconductor.scm (r-biomart): Update to 2.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aa3438067c6..aaa32b06f5e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3052,13 +3052,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.50.3") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "01mv05fj5iqvjb5xz9k92kx1a9d95mprb6isy57n0x20vd3cxdx1")))) + "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) From e56181a34e5f4e814739f77eda21e13a8411bd63 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:36 +0200 Subject: [PATCH 0312/1394] gnu: r-biocparallel: Update to 1.30.2. * gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.30.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aaa32b06f5e..a94105e68f9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3090,13 +3090,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.28.3") + (version "1.30.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0lkp7m2l66zq8yl788mkvi9kpb1haywxpf6ip9xl5y6iwm1w2b8p")))) + "0rqvwhs6d8ls1rq7j5ywl5k0qgblxpzimilyw335bi1yad5s10h3")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) From 6479274a0b5da9c80d5a7c565d4988b8860c970d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:36 +0200 Subject: [PATCH 0313/1394] gnu: r-biovizbase: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-biovizbase): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a94105e68f9..cefc73ca7bb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3171,14 +3171,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "0kg71p7sqfvxal0c19zrws1ffaqgyi8p605l3z6mkq5ldi26pajz")))) + "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs From 417481b3b0ef331bca789e3adad9ee7084aa5fba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:36 +0200 Subject: [PATCH 0314/1394] gnu: r-bsgenome: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cefc73ca7bb..72e7f7f1eac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3213,13 +3213,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1b023dpy8ygq0kd6qy0mk97c66gzpf39y2s0n89kmv61z5sg0jyi")))) + "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) From b7f95b40a86a2884b2b8e72e01b2888958265206 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:36 +0200 Subject: [PATCH 0315/1394] gnu: r-category: Update to 2.62.0. * gnu/packages/bioconductor.scm (r-category): Update to 2.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 72e7f7f1eac..e39405eef09 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3244,14 +3244,14 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "164zp4la9rqnp5vpn2y2p6plc5yxyk2kmn0z3d2flla54zc1b427")))) + "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs From 5e9e69ccd8020629bd68651feedaaeb03b908054 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:37 +0200 Subject: [PATCH 0316/1394] gnu: r-chipseeker: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e39405eef09..12e336caab6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3275,13 +3275,13 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.30.3") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "1f9m1p1viiigkmv15r2mknjrfw047jw1fylpqz5ipigc3jrphj1g")))) + "001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7")))) (build-system r-build-system) (native-inputs (list r-knitr)) From d66077a5ad9d2073a529ceee4594c117d66bd628 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:37 +0200 Subject: [PATCH 0317/1394] gnu: r-chipseq: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-chipseq): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 12e336caab6..7c25d97adfd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3321,14 +3321,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6")))) + "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics From d15ab4ed30527d9d6f25a03d6973efdca501f56f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:37 +0200 Subject: [PATCH 0318/1394] gnu: r-complexheatmap: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.12.0. [propagated-inputs]: Add r-codetools. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c25d97adfd..2f6b0855584 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3347,20 +3347,21 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "124w74mk0zk035wyr7cimblzx5blags4n5c8f83mp7iimxcb4gcn")))) + "15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) (propagated-inputs (list r-circlize r-clue + r-codetools r-colorspace r-digest r-doparallel From d29abfbd40735e41f33f394c3cafd97ffd3bd674 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:37 +0200 Subject: [PATCH 0319/1394] gnu: r-copywriter: Update to 2.28.0. * gnu/packages/bioconductor.scm (r-copywriter): Update to 2.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2f6b0855584..af4640eb472 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3387,14 +3387,14 @@ self-defined annotation graphics.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0xm5gjzi4r1xzyn7r669blqxhyhmbk9rh9k2gn696j14hbhc1hcy")))) + "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs From a83d8ee1eb325e7fa5ecd5cf47d0a4bf8ea426b1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:37 +0200 Subject: [PATCH 0320/1394] gnu: r-deseq2: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-deseq2): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index af4640eb472..bd09bae583b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3458,14 +3458,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0whk29zrmv9mrlc4w5ghy0fd29v8hfr8jccwgrn59mf3mkmfb2b9")))) + "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs From ea0c72bed0109211145e0b50e28a754677da0a10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:37 +0200 Subject: [PATCH 0321/1394] gnu: r-dexseq: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-dexseq): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bd09bae583b..827d82e26fd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3496,14 +3496,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1wd4bjd0a53s689yvb2lxzdiy0synh6ncfcly3cfw37kpdj8lds1")))) + "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs From 380384a209535e6b33408bad306b88bd6582ee07 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:37 +0200 Subject: [PATCH 0322/1394] gnu: r-diffcyt: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-diffcyt): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 827d82e26fd..96dded4bccb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3541,13 +3541,13 @@ exploration of the results.") (define-public r-diffcyt (package (name "r-diffcyt") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "diffcyt" version)) (sha256 - (base32 "1yc9mlc0ifb7h6rzskq97bsdq1kwdp5qq9l9mciwyxf6yjkmv5ni")))) + (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb")))) (properties `((upstream-name . "diffcyt"))) (build-system r-build-system) (propagated-inputs From 12a8b7bca3c92f7718192dd1849603a60ed0b391 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:38 +0200 Subject: [PATCH 0323/1394] gnu: r-dirichletmultinomial: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-dirichletmultinomial): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 96dded4bccb..70a81cf35ab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3579,14 +3579,14 @@ adapted from transcriptomics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "06nallp9jj2vmaa7d18g6hiymjc109szdv8sp51r87n7s38bvyq6")))) + "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) From 1d19d45fe7373f5aec3a937b4c74827e99d39baa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:38 +0200 Subject: [PATCH 0324/1394] gnu: r-edaseq: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-edaseq): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 70a81cf35ab..dea0dd42de9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3606,14 +3606,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-edaseq (package (name "r-edaseq") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "1vygfdxbjcww7sqzc3j7sp7w13dx10vlzy9z31flf7345qp6blj7")))) + "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs From 9d030069d45593902c2bd0a4ddca8ee0bc427094 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:38 +0200 Subject: [PATCH 0325/1394] gnu: r-edger: Update to 3.38.1. * gnu/packages/bioconductor.scm (r-edger): Update to 3.38.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dea0dd42de9..a747353f6f3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3646,13 +3646,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.36.0") + (version "3.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1d18kdfi9vjhhw5kwfy5airrd3c16fh4wbwppbhwgawm038mwavk")))) + "1q933m76155gy30wgps2gdd8pxzsfhppydjqn0fhjrwj6kqz8mik")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs From 89b669ba0e9554f8acead4873ea834be4cb9a891 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:38 +0200 Subject: [PATCH 0326/1394] gnu: r-ensembldb: Update to 2.20.1. * gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.20.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a747353f6f3..6eed1808a73 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3671,14 +3671,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.18.4") + (version "2.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1nsdcsghhh3ikv0hbn1aazdam7a6pqf1p6rz68ll2h6965kl4qzp")))) + "183rs74ngfvn9xz36csch495pqaash90yhhikm73m7b2bc37ziwz")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From b604766021012ce8bc0762b60930687ee9db0301 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:38 +0200 Subject: [PATCH 0327/1394] gnu: r-fastseg: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-fastseg): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6eed1808a73..11ed46fe4ec 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3716,14 +3716,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80")))) + "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-iranges From 3fd4c8f29f2312b335922d318c800e99879d6c11 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:38 +0200 Subject: [PATCH 0328/1394] gnu: r-gage: Update to 2.46.0. * gnu/packages/bioconductor.scm (r-gage): Update to 2.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11ed46fe4ec..4ec4e2aef7b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3743,14 +3743,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar")))) + "03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) From cb6e76dc6306bc0ff3cd60f02ad55ea5bb645223 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:39 +0200 Subject: [PATCH 0329/1394] gnu: r-genefilter: Update to 1.78.0. * gnu/packages/bioconductor.scm (r-genefilter): Update to 1.78.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4ec4e2aef7b..aa983861a08 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3771,14 +3771,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2")))) + "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) From b755e0d623c7ad3ada96c5a4b3d57179fff0762d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:39 +0200 Subject: [PATCH 0330/1394] gnu: r-geneoverlap: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-geneoverlap): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aa983861a08..c86da42aeea 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3795,13 +3795,13 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm")))) + "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-gplots)) From 09ae5950163d0fb8b93f5ee82d8199728ef04b3d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:39 +0200 Subject: [PATCH 0331/1394] gnu: r-genomation: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-genomation): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c86da42aeea..0d5bcd004fd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3814,13 +3814,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j")))) + "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79")))) (build-system r-build-system) (propagated-inputs (list r-biostrings From 4966e9e9256382578d8f2935e5c3f6a20b4f1a4f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:39 +0200 Subject: [PATCH 0332/1394] gnu: r-genomeinfodb: Update to 1.32.2. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.32.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0d5bcd004fd..9e96a71fc5f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3861,13 +3861,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.30.1") + (version "1.32.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1ly851w6xy144qvmpdv7p64yc45bqxmvny2rzgz691h3qbin3x55")))) + "1n37bwb2fqmdgqbn19rgsd2qn8vbdhv6khdwjr7v12bwabcbx9xh")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) From 1a04133411c0622028a9ed84d7a5195cd1aa41d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:39 +0200 Subject: [PATCH 0333/1394] gnu: r-genomicalignments: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9e96a71fc5f..0196aafe356 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3888,13 +3888,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9")))) + "1ifmlc0488f5yzcf4p92dmdc7psxl5c0aa7qpxjk0a07gf7lldbi")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) From fa516541c3a7cea51150961e275e45f60bb97153 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:39 +0200 Subject: [PATCH 0334/1394] gnu: r-genomicfeatures: Update to 1.48.1. * gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.48.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0196aafe356..2ade269bd4c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3921,13 +3921,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.46.5") + (version "1.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1fhahqh87cikfrwqkm2z4nq3jyi530qvsbmf09j2hyhsm87hhrgg")))) + "18ain5s0ry6w0ki4c0czvwax2ncigrldyac30a6mlbzyaga6i54h")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) From d14aeab8b84f0f2f8be2635c7eb1988a020c0a1a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:39 +0200 Subject: [PATCH 0335/1394] gnu: r-genomicfiles: Update to 1.32.1. * gnu/packages/bioconductor.scm (r-genomicfiles): Update to 1.32.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2ade269bd4c..bb3d945ac55 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3965,14 +3965,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.30.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "0i5y6dk6z18yqj5k4zy756c6l57z9jq2w5a5dksh2di4qgdgjx3x")))) + "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs From bf93ff28c589c0b78c6a1c84ce342eb5803e315d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:40 +0200 Subject: [PATCH 0336/1394] gnu: r-genomicranges: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-genomicranges): Update to 1.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bb3d945ac55..61dcee02eaf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3999,13 +3999,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.46.1") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "133r27wsdyppjv9kq0d2xamx007lkf416nnlaygs4hs3a76p9xwx")))) + "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) From 5c3a303d308ec87f08ef0ddf3f9b7096a241462b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:40 +0200 Subject: [PATCH 0337/1394] gnu: r-gostats: Update to 2.62.0. * gnu/packages/bioconductor.scm (r-gostats): Update to 2.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 61dcee02eaf..d1fec5992fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4026,14 +4026,14 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-gostats (package (name "r-gostats") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "1f8wqdl0swnvs59i6ljjcaglfqv314n8zxy4crpx806gbjzpn76z")))) + "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs From 3e1dbcb3bf44cc902caa94a2d84991f1f754f78e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:40 +0200 Subject: [PATCH 0338/1394] gnu: r-gseabase: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-gseabase): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d1fec5992fb..e69149405b8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4057,14 +4057,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1i8rryvagxk2pd8nl4a6yldwv82yx869nvv95jf8v00bna08f4d6")))) + "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs From 3daf94f147f9ae3fb3416f004e43927faab75e36 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:40 +0200 Subject: [PATCH 0339/1394] gnu: r-hpar: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-hpar): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e69149405b8..23af48be71b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4086,14 +4086,14 @@ Enrichment Analysis} (GSEA).") (define-public r-hpar (package (name "r-hpar") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76")))) + "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj")))) (build-system r-build-system) (native-inputs (list r-knitr)) From bb2b2f6543988702b70e0b1ff9ff0570ee417156 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:40 +0200 Subject: [PATCH 0340/1394] gnu: r-rhtslib: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-rhtslib): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 23af48be71b..b2ea841270c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4106,14 +4106,14 @@ the Human Protein Atlas project.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "0pwmzwjf6agfp3bq6w8s3piwmzwjdd474qd8zmbzrm772qbadfr4")))) + "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, From cd9b5f002956de52be1a4b26c860d480d89fe5cd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:40 +0200 Subject: [PATCH 0341/1394] gnu: r-impute: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-impute): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b2ea841270c..ceb97ef88e3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4135,13 +4135,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5")))) + "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2")))) (native-inputs (list gfortran)) (build-system r-build-system) From a6cb10afc359666bffa47490484db66150dc02e5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:40 +0200 Subject: [PATCH 0342/1394] gnu: r-interactivedisplaybase: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-interactivedisplaybase): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ceb97ef88e3..d9438bb9594 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4155,14 +4155,14 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "1pi887192k1jifb4k3pf2jn5hcl1xmmy6vwl22r9njsprdyb3kab")))) + "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) From 2a3372953d88fcc7bdf5f740aafac75633918bd0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:41 +0200 Subject: [PATCH 0343/1394] gnu: r-keggrest: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-keggrest): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d9438bb9594..f9c6f6f8ba7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4180,14 +4180,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1np3i1k7rki9akh70156ggmid52yy0is9q5vd3s45ra7an0ap279")))) + "0hzlm6nzmx0iyjh063512a3ghc1xqb58g5z2bnd2wl4y42iww7bg")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs From cb17da65a5c2241d7cfb29f3d98a77ed8b70441c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:41 +0200 Subject: [PATCH 0344/1394] gnu: r-lfa: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-lfa): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f9c6f6f8ba7..1490a0e3d59 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4204,13 +4204,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lfa (package (name "r-lfa") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "02b90xjb2lfm86hbsdrvzpv20pijnq78ibz4dwjzqd9v4xhia3wr")))) + (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) From 0cb9ffc4e3475b6f43451c1d06bfe6742b63413b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:41 +0200 Subject: [PATCH 0345/1394] gnu: r-limma: Update to 3.52.1. * gnu/packages/bioconductor.scm (r-limma): Update to 3.52.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1490a0e3d59..9db0e78df0c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4225,13 +4225,13 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.50.3") + (version "3.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1p46sif1aygmw2p8ifiylxrrbfbgvcsa0zp40nxlxawc7h56rybp")))) + "193l3z2jv0kr91nl4r64p3jzb2rai9k8akx1zw7303nsnwpiiaay")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") From 56741afedd88dbf3fe6bca566b88a9af19c52a5f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:41 +0200 Subject: [PATCH 0346/1394] gnu: r-methylkit: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-methylkit): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9db0e78df0c..b422b5d6010 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4244,13 +4244,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "02px46h2ynprss7kwll3i0jz0clrdg0bys70jacd432xw34nm2sx")))) + "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs From 8ec1ca001d2494e3f024aa1a4428bb2183bb7551 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:41 +0200 Subject: [PATCH 0347/1394] gnu: r-mutationalpatterns: Update to 3.6.0. * gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b422b5d6010..86a58958113 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4318,14 +4318,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.4.1") + (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "0i6fq6736gvrqn45r7nrhl0ns45qwj1bl4yc6qlalw2g46mjxf6k")))) + "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg")))) (build-system r-build-system) (native-inputs (list r-knitr)) From d6f683b561aa2ed7b8a9ffacc33c1a8b414099ce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:41 +0200 Subject: [PATCH 0348/1394] gnu: r-msnbase: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-msnbase): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 86a58958113..28ca320fad9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4364,14 +4364,14 @@ in SNV base substitution data.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.20.4") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0d3b0i154dyz1wvy2jwf5831bzbmalw7rzvxj8rd7658zjhghgzc")))) + "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs From d6fe1e2d120e4254c3c0b50420756fa5c29374c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:42 +0200 Subject: [PATCH 0349/1394] gnu: r-msnid: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-msnid): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28ca320fad9..8b99fecef11 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4409,14 +4409,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0dks5h3vp9ly8x24px2rl5blqicxybpxjnxvg2p1bwq8zvjkm38p")))) + "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments From 3eb763c2bad4eeecc080656ce04ecd3ed858e0dc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:42 +0200 Subject: [PATCH 0350/1394] gnu: r-mzid: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-mzid): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8b99fecef11..3daec564013 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4466,14 +4466,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0r001amd4m99cv0ixw38rpz0zv0xqb0qyvs16bz1i4a756391qri")))) + "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs From d1134b61fda491037e33364ef19183ec360d0854 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:42 +0200 Subject: [PATCH 0351/1394] gnu: r-mzr: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-mzr): Update to 2.30.0. [propagated-inputs]: Remove r-zlibbioc. [inputs]: Replace boost-for-mysql with boost. --- gnu/packages/bioconductor.scm | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3daec564013..eab73f7f05a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4497,19 +4497,17 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1azq0wjjy6n5xc721gjz6afm43ajz15b4p34vgsdjzwg9qn1vrs1")) + "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds")) (modules '((guix build utils))) (snippet - '(begin - (delete-file-recursively "src/boost") - #t)))) + '(delete-file-recursively "src/boost")))) (properties `((upstream-name . "mzR"))) (build-system r-build-system) (arguments @@ -4523,12 +4521,9 @@ specific parser.") (("\\ARCH_OBJS=" line) (string-append line "\nBOOST_LIBS=-lboost_system -lboost_regex \ --lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) - #t))))) +-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))))))) (inputs - (list ;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.28.0. - boost-for-mysql ; use this instead of the bundled boost sources + (list boost ; use this instead of the bundled boost sources zlib)) (propagated-inputs (list r-biobase @@ -4536,8 +4531,7 @@ specific parser.") r-ncdf4 r-protgenerics r-rcpp - r-rhdf5lib - r-zlibbioc)) + r-rhdf5lib)) (native-inputs (list r-knitr)) (home-page "https://github.com/sneumann/mzR/") From e3878bc3c075c0ec9cc75cde7df839521b6ddf56 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:42 +0200 Subject: [PATCH 0352/1394] gnu: r-organismdbi: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eab73f7f05a..0e33da51acf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4548,14 +4548,14 @@ previously been used in XCMS.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0zp6x2iqhn9s3xp07yilnr6hn73acvkdai5xip4iiwjdlnfffj83")))) + "1xklaiyd4mv9sf9211flq1s68fhdn53y2i4l1k2ib39a4l6y9cyr")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs From d4201b5f6185235737be4ca35b5d984023ed5377 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:42 +0200 Subject: [PATCH 0353/1394] gnu: r-pcamethods: Update to 1.88.0. * gnu/packages/bioconductor.scm (r-pcamethods): Update to 1.88.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0e33da51acf..116359fcd6a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4580,14 +4580,14 @@ the fact that each of these packages implements a select methods.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.86.0") + (version "1.88.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1fj2v6sna4lbw7ar9h93y2g4pzylqqp7760ih425gcai7s19xdrg")))) + "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs From 2b7c604ebff15a1e326e24373260ddaeccac408d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:42 +0200 Subject: [PATCH 0354/1394] gnu: r-protgenerics: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-protgenerics): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 116359fcd6a..bcf4127a4b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4649,14 +4649,14 @@ chromosome. Both tumor-normal paired and tumor-only analyses are supported.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "0x53pk7h47gjza1q5pz7jb1qqhwa9z2rr5fr61qc92zl3mqk57m0")))) + "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") From 1a873db6b28dfb816854749d19b0abd5a7e895dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:42 +0200 Subject: [PATCH 0355/1394] gnu: r-rbgl: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-rbgl): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bcf4127a4b9..36d33898455 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4669,14 +4669,14 @@ proteomics packages.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0k2p1lwdvix4n742a97lv988rx5kg8cvcmzgyzj0538n1nz0lxk0")))) + "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs From 9d05a948ea144200b0ddc27dc1fe3058dc97ed09 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:43 +0200 Subject: [PATCH 0356/1394] gnu: r-rcas: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-rcas): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 36d33898455..9edb17f78fa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4691,13 +4691,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "02zwz7c8ljmdcfxj54xns0a31sj616x63q63wxhxa1nb4dhgmvk7")))) + "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs From 21669d75f6844f8fd3a469a9bbd4b29e9dae0706 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:43 +0200 Subject: [PATCH 0357/1394] gnu: r-regioner: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-regioner): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9edb17f78fa..9e6ba1f1f97 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4741,14 +4741,14 @@ library implementing most of the pipeline's features.") (define-public r-regioner (package (name "r-regioner") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0k500fdmv5l0v7b9pj73bjk3h9k261mfqi6vl52khlw0fafn9b6p")))) + "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs From de8b8c86e628e724db4867b898e000c7c067fb78 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:43 +0200 Subject: [PATCH 0358/1394] gnu: r-reportingtools: Update to 2.36.0. * gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9e6ba1f1f97..f639211c9f2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4772,14 +4772,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "06kwf87h84xgswkrm7brmgr9aj1nf6cxp24hrfymkzq2pha5y5j7")))) + "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) From 3c31e7e249403385441bb7bd0e47fc9cb5ddcf98 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:43 +0200 Subject: [PATCH 0359/1394] gnu: r-rhdf5: Update to 2.40.0. * gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f639211c9f2..6aa58f17e3b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4822,13 +4822,13 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.38.1") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "1mlwp7bblhbpmd90sxj02zpq1q3fyg8v7ankyjb1y284xaymp02y")))) + "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff")))) (build-system r-build-system) (propagated-inputs (list r-rhdf5filters r-rhdf5lib)) From a8c63ab6103201d57b0da82a773f942a5cfccabb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:43 +0200 Subject: [PATCH 0360/1394] gnu: r-rhdf5filters: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6aa58f17e3b..3869f6f7eb0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4849,14 +4849,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "05b015pyp3g1crmm2d3ldsa7r5w0khmf87qbl4fv16r6pdggha78")))) + "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs From 990ee0c7ccf2fb2253831a38405fa1afba56fea6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:43 +0200 Subject: [PATCH 0361/1394] gnu: r-rsamtools: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-rsamtools): Update to 2.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3869f6f7eb0..39354a5e235 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4875,13 +4875,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0v6b3j45ivd9f04fpfs1vjwby5pi30mf5683bjxim01vi2krj9yh")))) + "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) From ea283a3cda0089937baa8c43c3d9447673bfe8c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:44 +0200 Subject: [PATCH 0362/1394] gnu: r-rtracklayer: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 39354a5e235..c73f63955ce 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4940,13 +4940,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "11bh9khra2qdmicppi6ya43kf8f1z13ak92vkl6nr5f20k54cphc")))) + "1d9sak1xrrkcvj0q3vnp6w2k0nx2k2ajhsbq0dyb4nhcghp5w8fd")))) (build-system r-build-system) (arguments `(#:phases From 021ab21b578cd2b6476fc8997904c2ea95a01d3a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:44 +0200 Subject: [PATCH 0363/1394] gnu: r-scannotatr: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-scannotatr): Update to 1.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c73f63955ce..0a5329b1939 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5019,13 +5019,13 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-scannotatr (package (name "r-scannotatr") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scAnnotatR" version)) (sha256 - (base32 "08jq04ckjw8a5y753almc5bl8vnn4j6qp2zb7bb9w3ql3ddy7b21")))) + (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b")))) (properties `((upstream-name . "scAnnotatR"))) (build-system r-build-system) (propagated-inputs From a260fc5a905c5fae03259511be1ced4524d0686d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:44 +0200 Subject: [PATCH 0364/1394] gnu: r-scdblfinder: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-scdblfinder): Update to 1.10.0. [propagated-inputs]: Add r-genomeinfodb, r-genomicranges, r-iranges, r-rsamtools, and r-rtracklayer. --- gnu/packages/bioconductor.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a5329b1939..d42d838133b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5056,13 +5056,13 @@ cell types based on specific research needs.") (define-public r-scdblfinder (package (name "r-scdblfinder") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 - (base32 "0wzmmcsnjybgzbc5rn4i72n26j9n59dfy1zg8ij0q8p4276jplsd")))) + (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0")))) (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs @@ -5072,9 +5072,14 @@ cell types based on specific research needs.") r-biocsingular r-bluster r-delayedarray + r-genomeinfodb + r-genomicranges r-igraph + r-iranges r-mass r-matrix + r-rsamtools + r-rtracklayer r-s4vectors r-scater r-scran From 5346b424cccfa3cb5d10c73d880ca60a239e35fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:44 +0200 Subject: [PATCH 0365/1394] gnu: r-seqlogo: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-seqlogo): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d42d838133b..bfafe4451ba 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5101,14 +5101,14 @@ comprehensive scDblFinder method.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "013hwj2lp29nqa8mkvm25aliarg0k725crg4cpsbj0iiskyrs6rl")))) + "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs From 27588f020d00efbd2638695f39743bb1a5abd942 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:44 +0200 Subject: [PATCH 0366/1394] gnu: r-seqpattern: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-seqpattern): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bfafe4451ba..fc6802ee0fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5124,13 +5124,13 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "1mik575qaxw9h9qyjn971207pfgbc8p1mx60jrb20jbrrihgg2na")))) + "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) From 6d2b2e0ad98675a266c23586567726da9dd67d24 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:44 +0200 Subject: [PATCH 0367/1394] gnu: r-shortread: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-shortread): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fc6802ee0fc..dbcb63ab081 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5147,14 +5147,14 @@ reference point and sorted by a user defined feature.") (define-public r-shortread (package (name "r-shortread") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "1p17v15wd3v6w9ligpjjk28vy8k2ql57y2hhm8y6vnv9y3nagjsx")))) + "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs From 9b935eaa562a7d60d2bd6b4c09f2f327eb254f2b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:45 +0200 Subject: [PATCH 0368/1394] gnu: r-simplifyenrichment: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 1.6.0. [propagated-inputs]: Add r-colorspace and r-globaloptions. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dbcb63ab081..4f437d271bd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5190,14 +5190,14 @@ ungapped alignment formats.") (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "05d9yjd8s7q1q78qmnx5xfrz9ppswc2cpfmjj47d338w783lwk98")))) + "1g3kfa17p60jkk4l34vc5hdq83w082qsxbjvpqw7r9rdd8d79z2q")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) @@ -5207,9 +5207,11 @@ ungapped alignment formats.") r-circlize r-clue r-cluster + r-colorspace r-complexheatmap r-digest r-getoptlong + r-globaloptions r-go-db r-gosemsim r-matrix From 909d580b9aa43414b0f75331467b0cf24e103001 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:45 +0200 Subject: [PATCH 0369/1394] gnu: r-transcriptr: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-transcriptr): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f437d271bd..a58d4954f16 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5231,13 +5231,13 @@ and comparing the clusterings.") (define-public r-transcriptr (package (name "r-transcriptr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "transcriptR" version)) (sha256 - (base32 "1p5l2z3szx3qh02x7r81ajl7yc5wqsri6q6pzw83livmalcli5yy")))) + (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03")))) (properties `((upstream-name . "transcriptR"))) (build-system r-build-system) (propagated-inputs From 3f873a27e0c5f0c7cd5c9865d9c1a9a052af0b84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:45 +0200 Subject: [PATCH 0370/1394] gnu: r-trajectoryutils: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-trajectoryutils): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a58d4954f16..d7121c37083 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5281,14 +5281,14 @@ able to deal also with novel and case specific events.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "0pzm1h69bg04a2v09r8c6pb3pix6f3n5dylvbv7wsp574qfaqyd1")))) + "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) From 8d1ab3f57d31be4e4a09232eed08bf79f9884746 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:45 +0200 Subject: [PATCH 0371/1394] gnu: r-slingshot: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-slingshot): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d7121c37083..02ded686622 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5308,13 +5308,13 @@ structures to hold pseudotime inference results.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.2.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "10kjpmckhzjf41yfhzg7c8idqa9cxz33r4rza6rwihnqnw1liff3")))) + "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2")))) (build-system r-build-system) (propagated-inputs (list r-igraph From ed19cbbf15b2b5f9530b3093c4b7ae6275d114b4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:45 +0200 Subject: [PATCH 0372/1394] gnu: r-stager: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-stager): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 02ded686622..fc26df4d821 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5340,13 +5340,13 @@ graph construction.") (define-public r-stager (package (name "r-stager") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "stageR" version)) (sha256 - (base32 "0vpx0v04hgkhzi0bm7ipnb9xr37n5wvnnr45lljgni8pwabfkf6y")))) + (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y")))) (properties `((upstream-name . "stageR"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) From d044d62102711c8a9ba36086c42108665ff3360a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:45 +0200 Subject: [PATCH 0373/1394] gnu: r-stringdb: Update to 2.8.4. * gnu/packages/bioconductor.scm (r-stringdb): Update to 2.8.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fc26df4d821..28494b828d0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5363,13 +5363,13 @@ Biology at (define-public r-stringdb (package (name "r-stringdb") - (version "2.6.5") + (version "2.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "0n2r2zc2sx1a2a8wqqxz6z7i4ynaj18iwbwgif7469n13agji5mv")))) + (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs From 803722761790eab8b4518c865e5c698f11c2ea5e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:45 +0200 Subject: [PATCH 0374/1394] gnu: r-structuralvariantannotation: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-structuralvariantannotation): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28494b828d0..6f96758cbdb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5396,13 +5396,13 @@ that integrates the various evidences.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "009l27kb9gvwwf57dwxfribhfhvn4z5pw8yc847l6pkbzqggx678")))) + (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6")))) (build-system r-build-system) (propagated-inputs (list r-assertthat From a0734f8bdd354ff4afc7fb0bda57e629f431e9c4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:46 +0200 Subject: [PATCH 0375/1394] gnu: r-summarizedexperiment: Update to 1.26.1. * gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.26.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6f96758cbdb..2fd092dbf05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5433,13 +5433,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.24.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "0qpnx2aii9vs7fcp0ax5j77ysbhi4qhjhm35vnygs3isbrjn925a")))) + "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) From 02c26f40b7f7b90e5a3ffe231cf1f93666acf1b2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:46 +0200 Subject: [PATCH 0376/1394] gnu: r-sva: Update to 3.44.0. * gnu/packages/bioconductor.scm (r-sva): Update to 3.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2fd092dbf05..009e0c2c6e0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5467,14 +5467,14 @@ samples.") (define-public r-sva (package (name "r-sva") - (version "3.42.0") + (version "3.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj")))) + "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4")))) (build-system r-build-system) (propagated-inputs (list r-edger From de403d02ad89c58dbbf9b709411ce2e2b4d197aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:46 +0200 Subject: [PATCH 0377/1394] gnu: r-systempiper: Update to 2.2.2. * gnu/packages/bioconductor.scm (r-systempiper): Update to 2.2.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 009e0c2c6e0..6f860c82830 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5498,14 +5498,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.0.8") + (version "2.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "0ajlw9yg6fha76rkkmsk5niq99s33k9437bkgi9whgh3pa6bkab2")))) + "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs From 47cdb428405722277fc3be3513191c52d91279ce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:46 +0200 Subject: [PATCH 0378/1394] gnu: r-topgo: Update to 2.48.0. * gnu/packages/bioconductor.scm (r-topgo): Update to 2.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6f860c82830..b612afa42ea 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5541,13 +5541,13 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "01vykf8bzwm2k7cfj09r6il6qaycjy10wpaxbn13f21p66r5nlm2")))) + "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) From 131135458e696b55824e77c0639e5b3d3f93f7e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:46 +0200 Subject: [PATCH 0379/1394] gnu: r-tximport: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-tximport): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b612afa42ea..17523b29712 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5574,13 +5574,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4")))) + "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x")))) (build-system r-build-system) (native-inputs (list r-knitr)) From a9d0efc639c3a79d5a8f98e52044077dc6b75af1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:46 +0200 Subject: [PATCH 0380/1394] gnu: r-variantannotation: Update to 1.42.1. * gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.42.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 17523b29712..ce0eb1bb51b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5631,13 +5631,13 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.40.0") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1r9kayp0hxcwls08lv2fh0cmf9ks0lqx3k31c1zn4asw4dyqpgva")))) + "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs From be389d989dd508704ef4df4dec06f86d9c46a148 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:46 +0200 Subject: [PATCH 0381/1394] gnu: r-vsn: Update to 3.64.0. * gnu/packages/bioconductor.scm (r-vsn): Update to 3.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ce0eb1bb51b..b74f2c1e2a0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5669,14 +5669,14 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.62.0") + (version "3.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x")))) + "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf")))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) From e7a0b1411599b35f45de75a484ff5869d530b7ee Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:47 +0200 Subject: [PATCH 0382/1394] gnu: r-xina: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-xina): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b74f2c1e2a0..bc8c5c76efb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5738,13 +5738,13 @@ inference.") (define-public r-xina (package (name "r-xina") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XINA" version)) (sha256 - (base32 "14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp")))) + (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g")))) (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs From 036dcaed7dd6714668202edde469d4a38ac14002 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:47 +0200 Subject: [PATCH 0383/1394] gnu: r-xmapbridge: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-xmapbridge): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bc8c5c76efb..8428a49aaf6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5774,13 +5774,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.") (define-public r-xmapbridge (package (name "r-xmapbridge") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 - (base32 "1zsqhisbq6f9qgw9f0a6ixxh635h3qm17117yfns5nnfw73ndlgi")))) + (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10")))) (properties `((upstream-name . "xmapbridge"))) (build-system r-build-system) (home-page "https://git.bioconductor.org/packages/xmapbridge") From 2b36da17849146e5775e603a9e4562bc36542ba8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:47 +0200 Subject: [PATCH 0384/1394] gnu: r-xvector: Update to 0.36.0. * gnu/packages/bioconductor.scm (r-xvector): Update to 0.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8428a49aaf6..512957d4dff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5801,13 +5801,13 @@ describing each of the graphs.") (define-public r-xvector (package (name "r-xvector") - (version "0.34.0") + (version "0.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "07r4qgmnifw9jk2srjg0cvl310j0f9y35jrg0zqhlvhmyhg6n2c0")))) + "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) From 2bc32aa065bb2e86f328e694ad54572d0a4b8393 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:47 +0200 Subject: [PATCH 0385/1394] gnu: r-zlibbioc: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-zlibbioc): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 512957d4dff..4ef9dfe6c94 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5835,13 +5835,13 @@ describing each of the graphs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0a0dl7z58zxdj6938zbxixphgljj1giylk1nd05bb7qsccmp0xhj")))) + "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) From 2b652812e8df0f59e0a76802226657013ba40c4d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:47 +0200 Subject: [PATCH 0386/1394] gnu: r-zellkonverter: Update to 1.6.1. * gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4ef9dfe6c94..ce227b34532 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5854,13 +5854,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.4.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "1ihp2f23lpdfgf3qliy22vrq8czm353hyhqf74r5r712190k6pgg")))) + (base32 "1w3qi35vk289cpky1pb0wgg1hr55s5kdw7np98i9c1vmwi3gvwr7")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs From 4268f796c8de69f0aee771ac2ef1429c1f8a8824 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:47 +0200 Subject: [PATCH 0387/1394] gnu: r-geneplotter: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ce227b34532..e01d2f4ef5c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5886,14 +5886,14 @@ saving AnnData objects to disk.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8")))) + "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc")))) (build-system r-build-system) (propagated-inputs (list r-annotate From 4ee5d02e70acdc43de6d3026886f2589fa2a2768 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:47 +0200 Subject: [PATCH 0388/1394] gnu: r-oligoclasses: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e01d2f4ef5c..835f9712fd3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5911,14 +5911,14 @@ saving AnnData objects to disk.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1ia2f19swiwb0552nfwkai4gl0av07cj75b6jwiviqa1bli09264")))) + "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs From 8a2e344cf7c5b4d5397767ae3525f217d2f43d4a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:48 +0200 Subject: [PATCH 0389/1394] gnu: r-oligo: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-oligo): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 835f9712fd3..0e7eecacc76 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5946,14 +5946,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6")))) + "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) From ec76f7ca9bdca96f11f06a554ca59f39e23d1e06 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:48 +0200 Subject: [PATCH 0390/1394] gnu: r-qvalue: Update to 2.28.0. * gnu/packages/bioconductor.scm (r-qvalue): Update to 2.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0e7eecacc76..6996d9037dd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5982,14 +5982,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138")))) + "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) From 21db7a48e04b266ddd131ee4cca1cad263bf19ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:48 +0200 Subject: [PATCH 0391/1394] gnu: r-apeglm: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-apeglm): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6996d9037dd..0287df0423d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6036,13 +6036,13 @@ integration with @code{Rcpp}.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "11w4vyc1sllmm5lh42krhidazid78n4s3lhikpy9kk2l57jmifbr")))) + "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs From 84fc29bad68605b24ab4c0948e76f5380442108d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:48 +0200 Subject: [PATCH 0392/1394] gnu: r-greylistchip: Update to 1.28.1. * gnu/packages/bioconductor.scm (r-greylistchip): Update to 1.28.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0287df0423d..08731b742d4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6063,13 +6063,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.26.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "1h7h27q6l9d8j0shklyrh135zrwx56v4zzmm21cj1b7dvmwvpbcv")))) + "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs From 7bc3e13bf5221b8e83afa5a5c2e92ffaec23de96 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:48 +0200 Subject: [PATCH 0393/1394] gnu: r-diffbind: Update to 3.6.1. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.6.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 08731b742d4..afc5100c70c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6090,14 +6090,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.4.11") + (version "3.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1xprj3x3s3yh6fwsdcl4zgfbhn640422x1lhhrmvdr836jr8sxcj")))) + "0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs From f6c66051021bd0f95b69f791043bc2771c53de27 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:48 +0200 Subject: [PATCH 0394/1394] gnu: r-mbkmeans: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-mbkmeans): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index afc5100c70c..a75f13036b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6168,13 +6168,13 @@ processing to visualization and annotation.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k")))) + "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg")))) (build-system r-build-system) (native-inputs (list r-knitr)) From de49b64b6945399faa7dda3026265ab16576a40d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:49 +0200 Subject: [PATCH 0395/1394] gnu: r-multtest: Update to 2.52.0. * gnu/packages/bioconductor.scm (r-multtest): Update to 2.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a75f13036b2..35137a27275 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6200,14 +6200,14 @@ large datasets, including support for on-disk data representation.") (define-public r-multtest (package (name "r-multtest") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns")))) + "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82")))) (build-system r-build-system) (propagated-inputs (list r-survival r-biocgenerics r-biobase r-mass)) From d825e79fc849e0f3be03562ec49d098e957c1628 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:49 +0200 Subject: [PATCH 0396/1394] gnu: r-graph: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-graph): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 35137a27275..739219b151b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6235,13 +6235,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0")))) + "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) From ef5c266f23098aa3aebbc61fc9321479f4818c8f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:49 +0200 Subject: [PATCH 0397/1394] gnu: r-chippeakanno: Update to 3.30.0. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 739219b151b..c34da5c5750 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6328,14 +6328,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.28.1") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0v2qz3rp5lmj3s1ziahjqym6cjlh4wdvf050k1x6dx8404jhi8kw")))) + "1ch636j3zd6hcfnl455vjs36wffrdhwzyvkbikcwjg7idiknjdkf")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs From a1da6d7d45e9efc946212d51988b26f5616695fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:49 +0200 Subject: [PATCH 0398/1394] gnu: r-matrixgenerics: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c34da5c5750..5676874ff5b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6382,13 +6382,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1s75p8rrmj24r0vcbaiyw8xg8y84j388mv6iawai7pypfcl8s1z3")))) + "0s7s39v9lqniirjgp8lbmffw0c8rsp6bndgzy1zlyh5vivfih0f5")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) From a7c3f7f2b1079169b13aed00ba32749f9f64f53b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:49 +0200 Subject: [PATCH 0399/1394] gnu: r-marray: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-marray): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5676874ff5b..cea0fa6f60f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6409,12 +6409,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz")))) + (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i")))) (build-system r-build-system) (propagated-inputs (list r-limma)) From 7188427b5c6ba5ab991c3db35a598e8bb879ad02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:49 +0200 Subject: [PATCH 0400/1394] gnu: r-cghbase: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-cghbase): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cea0fa6f60f..30d83e4c28f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6428,12 +6428,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1kfxw126bddfy67cmf8dca9qq4bg7fkxjf8iaikplhvs5hl7bp4d")))) + (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs From 3dd1b0508d54520eb0d655b112f79bc9d8f13547 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:50 +0200 Subject: [PATCH 0401/1394] gnu: r-cghcall: Update to 2.58.0. * gnu/packages/bioconductor.scm (r-cghcall): Update to 2.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 30d83e4c28f..fdabba3fd51 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6447,12 +6447,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1r4y8zakgmdbnpwgp14kwh4iwqgqcmjq2yg4nc7j37p09bw1c8zr")))) + (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs From ecd2d01d1e81924e1f40bef6c9a7ddf0889324cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:50 +0200 Subject: [PATCH 0402/1394] gnu: r-qdnaseq: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fdabba3fd51..0531d3c1e0d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6466,12 +6466,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1sza9br8agpdz1k9fn5wisir44sj8v0rk4wbx35d2c2kp9q70pqj")))) + (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs From d6559d1e1b8b7a94305a62a3ab25f32b96a51ae5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:50 +0200 Subject: [PATCH 0403/1394] gnu: r-bayseq: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-bayseq): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0531d3c1e0d..8f87da38d49 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6498,14 +6498,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "1zgxwb287ccz4wqsjxmffknnzziv12l4yrw7df912dxz6yccvd8r")))) + "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs From d47ffaf7ee4661736ef122f6ad825deded9321a2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:50 +0200 Subject: [PATCH 0404/1394] gnu: r-chipcomp: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8f87da38d49..6b9a512a115 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6522,14 +6522,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "1wdy92y5l3wa3zgg59w69rd7gdwf4z1waa4i2cccniccz463p1xq")))) + "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs From 2a8444ca5c0fce4afaf205ceef3f86c12088f2c5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:50 +0200 Subject: [PATCH 0405/1394] gnu: r-riboprofiling: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6b9a512a115..b1f5a5d5772 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6556,14 +6556,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "1szlzvm8ggjc40k4z2fxxa2h28g6j9wj2g5aw480v9hgyvvdw5lx")))) + "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs From 292efe0ae2db337beea30e0f4406d35829e42dc1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:50 +0200 Subject: [PATCH 0406/1394] gnu: r-riboseqr: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b1f5a5d5772..ffc92828501 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6597,14 +6597,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "0nnhjvjl4c9yyfzjf8kcj4yky5cdimicp7lz008sczy19jq4vjhd")))) + "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs From 6695c4e33b821aab4c2026ae93718978577c01ce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:51 +0200 Subject: [PATCH 0407/1394] gnu: r-interactionset: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-interactionset): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ffc92828501..38c16008fdc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6625,14 +6625,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "19m2mpby73zanai68rlqvzx9zccli4dz4kix93acrw9755xp3bsw")))) + "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) From 120329918b3e1657477ec433ba4dc915eb8c0d7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:51 +0200 Subject: [PATCH 0408/1394] gnu: r-genomicinteractions: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 38c16008fdc..519dc4aeb32 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6659,14 +6659,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "090kxq5jn1jfr9fgbkvbjr5g4bcxzgsaal3gc9yx1n7pgmhccfmb")))) + "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) From 6d9a73c84717c6e1b669a61ac69d9a7b7d004083 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:51 +0200 Subject: [PATCH 0409/1394] gnu: r-ctc: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-ctc): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 519dc4aeb32..422cfc54bef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6700,14 +6700,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx")))) + "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb")))) (build-system r-build-system) (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") From 53b152b2cf978082afa45cac71370d899c54e782 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:51 +0200 Subject: [PATCH 0410/1394] gnu: r-goseq: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-goseq): Update to 1.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 422cfc54bef..3657de957e4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6720,14 +6720,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0")))) + "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 09d473505553dbe161a053870a2bd8ca4e78b712 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:51 +0200 Subject: [PATCH 0411/1394] gnu: r-glimma: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-glimma): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3657de957e4..1baf6d9660a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6746,14 +6746,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0qkbx9n2vb7kvb5f00csnbffy5bm7hhbdvkx2isgzi0wv0y59kx9")))) + "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs From a028875b639fc2a2e941e0de7243fdff00fa46c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:51 +0200 Subject: [PATCH 0412/1394] gnu: r-rots: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-rots): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1baf6d9660a..9f2749dff47 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6779,14 +6779,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "0qhy984y83a3nf4zw54rasw3vn932q4zb3gljifkw701jnrzqmki")))) + "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs From 86dd93110e17ad6f1a3ca1520d049ed83008c2ce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:52 +0200 Subject: [PATCH 0413/1394] gnu: r-plgem: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-plgem): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f2749dff47..28355296e3c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6802,14 +6802,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3")))) + "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) From d6c3acb1c2bf774ef665ac64a4218607ce7cffaa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:52 +0200 Subject: [PATCH 0414/1394] gnu: r-inspect: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-inspect): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28355296e3c..02d5befe6f0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6826,14 +6826,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "072kv5k3giyll1clzrg0anqhyl4qbi7cjnmkqz25zdl5bab9l7jk")))) + "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs From 8b475c3e92fe5da86e719cef7de7f10f6d9efcaf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:52 +0200 Subject: [PATCH 0415/1394] gnu: r-dnabarcodes: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 02d5befe6f0..1076b5751c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6872,14 +6872,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg")))) + "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs From 0190978dcf73f224172ddd6d29134a1b909dd2fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:52 +0200 Subject: [PATCH 0416/1394] gnu: r-ruvseq: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1076b5751c1..59b13dbd00c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6899,14 +6899,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "1a19klscykdgsd7izcxyr45ml7g0gpdj65gvbaw124mal2p4zi9q")))) + "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs From ccee3dcc6b33fc89fd0252b1756f3a0332f4606c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:52 +0200 Subject: [PATCH 0417/1394] gnu: r-biocneighbors: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59b13dbd00c..761b194dd2e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6924,14 +6924,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "04in8l6j7frgm0a5dzphazfhn9cm8w775z5yir712jxa37mh1agr")))) + "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs From 80266651911ac6ef08fad9f9d44d87b7bd7981a9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:52 +0200 Subject: [PATCH 0418/1394] gnu: r-scaledmatrix: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 761b194dd2e..69f2830806d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6952,14 +6952,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "0vz8441gl5gycy1ypybwhq97bnyvhhlg6gxpi1dsdy2c9b6d81kc")))) + "0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs From 21715b19d3448b036c490e5062e25a8c02b073f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:53 +0200 Subject: [PATCH 0419/1394] gnu: r-treeio: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-treeio): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 69f2830806d..def4da17bcc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6978,14 +6978,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "19i8jhvycv57zbxhpn5gx5ymdiws64kc3nidc00xh1j9a8xkj1aq")))) + "1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs From e2ec50a93811d09cb3ad468339b44046da2d08ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:53 +0200 Subject: [PATCH 0420/1394] gnu: r-ggtree: Update to 3.4.0. * gnu/packages/bioconductor.scm (r-ggtree): Update to 3.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index def4da17bcc..176de7575b8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7010,14 +7010,14 @@ platform for merging tree with associated data and converting file formats.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.2.1") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "0qk39gdpy4kznjhmvi25y2spcdj2r1i6mv673vx8dzf66zfs20v8")))) + "033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs From a2cc02fea86ba6e1d3fc839f839023935901bbbf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:53 +0200 Subject: [PATCH 0421/1394] gnu: r-metapod: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-metapod): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 176de7575b8..170bdcf2511 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7047,14 +7047,14 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "1s8dfzpgbpxbn3jvx891gvw3jyn43nlxb73yv1vjn85brk9zbqpk")))) + "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs From 5aad4672519a77a3f7fd97e570ea08ae0d042274 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:53 +0200 Subject: [PATCH 0422/1394] gnu: r-biocsingular: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 170bdcf2511..28e18bd45ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7076,14 +7076,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "0dkh6a23qymjcynppmpp3k1mzpfadv8dqyz410pxkqsxig4ldd4n")))) + "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs From 0258381d438198e1cb009c13ebff4e1ca7bb7757 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:53 +0200 Subject: [PATCH 0423/1394] gnu: r-destiny: Update to 3.10.0. * gnu/packages/bioconductor.scm (r-destiny): Update to 3.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28e18bd45ff..3f45a15216b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7111,14 +7111,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.8.1") + (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1f2mp2sxbf1zi61npj5rl5pl7z30rkj5953521iiv0w99mdfwhsc")))) + "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 9641d32660e05a65475ee038804ade23a78786b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:53 +0200 Subject: [PATCH 0424/1394] gnu: r-savr: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-savr): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3f45a15216b..182a9132eec 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7155,14 +7155,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "0dwl94j5dm5ngn8lyyc4bd9ihd1nqincvq26najjn6lw0x55ciky")))) + "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs From f8bab3c5e7be274c0ed00e3d5339c51dd21292a2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:53 +0200 Subject: [PATCH 0425/1394] gnu: r-chipexoqual: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-chipexoqual): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 182a9132eec..1c4b684a387 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7177,14 +7177,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk")))) + "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs From db8cb101d63e40a04ce4e587b1007d606a7fc779 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:54 +0200 Subject: [PATCH 0426/1394] gnu: r-copynumber: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-copynumber): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1c4b684a387..82df9ac4bfd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7217,13 +7217,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534")))) + "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors r-iranges r-genomicranges r-biocgenerics)) From 9af002ee184e6106103d7561f14030864abcc6ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:54 +0200 Subject: [PATCH 0427/1394] gnu: r-dnacopy: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 82df9ac4bfd..c1925cd3136 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7237,14 +7237,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm")))) + "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) From 3de4ed3fc62fd095b34dd703ae48dc93f674bf38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:54 +0200 Subject: [PATCH 0428/1394] gnu: r-ebseq: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-ebseq): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c1925cd3136..2fe20065f19 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7335,14 +7335,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "1p8i04v5h6mbc8zqbf3rifbwwylzzc1fqrkhh0a0mbcgq2nv7i9m")))) + "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs From 266df31f5de9deaf1de6255b8bb4029c319b1fae Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:54 +0200 Subject: [PATCH 0429/1394] gnu: r-karyoploter: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2fe20065f19..d517abf5aa2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7357,13 +7357,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.20.3") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "0bcc1ln7602lrbm9wckgyfd9slsqiljjmymj28rfpax1n8rbq44m")))) + "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 5a23854532448a02d705f92884191faf6eee933b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:54 +0200 Subject: [PATCH 0430/1394] gnu: r-lpsymphony: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d517abf5aa2..cad35d65fda 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7395,14 +7395,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs")))) + "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g")))) (build-system r-build-system) (inputs (list zlib)) From 00da479a7b497ef56acf6aa32a511884667b09b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:54 +0200 Subject: [PATCH 0431/1394] gnu: r-ihw: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-ihw): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cad35d65fda..fc5d8687ae6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7424,14 +7424,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "0vgij5zyaw3fh7arkg4jy1mizsqzbkcsjl05mh3ng2bqh30kyqqx")))) + "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs From 76ec28f63b90f504f3da6aa20241a6bd6683ba84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:55 +0200 Subject: [PATCH 0432/1394] gnu: r-icobra: Update to 1.24.1. * gnu/packages/bioconductor.scm (r-icobra): Update to 1.24.1. [propagated-inputs]: Add r-markdown. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fc5d8687ae6..07afc46558d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7453,14 +7453,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.22.2") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1ln8l2cp6dqg6zv7s0qnmw5ii93v5sgp0b1nwswl52zdd8mivwxy")))) + "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -7468,6 +7468,7 @@ independent of the p-value under the null hypothesis.") r-dt r-ggplot2 r-limma + r-markdown r-reshape2 r-rocr r-scales From 70f5a747786d4ff8dd7470ceb86c048618f4a5c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:55 +0200 Subject: [PATCH 0433/1394] gnu: r-residualmatrix: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-residualmatrix): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07afc46558d..ddc9b7d2fde 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7490,14 +7490,14 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "0xsn4fm34a7xpkgmx3a1j2xzdaxf2hyla1062wqn04kw0k9y29vg")))) + "1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) From 2fb6818ab88dc93728ab2eb411ccf43d410d777b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:55 +0200 Subject: [PATCH 0434/1394] gnu: r-mast: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-mast): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ddc9b7d2fde..d60a0d9a7c7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7562,14 +7562,14 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "14h6giny9lhzqjsx3h7gdhsm8wfwnvp5zsl4avrflip0jmsn45yy")))) + "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs From 84d78abd525a0fbe2cc88b98f2389d565cd6c265 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:55 +0200 Subject: [PATCH 0435/1394] gnu: r-monocle: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-monocle): Update to 2.24.0. [propagated-inputs]: Remove r-densityclust; add r-leidenbase. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d60a0d9a7c7..e331dc3326f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7597,14 +7597,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85")))) + "1fyqd7qhij2iyx9vdmgnx2qf0w3kwbkmg805539zrmxry8cwfldb")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -7613,13 +7613,13 @@ single cell assay data.") r-cluster r-combinat r-ddrtree - r-densityclust r-dplyr r-fastica r-ggplot2 r-hsmmsinglecell r-igraph r-irlba + r-leidenbase r-limma r-mass r-matrix From 579e05dd9aed907108351ec75875292857f8ce9f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:55 +0200 Subject: [PATCH 0436/1394] gnu: r-noiseq: Update to 2.40.0. * gnu/packages/bioconductor.scm (r-noiseq): Update to 2.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e331dc3326f..dee24e34fcc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7782,14 +7782,14 @@ user-defined and/or data-driven sets of hypotheses.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "0mmvzf8y4gm84hgjdpf86b1y37237wp5mc3x1g6sdiz9qi8l356v")))) + "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs From 4221d4588b522fc3eebeff8654021f2c7a5efadb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:55 +0200 Subject: [PATCH 0437/1394] gnu: r-scdd: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-scdd): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dee24e34fcc..42c656a8938 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7808,14 +7808,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "0gjdjkpkm9zc9hzzb6r2mknl4zyg7s2lgqppmzzhgcnvlmgvm5b5")))) + "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs From 52b158dca519b0c884c6ad61b304918d1987724f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:56 +0200 Subject: [PATCH 0438/1394] gnu: r-scone: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-scone): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 42c656a8938..101f93decd2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7846,14 +7846,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1")))) + "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851")))) (build-system r-build-system) (propagated-inputs (list r-aroma-light From 6303dcbc85bd3380f5dafad18b9bb58ea1be1e08 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:56 +0200 Subject: [PATCH 0439/1394] gnu: r-geoquery: Update to 2.64.2. * gnu/packages/bioconductor.scm (r-geoquery): Update to 2.64.2. [propagated-inputs]: Remove r-httr; add r-curl. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 101f93decd2..5521525f055 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7890,21 +7890,21 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.62.2") + (version "2.64.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1hncr0p54qdg82a771yjjm4w1k2myrc26jzvci3g37mq7bgv3mxw")))) + "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-curl r-data-table r-dplyr - r-httr r-limma r-magrittr r-r-utils From 125c06af915b38be5b544132b46842b439428ea6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:56 +0200 Subject: [PATCH 0440/1394] gnu: r-illuminaio: Update to 0.38.0. * gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5521525f055..0a0b69fc735 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7925,14 +7925,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.36.0") + (version "0.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m")))) + "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62")))) (build-system r-build-system) (propagated-inputs (list r-base64)) From 4ff4b93aa00698069f725b412ba9b0f9ec20b034 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:56 +0200 Subject: [PATCH 0441/1394] gnu: r-siggenes: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-siggenes): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a0b69fc735..dbaef9d4299 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7946,14 +7946,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9")))) + "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest r-scrime)) From 2246d7a2d99bc65e9d5363f3cdb7dce471aca373 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:56 +0200 Subject: [PATCH 0442/1394] gnu: r-bumphunter: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dbaef9d4299..01c57d5f73c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7970,14 +7970,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv")))) + "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From f36df22ceb5357efb07c2b778b10fd98cf8c68ac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:56 +0200 Subject: [PATCH 0443/1394] gnu: r-minfi: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-minfi): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 01c57d5f73c..5cc13c8313f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8004,14 +8004,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx")))) + "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6")))) (build-system r-build-system) (propagated-inputs (list r-beanplot From a02d652e447c301abf219e5b30ea76e0d50810ea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:57 +0200 Subject: [PATCH 0444/1394] gnu: r-methylumi: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-methylumi): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5cc13c8313f..13b480a54c3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8055,14 +8055,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.40.1") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka")))) + "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww")))) (build-system r-build-system) (propagated-inputs (list r-annotate From 9ccc0373b139a18b0643991ef165498f5b04388c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:57 +0200 Subject: [PATCH 0445/1394] gnu: r-lumi: Update to 2.48.0. * gnu/packages/bioconductor.scm (r-lumi): Update to 2.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 13b480a54c3..74ece667b2a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8102,14 +8102,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in")))) + "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d")))) (build-system r-build-system) (propagated-inputs (list r-affy From 176a6ccb737e02d398716e0c6f85b19fcccffef5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:57 +0200 Subject: [PATCH 0446/1394] gnu: r-linnorm: Update to 2.20.0. * gnu/packages/bioconductor.scm (r-linnorm): Update to 2.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74ece667b2a..d34d91f9e8f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8141,14 +8141,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1bdnglznsfs1kdscqyjv595wiy09khcv9kxm4fmbnmksisqjz5qj")))) + "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs From 82ce69aeda22dd9dd6a2e1113334e3df0ad31dd2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:57 +0200 Subject: [PATCH 0447/1394] gnu: r-ioniser: Update to 2.20.0. * gnu/packages/bioconductor.scm (r-ioniser): Update to 2.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d34d91f9e8f..f1583e120a0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8202,14 +8202,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "1hdg446z5s616aaalzz49if1wp9nmzm2mbyva82m1vz8i7ih9m4h")))) + "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs From 0ff26b744a7cb82e097fb7d123d21b7ba0fa9dcc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:57 +0200 Subject: [PATCH 0448/1394] gnu: r-tradeseq: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-tradeseq): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1583e120a0..1c2e6747cf2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8293,13 +8293,13 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j")))) + "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0")))) (build-system r-build-system) (propagated-inputs (list r-biobase From a88487870b4f4e8cdbddab38325885c5bd749198 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:57 +0200 Subject: [PATCH 0449/1394] gnu: r-varianttools: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-varianttools): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1c2e6747cf2..11e71d86d56 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8362,14 +8362,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "0079dsgav4q03c4i0dhggc88iifd828n73kjv3sahim9akafdshl")))) + "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs From c2c13118814fb9271e2c28b4823dbeb0656c166f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:57 +0200 Subject: [PATCH 0450/1394] gnu: r-heatplus: Update to 3.4.0. * gnu/packages/bioconductor.scm (r-heatplus): Update to 3.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11e71d86d56..483e8ff41fd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8402,14 +8402,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.2.0") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0yrnjrbfn8vjzvp2742lyxdqca4s18h73j44qxw7ib95x3p4lndf")))) + "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs From 50bad20ace5fc5b40175f69def41476387746393 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:58 +0200 Subject: [PATCH 0451/1394] gnu: r-gosemsim: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 483e8ff41fd..ad88b14b59a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8427,14 +8427,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "15qi69kkgah7g25bymk9q1xf16hp1rd040fglg0svnydylg2d0ab")))) + "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs From dde65de5d3400c5f72bc47d3e36d082fcf417c72 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:58 +0200 Subject: [PATCH 0452/1394] gnu: r-anota: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-anota): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ad88b14b59a..55c11431a6f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8454,14 +8454,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f")))) + "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c")))) (build-system r-build-system) (propagated-inputs (list r-multtest r-qvalue)) From 9c44834a76e5312bd25938777210cfa1be4011a9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:58 +0200 Subject: [PATCH 0453/1394] gnu: r-sigpathway: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 55c11431a6f..58233fac7b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8484,14 +8484,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1c46m1gbgiygcj8m65h8iwzk3fkp6nynd6rk1f5qdh7kw5ap28f9")))) + "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") From 8b9d7ec80804981a2e3d28ea6b3f0611fe15903a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:58 +0200 Subject: [PATCH 0454/1394] gnu: r-fcscan: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-fcscan): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 58233fac7b9..5b8ff807a55 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8506,13 +8506,13 @@ phenotype of interest.") (define-public r-fcscan (package (name "r-fcscan") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "0b161ayq4m9xxfs0lgw632lgygzabz8gjl0n75050pa7qaazknvd")))) + (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs From cf8935a13073a9556ae332a74538bb1f015fe714 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:58 +0200 Subject: [PATCH 0455/1394] gnu: r-fgsea: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-fgsea): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5b8ff807a55..a0fc9fdef36 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8539,14 +8539,14 @@ presence of additional sites within the allowed window size.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9")))) + "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg")))) (build-system r-build-system) (propagated-inputs (list r-bh From 00c890fa471aa0609e70d0ddb5dd9f509c5b5896 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:58 +0200 Subject: [PATCH 0456/1394] gnu: r-dose: Update to 3.22.0. * gnu/packages/bioconductor.scm (r-dose): Update to 3.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a0fc9fdef36..1aa140748fd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8571,14 +8571,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.20.1") + (version "3.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "10kknaqz40pb6v0fcjzp12hfpi6k5kvlqnyxx1k3y0h0wdg8hs3n")))) + "11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs From 7dee98b9aa716885b8afa8a517613299087ca76c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:58 +0200 Subject: [PATCH 0457/1394] gnu: r-enrichplot: Update to 1.16.1. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.16.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1aa140748fd..0c1dfd55221 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8606,14 +8606,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.14.2") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "1rjiqmc32c9gxckgrgbypxpp0m8y0kahvhzvjzymda25xp8zqjs2")))) + "17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02")))) (build-system r-build-system) (propagated-inputs (list r-aplot From 54cd450ba8613c46df7e76b3f08c53965e20bd1a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:59 +0200 Subject: [PATCH 0458/1394] gnu: r-clusterprofiler: Update to 4.4.1. * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.4.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0c1dfd55221..04228c213a8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8644,14 +8644,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.2.2") + (version "4.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1y8ay3fxvcc7a7yqvfc95jfn800ikvs56j17byyp6v08w2j00y76")))) + "03bg3agisrm4q10gg57dksvd1ws37if6a1gwcxaybb4c50zadm8p")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) From a47875ef726c91ee528a5c57b1e36873e72dab94 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:59 +0200 Subject: [PATCH 0459/1394] gnu: r-clusterexperiment: Update to 2.16.0. * gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 04228c213a8..2aaf8f5742d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8681,13 +8681,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc")))) + "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f")))) (build-system r-build-system) (native-inputs (list r-knitr)) From 479dc1bd20acb341d911ed00f2613467ccfb97cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:59 +0200 Subject: [PATCH 0460/1394] gnu: r-mlinterfaces: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2aaf8f5742d..66d341985d8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8727,14 +8727,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1nzy04fqwzb0ywiafgx3m3i2n1b0g4pcg8mlgh8yz5d3mmna4kag")))) + "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs From c75a555b5dc87d7dc9620121fb66f8a339622685 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:59 +0200 Subject: [PATCH 0461/1394] gnu: r-annaffy: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-annaffy): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 66d341985d8..ed827544695 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8769,14 +8769,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "0crj37v571005brdd0ypfx2a7d1f829xxj2hahp2gy8aj9xm4s8l")))) + "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq")))) (build-system r-build-system) (arguments `(#:phases From b80a4781aebf5c1394779ec77d9755caf9224061 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:59 +0200 Subject: [PATCH 0462/1394] gnu: r-a4core: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-a4core): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ed827544695..2292bb6b1c7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8801,14 +8801,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "074aa52y6c70417lxwrclk613gbs7zv3326g9ndbbzzs5pmnh1y0")))) + "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs From 72a0c0fda2720be87a14934239e749fb1abebb7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:44:59 +0200 Subject: [PATCH 0463/1394] gnu: r-a4classif: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-a4classif): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2292bb6b1c7..6fa4cca6cd6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8825,14 +8825,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "0q50d41n7drj5c9x6njyvzr6bj7glmkp1vpyz6cpj97j2v9nikwb")))) + "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs From 47241c78a0e54b00528959d5c91aecdca8969125 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:00 +0200 Subject: [PATCH 0464/1394] gnu: r-a4preproc: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6fa4cca6cd6..a357751dcaf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8855,14 +8855,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "1qzr54w1qys1ppd71i5b57503dijfnnbn516a2mfk5l9l7wr728d")))) + "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs From 2fa91cea9c85688472ee684dc0f36a6d4ed7cb47 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:00 +0200 Subject: [PATCH 0465/1394] gnu: r-a4reporting: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a357751dcaf..9f6235b7d9a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8879,14 +8879,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "1vyah71gm4ngsgy0y10cdxa9b1g810gqa5pbvb3krh5i6h35smwr")))) + "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs From c5a596f8b3e649af56f3c0decc980f03d07f915e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:00 +0200 Subject: [PATCH 0466/1394] gnu: r-a4base: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-a4base): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f6235b7d9a..a5fb2f3457a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8903,14 +8903,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "0rddxnflvbc6z4sj2h8js8yfh0zhrrwj8fk00wicaqp4rkr5yaxy")))) + "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs From 73ed8b2361a57c54f2468bb0f235d2042b850008 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:00 +0200 Subject: [PATCH 0467/1394] gnu: r-a4: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-a4): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a5fb2f3457a..83d2bca8900 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8934,14 +8934,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m")))) + "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r")))) (build-system r-build-system) (propagated-inputs (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) From 83b5c68b442f8b2300d73c1980b784ecd248950d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:00 +0200 Subject: [PATCH 0468/1394] gnu: r-abseqr: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-abseqr): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 83d2bca8900..f549778cdcc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8955,14 +8955,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "1v9g71x689ly107c0qmc5iv8qk63nn6lp7yd03jf7hlcafmvqsvz")))) + "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs From 9dba02ad15280f8544f1a6c193cb082194fd3fd5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:00 +0200 Subject: [PATCH 0469/1394] gnu: r-bacon: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-bacon): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f549778cdcc..f3ee55b880f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9003,14 +9003,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc")))) + "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-ellipse r-ggplot2)) From bd510b8d7411655642801e3f989700a435963d78 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:00 +0200 Subject: [PATCH 0470/1394] gnu: r-rgadem: Update to 2.44.0. * gnu/packages/bioconductor.scm (r-rgadem): Update to 2.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f3ee55b880f..2f9cc79a53e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9028,14 +9028,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "1v8xgqqv7m2kyc38x9ppwsv87ivll5ppd6z76zcxj5yspkkrqw3v")))) + "013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs From d124f0fe205de52d116c98452e40f8484e145ea8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:01 +0200 Subject: [PATCH 0471/1394] gnu: r-motifdb: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-motifdb): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2f9cc79a53e..1c4d617a42e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9082,12 +9082,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "0a2zg26zzk7bj5c33mbwl8dx9lh1hns8q8kwp09rbfjdichv7425")))) + (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs From ef522a58285bd6733278ffd467852f578f2a3aa9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:01 +0200 Subject: [PATCH 0472/1394] gnu: r-motifbreakr: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.10.0. [propagated-inputs]: Remove r-grimport. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1c4d617a42e..6e0ed07adff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9109,12 +9109,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0lrgy64sv2ma6kylp4lsbwkg6ci1kn6qkk0cvzw3m4k3bgia1npj")))) + (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -9124,7 +9124,6 @@ frequency matrices from nine public sources, for multiple organisms.") r-bsgenome r-genomeinfodb r-genomicranges - r-grimport r-gviz r-iranges r-matrixstats From 81880b4cb7e2214e946cbd6c1d72b4ba49d75aa1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:01 +0200 Subject: [PATCH 0473/1394] gnu: r-motifstack: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-motifstack): Update to 1.40.0. [propagated-inputs]: Add r-tfbstools. --- gnu/packages/bioconductor.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6e0ed07adff..ebf5696d0be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9159,18 +9159,23 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "1ck6bbnrab8mbf70alfdsrcv6lq0fkvcy3klhcwyxxir7r9sgbaz")))) + "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs - (list r-ade4 r-biostrings r-ggplot2 r-htmlwidgets r-xml)) + (list r-ade4 + r-biostrings + r-ggplot2 + r-htmlwidgets + r-tfbstools + r-xml)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/motifStack/") From 8f957d34f18d2b7f5213c652f93fc5e110e62439 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:01 +0200 Subject: [PATCH 0474/1394] gnu: r-genomicscores: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ebf5696d0be..d491511a136 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9191,14 +9191,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.6.1") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "17v2v7aklljy17nivwmani2jxkbffqs2yr38hlspjlvgpidpf9ln")))) + "0zq9k4189dlc14f9rknsc1ffhpjzb2f4fzdaszfdbnd4rr43b79i")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs From 5fce56ab4b61ea6d7dedd1b34180d2d89c3edc19 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:01 +0200 Subject: [PATCH 0475/1394] gnu: r-atacseqqc: Update to 1.20.2. * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.20.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d491511a136..4979948d1a5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9228,14 +9228,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.18.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "1jmlialnhs9df1hv6l4qk2c4qjyjbz9mdj8vr52ms8vlxlxplz6c")))) + "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs From d3ff3a75cd02fa9a5f920a1762410f8c48bc9bf4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:01 +0200 Subject: [PATCH 0476/1394] gnu: r-gofuncr: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4979948d1a5..c1774a0368f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9275,14 +9275,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "08n1d03i4l2dl47axmrziiypi83yffndf0ww1b32skyjm2r0x127")))) + "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs From 4e95453274b4a926dd5848dea8104dd986f299b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:02 +0200 Subject: [PATCH 0477/1394] gnu: r-annotationtools: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c1774a0368f..eab102c4001 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9380,14 +9380,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "0grdswbf8nj0qwl0n5pqsir9242dry85j6m688j81gwwjgmzidvh")))) + "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) From 00eda6acec4237298e8361790eb582d36a805ae2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:02 +0200 Subject: [PATCH 0478/1394] gnu: r-allelicimbalance: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eab102c4001..64107de6d4b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9405,14 +9405,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "1s6arjd0nxgxyqy7vhqcb78k0ss7vwrhv41pm346hs1nyr5dkzaq")))) + "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) From 5bd8b53432f063e4452c14c8e68c1c084cf5883f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:02 +0200 Subject: [PATCH 0479/1394] gnu: r-aucell: Update to 1.18.1. * gnu/packages/bioconductor.scm (r-aucell): Update to 1.18.1. [propagated-inputs]: Remove r-s4vectors; add r-delayedarray and r-delayedmatrixstats. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 64107de6d4b..c91075198d7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9448,23 +9448,24 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.16.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "1lclf8hkhrm6g5fp8yhvjxnwgf8p0j9ffxsmcybz4rjvmwkiz5dp")))) + "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-data-table + r-delayedarray + r-delayedmatrixstats r-gseabase r-mixtools r-r-utils - r-s4vectors r-shiny r-summarizedexperiment)) (native-inputs From f27b8dfc8bced30bd9c8a2460b233a3a1630b674 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:02 +0200 Subject: [PATCH 0480/1394] gnu: r-ebimage: Update to 4.38.0. * gnu/packages/bioconductor.scm (r-ebimage): Update to 4.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c91075198d7..1a48027e29c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9488,14 +9488,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.36.0") + (version "4.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "030vpn55ppfqq4408c4db4w40d17x1yq6zajb11p2glikvm1q619")))) + "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs From ba6664485619942367ebb13e73c229b59e21a67e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:02 +0200 Subject: [PATCH 0481/1394] gnu: r-yamss: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-yamss): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1a48027e29c..0fb6eb2ad4e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9527,14 +9527,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab")))) + "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics From 342986b172ed08b18013ed52c9ff140d9e190261 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:02 +0200 Subject: [PATCH 0482/1394] gnu: r-gtrellis: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0fb6eb2ad4e..99f566ac084 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9560,14 +9560,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl")))) + "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-genomicranges r-getoptlong r-iranges)) From 648b99f7f61153e7d164e674df0576529eb0cf40 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:02 +0200 Subject: [PATCH 0483/1394] gnu: r-somaticsignatures: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 99f566ac084..9e6aef4d111 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9586,14 +9586,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "1dxzfkvljnydv7kfybfa52dwcbkkci2r8gjspjf90k2bxf10phql")))) + "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) From e5694d7e9f95540f279e3e07d9a2c132141576b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:03 +0200 Subject: [PATCH 0484/1394] gnu: r-yapsa: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-yapsa): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9e6aef4d111..0580aed2917 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9625,14 +9625,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "08r05fzpraggbxv15lx0b68kjlkysp0rcdlm6n9avzmlsdqplb2h")))) + "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs From 3fa5b905620c11acd25bf4c8f9bb3cd095dfdfe2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:03 +0200 Subject: [PATCH 0485/1394] gnu: r-gcrma: Update to 2.68.0. * gnu/packages/bioconductor.scm (r-gcrma): Update to 2.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0580aed2917..4ef1c2afb82 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9674,14 +9674,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.66.0") + (version "2.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001")))) + "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d")))) (build-system r-build-system) (propagated-inputs (list r-affy From 1ebbd9ee55d8ec24c74c9ce605ec454e8e15d3a5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:03 +0200 Subject: [PATCH 0486/1394] gnu: r-quantro: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-quantro): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4ef1c2afb82..86311bfa6e8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9756,14 +9756,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq")))) + "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 8ae5967136245fcae0c580580daee4ae6356752c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:03 +0200 Subject: [PATCH 0487/1394] gnu: r-yarn: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-yarn): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 86311bfa6e8..2f36fd89839 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9789,14 +9789,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d")))) + "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 63035ab55bd1850dcc9678459a84dbf26e52e4b2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:03 +0200 Subject: [PATCH 0488/1394] gnu: r-roar: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-roar): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2f36fd89839..9f3ab5a3bc0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9826,14 +9826,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347")))) + "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics From 9873a3a710aa182c2deaeb06396290d9f678e9c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:04 +0200 Subject: [PATCH 0489/1394] gnu: r-massspecwavelet: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.62.0. [propagated-inputs]: Remove r-waveslim. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f3ab5a3bc0..2c82898e210 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9894,19 +9894,19 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.60.1") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "00irq3i5kfck7rnm8ll7rqhqfpp3bisv2h8is50a7wbd7480z7ij")))) + "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) - (propagated-inputs - (list r-waveslim)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/MassSpecWavelet/") (synopsis "Mass spectrum processing by wavelet-based algorithms") (description From d01f1c34241c40b89f3ce78467e432c3eb4c123b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:04 +0200 Subject: [PATCH 0490/1394] gnu: r-xcms: Update to 3.18.0. * gnu/packages/bioconductor.scm (r-xcms): Update to 3.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c82898e210..ae5a973921f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9918,14 +9918,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.16.1") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143")))) + "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm")))) (build-system r-build-system) (propagated-inputs (list r-biobase From ec91ec29f1bd44ea65b91a210b873f82b1e22982 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:04 +0200 Subject: [PATCH 0491/1394] gnu: r-wppi: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-wppi): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae5a973921f..b70b008b93d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9959,13 +9959,13 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wppi (package (name "r-wppi") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wppi" version)) (sha256 (base32 - "1spwa8p6w3pyw21dvd1lrhcz1sphdsmsd408jv55ss9nbgvgrp23")))) + "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f")))) (properties `((upstream-name . "wppi"))) (build-system r-build-system) ;; This is necessary because omnipathr attempts to write a configuration From d59260a1dd59789705dac27b61068250bf216f44 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:04 +0200 Subject: [PATCH 0492/1394] gnu: r-wrench: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-wrench): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b70b008b93d..7a5887d06e9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10000,14 +10000,14 @@ scores and a path search algorithm.") (define-public r-wrench (package (name "r-wrench") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1vzv7sswijgb8nq58yrc19wlw2nnpjvans86fqqzs4p8wvq8j06n")))) + "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs From c0de7bad0a7308e78bcf09708d926e6be2fdecce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:04 +0200 Subject: [PATCH 0493/1394] gnu: r-wiggleplotr: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7a5887d06e9..0d7158cbdcb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10024,14 +10024,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi")))) + "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i")))) (build-system r-build-system) (propagated-inputs (list r-assertthat From 30b9b1774b53049428318a422f87e10961e8793b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:04 +0200 Subject: [PATCH 0494/1394] gnu: r-widgettools: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-widgettools): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0d7158cbdcb..f2cf3fd8c62 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10058,14 +10058,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "0jajfh78116wjfwbmzfvcbxswai4jj9ypzmfhs5j5iypaf8zff8j")))) + "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") From 6885db9d14e9a6b6dec351da95ae717f25c88168 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:04 +0200 Subject: [PATCH 0495/1394] gnu: r-webbioc: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-webbioc): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f2cf3fd8c62..a94d44f5ad2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10079,14 +10079,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17")))) + "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah")))) (build-system r-build-system) (inputs (list netpbm perl)) From 40d384423c24f1b08e1d0605e14585aa335c40bf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:05 +0200 Subject: [PATCH 0496/1394] gnu: r-zinbwave: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-zinbwave): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a94d44f5ad2..2a079242616 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10111,14 +10111,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq")))) + "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel From 74abb0cfca6b9cc15e1102ac4e6e09ee28fe37f0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:05 +0200 Subject: [PATCH 0497/1394] gnu: r-zfpkm: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2a079242616..a06af1b7d8a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10144,14 +10144,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "0fk05vrmyyrhmkwi06lsi553mlpqj3fgwhk1kygz83iqv5z2vfw9")))) + "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs From 7ddf44ccafee26c1484d6f4c10787c23fd0c4aeb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:05 +0200 Subject: [PATCH 0498/1394] gnu: r-rbowtie2: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-rbowtie2): Update to 2.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a06af1b7d8a..476dbf332e6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10169,14 +10169,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "0xpvrx2ak9x913sym4l46ycwbnmpcdwb3bf3dfd2gsp0krv8vh1x")))) + "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs From fee94f676b57c4d225c6b39d42737a5d8be10ebb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:05 +0200 Subject: [PATCH 0499/1394] gnu: r-progeny: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-progeny): Update to 1.18.0. [propagated-inputs]: Add r-decoupler and r-reshape2. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 476dbf332e6..8991077023a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10196,21 +10196,23 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y")))) + "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b")))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-decoupler r-dplyr r-ggplot2 r-ggrepel r-gridextra + r-reshape2 r-tidyr)) (native-inputs (list r-knitr)) From 8fdd1a8aabfbd9171a96156e97337348adc7f133 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:05 +0200 Subject: [PATCH 0500/1394] gnu: r-arrmnormalization: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8991077023a..024c01d28b6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10228,14 +10228,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "1ryqr3mpakjml0jhbk28k2z511sdl87wxdczxq1rwx98s0pc9mnh")))) + "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) From 143a3dd032bba6d1f3db353ae52810928340033e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:05 +0200 Subject: [PATCH 0501/1394] gnu: r-biocfilecache: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 024c01d28b6..fbce487aad9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10251,14 +10251,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.2.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "0gaj0z6dk2p2vhvqz685xwd5q2mkvpimh2493p3w04s2rlsvi3jb")))) + "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs From bd518b3b8a69c980142f343ee51200b45b882bcc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:06 +0200 Subject: [PATCH 0502/1394] gnu: r-iclusterplus: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbce487aad9..21aa9044e96 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10284,14 +10284,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b")))) + "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) From ac90ccab42e350ffe613c0e0437e83b2eb5f7758 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:06 +0200 Subject: [PATCH 0503/1394] gnu: r-rbowtie: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 21aa9044e96..8e7a3e4edcc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10314,14 +10314,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr")))) + "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (arguments From 5e39a816fe1df2917c3b167f55d2a63ac8931c00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:06 +0200 Subject: [PATCH 0504/1394] gnu: r-sgseq: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-sgseq): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e7a3e4edcc..49aa2308773 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10350,14 +10350,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "15l0r6svs27k82dd472is26shwayz6rs5ylg5gpf3mldr7sa5kja")))) + "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs From 9360c7f1668d25a044275186d4338acc4dca1e26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:06 +0200 Subject: [PATCH 0505/1394] gnu: r-rhisat2: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 49aa2308773..b41de4730eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10393,14 +10393,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "092rws9vjxgm2jpkbp6ign47zmillyyidnc7ylcbn4zr9j5lwv0y")))) + "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments From 2a5a695855a30ddc621c64554d25a181719c2e4c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:06 +0200 Subject: [PATCH 0506/1394] gnu: r-quasr: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-quasr): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b41de4730eb..eebcbe5f5f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10431,14 +10431,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "0d292xgaq8d3cdpa9anabda03lis46xc29iw9c5k5i3sj7dcr4g5")))) + "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs From e037f48fcc30ab0678d6e0f9a186341751c7725d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:06 +0200 Subject: [PATCH 0507/1394] gnu: r-rqc: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-rqc): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eebcbe5f5f6..5de5750d5e3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10473,14 +10473,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "0hcxkrfja0gmd8r2llijdvaw2xiiplk037305inimz0qna6w2071")))) + "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs From e5b0fac414fc83ffc8a400448c2490e93da0e0bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:06 +0200 Subject: [PATCH 0508/1394] gnu: r-birewire: Update to 3.28.0. * gnu/packages/bioconductor.scm (r-birewire): Update to 3.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5de5750d5e3..8ab40d7e1ec 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10516,14 +10516,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.26.5") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "041i5d08bsc5jqx3309fixjacizs4yi992cwazxghm8mrk3kicbr")))) + "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs From ea931c7223c266696780ac028bcb4fe2f55057bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:07 +0200 Subject: [PATCH 0509/1394] gnu: r-multidataset: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-multidataset): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ab40d7e1ec..30dfc9e9806 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10569,14 +10569,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "17asldnxqvp3sijx7nbi2lbbgnq4iq8z72qlg9080sm5lga1yy1s")))) + "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs From bc2d0114f8ef7c0df14f78879eab0772bb3d9be5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:07 +0200 Subject: [PATCH 0510/1394] gnu: r-ropls: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-ropls): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 30dfc9e9806..f91c7b559fe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10606,14 +10606,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.26.4") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "19f3wd55860x959h5n7mrivyjdas5b3jmx74lf24xnx23g26f8rn")))) + "1i9g32mjknrd2lbz2nisc7nr0gk9byx9aik1i7xdwmq4ndxf8rf7")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multidataset)) From 9986cc0bdfb4b1f8989d537642c333e61539fa7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:07 +0200 Subject: [PATCH 0511/1394] gnu: r-biosigner: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-biosigner): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f91c7b559fe..98370a1b4fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10643,14 +10643,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z")))) + "11w28nlz0f06idbna5k9xs891w516401l1zab5gg7s0z3xxaki4f")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071 r-multidataset r-randomforest r-ropls)) From eab93418bf72f48f325e88ec36dce2e4db497140 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:07 +0200 Subject: [PATCH 0512/1394] gnu: r-annotatr: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-annotatr): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 98370a1b4fb..9de1028086c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10672,14 +10672,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i")))) + "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 44b596f088f3d25303a1dae29281ac25287adcea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:07 +0200 Subject: [PATCH 0513/1394] gnu: r-rsubread: Update to 2.10.1. * gnu/packages/bioconductor.scm (r-rsubread): Update to 2.10.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9de1028086c..bcd357fc856 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10713,14 +10713,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.8.2") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "078zcchw9xl6vs2wihzzji349vq0m1a039m86jdlvb7nc3i1imfk")))) + "1cf80gmzz4c1pvif3350ifsmsbfplyl2na39n8g3x0zkwpl6ijdc")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) From 73b695f06d5ce9f677f62fb7e62991cd2559a556 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:07 +0200 Subject: [PATCH 0514/1394] gnu: r-flowutils: Update to 1.59.0. * gnu/packages/bioconductor.scm (r-flowutils): Update to 1.59.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bcd357fc856..d0adc8b4f09 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10739,14 +10739,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.58.0") + (version "1.59.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "0rgybkzbn8c3kpbz0ddghp1np0gka0cgiqvkk5jbnhlgf4s07161")))) + "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs From d44194e8079c0564bca6c609c8990e4c98e45ec3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:08 +0200 Subject: [PATCH 0515/1394] gnu: r-consensusclusterplus: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-consensusclusterplus): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d0adc8b4f09..5fa21f0777d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10765,14 +10765,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "13z43qbk9z7mvy8v8k185m6n020i6ahb18pm4q88rs75qlklzdkr")))) + "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) From 3f7c9b93a20b1d5340b2866abba0221fbf6b9a1d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:08 +0200 Subject: [PATCH 0516/1394] gnu: r-cytolib: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-cytolib): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5fa21f0777d..16a0ebca5e4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10831,14 +10831,14 @@ of the analyses while minimizing technical noise.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.6.2") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "0ycr4wmkfi0rvzwicblkfjgppk72gwwpim0rfiz1s44lycsf4py5")))) + "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs From e5a261cd3452483a7d4ae2b3a47753a90e22825b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:08 +0200 Subject: [PATCH 0517/1394] gnu: r-flowcore: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-flowcore): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 16a0ebca5e4..a7205b2bda3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10860,14 +10860,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "0zbd2hrdbb6r0np6nd3ab8nlcf9l57vcwnnhbqkbas8y0c2i2mwp")))) + "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs From 739beb90c4a47893ba3e7b64a1e0ccdf56efa009 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:08 +0200 Subject: [PATCH 0518/1394] gnu: r-flowmeans: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-flowmeans): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a7205b2bda3..24427e967df 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10892,14 +10892,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "0iy8hvi0inj1ylhdx6q4mya9k55iazprz6fdrnq1mxb2iyndzsl6")))) + "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs From 7db8599d851baef54b87d554c9bd8b22157d7983 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:08 +0200 Subject: [PATCH 0519/1394] gnu: r-ncdfflow: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24427e967df..b810214fc29 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10915,14 +10915,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "1c6wb2x24ydqp5nxrx6bhj6f13x9djfy9awkc7zn63xkag7mvvar")))) + "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs From edbabc91cc0e86e73b6cbb75dc78e4a92cd7981e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:08 +0200 Subject: [PATCH 0520/1394] gnu: r-ggcyto: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b810214fc29..2c8560757b0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10946,14 +10946,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "17dnmsa92gc2za36c3klgd7rklqlxrhkzs5ksnrc1am6a4knc0p1")))) + "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs From 2c76fce33afb22dd8e621e4f52ee4296b8a30669 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:08 +0200 Subject: [PATCH 0521/1394] gnu: r-flowviz: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-flowviz): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c8560757b0..99321dfb05e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10983,14 +10983,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "039sh7qn25gp2b34khs8dyrdpxyapsjlprrvxlz8f7dl8gmggl04")))) + "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs From 9305453a669876869a2c9de98704ff73df36f245 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:09 +0200 Subject: [PATCH 0522/1394] gnu: r-flowclust: Update to 3.34.0. * gnu/packages/bioconductor.scm (r-flowclust): Update to 3.34.0. [propagated-inputs]: Remove r-clue, r-corpcor, r-ellipse, r-flowviz, and r-mnormt. --- gnu/packages/bioconductor.scm | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 99321dfb05e..2790abd1cdb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11014,14 +11014,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.32.0") + (version "3.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "0ch7mkq40qcnxwgzy51vjdlwyzx4bvp03vpdm6dwjc6qy8a6qfzi")))) + "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -11030,13 +11030,8 @@ statistics to the plot.") (propagated-inputs (list r-biobase r-biocgenerics - r-clue - r-corpcor - r-ellipse r-flowcore - r-flowviz - r-graph - r-mnormt)) + r-graph)) (inputs (list gsl)) (native-inputs From cf72f829dc0eb60d708667483ad00a5b4d1d48c9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:09 +0200 Subject: [PATCH 0523/1394] gnu: r-rprotobuflib: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-rprotobuflib): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2790abd1cdb..9471e329e0e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11048,14 +11048,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "04qlhbhdchpr35rdc6jc3y8fy6znnfrdlsb8am04agbrvpjgrx10")))) + "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -11064,7 +11064,7 @@ model with Box-Cox transformation.") (add-after 'unpack 'unpack-bundled-sources (lambda _ (with-directory-excursion "src" - (invoke "tar" "xf" "protobuf-3.13.0.tar.gz"))))))) + (invoke "tar" "xf" "protobuf-3.8.0.tar.gz"))))))) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/RProtoBufLib/") From 6b078537858891234cb3a2b9ebe515d161006093 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:09 +0200 Subject: [PATCH 0524/1394] gnu: r-flowworkspace: Update to 4.8.0. * gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9471e329e0e..f556120ea59 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11077,14 +11077,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.6.0") + (version "4.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "11ni7kgk9s1fz3lvg85s6r7x2fhk4m7cdpilji05ya12jsyr3fig")))) + "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs From 1d6586a8c7de69c7afd4b7fd04adeb1754cc29fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:09 +0200 Subject: [PATCH 0525/1394] gnu: r-flowstats: Update to 4.8.0. * gnu/packages/bioconductor.scm (r-flowstats): Update to 4.8.0. [propagated-inputs]: Add r-corpcor and r-mnormt. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f556120ea59..8b9e3db7305 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11131,20 +11131,21 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.6.0") + (version "4.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "0jjfq66m4lbpkynwxaparkd05znhp3jl9ccj37gyghly294x3rm9")))) + "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-cluster + r-corpcor r-fda r-flowcore r-flowviz @@ -11153,6 +11154,7 @@ matches the flowJo analysis.") r-ks r-lattice r-mass + r-mnormt r-ncdfflow r-rcolorbrewer r-rrcov)) From 31604d4afc28311a40f10043e2f2bb36ff9ee2ec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:09 +0200 Subject: [PATCH 0526/1394] gnu: r-opencyto: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-opencyto): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8b9e3db7305..7b8c4925dc2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11169,14 +11169,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "11svr1lk383pkm4npwrnf3h37b3drjsmcwcgdbb45x8k2k95z2fm")))) + "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs From 74abd80a3fa9ad6fa039a5c2c8736402fb899a49 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:09 +0200 Subject: [PATCH 0527/1394] gnu: r-cytoml: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-cytoml): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7b8c4925dc2..85b4918b068 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11213,14 +11213,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "16rgsc2dz5b8lm3ma8nh9wiknrdnvfjcsij7809rmcfs0gn1arcz")))) + "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs From 2b9201ae8a4ebc74841a2dfd8a5cb6158d00bf63 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:10 +0200 Subject: [PATCH 0528/1394] gnu: r-flowsom: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-flowsom): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 85b4918b068..90bb0f3698d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11265,14 +11265,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "062xrv8li2z849qa8mv5dhafqli6ziz099ikjfvi7v2fr7174p8f")))) + "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs From af575f5b379b1e74bcc574c9f65ed28d5de3ad66 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:10 +0200 Subject: [PATCH 0529/1394] gnu: r-mixomics: Update to 6.20.0. * gnu/packages/bioconductor.scm (r-mixomics): Update to 6.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90bb0f3698d..a0aa2645403 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11308,14 +11308,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.18.1") + (version "6.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "1wpskrnl2bry9m4k2djhjddcd8gpwf51gp5c3si1y7qxja78ql9f")))) + "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs From b1f4698988f71ba9a07648da2bde79ff133fc406 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:10 +0200 Subject: [PATCH 0530/1394] gnu: r-depecher: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-depecher): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a0aa2645403..87cf96d42bd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11354,14 +11354,14 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9")))) + "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs From d88de74e61e28d1abb4e0a4ed9189b84875e95fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:10 +0200 Subject: [PATCH 0531/1394] gnu: r-rcistarget: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.16.0. [propagated-inputs]: Remove r-feather; add r-s4vectors. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 87cf96d42bd..e4098dc4799 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11400,14 +11400,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1qarr7xd71kz1haccj65x7sc7pc4v6xpqcfa3rkyp2bk240gigi7")))) + "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -11416,11 +11416,11 @@ data, to only emphasize the data that actually matters.") r-biocgenerics r-data-table r-dplyr - r-feather r-genomeinfodb r-genomicranges r-gseabase r-r-utils + r-s4vectors r-summarizedexperiment r-tibble)) (native-inputs From 876f7f9c50cb6dbbafcc357939ebce6f5a684acb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:10 +0200 Subject: [PATCH 0532/1394] gnu: r-chicago: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-chicago): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e4098dc4799..fd20fbd65e8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11442,14 +11442,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "0nz9v37p7zl8yw3ykdbsb3izcwgx349wvrhwfyyn9h3jxjfafngn")))) + "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs From 54e790e6849a4a5e27f87d4728faa6876a99c9b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:11 +0200 Subject: [PATCH 0533/1394] gnu: r-cicero: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-cicero): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fd20fbd65e8..b57824ec984 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11464,14 +11464,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7")))) + "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5")))) (build-system r-build-system) (propagated-inputs (list r-assertthat From 840ffa0bfaa45d926f3f272d2cab0156f7e1af4d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:11 +0200 Subject: [PATCH 0534/1394] gnu: r-circrnaprofiler: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b57824ec984..59c78b7cb2d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11531,14 +11531,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "0l83r9idhrha1m21vpnw917m5dlldji49zvx4d25m5g3ia1pkhpf")))) + "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) From 8ad4197c235bacf188d1b4ce21c8b7ef0559216c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:11 +0200 Subject: [PATCH 0535/1394] gnu: r-genie3: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-genie3): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59c78b7cb2d..1eac98e080f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11666,14 +11666,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0ms769267pimrx3xwwkgjy03qilkxxs7xwhzfca01f65i4n3l6fw")))) + "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs From 0a649904286665fa02f90ab0251ff305c3601a4d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:11 +0200 Subject: [PATCH 0536/1394] gnu: r-roc: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-roc): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1eac98e080f..e49ed9b2c8a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11690,14 +11690,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "1mgxpv5p6gnv04wzkcryrg5as5xrxvlqlkkcbv0k1bx9y6ykijy9")))) + "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs From 0c611d7f4fdbd93ad0cef2ee9f356c8f70ebc4dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:11 +0200 Subject: [PATCH 0537/1394] gnu: r-watermelon: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-watermelon): Update to 2.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e49ed9b2c8a..912b3ed6e9b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11712,14 +11712,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") (define-public r-watermelon (package (name "r-watermelon") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "1kzkg3cnm5pcs6blpw1qn7na6z3kar93v67680wsxa6qxxdiggk3")))) + "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs From c9bdb12ba353202a546bd5ff441390cb03f7c540 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:11 +0200 Subject: [PATCH 0538/1394] gnu: r-gdsfmt: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 912b3ed6e9b..a36ea34589f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11750,14 +11750,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "147i33sb65n3cl3ibmjzgfm7i4ljy640k18mzknvc18v1906j9vp")) + "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. From c272bc0b1924a936ab36496ad65631b9bf290a8f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:12 +0200 Subject: [PATCH 0539/1394] gnu: r-bigmelon: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a36ea34589f..ebc2e97d2a3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11806,14 +11806,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "0ksbmybi8wsg515b4k9ij1xqqk9i90pyap2wq5w3c49qgc0pqali")))) + "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs From d68798fbd9fc71953cfeb9be60131afbe002c053 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:12 +0200 Subject: [PATCH 0540/1394] gnu: r-seqbias: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-seqbias): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ebc2e97d2a3..e48e401ad7b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11837,14 +11837,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "1q608c1madij8l52ljl3w52vi3cssr6ikny84yj6n8s7yvpx5jpr")))) + "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs From 988ed7b0901dcf4ea8743eb7e0f069cbfec3c3e2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:12 +0200 Subject: [PATCH 0541/1394] gnu: r-reqon: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-reqon): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e48e401ad7b..33df5cbc7be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11861,14 +11861,14 @@ genome sequence.") (define-public r-reqon (package (name "r-reqon") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "14v79vg3pmpkbzgn8xqd020jdwcs8g57d46bzl23yi3w1rsfbrb1")))) + "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs From 6291ee1e5b40f22249fa6b9a723aa0ca5943d77b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:12 +0200 Subject: [PATCH 0542/1394] gnu: r-wavcluster: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-wavcluster): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 33df5cbc7be..7de727b69e8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11884,14 +11884,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "1a1zhckrgq5yl51acj5piyh2hq70q6hhpym4cawzdssxhcbq70bk")))) + "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs From 9825c2b03d3d263229761963b4e53388fb757dd7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:12 +0200 Subject: [PATCH 0543/1394] gnu: r-timeseriesexperiment: Update to 1.13.0. * gnu/packages/bioconductor.scm (r-timeseriesexperiment): Update to 1.13.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7de727b69e8..c7d339f0116 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11931,14 +11931,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d")))) + "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) From 286bed66fd9fe5ca59a129a26c8835ab4c0540cd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:12 +0200 Subject: [PATCH 0544/1394] gnu: r-variantfiltering: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c7d339f0116..e8978c00ec2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11972,14 +11972,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "15js8xzi9rsgkjkqcshzk3r3g85kdnxn5v2hi6l5s4yxj9lnq12p")))) + "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) From f27a511f7af5e8b1aa2fa9001538bddd68b946a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:13 +0200 Subject: [PATCH 0545/1394] gnu: r-variancepartition: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e8978c00ec2..4fc74534637 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12078,14 +12078,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "14aki7d9xl4rhhzv3cl09mbj1q7xhxg69s4kzms9hfv3cqjryqd7")))) + "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) From faaa54d0a88f79df01b4234dc47a6715ef2d7b76 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:13 +0200 Subject: [PATCH 0546/1394] gnu: r-htqpcr: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-htqpcr): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4fc74534637..6ff4ef34eb0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12126,14 +12126,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "1d7qj5yv6kzqmdrnp5pd8qv1yr4bg8cs39p8ib0i0k8b4wr97kq3")))) + "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs From 6f5cd0539527bd3ef66010e5c8115119441632ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:13 +0200 Subject: [PATCH 0547/1394] gnu: r-unifiedwmwqpcr: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6ff4ef34eb0..4fec83e68e6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12156,14 +12156,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "0kw26bm2yyna38q5r4zb2alpa3j4gx7v970419mnjlif4g0hmggk")))) + "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) From fffa2581c35670655f1225969c67f2a6fdc420d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:13 +0200 Subject: [PATCH 0548/1394] gnu: r-universalmotif: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4fec83e68e6..a95a0a8b5e4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12180,14 +12180,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.12.4") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "01skcvzd815m3c15ka2pk7z6bggc4l8bhvaf4z9v95i36k4mn5zd")))) + "0n2msyyy1xhapkd66j4xwabg4qfd62l01p1nmafjwifnjsx45xvp")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) From ac1b83ff821c823445a8f1c752aa30d39b56a2c1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:13 +0200 Subject: [PATCH 0549/1394] gnu: r-ace: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-ace): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a95a0a8b5e4..1a7ef1c31ba 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12228,13 +12228,13 @@ motifs, and others.") (define-public r-ace (package (name "r-ace") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACE" version)) (sha256 (base32 - "1nkbxldn5ba4fzfh4skwjc37gm6apwp09vzwnj2jw3b7ivmr0yr6")))) + "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m")))) (properties `((upstream-name . "ACE"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) From 0b03a2f3245711fdafdd3b8a72bd2a1543bb3b1b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:13 +0200 Subject: [PATCH 0550/1394] gnu: r-acgh: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-acgh): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1a7ef1c31ba..09e74d2f16e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12257,13 +12257,13 @@ of @dfn{tumor cells} (cells with divergent segments).") (define-public r-acgh (package (name "r-acgh") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aCGH" version)) (sha256 (base32 - "1r1q6iq3g7svfn5m4jxlxp413djb40mvf6lh595y86sgwav5k6l4")))) + "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d")))) (properties `((upstream-name . "aCGH"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-cluster r-multtest r-survival)) From 7fd611926e4149510451c42079ace047377a976b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:14 +0200 Subject: [PATCH 0551/1394] gnu: r-acme: Update to 2.52.0. * gnu/packages/bioconductor.scm (r-acme): Update to 2.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 09e74d2f16e..9a6c6e0253f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12281,13 +12281,13 @@ printing and plotting @code{aCGH} objects.") (define-public r-acme (package (name "r-acme") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACME" version)) (sha256 (base32 - "0h4bqbbqcwc938q7lysk5l35f64xz9d1bsniv2wshmlr4rr0zpcg")))) + "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25")))) (properties `((upstream-name . "ACME"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics)) From 58386d0f408bd0b335a8f29209fbb6531ba35a53 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:14 +0200 Subject: [PATCH 0552/1394] gnu: r-acde: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-acde): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9a6c6e0253f..e70e21c2072 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12308,13 +12308,13 @@ on whole-genome tiling array experiments quite easily with enough memory.") (define-public r-acde (package (name "r-acde") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "acde" version)) (sha256 (base32 - "13ks87am73m3bjn9ljapxml2a9cxdpgv9flwvly8aqmi3ndxyqi6")))) + "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2")))) (properties `((upstream-name . "acde"))) (build-system r-build-system) (propagated-inputs (list r-boot)) From c988069a9dd8b44aa804a2577f6855585efbe90f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:14 +0200 Subject: [PATCH 0553/1394] gnu: r-bgmix: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-bgmix): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e70e21c2072..a97f89777f3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12401,14 +12401,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "0x1sx319yfxgkscr9r62msq00ddvmzryzn42wy4dh5pvjmgifkkn")))) + "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs From 8c4e6cfb294dfff6be6178abe380c5c41e50b994 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:14 +0200 Subject: [PATCH 0554/1394] gnu: r-bgx: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-bgx): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a97f89777f3..f31d8b22a36 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12423,14 +12423,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0z3isnpyf9s11807dprxmd105lb0k4l7r1sygad30ncjvpldifzm")))) + "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs From 3a938a581350cf7ee8b7730d96c44d6bbd1afada Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:14 +0200 Subject: [PATCH 0555/1394] gnu: r-bhc: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-bhc): Update to 1.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f31d8b22a36..9f1e5a388eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12445,14 +12445,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "09nw4ljc9sn7iw09ha0m614hmdjj193xhhav5x5p07l501kks6h2")))) + "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") From 0e4dc0e9bfaa58aa602cbc8adaddf382ba9f990b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:14 +0200 Subject: [PATCH 0556/1394] gnu: r-bicare: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-bicare): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f1e5a388eb..082a568f85a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12471,14 +12471,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "1g8vrsc05cysb36gsw8sfmr6dgbh4aji37vcq9qwkmkv3jgvnlf6")))) + "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs From 5ab4747f7716eafd35f8e163b30e0b20289fdf05 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:14 +0200 Subject: [PATCH 0557/1394] gnu: r-bifet: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-bifet): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 082a568f85a..4afce5f7bd3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12493,14 +12493,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "0vidypvphnj76g4ra5ijrgqx2dnzw0fmvdvz35gsqswrr3k20jkk")))) + "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs From 39bd70c43cbe062b49a8b15037d57c9986919801 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:15 +0200 Subject: [PATCH 0558/1394] gnu: r-rsbml: Update to 2.54.0. * gnu/packages/bioconductor.scm (r-rsbml): Update to 2.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4afce5f7bd3..c32be2228d4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12522,14 +12522,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "0mdyr637sgasc156cv8i2s2mpl1hdvilfwwkhvw7l95pl90gnsh2")))) + "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs From 631c408da79b28ae74942d6aa124c977a73de5c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:15 +0200 Subject: [PATCH 0559/1394] gnu: r-hypergraph: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-hypergraph): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c32be2228d4..0123994d308 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12548,14 +12548,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "0xnyl9qh5p32ifvzkcl5g4a38zbnwykqzrp8gwz076a0ksiqqdxf")))) + "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs From a13a4d1e8f71996837e400b9f57d5d23020ab5ee Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:15 +0200 Subject: [PATCH 0560/1394] gnu: r-hyperdraw: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-hyperdraw): Update to 1.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0123994d308..5e8261a4202 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12570,14 +12570,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj")))) + "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs (list graphviz)) From e273f1ab82e19be5e0ea7bc3eb7bbdf023dcb057 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:15 +0200 Subject: [PATCH 0561/1394] gnu: r-biggr: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-biggr): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5e8261a4202..db8cada73af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12592,14 +12592,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "1g01666wwznk148776s4vr1hfi3dfl448dhgk4d1qy2wv6sxh9kr")))) + "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs From a2e334d20c4ea394a87b932e26428b2940cd05d9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:15 +0200 Subject: [PATCH 0562/1394] gnu: r-bigpint: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-bigpint): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db8cada73af..e51911732fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12656,14 +12656,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "0b0l0v9p7a5da3x18d0pqn41ilgxfyzapjaawgsshcfm5mjq5d7q")))) + "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs From 985723a862830d9cc76e6b9ca5c0df271144f563 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:15 +0200 Subject: [PATCH 0563/1394] gnu: r-chemminer: Update to 3.48.0. * gnu/packages/bioconductor.scm (r-chemminer): Update to 3.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e51911732fc..4c8d83bcae6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12699,14 +12699,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.46.0") + (version "3.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "069xd7if7fs69afmamgl6wrkzpnk97ic6z5ix4vvlzkb078dm0p8")))) + "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs From 3d99b6af6030bfe72fd203e278061e9d87cdec95 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:16 +0200 Subject: [PATCH 0564/1394] gnu: r-fmcsr: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-fmcsr): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4c8d83bcae6..8bf3e1cfa4c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12742,13 +12742,13 @@ structures.") (define-public r-fmcsr (package (name "r-fmcsr") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fmcsR" version)) (sha256 - (base32 "0mshslfj7jsix1yc03s54spbbi56zspic49kfsjfv8npikj1i5w0")))) + (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30")))) (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs From 4bb7bb8db382fa246efdd0198b653c06a384ed93 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:16 +0200 Subject: [PATCH 0565/1394] gnu: r-bioassayr: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8bf3e1cfa4c..24a2e0cbfad 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12771,14 +12771,14 @@ searching and clustering.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0pa8d7p9asp36wddkg779i3b9m12rxik56c54bmclnammr0cz89i")))) + "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs From 63726dee635ac5a98f1529d6953622c02dd9652c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:16 +0200 Subject: [PATCH 0566/1394] gnu: r-biobroom: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-biobroom): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24a2e0cbfad..24f80a1e18d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12806,14 +12806,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "034gbywrscv23kk1qnk7sc7dxdckmf60wh29fz65v1n28mkf180r")))) + "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs From 8f240ba849787b80c05d7fc47edce5272791b14e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:16 +0200 Subject: [PATCH 0567/1394] gnu: r-graphite: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-graphite): Update to 1.42.0. [propagated-inputs]: Remove r-checkmate; add r-rlang. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24f80a1e18d..662d1e86163 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12835,18 +12835,18 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "0wmdv4j6dinszxwpz2jddshkh1ahbhm2fxh6vhjsk4grw38i1lfr")))) + "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs - (list r-annotationdbi r-checkmate r-graph r-httr r-rappdirs)) + (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description From 449b0f0920652c6f7e44241a8c16f2dd753aa96c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:16 +0200 Subject: [PATCH 0568/1394] gnu: r-reactomepa: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-reactomepa): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 662d1e86163..475000aa99f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12858,14 +12858,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1f4kd5cql7knnqaq3ba48kkypw8p60lkfdsnpqxcabdj30gqp55b")))) + "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs From 89c507900714f1b4cb581594e8f411b69d010b59 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:16 +0200 Subject: [PATCH 0569/1394] gnu: r-ebarrays: Update to 2.60.0. * gnu/packages/bioconductor.scm (r-ebarrays): Update to 2.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 475000aa99f..50261324f9f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12890,14 +12890,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "10dw6c93rmpknzf4cnhw3y7lb27q4xq7x7wirl2a7qywdj0yj2g6")))) + "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs From 98074b055352ce048ec3db0ea11c1057cc8b32c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:17 +0200 Subject: [PATCH 0570/1394] gnu: r-bioccheck: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.32.0. [propagated-inputs]: Remove r-optparse. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 50261324f9f..36273aafb08 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12934,13 +12934,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "0w9ddicyp9i8rxf92n9pghd9s6bb8jdjikaylrmkydhb7jbhan0y")))) + "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -12949,7 +12949,6 @@ monograph.") r-graph r-httr r-knitr - r-optparse r-biocmanager r-biocviews r-stringdist)) From d377dd0e2b21f40bf40cef1955dca8d101a98b1b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:17 +0200 Subject: [PATCH 0571/1394] gnu: r-biocgraph: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-biocgraph): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 36273aafb08..b34ad25f505 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12963,14 +12963,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "0c7r0c1kx22dlwi6d1ldbkkbf53yi0p3vmgbwzrbkn3cina7bcxq")))) + "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs From 52a79b24b6e653e4239c8f7a5dfbc70625c01f6c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:17 +0200 Subject: [PATCH 0572/1394] gnu: r-biocstyle: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b34ad25f505..d0347b2c8bd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12985,13 +12985,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "0xx6xr01sb5wig94515zxgw24r9fv0g962ajy87741civhq32lbd")))) + "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) From ad6185a57cdd6dba0bbceef362ead5d96804331b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:17 +0200 Subject: [PATCH 0573/1394] gnu: r-biocviews: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-biocviews): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d0347b2c8bd..da0e758f3c9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13009,13 +13009,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.62.1") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1v6himzp546dpb990vv0nlya21w8x2x30137rsmahjzg942nzs9r")))) + "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) From a2756089efb70180b3b3bf6351705f9a96d8885c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:17 +0200 Subject: [PATCH 0574/1394] gnu: r-experimenthub: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-experimenthub): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index da0e758f3c9..8ecc66d8d02 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13037,14 +13037,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.2.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "0lvd6hyqdfsn5ji714v46qdrb8vr1y38lv0pgw8priab0hpqrbm5")))) + "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs From c3733497e0b61ce13665d56a444cadf555380477 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:18 +0200 Subject: [PATCH 0575/1394] gnu: r-grohmm: Update to 1.30.1. * gnu/packages/bioconductor.scm (r-grohmm): Update to 1.30.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ecc66d8d02..6778e70d5a2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13071,14 +13071,14 @@ access.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.28.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1jcj29df4prknqwbydca1jb9w6njacjhwwk9jp0r5mvb88xrm60s")))) + "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs From 4028c2b3b5d2173fda2b1d1f60f0722d7323797b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:18 +0200 Subject: [PATCH 0576/1394] gnu: r-multiassayexperiment: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6778e70d5a2..f255cb599bc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13098,14 +13098,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "1h3b8vqlbd04amjprxd1814zksdrbi01a0xn3906vkbqi43hfyn9")))) + "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) From e833302c582803b25c3ea52ccecc3de48066f89b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:18 +0200 Subject: [PATCH 0577/1394] gnu: r-bioconcotk: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-bioconcotk): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f255cb599bc..7105f28b582 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13133,14 +13133,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1h5s6wbc5n5x5d28rynxpcmaklxdhf72g9gg9fy8cg77niipvxd9")))) + "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs From b86b657862e2e3500054ecaefab8ab0d69d98ba1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:18 +0200 Subject: [PATCH 0578/1394] gnu: r-biocor: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-biocor): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7105f28b582..f00eda567b3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13178,14 +13178,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "0ii4g7438lb34ykidkbxw3v3k289k662rgbgayf9gak5avpkb2cq")))) + "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs From d5875494dd5b466fb0f4e4869f088821d42d2ab4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:18 +0200 Subject: [PATCH 0579/1394] gnu: r-biocpkgtools: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f00eda567b3..7b866c7cbd2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13205,14 +13205,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.12.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "1yz2sgx4xrnw22k3d6q6hkj213bnbb4hbr5ymxnmjnsz551s75ny")))) + "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs From 22300462dd61e452142d673864ab5727c7980766 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:18 +0200 Subject: [PATCH 0580/1394] gnu: r-biocset: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-biocset): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7b866c7cbd2..e19156e15cc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13253,14 +13253,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1x5ar9byr85iap2x6y66j31fi17wr31awx1gl3z01sckp0dldx6w")))) + "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs From a56e8ec8fbd02c100f9938dbc604101f79ea3f91 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:19 +0200 Subject: [PATCH 0581/1394] gnu: r-biocworkflowtools: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e19156e15cc..4abc46e8625 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13291,14 +13291,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "1j9s8w5y8savcmh70npkanxacq1kipxnwk1wsiw5hwnp1p13ldaa")))) + "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) From 9f3d204c3a5144fcee90b5c98226b68c7b80eabf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:19 +0200 Subject: [PATCH 0582/1394] gnu: r-biodist: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-biodist): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4abc46e8625..a7173ae1dad 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13324,14 +13324,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "0y35c9sdq5x4q64ip0wgqz59mh01l71k1pp6n8vqbr667nwg0gdp")))) + "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs From 0f1295e9e9658db831db34cb24429938bf9a8c0d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:19 +0200 Subject: [PATCH 0583/1394] gnu: r-pcatools: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-pcatools): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a7173ae1dad..68a4407305b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13346,14 +13346,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "10kfhsxhsjpzal3yvcqg769h5fz99cqqjq217cj9jip3jfh2m2h4")))) + "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs From dd33e8b062ca71206ee8333b4bb293ae19a75ed2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:19 +0200 Subject: [PATCH 0584/1394] gnu: r-rgreat: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-rgreat): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 68a4407305b..4e190805b7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13392,14 +13392,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0kr61mhxp9phn1136fci450zwfhsipchmlm8d5rgib4lh0zbxrhl")))) + "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs From 3e7b5a45e46d1a0817143d7ba040a6155a7f447a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:19 +0200 Subject: [PATCH 0585/1394] gnu: r-m3c: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-m3c): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4e190805b7e..cb87b85358f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13416,14 +13416,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "0jsql5wd58hs5mnn9wq5b4kl3z57y6amykirfb3k047zpyi8ijnh")))) + "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs From 0a9838b17d0eeff58f5fcfabc65dae24f19d0c6a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:20 +0200 Subject: [PATCH 0586/1394] gnu: r-icens: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-icens): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cb87b85358f..4e5937dee42 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13449,14 +13449,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "08jd7g28mazvwd3qbq8y26czmkz45avp4vy8l7i5d6qajwzqzgzs")))) + "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs From 16419c4639c08526fc8699d2f262bc1e1e4c9a70 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:20 +0200 Subject: [PATCH 0587/1394] gnu: r-preprocesscore: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4e5937dee42..a0e3f2da4b5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13572,14 +13572,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1i93vdqa6pwzamiryp3lv6cyvhx9shs01is0q6vbmdvcbii2vf3x")))) + "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) From c8e364b60901a46d22442fd46c492ad80b6fdf98 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:20 +0200 Subject: [PATCH 0588/1394] gnu: r-s4vectors: Update to 0.34.0. * gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a0e3f2da4b5..bb8559fb6bd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13593,13 +13593,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.32.4") + (version "0.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "17dvypxcwp8c7ih23hi2366110by6zq1mjgxkmlbiklzachg9780")))) + "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) From 3c57f6d2a0ac98709a06ea5568718c1e60082a0c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:20 +0200 Subject: [PATCH 0589/1394] gnu: r-rgraphviz: Update to 2.40.0. * gnu/packages/bioconductor.scm (r-rgraphviz): Update to 2.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bb8559fb6bd..aeb1b084f6f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13660,14 +13660,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "0fyv1ybpahkwz3fawzxgxfnshi8y7c18262rgdmqwdl5662vv1p7")))) + "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments From 8b7e1da3b68542d50efb210aadad87acae01bafc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:20 +0200 Subject: [PATCH 0590/1394] gnu: r-fithic: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-fithic): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aeb1b084f6f..2f841b3e3e2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13698,13 +13698,13 @@ objects from the @code{graph} package.") (define-public r-fithic (package (name "r-fithic") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "0a3d2bxp98lmbf3i864zgfwxwvxyqfcrh75z9yz7ra7y44pkjr4y")))) + "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs From 0b0bce35562e70d46740978fb7e09e6cfa0e4653 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:20 +0200 Subject: [PATCH 0591/1394] gnu: r-hitc: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-hitc): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2f841b3e3e2..8d203b780cf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13722,13 +13722,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "1ckiwqfq86k8p3y36iwr7k3y6g4z80n8hb047c0i2491lrn23rhx")))) + "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs From 59519a14deb73c878bfa57c3a59c70f8ef54d714 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:21 +0200 Subject: [PATCH 0592/1394] gnu: r-hdf5array: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8d203b780cf..1b9ee8ed2f2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13751,14 +13751,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1al4a88pgdl7hfhphsnwl1gg1c1kmw37wcdr4v4pfsw5l8ff7nx4")))) + "0s9vj74359ckmwl8r951jxrzkidslwdl9qamkhz8ilw8b5awxyw4")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs From 3db60a25a73030fc6bf158fae398d3517888e2ad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:21 +0200 Subject: [PATCH 0593/1394] gnu: r-rhdf5lib: Update to 1.18.2. * gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.18.2. [source]: Adjust snippet. [arguments]: Update build phase 'do-not-use-bundled-hdf5. --- gnu/packages/bioconductor.scm | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b9ee8ed2f2..73995c02558 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13782,22 +13782,21 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.16.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0yly9s3wdnhd9ci2jxfkql38ibv35yzs38a6g6ashbg1m5kgwd9p")) + "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled binaries (delete-file-recursively "src/wininclude/") - (delete-file-recursively "src/winlib-8.3.0/") - (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz") - #t)))) + (delete-file-recursively "src/winlib/") + (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz"))))) (properties `((upstream-name . "Rhdf5lib"))) (build-system r-build-system) (arguments @@ -13806,11 +13805,8 @@ block processing.") (add-after 'unpack 'do-not-use-bundled-hdf5 (lambda* (#:key inputs #:allow-other-keys) (for-each delete-file '("configure" "configure.ac")) - ;; Do not make other packages link with the proprietary libsz. (substitute* "R/zzz.R" - ((" \"%s/libsz.a\"") "") - (("patharch, .getDynamicLinks") - ".getDynamicLinks")) + (("return\\(links\\)") "return(\" -lz\")")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) @@ -13829,6 +13825,8 @@ block processing.") "hdf5/src/libhdf5.settings") (rename-file "Makevars.in" "Makevars") (substitute* "Makevars" + (("@BUILD_HDF5@") "") + (("@COPY_SZIP@") "") (("@ZLIB_LIB@") "-lz") (("@ZLIB_INCLUDE@") "") (("HDF5_CXX_LIB=.*") From 18fd5759c70e29789fe8ce88e775f7bee720a740 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:21 +0200 Subject: [PATCH 0594/1394] gnu: r-beachmat: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-beachmat): Update to 2.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 73995c02558..b53e8390a29 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13862,14 +13862,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb")))) + "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) From bde757d11d8e2a302a8bee4b31fdd7138418e7c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:21 +0200 Subject: [PATCH 0595/1394] gnu: r-cner: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-cner): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b53e8390a29..0fe839047dc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13888,13 +13888,13 @@ matrices.") (define-public r-cner (package (name "r-cner") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2")))) + (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs (list zlib)) From 7c9793b3e8ef654538e8b0b49549c8afdd131cf2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:21 +0200 Subject: [PATCH 0596/1394] gnu: r-tfbstools: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-tfbstools): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0fe839047dc..a8a673cf4ce 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13936,14 +13936,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "0j5gv145fczzdspwhbywlg47y05pgnkra9jg7bn4wa1k0cf5pr9g")))) + "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs From e213375069ef72aab745183e9760c5fb68e35c92 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:21 +0200 Subject: [PATCH 0597/1394] gnu: r-maftools: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-maftools): Update to 2.12.0. [propagated-inputs]: Add r-dnacopy. --- gnu/packages/bioconductor.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a8a673cf4ce..feda9ccc1f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13982,17 +13982,22 @@ provides a wrapper of de novo motif discovery software.") (define-public r-maftools (package (name "r-maftools") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maftools" version)) (sha256 - (base32 "1s8w3xwwigz803l81bs9cb2dbvvw5r9z8jjcav1rmh9wm8909nfd")))) + (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6")))) (properties `((upstream-name . "maftools"))) (build-system r-build-system) (propagated-inputs - (list r-data-table r-rcolorbrewer r-rhtslib r-survival r-zlibbioc)) + (list r-data-table + r-dnacopy + r-rcolorbrewer + r-rhtslib + r-survival + r-zlibbioc)) (native-inputs (list r-knitr)) (home-page "https://github.com/PoisonAlien/maftools") (synopsis "Summarize, analyze and visualize MAF files") From 3ef47df3b611062574f950fb8a777adecabe5618 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:22 +0200 Subject: [PATCH 0598/1394] gnu: r-motifmatchr: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-motifmatchr): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index feda9ccc1f4..db4417bbeea 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14011,14 +14011,14 @@ customizable visualzations with minimal effort.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "0f7j54zdn51h1gcn81vqs8avmschjwqprjcfpvsi00q4fna3fg7z")))) + "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs From d9d9f78391009b122662db1ed279dff3e36aff28 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:22 +0200 Subject: [PATCH 0599/1394] gnu: r-chromvar: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-chromvar): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db4417bbeea..e9157793efa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14045,13 +14045,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "0ylsfr540l763bh010irbcavlskahyb1769pppimdgn22gyr3spk")))) + (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs From decd8480f6d86931c1f9918131604c5ccc1d98e5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:22 +0200 Subject: [PATCH 0600/1394] gnu: r-singlecellexperiment: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e9157793efa..25857f93ddf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14092,14 +14092,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "01075vbs8hy399pxalav9rbkz4djvl84ip559jkz51fypd0m4i39")))) + "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) From 816a1ba4dc7bff61b22634c2dbcede300070ae3a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:22 +0200 Subject: [PATCH 0601/1394] gnu: r-singler: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-singler): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 25857f93ddf..2905b0398dd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14120,13 +14120,13 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "0j0h6ipm65wv38qx40z16h01mfirpshfn4lhlwlg2nri4vmihlpi")))) + (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs From a8fbcbdb7aa17f7c0d72e2f896ae594bba555a17 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:22 +0200 Subject: [PATCH 0602/1394] gnu: r-scuttle: Update to 1.6.2. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.6.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2905b0398dd..244cb1b9e66 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14152,14 +14152,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.4.0") + (version "1.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1dbdb6yc6wk01dljy1vy6f0lf44crc5rxxnc4bhjk8i4iljz8467")))) + "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs From 9631f2190aac830bf27322e5d3c7eff7e2153099 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:22 +0200 Subject: [PATCH 0603/1394] gnu: r-scater: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-scater): Update to 1.24.0. [propagated-inputs]: Add r-rcppml. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 244cb1b9e66..cc1469e24b7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14187,13 +14187,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg")))) + "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -14209,6 +14209,7 @@ of other packages.") r-gridextra r-matrix r-rcolorbrewer + r-rcppml r-rlang r-rtsne r-s4vectors From 5f04cf7bdb81d1878b0ba621922250de7e595e6d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:23 +0200 Subject: [PATCH 0604/1394] gnu: r-scran: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-scran): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cc1469e24b7..d0e15d26cce 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14229,14 +14229,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "06lcxya6rpa8dv0il7m7fwyx0ci1y1jn16ff5lmvzf2mnr6q7lic")))) + "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w")))) (build-system r-build-system) (propagated-inputs (list r-beachmat From eca29a788b141c35be821d6ef290fe17c611050e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:23 +0200 Subject: [PATCH 0605/1394] gnu: r-sparsematrixstats: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d0e15d26cce..0490e630073 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14272,14 +14272,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0ifqj4a6mn4749sr62gq3dwd6mmbbzdx5mh5b5663vcgl1kw96x1")))) + "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) From 9381702bbc619756599c084578fcdf391b6c1b79 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:23 +0200 Subject: [PATCH 0606/1394] gnu: r-delayedmatrixstats: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0490e630073..b4018b6b830 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14297,14 +14297,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1pqwkk39rfhcnhmgchk0gfmm4jgasl19yq0nhhwsfj45y2vk6kjk")))) + "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) From ec7849c360479ab6818d99ce753e523ff10cf927 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:23 +0200 Subject: [PATCH 0607/1394] gnu: r-mscoreutils: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4018b6b830..af8f4332c08 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14333,14 +14333,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.6.2") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "0614a830gf676ck8j5lkm04158pfvhjb61p3xfdd69gg3d44mk1d")))) + "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs From d34a40c4c03e34a2cfc8514cd217e0b10e09665e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:23 +0200 Subject: [PATCH 0608/1394] gnu: r-msfeatures: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-msfeatures): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index af8f4332c08..70ecf15e230 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14362,13 +14362,13 @@ within the R for Mass Spectrometry packages.") (define-public r-msfeatures (package (name "r-msfeatures") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsFeatures" version)) (sha256 - (base32 "020ifrijlzdd3qk4bhd9z4knj5d87ildrkl3wcmxvwkvs9rbh8rq")))) + (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3")))) (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs From f185bf805c22d08e6bdd9f8bb1b1def85a263a5c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:23 +0200 Subject: [PATCH 0609/1394] gnu: r-biocio: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-biocio): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 70ecf15e230..2d8a470f037 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14392,14 +14392,14 @@ the respective packages (such as e.g. @code{xcms}).") (define-public r-biocio (package (name "r-biocio") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "1qg6v961sbj7qwyjx4z720f6h0kq693p7gc8q99my7gqkbbcxrfr")))) + "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs From d99da8bb1c289863d979640e4970f002d8683d43 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:24 +0200 Subject: [PATCH 0610/1394] gnu: r-msmseda: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-msmseda): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2d8a470f037..107715aa32c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14425,14 +14425,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "1jammjkjjkcqad2ki02l2pdf4jybyh71hv463aya2ylmzsin5vi9")))) + "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs From e4a8e6dab4acb2741fd275a54a022c9761b2abaf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:24 +0200 Subject: [PATCH 0611/1394] gnu: r-msmstests: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-msmstests): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 107715aa32c..255b8c39aa1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14448,14 +14448,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "0xmjgd8rqpb8i7d46pvnj7da2di8bwfdncr48b8hgylkc98ghznb")))) + "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs From 1b75b53a0e0c60afabdf7f25b403a819261ad1bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:24 +0200 Subject: [PATCH 0612/1394] gnu: r-catalyst: Update to 1.20.1. * gnu/packages/bioconductor.scm (r-catalyst): Update to 1.20.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 255b8c39aa1..65453b78b3b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14477,14 +14477,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.18.1") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "0dvcs7nz1yawcrsf9lqiwdcrvjmbs8ajrmvj0ji4qq2a86n3dkg0")))) + "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs From 534743333e0a9c9e9a3d7aa2d01f76814ca0ae39 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:24 +0200 Subject: [PATCH 0613/1394] gnu: r-erma: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-erma): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 65453b78b3b..51c97e5d50f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14540,14 +14540,14 @@ preprocessing of cytometry data, including: (define-public r-erma (package (name "r-erma") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z")))) + "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 97ea85bfcff36f790b8cb07dba243e36e3d3db43 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:24 +0200 Subject: [PATCH 0614/1394] gnu: r-ggbio: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-ggbio): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 51c97e5d50f..07a36926007 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14580,14 +14580,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "1svmjaa3gisi39sl52337drvd54havcy5pjmwrykgykz5flid2m7")))) + "1lvms07ba99nzf10gpn50wjca84nj5jrb6902z069p2bfi4xyd27")))) (build-system r-build-system) (arguments `(#:phases From b6f77fdc872d6d9dec27fe99cc14f66a3e6e9e74 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:25 +0200 Subject: [PATCH 0615/1394] gnu: r-gviz: Update to 1.40.1. * gnu/packages/bioconductor.scm (r-gviz): Update to 1.40.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07a36926007..b1ceff5ad81 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14748,14 +14748,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.38.4") + (version "1.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "14qybi5b3h9z5b0m127jf7z695amf612rh5wq2g2n1yirfhzbdja")))) + "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs From ee71b376ecfadb220066d24acebff0a4d1665543 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:25 +0200 Subject: [PATCH 0616/1394] gnu: r-gwascat: Update to 2.28.1. * gnu/packages/bioconductor.scm (r-gwascat): Update to 2.28.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b1ceff5ad81..0c1ffcf1613 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14797,14 +14797,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.26.0") + (version "2.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx")))) + "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 564024c01f6461f3249e4811cff3a0980cdb7e87 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:25 +0200 Subject: [PATCH 0617/1394] gnu: r-kegggraph: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0c1ffcf1613..73478299c5d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14831,13 +14831,13 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "1qqvbv1sq9j570syb2802ya2ffg1k8f1w986wr6ksqkwxb9qbbm4")))) + (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs From c8f930d575792b16cafa7ae6b08d461308f092a8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:25 +0200 Subject: [PATCH 0618/1394] gnu: r-ldblock: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-ldblock): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 73478299c5d..6aaac8c0c4b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14855,14 +14855,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg")))) + "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics From c784304f9ba451c18631b22a08381bfc45371642 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:25 +0200 Subject: [PATCH 0619/1394] gnu: r-pathview: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-pathview): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6aaac8c0c4b..f4c8cdadc73 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14979,13 +14979,13 @@ other functional sequencing data.") (define-public r-pathview (package (name "r-pathview") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "1jdl81lvrsz03b1nws90nssf2clipipzaqvwm1pq57mvshnlnkjr")))) + (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs From 93b59aca4c3c11b62af38cb306259be73f828cba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:25 +0200 Subject: [PATCH 0620/1394] gnu: r-snpstats: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-snpstats): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f4c8cdadc73..592af1b0d96 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15013,14 +15013,14 @@ large-scale and fully automated analysis.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq")))) + "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs (list zlib)) From 80f63620c5bd9b64a4ccca3921de36330580c35e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:26 +0200 Subject: [PATCH 0621/1394] gnu: r-chromstar: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-chromstar): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 592af1b0d96..f863adc249d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15037,14 +15037,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "1akcmxzn4j9ph4n3lsgfh8fh8hrb28jjamz037w59bsdkcv6wyjq")))) + "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs From 8467426bba938c12a966a943e5904f5751cbf14c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:26 +0200 Subject: [PATCH 0622/1394] gnu: r-guitar: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-guitar): Update to 2.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f863adc249d..b63ebd8b954 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15075,14 +15075,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "082yja4mmsq77sllv3c88agxjbb6jxwil2krb8fkfsijvyyx11c9")))) + "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs From d57d65a6284ed917437bc2d17cb89099473eb2cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:26 +0200 Subject: [PATCH 0623/1394] gnu: r-sushi: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-sushi): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b63ebd8b954..63c273d5291 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15107,13 +15107,13 @@ starting site, start codon, stop codon and transcription ending site.") (define-public r-sushi (package (name "r-sushi") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "073mh1d063ph5zk1d8kipgblr4l1ixqbxflhq4669761fi2frlw4")))) + "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs From c2a8c4c248441b37683c9e7ebf97f01cab381f95 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:26 +0200 Subject: [PATCH 0624/1394] gnu: r-ballgown: Update to 2.28.0. * gnu/packages/bioconductor.scm (r-ballgown): Update to 2.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 63c273d5291..691f9a95b71 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15128,14 +15128,14 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf")))) + "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs From 64c3498d9fe6a99f5fb785ef39d66ae760627300 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:26 +0200 Subject: [PATCH 0625/1394] gnu: r-megadepth: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-megadepth): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 691f9a95b71..ec2d5488b32 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15162,14 +15162,14 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r")))) + "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) (inputs (list megadepth)) From 460680ef90cfe3c8f4d95b7bf3108111ca2af08f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:26 +0200 Subject: [PATCH 0626/1394] gnu: r-beclear: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-beclear): Update to 2.12.0. [propagated-inputs]: Remove r-outliers; add r-dixontest. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec2d5488b32..cd41cc5f108 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15195,23 +15195,23 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "1njb1lfd4wmsrfw06jc8z8vdk14nmcw9lwyvbxr7z1zg4h8v6c29")))) + "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs (list r-abind r-biocparallel r-data-table + r-dixontest r-futile-logger r-matrix - r-outliers r-rcpp r-rdpack)) (native-inputs From 00025cdd230569993c72322f27809191fe2dbf8c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:27 +0200 Subject: [PATCH 0627/1394] gnu: r-bgeecall: Update to 1.12.1. * gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.12.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cd41cc5f108..010b7628618 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15228,14 +15228,14 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "0rbbl8m48qcvl26lnf27jq108p7pi84m9ac3qcpjc0ax5wywbv16")))) + "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs From 24c13f9d64c336ec0a611ca3cac35a7f70eb8b9c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:27 +0200 Subject: [PATCH 0628/1394] gnu: r-bgeedb: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 010b7628618..bd476a2bb7f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15264,14 +15264,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.20.1") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "0mrw7fwjx8k0a5c3iw2j94h1yn5pkvqil7fbzih9xiafnpbn374m")))) + "093zk43x8i9ajaqsdhndkyal3dizllr3g85ziavb3k73dzvarzsc")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs From 395f152b926932a81cf151f34fea0502738afe98 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:45:27 +0200 Subject: [PATCH 0629/1394] gnu: r-biobtreer: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-biobtreer): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bd476a2bb7f..db192834aad 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15298,14 +15298,14 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "0m9gx2g5ishbbh7aqp09mpknhr7q1v5ap0s6xp6ccj01pz2gkk8s")))) + "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs From c4f8b5759a7f9c45282236793d1c86a7c2eb2e5d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:47 +0200 Subject: [PATCH 0630/1394] gnu: r-minet: Update to 3.54.0. * gnu/packages/bioconductor.scm (r-minet): Update to 3.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db192834aad..ccec896ae33 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15322,14 +15322,14 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.52.0") + (version "3.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "0nhgvgci4r9pjfsnvxyj2q8im1wvig4zmfx2kidw8f63x2ip2rbd")))) + "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs From 3c65a7d577f473144e0b483d63514863690fe0ff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:47 +0200 Subject: [PATCH 0631/1394] gnu: r-genetclassifier: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-genetclassifier): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ccec896ae33..b7c41d0f1d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15344,14 +15344,14 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1phyphdc1i55ab1a05633b0p41q8n7w0byp1plgcav2s3h8mk1km")))) + "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) From 5d2c07021cd120215bd3136e0e2ed0f899659516 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:47 +0200 Subject: [PATCH 0632/1394] gnu: r-dir-expiry: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b7c41d0f1d1..d3e8b77edcc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15369,14 +15369,14 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00")))) + "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs (list r-filelock)) From 90e56ba6e3ba7909863236e0976901d152303b20 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:47 +0200 Subject: [PATCH 0633/1394] gnu: r-basilisk-utils: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3e8b77edcc..238c01a51f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15393,14 +15393,14 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "0578rq2yz24sv7anb7vp0a0y35944ag1l8ca6haanb03wl97wm99")))) + "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) From b007802e4bbe89c305aa2b6f457d4d2e0907187e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:47 +0200 Subject: [PATCH 0634/1394] gnu: r-basilisk: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-basilisk): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 238c01a51f4..b17ac0e9d5d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15417,14 +15417,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "1cdkpngv9qybd9yxc3i2201p433vkkahs71v28x6lgs5l2wz3m1a")))) + "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs From 6766fbb003995adf12a13ecd0e9ac96186e34937 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:47 +0200 Subject: [PATCH 0635/1394] gnu: r-biocthis: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-biocthis): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b17ac0e9d5d..f0e5760412c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15443,14 +15443,14 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "0kh5lmv992v4r5r58x29403cll0zxr9fx4ar81nrzvnch5668v39")))) + "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments From 259c003f026b82768c8d4b5c2e82ae97eb8fee79 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:48 +0200 Subject: [PATCH 0636/1394] gnu: r-biocdockermanager: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-biocdockermanager): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f0e5760412c..1900ee217cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15477,14 +15477,14 @@ Bioconductor-friendly.") (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "1kpdmpcngnl667bfffp9bkf8c31ipmhsncq0h9bf3a4k8b83pi0w")))) + "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) From 12ee563b41466cae1609790e5712dd1209ab4948 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:48 +0200 Subject: [PATCH 0637/1394] gnu: r-biodb: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-biodb): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1900ee217cb..0e3c8b85ca0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15507,14 +15507,14 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "0b5zva16r4kz8736h3djjgmh35nxmlin4f374rb4i2s55zsrb638")))) + "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs From eb18527e5ff5dad0cf90f005309829caecb213ac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:48 +0200 Subject: [PATCH 0638/1394] gnu: r-biomformat: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-biomformat): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0e3c8b85ca0..5a0145898d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15552,14 +15552,14 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817")))) + "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs From a3a8109fe854fcfd6202ccf3327ef87d00222adc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:48 +0200 Subject: [PATCH 0639/1394] gnu: r-mvcclass: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5a0145898d2..59e70896f38 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15581,14 +15581,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "088gzh33vjkjf78xczqfs89pyg0k7c3533yfvijqxl84ni2ky78z")))) + "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") From 7fe83026b7491108c6bbfd76a13b0c8cb57d2406 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:48 +0200 Subject: [PATCH 0640/1394] gnu: r-biomvcclass: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59e70896f38..a3f283f18d6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15601,14 +15601,14 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "0jqgazwz35gz11a7vzanyy2yalzalx0z0rw6y18nmk8dbv01nv2j")))) + "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs From 3391ff6ddb813ddc7865a36a691bd0fbadea58c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:48 +0200 Subject: [PATCH 0641/1394] gnu: r-biomvrcns: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-biomvrcns): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3f283f18d6..0ddbdc2f789 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15623,14 +15623,14 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy")))) + "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs From f5262fa4edf71742fdf93d142b6fd89a5b3a2fc2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:49 +0200 Subject: [PATCH 0642/1394] gnu: r-bionero: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-bionero): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0ddbdc2f789..3e80b2ab8b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15648,14 +15648,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "0ddrzv1g46hvm52dzrcj5nbyyw9a16cqk8zg20wnkrh3qw1h4d9p")))) + "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs From 8fe9bcf0a4aa8570971ef29b952873e9e3d59e15 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:49 +0200 Subject: [PATCH 0643/1394] gnu: r-bionet: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-bionet): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3e80b2ab8b9..9bf94f9ff41 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15704,14 +15704,14 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "05rj14jn4gn0hfn57amf19b8fqwkd3y2ji3mg7m1yg1w7n4qxqsg")))) + "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs From dba6a33e3d57128442f1c5bf63e1c57f7391a013 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:49 +0200 Subject: [PATCH 0644/1394] gnu: r-bionetstat: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9bf94f9ff41..7818d392956 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15733,14 +15733,14 @@ scoring subnetwork.") (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "13br8x4809hrr4ibz6iy5qjza9j6cazmkpvfikvw6bs588csxwf8")))) + "0f387j35lj32ryiw48jz8gc08al2lmmv9zvbbgyjq9wmqlca3dfb")))) (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs From e8e3d333f0fd45904a692b8cde8364a8a88528c9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:49 +0200 Subject: [PATCH 0645/1394] gnu: r-bioqc: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-bioqc): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7818d392956..346c15acfa6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15775,14 +15775,14 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "190336qk0plg79gzvfn6wfplsi8nq0nj8508g7m0w3z6bdgwy407")))) + "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs From 4b3f9a16f2b7a3db728e11747366d1cb94039489 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:49 +0200 Subject: [PATCH 0646/1394] gnu: r-biotip: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-biotip): Update to 1.10.0. [propagated-inputs]: Remove r-hmisc; add r-scran. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 346c15acfa6..3a65c554a5a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15801,23 +15801,23 @@ optimised for high performance.") (define-public r-biotip (package (name "r-biotip") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "0xmy5c4i9gf6d04gara6lbnnldqmzjaascb2pd2ih60jw2mvl4ys")))) + "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-genomicranges - r-hmisc r-igraph r-mass r-psych + r-scran r-stringr)) (native-inputs (list r-knitr)) From 397bdc4329bbefc31b6b37216955bcae7d987577 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:50 +0200 Subject: [PATCH 0647/1394] gnu: r-biotmle: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-biotmle): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3a65c554a5a..509e3305ab4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15831,14 +15831,14 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "0p3iavf9059qa8qvfvqzskfc5gki3z0ivkkqdwg5anvf0wv2k47g")))) + "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs From 4ab8327ba4ac42bbf39fffe6cddf9ae61e1d73be Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:50 +0200 Subject: [PATCH 0648/1394] gnu: r-bsseq: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-bsseq): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 509e3305ab4..a672997607c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15873,14 +15873,14 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d")))) + "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs From b1c215755a952bd058c97c885d159401887135da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:50 +0200 Subject: [PATCH 0649/1394] gnu: r-dmrseq: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a672997607c..982902e2105 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15919,14 +15919,14 @@ visualizing bisulfite sequencing data.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "1d6y6rbvcgprmzqkdzxg5csf0yv845d9vw10pcd1pzyndrama1vd")))) + "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs From 6f31f4618a20d5702c08324cd61fa2ef72ac366d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:50 +0200 Subject: [PATCH 0650/1394] gnu: r-omnipathr: Update to 3.4.0. * gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.4.0. [propagated-inputs]: Add r-withr. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 982902e2105..f651b33ebeb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15965,13 +15965,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.2.8") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "0vr16ar3rbjsfw4qz2g86lbhvmqwgq0vcahc6vrc4d9rdjxwg6sb")))) + (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -16001,6 +16001,7 @@ interest on transformed methylation proportions.") r-tibble r-tidyr r-tidyselect + r-withr r-xml2 r-yaml)) (native-inputs (list r-knitr)) From a4f03b0a55f2fcdddc45802948c2c3358894e466 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:50 +0200 Subject: [PATCH 0651/1394] gnu: r-biscuiteer: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.10.0. [propagated-inputs]: Add r-iranges. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f651b33ebeb..2d6de0e259d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16018,14 +16018,14 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "16ds322b21g8ys5c3lkrvi70i82f9rxvnknbiqx4sp6f2l01j5yj")))) + "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs @@ -16043,6 +16043,7 @@ for ligand activity prediction from transcriptomics data.") r-hdf5array r-homo-sapiens r-impute + r-iranges r-matrix r-matrixstats r-mus-musculus From 5ec7143f69b2d567683d6901754051f147fd495c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:50 +0200 Subject: [PATCH 0652/1394] gnu: r-tcgabiolinks: Update to 2.24.1. * gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.24.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2d6de0e259d..c2c8b654dae 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16070,13 +16070,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.22.4") + (version "2.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "071wz6dm6dypbfzvxd6j67l1iawlb6d5sfzq871zh06fzaxjm332")))) + (base32 "0kw4lrg8xm0ipj7f7h1rwfj7a8mknkril1pn05x08mx13f7p5p14")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs From e290d834d908c95b7cde9d5fffb10ad781cc8f50 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:51 +0200 Subject: [PATCH 0653/1394] gnu: r-tricycle: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-tricycle): Update to 1.4.0. [propagated-inputs]: Add r-ggnewscale. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c2c8b654dae..6bdeaf0a673 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16125,27 +16125,29 @@ starburst plots) in order to easily develop complete analysis pipelines.") (define-public r-tricycle (package (name "r-tricycle") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 - "19yh7yif8630j845m9rddva2z0xy4jcw9j4hvyr076jqbyxz998r")))) + "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) - (propagated-inputs (list r-annotationdbi - r-circular - r-dplyr - r-genomicranges - r-ggplot2 - r-iranges - r-rcolorbrewer - r-s4vectors - r-scater - r-scattermore - r-singlecellexperiment - r-summarizedexperiment)) + (propagated-inputs + (list r-annotationdbi + r-circular + r-dplyr + r-genomicranges + r-ggnewscale + r-ggplot2 + r-iranges + r-rcolorbrewer + r-s4vectors + r-scater + r-scattermore + r-singlecellexperiment + r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/hansenlab/tricycle") (synopsis "Transferable representation and inference of cell cycle") From e0be852a1ea00ec9b44e7df722021252fe5643d5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:51 +0200 Subject: [PATCH 0654/1394] gnu: r-tximeta: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-tximeta): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6bdeaf0a673..7c27ace4539 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16164,14 +16164,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.12.4") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "1lm2r64d6sdfzvxcabgs0214cdc5dl9pfx562acjcxz5mb101g9g")))) + "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs From 319fa58dac2499525c1e340ee7bb3200f1c37239 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 12:46:51 +0200 Subject: [PATCH 0655/1394] gnu: r-phyloseq: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c27ace4539..5d94d25d5db 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16205,13 +16205,13 @@ reproducibility.") (define-public r-phyloseq (package (name "r-phyloseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 - (base32 "0k0aj8f7g1vr7l0qcc507b3w67zc1k9x7sdblm7mjb20zqr3916s")))) + (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs From 549a9e6f6a86a72af4733ca22280c3b5a29acc0a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:20 +0200 Subject: [PATCH 0656/1394] gnu: r-leidenbase: Update to 0.1.9. * gnu/packages/bioconductor.scm (r-leidenbase): Update to 0.1.9. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5d94d25d5db..e1cc32d8fd3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7652,11 +7652,11 @@ qPCR data, but could be used with other types as well.") (license license:artistic2.0))) (define-public r-leidenbase - (let ((commit "430f22af6982cc7d2e6e77f6b0df47bc970dcbce") + (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96") (revision "1")) (package (name "r-leidenbase") - (version (git-version "0.1.3" revision commit)) + (version (git-version "0.1.9" revision commit)) (source (origin (method git-fetch) @@ -7666,7 +7666,7 @@ qPCR data, but could be used with other types as well.") (file-name (git-file-name name version)) (sha256 (base32 - "0ylqsmdpv4xq6f6ldxvwkhk33a9i1jcgk60zvksk3iplykfzd6c0")))) + "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f")))) (properties `((upstream-name . "leidenbase"))) (build-system r-build-system) (inputs From 3d93251ea58129c3dac450b3ace76a7e9549efc7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:54 +0200 Subject: [PATCH 0657/1394] gnu: r-bsgenome-hsapiens-ucsc-hg19: Update to 1.4.3. * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): Update to 1.4.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e1cc32d8fd3..02c8612b23e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -696,14 +696,14 @@ annotations for the genome of the model mouse Mus musculus.") (define-public r-bsgenome-hsapiens-ucsc-hg19 (package (name "r-bsgenome-hsapiens-ucsc-hg19") - (version "1.4.0") + (version "1.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19" version 'annotation)) (sha256 (base32 - "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) + "06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) (build-system r-build-system) From 8ee1246a38649d0a57b8f36161a4744f8efe16f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:54 +0200 Subject: [PATCH 0658/1394] gnu: r-bsgenome-hsapiens-ucsc-hg38: Update to 1.4.4. * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38): Update to 1.4.4. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 02c8612b23e..0211ccdc41b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -720,14 +720,13 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.") (define-public r-bsgenome-hsapiens-ucsc-hg38 (package (name "r-bsgenome-hsapiens-ucsc-hg38") - (version "1.4.1") + (version "1.4.4") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38" version 'annotation)) (sha256 - (base32 - "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi")))) + (base32 "03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) (build-system r-build-system) From 5efae7b049ed2747061058c1aaf50a1aeef24cca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:55 +0200 Subject: [PATCH 0659/1394] gnu: r-txdb-hsapiens-ucsc-hg38-knowngene: Update to 3.15.0. * gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg38-knowngene): Update to 3.15.0. [propagated-inputs]: Add r-annotationdbi. --- gnu/packages/bioconductor.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0211ccdc41b..88b697d4ff6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -891,19 +891,18 @@ track. The database is exposed as a @code{TxDb} object.") (define-public r-txdb-hsapiens-ucsc-hg38-knowngene (package (name "r-txdb-hsapiens-ucsc-hg38-knowngene") - (version "3.4.6") + (version "3.15.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" version 'annotation)) (sha256 - (base32 - "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) + (base32 "1y9fqhkk5wgny43bxc0j82afy49vz34rblcmcfmwavngdkpnj879")))) (properties `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) (build-system r-build-system) (propagated-inputs - (list r-genomicfeatures)) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") (synopsis "Annotation package for human genome in TxDb format") From 7feae8098c5effe4428840f594d3a149c06ee56a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:55 +0200 Subject: [PATCH 0660/1394] gnu: r-pfam-db: Update to 3.15.0. * gnu/packages/bioconductor.scm (r-pfam-db): Update to 3.15.0. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 88b697d4ff6..88a5742689b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1079,14 +1079,13 @@ data (chip hgu133plus2) assembled using data from public repositories.") (define-public r-pfam-db (package (name "r-pfam-db") - (version "3.8.2") + (version "3.15.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PFAM.db" version 'annotation)) (sha256 - (base32 - "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) + (base32 "03vjfb9vx1gxrw1jkq6y4i46qhjj9z2mkdiflglbd6kpfrgnl0z7")))) (properties `((upstream-name . "PFAM.db"))) (build-system r-build-system) (propagated-inputs From c89eb68ede7ea479e43374ce1b2ee0526333aa7c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:55 +0200 Subject: [PATCH 0661/1394] gnu: r-adductdata: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-adductdata): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 88a5742689b..9bc23d2f725 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1166,13 +1166,12 @@ All datasets are restricted to protein coding genes.") (define-public r-adductdata (package (name "r-adductdata") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductData" version 'experiment)) (sha256 - (base32 - "0bp74p06gskwn2xl1srpnmsq27ajsrlynkzw6fcmvwwjcrzljmnj")))) + (base32 "02r7p1645vhhf7wn5x0aklmf7l97h6fjb8v9mldim4waccmpyg48")))) (properties `((upstream-name . "adductData"))) (build-system r-build-system) (propagated-inputs (list r-annotationhub r-experimenthub)) From 9db43e49792329806ecbdcfa30f28c0931835157 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:55 +0200 Subject: [PATCH 0662/1394] gnu: r-aneufinderdata: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-aneufinderdata): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9bc23d2f725..36cf2062636 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1187,17 +1187,17 @@ albumin} (HSA).") (define-public r-aneufinderdata (package (name "r-aneufinderdata") - (version "1.18.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinderData" version 'experiment)) (sha256 - (base32 - "02vb3kmza5hv8bc424fdmfif608xvpdb759w8882kac8izpv29ks")))) + (base32 "0cncb8km0sc2xh95rgnnm38kys5ml0n8gh8cl6x7ls1xh9sm83f7")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/AneuFinderData/") (synopsis "Data package for @code{AneuFinder}") - (description "This package contains data used by @code{AneuFinder}.") + (description "This package contains whole-genome single cell sequencing data for +demonstration purposes in the @code{AneuFinder} package.") (license license:artistic2.0))) (define-public r-arrmdata From ccb66a16a06fdfc764560665858e62caf41e552b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:55 +0200 Subject: [PATCH 0663/1394] gnu: r-arrmdata: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 36cf2062636..6eae1e16863 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1203,13 +1203,12 @@ demonstration purposes in the @code{AneuFinder} package.") (define-public r-arrmdata (package (name "r-arrmdata") - (version "1.18.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmData" version 'experiment)) (sha256 - (base32 - "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) + (base32 "1cjzr58426s9z2bwjz3wzlkh52fv0q85cw4gbjnhwakh9sr3dd5p")))) (properties `((upstream-name . "ARRmData"))) (build-system r-build-system) From 3ce819d5635aff3540f55dd0bcc13e034a72c67d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:55 +0200 Subject: [PATCH 0664/1394] gnu: r-biscuiteerdata: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6eae1e16863..401461bfac5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1222,14 +1222,13 @@ from Illumina 450k methylation arrays.") (define-public r-biscuiteerdata (package (name "r-biscuiteerdata") - (version "1.6.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteerData" version 'experiment)) (sha256 - (base32 - "1d7zibjf0qccmdnzdxh7wy1h943yhnbf8zdix72486pvhzm124zj")))) + (base32 "0nda6b8mkv93s513y0xfgxvi7zn8v07jx323ii709rknlncm6qqw")))) (properties `((upstream-name . "biscuiteerData"))) (build-system r-build-system) From 1413f9f214cb8ac8e23db87d3be642da79385a55 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:56 +0200 Subject: [PATCH 0665/1394] gnu: r-celldex: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-celldex): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 401461bfac5..a57cf52957a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1245,13 +1245,13 @@ biscuiteer.") (define-public r-celldex (package (name "r-celldex") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "celldex" version 'experiment)) (sha256 - (base32 "04w60fx3s3wlirmr65nsz6d7ig48j9fzimdr8kbdqv1g80ivdcq1")))) + (base32 "1fjldmhb9yg6yr3aq5ldvc8xwqw71ix4cdlr53xxckgwljjq7x10")))) (properties `((upstream-name . "celldex"))) (build-system r-build-system) (propagated-inputs From e437cf10a45e69b332234c13335db5dc7a4a07ff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:56 +0200 Subject: [PATCH 0666/1394] gnu: r-chromstardata: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-chromstardata): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a57cf52957a..3dd66890d71 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1274,14 +1274,13 @@ single-cell data or deconvolution of bulk RNA-seq.") (define-public r-chromstardata (package (name "r-chromstardata") - (version "1.16.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaRData" version 'experiment)) (sha256 - (base32 - "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab")))) + (base32 "1ajwnkibpi01c93nrplxhy6grw8jj5219g4pii4rkan4k5815kv1")))) (properties `((upstream-name . "chromstaRData"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/chromstaRData/") From 7a58c9af46041ee069d8143549431bcde08bc2f8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:56 +0200 Subject: [PATCH 0667/1394] gnu: r-copyhelper: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3dd66890d71..651bdec63d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1293,14 +1293,13 @@ chromstaR package.") (define-public r-copyhelper (package (name "r-copyhelper") - (version "1.6.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopyhelpeR" version 'experiment)) (sha256 - (base32 - "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) + (base32 "0klrnxck0q14birnpwzkiwmj77hwdn6gazvdg0lqn9y6j5mbkyx1")))) (properties `((upstream-name . "CopyhelpeR"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/CopyhelpeR/") From d24b0702b60e7052eabcd2f94b6682ad29b24c1d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:56 +0200 Subject: [PATCH 0668/1394] gnu: r-genelendatabase: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 651bdec63d1..48dd1b62317 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1316,14 +1316,13 @@ GenomicRanges Bioconductor package.") (define-public r-genelendatabase (package (name "r-genelendatabase") - (version "1.18.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) (sha256 - (base32 - "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) + (base32 "0p4rmd3qszsnyn47mfbk96zfa0bhpyyvsh4ma1ligjrsnmkicsaz")))) (properties `((upstream-name . "geneLenDataBase"))) (build-system r-build-system) From 4f2ac5f19f23be9b5a3bbf762111b0d4cf2f6d9d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:56 +0200 Subject: [PATCH 0669/1394] gnu: r-genomationdata: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-genomationdata): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 48dd1b62317..d17389e2ef1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1338,13 +1338,13 @@ genomes and gene ID formats, largely based on the UCSC table browser.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "genomationData" version 'experiment)) - (sha256 - (base32 - "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g")))) + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "genomationData" version 'experiment)) + (sha256 + (base32 "0ckdgmarndpz6r0y9sd4nmypzjgivj32w2890yl15xmxkx4397fh")))) (properties `((upstream-name . "genomationData"))) (build-system r-build-system) From 3ff4e48e85be24316756515ad4f4680079e14266 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:56 +0200 Subject: [PATCH 0670/1394] gnu: r-pasilla: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-pasilla): Update to 1.24.0. [propagated-inputs]: Remove r-biocstyle, r-knitr, and r-rmarkdown. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d17389e2ef1..8329c4feb92 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1364,16 +1364,16 @@ downloaded from Encode.") (define-public r-pasilla (package (name "r-pasilla") - (version "1.14.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "pasilla" version 'experiment)) - (sha256 - (base32 - "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pasilla" version 'experiment)) + (sha256 + (base32 "1vsxh7mv2krkbdqs5gsgjsxarjbll0bpyk94syrwh56z67n7jyib")))) (build-system r-build-system) - (propagated-inputs - (list r-biocstyle r-dexseq r-knitr r-rmarkdown)) + (propagated-inputs (list r-dexseq)) + (native-inputs (list r-knitr)) (home-page "https://www.bioconductor.org/packages/pasilla/") (synopsis "Data package with per-exon and per-gene read counts") (description "This package provides per-exon and per-gene read counts From 15e10974ef22940242623377e46fb3e56b56ae6e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:56 +0200 Subject: [PATCH 0671/1394] gnu: r-hsmmsinglecell: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8329c4feb92..f31879bbb67 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1385,13 +1385,13 @@ by Brooks et al., Genome Research 2011.") (define-public r-hsmmsinglecell (package (name "r-hsmmsinglecell") - (version "1.2.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) - (sha256 - (base32 - "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) + (sha256 + (base32 "12whx0pl9461xbak5r9zi6ggx5is8sk6mgrbjwlmx3mbr9am116v")))) (properties `((upstream-name . "HSMMSingleCell"))) (build-system r-build-system) From e06ee7a745ed82d349e111a103abacb957324042 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:56 +0200 Subject: [PATCH 0672/1394] gnu: r-all: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-all): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f31879bbb67..a60e621ac44 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1414,13 +1414,13 @@ resulting in a complete gene expression profile for each cell.") (define-public r-all (package (name "r-all") - (version "1.26.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "ALL" version 'experiment)) - (sha256 - (base32 - "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ALL" version 'experiment)) + (sha256 + (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z")))) (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs From c56b553e97777dccc2619b5c75525d745b2641e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:57 +0200 Subject: [PATCH 0673/1394] gnu: r-affydata: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-affydata): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a60e621ac44..e643513b897 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1438,14 +1438,13 @@ the form of an @code{exprSet} object.") (define-public r-affydata (package (name "r-affydata") - (version "1.32.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affydata" version 'experiment)) (sha256 - (base32 - "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) + (base32 "1d8ims7hks536v739r5hhfkkzyzqrf398aqal3hzyfm0psv15jbp")))) (properties `((upstream-name . "affydata"))) (build-system r-build-system) (propagated-inputs From 1c4d0fc9a9d3c324f930b04d6c230154db6da641 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:57 +0200 Subject: [PATCH 0674/1394] gnu: r-gagedata: Update to 2.34.0. * gnu/packages/bioconductor.scm (r-gagedata): Update to 2.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e643513b897..b4ce9d6f9e7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1460,13 +1460,13 @@ package @code{affy}.") (define-public r-gagedata (package (name "r-gagedata") - (version "2.28.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gageData" version 'experiment)) (sha256 - (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn")))) + (base32 "00s2aig9r0bvk45brc0shildrgl2z0i0k8xlvqc9h1s274nnslk9")))) (properties `((upstream-name . "gageData"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/gageData") From 9d538de266257307c0072253c001bb1302372596 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:57 +0200 Subject: [PATCH 0675/1394] gnu: r-curatedtcgadata: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.18.0. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4ce9d6f9e7..aa980ed9b41 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1486,14 +1486,13 @@ yeast are also included.") (define-public r-curatedtcgadata (package (name "r-curatedtcgadata") - (version "1.8.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) (sha256 - (base32 - "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) + (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr")))) (properties `((upstream-name . "curatedTCGAData"))) (build-system r-build-system) @@ -1504,6 +1503,7 @@ yeast are also included.") r-multiassayexperiment r-s4vectors r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/curatedTCGAData/") (synopsis "Curated data from The Cancer Genome Atlas") (description From 79158a5624a587395e36125ad5d0cc369c841af4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 15:16:57 +0200 Subject: [PATCH 0676/1394] gnu: r-tcgabiolinksgui-data: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aa980ed9b41..be946ae667d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1519,13 +1519,13 @@ across the entire multi-'omics experiment.") (define-public r-tcgabiolinksgui-data (package (name "r-tcgabiolinksgui-data") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment)) (sha256 - (base32 "08zmlvycq3jz1zy0715x9f21nf3465c51k7w2jq12sfbap36pmjm")))) + (base32 "1mb2z59acs1pi1gqvgjyh62wnmbxskc5l0p42gpjajsjip5x1x7g")))) (properties `((upstream-name . "TCGAbiolinksGUI.data"))) (build-system r-build-system) (native-inputs (list r-knitr)) From 66bfe558481a2431810d7a2d2436d06d6f8daab7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 28 May 2022 17:03:02 +0200 Subject: [PATCH 0677/1394] gnu: Add r-msdata. * gnu/packages/bioconductor.scm (r-msdata): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index be946ae667d..518224306f7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1361,6 +1361,29 @@ genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.") (license license:gpl3+))) +(define-public r-msdata + (package + (name "r-msdata") + (version "0.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "msdata" version 'experiment)) + (sha256 + (base32 "0nqb7d7fa9l15bxy3s9wmy2h79jb6ldwww0hzk5mifabacmzx691")))) + (properties `((upstream-name . "msdata"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/msdata") + (synopsis "Various Mass Spectrometry raw data example files") + (description + "This package provides Ion Trap positive ionization mode data in mzML file +format. It includes a subset from 500-850 m/z and 1190-1310 seconds, +including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex +III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5; +LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example +files for various search engines.") + (license license:gpl2+))) + (define-public r-pasilla (package (name "r-pasilla") From b04ae71defe0bd2a5fbd2df07d55cfe3eb40cba9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 28 May 2022 23:03:45 +0200 Subject: [PATCH 0678/1394] services: herd: Add 'wait-for-service'. * gnu/services/herd.scm (wait-for-service): New procedure. --- gnu/services/herd.scm | 36 +++++++++++++++++++++++++++++++++++- 1 file changed, 35 insertions(+), 1 deletion(-) diff --git a/gnu/services/herd.scm b/gnu/services/herd.scm index 80d08f849e1..a7c845b4b04 100644 --- a/gnu/services/herd.scm +++ b/gnu/services/herd.scm @@ -58,7 +58,8 @@ load-services/safe start-service stop-service - restart-service)) + restart-service + wait-for-service)) ;;; Commentary: ;;; @@ -313,6 +314,39 @@ when passed a service with an already-registered name." (with-shepherd-action name ('restart) result result)) +(define* (wait-for-service name #:key (timeout 20)) + "Wait for the service providing NAME, a symbol, to be up and running, and +return its \"running value\". Give up after TIMEOUT seconds and raise a +'&shepherd-error' exception. Raise a '&service-not-found-error' exception +when NAME is not found." + (define (relevant-service? service) + (memq name (live-service-provision service))) + + (define start + (car (gettimeofday))) + + ;; Note: As of Shepherd 0.9.1, we cannot just call the 'start' method and + ;; wait for it: it would spawn an additional elogind process. Thus, poll. + (let loop ((attempts 0)) + (define services + (current-services)) + + (define now + (car (gettimeofday))) + + (when (>= (- now start) timeout) + (raise (condition (&shepherd-error)))) ;XXX: better exception? + + (match (find relevant-service? services) + (#f + (raise (condition (&service-not-found-error + (service name))))) + (service + (or (live-service-running service) + (begin + (sleep 1) + (loop (+ attempts 1)))))))) + ;; Local Variables: ;; eval: (put 'alist-let* 'scheme-indent-function 2) ;; eval: (put 'with-shepherd 'scheme-indent-function 1) From f383838a091835b86d4a6ff1c256498bcdecadad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 27 May 2022 22:41:55 +0200 Subject: [PATCH 0679/1394] services: elogind: When started by dbus-daemon, wait for the Shepherd service. Fixes . Previously shepherd and dbus-daemon would race to start elogind. In some cases (for instance if one logs in quickly enough on the tty), dbus-daemon would "win" and start elogind before shepherd has had a chance to do it. Consequently, shepherd would fail to start elogind and mark it as stopped and disabled, in turn preventing services that depend on it such as 'xorg-server' from starting. * gnu/services/desktop.scm (elogind-dbus-service): Rewrite to refer to a wrapper that waits for the 'elogind' Shepherd service. --- gnu/services/desktop.scm | 58 +++++++++++++++++++++++++++++++++++++--- 1 file changed, 54 insertions(+), 4 deletions(-) diff --git a/gnu/services/desktop.scm b/gnu/services/desktop.scm index 24fd43a207c..0499071436a 100644 --- a/gnu/services/desktop.scm +++ b/gnu/services/desktop.scm @@ -1075,10 +1075,60 @@ include the @command{udisksctl} command, part of UDisks, and GNOME Disks." ("HybridSleepMode" (sleep-list elogind-hybrid-sleep-mode)))) (define (elogind-dbus-service config) - (list (wrapped-dbus-service (elogind-package config) - "libexec/elogind/elogind" - `(("ELOGIND_CONF_FILE" - ,(elogind-configuration-file config)))))) + "Return a @file{org.freedesktop.login1.service} file that tells D-Bus how to +\"start\" elogind. In practice though, our elogind is started when booting by +shepherd. Thus, the @code{Exec} line of this @file{.service} file does not +explain how to start elogind; instead, it spawns a wrapper that waits for the +@code{elogind} shepherd service. This avoids a race condition where both +@command{shepherd} and @command{dbus-daemon} would attempt to start elogind." + ;; For more info on the elogind startup race, see + ;; . + + (define elogind + (elogind-package config)) + + (define wrapper + (program-file "elogind-dbus-shepherd-sync" + (with-imported-modules '((gnu services herd)) + #~(begin + (use-modules (gnu services herd) + (srfi srfi-34)) + + (guard (c ((service-not-found-error? c) + (format (current-error-port) + "no elogind shepherd service~%") + (exit 1)) + ((shepherd-error? c) + (format (current-error-port) + "elogind shepherd service not \ +started~%") + (exit 2))) + (wait-for-service 'elogind)))))) + + (define build + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils) + (ice-9 match)) + + (define service-directory + "/share/dbus-1/system-services") + + (mkdir-p (dirname (string-append #$output service-directory))) + (copy-recursively (string-append #$elogind service-directory) + (string-append #$output service-directory)) + (symlink (string-append #$elogind "/etc") ;for etc/dbus-1 + (string-append #$output "/etc")) + + ;; Replace the "Exec=" line of the 'org.freedesktop.login1.service' + ;; file with one that refers to WRAPPER instead of elogind. + (match (find-files #$output "\\.service$") + ((file) + (substitute* file + (("Exec[[:blank:]]*=.*" _) + (string-append "Exec=" #$wrapper "\n")))))))) + + (list (computed-file "elogind-dbus-service-wrapper" build))) (define (pam-extension-procedure config) "Return an extension for PAM-ROOT-SERVICE-TYPE that ensures that all the PAM From 371a83b764c4993d198666e1674454eecbefcdf1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 27 May 2022 10:07:26 +0200 Subject: [PATCH 0680/1394] scripts/import: Use pretty printer from (guix scripts style). * guix/scripts/import.scm (guix-import): Use pretty-print-with-comments. (newline-rewriting-port): Remove procedure. --- guix/scripts/import.scm | 39 +++------------------------------------ 1 file changed, 3 insertions(+), 36 deletions(-) diff --git a/guix/scripts/import.scm b/guix/scripts/import.scm index fa79f3211ec..62aa7bdbc54 100644 --- a/guix/scripts/import.scm +++ b/guix/scripts/import.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2012, 2013, 2014, 2020, 2021 Ludovic Courtès ;;; Copyright © 2014 David Thompson ;;; Copyright © 2018 Kyle Meyer -;;; Copyright © 2019 Ricardo Wurmus +;;; Copyright © 2019, 2022 Ricardo Wurmus ;;; Copyright © 2021 Simon Tournier ;;; Copyright © 2021 Xinglu Chen ;;; Copyright © 2022 Philip McGrath @@ -25,6 +25,7 @@ (define-module (guix scripts import) #:use-module (guix ui) #:use-module (guix scripts) + #:use-module (guix scripts style) #:use-module (guix utils) #:use-module (srfi srfi-1) #:use-module (srfi srfi-11) @@ -32,41 +33,9 @@ #:use-module (srfi srfi-37) #:use-module (ice-9 format) #:use-module (ice-9 match) - #:use-module (ice-9 pretty-print) #:export (%standard-import-options guix-import)) - -;;; -;;; Helper. -;;; - -(define (newline-rewriting-port output) - "Return an output port that rewrites strings containing the \\n escape -to an actual newline. This works around the behavior of `pretty-print' -and `write', which output these as \\n instead of actual newlines, -whereas we want the `description' field to contain actual newlines -rather than \\n." - (define (write-string str) - (let loop ((chars (string->list str))) - (match chars - (() - #t) - ((#\\ #\n rest ...) - (newline output) - (loop rest)) - ((chr rest ...) - (write-char chr output) - (loop rest))))) - - (make-soft-port (vector (cut write-char <>) - write-string - (lambda _ #t) ; flush - #f - (lambda _ #t) ; close - #f) - "w")) - ;;; ;;; Command line options. @@ -119,9 +88,7 @@ Run IMPORTER with ARGS.\n")) ((importer args ...) (if (member importer importers) (let ((print (lambda (expr) - (pretty-print expr (newline-rewriting-port - (current-output-port)) - #:max-expr-width 80)))) + (pretty-print-with-comments (current-output-port) expr)))) (match (apply (resolve-importer importer) args) ((and expr (or ('package _ ...) ('let _ ...) From a4b90009c7c3987417f2ef1bd06dc8dacd543249 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Fri, 27 May 2022 18:40:12 +0200 Subject: [PATCH 0681/1394] gnu: Add r-googlevis. * gnu/packages/cran.scm (r-googlevis): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0fdcfb3cb93..95de77e3a76 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -402,6 +402,33 @@ Distance (EMD).") (description "This package lets you manage Google Drive files from R.") (license license:expat))) +(define-public r-googlevis + (package + (name "r-googlevis") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "googleVis" version)) + (sha256 + (base32 "1s82xcs6zrlmnhay764bspzwvabfyi35nq6fwdrrk3v79q13c5jz")))) + (properties `((upstream-name . "googleVis"))) + (build-system r-build-system) + (propagated-inputs (list r-jsonlite)) + (native-inputs (list r-knitr)) + (home-page "https://mages.github.io/googleVis/") + (synopsis "R interface to Google Charts") + (description + "The @code{googleVis} package provides an interface between R and the Google +Charts API. Google Charts offer interactive charts which can be embedded into +web pages. The functions of the @code{googleVis} package allow the user to +visualise data stored in R data frames with Google Charts without uploading +the data to Google. The output of a @code{googleVis} function is HTML code +that contains the data and references to JavaScript functions hosted by +Google. @code{googleVis} makes use of the internal R HTTP server to display +the output locally.") + (license license:gpl2+))) + (define-public r-guix-install (package (name "r-guix-install") From add551f651cf6c2359baf5493c7a9d920b7d511d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 29 May 2022 00:18:48 +0200 Subject: [PATCH 0682/1394] gnu: pigx-chipseq: Fix build. * gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build system. --- gnu/packages/bioinformatics.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 239a8c13df1..ced3b642e99 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11094,6 +11094,15 @@ expression report comparing samples in an easily configurable manner.") (modify-phases %standard-phases (add-before 'bootstrap 'autoreconf (lambda _ + ;; This was fixed in commit + ;; 0b1c9f7f2e4d0ff601f1de95ab8b2953f4d5dbc7, but there is no + ;; release with this fix. + (call-with-output-file "VERSION" + (lambda (port) (display ,version port))) + ;; See https://github.com/BIMSBbioinfo/pigx_chipseq/issues/176 + (substitute* "m4/ax_r_package.m4" + (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") + "if(system.file(package=\"PKG\") == \"\")")) (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ From b64f4a12451062d7436a0463e6c50d1cef4a75ac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 29 May 2022 00:29:19 +0200 Subject: [PATCH 0683/1394] gnu: pigx-scrnaseq: Fix build. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Add autoreconf step to work around m4 macro bug and missing VERSION file. [native-inputs]: Add autoconf and automake. --- gnu/packages/bioinformatics.scm | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ced3b642e99..1b118908da0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11258,8 +11258,20 @@ methylation and segmentation.") "1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885")))) (build-system gnu-build-system) (arguments - '(#:phases + `(#:phases (modify-phases %standard-phases + (add-before 'bootstrap 'autoreconf + (lambda _ + ;; This was fixed in commit + ;; c4ac067438ae9312b5786a72e2bfb3d795e3ec8a, but there is no + ;; release with this fix. + (call-with-output-file "VERSION" + (lambda (port) (display ,version port))) + ;; https://github.com/BIMSBbioinfo/pigx_scrnaseq/issues/59 + (substitute* "m4/ax_r_package.m4" + (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") + "if(system.file(package=\"PKG\") == \"\")")) + (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-additional-environment-variables (lambda _ ;; Needed because of loompy @@ -11308,6 +11320,8 @@ methylation and segmentation.") r-singlecellexperiment r-stringr r-yaml)) + (native-inputs + (list autoconf automake)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") (description From df3e5cfa05c45439fee30375cde21f4c3d32e26b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 29 May 2022 00:34:29 +0200 Subject: [PATCH 0684/1394] gnu: pigx-bsseq: Fix build. * gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system in 'autoreconf phase. --- gnu/packages/bioinformatics.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1b118908da0..0945bddbe74 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11191,6 +11191,15 @@ in an easily configurable manner.") (modify-phases %standard-phases (add-before 'bootstrap 'autoreconf (lambda _ + ;; This was fixed in commit + ;; d56ac732524da659afbbb0972f7a87fa178ae58e, but there is no + ;; release with this fix. + (call-with-output-file "VERSION" + (lambda (port) (display ,version port))) + ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/181 + (substitute* "m4/ax_r_package.m4" + (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") + "if(system.file(package=\"PKG\") == \"\")")) (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ From cb115ba7220d7db12ccb761a1261a778ec583ae2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 29 May 2022 00:39:19 +0200 Subject: [PATCH 0685/1394] gnu: pigx-sars-cov-2: Fix build. * gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add 'autoreconf phase to patch build system. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0945bddbe74..1d8397c1aa5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11359,6 +11359,13 @@ based methods.") `(#:tests? #f ;requires huge kraken database #:phases (modify-phases %standard-phases + (add-before 'bootstrap 'autoreconf + (lambda _ + ;; https://github.com/BIMSBbioinfo/pigx_sars-cov-2/issues/123 + (substitute* "m4/ax_r_package.m4" + (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") + "if(system.file(package=\"PKG\") == \"\")")) + (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) From a5f4c03df18f8f76d570b996399a4adf0fc297c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Fri, 27 May 2022 18:40:13 +0200 Subject: [PATCH 0686/1394] gnu: Add r-scmap. * gnu/packages/bioconductor.scm (r-scmap): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4baa80dcb13..19621171322 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5049,6 +5049,48 @@ includes methods formerly found in the scran package, and the new fast and comprehensive scDblFinder method.") (license license:gpl3))) +(define-public r-scmap + (package + (name "r-scmap") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scmap" version)) + (sha256 + (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l")))) + (properties `((upstream-name . "scmap"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-dplyr + r-e1071 + r-ggplot2 + r-googlevis + r-matrixstats + r-proxy + r-randomforest + r-rcpp + r-rcpparmadillo + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hemberg-lab/scmap") + (synopsis "Tool for unsupervised projection of single cell RNA-seq data") + (description + "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the +composition of complex tissues since the technology allows researchers to +define cell-types using unsupervised clustering of the transcriptome. +However, due to differences in experimental methods and computational +analyses, it is often challenging to directly compare the cells identified in +two different experiments. @code{scmap} is a method for projecting cells from +a scRNA-seq experiment onto the cell-types or individual cells identified in a +different experiment.") + (license license:gpl3))) + (define-public r-seqlogo (package (name "r-seqlogo") From 926fcb488b756fb5d6c4c129c4348650919e5835 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 29 May 2022 08:46:17 +0300 Subject: [PATCH 0687/1394] gnu: clang-from-llvm: Fix building on riscv64-linux. * gnu/packages/llvm.scm (clang-from-llvm)[arguments]: When building for riscv64-linux add configure-flags and make-flags to ensure linking with '-latomic'. --- gnu/packages/llvm.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index aedf039ff41..d3b16f27594 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -216,7 +216,15 @@ given PATCHES. When TOOLS-EXTRA is given, it must point to the ;; Use a sane default include directory. (string-append "-DC_INCLUDE_DIRS=" (assoc-ref %build-inputs "libc") - "/include")) + "/include") + ,@(if (target-riscv64?) + (list "-DLIBOMP_LIBFLAGS=-latomic" + "-DCMAKE_SHARED_LINKER_FLAGS=-latomic") + `())) + + ,@(if (target-riscv64?) + `(#:make-flags '("LDFLAGS=-latomic")) + '()) ;; Don't use '-g' during the build to save space. #:build-type "Release" From 89e926201234a4fe5474dc97504474323dd03f0a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 29 May 2022 11:44:09 +0200 Subject: [PATCH 0688/1394] gnu: r-bsgenome-hsapiens-ucsc-hg19-masked: Update to 1.3.993. * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): Update to 1.3.993. --- gnu/packages/bioconductor.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 518224306f7..59b921af824 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -358,14 +358,14 @@ provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") (define-public r-bsgenome-hsapiens-ucsc-hg19-masked (package (name "r-bsgenome-hsapiens-ucsc-hg19-masked") - (version "1.3.99") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked" - version 'annotation)) - (sha256 - (base32 - "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) + (version "1.3.993") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked" + version 'annotation)) + (sha256 + (base32 "19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) (build-system r-build-system) From b456086c65976cc01593b9547418a1449328366b Mon Sep 17 00:00:00 2001 From: Rene Saavedra Date: Fri, 20 May 2022 13:13:49 -0500 Subject: [PATCH 0689/1394] gnu: apostrophe: Build with correct webkitgtk. * gnu/packages/gnome.scm (apostrophe)[inputs]: Replace webkitgtk with webkitgtk-with-libsoup2. Signed-off-by: Efraim Flashner --- gnu/packages/gnome.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 4a90245bff5..7868063a05e 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -12027,7 +12027,7 @@ GTK+. It integrates well with the GNOME desktop environment.") python-pygobject python-pyenchant python-pypandoc - webkitgtk)) + webkitgtk-with-libsoup2)) (native-inputs (list gettext-minimal `(,glib "bin") From d540e686ef0f1e40962be144388784da25cf7893 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 24 May 2022 10:52:20 +0300 Subject: [PATCH 0690/1394] gnu: Add pbuilder. * gnu/packages/debian.scm (pbuilder): New variable. --- gnu/packages/debian.scm | 151 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 150 insertions(+), 1 deletion(-) diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm index 03a1778a364..5ff09393b9b 100644 --- a/gnu/packages/debian.scm +++ b/gnu/packages/debian.scm @@ -36,10 +36,13 @@ #:use-module (gnu packages gettext) #:use-module (gnu packages gnupg) #:use-module (gnu packages guile) + #:use-module (gnu packages linux) + #:use-module (gnu packages man) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) - #:use-module (gnu packages wget)) + #:use-module (gnu packages wget) + #:use-module (srfi srfi-26)) (define-public debian-archive-keyring (package @@ -418,6 +421,152 @@ other apt sources typically provided by open source developers.") handling the installation and removal of Debian software packages.") (license license:gpl2+))) +(define-public pbuilder + (package + (name "pbuilder") + (version "0.231") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://salsa.debian.org/pbuilder-team/pbuilder.git/") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0z6f1fgcrkfql9ayc3d0nxra2y6cn91xd5lvr0hd8gdlp9xdvxbc")))) + (build-system gnu-build-system) + (arguments + (list + #:modules `((guix build gnu-build-system) + (guix build utils) + (srfi srfi-26)) + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; no configure script + (add-after 'unpack 'patch-source + (lambda* (#:key inputs outputs #:allow-other-keys) + + ;; Documentation requires tldp-one-page.xsl + (substitute* "Makefile" + ((".*-C Documentation.*") "")) + + ;; Don't create #$output/var/cache/pbuilder/... + (substitute* '("Makefile" + "pbuildd/Makefile") + ((".*/var/cache/pbuilder.*") "")) + + ;; Find the correct fallback location. + (substitute* '("pbuilder-checkparams" + "pbuilder-loadconfig" + "pbuilder-satisfydepends-apt" + "pbuilder-satisfydepends-aptitude" + "pbuilder-satisfydepends-classic" + "t/test_pbuilder-satisfydepends-classic") + (("\\$PBUILDER_ROOT(/usr)?") #$output)) + + ;; Some hardcoded paths + (substitute* '("debuild-pbuilder" + "pbuilder" + "pbuilder-buildpackage" + "pbuilderrc" + "pdebuild" + "pdebuild-checkparams" + "pdebuild-internal") + (("/usr/lib/pbuilder") + (string-append #$output "/lib/pbuilder"))) + (substitute* "pbuildd/buildd-config.sh" + (("/usr/share/doc/pbuilder") + (string-append #$output "/share/doc/pbuilder"))) + (substitute* "pbuilder-unshare-wrapper" + (("/(s)?bin/ifconfig") "ifconfig") + (("/(s)?bin/ip") (search-input-file inputs "/sbin/ip"))) + (substitute* "Documentation/Makefile" + (("/usr") "")) + + ;; Ensure PATH works both in Guix and within the Debian chroot. + (substitute* "pbuilderrc" + (("PATH=\"/usr/sbin:/usr/bin:/sbin:/bin") + "PATH=\"$PATH:/usr/sbin:/usr/bin:/sbin:/bin")))) + (add-after 'install 'create-etc-pbuilderrc + (lambda* (#:key outputs #:allow-other-keys) + (with-output-to-file (string-append #$output "/etc/pbuilderrc") + (lambda () + (format #t "# A couple of presets to make this work more smoothly.~@ + MIRRORSITE=\"http://deb.debian.org/debian\"~@ + if [ -r /run/setuid-programs/sudo ]; then~@ + PBUILDERROOTCMD=\"/run/setuid-programs/sudo -E\"~@ + fi~@ + PBUILDERSATISFYDEPENDSCMD=\"~a/lib/pbuilder/pbuilder-satisfydepends-apt\"~%" + #$output))))) + (add-after 'install 'install-manpages + (lambda* (#:key outputs #:allow-other-keys) + (let ((man (string-append #$output "/share/man/"))) + (install-file "debuild-pbuilder.1" (string-append man "man1")) + (install-file "pdebuild.1" (string-append man "man1")) + (install-file "pbuilder.8" (string-append man "man8")) + (install-file "pbuilderrc.5" (string-append man "man5"))))) + (add-after 'install 'wrap-programs + (lambda* (#:key inputs outputs #:allow-other-keys) + (for-each + (lambda (file) + (wrap-script file + `("PATH" ":" prefix + ,(map (compose dirname (cut search-input-file inputs <>)) + (list "/bin/cut" + "/bin/dpkg" + "/bin/grep" + "/bin/perl" + "/bin/sed" + "/bin/which" + "/sbin/debootstrap"))))) + (cons* + (string-append #$output "/bin/pdebuild") + (string-append #$output "/sbin/pbuilder") + (find-files (string-append #$output "/lib/pbuilder")))))) + ;; Move the 'check phase to after 'install. + (delete 'check) + (add-after 'validate-runpath 'check + (assoc-ref %standard-phases 'check))) + #:make-flags + ;; No PREFIX, use DESTDIR instead. + #~(list (string-append "DESTDIR=" #$output) + (string-append "SYSCONFDIR=" #$output "/etc") + (string-append "BINDIR=" #$output "/bin") + (string-append "PKGLIBDIR=" #$output "/lib/pbuilder") + (string-append "SBINDIR=" #$output "/sbin") + (string-append "PKGDATADIR=" #$output "/share/pbuilder") + (string-append "EXAMPLEDIR=" #$output "/share/doc/pbuilder/examples") + "PBUILDDDIR=/share/doc/pbuilder/examples/pbuildd/"))) + (inputs + (list dpkg + debootstrap + grep + guile-3.0 ; for wrap-script + iproute + perl + which)) + (native-inputs + (list man-db + util-linux)) + (home-page "https://pbuilder-team.pages.debian.net/pbuilder/") + (synopsis "Personal package builder for Debian packages") + (description + "@code{pbuilder} is a personal package builder for Debian packages. +@itemize +@item@code{pbuilder} constructs a chroot system, and builds a package inside the +chroot. It is an ideal system to use to check that a package has correct +build-dependencies. It uses @code{apt} extensively, and a local mirror, or a +fast connection to a Debian mirror is ideal, but not necessary. +@item@code{pbuilder create} uses debootstrap to create a chroot image. +@item@code{pbuilder update} updates the image to the current state of +testing/unstable/whatever. +@item@code{pbuilder build} takes a @code{*.dsc} file and builds a binary in the +chroot image. +@item@code{pdebuild} is a wrapper for Debian Developers, to allow running +@code{pbuilder} just like @code{debuild}, as a normal user. +@end itemize") + (license license:gpl2+))) + (define-public reprepro (package (name "reprepro") From 69af8a68375006e09489899f89f37e6f6d693449 Mon Sep 17 00:00:00 2001 From: cage Date: Fri, 27 May 2022 20:04:33 +0200 Subject: [PATCH 0691/1394] gnu: telescope: Update to 0.8.1. * gnu/packages/web-browsers.scm (telescope): Update to 0.8.1. [home-page]: Update to new upstream home-page. Signed-off-by: Efraim Flashner --- gnu/packages/web-browsers.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index 01d71324ba5..a98eb849a00 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -923,14 +923,14 @@ interface.") (define-public telescope (package (name "telescope") - (version "0.7.1") + (version "0.8.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/omar-polo/telescope/releases/download/" version "/telescope-" version ".tar.gz")) (sha256 - (base32 "055iqld99l4jshs10mhl2ml0p74wcyyv5kxjy8izzysw9lnkjjb5")))) + (base32 "1fblm3mjddhjmcj1c065n9440n72ld037bdjdlyk1fpwd240m1pa")))) (build-system gnu-build-system) (arguments `(#:tests? #f)) ;no tests @@ -938,7 +938,7 @@ interface.") (list gettext-minimal pkg-config)) (inputs (list libevent libressl ncurses)) - (home-page "https://git.omarpolo.com/telescope/about/") + (home-page "https://telescope.omarpolo.com/") (synopsis "Gemini client with a terminal interface") (description "Telescope is a w3m-like browser for Gemini.") (license license:x11))) From c62be7d53041ce03054371fb320688c6f5800596 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 29 May 2022 16:23:48 +0300 Subject: [PATCH 0692/1394] gnu: wgetpaste: Add missing input. * gnu/packages/wget.scm (wgetpaste)[inputs]: Add bash-minimal. --- gnu/packages/wget.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index 7c8c961dfb3..95baed25a76 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -24,6 +24,7 @@ (define-module (gnu packages wget) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) + #:use-module (gnu packages bash) #:use-module (gnu packages compression) #:use-module (gnu packages documentation) #:use-module (gnu packages gnunet) @@ -124,7 +125,7 @@ in downloaded documents to relative links.") #t)))) #:tests? #f)) ; no test target (inputs - (list wget xclip)) + (list bash-minimal wget xclip)) (home-page "https://wgetpaste.zlin.dk/") (synopsis "Script that automates pasting to a number of pastebin services") (description From 50970a28b768c98ed45ed0201e201f5da8d993e4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 29 May 2022 16:25:35 +0300 Subject: [PATCH 0693/1394] gnu: wgetpaste: Remove trailing #t from phases. * gnu/packages/wget.scm (wgetpaste)[arguments]: Remove trailing #t from phases. --- gnu/packages/wget.scm | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index 95baed25a76..a2131785a76 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -100,16 +100,14 @@ in downloaded documents to relative links.") (substitute* "wgetpaste" ;; dpaste blocks Tor users. Use a better default. (("DEFAULT_SERVICE:-dpaste") - "DEFAULT_SERVICE-bpaste")) - #t)) + "DEFAULT_SERVICE-bpaste")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin")) (zsh (string-append out "/share/zsh/site-functions"))) (install-file "wgetpaste" bin) - (install-file "_wgetpaste" zsh) - #t))) + (install-file "_wgetpaste" zsh)))) (add-after 'install 'wrap-program ;; /bin/wgetpaste prides itself on relying only on the following ;; inputs, and doesn't need to execute arbitrary commands, so @@ -121,8 +119,7 @@ in downloaded documents to relative links.") ,(delete-duplicates (map (lambda (command) (dirname (which command))) (list "bash" "mktemp" "sed" "sort" "tee" "tr" - "wget" "xclip"))))) - #t)))) + "wget" "xclip"))))))))) #:tests? #f)) ; no test target (inputs (list bash-minimal wget xclip)) From e4fe344a5c64063f8201a637973aa366a3ded200 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 29 May 2022 16:29:36 +0300 Subject: [PATCH 0694/1394] gnu: nmap: Honor tests? flag. * gnu/packages/admin.scm (nmap)[arguments]: In custom 'check phase honor the #:tests? flag. --- gnu/packages/admin.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index af75dee6975..4e655551bd8 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -3191,10 +3191,12 @@ rules is done with the @code{auditctl} utility.") (,(python-path ndiff))))))) ;; These are the tests that do not require network access. (replace 'check - (lambda _ (invoke "make" - "check-nse" - "check-ndiff" - "check-dns")))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "make" + "check-nse" + "check-ndiff" + "check-dns"))))) ;; Nmap can't cope with out-of-source building. #:out-of-source? #f)) (home-page "https://nmap.org/") From 46ed423e286acdd61b8a1325a106a64e9efcfe19 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 29 May 2022 16:31:59 +0300 Subject: [PATCH 0695/1394] gnu: git-annex: Update to 10.20220525. * gnu/packages/haskell-apps.scm (git-annex): Update to 10.20220525. --- gnu/packages/haskell-apps.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/haskell-apps.scm b/gnu/packages/haskell-apps.scm index 5579ef58eab..572e9a062f0 100644 --- a/gnu/packages/haskell-apps.scm +++ b/gnu/packages/haskell-apps.scm @@ -304,14 +304,14 @@ to @code{cabal repl}).") (define-public git-annex (package (name "git-annex") - (version "10.20220504") + (version "10.20220525") (source (origin (method url-fetch) (uri (string-append "https://hackage.haskell.org/package/" "git-annex/git-annex-" version ".tar.gz")) (sha256 - (base32 "10pp58b7glwi1yckrij49d1iq99pc4dpkkbkb1qqiif9dr9672f3")))) + (base32 "1nrwa4qm3xkr11x0b0c1mx052zhd7lz9w97xf0ycdkhsyc6vbiy6")))) (build-system haskell-build-system) (arguments `(#:configure-flags From 1ed40eee39240462b1454e75dedf74408c1c3c78 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 29 May 2022 16:31:59 +0300 Subject: [PATCH 0696/1394] gnu: mutt: Update to 2.2.5. * gnu/packages/mail.scm (mutt): Update to 2.2.5. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 2b6c5ebb8f5..b44ba90582f 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -556,7 +556,7 @@ aliasing facilities to work just as they would on normal mail.") (define-public mutt (package (name "mutt") - (version "2.2.4") + (version "2.2.5") (source (origin (method url-fetch) (uri (list @@ -566,7 +566,7 @@ aliasing facilities to work just as they would on normal mail.") version ".tar.gz"))) (sha256 (base32 - "0q70qrsjvmkfns1qxc0il2rlmfjwzbmfg89zlch0iqghpyz7c9xq")) + "0ivyfld4a4sfzsdiaajqiarvfx4i85g1smbb2b5dqjkrb48pi2zz")) (patches (search-patches "mutt-store-references.patch")))) (build-system gnu-build-system) (inputs From 9cd22702b87f873f7e307c99b406fb758e5a307c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 29 May 2022 16:31:59 +0300 Subject: [PATCH 0697/1394] gnu: wget: Update to 1.21.3. * gnu/packages/wget.scm (wget): Update to 1.21.3. --- gnu/packages/wget.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index a2131785a76..960569f3edd 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -45,7 +45,7 @@ (define-public wget (package (name "wget") - (version "1.21.1") + (version "1.21.3") (source (origin (method url-fetch) @@ -53,7 +53,7 @@ version ".tar.lz")) (sha256 (base32 - "1bchzkacjsc5c0x01ngaana9fs5j12wfw1c8qxps1yp68x9vx6yv")))) + "19afmyr1i3zwdwr8wkyz8q6z5764ik3dm87as194g78l8xggplnv")))) (build-system gnu-build-system) (inputs (list gnutls libidn2 libpsl)) From e8b2219152ae6afed8a7fb5d81759ae6a9e32cec Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 29 May 2022 19:26:47 +0300 Subject: [PATCH 0698/1394] gnu: lagrange: Update to 1.13.6. * gnu/packages/web-browsers.scm (lagrange): Update to 1.13.6. [source]: Adjust snippet to remove another bundled library. --- gnu/packages/web-browsers.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index a98eb849a00..5ae44147ef3 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -707,7 +707,7 @@ is fully configurable and extensible in Common Lisp.") (define-public lagrange (package (name "lagrange") - (version "1.12.1") + (version "1.13.6") (source (origin (method url-fetch) @@ -715,13 +715,14 @@ is fully configurable and extensible in Common Lisp.") (string-append "https://git.skyjake.fi/skyjake/lagrange/releases/" "download/v" version "/lagrange-" version ".tar.gz")) (sha256 - (base32 "10v4bp5h1qq24by61yw52rr13m23smfj2whxfzcxc34qgsdjsd4a")) + (base32 "19xaw6lspl4mjx1wls0s15l97dzfkv20gph652yzwk6ia3ly92bs")) (modules '((guix build utils))) (snippet '(begin ;; TODO: unbundle fonts. (delete-file-recursively "lib/fribidi") - (delete-file-recursively "lib/harfbuzz"))))) + (delete-file-recursively "lib/harfbuzz") + (delete-file-recursively "lib/sealcurses"))))) (build-system cmake-build-system) (arguments `(#:tests? #false ;no tests From 92a83f38b50535694c2b62e17aa4a509b0a63a65 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sun, 29 May 2022 21:29:43 +0200 Subject: [PATCH 0699/1394] gnu: python-ua-parser: Update to 0.10.0. * gnu/packages/python-xyz.scm (python-ua-parser): Update to 0.10.0. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index fe1896efca5..58599304e55 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9751,14 +9751,14 @@ toolkit. Use it to build trees of widgets.") (define-public python-ua-parser (package (name "python-ua-parser") - (version "0.8.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (pypi-uri "ua-parser" version)) (sha256 (base32 - "1jwdf58rhchjzzrad405pviv0iq24xa2xmmmdgcm2c8s6b4wzfwp")))) + "0csh307zfz666kkk5idrw3crj1x8q8vsqgwqil0r1n1hs4p7ica7")))) (build-system python-build-system) (arguments `(#:tests? #f)) ;no test suite in release From 31a9d8677c86c4fcccecc3f0eadc373904a0f27c Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sun, 29 May 2022 21:30:45 +0200 Subject: [PATCH 0700/1394] gnu: python-user-agents: Update to 2.2.0. * gnu/packages/python-xyz.scm (python-user-agents): Update to 2.2.0. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 58599304e55..38c5fbb8082 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9776,14 +9776,14 @@ toolkit. Use it to build trees of widgets.") (define-public python-user-agents (package (name "python-user-agents") - (version "1.1.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (pypi-uri "user-agents" version)) (sha256 (base32 - "0fc00cd3j8dahq1zzn8pkgfgd7lq37bp2scmdma2n1c049vicgb4")))) + "09mddriffm9rkwr30081fy9n3cn976ms8pwc8p8hhlxnilbjavfk")))) (build-system python-build-system) (arguments `(#:tests? #f)) ;missing devices.json test file in release From d1f4b6dc8326f2d99c3692f109b2ce5c608d53bc Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sun, 29 May 2022 22:19:52 +0200 Subject: [PATCH 0701/1394] gnu: python-translate-toolkit: Update to 3.6.2. * gnu/packages/python-xyz.scm (python-translate-toolkit): Update to 3.6.2. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 38c5fbb8082..acd5954fb6e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20802,13 +20802,13 @@ while only declaring the test-specific fields.") (define-public python-translate-toolkit (package (name "python-translate-toolkit") - (version "3.5.1") + (version "3.6.2") (source (origin (method url-fetch) (uri (pypi-uri "translate-toolkit" version ".tar.gz")) (sha256 - (base32 "020pp7pbpnavxd41z90vyzzx06ci57mx9drkgbsb89wxxx4gal9v")))) + (base32 "0m4cpsp7x7h5m5agg4ybscf7y86wla46q2lvxpi2myplb6qlgcli")))) (build-system python-build-system) (native-inputs (list python-pytest python-sphinx)) From 98e2f4fbebb8b08784401e2095123fcd3d3a32cb Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 12 May 2022 14:07:40 +0200 Subject: [PATCH 0702/1394] gnu: openjdk: Update to 17.0.3. * gnu/packages/java.scm (openjdk17): Update to 17.0.3. --- gnu/packages/java.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 36baefaa7a8..336e84e3e5e 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -2252,7 +2252,7 @@ new Date();")) (package (inherit openjdk16) (name "openjdk") - (version "17.0.2") + (version "17.0.3") (source (origin (method git-fetch) (uri (git-reference @@ -2261,7 +2261,7 @@ new Date();")) (file-name (git-file-name name version)) (sha256 (base32 - "0zwv5pnh7rb7a6689jlhjfcc92bsiy0xbhdxyj93096ah4n3hqhj")) + "0slmd6ww947gxpp4yr2wmr5z975bg86qh7zqfp2radf2q77ql65b")) (patches (search-patches "openjdk-15-xcursor-no-dynamic.patch")))) (native-inputs From 40530ffd15ece6ec610a43221293010fe3b9234b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 29 May 2022 22:58:56 +0200 Subject: [PATCH 0703/1394] store: Record cache lookups in 'references/cached'. * guix/store.scm (references/cached): Add call to 'record-cache-lookup!'. --- guix/store.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/guix/store.scm b/guix/store.scm index 82fca14cd90..efba07bdcdc 100644 --- a/guix/store.scm +++ b/guix/store.scm @@ -1840,8 +1840,10 @@ This is a mutating version that should be avoided. Prefer the functional (define (references/cached store item) "Like 'references', but cache results." - (let ((cache (store-connection-cache store %reference-cache-id))) - (match (vhash-assoc item cache) + (let* ((cache (store-connection-cache store %reference-cache-id)) + (value (vhash-assoc item cache))) + (record-cache-lookup! %reference-cache-id value cache) + (match value ((_ . references) references) (#f From 3d1b2bc740b880c474ee3b178d078a7222315c74 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Wed, 18 May 2022 17:31:18 +0000 Subject: [PATCH 0704/1394] gnu: wla-dx: Update to 10.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/assembly.scm (wla-dx): Update to 10.1. [native-inputs]: Use new style. [arguments]: Add custom 'check phase to run run_tests.sh. Signed-off-by: Ludovic Courtès --- gnu/packages/assembly.scm | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm index b2830716e10..ca50b00a06d 100644 --- a/gnu/packages/assembly.scm +++ b/gnu/packages/assembly.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2020 B. Wilson ;;; Copyright © 2021 Maxim Cournoyer ;;; Copyright © 2021 Guillaume Le Vaillant +;;; Copyright © 2022 Felix Gruber ;;; ;;; This file is part of GNU Guix. ;;; @@ -342,7 +343,7 @@ package for the Game Boy and Game Boy Color. It consists of: (define-public wla-dx (package (name "wla-dx") - (version "9.12") + (version "10.1") (source (origin (method git-fetch) (uri (git-reference @@ -351,12 +352,20 @@ package for the Game Boy and Game Boy Color. It consists of: (file-name (git-file-name name version)) (sha256 (base32 - "1wlbqv2rgk9q6m9an1mi0i29250zl8lw7zipki2bbi9mczpyczli")))) + "1nh2k2xn5fj389gq68f3fxgrxakgn8c6dw2ffqay86s3706hac9w")))) (build-system cmake-build-system) - (native-inputs - `(("sphinx" ,python-sphinx))) ; to generate man pages + (native-inputs (list python-sphinx)) ; to generate man pages (arguments - `(#:tests? #f)) ; no tests + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'copy-tests-to-build-directory + (lambda _ + (copy-recursively "../source/tests" "tests"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (let ((sh (which "sh"))) + (when tests? + (invoke sh "../source/run_tests.sh")))))))) (home-page "https://github.com/vhelin/wla-dx") (synopsis "Assemblers for various processors") (description "WLA DX is a set of tools to assemble assembly files to From 6dacd15381f5cb42653c207715b8d5c133f93129 Mon Sep 17 00:00:00 2001 From: Wiktor Zelazny Date: Wed, 18 May 2022 16:20:23 +0000 Subject: [PATCH 0705/1394] gnu: Add python-climin. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-science.scm (python-climin): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/python-science.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 6bc726fc833..1e0910b46f4 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -18,6 +18,7 @@ ;;; Copyright © 2022 Malte Frank Gerdes ;;; Copyright © 2022 Guillaume Le Vaillant ;;; Copyright © 2022 Paul A. Patience +;;; Copyright © 2022 Wiktor Żelazny ;;; ;;; This file is part of GNU Guix. ;;; @@ -1291,3 +1292,24 @@ build applications with traitlets in combination with the scipy stack.") (description "This package is an implementation of the Promises/A+ specification and test suite in Python.") (license license:expat))) + +(define-public python-climin + (package + (name "python-climin") + (version "0.1a1") + (source (origin + (method url-fetch) + (uri (pypi-uri "climin" version)) + (sha256 + (base32 + "1wpjisd5zzi5yvjff02hnxn84822k8sdxvvd33lil2x79wdb36rv")))) + (build-system python-build-system) + (native-inputs (list python-nose)) + (propagated-inputs (list python-numpydoc python-numpy python-scipy)) + (home-page "https://github.com/BRML/climin") + (synopsis "Optimization for machine learning") + (description + "@command{climin} is a Python package for optimization, +heavily biased to machine learning scenarios. It works on top of +@command{numpy} and (partially) @command{gnumpy}.") + (license license:bsd-3))) From 6400f08d0749bf68250c28448e64c295bef6695d Mon Sep 17 00:00:00 2001 From: Wiktor Zelazny Date: Wed, 18 May 2022 16:20:27 +0000 Subject: [PATCH 0706/1394] gnu: Add python-paramz. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-science.scm (python-paramz): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/python-science.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 1e0910b46f4..1cab2a389bd 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1313,3 +1313,37 @@ specification and test suite in Python.") heavily biased to machine learning scenarios. It works on top of @command{numpy} and (partially) @command{gnumpy}.") (license license:bsd-3))) + +(define-public python-paramz + (package + (name "python-paramz") + (version "0.9.5") + (source (origin + (method url-fetch) + (uri (pypi-uri "paramz" version)) + (sha256 + (base32 + "16hbh97kj6b1c2gw22rqnr3w3nqkszh9gj8vgx738gq81wf225q9")))) + (build-system python-build-system) + (propagated-inputs (list python-decorator python-numpy python-scipy + python-six)) + (home-page "https://github.com/sods/paramz") + (synopsis "The Parameterization Framework") + (description + "@command{paramz} is a lightweight parameterization framework +for parameterized model creation and handling. Its features include: + +@itemize + @item Easy model creation with parameters. + @item Fast optimized access of parameters for optimization routines. + @item Memory efficient storage of parameters (only one copy in memory). + @item Renaming of parameters. + @item Intuitive printing of models and parameters. + @item Gradient saving directly inside parameters. + @item Gradient checking of parameters. + @item Optimization of parameters. + @item Jupyter notebook integration. + @item Efficient storage of models, for reloading. + @item Efficient caching. +@end itemize") + (license license:bsd-3))) From acb08304c862d65679086a9f160240bfd598289d Mon Sep 17 00:00:00 2001 From: Wiktor Zelazny Date: Wed, 18 May 2022 16:20:30 +0000 Subject: [PATCH 0707/1394] gnu: Add python-gpy. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-science.scm (python-gpy): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/python-science.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 1cab2a389bd..af91f73ec1f 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1347,3 +1347,31 @@ for parameterized model creation and handling. Its features include: @item Efficient caching. @end itemize") (license license:bsd-3))) + +(define-public python-gpy + (package + (name "python-gpy") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "GPy" version)) + (sha256 + (base32 + "1yx65ajrmqp02ykclhlb0n8s3bx5r0xj075swwwigiqaippr7dx2")))) + (build-system python-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (add-before 'check 'remove-plotting-tests + ;; These fail + (lambda _ + (delete-file "GPy/testing/plotting_tests.py")))))) + (native-inputs (list python-cython python-nose python-climin)) + (propagated-inputs (list python-numpy python-paramz python-scipy + python-six)) + (home-page "https://sheffieldml.github.io/GPy/") + (synopsis "The Gaussian Process Toolbox") + (description + "@command{GPy} is a Gaussian Process (GP) framework written in +Python, from the Sheffield machine learning group. GPy implements a range of +machine learning algorithms based on GPs.") + (license license:bsd-3))) From 7f63a6aefc8ae146150be2fb6897b1b2c9fd1907 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 29 May 2022 22:02:28 -0400 Subject: [PATCH 0708/1394] gnu: icecat: Update to 91.9.1-guix0-preview1 [security fixes]. Includes fixes for CVE-2022-1529 and CVE-2022-1802. * gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes. --- gnu/packages/gnuzilla.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 96c51cf8db8..f3eb1f7b57d 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -716,8 +716,8 @@ in C/C++.") ;; XXXX: Workaround 'snippet' limitations. (define computed-origin-method (@@ (guix packages) computed-origin-method)) -(define %icecat-version "91.9.0-guix0-preview1") -(define %icecat-build-id "20220503000000") ;must be of the form YYYYMMDDhhmmss +(define %icecat-version "91.9.1-guix0-preview1") +(define %icecat-build-id "20220520000000") ;must be of the form YYYYMMDDhhmmss ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat' @@ -739,11 +739,11 @@ in C/C++.") "firefox-" upstream-firefox-version ".source.tar.xz")) (sha256 (base32 - "175sakp772hx5c45zc1isbibhpvw7xb4l2lwaf9pvxig9j9ymgml")))) + "0q5mmgjy9qpcvkpcwf0ic7kjwr7zk601wvi81wm3qdz4g56py3h9")))) - (upstream-icecat-base-version "91.9.0") ; maybe older than base-version + (upstream-icecat-base-version "91.9.1") ; maybe older than base-version ;;(gnuzilla-commit (string-append "v" upstream-icecat-base-version)) - (gnuzilla-commit "d7d3e9a33d2b3b78a6e08060684580c72c0d6e93") + (gnuzilla-commit "c5a087823119d3e3109cca9cab222ee926d7a2a2") (gnuzilla-source (origin (method git-fetch) @@ -755,7 +755,7 @@ in C/C++.") (string-take gnuzilla-commit 8))) (sha256 (base32 - "0mp6mknnhha88932v6pmfadjbnnvkcrsi1ljmcrcz7pb9y81gxn0")))) + "1ry5nrb74xr2lah2mijpjymv0kbq0731qli60s3rb93l5f6bkp0j")))) ;; 'search-patch' returns either a valid file name or #f, so wrap it ;; in 'assume-valid-file-name' to avoid 'local-file' warnings. From 48efbde7a944acfe4fc944bf27bfa9ff82592024 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Mon, 30 May 2022 09:03:02 +0200 Subject: [PATCH 0709/1394] gnu: virtuoso-ose: Update to 7.2.7. * gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.7; Run autogen after applying the patch below. * gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch: New file. --- gnu/packages/databases.scm | 26 +++- ...tuoso-ose-remove-pre-built-jar-files.patch | 117 ++++++++++++++++++ 2 files changed, 141 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 2d72c78233b..a161e299072 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -100,6 +100,7 @@ #:use-module (gnu packages gnome) #:use-module (gnu packages gnupg) #:use-module (gnu packages golang) + #:use-module (gnu packages gperf) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) #:use-module (gnu packages icu4c) @@ -3229,14 +3230,30 @@ Memory-Mapped Database} (LMDB), a high-performance key-value store.") (define-public virtuoso-ose (package (name "virtuoso-ose") - (version "7.2.6") + (version "7.2.7") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/virtuoso/virtuoso/" version "/" "virtuoso-opensource-" version ".tar.gz")) (sha256 - (base32 "0ly7s7a3w2a2zhhi9rq9k2qlnzapqbbc1rcdqb3zqqpgg81krz9q")))) + (base32 "1853ln0smiilf3pni70gq6nmi9ps039cy44g6b5i9d2z1n9hnj02")) + (patches (search-patches "virtuoso-ose-remove-pre-built-jar-files.patch")) + (modules '((guix build utils))) + ;; This snippet removes pre-built Java archives. + (snippet + '(for-each delete-file-recursively + (list "binsrc/hibernate" + "binsrc/jena" + "binsrc/jena2" + "binsrc/jena3" + "binsrc/jena4" + "binsrc/rdf4j" + "binsrc/sesame" + "binsrc/sesame2" + "binsrc/sesame3" + "binsrc/sesame4" + "libsrc/JDBCDriverType4"))))) (build-system gnu-build-system) (arguments `(#:tests? #f ; Tests require a network connection. @@ -3247,6 +3264,9 @@ Memory-Mapped Database} (LMDB), a high-performance key-value store.") "--enable-static=no") #:phases (modify-phases %standard-phases + (replace 'bootstrap + (lambda _ + (invoke "sh" "autogen.sh"))) ;; Even with "--enable-static=no", "libvirtuoso-t.a" is left in ;; the build output. The following phase removes it. (add-after 'install 'remove-static-libs @@ -3256,6 +3276,8 @@ Memory-Mapped Database} (LMDB), a high-performance key-value store.") (delete-file (string-append lib "/" file))) '("libvirtuoso-t.a" "libvirtuoso-t.la")))))))) + (native-inputs + (list autoconf automake bison flex gperf libtool)) (inputs (list openssl net-tools readline zlib)) (home-page "http://vos.openlinksw.com/owiki/wiki/VOS/") diff --git a/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch b/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch new file mode 100644 index 00000000000..17413c71aea --- /dev/null +++ b/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch @@ -0,0 +1,117 @@ +This patch disables build targets that contain pre-built Java archives that +would be copied to the build's output. + +Patch by Roel Janssen +*** a-virtuoso-opensource-7.2.7/binsrc/Makefile.am 1970-01-01 01:00:01.000000000 +0100 +--- b-virtuoso-opensource-7.2.7/binsrc/Makefile.am 2022-05-27 12:20:52.909135774 +0200 +*************** +*** 19,25 **** + # + # + +! SUBDIRS = dav mono virtuoso tests rdf_mappers driver maildrop sqldoc hosting bpel fct tutorial conductor samples vsp ws sync vspx vad cached_resources virtodbc virtoledb virtuoso_sink xddl VirtuosoClient.Net oat isparql jena jena2 jena3 jena4 sesame sesame2 sesame3 sesame4 redland hibernate dbpedia rdb2rdf rdf4j + + + # ---------------------------------------------------------------------- +--- 19,25 ---- + # + # + +! SUBDIRS = dav mono virtuoso tests rdf_mappers driver maildrop sqldoc hosting bpel fct tutorial conductor samples vsp ws sync vspx vad cached_resources virtodbc virtoledb virtuoso_sink xddl VirtuosoClient.Net oat isparql redland dbpedia rdb2rdf + + + # ---------------------------------------------------------------------- +*** a-virtuoso-opensource-7.2.7/configure.ac 1970-01-01 01:00:01.000000000 +0100 +--- b-virtuoso-opensource-7.2.7/configure.ac 2022-05-27 12:27:51.879208018 +0200 +*************** +*** 57,64 **** + dnl AM_INIT_AUTOMAKE([1.8]) + dnl AM_INIT_AUTOMAKE([1.9 tar-ustar]) + dnl +! AM_INIT_AUTOMAKE([1.9 tar-ustar]) +! + AM_MAINTAINER_MODE + + +--- 57,63 ---- + dnl AM_INIT_AUTOMAKE([1.8]) + dnl AM_INIT_AUTOMAKE([1.9 tar-ustar]) + dnl +! AM_INIT_AUTOMAKE([1.9 tar-ustar subdir-objects]) + AM_MAINTAINER_MODE + + +*************** +*** 3157,3163 **** + binsrc/dbpedia/Makefile + binsrc/driver/Makefile + binsrc/fct/Makefile +- binsrc/hibernate/Makefile + binsrc/hosting/Makefile + binsrc/hosting/mono/Makefile + binsrc/hosting/mono/tests/Makefile +--- 3156,3161 ---- +*************** +*** 3169,3184 **** + binsrc/hosting/ruby/Makefile + binsrc/hosting/shapefileio/Makefile + binsrc/isparql/Makefile +- binsrc/jena/Makefile +- binsrc/jena2/Makefile +- binsrc/jena3/Makefile +- binsrc/jena4/Makefile + binsrc/maildrop/Makefile + binsrc/mono/Makefile + binsrc/oat/Makefile + binsrc/rdf_mappers/Makefile + binsrc/rdb2rdf/Makefile +- binsrc/rdf4j/Makefile + binsrc/redland/Makefile + binsrc/samples/demo/Makefile + binsrc/samples/hslookup/Makefile +--- 3167,3177 ---- +*************** +*** 3191,3200 **** + binsrc/samples/webapp/Makefile + binsrc/samples/xpath/Makefile + binsrc/samples/xquery/Makefile +- binsrc/sesame/Makefile +- binsrc/sesame2/Makefile +- binsrc/sesame3/Makefile +- binsrc/sesame4/Makefile + binsrc/sqldoc/Makefile + binsrc/sync/Makefile + binsrc/tests/biftest/Makefile +--- 3184,3189 ---- +*************** +*** 3236,3245 **** + docsrc/stylesheets/Makefile + docsrc/xmlsource/Makefile + libsrc/Dk/Makefile +- libsrc/JDBCDriverType4/Makefile +- libsrc/JDBCDriverType4/testsuite_4.0/Makefile +- libsrc/JDBCDriverType4/virtuoso/jdbc/Makefile +- libsrc/JDBCDriverType4/virtuoso/Makefile + libsrc/langfunc/Makefile + libsrc/odbcsdk/Makefile + libsrc/plugin/Makefile +--- 3225,3230 ---- +*** a-virtuoso-opensource-7.2.7/libsrc/Makefile.am 1970-01-01 01:00:01.000000000 +0100 +--- b-virtuoso-opensource-7.2.7/libsrc/Makefile.am 2022-05-27 12:30:12.658593011 +0200 +*************** +*** 19,25 **** + # + # + +! SUBDIRS = util zlib odbcsdk Dk Thread langfunc Wi plugin Tidy Xml.new JDBCDriverType4 + + noinst_HEADERS = Dk.h libutil.h + +--- 19,25 ---- + # + # + +! SUBDIRS = util zlib odbcsdk Dk Thread langfunc Wi plugin Tidy Xml.new + + noinst_HEADERS = Dk.h libutil.h + From e5dd864e68ee894f207c7c442416d52d120beca0 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 30 May 2022 09:04:50 +0300 Subject: [PATCH 0710/1394] gnu: links: Update to 2.27. * gnu/packages/web-browsers.scm (links): Update to 2.27. --- gnu/packages/web-browsers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index 5ae44147ef3..ead9e9749e8 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -158,14 +158,14 @@ management, extensions such as advertisement blocker and colorful tabs.") (define-public links (package (name "links") - (version "2.26") + (version "2.27") (source (origin (method url-fetch) (uri (string-append "http://links.twibright.com/download/" "links-" version ".tar.bz2")) (sha256 (base32 - "1jy90k04kl7y3l8jzg5jx7fglyqzngng0964j7j67gjxy9vkanzh")))) + "1d7bz6bbis94jq82xydwnazaczzmb1ij62pbmf0dxkg7xpycppfq")))) (build-system gnu-build-system) (arguments (list From d56506aad52d6ad757bd04a8559e3ed1411b237e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 30 May 2022 10:19:50 +0300 Subject: [PATCH 0711/1394] gnu: yt-dlp: Update to 2022.05.18. * gnu/packages/video.scm (yt-dlp): Update to 2022.05.18. [inputs]: Add python-brotli and python-certifi. --- gnu/packages/video.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 022c615f49f..31e3218320f 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2463,7 +2463,7 @@ YouTube.com and many more sites.") (define-public yt-dlp (package/inherit youtube-dl (name "yt-dlp") - (version "2022.02.04") + (version "2022.05.18") (source (origin (method url-fetch) (uri (string-append "https://github.com/yt-dlp/yt-dlp/" @@ -2471,7 +2471,7 @@ YouTube.com and many more sites.") version "/yt-dlp.tar.gz")) (sha256 (base32 - "1qx8sx47lzyrcl00r2657zjaq0mwfbzjyfnv5lr5dlm552f13pf8")) + "0wiiwqj8m4z6lladmrsp9354ddwlhn2gf0b39j271001g6fyi82r")) (snippet '(begin ;; Delete the pre-generated files, except for the man page @@ -2514,7 +2514,9 @@ YouTube.com and many more sites.") (when tests? (invoke "pytest" "-k" "not download")))))))) (inputs - `(("python-mutagen" ,python-mutagen) + `(("python-brotli" ,python-brotli) + ("python-certifi" ,python-certifi) + ("python-mutagen" ,python-mutagen) ("python-pycryptodomex" ,python-pycryptodomex) ("python-websockets" ,python-websockets) ,@(package-inputs youtube-dl))) From 1a8519dd017b641186bc5dd26e675fd4601287ac Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 30 May 2022 10:20:47 +0300 Subject: [PATCH 0712/1394] gnu: yt-dlp: Remove trailing #t. * gnu/packages/video.scm (yt-dlp)[source]: Remove trailing #t from snippet. [arguments]: Remove trailing #t from phases. --- gnu/packages/video.scm | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 31e3218320f..bddfbf1128a 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2481,8 +2481,7 @@ YouTube.com and many more sites.") ;;"yt-dlp.1" "completions/bash/yt-dlp" "completions/fish/yt-dlp.fish" - "completions/zsh/_yt-dlp")) - #t)))) + "completions/zsh/_yt-dlp")))))) (arguments (substitute-keyword-arguments (package-arguments youtube-dl) ((#:tests? _) #t) @@ -2493,8 +2492,7 @@ YouTube.com and many more sites.") (lambda _ (substitute* "yt_dlp/postprocessor/ffmpeg.py" (("\\.get_param\\('ffmpeg_location'\\)" match) - (format #f "~a or '~a'" match (which "ffmpeg")))) - #t)) + (format #f "~a or '~a'" match (which "ffmpeg")))))) (replace 'build-generated-files (lambda _ ;; Avoid the yt-dlp.1 target, which requires pandoc. @@ -2506,8 +2504,7 @@ YouTube.com and many more sites.") (("'etc/") (string-append "'" prefix "/etc/")) (("'share/") - (string-append "'" prefix "/share/")))) - #t)) + (string-append "'" prefix "/share/")))))) (delete 'install-completion) (replace 'check (lambda* (#:key tests? #:allow-other-keys) From 4259a6516a7c8617e59e00b1c4959c4f8d136794 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 30 May 2022 10:42:47 +0300 Subject: [PATCH 0713/1394] gnu: virtuoso-ose: Register patch. This is a follow-up to 48efbde7a944acfe4fc944bf27bfa9ff82592024. * gnu/local.mk (dist_patch_DATA): Register patch. --- gnu/local.mk | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/local.mk b/gnu/local.mk index bc82c5ba9f2..182c0dd4a9c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1931,6 +1931,7 @@ dist_patch_DATA = \ %D%/packages/patches/vinagre-newer-freerdp.patch \ %D%/packages/patches/vinagre-newer-rdp-parameters.patch \ %D%/packages/patches/virglrenderer-CVE-2017-6386.patch \ + %D%/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch \ %D%/packages/patches/vsearch-unbundle-cityhash.patch \ %D%/packages/patches/vte-CVE-2012-2738-pt1.patch \ %D%/packages/patches/vte-CVE-2012-2738-pt2.patch \ From acada2580fa249cd3aad074c310ef2e6e1a9022f Mon Sep 17 00:00:00 2001 From: Evgenii Lepikhin Date: Sat, 2 Apr 2022 00:54:32 +0300 Subject: [PATCH 0714/1394] gnu: Add rust-nom-locate-4. * gnu/packages/crates-io.scm (rust-nom-locate-4): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 7301084382c..1ffce539491 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -25,6 +25,7 @@ ;;; Copyright © 2021 Nicolas Graves ;;; Copyright © 2022 Aleksandr Vityazev ;;; Copyright © 2022 Marius Bakke +;;; Copyright © 2022 Evgenii Lepikhin ;;; ;;; This file is part of GNU Guix. ;;; @@ -37548,6 +37549,30 @@ combinators library.") (description "This package derives custom nom parsers from structs.") (license (list license:expat license:asl2.0)))) +(define-public rust-nom-locate-4 + (package + (name "rust-nom-locate") + (version "4.0.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "nom_locate" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0186n5qbpiyhpas3nk8y4ynnbdghl4nx958bkq4a6a9hr8v48y9p")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bytecount" ,rust-bytecount-0.6) + ("rust-memchr" ,rust-memchr-2) + ("rust-nom" ,rust-nom-7) + ("rust-stable-deref-trait" ,rust-stable-deref-trait-1)))) + (home-page "https://github.com/fflorent/nom_locate") + (synopsis "Special input type for nom to locate tokens") + (description "This crate provides the @code{LocatedSpan} struct that +encapsulates the data.") + (license (list license:expat)))) + (define-public rust-noop-proc-macro-0.3 (package (name "rust-noop-proc-macro") From 30cf5284b2be9e363e624c42436ada524a63dc39 Mon Sep 17 00:00:00 2001 From: Evgenii Lepikhin Date: Sat, 2 Apr 2022 00:54:33 +0300 Subject: [PATCH 0715/1394] gnu: Add rust-pretty-0.11. * gnu/packages/crates-io.scm (rust-pretty-0.11) New variable. (rust-pretty-0.5): Inherit from rust-pretty-0.11. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 41 ++++++++++++++++++++++++++++++-------- 1 file changed, 33 insertions(+), 8 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 1ffce539491..6d86b60bba9 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -44364,8 +44364,40 @@ functions.") (("rust-predicates-core" ,rust-predicates-core-0.9) ("rust-treeline" ,rust-treeline-0.1)))))) +(define-public rust-pretty-0.11 + (package + (name "rust-pretty") + (version "0.11.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "pretty" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1282l4pa9hhamvbnd5mjrwhdgcsjy1l1lj44i0m4pczsf1cd3br9")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-arrayvec" ,rust-arrayvec-0.5) + ("rust-log" ,rust-log-0.4) + ("rust-termcolor" ,rust-termcolor-1) + ("rust-typed-arena" ,rust-typed-arena-2) + ("rust-unicode-segmentation" ,rust-unicode-segmentation-1)) + #:cargo-development-inputs + (("rust-criterion" ,rust-criterion-0.3) + ("rust-difference" ,rust-difference-2) + ("rust-env-logger" ,rust-env-logger-0.9) + ("rust-tempfile" ,rust-tempfile-3)))) + (home-page "https://github.com/Marwes/pretty.rs") + (synopsis "Pretty printing combinators for Rust") + (description + "This crate provides functionality for defining pretty printers. It is +particularly useful for printing structured recursive data like trees.") + (license license:expat))) + (define-public rust-pretty-0.5 (package + (inherit rust-pretty-0.11) (name "rust-pretty") (version "0.5.2") (source @@ -44375,18 +44407,11 @@ functions.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "1lzn7d60l79vsdwcfgrh6jmk193nzwh1j36r8p9cv3n8dyghs37n")))) - (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs (("rust-termcolor" ,rust-termcolor-0.3) - ("rust-typed-arena" ,rust-typed-arena-1)))) - (home-page "https://github.com/Marwes/pretty.rs") - (synopsis "Pretty printing combinators for Rust") - (description - "This crate provides functionality for defining pretty printers. It is -particularly useful for printing structured recursive data like trees.") - (license license:expat))) + ("rust-typed-arena" ,rust-typed-arena-1)))))) (define-public rust-pretty-assertions-0.7 (package From 4b18cb437ae06162868e6de25567b58929f82d18 Mon Sep 17 00:00:00 2001 From: Evgenii Lepikhin Date: Sat, 2 Apr 2022 00:54:34 +0300 Subject: [PATCH 0716/1394] gnu: Add rust-located-yaml-0.2. * gnu/packages/crates-io.scm (rust-located-yaml-0.2) New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 6d86b60bba9..9db1348b8dc 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -32383,6 +32383,29 @@ by inspecting the system for user preference.") ("rust-regex" ,rust-regex-1) ("rust-winapi" ,rust-winapi-0.3)))))) +(define-public rust-located-yaml-0.2 + (package + (name "rust-located-yaml") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "located_yaml" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0xnx5al5v7d9syspj0irm22alwc3a9adikqxpbyyf6vsz3k8xilv")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-linked-hash-map" ,rust-linked-hash-map-0.5) + ("rust-serde" ,rust-serde-1) + ("rust-yaml-rust" ,rust-yaml-rust-0.4)))) + (home-page "https://github.com/johnlepikhin/located_yaml") + (synopsis "YAML parser with saved positions") + (description + "YAML parser which provides AST with saved tokens positions.") + (license (list license:expat)))) + (define-public rust-lock-api-0.4 (package (name "rust-lock-api") From 4f5a71d5b7c13fed7487130a861927c697dd8de6 Mon Sep 17 00:00:00 2001 From: Evgenii Lepikhin Date: Mon, 30 May 2022 11:01:57 +0300 Subject: [PATCH 0717/1394] gnu: Add rust-minimal-lexical-0.2. * gnu/packages/crates-io.scm (rust-minimal-lexical-0.2): New variable. (rust-minimal-lexical-0.1): Inherit from rust-minimal-lexical-0.2. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++------ 1 file changed, 21 insertions(+), 6 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 9db1348b8dc..5098e1d7355 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -34708,8 +34708,28 @@ file's MIME type by its extension.") ;; No copyright headers in the source code. LICENSE indicates gpl3. (license license:gpl3))) +(define-public rust-minimal-lexical-0.2 + (package + (name "rust-minimal-lexical") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "minimal-lexical" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "16ppc5g84aijpri4jzv14rvcnslvlpphbszc7zzp6vfkddf4qdb8")))) + (build-system cargo-build-system) + (home-page "https://github.com/Alexhuszagh/minimal-lexical") + (synopsis "Float parsing conversion routines") + (description "This is a minimal version of rust-lexical, meant to allow +efficient round-trip float parsing. Minimal-lexical implements a correct, fast +float parser.") + (license (list license:expat license:asl2.0)))) + (define-public rust-minimal-lexical-0.1 (package + (inherit rust-minimal-lexical-0.2) (name "rust-minimal-lexical") (version "0.1.4") (source @@ -34718,12 +34738,7 @@ file's MIME type by its extension.") (uri (crate-uri "minimal-lexical" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0xynhr97vyv5n5lls41dl7bfa3ba122lix9mqij1l7yprl6n6r4w")))) - (build-system cargo-build-system) - (home-page "https://github.com/Alexhuszagh/minimal-lexical") - (synopsis "Fast float parsing conversion routines") - (description "Fast float parsing conversion routines.") - (license (list license:expat license:asl2.0)))) + (base32 "0xynhr97vyv5n5lls41dl7bfa3ba122lix9mqij1l7yprl6n6r4w")))))) (define-public rust-miniz-oxide-0.4 (package From 6ec464ced7660b5aafd5f8e45fe55fa4d33a2667 Mon Sep 17 00:00:00 2001 From: Evgenii Lepikhin Date: Mon, 30 May 2022 11:05:44 +0300 Subject: [PATCH 0718/1394] gnu: rust-nom-7: Update to 7.1.1. * gnu/packages/crates-io.scm (rust-nom-7): Update to 7.1.1. [arguments]: In cargo-inputs replace rust-minimal-lexical-0.1 with 0.2. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 5098e1d7355..415f9ec6c3a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -37361,7 +37361,7 @@ implementation (which is unstable / requires nightly).") (define-public rust-nom-7 (package (name "rust-nom") - (version "7.0.0") + (version "7.1.1") (source (origin (method url-fetch) @@ -37370,13 +37370,13 @@ implementation (which is unstable / requires nightly).") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1ha24yclw4m74gi9p5c3d68rhrrcb7qvkgicz153p5cahck9vzbz")))) + "0djc3lq5xihnwhrvkc4bj0fd58sjf632yh6hfiw545x355d3x458")))) (build-system cargo-build-system) (arguments `(#:tests? #f ; Tests require example directory, not included in tarball. #:cargo-inputs (("rust-memchr" ,rust-memchr-2) - ("rust-minimal-lexical" ,rust-minimal-lexical-0.1) + ("rust-minimal-lexical" ,rust-minimal-lexical-0.2) ("rust-version-check" ,rust-version-check-0.9)) #:cargo-development-inputs (("rust-criterion" ,rust-criterion-0.3) From 69b27be15d1801b994bafa4c4cc01c790a27b5a8 Mon Sep 17 00:00:00 2001 From: Evgenii Lepikhin Date: Sat, 2 Apr 2022 00:54:36 +0300 Subject: [PATCH 0719/1394] gnu: Add rust-serde-regex-1. * gnu/packages/crates-io.scm (rust-serde-regex-1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 415f9ec6c3a..86313f5e4fd 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -54670,6 +54670,30 @@ using nested parameters, similar to those used by @code{qs} for Node, and commonly used by Ruby on Rails via Rack.") (license (list license:expat license:asl2.0)))) +(define-public rust-serde-regex-1 + (package + (name "rust-serde-regex") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde_regex" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1pxsnxb8c198szghk1hvzvhva36w2q5zs70hqkmdf5d89qd6y4x8")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-regex" ,rust-regex-1)) + #:cargo-development-inputs + (("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-json" ,rust-serde-json-1)))) + (home-page "https://github.com/tailhook/serde-regex") + (synopsis "Serde wrapper to serialize regular expressions as strings") + (description "This package provides a serde wrapper, that can be used to +serialize regular expressions as strings.") + (license (list license:expat license:asl2.0)))) + (define-public rust-serde-repr-0.1 (package (name "rust-serde-repr") From 19e1045352d33ae8074b0a6e891bfd4f6d95c134 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 31 Aug 2021 10:25:24 +0300 Subject: [PATCH 0720/1394] gnu: nss: Adjust make-flags for riscv64-linux. * gnu/packages/nss.scm (nss)[arguments]: When building for riscv64-linux don't build the binaries with gtest. --- gnu/packages/nss.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/gnu/packages/nss.scm b/gnu/packages/nss.scm index aae88860952..bf2003d927a 100644 --- a/gnu/packages/nss.scm +++ b/gnu/packages/nss.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2021 Mark H Weaver -;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner +;;; Copyright © 2016, 2017, 2018, 2019, 2021 Efraim Flashner ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2020, 2021 Marius Bakke ;;; Copyright © 2020 Jonathan Brielmaier @@ -144,6 +144,11 @@ in the Mozilla clients.") (list "-C" "nss" (string-append "PREFIX=" out) "NSDISTMODE=copy" "NSS_USE_SYSTEM_SQLITE=1" + ;; The gtests fail to compile on riscv64. + ;; Skipping them doesn't affect the test suite. + ,@(if (target-riscv64?) + `("NSS_DISABLE_GTESTS=1") + '()) (string-append "NSPR_INCLUDE_DIR=" nspr "/include/nspr") ;; Add $out/lib/nss to RPATH. (string-append "RPATH=" rpath) From a037815f628326952fa78230189898a0505c5ca4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 30 May 2022 15:26:17 +0300 Subject: [PATCH 0721/1394] gnu: nss: Skip tests on riscv64-linux. * gnu/packages/nss.scm (nss)[arguments]: Skip tests when building for riscv64-linux. --- gnu/packages/nss.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/nss.scm b/gnu/packages/nss.scm index bf2003d927a..5e719ad5b8f 100644 --- a/gnu/packages/nss.scm +++ b/gnu/packages/nss.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2021 Mark H Weaver -;;; Copyright © 2016, 2017, 2018, 2019, 2021 Efraim Flashner +;;; Copyright © 2016-2019, 2021, 2022 Efraim Flashner ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2020, 2021 Marius Bakke ;;; Copyright © 2020 Jonathan Brielmaier @@ -158,6 +158,9 @@ in the Mozilla clients.") (ice-9 ftw) (ice-9 match) (srfi srfi-26)) + #:tests? ,(not (or (%current-target-system) + ;; Tests take more than 30 hours on riscv64-linux. + (target-riscv64?))) #:phases (modify-phases %standard-phases (replace 'configure From dc26d0f94e7e210cd4d824943f32ee3081ac4967 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 30 May 2022 15:28:04 +0300 Subject: [PATCH 0722/1394] gnu: hello: Update to 2.12.1. * gnu/packages/base.scm (hello): Update to 2.12.1. --- gnu/packages/base.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index c3b33e37510..b8534655780 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -85,14 +85,14 @@ (define-public hello (package (name "hello") - (version "2.12") + (version "2.12.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/hello/hello-" version ".tar.gz")) (sha256 (base32 - "1ayhp9v4m4rdhjmnl2bq3cibrbqqkgjbl3s7yk2nhlh8vj3ay16g")))) + "086vqwk2wl8zfs47sq2xpjc9k066ilmb8z6dn0q6ymwjzlm196cd")))) (build-system gnu-build-system) (synopsis "Hello, GNU world: An example GNU package") (description From d2a9142852e33c2114dbc25e24477af94ac069a5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 30 May 2022 15:28:04 +0300 Subject: [PATCH 0723/1394] gnu: gcc-9: Update to 9.5.0. * gnu/packages/gcc.scm (gcc-9): Update to 9.5.0. --- gnu/packages/gcc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index 6823b41ee0d..cd144772b8b 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -641,14 +641,14 @@ It also includes runtime support libraries for these languages.") (define-public gcc-9 (package (inherit gcc-8) - (version "9.4.0") + (version "9.5.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/gcc/gcc-" version "/gcc-" version ".tar.xz")) (sha256 (base32 - "13l3p6g2krilaawbapmn9zmmrh3zdwc36mfr3msxfy038hps6pf9")) + "13ygjmd938m0wmy946pxdhz9i1wq7z4w10l6pvidak0xxxj9yxi7")) (patches (search-patches "gcc-9-strmov-store-file-names.patch" "gcc-9-asan-fix-limits-include.patch" "gcc-5.0-libvtv-runpath.patch")) From bfcae1efbb524e8d4ea404ba5985d5219ac63612 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 15:16:35 +0200 Subject: [PATCH 0724/1394] gnu: r-batchelor: Update to 1.12.1. * gnu/packages/bioconductor.scm (r-batchelor): Update to 1.12.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4d3f86bfd3a..176f7ecc6d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7574,14 +7574,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "0axkic11bwjbw8apwxx6p51s7jvlwhq7xi1bdknn54k86axq84dr")))) + "1zyvjr9nwfh0cdqk4kwmr30yhh05picyab1hpnpn737xvn525jfi")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs From d3cb071050f345f37a95c5c97ec41fb2029de201 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 15:30:47 +0200 Subject: [PATCH 0725/1394] gnu: r-qpdf: Update to 1.2.0. * gnu/packages/cran.scm (r-qpdf): Update to 1.2.0. [source]: Remove trailing #T from snippet. [arguments]: Remove trailing #T from 'configure phase. [inputs]: Add libjpeg-turbo. --- gnu/packages/cran.scm | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5a8285b3422..c7ba9e6e695 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30818,32 +30818,29 @@ Also support writing data frame into ODS file.") (define-public r-qpdf (package (name "r-qpdf") - (version "1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "qpdf" version)) (sha256 (base32 - "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi")) + "1a1d7zad2l94z068mic6dg9wr9bq8mlmqszrj8vxps1441mb6gfh")) (modules '((guix build utils))) (snippet '(begin ;; unvendor libqpdf (delete-file-recursively "src/libqpdf") - (delete-file-recursively "src/include/qpdf") - #t)))) + (delete-file-recursively "src/include/qpdf"))))) (properties `((upstream-name . "qpdf"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'configure - (lambda _ - (setenv "EXTERNAL_QPDF" "1") - #t))))) + (lambda _ (setenv "EXTERNAL_QPDF" "1")))))) (inputs - (list zlib qpdf)) + (list libjpeg-turbo qpdf zlib)) (propagated-inputs (list r-askpass r-curl r-rcpp)) (native-inputs (list pkg-config)) From 56373df33a3a84db68a5c8896fcf3e86b4616b63 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 15:34:28 +0200 Subject: [PATCH 0726/1394] gnu: r-gee: Update to 4.13-23. * gnu/packages/cran.scm (r-gee): Update to 4.13-23. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c7ba9e6e695..7a18cfd69eb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11782,14 +11782,14 @@ analysis.") (define-public r-gee (package (name "r-gee") - (version "4.13-22") + (version "4.13-23") (source (origin (method url-fetch) (uri (cran-uri "gee" version)) (sha256 (base32 - "1wbwn7bjqz09l6clh43dy3x5qgv9b9wwn7xnfw9fkkrhn6rvc3rw")))) + "0v0fam678pqqkxmj95f1pwsi08y1rbz1wxnp1ig81jvpn0xpq8gq")))) (properties `((upstream-name . "gee"))) (build-system r-build-system) (native-inputs From 7815efe731fc24c87e36c1df5379b7f851bf9277 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 15:34:34 +0200 Subject: [PATCH 0727/1394] gnu: r-cobs: Update to 1.3-5. * gnu/packages/cran.scm (r-cobs): Update to 1.3-5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7a18cfd69eb..4f09eca19e6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16378,14 +16378,14 @@ numbers (e.g. concentrations).") (define-public r-cobs (package (name "r-cobs") - (version "1.3-4") + (version "1.3-5") (source (origin (method url-fetch) (uri (cran-uri "cobs" version)) (sha256 (base32 - "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1")))) + "04f6a6gp11p93j2k35mbrfqgjx5qsgi3dj1085a5v5s0z6l7vbkz")))) (build-system r-build-system) (propagated-inputs (list r-quantreg r-sparsem)) From 0880acbcb56c401ad912979b3e7ab42b36fea0dc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 15:34:39 +0200 Subject: [PATCH 0728/1394] gnu: r-clue: Update to 0.3-61. * gnu/packages/cran.scm (r-clue): Update to 0.3-61. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4f09eca19e6..c7e182c9324 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19851,14 +19851,14 @@ experiments in a well-organized and reproducible way.") (define-public r-clue (package (name "r-clue") - (version "0.3-60") + (version "0.3-61") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 - "0apgpdnn74mqg2bnr8yjyxgyvdl411h0r2b1r2xd67k21pyxs8bd")))) + "0cfw2k1kh4a8imdv7b5qw977xd6indampsabhfldj3rqrqb1ncbi")))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/clue/") From 440bd1b617aef76d278194668fc92748ee360a38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 15:34:46 +0200 Subject: [PATCH 0729/1394] gnu: r-parameters: Update to 0.18.1. * gnu/packages/cran.scm (r-parameters): Update to 0.18.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c7e182c9324..a314ce571ab 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20793,14 +20793,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.18.0") + (version "0.18.1") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "0r6bj29frhqyv75cviw0p8kns6h8z10n7g7khyk0hzq2fqjsjrwh")))) + "0zcypf3fi745pa18vpqgx3q9izhkkmpcvcv1gv8pxawyq9mw8ag9")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs From 85e77d93ac5da2b0a2027a2b8e8a922e4d381938 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 15:34:52 +0200 Subject: [PATCH 0730/1394] gnu: r-tree: Update to 1.0-42. * gnu/packages/cran.scm (r-tree): Update to 1.0-42. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a314ce571ab..2bbb3f6a157 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22655,13 +22655,13 @@ management} (aCRM).") (define-public r-tree (package (name "r-tree") - (version "1.0-41") + (version "1.0-42") (source (origin (method url-fetch) (uri (cran-uri "tree" version)) (sha256 (base32 - "13jwdxx3na16mly176n01zdkaqn4a8x9fc43rq5xx5vx31drkkr1")))) + "1q3jgkhl5d4d8c396cyvkw60094p0z0a3x7xwhdbi8gl4c2c65ss")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/tree/") (synopsis "Classification and regression trees") From eba783130fa32fa10710bb43b9c00929d55e6c2c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 15:34:59 +0200 Subject: [PATCH 0731/1394] gnu: r-chron: Update to 2.3-57. * gnu/packages/statistics.scm (r-chron): Update to 2.3-57. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 43b9c1b8044..c95fbff54a8 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1943,13 +1943,13 @@ and density estimation.") (define-public r-chron (package (name "r-chron") - (version "2.3-56") + (version "2.3-57") (source (origin (method url-fetch) (uri (cran-uri "chron" version)) (sha256 (base32 - "0p9zz96jfyf139924hdwkzhr8knkjvx6547ac53rknm3a6wwngl6")))) + "0cn2367mw27qf2nj8d1i182ns3nlzlkgix6c18mc3byihimdhicn")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/chron") (synopsis "Chronological R objects which can handle dates and times") From 281bf7274529ae47f007a2b1eceacb5f25d12c0d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 15:35:04 +0200 Subject: [PATCH 0732/1394] gnu: r-lmom: Update to 2.9. * gnu/packages/statistics.scm (r-lmom): Update to 2.9. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c95fbff54a8..5e6e9ba8371 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -6835,13 +6835,13 @@ Annealing\" @url{doi:10.1145/3025453.3025912}.") (define-public r-lmom (package (name "r-lmom") - (version "2.8") + (version "2.9") (source (origin (method url-fetch) (uri (cran-uri "lmom" version)) (sha256 - (base32 "1lnj41gynaar5isyijg5nbll64qdxa12dnqvz7lxhaclqcjskqna")))) + (base32 "145va4dhl767mywk36xcmqilm21sfkqhcqi0s07qgq3k39sn4gin")))) (properties `((upstream-name . "lmom"))) (build-system r-build-system) (native-inputs (list gfortran)) From 1ae0e1dc29109cef20dbe9d26eb1c855694716b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 30 May 2022 15:58:05 +0200 Subject: [PATCH 0733/1394] store: 'map/accumulate-builds' preserves caches. Fixes . Starting from the switch to functional object caches ca. 9e5812ac59b01ff011ec0c5b0f437dfe85d6fcc7, we would be losing accumulated caches when aborting to the build handler. This patch fixes that. In particular, by preserving '%reference-cache-id', we avoid redundant 'query-references' RPCs, which accounted for a large part of the extra processing time. * guix/store.scm (build-accumulator): When returning an node, call 'set-store-connection-caches!' before and after to preserve caches. (map/accumulate-builds): Pass STORE as the first argument to the continuation. --- guix/store.scm | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/guix/store.scm b/guix/store.scm index efba07bdcdc..6bdd071b488 100644 --- a/guix/store.scm +++ b/guix/store.scm @@ -1337,7 +1337,17 @@ object, only for build requests on EXPECTED-STORE." (if (and (eq? (store-connection-socket store) (store-connection-socket expected-store)) (= mode (build-mode normal))) - (unresolved things continue) + (begin + ;; Preserve caches accumulated up to this handler invocation. + (set-store-connection-caches! expected-store + (store-connection-caches store)) + + (unresolved things + (lambda (new-store value) + ;; Borrow caches from NEW-STORE. + (set-store-connection-caches! + store (store-connection-caches new-store)) + (continue value)))) (continue #t)))) (define default-cutoff @@ -1397,7 +1407,8 @@ CUTOFF is the threshold above which we stop accumulating unresolved nodes." (if (unresolved? obj) ;; Pass #f because 'build-things' is now ;; unnecessary. - ((unresolved-continuation obj) #f) + ((unresolved-continuation obj) + store #f) obj)) result #:cutoff cutoff) (map/accumulate-builds store proc rest #:cutoff cutoff))))) From 61d4f9e89da8471ecf4df93ab25c0d707797122a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 30 May 2022 12:21:50 +0200 Subject: [PATCH 0734/1394] tests: Adjust crate importer test to spdx changes. This is a followup to 95b0544fcfa1a663435a9ac84db94312b938022b. * tests/crate.scm ("licenses: MIT/Apache-2.0 AND BSD-2-Clause"): Adjust expected result. --- tests/crate.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/crate.scm b/tests/crate.scm index b6c3a7ee2e6..720fcb212c9 100644 --- a/tests/crate.scm +++ b/tests/crate.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 David Thompson ;;; Copyright © 2016 David Craven -;;; Copyright © 2019, 2020 Ludovic Courtès +;;; Copyright © 2019, 2020, 2022 Ludovic Courtès ;;; Copyright © 2020 Martin Becze ;;; ;;; This file is part of GNU Guix. @@ -572,7 +572,7 @@ (string->license "Apache-2.0 WITH LLVM-exception")) (test-equal "licenses: MIT/Apache-2.0 AND BSD-2-Clause" - '(license:expat license:asl2.0 unknown-license!) + '(license:expat license:asl2.0 license:bsd-2) (string->license "MIT/Apache-2.0 AND BSD-2-Clause")) (test-equal "licenses: MIT/Apache-2.0" From 7750f220bedb5f7a24e7429a4ccd794f9d07e4aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 30 May 2022 12:23:00 +0200 Subject: [PATCH 0735/1394] gnu: tor: Record the file name of 'torsocks' in 'torify'. * gnu/packages/tor.scm (tor)[arguments]: Add 'adjust-torify' phase. [inputs]: Add TORSOCKS. --- gnu/packages/tor.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 277acf47545..4c4ccbb0037 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -73,6 +73,16 @@ "--enable-zstd") #:phases #~(modify-phases %standard-phases + (add-before 'build 'adjust-torify + (lambda* (#:key inputs #:allow-other-keys) + ;; Record in 'torify' the absolute file name of 'torsocks'. + (let ((torsocks (search-input-file + inputs "/bin/torsocks"))) + (substitute* "contrib/client-tools/torify" + (("pathfind torsocks") + "true") + (("exec torsocks") + (string-append "exec " torsocks)))))) (add-before 'check 'skip-practracker ;; This is a style linter. It doesn't get to throw fatal errors. (lambda _ @@ -98,6 +108,7 @@ (list libevent libseccomp openssl + torsocks xz zlib `(,zstd "lib"))) From 56dddd05e85c1233870bbf7157bbb6f7972329be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 30 May 2022 12:26:25 +0200 Subject: [PATCH 0736/1394] gnu: emacs-w3m: Update to 20220508.2259. * gnu/packages/emacs-xyz.scm (emacs-w3m): Update to 20220508.2259. [source]: Switch to 'git-fetch'. --- gnu/packages/emacs-xyz.scm | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 31822dc6414..94b2571a155 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès +;;; Copyright © 2013-2022 Ludovic Courtès ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Mark H Weaver ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Alex Kost ;;; Copyright © 2015 Federico Beffa @@ -2155,18 +2155,17 @@ or unexpected behavior inside an elisp configuration file (typically ;; Emacs-w3m follows a "rolling release" model. (package (name "emacs-w3m") - (version "2018-11-11") - (source - (origin - (method cvs-fetch) - (uri (cvs-reference - (root-directory - ":pserver:anonymous@cvs.namazu.org:/storage/cvsroot") - (module "emacs-w3m") - (revision version))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 "0nvahdbjs12zg7zsk4gql02mvnv56cf1rwj2f5p42lwp3xvswiwp")))) + (version "20220508.2259") + (source (origin + ;; "Officially" this is still on cvs.namazu.org, but that repo + ;; seems to be unreachable. + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-w3m/emacs-w3m.git") + (commit "bbcebbe20ebfa807a3e4beaadf40ce6f4be213e7"))) + (sha256 + (base32 + "0y892n8jaxzyxi1fgyklc7zfh57ibp4yyywmif69dm28hykj6lmz")))) (build-system gnu-build-system) (native-inputs (list autoconf texinfo emacs-minimal)) (inputs (list w3m imagemagick)) From 3f31525546647a4936e4692b630efda6afac3715 Mon Sep 17 00:00:00 2001 From: Morgan Smith Date: Wed, 25 May 2022 17:37:32 -0400 Subject: [PATCH 0737/1394] gnu: GCC: Add cross environment variables patch to GCC 12. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/patches/gcc-12-cross-environment-variables.patch : New file. * gnu/local.mk (dist_patch_DATA): Add gcc-12-cross-environment-variables.patch. * gnu/packages/cross-base.scm (cross-gcc)[source](patches): Apply the patch. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/cross-base.scm | 3 ++ .../gcc-12-cross-environment-variables.patch | 54 +++++++++++++++++++ 3 files changed, 58 insertions(+) create mode 100644 gnu/packages/patches/gcc-12-cross-environment-variables.patch diff --git a/gnu/local.mk b/gnu/local.mk index 182c0dd4a9c..3de938e5d03 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1131,6 +1131,7 @@ dist_patch_DATA = \ %D%/packages/patches/gcc-9-strmov-store-file-names.patch \ %D%/packages/patches/gcc-12-strmov-store-file-names.patch \ %D%/packages/patches/gcc-10-cross-environment-variables.patch \ + %D%/packages/patches/gcc-12-cross-environment-variables.patch \ %D%/packages/patches/gcolor3-update-libportal-usage.patch \ %D%/packages/patches/gd-fix-tests-on-i686.patch \ %D%/packages/patches/gd-brect-bounds.patch \ diff --git a/gnu/packages/cross-base.scm b/gnu/packages/cross-base.scm index 93e4f8a445f..9c98c923fff 100644 --- a/gnu/packages/cross-base.scm +++ b/gnu/packages/cross-base.scm @@ -242,6 +242,9 @@ target that libc." (append (origin-patches (package-source xgcc)) (append (cond + ((version>=? (package-version xgcc) "12.0") + (search-patches "gcc-12-cross-environment-variables.patch" + "gcc-cross-gxx-include-dir.patch")) ((version>=? (package-version xgcc) "10.0") (search-patches "gcc-10-cross-environment-variables.patch" "gcc-cross-gxx-include-dir.patch")) diff --git a/gnu/packages/patches/gcc-12-cross-environment-variables.patch b/gnu/packages/patches/gcc-12-cross-environment-variables.patch new file mode 100644 index 00000000000..8787f094c0d --- /dev/null +++ b/gnu/packages/patches/gcc-12-cross-environment-variables.patch @@ -0,0 +1,54 @@ +Search path environment variables for cross-compilers. See the discussion +at . + +Note: Touch 'C_INCLUDE_PATH' et al. rather than 'CPATH', as discussed +at . + +diff --git a/gcc/gcc.cc b/gcc/gcc.cc +--- a/gcc/gcc.cc ++++ b/gcc/gcc.cc +@@ -4832,7 +4832,7 @@ process_command (unsigned int decoded_options_count, + } + + temp = env.get (LIBRARY_PATH_ENV); +- if (temp && *cross_compile == '0') ++ if (temp) + { + const char *startp, *endp; + char *nstore = (char *) alloca (strlen (temp) + 3); +diff --git a/gcc/incpath.cc b/gcc/incpath.cc +--- a/gcc/incpath.cc ++++ b/gcc/incpath.cc +@@ -480,8 +480,8 @@ register_include_chains (cpp_reader *pfile, const char *sysroot, + int stdinc, int cxx_stdinc, int verbose) + { + static const char *const lang_env_vars[] = +- { "C_INCLUDE_PATH", "CPLUS_INCLUDE_PATH", +- "OBJC_INCLUDE_PATH", "OBJCPLUS_INCLUDE_PATH" }; ++ { "CROSS_C_INCLUDE_PATH", "CROSS_CPLUS_INCLUDE_PATH", ++ "CROSS_OBJC_INCLUDE_PATH", "CROSS_OBJCPLUS_INCLUDE_PATH" }; + cpp_options *cpp_opts = cpp_get_options (pfile); + size_t idx = (cpp_opts->objc ? 2: 0); + +@@ -492,7 +492,7 @@ register_include_chains (cpp_reader *pfile, const char *sysroot, + + /* CPATH and language-dependent environment variables may add to the + include chain. */ +- add_env_var_paths ("CPATH", INC_BRACKET); ++ add_env_var_paths ("CROSS_CPATH", INC_BRACKET); + add_env_var_paths (lang_env_vars[idx], INC_SYSTEM); + + target_c_incpath.extra_pre_includes (sysroot, iprefix, stdinc); +diff --git a/gcc/system.h b/gcc/system.h +--- a/gcc/system.h ++++ b/gcc/system.h +@@ -1317,4 +1317,6 @@ endswith (const char *str, const char *suffix) + return memcmp (str + str_len - suffix_len, suffix, suffix_len) == 0; + } + ++#define LIBRARY_PATH_ENV "CROSS_LIBRARY_PATH" ++ + #endif /* ! GCC_SYSTEM_H */ +-- +2.36.1 + From 7d8f6a5db5069ad614ca58ec3a995335fdf4fac8 Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Tue, 3 May 2022 17:55:02 +0000 Subject: [PATCH 0738/1394] gnu: rsync: Update to 3.2.4. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/rsync.scm (rsync): Update to 3.2.4. Signed-off-by: Ludovic Courtès --- gnu/packages/rsync.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/rsync.scm b/gnu/packages/rsync.scm index 13717f0249d..2b3673c90c5 100644 --- a/gnu/packages/rsync.scm +++ b/gnu/packages/rsync.scm @@ -39,14 +39,14 @@ (define-public rsync (package (name "rsync") - (version "3.2.3") + (version "3.2.4") (source (origin (method url-fetch) (uri (string-append "https://rsync.samba.org/ftp/rsync/src/rsync-" version ".tar.gz")) (sha256 (base32 - "03p5dha9g9krq61mdbcrjkpz5nglri0009ks2vs9k97f9i83rk5y")))) + "1lgslprbfirl9p9ca16syh0pzr4kgmrzdxwwayvb0ll0s0w1hxkg")))) (build-system gnu-build-system) (arguments `(#:configure-flags From 092ee3515520c759174d235910aefc3a54b00b97 Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Tue, 3 May 2022 17:54:16 +0000 Subject: [PATCH 0739/1394] gnu: casync: Update to 99559cd1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/sync.scm (casync): Update to 99559cd1. [source]: Remove patch. [arguments]: Fix installation. [native-inputs]: Add python. [inputs]: Add eudev. * gnu/packages/patches/casync-renameat2-declaration.patch: Delete file. * gnu/local.mk: Remove it. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 - .../casync-renameat2-declaration.patch | 27 -------- gnu/packages/sync.scm | 67 ++++++++++--------- 3 files changed, 37 insertions(+), 58 deletions(-) delete mode 100644 gnu/packages/patches/casync-renameat2-declaration.patch diff --git a/gnu/local.mk b/gnu/local.mk index 3de938e5d03..f6aae15e767 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -926,7 +926,6 @@ dist_patch_DATA = \ %D%/packages/patches/calibre-no-updates-dialog.patch \ %D%/packages/patches/calibre-remove-test-sqlite.patch \ %D%/packages/patches/calibre-remove-test-unrar.patch \ - %D%/packages/patches/casync-renameat2-declaration.patch \ %D%/packages/patches/catdoc-CVE-2017-11110.patch \ %D%/packages/patches/circos-remove-findbin.patch \ %D%/packages/patches/cdparanoia-fpic.patch \ diff --git a/gnu/packages/patches/casync-renameat2-declaration.patch b/gnu/packages/patches/casync-renameat2-declaration.patch deleted file mode 100644 index 74c2ca7b3ca..00000000000 --- a/gnu/packages/patches/casync-renameat2-declaration.patch +++ /dev/null @@ -1,27 +0,0 @@ -Fix build failure on glibc 2.28 where 'renameat2' would end up being -declared twice: . - -From 625244ca47e8ee1375d2d0092271bfd13b0913ea Mon Sep 17 00:00:00 2001 -From: Daniel Mack -Date: Tue, 13 Nov 2018 17:52:48 +0100 -Subject: [PATCH] meson.build: pass -D_GNU_SOURCE when checking for functions - -As described in #166, -D_GNU_SOURCE needs to be passed to the meson function -availability checker. h/t to @tomeon for providing a link to the solution as -well. ---- - meson.build | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/meson.build b/meson.build -index f42ed16..c0f741e 100644 ---- a/meson.build -+++ b/meson.build -@@ -78,6 +78,6 @@ foreach ident : [ - ['copy_file_range', '''#include - #include '''], - ] -- have = cc.has_function(ident[0], prefix : ident[1]) -+ have = cc.has_function(ident[0], args : '-D_GNU_SOURCE', prefix : ident[1]) - conf.set10('HAVE_' + ident[0].to_upper(), have) - endforeach diff --git a/gnu/packages/sync.scm b/gnu/packages/sync.scm index 801aef3f443..3dfaf407963 100644 --- a/gnu/packages/sync.scm +++ b/gnu/packages/sync.scm @@ -451,35 +451,42 @@ written in @command{scsh}. It makes use of @command{unison} and (license license:expat)))) (define-public casync - (package - (name "casync") - (version "2") - (home-page "https://github.com/systemd/casync/") - (source (origin - (method git-fetch) - (uri (git-reference - (url home-page) - (commit (string-append "v" version)))) - (sha256 - (base32 - "0znkp3fcksrykcsv06y2mjvf2lbwmin25snmvfa8i5qfm3f4rm88")) - (file-name (string-append name "-" version "-checkout")) - (patches (search-patches "casync-renameat2-declaration.patch")))) - (build-system meson-build-system) - (native-inputs - (list pkg-config python-sphinx rsync)) ;for tests - (inputs - (list xz ;for liblzma - `(,zstd "lib") - curl - acl - libselinux - fuse - openssl - zlib)) - (synopsis "File synchronization and backup system") - (description - "casync is a @dfn{content-addressable data synchronizer} that can be used + (let ((commit "99559cd1d8cea69b30022261b5ed0b8021415654") + (revision "0")) + (package + (name "casync") + (version (git-version "2" revision commit)) + (home-page "https://github.com/systemd/casync/") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (sha256 + (base32 + "139g82rkwv1kzss6crfmw3p01xnyjzz66b1ckprpbfncxb24047w")) + (file-name (string-append name "-" version "-checkout")))) + (build-system meson-build-system) + (arguments + `(#:configure-flags + (let ((out (assoc-ref %outputs "out"))) + (list (string-append "-Dudevrulesdir=" + out "/lib/udev/rules.d"))))) + (native-inputs + (list pkg-config python python-sphinx rsync)) ;for tests + (inputs + (list xz ;for liblzma + `(,zstd "lib") + curl + acl + libselinux + eudev + fuse + openssl + zlib)) + (synopsis "File synchronization and backup system") + (description + "casync is a @dfn{content-addressable data synchronizer} that can be used as the basis of a backup system. It is: @itemize @@ -490,7 +497,7 @@ large file systems or directory trees; over the Internet in an HTTP and CDN friendly way; @item An efficient backup system. @end itemize\n") - (license license:lgpl2.1+))) + (license license:lgpl2.1+)))) (define-public rclone (package From 38f3d38eadf435c76306f2fc65f4b70ba49c8392 Mon Sep 17 00:00:00 2001 From: Rene Saavedra Date: Mon, 23 May 2022 15:09:29 -0500 Subject: [PATCH 0740/1394] gnu: xpad: Update to 5.8.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnome.scm (xpad): Update to 5.8.0. [inputs]: Replace gtksourceview-3 with gtksourceview. Signed-off-by: Ludovic Courtès --- gnu/packages/gnome.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 7868063a05e..81b74a2497c 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -10211,7 +10211,7 @@ is suitable as a default application in a Desktop environment.") (define-public xpad (package (name "xpad") - (version "5.1.0") + (version "5.8.0") (source (origin (method url-fetch) @@ -10220,13 +10220,13 @@ is suitable as a default application in a Desktop environment.") name "-" version ".tar.bz2")) (sha256 (base32 - "0l0g5x8g6dwhf5ksnqqrjjsycy57kcvdslkmsr6bl3vrsjd7qml3")))) + "1sc2dz4yxx6glnqpnhiby85g2blnsfn8d3fvbaqhdi2hi0q54q7j")))) (build-system gnu-build-system) (native-inputs (list autoconf automake `(,gtk+ "bin") intltool pkg-config)) (inputs - (list gtksourceview-3 libsm)) + (list gtksourceview libsm)) (home-page "https://wiki.gnome.org/Apps/Xpad") (synopsis "Virtual sticky note") (description From b67fd51902014bf5ab21fd9a93f2ac710cb173bd Mon Sep 17 00:00:00 2001 From: jgart Date: Mon, 23 May 2022 13:58:59 -0500 Subject: [PATCH 0741/1394] gnu: pre-commit: Update to 2.19.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/version-control.scm (pre-commit): Update to 2.19.0. Signed-off-by: Ludovic Courtès --- gnu/packages/version-control.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 9d0786d2d9c..30d15919abe 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1651,7 +1651,7 @@ visualize your public Git repositories on a web interface.") (define-public pre-commit (package (name "pre-commit") - (version "2.18.1") + (version "2.19.0") (source (origin (method git-fetch) ; no tests in PyPI release @@ -1660,7 +1660,7 @@ visualize your public Git repositories on a web interface.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "08c1nxqyqmy5sbmfnpvc8z82cx1rv9q290w7x2mrm0nd718s9yvp")))) + (base32 "102z1n6wjrmk5h4p59l929bi0r91bl3vz62j4k6sz2j7k0a791g5")))) (build-system python-build-system) (arguments `(#:phases From 5e5e37fbc47236651d59448da60860c88e9241ed Mon Sep 17 00:00:00 2001 From: ykonai Date: Mon, 23 May 2022 01:43:01 +0200 Subject: [PATCH 0742/1394] gnu: rspamd: Update to 3.2 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/mail.scm (rspamd): Update to 3.2 I also added a new build option, that changes the LOCAL_CONFDIR variable to /etc/rspamd. This allows for rspamd configuration via the /etc/rspamd/local.d and override.d directories, which by default were located in the PREFIX which is in /gnu/store. Signed-off-by: Ludovic Courtès --- gnu/packages/mail.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index b44ba90582f..c0b43f7c7fa 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -4365,7 +4365,7 @@ on RFC 3501 and original @code{imaplib} module.") (define-public rspamd (package (name "rspamd") - (version "2.7") + (version "3.2") (source (origin (method git-fetch) @@ -4373,11 +4373,12 @@ on RFC 3501 and original @code{imaplib} module.") (url "https://github.com/rspamd/rspamd") (commit version))) (sha256 - (base32 "0fw6nbfc3xqapzq5nydakwgpw6cz6vb3qby2aqlr06lzf87d3hic")) + (base32 "122d5m1nfxxz93bhsk8lm4dazvdknzphb0a1188m7bsa4iynbfv2")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments - '(#:configure-flags '("-DENABLE_LUAJIT=ON"))) + '(#:configure-flags '("-DENABLE_LUAJIT=ON" + "-DLOCAL_CONFDIR=/etc/rspamd"))) (inputs (list openssl glib @@ -4386,7 +4387,7 @@ on RFC 3501 and original @code{imaplib} module.") sqlite file icu4c - pcre + pcre2 zlib perl libsodium)) From 8d5b27cae9e9727573ccb2b8ae7e40f89c869b56 Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Sun, 22 May 2022 16:28:33 -0400 Subject: [PATCH 0743/1394] gnu: emacs-vterm: Update to 0.0.1-1.b447235. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-vterm): Update to 0.0.1-1.b447235. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 94b2571a155..8fe450cf7be 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -24175,8 +24175,8 @@ stored playlists.") (define-public emacs-vterm (let ((version "0.0.1") - (revision "0") - (commit "a670b786539d3c8865d8f68fe0c67a2d4afbf1aa")) + (revision "1") + (commit "b44723552f86407d528c4a6c8057382c061b008e")) (package (name "emacs-vterm") (version (git-version version revision commit)) @@ -24188,7 +24188,7 @@ stored playlists.") (file-name (git-file-name name version)) (sha256 (base32 - "0s244crjkbzl2jhp9m4sm1xdhbpxwph0m3jg18livirgajvdz6hn")))) + "0rq2skwylvc7s4vfpbbsdykws4akyp9sc6xgrh2ql5yydhhnv2h3")))) (build-system emacs-build-system) (arguments `(#:modules ((guix build emacs-build-system) From d730bbbbb3d47d566bd24d0b4a44dcc808435f24 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 18 May 2022 21:31:18 +0100 Subject: [PATCH 0744/1394] gnu: Add calceph. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/astronomy.scm (calceph): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/astronomy.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index cd0949b04f6..86705bbf19f 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -39,6 +39,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages curl) #:use-module (gnu packages fontutils) + #:use-module (gnu packages gcc) #:use-module (gnu packages gettext) #:use-module (gnu packages gl) #:use-module (gnu packages glib) @@ -71,6 +72,40 @@ #:use-module (ice-9 match) #:use-module (srfi srfi-1)) +(define-public calceph + (package + (name "calceph") + (version "3.5.1") + (source + (origin + (method url-fetch) + (uri (string-append + "https://www.imcce.fr/content/medias/recherche/equipes/asd/calceph/calceph-" + version ".tar.gz")) + (sha256 + (base32 "078wn773pwf4pg9m0h0l00g4aq744pq1rb6kz6plgdpzp3hhpk1k")))) + (build-system gnu-build-system) + (native-inputs + (list gfortran)) + (home-page "https://www.imcce.fr/inpop/calceph") + (synopsis "Astronomical library to access the binary planetary ephemeris files") + (description + "The CALCEPH Library is designed to access the binary planetary ephemeris files, +such INPOPxx and JPL DExxx ephemeris files, (called @code{original JPL binary} or +@code{INPOP 2.0 or 3.0 binary} ephemeris files in the next sections) and the SPICE +kernel files (called @code{SPICE} ephemeris files in the next sections). At the +moment, supported SPICE files are: + +@itemize +@item text Planetary Constants Kernel (KPL/PCK) files; +@item binary PCK (DAF/PCK) files; +@item binary SPK (DAF/SPK) files containing segments of type 1, 2, 3, 5, 8, 9, +12, 13, 17, 18, 19, 20, 21, 102, 103 and 120; +@item meta kernel (KPL/MK) files; +@item frame kernel (KPL/FK) files (only basic support). +@end itemize\n") + (license license:cecill))) + (define-public cfitsio (package (name "cfitsio") From fed51b26141548a5bae349a5e1d8d6f681320f4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 30 May 2022 16:34:12 +0200 Subject: [PATCH 0745/1394] gnu: calceph: Add 'release-monitoring-url' property. * gnu/packages/astronomy.scm (calceph)[properties]: New field. --- gnu/packages/astronomy.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 86705bbf19f..93c45d57804 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -88,6 +88,7 @@ (native-inputs (list gfortran)) (home-page "https://www.imcce.fr/inpop/calceph") + (properties `((release-monitoring-url . ,home-page))) (synopsis "Astronomical library to access the binary planetary ephemeris files") (description "The CALCEPH Library is designed to access the binary planetary ephemeris files, From df43e8d45c6af3235dd66b6d2ffebbbbf0899bda Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Mon, 30 May 2022 20:57:37 +0200 Subject: [PATCH 0746/1394] gnu: quodlibet: Correct wrappers. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/music.scm (quodlibet)[#:phases]: Rename ‘wrap-gi-typelib’ to ‘wrap-extra-paths’. Use ‘=’ for GI_TYPELIB_PATH. Add ‘GST_PLUGIN_SYSTEM_PATH’ with suffix binding. --- gnu/packages/music.scm | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 9011f262a47..f00fe715c84 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -6919,14 +6919,17 @@ streaming audio server.") (format #t "test suite not run~%")))) (add-after 'install 'glib-or-gtk-wrap ; ensure icons loaded (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)) - (add-after 'install 'wrap-gi-typelib ; GObject Introspection + (add-after 'install 'wrap-extra-paths (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) - (gi-typelib-path (getenv "GI_TYPELIB_PATH"))) - (for-each (lambda (prog) - (wrap-program (string-append out "/bin/" prog) - `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path)))) - '("exfalso" "quodlibet")))))))) + (gi-typelib-path (getenv "GI_TYPELIB_PATH")) + (gst-plugins-path (getenv "GST_PLUGIN_SYSTEM_PATH"))) + (for-each + (lambda (prog) + (wrap-program (string-append out "/bin/" prog) + `("GI_TYPELIB_PATH" ":" = (,gi-typelib-path)) + `("GST_PLUGIN_SYSTEM_PATH" ":" suffix (,gst-plugins-path)))) + '("exfalso" "quodlibet")))))))) (native-inputs (list xvfb-run gettext-minimal)) (inputs (list adwaita-icon-theme From 216fb59b9b854c565b48a9497c21757f8db72cb5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 21:00:37 +0200 Subject: [PATCH 0747/1394] gnu: non-sequencer: Update to 1.9.5-5.257ec59. * gnu/packages/music.scm (non-sequencer): Update to 1.9.5-5.257ec59. [source]: Use fork as old repository is defunct; use git-file-name and git-version. [arguments]: Remove python-2; add phase to replace bundled waf. [native-inputs]: Add python-waf. (non-session-manager)[native-inputs]: Add python-waf. (non-mixer)[inputs]: Add lv2 and lilv. [native-inputs]: Add python-waf. (non-timeline)[native-inputs]: Add python-waf. --- gnu/packages/music.scm | 29 +++++++++++++++++------------ 1 file changed, 17 insertions(+), 12 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index f00fe715c84..6a26b30a91b 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -1752,20 +1752,20 @@ music theorist Paul Nauert's quantization grids or Q-Grids, for short.") (define-public non-sequencer ;; The latest tagged release is three years old and uses a custom build ;; system, so we take the last commit. - (let ((commit "5ae43bb27c42387052a73e5ffc5d33efb9d946a9") - (revision "4")) + (let ((commit "257ec5951e7d4086344d98c99ebbe569f7c31211") + (revision "5")) (package (name "non-sequencer") - (version (string-append "1.9.5-" revision "." (string-take commit 7))) + (version (git-version "1.9.5" revision commit)) (source (origin (method git-fetch) (uri (git-reference - (url "git://git.tuxfamily.org/gitroot/non/non.git") + (url "https://github.com/falkTX/non/") (commit commit))) (sha256 (base32 - "1cljkkyi9dxqpqhx8y6l2ja4zjmlya26m26kqxml8gx08vyvddhx")) - (file-name (string-append name "-" version "-checkout")))) + "0h6ycm3nbb5lvjvhymz5xlj8wqm3z3ggzn4ghmw6xyzd0l7c3m8b")) + (file-name (git-file-name name version)))) (build-system waf-build-system) (arguments `(#:tests? #f ;no "check" target @@ -1776,11 +1776,16 @@ music theorist Paul Nauert's quantization grids or Q-Grids, for short.") (%current-system)))) '("--disable-sse") '())) - #:python ,python-2)) + #:phases + (modify-phases %standard-phases + (add-before 'configure 'setup-waf + (lambda* (#:key inputs #:allow-other-keys) + (let ((waf (assoc-ref inputs "python-waf"))) + (copy-file (string-append waf "/bin/waf") "waf"))))))) (inputs (list jack-1 libsigc++-2 liblo ntk)) (native-inputs - (list pkg-config)) + (list python-waf pkg-config)) (home-page "https://non.tuxfamily.org/wiki/Non%20Sequencer") (synopsis "Pattern-based MIDI sequencer") (description @@ -1802,7 +1807,7 @@ transport is rolling.") (inputs (list jack-1 liblo ntk)) (native-inputs - (list pkg-config)) + (list python-waf pkg-config)) (home-page "https://non.tuxfamily.org/nsm/") (synopsis "Audio session management") (description @@ -1820,9 +1825,9 @@ communicate with the session management daemon.") `(cons "--project=mixer" (delete "--project=sequencer" ,flags))))) (inputs - (list jack-1 liblo ladspa lrdf ntk)) + (list jack-1 liblo ladspa lrdf ntk lv2 lilv)) (native-inputs - (list pkg-config)) + (list python-waf pkg-config)) (home-page "https://non.tuxfamily.org/wiki/Non%20Mixer") (synopsis "Modular digital audio mixer") (description @@ -1844,7 +1849,7 @@ studio.") (inputs (list jack-1 liblo libsndfile ntk)) (native-inputs - (list pkg-config)) + (list python-waf pkg-config)) (home-page "https://non.tuxfamily.org/wiki/Non%20Timeline") (synopsis "Modular digital audio timeline arranger") (description From 1257c4c663b83c3724b4f003b0f55ea418385bef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 22:13:51 +0200 Subject: [PATCH 0748/1394] gnu: Add python-session-info. * gnu/packages/python-xyz.scm (python-session-info): New variable. --- gnu/packages/python-xyz.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index acd5954fb6e..9c0851ea44b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10485,6 +10485,25 @@ and statistical routines from scipy and statsmodels.") (base32 "1bjnshjz4d6z3vrwfwall1a3yh8h3a1h47c3fg7458x9426alcys"))))))) +(define-public python-session-info + (package + (name "python-session-info") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "session_info" version)) + (sha256 + (base32 + "1dxnrgaxd2nb44n423mnrx119hmnh2yxdnzaw8mg60x7rh1mxniw")))) + (build-system python-build-system) + (propagated-inputs (list python-stdlib-list)) + (home-page "https://gitlab.com/joelostblom/session_info") + (synopsis "Output version information for modules currently loaded") + (description + "This package outputs version information for modules loaded in the current +session, Python, and the OS.") + (license license:bsd-3))) + (define-public python-mpmath (package (name "python-mpmath") From 7c8f3dfa34bf644066035a352ddf8f5191b3ec80 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 22:40:02 +0200 Subject: [PATCH 0749/1394] gnu: python-dask: Update to 2022.05.2. * gnu/packages/python-xyz.scm (python-dask): Update to 2022.05.2. --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9c0851ea44b..4a5db7c87b5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24844,16 +24844,16 @@ decisions with any given backend.") (define-public python-dask (package (name "python-dask") - (version "2021.11.2") + (version "2022.05.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/dask/dask/") - (commit "5a8275dd53193b47457cdfadc0e2356ea3eb6ccd"))) + (commit "8db1597c9745543df3129399bead5fbc95a54571"))) (file-name (git-file-name name version)) (sha256 - (base32 "0h8w7c03mn6s2mmwbqd2sqay3k4vaqiwlsbvliziggw28042zfw2")) + (base32 "1xfk3wml972z502w5ii5mn03ls3rg5p4hqgl0hkicgpmzlyz9kph")) (snippet ;; Delete generated copy of python-versioneer. We recreate it below. '(delete-file "versioneer.py")))) From ca2516f0653c33494701ad02638bf5d7c5c74f25 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 22:59:14 +0200 Subject: [PATCH 0750/1394] gnu: python-leidenalg: Update to 0.8.10. * gnu/packages/graph.scm (python-leidenalg): Update to 0.8.10. [arguments]: Patch setup.py. [native-inputs]: Remove python-setuptools; add python-setuptools-scm. --- gnu/packages/graph.scm | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 6d1575a0bda..0b8e76f676a 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -495,14 +495,14 @@ Faiss library."))) (define-public python-leidenalg (package (name "python-leidenalg") - (version "0.7.0") + (version "0.8.10") (source (origin (method url-fetch) (uri (pypi-uri "leidenalg" version)) (sha256 (base32 - "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1")))) + "1hbvagp1yyazvl7cid7mii5263qi48lpkq543n5w71qysgz1f0v7")))) (build-system python-build-system) (arguments '(#:tests? #f ;tests are not included @@ -510,12 +510,14 @@ Faiss library."))) (add-after 'unpack 'fix-requirements (lambda _ (substitute* "setup.py" + (("self.external = False") + "self.external = True") + (("self.use_pkgconfig = False") + "self.use_pkgconfig = True") (("python-igraph >=") "igraph >="))))))) (native-inputs - ;; XXX: setuptools >= 58 as shipped with Python 3.9+ removes support - ;; for lib2to3, so use this older variant. - (list pkg-config python-setuptools)) + (list pkg-config python-setuptools-scm)) (inputs (list igraph)) (propagated-inputs From 0bcd28e58cb8f06bc6d0e47da22cef3d834a6da7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 23:07:52 +0200 Subject: [PATCH 0751/1394] gnu: python-scanpy: Update to 1.9.1. * gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.1. [arguments]: Add phase 'set-numba-cache-dir; disable more broken tests. [propagated-inputs]: Add python-dask and python-session-info; replace python-louvain-0.7 with python-louvain. --- gnu/packages/bioinformatics.scm | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1d8397c1aa5..23c0024e52b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12248,7 +12248,7 @@ implementation differs in these ways: (define-public python-scanpy (package (name "python-scanpy") - (version "1.8.2") + (version "1.9.1") (source (origin (method git-fetch) @@ -12258,7 +12258,7 @@ implementation differs in these ways: (file-name (git-file-name name version)) (sha256 (base32 - "14zax23lqinv7xyv3491vpl3ydi38naiwaxg5mkfs5zk2406cqdr")))) + "0k524xnx3dvpz5yx65p316wghvi01zs17is8w2m3w2qywiswk0sl")))) (build-system python-build-system) (arguments `(#:phases @@ -12278,6 +12278,10 @@ implementation differs in these ways: (invoke "python" "-m" "pip" "install" wheel (string-append "--prefix=" out))) (find-files "dist" "\\.whl$"))))) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp"))) (replace 'check (lambda* (#:key tests? inputs #:allow-other-keys) (when tests? @@ -12285,6 +12289,7 @@ implementation differs in these ways: (delete-file-recursively "scanpy/tests/notebooks") (delete-file "scanpy/tests/test_clustering.py") (delete-file "scanpy/tests/test_datasets.py") + (delete-file "scanpy/tests/test_normalization.py") (delete-file "scanpy/tests/test_score_genes.py") (delete-file "scanpy/tests/test_highly_variable_genes.py") @@ -12293,6 +12298,9 @@ implementation differs in these ways: (delete-file "scanpy/tests/test_preprocessing.py") (delete-file "scanpy/tests/test_read_10x.py") + ;; These two fail with "ValueError: I/O operation on closed file." + (delete-file "scanpy/tests/test_neighbors_key_added.py") + ;; TODO: these fail with TypingError and "Use of unsupported ;; NumPy function 'numpy.split'". (delete-file "scanpy/tests/test_metrics.py") @@ -12318,17 +12326,20 @@ implementation differs in these ways: " and not test_clustermap" ;; These try to connect to the network + " and not test_scrublet_plots" " and not test_plot_rank_genes_groups_gene_symbols" + " and not test_pca_n_pcs" " and not test_pca_chunked" " and not test_pca_sparse" " and not test_pca_reproducible")))))))) (propagated-inputs (list python-anndata + python-dask python-h5py python-igraph python-joblib python-legacy-api-wrap - python-louvain-0.7 + python-louvain python-matplotlib python-natsort python-networkx @@ -12339,6 +12350,7 @@ implementation differs in these ways: python-scikit-learn python-scipy python-seaborn + python-session-info python-sinfo python-statsmodels python-tables From f12d08c6d2a306d1e103af44e2260b8aa7f1d91d Mon Sep 17 00:00:00 2001 From: Pierre Langlois Date: Tue, 17 May 2022 20:46:09 +0100 Subject: [PATCH 0752/1394] gnu: python-click@8: Remove redundant package. The python-click package is already version 8. * gnu/packages/python-xyz.scm (python-click-8): Remove variable. (python-proselint)[propagated-inputs]: Depend on python-click. --- gnu/packages/python-xyz.scm | 16 ++-------------- 1 file changed, 2 insertions(+), 14 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4a5db7c87b5..a8ad4dd7786 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -61,7 +61,7 @@ ;;; Copyright © 2019 Jack Hill ;;; Copyright © 2019, 2020, 2021 Guillaume Le Vaillant ;;; Copyright © 2019, 2020 Alex Griffin -;;; Copyright © 2019, 2020, 2021 Pierre Langlois +;;; Copyright © 2019, 2020, 2021, 2022 Pierre Langlois ;;; Copyright © 2019 Jacob MacDonald ;;; Copyright © 2019, 2020, 2021 Giacomo Leidi ;;; Copyright © 2019 Wiktor Żelazny @@ -3657,18 +3657,6 @@ with sensible defaults out of the box.") (base32 "0njsm0wn31l21bi118g5825ma5sa3rwn7v2x4wjd7yiiahkri337")))) (arguments `()))) -(define-public python-click-8 - (package (inherit python-click) - (name "python-click") - (version "8.1.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "click" version)) - (sha256 - (base32 "0whs38a2i0561kwbgigs6vic9r0a1887m2v1aw3rmv6r2kz0g5s7")))) - (arguments `()))) - (define-public python-cligj (package (name "python-cligj") @@ -18375,7 +18363,7 @@ characters, mouse support, and auto suggestions.") (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - (list python-click-8 python-future python-six)) + (list python-click python-future python-six)) (home-page "https://github.com/amperser/proselint") (synopsis "Linter for prose") (description "@code{python-proselint} is a linter for English prose, that From b8fc3403d3c09c00a4b0ab68c9f4f296928479b9 Mon Sep 17 00:00:00 2001 From: Pierre Langlois Date: Tue, 17 May 2022 20:46:53 +0100 Subject: [PATCH 0753/1394] gnu: gandi.cli: Fix by downgrading python-click. * gnu/packages/python-xyz.scm (python-click-7): New variable. * gnu/packages/networking.scm (gandi.cli)[inputs]: Depend on python-click-7. --- gnu/packages/networking.scm | 3 ++- gnu/packages/python-xyz.scm | 12 ++++++++++++ 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 99145b2b470..2d1cb50f4ad 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -48,6 +48,7 @@ ;;; Copyright © 2021 Guillaume Le Vaillant ;;; Copyright © 2021 Maxime Devos ;;; Copyright © 2022 Simon South +;;; Copyright © 2022 Pierre Langlois ;;; ;;; This file is part of GNU Guix. ;;; @@ -1655,7 +1656,7 @@ round-robin fashion.") (propagated-inputs (list openssh)) ; used by gandi/cli/modules/iass.py (inputs - (list openssl python-click python-ipy python-pyyaml python-requests)) + (list openssl python-click-7 python-ipy python-pyyaml python-requests)) (home-page "https://cli.gandi.net") (synopsis "Command-line interface to the Gandi.net Web API") (description diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a8ad4dd7786..9ba7266fa94 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3645,6 +3645,18 @@ composable way with as little code as necessary. Its name stands for with sensible defaults out of the box.") (license license:bsd-3))) +(define-public python-click-7 + (package (inherit python-click) + (name "python-click") + (version "7.1.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "click" version)) + (sha256 + (base32 "06kbzd6sjfkqan3miwj9wqyddfxc2b6hi7p5s4dvqjb3gif2bdfj")))) + (arguments `()))) + (define-public python-click-5 (package (inherit python-click) (name "python-click") From 6169c582d154f65a9834a4e07226de4fc98ea67f Mon Sep 17 00:00:00 2001 From: yarl baudig Date: Mon, 30 May 2022 09:20:24 +0200 Subject: [PATCH 0754/1394] gnu: emacs-helpful: Update to 0.19 * gnu/packages/patches/emacs-helpful-docstring-test.patch: New file. * gnu/packages/emacs-xyz.scm (emacs-helpful): Update to 0.19. [source]: Use the patch. * gnu/local.mk (dist_patch_DATA): Register the patch. Signed-off-by: Liliana Marie Prikler --- gnu/local.mk | 1 + gnu/packages/emacs-xyz.scm | 6 ++++-- .../emacs-helpful-fix-docstring-test.patch | 18 ++++++++++++++++++ 3 files changed, 23 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/emacs-helpful-fix-docstring-test.patch diff --git a/gnu/local.mk b/gnu/local.mk index f6aae15e767..bb2913c3a26 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1028,6 +1028,7 @@ dist_patch_DATA = \ %D%/packages/patches/emacs-git-email-missing-parens.patch \ %D%/packages/patches/emacs-fix-scheme-indent-function.patch \ %D%/packages/patches/emacs-json-reformat-fix-tests.patch \ + %D%/packages/patches/emacs-helpful-fix-docstring-test.patch \ %D%/packages/patches/emacs-highlight-stages-add-gexp.patch \ %D%/packages/patches/emacs-hyperbole-toggle-messaging.patch \ %D%/packages/patches/emacs-libgit-use-system-libgit2.patch \ diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 8fe450cf7be..22d723c879f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20130,7 +20130,7 @@ downloading manager for Emacs.") (define-public emacs-helpful (package (name "emacs-helpful") - (version "0.18") + (version "0.19") (source (origin (method git-fetch) @@ -20139,7 +20139,9 @@ downloading manager for Emacs.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0gdjxykqkal2x765mi51m99i5ql23i1fy909wy4mzj5ajhjfgqcc")))) + (base32 "0qwsifzsjw95l83m7z07fr9h1sqbhggwmcps1qgbddpan2a8ab8a")) + ;; Cherry-picked from upstream, remove when bumping to 0.20. + (patches (search-patches "emacs-helpful-fix-docstring-test.patch")))) (build-system emacs-build-system) (propagated-inputs (list emacs-elisp-refs emacs-dash emacs-s emacs-f emacs-shut-up)) diff --git a/gnu/packages/patches/emacs-helpful-fix-docstring-test.patch b/gnu/packages/patches/emacs-helpful-fix-docstring-test.patch new file mode 100644 index 00000000000..de40010fa24 --- /dev/null +++ b/gnu/packages/patches/emacs-helpful-fix-docstring-test.patch @@ -0,0 +1,18 @@ +This patch fixing a build failure has been cherry-picked from upstream. +Originally submitted as pull request by Erik Šabič. +See also . +diff --git a/test/helpful-unit-test.el b/test/helpful-unit-test.el +index a07aa8e..8a95129 100644 +--- a/test/helpful-unit-test.el ++++ b/test/helpful-unit-test.el +@@ -119,7 +119,9 @@ bar"))) + (should + (equal + (helpful--docstring #'test-foo-advised t) +- "Docstring here too."))) ++ (if (version< emacs-version "28") ++ "Docstring here too." ++ "Docstring here too.\n\nThis function has :around advice: `ad-Advice-test-foo-advised'.")))) + + (defun test-foo-no-docstring () + nil) From 8b680b00d49bdd1064918ffd221ffbcc11ba902a Mon Sep 17 00:00:00 2001 From: Pavel Shlyak Date: Thu, 26 May 2022 21:00:51 +0300 Subject: [PATCH 0755/1394] image: Add fat32 support. * gnu/build/image.scm (make-vfat-image): Pass fs-bits as an argument and force 1kb logical sector size only if "ESP" flag is set. (make-partition-image): Add "fat32" partition type, support explicit "fat16" type with vfat alias. * gnu/system/image.scm (partition->dos-type partition): Return file system IDs for "fat16" and "fat32" partitions. (partition->gpt-type partition): Ditto. Signed-off-by: Mathieu Othacehe --- gnu/build/image.scm | 24 ++++++++++++++---------- gnu/system/image.scm | 8 ++++++-- 2 files changed, 20 insertions(+), 12 deletions(-) diff --git a/gnu/build/image.scm b/gnu/build/image.scm index 3e8b94e2d65..ddfd34c111a 100644 --- a/gnu/build/image.scm +++ b/gnu/build/image.scm @@ -95,16 +95,18 @@ turn doesn't take any constant overhead into account, force a 1-MiB minimum." (estimate-partition-size root) size))))))) -(define* (make-vfat-image partition target root) +(define* (make-vfat-image partition target root fs-bits) "Handle the creation of VFAT partition images. See 'make-partition-image'." (let ((size (partition-size partition)) - (label (partition-label partition))) - (invoke "fakeroot" "mkdosfs" "-n" label "-C" target - "-F" "16" "-S" "1024" - (size-in-kib - (if (eq? size 'guess) - (estimate-partition-size root) - size))) + (label (partition-label partition)) + (flags (partition-flags partition))) + (apply invoke "fakeroot" "mkdosfs" "-n" label "-C" target + "-F" (number->string fs-bits) + (size-in-kib + (if (eq? size 'guess) + (estimate-partition-size root) + size)) + (if (member 'esp flags) (list "-S" "1024") '())) (for-each (lambda (file) (unless (member file '("." "..")) (invoke "mcopy" "-bsp" "-i" target @@ -120,8 +122,10 @@ ROOT directory to populate the image." (cond ((string-prefix? "ext" type) (make-ext-image partition target root)) - ((string=? type "vfat") - (make-vfat-image partition target root)) + ((or (string=? type "vfat") (string=? type "fat16")) + (make-vfat-image partition target root 16)) + ((string=? type "fat32") + (make-vfat-image partition target root 32)) (else (raise (condition (&message diff --git a/gnu/system/image.scm b/gnu/system/image.scm index dd32e58c2d5..f02f6e0b8c2 100644 --- a/gnu/system/image.scm +++ b/gnu/system/image.scm @@ -312,7 +312,9 @@ used in the image." (cond ((member 'esp flags) "0xEF") ((string-prefix? "ext" file-system) "0x83") - ((string=? file-system "vfat") "0x0E") + ((or (string=? file-system "vfat") + (string=? file-system "fat16")) "0x0E") + ((string=? file-system "fat32") "0x0C") (else (raise (condition (&message @@ -329,7 +331,9 @@ used in the image." (cond ((member 'esp flags) "U") ((string-prefix? "ext" file-system) "L") - ((string=? file-system "vfat") "F") + ((or (string=? file-system "vfat") + (string=? file-system "fat16") + (string=? file-system "fat32")) "F") (else (raise (condition (&message From 098d0012f56b7eb654a0e8412d5030584b163c12 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 30 May 2022 23:30:24 +0200 Subject: [PATCH 0756/1394] gnu: python-fsspec: Update to 2022.5.0. * gnu/packages/python-xyz.scm (python-fsspec): Update to 2022.5.0. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9ba7266fa94..3ac9adee1ee 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24821,14 +24821,14 @@ append on old values. Partd excels at shuffling operations.") (define-public python-fsspec (package (name "python-fsspec") - (version "0.6.1") + (version "2022.5.0") (source (origin (method url-fetch) (uri (pypi-uri "fsspec" version)) (sha256 (base32 - "1g9ba8v04s1nrh7pvzfm2md7ivl2mrz3hcq3y9d1a44gd62h17zj")))) + "1d43qiz8g395042a52yswz6j7q41gvrv3k53wvxn1rs4bk3mjm3s")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; there are none (home-page "https://github.com/intake/filesystem_spec") From 3d5144db5a8ee87fd75693d68c0ed0f84a7d4d20 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 31 May 2022 15:15:34 +0200 Subject: [PATCH 0757/1394] gnu: r-haven: Fix build. * gnu/packages/cran.scm (r-haven)[arguments]: Adjust 'unbundle-readstat phase. Reported-by: Jonas Freimuth. --- gnu/packages/cran.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2bbb3f6a157..26e3e0e87af 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3493,9 +3493,12 @@ including functions for geolocation and routing.") (modify-phases %standard-phases (add-after 'unpack 'unbundle-readstat (lambda _ - ;; Not required, since we’re not building readstat. - (substitute* "src/Makevars" - (("-lz") "-lreadstat"))))))) + ;; We’re not building readstat. + (substitute* "configure" + (("exit 1") "")) ;don't be so dramatic! + (substitute* '("src/Makevars.in" + "configure") + (("^PKG_LIBS=.*") "PKG_LIBS=\"-lreadstat\"\n"))))))) (inputs (list readstat)) (native-inputs From 07909eb09210597df998d2b88ec555bb648f8066 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 31 May 2022 15:17:00 +0200 Subject: [PATCH 0758/1394] gnu: python-distributed: Update to 2022.05.2. * gnu/packages/python-science.scm (python-distributed): Update to 2022.05.2. [arguments]: Remove 'sanity-check phase; adjust 'check phase. [propagated-inputs]: Add python-urllib3. [native-inputs]: Add python-pytest-timeout and python-flaky. --- gnu/packages/python-science.scm | 148 +++++++++++++++++++++++++++++--- 1 file changed, 134 insertions(+), 14 deletions(-) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index af91f73ec1f..5fbb7fd1c82 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1016,7 +1016,7 @@ and more (define-public python-distributed (package (name "python-distributed") - (version "2021.11.2") + (version "2022.05.2") (source (origin ;; The test files are not included in the archive on pypi @@ -1027,7 +1027,7 @@ and more (file-name (git-file-name name version)) (sha256 (base32 - "1p20cbyabzl7rs8y3ydzszsskh4kw088m252ghgairhs0p2f95hl")) + "009jrlk7kmazrd3nkl217cl3x5ddg7kw9mqdgq1z9knv5h1rm8qv")) ;; Delete bundled copy of python-versioneer. (snippet '(delete-file "versioneer.py")))) (build-system python-build-system) @@ -1053,23 +1053,139 @@ and more (("\"dask-worker\"") (format #false "\"~a/bin/dask-worker\"" (assoc-ref outputs "out")))))) + ;; ERROR: distributed==2022.5.2 + ;; ContextualVersionConflict (locket 0.2.0 + ;; (/gnu/store/...-python-locket-0.2.0/lib/python3.9/site-packages), + ;; Requirement.parse('locket>=1.0.0'), {'distributed'}) + (delete 'sanity-check) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (setenv "DISABLE_IPV6" "1") - (invoke "pytest" "-vv" "distributed" - "-m" "not slow and not gpu and not ipython and not avoid_ci" + ;; The integration tests are all problematic to some + ;; degree. They either require network access or some + ;; other setup. We only run the tests in + ;; distributed/tests. + (for-each (lambda (dir) + (delete-file-recursively + (string-append "distributed/" dir "/tests"))) + (list "cli" "comm" "dashboard" "deploy" "diagnostics" + "http" "http/scheduler" "http/worker" + "protocol" "shuffle")) + (invoke "python" "-m" "pytest" "-vv" "distributed" + "-m" + (string-append "not slow" + " and not flaky" + " and not gpu" + " and not ipython" + " and not avoid_ci") "-k" - ;; TODO: These tests fail for unknown reasons: (string-append - ;; TimeoutExpired - "not test_text" - ;; AssertionError - " and not test_version_option" - ;; "The 'distributed' distribution was not found" - " and not test_register_backend_entrypoint" - ;; "AttributeError: module 'distributed.dashboard' has no attribute 'scheduler'" - " and not test_get_client_functions_spawn_clusters")))))))) + ;; These fail because they require network access, + ;; specifically access to 8.8.8.8. + "not " + (string-join + (list + "TestClientSecurityLoader.test_security_loader" + "test_BatchedSend" + "test_allowed_failures_config" + "test_async_context_manager" + "test_async_with" + "test_client_repr_closed_sync" + "test_close_closed" + "test_close_fast_without_active_handlers" + "test_close_grace_period_for_handlers" + "test_close_loop_sync" + "test_close_properly" + "test_close_twice" + "test_compression" + "test_connection_pool" + "test_connection_pool_close_while_connecting" + "test_connection_pool_detects_remote_close" + "test_connection_pool_outside_cancellation" + "test_connection_pool_remove" + "test_connection_pool_respects_limit" + "test_connection_pool_tls" + "test_counters" + "test_dashboard_host" + "test_dashboard_link_cluster" + "test_dashboard_link_inproc" + "test_deserialize_error" + "test_dont_override_default_get" + "test_errors" + "test_fail_to_pickle_target_2" + "test_file_descriptors_dont_leak" + "test_finished" + "test_get_client_functions_spawn_clusters" + "test_host_uses_scheduler_protocol" + "test_identity_inproc" + "test_identity_tcp" + "test_large_packets_inproc" + "test_locked_comm_drop_in_replacement" + "test_locked_comm_intercept_read" + "test_locked_comm_intercept_write" + "test_multiple_listeners" + "test_no_dangling_asyncio_tasks" + "test_plugin_exception" + "test_plugin_internal_exception" + "test_plugin_multiple_exceptions" + "test_ports" + "test_preload_import_time" + "test_queue_in_task" + "test_quiet_client_close" + "test_rebalance_sync" + "test_repr_localcluster" + "test_require_encryption" + "test_rpc_default" + "test_rpc_inproc" + "test_rpc_message_lifetime_default" + "test_rpc_message_lifetime_inproc" + "test_rpc_message_lifetime_tcp" + "test_rpc_serialization" + "test_rpc_tcp" + "test_rpc_tls" + "test_rpc_with_many_connections_inproc" + "test_rpc_with_many_connections_tcp" + "test_scheduler_file" + "test_security_dict_input_no_security" + "test_security_loader" + "test_security_loader_ignored_if_explicit_security_provided" + "test_security_loader_ignored_if_returns_none" + "test_send_after_stream_start" + "test_send_before_close" + "test_send_before_start" + "test_send_recv_args" + "test_send_recv_cancelled" + "test_sending_traffic_jam" + "test_serializers" + "test_server" + "test_server_comms_mark_active_handlers" + "test_shutdown" + "test_shutdown_localcluster" + "test_teardown_failure_doesnt_crash_scheduler" + "test_threadpoolworkers_pick_correct_ioloop" + "test_tls_listen_connect" + "test_tls_temporary_credentials_functional" + "test_variable_in_task" + "test_worker_preload_text" + "test_worker_uses_same_host_as_nanny") + " and not ") + + ;; These fail because it doesn't find dask[distributed] + " and not test_quiet_close_process" + + ;; This one fails because of a silly assert failure: + ;; '2022.05.2' == '2022.5.2' + " and not test_version" + " and not test_git_revision" + + ;; Recursion stack failure. No idea what they + ;; expected to happen. + " and not test_stack_overflow" + + ;; These tests are rather flaky + " and not test_quiet_quit_when_cluster_leaves" + " and not multiple_clients_restart")))))))) (propagated-inputs (list python-click python-cloudpickle @@ -1083,9 +1199,13 @@ and more python-tblib python-toolz python-tornado-6 + python-urllib3 python-zict)) (native-inputs - (list python-pytest python-versioneer)) + (list python-pytest + python-pytest-timeout + python-flaky + python-versioneer)) (home-page "https://distributed.dask.org") (synopsis "Distributed scheduler for Dask") (description "Dask.distributed is a lightweight library for distributed From 34c8558af2d0a72a7f90dab9106addbf9b3e6c5f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 27 May 2022 09:59:12 -0400 Subject: [PATCH 0759/1394] gnu: guile-ac-d-bus: Build and install info manual. * gnu/packages/guile-xyz.scm (guile-ac-d-bus) [arguments]: Use gexps. [phases]{build-doc, install-doc}: New phases. [native-inputs]: Add texinfo. --- gnu/packages/guile-xyz.scm | 72 +++++++++++++++++++++----------------- 1 file changed, 40 insertions(+), 32 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 2c18fc138c0..0b1537a9639 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -3846,42 +3846,50 @@ and space linear in the size of the input text.") "0rl809qimhgz6b0rixakb42r2l4g53jr09a2g0s1hxgab0blz0kb")))) (build-system guile-build-system) (arguments - `(#:implicit-inputs? #f ;needs nothing but Guile - #:compile-flags '("--r6rs" "-Wunbound-variable" "-Warity-mismatch") - #:phases (modify-phases %standard-phases - (add-before 'build 'adjust-for-guile - (lambda _ - ;; Adjust source file names for Guile. - (define (guile-sls->sls file) - (string-append (string-drop-right - file (string-length ".guile.sls")) - ".sls")) + (list + #:implicit-inputs? #f ;needs nothing but Guile + #:compile-flags #~(list "--r6rs" "-Wunbound-variable" "-Warity-mismatch") + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'adjust-for-guile + (lambda _ + ;; Adjust source file names for Guile. + (define (guile-sls->sls file) + (string-append (string-drop-right + file (string-length ".guile.sls")) + ".sls")) - ;; Remove files targeting other implementations: - ;; *.mosh.sls, etc. - (for-each delete-file - (find-files - "compat" - (lambda (file stat) - (not (string-contains file ".guile."))))) + ;; Remove files targeting other implementations: *.mosh.sls, + ;; etc. + (for-each delete-file + (find-files + "compat" + (lambda (file stat) + (not (string-contains file ".guile."))))) - ;; Rename *.guile.sls to *.sls so the ".guile" bit does - ;; not appear in .go file names. - (for-each (lambda (file) - (rename-file file (guile-sls->sls file))) - (find-files "compat" "\\.guile\\.sls")) + ;; Rename *.guile.sls to *.sls so the ".guile" bit does not + ;; appear in .go file names. + (for-each (lambda (file) + (rename-file file (guile-sls->sls file))) + (find-files "compat" "\\.guile\\.sls")) - ;; Move directories under d-bus/ to match module names. - (mkdir "d-bus") - (for-each (lambda (directory) - (rename-file directory - (string-append "d-bus/" - directory))) - '("compat" "protocol")) - - #t))))) + ;; Move directories under d-bus/ to match module names. + (mkdir "d-bus") + (for-each (lambda (directory) + (rename-file directory + (string-append "d-bus/" + directory))) + '("compat" "protocol")))) + (add-after 'build 'build-doc + (lambda _ + (with-directory-excursion "docs" + (invoke "makeinfo" "ac-d-bus")))) + (add-after 'install 'install-doc + (lambda _ + (install-file "docs/ac-d-bus.info" + (string-append #$output "/share/info"))))))) (native-inputs - (list guile-3.0)) + (list guile-3.0 texinfo)) (propagated-inputs (list guile-packrat)) (synopsis "D-Bus protocol implementation in R6RS Scheme") From d11d27e2e4a0e6d132127f5130533b0ce9d04481 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 27 May 2022 11:48:14 -0400 Subject: [PATCH 0760/1394] gnu: guile-ac-d-bus: Run test suite. * gnu/packages/patches/guile-ac-d-bus-fix-tests.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/guile-xyz.scm (guile-ac-d-bus) [source]: Apply patch. [phases]{check}: New phase. [native-inputs]: Add bash-minimal. --- gnu/local.mk | 1 + gnu/packages/guile-xyz.scm | 15 ++++++++-- .../patches/guile-ac-d-bus-fix-tests.patch | 28 +++++++++++++++++++ 3 files changed, 42 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/guile-ac-d-bus-fix-tests.patch diff --git a/gnu/local.mk b/gnu/local.mk index bb2913c3a26..93b4902151d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1236,6 +1236,7 @@ dist_patch_DATA = \ %D%/packages/patches/guile-3.0-relocatable.patch \ %D%/packages/patches/guile-linux-syscalls.patch \ %D%/packages/patches/guile-3.0-linux-syscalls.patch \ + %D%/packages/patches/guile-ac-d-bus-fix-tests.patch \ %D%/packages/patches/guile-cross-compilation.patch \ %D%/packages/patches/guile-fibers-destroy-peer-schedulers.patch \ %D%/packages/patches/guile-fibers-wait-for-io-readiness.patch \ diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 0b1537a9639..3c02a85bc39 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -3843,7 +3843,8 @@ and space linear in the size of the input text.") (file-name (git-file-name name version)) (sha256 (base32 - "0rl809qimhgz6b0rixakb42r2l4g53jr09a2g0s1hxgab0blz0kb")))) + "0rl809qimhgz6b0rixakb42r2l4g53jr09a2g0s1hxgab0blz0kb")) + (patches (search-patches "guile-ac-d-bus-fix-tests.patch")))) (build-system guile-build-system) (arguments (list @@ -3884,12 +3885,22 @@ and space linear in the size of the input text.") (lambda _ (with-directory-excursion "docs" (invoke "makeinfo" "ac-d-bus")))) + (add-after 'build-doc 'check + (lambda* (#:key (tests? #t) #:allow-other-keys) + (when tests? + ;; There is no locale for the ö character, which crashes + ;; substitute*; reset the conversion strategy to workaround it. + (with-fluids ((%default-port-conversion-strategy 'substitute)) + (substitute* (find-files "tests") + (("#!/usr/bin/env scheme-script") + (string-append "#!" (which "guile"))))) + (invoke "./run-tests.sh")))) (add-after 'install 'install-doc (lambda _ (install-file "docs/ac-d-bus.info" (string-append #$output "/share/info"))))))) (native-inputs - (list guile-3.0 texinfo)) + (list bash-minimal guile-3.0 texinfo)) (propagated-inputs (list guile-packrat)) (synopsis "D-Bus protocol implementation in R6RS Scheme") diff --git a/gnu/packages/patches/guile-ac-d-bus-fix-tests.patch b/gnu/packages/patches/guile-ac-d-bus-fix-tests.patch new file mode 100644 index 00000000000..19fd475c39f --- /dev/null +++ b/gnu/packages/patches/guile-ac-d-bus-fix-tests.patch @@ -0,0 +1,28 @@ +Submitted upstream: https://gitlab.com/weinholt/ac-d-bus/-/merge_requests/3 + +diff --git a/tests/test-signature.sps b/tests/test-signature.sps +index 278401b..cc5574f 100755 +--- a/tests/test-signature.sps ++++ b/tests/test-signature.sps +@@ -43,6 +43,7 @@ + (format-type-signature '(message BYTE BYTE BYTE BYTE UINT32 UINT32 + (ARRAY (STRUCT BYTE VARIANT))))) + ++(define fail-count (test-runner-fail-count (test-runner-get))) + (test-end) + +-(exit (if (zero? (test-runner-fail-count (test-runner-get))) 0 1)) ++(exit (if (zero? fail-count) 0 1)) +diff --git a/tests/test-wire.sps b/tests/test-wire.sps +index c3354bf..06ae73b 100755 +--- a/tests/test-wire.sps ++++ b/tests/test-wire.sps +@@ -147,6 +147,7 @@ + #x08 #x01 #x67 #x00 #x00 #x00 #x00 #x00 #x05 #x01 #x75 #x00 #x04 #x00 #x00 #x00 + #x07 #x01 #x73 #x00 #x06 #x00 #x00 #x00 #x3A #x31 #x2E #x32 #x39 #x38 #x00 #x00))) + ++(define fail-count (test-runner-fail-count (test-runner-get))) + (test-end) + +-(exit (if (zero? (test-runner-fail-count (test-runner-get))) 0 1)) ++(exit (if (zero? fail-count) 0 1)) From 2c4c504272643f6d42a03178b684eeb3f4615438 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 31 May 2022 20:45:05 +0300 Subject: [PATCH 0761/1394] gnu: python-sip-4: Update to 4.19.25. * gnu/packages/qt.scm (python-sip-4): Update to 4.19.25. --- gnu/packages/qt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index bf2a3e88c2f..ea82ab07d0e 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -2000,7 +2000,7 @@ module provides support functions to the automatically generated code.") (package (inherit python-sip) (name "python-sip") - (version "4.19.24") + (version "4.19.25") (source (origin (method url-fetch) @@ -2010,7 +2010,7 @@ module provides support functions to the automatically generated code.") "/sip-" version ".tar.gz"))) (sha256 (base32 - "1ra15vb5i9gkg2vdvh16cq9x2mmzw1yi3xphxs8q34q1pf83gkgd")))) + "04a23cgsnx150xq86w1z44b6vr2zyazysy9mqax0fy346zlr77dk")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-wrapper))) From be85c4d40fdbc72dba2ac1ed5f381f6da43d83ba Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 31 May 2022 19:53:32 +0200 Subject: [PATCH 0762/1394] gnu: ungoogled-chromium: Update to 102.0.5005.61-3. * gnu/packages/chromium.scm (%ungoogled-revision): Bump to latest. (%ungoogled-origin): Update hash. --- gnu/packages/chromium.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index 4c62acd2b55..5936ab23c31 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -313,7 +313,7 @@ '("third_party/blink/perf_tests")) (define %chromium-version "102.0.5005.61") -(define %ungoogled-revision (string-append %chromium-version "-1")) +(define %ungoogled-revision (string-append %chromium-version "-3")) (define %debian-revision "debian/102.0.5005.61-1") (define %ungoogled-origin @@ -324,7 +324,7 @@ (file-name (git-file-name "ungoogled-chromium" %ungoogled-revision)) (sha256 (base32 - "1hlyi6k894blkkqmqsizx72bag2vj6wlpza0fvi8db5wp6i5b58g")))) + "19i4ygxjm503dmck3bdqv3fcpda3dp9wr7z306pi6i1k989rbs8l")))) (define %debian-origin (origin From 20432b839b6bc9e30c156d412597b734a726940d Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 30 May 2022 18:11:43 -0400 Subject: [PATCH 0763/1394] gnu: icecat: Update to 91.10.0-guix0-preview1 [security fixes]. Includes fixes for CVE-2022-31736, CVE-2022-31737, CVE-2022-31738, CVE-2022-31739, CVE-2022-31740, CVE-2022-31741, CVE-2022-31742, and CVE-2022-31747. * gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes. --- gnu/packages/gnuzilla.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index f3eb1f7b57d..4728b5e3475 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -716,8 +716,8 @@ in C/C++.") ;; XXXX: Workaround 'snippet' limitations. (define computed-origin-method (@@ (guix packages) computed-origin-method)) -(define %icecat-version "91.9.1-guix0-preview1") -(define %icecat-build-id "20220520000000") ;must be of the form YYYYMMDDhhmmss +(define %icecat-version "91.10.0-guix0-preview1") +(define %icecat-build-id "20220531000000") ;must be of the form YYYYMMDDhhmmss ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat' @@ -739,11 +739,11 @@ in C/C++.") "firefox-" upstream-firefox-version ".source.tar.xz")) (sha256 (base32 - "0q5mmgjy9qpcvkpcwf0ic7kjwr7zk601wvi81wm3qdz4g56py3h9")))) + "1fz11rmbb0qjcp84wz7hmq7wy1zh9bk6vk47xwhrinmmifrqqnl2")))) - (upstream-icecat-base-version "91.9.1") ; maybe older than base-version + (upstream-icecat-base-version "91.10.0") ; maybe older than base-version ;;(gnuzilla-commit (string-append "v" upstream-icecat-base-version)) - (gnuzilla-commit "c5a087823119d3e3109cca9cab222ee926d7a2a2") + (gnuzilla-commit "4c39c619daf344f36962d958d809f6d42d3fce4e") (gnuzilla-source (origin (method git-fetch) @@ -755,7 +755,7 @@ in C/C++.") (string-take gnuzilla-commit 8))) (sha256 (base32 - "1ry5nrb74xr2lah2mijpjymv0kbq0731qli60s3rb93l5f6bkp0j")))) + "1fizsq0dphm40nj6vnvjp87v34iyg78gllv3jp5ssn43ln4jiyb7")))) ;; 'search-patch' returns either a valid file name or #f, so wrap it ;; in 'assume-valid-file-name' to avoid 'local-file' warnings. From 51b671596012e8c68a1a40a59f5d770b3a1e2484 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 28 Apr 2022 23:58:36 -0400 Subject: [PATCH 0764/1394] packages: Fix typo in package-superseded doc. * guix/packages.scm (package-superseded): Fix typo. --- guix/packages.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/packages.scm b/guix/packages.scm index 7ee65e9b6be..74253896182 100644 --- a/guix/packages.scm +++ b/guix/packages.scm @@ -662,7 +662,7 @@ interfaces." (assoc-ref (package-properties p) 'hidden?)) (define (package-superseded p) - "Return the package the supersedes P, or #f if P is still current." + "Return the package that supersedes P, or #f if P is still current." (assoc-ref (package-properties p) 'superseded)) (define (deprecated-package old-name p) From 6c956243bc7972644e947563a45e33d73042afdc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 25 Apr 2022 22:52:15 -0400 Subject: [PATCH 0765/1394] etc/committer: Prefix (sxml xpath) symbols to avoid name conflict. This avoids a naming conflict for 'filter', provided by both (srfi srfi-1) and (sxml xpath). * etc/committer.scm.in: Use 'use-modules' instead of 'import', and use a prefix for the (sxml xpath) module. (new-sexp): Adjust accordingly. (change-commit-message): Likewise. --- etc/committer.scm.in | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/etc/committer.scm.in b/etc/committer.scm.in index 5a57d51577a..3b37320e89c 100755 --- a/etc/committer.scm.in +++ b/etc/committer.scm.in @@ -6,6 +6,7 @@ ;;; Copyright © 2020, 2021 Ricardo Wurmus ;;; Copyright © 2021 Sarah Morgensen ;;; Copyright © 2021 Xinglu Chen +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -28,19 +29,19 @@ ;;; Code: -(import (sxml xpath) - (srfi srfi-1) - (srfi srfi-2) - (srfi srfi-9) - (srfi srfi-11) - (srfi srfi-26) - (ice-9 format) - (ice-9 popen) - (ice-9 match) - (ice-9 rdelim) - (ice-9 regex) - (ice-9 textual-ports) - (guix gexp)) +(use-modules ((sxml xpath) #:prefix xpath:) + (srfi srfi-1) + (srfi srfi-2) + (srfi srfi-9) + (srfi srfi-11) + (srfi srfi-26) + (ice-9 format) + (ice-9 popen) + (ice-9 match) + (ice-9 rdelim) + (ice-9 regex) + (ice-9 textual-ports) + (guix gexp)) (define* (break-string str #:optional (max-line-length 70)) "Break the string STR into lines that are no longer than MAX-LINE-LENGTH. @@ -214,10 +215,10 @@ corresponding to the top-level definition containing the staged changes." (define* (change-commit-message file-name old new #:optional (port (current-output-port))) "Print ChangeLog commit message for changes between OLD and NEW." (define (get-values expr field) - (match ((sxpath `(// ,field quasiquote *)) expr) + (match ((xpath:sxpath `(// ,field quasiquote *)) expr) (() ;; New-style plain lists - (match ((sxpath `(// ,field list *)) expr) + (match ((xpath:sxpath `(// ,field list *)) expr) ((inner) inner) (_ '()))) ;; Old-style labelled inputs @@ -234,7 +235,7 @@ corresponding to the top-level definition containing the staged changes." (define variable-name (second old)) (define version - (and=> ((sxpath '(// version *any*)) new) + (and=> ((xpath:sxpath '(// version *any*)) new) first)) (format port "gnu: ~a: Update to ~a.~%~%* ~a (~a): Update to ~a.~%" From 5e6efdfeecae82315862ebee95ce02bb868eb0f3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 25 Apr 2022 22:56:08 -0400 Subject: [PATCH 0766/1394] etc/committer: Teach it how to commit package removal. * etc/committer.scm.in (hunk-types): New variable. (): Rename hunk-definition? getter to 'hunk-type'. (diff-info): Mute a git warning by separating file names from arguments with '--'. Rename the 'definitions?' variable to 'type'. Use the 'addition type when a new package addition is detected, 'removal when removed else #f. (add-commit-message): Re-indent. (remove-commit-message): New procedure. (main)[definitions]: Make commit message conditional depending on whether it is an addition or removal. [changes]: Adjust indentation. --- etc/committer.scm.in | 164 ++++++++++++++++++++++++------------------- 1 file changed, 91 insertions(+), 73 deletions(-) diff --git a/etc/committer.scm.in b/etc/committer.scm.in index 3b37320e89c..e7f1ca8c45a 100755 --- a/etc/committer.scm.in +++ b/etc/committer.scm.in @@ -101,12 +101,16 @@ LINE-NO in PORT." (read-line port) (loop (1- i) last-top-level-sexp)))))) +;;; Whether the hunk contains a newly added package (definition), a removed +;;; package (removal) or something else (#false). +(define hunk-types '(addition removal #false)) + (define-record-type (make-hunk file-name old-line-number new-line-number diff-lines - definition?) + type) hunk? (file-name hunk-file-name) ;; Line number before the change @@ -115,8 +119,8 @@ LINE-NO in PORT." (new-line-number hunk-new-line-number) ;; The full diff to be used with "git apply --cached" (diff-lines hunk-diff-lines) - ;; Does this hunk add a definition? - (definition? hunk-definition?)) + ;; Does this hunk add or remove a package? + (type hunk-type)) ;one of 'hunk-types' (define* (hunk->patch hunk #:optional (port (current-output-port))) (let ((file-name (hunk-file-name hunk))) @@ -134,25 +138,30 @@ LINE-NO in PORT." ;; new definitions with changes to existing ;; definitions. "--unified=1" - "gnu"))) + "--" "gnu"))) (define (extract-line-number line-tag) (abs (string->number (car (string-split line-tag #\,))))) (define (read-hunk) (let loop ((lines '()) - (definition? #false)) + (type #false)) (let ((line (read-line port 'concat))) (cond ((eof-object? line) - (values (reverse lines) definition?)) + (values (reverse lines) type)) ((or (string-prefix? "@@ " line) (string-prefix? "diff --git" line)) (unget-string port line) - (values (reverse lines) definition?)) + (values (reverse lines) type)) (else (loop (cons line lines) - (or definition? - (string-prefix? "+(define" line)))))))) + (or type + (cond + ((string-prefix? "+(define" line) + 'addition) + ((string-prefix? "-(define" line) + 'removal) + (else #false))))))))) (define info (let loop ((acc '()) (file-name #f)) @@ -167,13 +176,13 @@ LINE-NO in PORT." (match (string-split line #\space) ((_ old-start new-start . _) (let-values - (((diff-lines definition?) (read-hunk))) + (((diff-lines type) (read-hunk))) (loop (cons (make-hunk file-name (extract-line-number old-start) (extract-line-number new-start) (cons (string-append line "\n") diff-lines) - definition?) acc) + type) acc) file-name))))) (else (loop acc file-name)))))) (close-pipe port) @@ -263,10 +272,18 @@ corresponding to the top-level definition containing the staged changes." (listify added)))))))))) '(inputs propagated-inputs native-inputs))) -(define* (add-commit-message file-name variable-name #:optional (port (current-output-port))) - "Print ChangeLog commit message for a change to FILE-NAME adding a definition." - (format port - "gnu: Add ~a.~%~%* ~a (~a): New variable.~%" +(define* (add-commit-message file-name variable-name + #:optional (port (current-output-port))) + "Print ChangeLog commit message for a change to FILE-NAME adding a +definition." + (format port "gnu: Add ~a.~%~%* ~a (~a): New variable.~%" + variable-name file-name variable-name)) + +(define* (remove-commit-message file-name variable-name + #:optional (port (current-output-port))) + "Print ChangeLog commit message for a change to FILE-NAME removing a +definition." + (format port "gnu: Remove ~a.~%~%* ~a (~a): Delete variable.~%" variable-name file-name variable-name)) (define* (custom-commit-message file-name variable-name message changelog @@ -345,66 +362,67 @@ modifying." (() (display "Nothing to be done.\n" (current-error-port))) (hunks - (let-values - (((definitions changes) - (partition hunk-definition? hunks))) + (let-values (((definitions changes) (partition hunk-type hunks))) + ;; Additions/removals. + (for-each + (lambda (hunk) + (and-let* ((define-line (find (cut string-match "(\\+|-)\\(define" <>) + (hunk-diff-lines hunk))) + (variable-name (and=> (string-tokenize define-line) + second)) + (commit-message-proc (match (hunk-type hunk) + ('addition add-commit-message) + ('removal remove-commit-message)))) + (commit-message-proc (hunk-file-name hunk) variable-name) + (let ((port (open-pipe* OPEN_WRITE + "git" "apply" + "--cached" + "--unidiff-zero"))) + (hunk->patch hunk port) + (unless (eqv? 0 (status:exit-val (close-pipe port))) + (error "Cannot apply"))) - ;; Additions. - (for-each (lambda (hunk) - (and-let* - ((define-line (find (cut string-prefix? "+(define" <>) - (hunk-diff-lines hunk))) - (variable-name (and=> (string-tokenize define-line) second))) - (add-commit-message (hunk-file-name hunk) variable-name) - (let ((port (open-pipe* OPEN_WRITE - "git" "apply" - "--cached" - "--unidiff-zero"))) - (hunk->patch hunk port) - (unless (eqv? 0 (status:exit-val (close-pipe port))) - (error "Cannot apply"))) + (let ((port (open-pipe* OPEN_WRITE "git" "commit" "-F" "-"))) + (commit-message-proc (hunk-file-name hunk) variable-name port) + (usleep %delay) + (unless (eqv? 0 (status:exit-val (close-pipe port))) + (error "Cannot commit")))) + (usleep %delay)) + definitions)) - (let ((port (open-pipe* OPEN_WRITE "git" "commit" "-F" "-"))) - (add-commit-message (hunk-file-name hunk) - variable-name port) - (usleep %delay) + ;; Changes. + (for-each + (match-lambda + ((new old . hunks) + (for-each (lambda (hunk) + (let ((port (open-pipe* OPEN_WRITE + "git" "apply" + "--cached" + "--unidiff-zero"))) + (hunk->patch hunk port) (unless (eqv? 0 (status:exit-val (close-pipe port))) - (error "Cannot commit")))) - (usleep %delay)) - definitions) - - ;; Changes. - (for-each (match-lambda - ((new old . hunks) - (for-each (lambda (hunk) - (let ((port (open-pipe* OPEN_WRITE - "git" "apply" - "--cached" - "--unidiff-zero"))) - (hunk->patch hunk port) - (unless (eqv? 0 (status:exit-val (close-pipe port))) - (error "Cannot apply"))) - (usleep %delay)) - hunks) - (define copyright-line - (any (lambda (line) (and=> (string-prefix? "+;;; Copyright ©" line) - (const line))) - (hunk-diff-lines (first hunks)))) - (cond - (copyright-line - (add-copyright-line copyright-line)) - (else - (let ((port (open-pipe* OPEN_WRITE "git" "commit" "-F" "-"))) - (change-commit-message* (hunk-file-name (first hunks)) - old new) - (change-commit-message* (hunk-file-name (first hunks)) - old new - port) - (usleep %delay) - (unless (eqv? 0 (status:exit-val (close-pipe port))) - (error "Cannot commit"))))))) - ;; XXX: we recompute the hunks here because previous - ;; insertions lead to offsets. - (new+old+hunks (diff-info))))))) + (error "Cannot apply"))) + (usleep %delay)) + hunks) + (define copyright-line + (any (lambda (line) (and=> (string-prefix? "+;;; Copyright ©" line) + (const line))) + (hunk-diff-lines (first hunks)))) + (cond + (copyright-line + (add-copyright-line copyright-line)) + (else + (let ((port (open-pipe* OPEN_WRITE "git" "commit" "-F" "-"))) + (change-commit-message* (hunk-file-name (first hunks)) + old new) + (change-commit-message* (hunk-file-name (first hunks)) + old new + port) + (usleep %delay) + (unless (eqv? 0 (status:exit-val (close-pipe port))) + (error "Cannot commit"))))))) + ;; XXX: we recompute the hunks here because previous + ;; insertions lead to offsets. + (new+old+hunks (diff-info)))))) (apply main (cdr (command-line))) From 5bc1ede86269b445c14afbf484fd8872c2275d4d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 26 Apr 2022 00:11:26 -0400 Subject: [PATCH 0767/1394] utils: Add a 'delete-expression' procedure. * guix/utils.scm: Fix copyright lines and order imports. (edit-expression): Fix typo in doc. Add a new 'include-trailing-newline?' keyword argument. Update doc. (delete-expression): New procedure. --- guix/utils.scm | 32 +++++++++++++++++++++----------- 1 file changed, 21 insertions(+), 11 deletions(-) diff --git a/guix/utils.scm b/guix/utils.scm index 44c46cb4a96..e169624ee62 100644 --- a/guix/utils.scm +++ b/guix/utils.scm @@ -8,12 +8,11 @@ ;;; Copyright © 2017 Mathieu Othacehe ;;; Copyright © 2018, 2020 Marius Bakke ;;; Copyright © 2020, 2021 Efraim Flashner -;;; Copyright © 2020 Maxim Cournoyer +;;; Copyright © 2020, 2021, 2022 Maxim Cournoyer ;;; Copyright © 2021 Simon Tournier ;;; Copyright © 2021 Chris Marusich ;;; Copyright © 2021 Maxime Devos ;;; Copyright © 2018 Steve Sprang -;;; Copyright © 2021 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -38,7 +37,6 @@ #:use-module (srfi srfi-26) #:use-module (srfi srfi-39) #:use-module (srfi srfi-71) - #:use-module (ice-9 ftw) #:use-module (rnrs io ports) ;need 'port-position' etc. #:use-module ((rnrs bytevectors) #:select (bytevector-u8-set!)) #:use-module (guix memoization) @@ -49,10 +47,11 @@ #:use-module ((guix combinators) #:select (fold2)) #:use-module (guix diagnostics) ;, &error-location, etc. #:use-module (ice-9 format) - #:use-module (ice-9 regex) - #:use-module (ice-9 match) - #:use-module (ice-9 format) + #:use-module (ice-9 ftw) #:use-module ((ice-9 iconv) #:prefix iconv:) + #:use-module (ice-9 match) + #:use-module (ice-9 regex) + #:use-module (ice-9 rdelim) #:use-module (ice-9 vlist) #:autoload (zlib) (make-zlib-input-port make-zlib-output-port) #:use-module (system foreign) @@ -133,6 +132,7 @@ readlink* go-to-location edit-expression + delete-expression filtered-port decompressed-port @@ -433,11 +433,13 @@ TARGET must be stat buffers as returned by 'stat'." (hash-set! %source-location-map target-key `(,@target-stamp ,source-map))))))) -(define* (edit-expression source-properties proc #:key (encoding "UTF-8")) +(define* (edit-expression source-properties proc #:key (encoding "UTF-8") + include-trailing-newline?) "Edit the expression specified by SOURCE-PROPERTIES using PROC, which should be a procedure that takes the original expression in string and returns a new -one. ENCODING will be used to interpret all port I/O, it default to UTF-8. -This procedure returns #t on success." +one. ENCODING will be used to interpret all port I/O, it defaults to UTF-8. +This procedure returns #t on success. When INCLUDE-TRAILING-NEWLINE? is true, +the trailing line is included in the edited expression." (define file (assq-ref source-properties 'filename)) (define line (assq-ref source-properties 'line)) (define column (assq-ref source-properties 'column)) @@ -446,10 +448,14 @@ This procedure returns #t on success." (call-with-input-file file (lambda (in) (let* ( ;; The start byte position of the expression. - (start (begin (go-to-location in (+ 1 line) (+ 1 column)) + (start (begin (go-to-location + in (+ 1 line) (+ 1 column)) (ftell in))) ;; The end byte position of the expression. - (end (begin (read in) (ftell in)))) + (end (begin (read in) + (when include-trailing-newline? + (read-line in)) + (ftell in)))) (seek in 0 SEEK_SET) ; read from the beginning of the file. (let* ((pre-bv (get-bytevector-n in start)) ;; The expression in string form. @@ -478,6 +484,10 @@ This procedure returns #t on success." (move-source-location-map! (stat in) (stat file) (+ 1 line)))))))))) +(define (delete-expression source-properties) + "Delete the expression specified by SOURCE-PROPERTIES." + (edit-expression source-properties (const "") #:include-trailing-newline? #t)) + ;;; ;;; Keyword arguments. From d7c4e7a0c238fa5e51b32a84e4c244d553f05621 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 26 Apr 2022 22:20:57 -0400 Subject: [PATCH 0768/1394] utils: Add a %guix-source-root-directory procedure. * guix/utils.scm (%guix-source-root-directory): New procedure. --- guix/utils.scm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/guix/utils.scm b/guix/utils.scm index e169624ee62..37b2e298008 100644 --- a/guix/utils.scm +++ b/guix/utils.scm @@ -78,6 +78,7 @@ substitute-keyword-arguments ensure-keyword-arguments + %guix-source-root-directory current-source-directory nix-system->gnu-triplet @@ -1031,6 +1032,10 @@ environment variable name like \"XDG_CONFIG_HOME\"; SUFFIX is a suffix like ;;; Source location. ;;; +(define (%guix-source-root-directory) + "Return the source root directory of the Guix found in %load-path." + (dirname (absolute-dirname "guix/packages.scm"))) + (define absolute-dirname ;; Memoize to avoid repeated 'stat' storms from 'search-path'. (mlambda (file) From 53cd5923ef97d8ef62a15aee3fb052cf845ee9da Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 15:54:32 -0400 Subject: [PATCH 0769/1394] diagnostics: Fix typo about 0-indexed COL in location. * guix/diagnostics.scm (source-properties->location): The location column is 0-indexed, not 1-indexed (the same as in source-properties, so the code is accurate). --- guix/diagnostics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/diagnostics.scm b/guix/diagnostics.scm index bf1ced8140e..9f0d558f2fe 100644 --- a/guix/diagnostics.scm +++ b/guix/diagnostics.scm @@ -232,7 +232,7 @@ macro-expansion time." by Guile's `source-properties', `frame-source', `current-source-location', etc." ;; In accordance with the GCS, start line and column numbers at 1. Note - ;; that unlike LINE and `port-column', COL is actually 1-indexed here... + ;; that unlike LINE and `port-column', COL is actually 0-indexed here... (match loc ((('line . line) ('column . col) ('filename . file)) ;common case (and file line col From 787a026f003fad544a81d3f13901603ee4e2469c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 12:56:49 -0400 Subject: [PATCH 0770/1394] gnu: Remove python-pytest-runner-2. * gnu/packages/check.scm (python-pytest-runner-2): Delete variable. (python2-pytest-runner): Likewise. --- gnu/packages/check.scm | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 8df5d874765..cb228c92001 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -1347,22 +1347,6 @@ Python's @code{random.seed}.") (define-public python2-pytest-runner (package-with-python2 python-pytest-runner)) -;; python-bleach 3.1.0 requires this ancient version of pytest-runner. -;; Remove once no longer needed. -(define-public python-pytest-runner-2 - (package - (inherit python-pytest-runner) - (version "2.12.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "pytest-runner" version)) - (sha256 - (base32 - "11ivjj9hfphkv4yfb2g74av4yy86y8gcbf7gbif0p1hcdfnxg3w6")))))) - -(define-public python2-pytest-runner-2 - (package-with-python2 python-pytest-runner-2)) - (define-public python-pytest-lazy-fixture (package (name "python-pytest-lazy-fixture") From 74641c7f66bc18a29aa92777a9616415eed6661e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:34:40 -0400 Subject: [PATCH 0771/1394] gnu: Remove python2-langkit. * gnu/packages/ada.scm (python2-langkit): Delete variable. --- gnu/packages/ada.scm | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/gnu/packages/ada.scm b/gnu/packages/ada.scm index a3bba245ecb..ea3e9c365b3 100644 --- a/gnu/packages/ada.scm +++ b/gnu/packages/ada.scm @@ -149,32 +149,3 @@ Ada system. Being an interpreter, it does not implement most representation clauses, and thus does not support systems programming close to the machine level.") (license license:gpl2+))) - -(define-public python2-langkit - (let ((commit "fe0bc8bf60dbd2937759810df76ac420d99fc15f") - (revision "0")) - (package - (name "python2-langkit") - (version (git-version "0.0.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/AdaCore/langkit") - (commit commit))) - (sha256 - (base32 - "1abqgw2p8pb1pm54my5kkbbixfhc6l0bwajdv1xlzyrh31xki3wx")) - (file-name (string-append name "-" version "-checkout")))) - (build-system python-build-system) - (propagated-inputs - (list python2-docutils python2-enum34 python2-funcy python2-mako)) - (arguments - `(#:python ,python-2 - #:tests? #f)) ; Tests would requite gprbuild (Ada). - (synopsis "Semantic analysis tool generator in Python") - (description "@code{Langkit} is a tool whose purpose is to make it easy -to create syntactic and semantic analysis engines. Write a language -specification in our Python DSL and Langkit will generate for you an -Ada library with bindings for the C and Python programming languages.") - (home-page "https://github.com/AdaCore/langkit/") - (license license:gpl3+)))) ; and gcc runtime library exception From cd46c8c34b4287f550d7744e31cf339dbd07dc45 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:34:44 -0400 Subject: [PATCH 0772/1394] gnu: Remove graphios. * gnu/packages/admin.scm (graphios): Delete variable. --- gnu/packages/admin.scm | 36 ------------------------------------ 1 file changed, 36 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 4e655551bd8..2d817fc00f1 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2567,42 +2567,6 @@ degradation and failure.") specified directories.") (license license:expat))) -(define-public graphios - (package - (name "graphios") - (version "2.0.3") - (source - (origin - (method url-fetch) - (uri (pypi-uri "graphios" version)) - (sha256 - (base32 - "1h87hvc315wg6lklbf4l7csd3n5pgljwrfli1p3nasdi0izgn66i")))) - (build-system python-build-system) - (arguments - ;; Be warned: Building with Python 3 succeeds, but the build process - ;; throws a syntax error that is ignored. - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-before 'build 'fix-setup.py - (lambda* (#:key outputs #:allow-other-keys) - ;; Fix hardcoded, unprefixed file names. - (let ((out (assoc-ref outputs "out"))) - (substitute* '("setup.py") - (("/etc") (string-append out "/etc")) - (("/usr") out) - (("distro_ver = .*") "distro_ver = ''")) - #t)))))) - (home-page "https://github.com/shawn-sterling/graphios") - (synopsis "Emit Nagios metrics to Graphite, Statsd, and Librato") - (description - "Graphios is a script to emit nagios perfdata to various upstream metrics -processing and time-series systems. It's currently compatible with Graphite, -Statsd, Librato and InfluxDB. Graphios can emit Nagios metrics to any number -of supported upstream metrics systems simultaneously.") - (license license:gpl2+))) - (define-public ansible-core (package (name "ansible-core") From cfce386aba9a052e4dfdb255e809f6b10f4f8242 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:34:56 -0400 Subject: [PATCH 0773/1394] gnu: Remove python2-pyalsaaudio. * gnu/packages/audio.scm (python2-pyalsaaudio): Delete variable. --- gnu/packages/audio.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 3639fe4b1a9..fd10574209d 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -4347,9 +4347,6 @@ It is currently fairly complete for PCM devices, and has some support for mixers.") (license license:psfl))) -(define-public python2-pyalsaaudio - (package-with-python2 python-pyalsaaudio)) - (define-public ldacbt (package (name "ldacbt") From a5a84babb985f3a3d242e3fb0e225dcc826875d5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:39:30 -0400 Subject: [PATCH 0774/1394] gnu: Remove ingen. * gnu/packages/music.scm (ingen): Delete variable. --- gnu/packages/music.scm | 85 ------------------------------------------ 1 file changed, 85 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 6a26b30a91b..8183ac942e1 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -4482,91 +4482,6 @@ filters, crossovers, simple gain plugins without zipper noise, switch box plugins, a switch trigger, a toggle switch, and a peakmeter.") (license license:gpl2+)))) -(define-public ingen - (let ((commit "cc4a4db33f4d126a07a4a498e053c5fb9a883be3") - (revision "2")) - (package - (name "ingen") - (version (string-append "0.0.0-" revision "." - (string-take commit 9))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://git.drobilla.net/ingen.git") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "1wg47vjw9djn99gbnsl2bcwj4xhdid61m4wrbn2nlp797flj91ic")))) - (build-system waf-build-system) - (arguments - `(#:python ,python-2 - #:tests? #f ; no "check" target - #:configure-flags (list "--no-webkit") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-wscript - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (substitute* "wscript" - ;; FIXME: Our version of lv2specgen.py does not behave as - ;; expected. Maybe this requires a development version of - ;; LV2. - (("lv2specgen.py") "touch ingen.lv2/ingen.html; echo") - ;; Add libraries to RUNPATH. - (("^(.+)target.*= 'src/ingen/ingen'," line prefix) - (string-append prefix - "linkflags=[\"-Wl,-rpath=" - out "/lib" "\"]," line))) - (substitute* '("src/wscript" - "src/server/wscript") - ;; Add libraries to RUNPATH. - (("bld.env.PTHREAD_LINKFLAGS" line) - (string-append line - " + [\"-Wl,-rpath=" out "/lib" "\"]"))) - (substitute* "src/client/wscript" - ;; Add libraries to RUNPATH. - (("^(.+)target.*= 'ingen_client'," line prefix) - (string-append prefix - "linkflags=[\"-Wl,-rpath=" - out "/lib" "\"]," line))) - (substitute* "src/gui/wscript" - ;; Add libraries to RUNPATH. - (("^(.+)target.* = 'ingen_gui.*" line prefix) - (string-append prefix - "linkflags=[\"-Wl,-rpath=" - out "/lib" "\"]," line)))) - #t))))) - (inputs - (list boost - python-rdflib - python - jack-1 - lv2 - lilv - raul-devel - ganv - suil - serd - sord - sratom - gtkmm-2)) - (native-inputs - (list pkg-config python-pygments)) - (home-page "https://drobilla.net/software/ingen") - (synopsis "Modular audio processing system") - (description "Ingen is a modular audio processing system for JACK and -LV2 based systems. Ingen is built around LV2 technology and a strict -separation of engine from user interface. The engine is controlled -exclusively through a protocol, and can execute as a headless process, with an -in-process GUI, or as an LV2 plugin. The GUI can run as a program which -communicates over a Unix or TCP/IP socket, or as an embeddable LV2 GUI which -communicates via LV2 ports. Any saved Ingen graph can be loaded as an LV2 -plugin on any system where Ingen is installed. This allows users to visually -develop custom plugins for use in other applications without programming.") - (license license:agpl3+)))) - (define-public qmidiarp (package (name "qmidiarp") From 94e8f2b9b513859d0883c714a911e1806c0a726a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:05 -0400 Subject: [PATCH 0775/1394] gnu: Remove raul. * gnu/packages/audio.scm (raul): Delete variable. --- gnu/packages/audio.scm | 26 -------------------------- 1 file changed, 26 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index fd10574209d..787e24dfe81 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -3163,32 +3163,6 @@ using Guix System.") ;; GNU Library (not Lesser) General Public License. (license license:lgpl2.0+))) -(define-public raul - (package - (name "raul") - (version "0.8.0") - (source (origin - (method url-fetch) - (uri (string-append "https://download.drobilla.net/raul-" - version ".tar.bz2")) - (sha256 - (base32 - "09ms40xc1x6qli6lxkwn5ibqh62nl9w7dq0b6jh1q2zvnrxwsd8b")))) - (build-system waf-build-system) - (arguments - `(#:python ,python-2 - #:tests? #f)) ; no check target - (inputs - (list glib boost)) - (native-inputs - (list pkg-config)) - (home-page "https://drobilla.net/software/raul/") - (synopsis "Real-time audio utility library") - (description - "Raul (Real-time Audio Utility Library) is a C++ utility library primarily -aimed at audio/musical applications.") - (license license:gpl2+))) - (define-public raul-devel (let ((commit "4db870b2b20b0a608ec0283139056b836c5b1624") (revision "1")) From 1a60e11a9835ccc25204f9787bcba1794d06f3c8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:39:51 -0400 Subject: [PATCH 0776/1394] gnu: Remove raul-devel. * gnu/packages/audio.scm (raul-devel): Delete variable. --- gnu/packages/audio.scm | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 787e24dfe81..ff786a680be 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -3163,23 +3163,6 @@ using Guix System.") ;; GNU Library (not Lesser) General Public License. (license license:lgpl2.0+))) -(define-public raul-devel - (let ((commit "4db870b2b20b0a608ec0283139056b836c5b1624") - (revision "1")) - (package (inherit raul) - (name "raul") - (version (string-append "0.8.9-" revision "." - (string-take commit 9))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://git.drobilla.net/raul.git") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "04fajrass3ymr72flx5js5vxc601ccrmx8ny8scp0rw7j0igyjdr"))))))) - (define-public resample (package (name "resample") From fd4668b1119753ae570f9f7ccf87bcf8c61636d4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:09 -0400 Subject: [PATCH 0777/1394] gnu: Remove python2-pyaudio. * gnu/packages/audio.scm (python2-pyaudio): Delete variable. --- gnu/packages/audio.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index ff786a680be..136004425a1 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2568,9 +2568,6 @@ compensation, (de)interleaving, and byte-swapping cross-platform audio input/output stream library.") (license license:expat))) -(define-public python2-pyaudio - (package-with-python2 python-pyaudio)) - (define-public python-pyliblo (package (name "python-pyliblo") From 7963e125681024ca58de2ce01597cd1706d2d1f5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:13 -0400 Subject: [PATCH 0778/1394] gnu: Remove python2-fastalite. * gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable. --- gnu/packages/bioinformatics.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 23c0024e52b..2073541ca5b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1306,9 +1306,6 @@ into separate processes; and more.") relying on a complex dependency tree.") (license license:expat))) -(define-public python2-fastalite - (package-with-python2 python-fastalite)) - (define-public biosoup (package (name "biosoup") From 9f4c958d62829ff56cd2703f82e22eb74b917b10 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:16 -0400 Subject: [PATCH 0779/1394] gnu: Remove grit. * gnu/packages/bioinformatics.scm (grit): Delete variable. --- gnu/packages/bioinformatics.scm | 42 --------------------------------- 1 file changed, 42 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2073541ca5b..2c5ad343f5a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4025,48 +4025,6 @@ standard linear mixed model resolver with application in @acronym{GWAS, genome-wide association studies}.") (license license:gpl3))) -(define-public grit - (package - (name "grit") - (version "2.0.5") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/nboley/grit") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'generate-from-cython-sources - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Delete these C files to force fresh generation from pyx sources. - (delete-file "grit/sparsify_support_fns.c") - (delete-file "grit/call_peaks_support_fns.c") - (substitute* "setup.py" - (("Cython.Setup") "Cython.Build")) - #t))))) - (inputs - (list python2-scipy python2-numpy python2-pysam python2-networkx)) - (native-inputs - (list python2-cython)) - ;; The canonical home page times out as of 2020-01-21. - (home-page "https://github.com/nboley/grit") - (synopsis "Tool for integrative analysis of RNA-seq type assays") - (description - "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify -full length transcript models. When none of these data sources are available, -GRIT can be run by providing a candidate set of TES or TSS sites. In -addition, GRIT can merge in reference junctions and gene boundaries. GRIT can -also be run in quantification mode, where it uses a provided GTF file and just -estimates transcript expression.") - (license license:gpl3+))) - (define-public hisat (package (name "hisat") From 98c4f97d18ad4cbc57459488e7d7edd0bd9d9a78 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:20 -0400 Subject: [PATCH 0780/1394] gnu: Remove ribodiff. * gnu/packages/bioinformatics.scm (ribodiff): Delete variable. --- gnu/packages/bioinformatics.scm | 46 --------------------------------- 1 file changed, 46 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2c5ad343f5a..32c6b29a68a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -840,52 +840,6 @@ frames} (ORFs) using ribosome profiling (ribo-seq) data. This package provides the Ribotaper pipeline.") (license license:gpl3+))) -(define-public ribodiff - (package - (name "ribodiff") - (version "0.2.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ratschlab/RiboDiff") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - ;; This test fails because of the matplotlib plotting backend. - (add-after 'unpack 'disable-plot-test - (lambda _ - (substitute* "src/ribodiff/functional_test_te.py" - (("pl\\.make_plots\\(data, opts\\)") "#")))) - ;; Generate an installable executable script wrapper. - (add-after 'unpack 'patch-setup.py - (lambda _ - (substitute* "setup.py" - (("^(.*)packages=.*" line prefix) - (string-append line "\n" - prefix "scripts=['scripts/TE.py'],\n")))))))) - (inputs - (list python2-numpy python2-matplotlib python2-scipy - python2-statsmodels)) - (native-inputs - (list python2-mock python2-nose)) - (home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") - (synopsis "Detect translation efficiency changes from ribosome footprints") - (description "RiboDiff is a statistical tool that detects the protein -translational efficiency change from Ribo-Seq (ribosome footprinting) and -RNA-Seq data. It uses a generalized linear model to detect genes showing -difference in translational profile taking mRNA abundance into account. It -facilitates us to decipher the translational regulation that behave -independently with transcriptional regulation.") - (license license:gpl3+))) - (define-public bioawk (package (name "bioawk") From d29d50a5565359bdd1a0217a0db8b0c3b75a401d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:24 -0400 Subject: [PATCH 0781/1394] gnu: Remove python2-pybigwig. * gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable. --- gnu/packages/bioinformatics.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 32c6b29a68a..ce1c1e8394c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2854,9 +2854,6 @@ files.") accessing bigWig files.") (license license:expat))) -(define-public python2-pybigwig - (package-with-python2 python-pybigwig)) - (define-public python-schema-salad (package (name "python-schema-salad") From 3d63c5f1ba4da00fd795e2e9a836806defc74378 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:30 -0400 Subject: [PATCH 0782/1394] gnu: tetoolkit: Update to 2.2.1b. * gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b. [python]: Delete argument. [phases]: Delete trailing #t. {make-writable}: Delete phase. {adjust-requirements}: New phase. {patch-invocations}: Use search-input-file. {wrap-program}: Use search-input-file. [inputs]: Remove python2-argparse. Replace python2-pysam with python-pysam. [home-page]: Update URL. --- gnu/packages/bioinformatics.scm | 53 +++++++++++++++++---------------- 1 file changed, 27 insertions(+), 26 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ce1c1e8394c..0a4c68e8c75 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2391,59 +2391,60 @@ high-throughput sequencing data – with an emphasis on simplicity.") (define-public tetoolkit (package (name "tetoolkit") - (version "2.0.3") + (version "2.2.1b") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/mhammell-laboratory/tetoolkit") + (url "https://github.com/mhammell-laboratory/TEtranscripts") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "1yzi0kfpzip8zpjb82x1ik6h22yzfyjiz2dv85v6as2awwqvk807")))) + "1m3xsydakhdan9gp9mfdz7llka5g6ak91d0mbl1cmmxq9qs6an4y")))) (build-system python-build-system) (arguments - `(#:python ,python-2 ; not guaranteed to work with Python 3 - #:phases + `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'make-writable + (add-after 'unpack 'adjust-requirements (lambda _ - (for-each make-file-writable (find-files ".")) - #t)) + (substitute* "setup.py" + ;; This defunct dependency isn't required for Python 3 (see: + ;; https://github.com/mhammell-laboratory/TEtranscripts/issues/111). + ((".*'argparse'.*") "")))) (add-after 'unpack 'patch-invocations (lambda* (#:key inputs #:allow-other-keys) (substitute* '("bin/TEtranscripts" "bin/TEcount") (("'sort ") - (string-append "'" (which "sort") " ")) + (string-append "'" (search-input-file inputs "bin/sort") " ")) (("'rm -f ") - (string-append "'" (which "rm") " -f ")) - (("'Rscript'") (string-append "'" (which "Rscript") "'"))) + (string-append "'" (search-input-file inputs "bin/rm") " -f ")) + (("'Rscript'") + (string-append "'" (search-input-file inputs "bin/Rscript") + "'"))) (substitute* "TEToolkit/IO/ReadInputs.py" - (("BamToBED") (which "bamToBed"))) + (("BamToBED") + (search-input-file inputs "bin/bamToBed"))) (substitute* "TEToolkit/Normalization.py" (("\"Rscript\"") - (string-append "\"" (which "Rscript") "\""))) - #t)) + (string-append "\"" (search-input-file inputs "bin/Rscript") + "\""))))) (add-after 'install 'wrap-program (lambda* (#:key outputs #:allow-other-keys) ;; Make sure the executables find R packages. - (let ((out (assoc-ref outputs "out"))) - (for-each - (lambda (script) - (wrap-program (string-append out "/bin/" script) - `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) - '("TEtranscripts" - "TEcount"))) - #t))))) + (for-each (lambda (script) + (wrap-program script + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) + (list (search-input-file outputs "bin/TEtranscripts") + (search-input-file outputs "bin/TEcount")))))))) (inputs - (list coreutils + (list bash-minimal + coreutils bedtools - python2-argparse - python2-pysam + python-pysam r-minimal r-deseq2)) - (home-page "https://github.com/mhammell-laboratory/tetoolkit") + (home-page "https://github.com/mhammell-laboratory/TEtranscripts") (synopsis "Transposable elements in differential enrichment analysis") (description "This is package for including transposable elements in differential From 8bcb07d08936b41e9e737d52586683cadfddea61 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:34 -0400 Subject: [PATCH 0783/1394] gnu: Remove pepr. * gnu/packages/bioinformatics.scm (pepr): Delete variable. --- gnu/packages/bioinformatics.scm | 26 -------------------------- 1 file changed, 26 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0a4c68e8c75..6f247cf4123 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8729,32 +8729,6 @@ regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.") (license license:gpl3+)))) -(define-public pepr - (package - (name "pepr") - (version "1.0.9") - (source (origin - (method url-fetch) - (uri (pypi-uri "PePr" version)) - (sha256 - (base32 - "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; python2 only - #:tests? #f)) ; no tests included - (propagated-inputs - (list python2-numpy python2-scipy python2-pysam)) - (home-page "https://github.com/shawnzhangyx/PePr") - (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data") - (description - "PePr is a ChIP-Seq peak calling or differential binding analysis tool -that is primarily designed for data with biological replicates. It uses a -negative binomial distribution to model the read counts among the samples in -the same group, and look for consistent differences between ChIP and control -group or two ChIP groups run under different conditions.") - (license license:gpl3+))) - (define-public filevercmp (let ((commit "1a9b779b93d0b244040274794d402106907b71b7") (revision "1")) From 725b56296253ad2e2f2079ac80c889965280feca Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:38 -0400 Subject: [PATCH 0784/1394] gnu: Remove python2-htseq. * gnu/packages/bioinformatics.scm (python2-htseq): Delete variable. --- gnu/packages/bioinformatics.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6f247cf4123..d9e5e5a54e8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4157,9 +4157,6 @@ HMMs).") from high-throughput sequencing assays.") (license license:gpl3+))) -(define-public python2-htseq - (package-with-python2 htseq)) - (define-public java-htsjdk (package (name "java-htsjdk") From 1010c05800a2df00257b6ef4ab530b069c7e1bfc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:41 -0400 Subject: [PATCH 0785/1394] gnu: Remove python2-pybedtools. * gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable. --- gnu/packages/bioinformatics.scm | 8 -------- 1 file changed, 8 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d9e5e5a54e8..d25dc8d1938 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -981,14 +981,6 @@ pybedtools extends BEDTools by offering feature-level manipulations from with Python.") (license license:gpl2+))) -(define-public python2-pybedtools - (let ((pybedtools (package-with-python2 python-pybedtools))) - (package - (inherit pybedtools) - (native-inputs - (modify-inputs (package-native-inputs pybedtools) - (prepend python2-pathlib)))))) - (define-public python-biom-format (package (name "python-biom-format") From d2c971e67b546fc94771ecae41340822ea67ac0a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:47 -0400 Subject: [PATCH 0786/1394] gnu: Remove bamm. * gnu/packages/bioinformatics.scm (bamm): Delete variable. --- gnu/packages/bioinformatics.scm | 79 --------------------------------- 1 file changed, 79 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d25dc8d1938..a4a2f50b397 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -211,85 +211,6 @@ tRNA consensus sequences and RNA structure. It also outputs the secondary structure of the predicted RNA.") (license license:gpl2))) -(define-public bamm - (package - (name "bamm") - (version "1.7.3") - (source (origin - (method git-fetch) - ;; BamM is not available on pypi. - (uri (git-reference - (url "https://github.com/Ecogenomics/BamM") - (commit version) - (recursive? #t))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5")) - (modules '((guix build utils))) - (snippet - `(begin - ;; Delete bundled htslib. - (delete-file-recursively "c/htslib-1.3.1"))))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; BamM is Python 2 only. - ;; Do not use bundled libhts. Do use the bundled libcfu because it has - ;; been modified from its original form. - #:configure-flags - ,#~(let ((htslib #$(this-package-input "htslib"))) - (list "--with-libhts-lib" (string-append htslib "/lib") - "--with-libhts-inc" (string-append htslib "/include/htslib"))) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'autogen - (lambda _ - (with-directory-excursion "c" - (let ((sh (which "sh"))) - (for-each make-file-writable (find-files "." ".*")) - ;; Use autogen so that 'configure' works. - (substitute* "autogen.sh" (("/bin/sh") sh)) - (setenv "CONFIG_SHELL" sh) - (invoke "./autogen.sh"))))) - (delete 'build) ;the build loops otherwise - (replace 'check - (lambda _ - ;; There are 2 errors printed, but they are safe to ignore: - ;; 1) [E::hts_open_format] fail to open file ... - ;; 2) samtools view: failed to open ... - (invoke "nosetests"))) - (add-after 'install 'wrap-executable - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (path (getenv "PATH")) - (pythonpath (getenv "GUIX_PYTHONPATH"))) - (wrap-program (string-append out "/bin/bamm") - `("PATH" ":" prefix (,path)) - `("GUIX_PYTHONPATH" ":" prefix (,pythonpath))))))))) - (native-inputs - (list autoconf - automake - libtool - zlib - python2-nose - python2-pysam)) - (inputs - (list htslib-1.3 ; At least one test fails on htslib-1.4+. - samtools - bwa - grep - sed - coreutils)) - (propagated-inputs - (list python2-numpy)) - (home-page "https://ecogenomics.github.io/BamM/") - (synopsis "Metagenomics-focused BAM file manipulator") - (description - "BamM is a C library, wrapped in python, to efficiently generate and -parse BAM files, specifically for the analysis of metagenomic data. For -instance, it implements several methods to assess contig-wise read coverage.") - (license license:lgpl3+))) - (define-public bamtools (package (name "bamtools") From bcdd45be6f1e5c5dfc77e1ef365fa0bb420ae74f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:51 -0400 Subject: [PATCH 0787/1394] gnu: Remove python2-dendropy. * gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable. --- gnu/packages/bioinformatics.scm | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a4a2f50b397..727d88ce27c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2955,22 +2955,6 @@ writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.") (license license:bsd-3))) -(define-public python2-dendropy - (let ((base (package-with-python2 python-dendropy))) - (package/inherit base - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'remove-failing-test - (lambda _ - ;; This test fails when the full test suite is run, as documented - ;; at https://github.com/jeetsukumaran/DendroPy/issues/74 - (substitute* "tests/test_dataio_nexml_reader_tree_list.py" - (("test_collection_comments_and_annotations") - "do_not_test_collection_comments_and_annotations")) - #t))) - ,@(package-arguments base)))))) - (define-public python-py2bit (package (name "python-py2bit") From bb35b50adc132c416f1d00c9c632e00327b889bf Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:55 -0400 Subject: [PATCH 0788/1394] gnu: Remove poretools. * gnu/packages/bioinformatics.scm (poretools): Delete variable. --- gnu/packages/bioinformatics.scm | 36 --------------------------------- 1 file changed, 36 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 727d88ce27c..e7c749c4534 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12909,42 +12909,6 @@ of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.") (license license:gpl3+)))) -(define-public poretools - ;; The latest release was in 2016 and the latest commit is from 2017 - ;; the recommended way to install is to clone the git repository - ;; https://poretools.readthedocs.io/en/latest/content/installation.html - (let ((commit "e426b1f09e86ac259a00c261c79df91510777407") - (revision "1")) - (package - (name "poretools") - (version (git-version "0.6.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/arq5x/poretools") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am")))) - (build-system python-build-system) - ;; requires python >=2.7, <3.0, and the same for python dependencies - (arguments `(#:python ,python-2)) - (inputs - (list hdf5)) - (propagated-inputs - (list python2-dateutil python2-h5py python2-matplotlib - python2-pandas python2-seaborn)) - (home-page "https://poretools.readthedocs.io") - (synopsis "Toolkit for working with nanopore sequencing data") - (description - "The MinION from Oxford Nanopore Technologies is a nanopore sequencer. -This @code{poretools} package is a flexible toolkit for exploring datasets -generated by nanopore sequencing devices for the purposes of quality control and -downstream analysis. Poretools operates directly on the native FAST5, a variant -of the Hierarchical Data Format (HDF5) standard.") - (license license:expat)))) - (define-public jamm (package (name "jamm") From 23e133a907905875f79736cd83b554eb0b487f95 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:35:58 -0400 Subject: [PATCH 0789/1394] gnu: Remove python2-warpedlmm. * gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable. --- gnu/packages/bioinformatics.scm | 41 --------------------------------- 1 file changed, 41 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e7c749c4534..916b84cba9e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5366,47 +5366,6 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") files and writing bioinformatics applications.") (license license:bsd-3))) -(define-public python2-warpedlmm - (package - (name "python2-warpedlmm") - (version "0.21") - (source - (origin - (method url-fetch) - (uri (pypi-uri "WarpedLMM" version ".zip")) - (sha256 - (base32 - "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; requires Python 2.7 - #:tests? #f ; test data are not included - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-weave - (lambda _ - (substitute* "warpedlmm/util/linalg.py" - (("from scipy import linalg, weave") - "from scipy import linalg\nimport weave")) - #t))))) - (propagated-inputs - (list python2-scipy - python2-numpy - python2-matplotlib - python2-fastlmm - python2-pandas - python2-pysnptools - python2-weave)) - (native-inputs - (list python2-mock python2-nose unzip)) - (home-page "https://github.com/PMBio/warpedLMM") - (synopsis "Implementation of warped linear mixed models") - (description - "WarpedLMM is a Python implementation of the warped linear mixed model, -which automatically learns an optimal warping function (or transformation) for -the phenotype as it models the data.") - (license license:asl2.0))) - (define-public prank (package (name "prank") From a94bc7798ac0516763b24823536ab251b55aa964 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:36:02 -0400 Subject: [PATCH 0790/1394] gnu: Remove miso. * gnu/packages/bioinformatics.scm (miso): Delete variable. --- gnu/packages/bioinformatics.scm | 48 --------------------------------- 1 file changed, 48 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 916b84cba9e..f73c8290f6b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5195,54 +5195,6 @@ unassembled metagenomic reads, but is mainly designed for full genomes and assembled metagenomic sequence.") (license license:gpl3+))) -(define-public miso - (let ((commit "b71402188000465e3430736a11ea118fd5639a4a") - (revision "1")) - (package - (name "miso") - (version (git-version "0.5.4" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/yarden/MISO/") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0x37ipwwvpxbkrg17gmq3hp92c9cphch8acd6cj7fqgnrjwd47g5")) - (modules '((guix build utils))) - (snippet - '(substitute* "setup.py" - ;; Use "gcc" instead of "cc" for compilation. - (("^defines") - "cc.set_executables( -compiler='gcc', -compiler_so='gcc', -linker_exe='gcc', -linker_so='gcc -shared'); defines"))))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; only Python 2 is supported - #:tests? #f)) ; no "test" target - (inputs - ;; Samtools must not be newer than 1.2. See - ;; https://github.com/yarden/MISO/issues/135 - (list samtools-1.2 python2-numpy python2-pysam python2-scipy - python2-matplotlib)) - (native-inputs - (list python2-mock ; for tests - python2-pytz)) ; for tests - (home-page "https://miso.readthedocs.io/en/fastmiso/") - (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") - (description - "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates -the expression level of alternatively spliced genes from RNA-Seq data, and -identifies differentially regulated isoforms or exons across samples. By -modeling the generative process by which reads are produced from isoforms in -RNA-Seq, the MISO model uses Bayesian inference to compute the probability -that a read originated from a particular isoform.") - (license license:gpl2)))) - (define-public muscle (package (name "muscle") From 850bd0c3291e37020d3114f830423d795e159986 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:36:05 -0400 Subject: [PATCH 0791/1394] gnu: Remove python2-screed. * gnu/packages/bioinformatics.scm (python2-screed): Delete variable. --- gnu/packages/bioinformatics.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f73c8290f6b..c16648e4a89 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6547,9 +6547,6 @@ Values such as sequence name, sequence description, sequence quality and the sequence itself can be retrieved from these databases.") (license license:bsd-3))) -(define-public python2-screed - (package-with-python2 python-screed)) - (define-public sra-tools (package (name "sra-tools") From 828797966991e1105d4c6df7c24c1c4b63d6165f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:36:09 -0400 Subject: [PATCH 0792/1394] gnu: Remove python2-pyfaidx. * gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable. --- gnu/packages/bioinformatics.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c16648e4a89..7f0b6bebea5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12370,9 +12370,6 @@ bgzipped text file that contains a pair of genomic coordinates per line.") fasta subsequences.") (license license:bsd-3))) -(define-public python2-pyfaidx - (package-with-python2 python-pyfaidx)) - (define-public python-cooler (package (name "python-cooler") From ba09192168ec7683e7a4456480b740892a797ad1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:36:13 -0400 Subject: [PATCH 0793/1394] gnu: Remove python2-pbcore. * gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable. --- gnu/packages/bioinformatics.scm | 33 --------------------------------- 1 file changed, 33 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7f0b6bebea5..735b1e5eeac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5285,39 +5285,6 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") (home-page "https://github.com/wwood/OrfM") (license license:lgpl3+))) -(define-public python2-pbcore - (package - (name "python2-pbcore") - (version "1.2.10") - (source (origin - (method url-fetch) - (uri (pypi-uri "pbcore" version)) - (sha256 - (base32 - "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ;pbcore < 2.0 requires Python 2.7 - #:phases (modify-phases %standard-phases - (add-after 'unpack 'remove-sphinx-dependency - (lambda _ - ;; Sphinx is only required for documentation tests, which - ;; we do not run; furthermore it depends on python2-sphinx - ;; which is no longer maintained. - (substitute* "requirements-dev.txt" - (("^sphinx") "")) - #t))))) - (propagated-inputs - (list python2-cython python2-numpy python2-pysam python2-h5py)) - (native-inputs - (list python2-nose python2-pyxb)) - (home-page "https://pacificbiosciences.github.io/pbcore/") - (synopsis "Library for reading and writing PacBio data files") - (description - "The pbcore package provides Python APIs for interacting with PacBio data -files and writing bioinformatics applications.") - (license license:bsd-3))) - (define-public prank (package (name "prank") From c30ab2c0b4d506c559cd35a21c1cadac65014f1a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:36:16 -0400 Subject: [PATCH 0794/1394] gnu: Remove pyicoteo. * gnu/packages/bioinformatics.scm (pyicoteo): Delete variable. --- gnu/packages/bioinformatics.scm | 39 --------------------------------- 1 file changed, 39 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 735b1e5eeac..40c060b2dc3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5406,45 +5406,6 @@ clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at once.") (license license:gpl3+))) -(define-public pyicoteo - (package - (name "pyicoteo") - (version "2.0.7") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; does not work with Python 3 - #:tests? #f)) ; there are no tests - (inputs - (list python2-matplotlib)) - (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo") - (synopsis "Analyze high-throughput genetic sequencing data") - (description - "Pyicoteo is a suite of tools for the analysis of high-throughput genetic -sequencing data. It works with genomic coordinates. There are currently six -different command-line tools: - -@enumerate -@item pyicoregion: for generating exploratory regions automatically; -@item pyicoenrich: for differential enrichment between two conditions; -@item pyicoclip: for calling CLIP-Seq peaks without a control; -@item pyicos: for genomic coordinates manipulation; -@item pyicoller: for peak calling on punctuated ChIP-Seq; -@item pyicount: to count how many reads from N experiment files overlap in a - region file; -@item pyicotrocol: to combine operations from pyicoteo. -@end enumerate\n") - (license license:gpl3+))) - (define-public prodigal (package (name "prodigal") From ddec4b81d6681d58469c70e3e9436df73a980036 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:36:20 -0400 Subject: [PATCH 0795/1394] gnu: Remove transmission-remote-cli. * gnu/packages/bittorrent.scm (transmission-remote-cli): Delete variable. --- gnu/packages/bittorrent.scm | 43 ------------------------------------- 1 file changed, 43 deletions(-) diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm index 0191bb8e1b8..1c9358b8967 100644 --- a/gnu/packages/bittorrent.scm +++ b/gnu/packages/bittorrent.scm @@ -255,49 +255,6 @@ Transmission BitTorrent daemon.") (home-page "https://github.com/tremc/tremc") (license l:gpl3+))) -(define-public transmission-remote-cli - (package - (name "transmission-remote-cli") - (version "1.7.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/fagga/transmission-remote-cli") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "09w9f8vrm61lapin8fmq4rgahr95y3c6wss10g0fgd0kl16f895v")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; only supports Python 2 - #:tests? #f ; no test suite - #:phases (modify-phases %standard-phases - ;; The software is just a Python script that must be - ;; copied into place. - (delete 'build) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (man (string-append out "/share/man/man1")) - ;; FIXME install zsh completions - (completions (string-append out "/etc/bash_completion.d"))) - (install-file "transmission-remote-cli" bin) - (install-file "transmission-remote-cli.1" man) - (install-file - (string-append - "completion/bash/" - "transmission-remote-cli-bash-completion.sh") - completions))))))) - (synopsis "Console client for the Transmission BitTorrent daemon") - (description "Transmission-remote-cli is a console client, with a curses -interface, for the Transmission BitTorrent daemon. This package is no longer -maintained upstream.") - (home-page "https://github.com/fagga/transmission-remote-cli") - (license l:gpl3+) - (properties `((superseded . ,tremc))))) - (define-public aria2 (package (name "aria2") From 4746f9fc63ef9c3faeca19aa4c6c2791c55c4f29 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:36:24 -0400 Subject: [PATCH 0796/1394] gnu: Remove python2-nose-timer. * gnu/packages/check.scm (python2-nose-timer): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index cb228c92001..0a64ee5adf5 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2917,9 +2917,6 @@ create data based on random numbers and yet remain repeatable.") (description "Shows how much time was needed to run individual tests.") (license license:expat))) -(define-public python2-nose-timer - (package-with-python2 python-nose-timer)) - (define-public python-freezegun (package (name "python-freezegun") From dc612d54fd2ff437acabeeca3d238c43f6cd740b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:36:33 -0400 Subject: [PATCH 0797/1394] gnu: Remove python2-pytest-catchlog. * gnu/packages/check.scm (python2-pytest-catchlog): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 0a64ee5adf5..f8a6fde6b0f 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2691,9 +2691,6 @@ pytest report.") a fork of pytest-capturelog.") (license license:expat))) -(define-public python2-pytest-catchlog - (package-with-python2 python-pytest-catchlog)) - (define-public python-nosexcover (package (name "python-nosexcover") From dc0da7e56f9e8d8df23c4f551301011f261c2265 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:36:46 -0400 Subject: [PATCH 0798/1394] gnu: Remove python2-testlib. * gnu/packages/check.scm (python2-testlib): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index f8a6fde6b0f..2e9ecba26db 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2048,9 +2048,6 @@ tools for mocking system commands and recording calls to those.") (home-page "https://github.com/trentm/testlib") (license license:expat))) -(define-public python2-testlib - (package-with-python2 python-testlib)) - ;;; The software provided by this package was integrated into pytest 2.8. (define-public python-pytest-cache (package From 94447313e875338ba59cbc417dc51ece11c949c9 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:36:50 -0400 Subject: [PATCH 0799/1394] gnu: Remove python2-nose2. * gnu/packages/check.scm (python2-nose2): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 2e9ecba26db..8c785fd7f25 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -947,9 +947,6 @@ better plugin api, being easier for users to configure, and simplifying internal interfaces and processes.") (license license:bsd-2))) -(define-public python2-nose2 - (package-with-python2 python-nose2)) - (define-public python-unittest2 (package (name "python-unittest2") From 099c5a90e407fedeca3423c306687d8c9e73005c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:37:04 -0400 Subject: [PATCH 0800/1394] gnu: Remove python2-pytest-capturelog. * gnu/packages/check.scm (python2-pytest-capturelog): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 8c785fd7f25..0cc5be8734f 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2659,9 +2659,6 @@ pytest report.") "Python-pytest-catchlog is a pytest plugin to catch log messages.") (license license:expat))) -(define-public python2-pytest-capturelog - (package-with-python2 python-pytest-capturelog)) - (define-public python-pytest-catchlog (package (name "python-pytest-catchlog") From 4178b304abc667e11d398412df90b4c4b1de1bc4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:38:09 -0400 Subject: [PATCH 0801/1394] gnu: Remove python2-python-paramunittest. * gnu/packages/check.scm (python2-python-paramunittest): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 0cc5be8734f..476292d6614 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2607,9 +2607,6 @@ cases. Since they are TestCase subclasses, they work with other test suites tha recognize TestCases.") (license license:bsd-2))) -(define-public python2-python-paramunittest - (package-with-python2 python-paramunittest)) - (define-public python-pytest-warnings (package (name "python-pytest-warnings") From 2af19eb9b5026fc96110ded4b7cb5c49343007bc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:41:07 -0400 Subject: [PATCH 0802/1394] gnu: Remove python2-rednose. * gnu/packages/check.scm (python2-rednose): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 476292d6614..70f3a05e025 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2828,9 +2828,6 @@ JSON APIs with Behave.") @command{nosetests} command of the Python Nose unit test framework.") (license license:bsd-3))) -(define-public python2-rednose - (package-with-python2 python-rednose)) - (define-public python-nose-random (package (name "python-nose-random") From ae2f3bed7616c42f3e3e4956e882832985f744e7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:41:11 -0400 Subject: [PATCH 0803/1394] gnu: Remove python2-minimock. * gnu/packages/check.scm (python2-minimock): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 70f3a05e025..dbb131ffc79 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -849,9 +849,6 @@ for every Python test framework. It supports nose, py.test, and unittest.") doctest.") (license license:expat))) -(define-public python2-minimock - (package-with-python2 python-minimock)) - (define-public python-mock (package (name "python-mock") From 359a0b6c2e99115f3dabbaeede0f322cf7e29b2d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:41:26 -0400 Subject: [PATCH 0804/1394] gnu: Remove python2-flexmock. * gnu/packages/check.scm (python2-flexmock): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index dbb131ffc79..d99be83c995 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2975,9 +2975,6 @@ time by mocking the datetime module.") mocks, stubs and fakes.") (license license:bsd-3))) -(define-public python2-flexmock - (package-with-python2 python-flexmock)) - (define-public python-flaky (package (name "python-flaky") From f9d31d90ec357e3ea3cdc6aa1b8123109937924c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:41:30 -0400 Subject: [PATCH 0805/1394] gnu: Remove python2-discover. * gnu/packages/check.scm (python2-discover): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index d99be83c995..e21707b89ef 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2722,9 +2722,6 @@ especially -cover-package.") backported from Python 2.7 for Python 2.4+.") (license license:bsd-3))) -(define-public python2-discover - (package-with-python2 python-discover)) - (define-public behave (package (name "behave") From 2abde9b9270f822794921147631d3f48dd3498fb Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:41:44 -0400 Subject: [PATCH 0806/1394] gnu: Remove python2-cov-core. * gnu/packages/check.scm (python2-cov-core): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index e21707b89ef..2369245982e 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -1951,9 +1951,6 @@ and @code{nose2-cov}. It is useful for developing coverage plugins for these testing frameworks.") (license license:expat))) -(define-public python2-cov-core - (package-with-python2 python-cov-core)) - (define-public python-codecov (package (name "python-codecov") From af6d88c803f2338cf199ec76f65e8fd25f774fe6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:41:50 -0400 Subject: [PATCH 0807/1394] gnu: Remove python2-pytest-flakes. * gnu/packages/check.scm (python2-pytest-flakes): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 2369245982e..2596b8aaa8b 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2494,9 +2494,6 @@ each of the environments.") (description "Pytest plugin for checking Python source code with pyflakes.") (license license:expat))) -(define-public python2-pytest-flakes - (package-with-python2 python-pytest-flakes)) - (define-public python-coverage-test-runner (package (name "python-coverage-test-runner") From 6e763df31c458db3fd628b80ef121a30d73ae286 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:41:57 -0400 Subject: [PATCH 0808/1394] gnu: Remove python2-pytest-subtesthack. * gnu/packages/check.scm (python2-pytest-subtesthack): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 2596b8aaa8b..a419e448ec0 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2132,9 +2132,6 @@ normally the case.") (home-page "https://github.com/untitaker/pytest-subtesthack/") (license license:unlicense))) -(define-public python2-pytest-subtesthack - (package-with-python2 python-pytest-subtesthack)) - (define-public python-pytest-sugar (package (name "python-pytest-sugar") From be6740df96defb6f5c7f69a73e8382bac990bac8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:42:09 -0400 Subject: [PATCH 0809/1394] gnu: Remove python2-nose-randomly. * gnu/packages/check.scm (python2-nose-randomly): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index a419e448ec0..ce5feca0205 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2863,9 +2863,6 @@ by resetting it to a repeatable number for each test, enabling the tests to create data based on random numbers and yet remain repeatable.") (license license:bsd-3))) -(define-public python2-nose-randomly - (package-with-python2 python-nose-randomly)) - (define-public python-nose-timer (package (name "python-nose-timer") From dbac9f890e3c12b9d82aa00604c779f0770b8299 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:42:22 -0400 Subject: [PATCH 0810/1394] gnu: Remove domainfinder. * gnu/packages/chemistry.scm (domainfinder): Delete variable. --- gnu/packages/chemistry.scm | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 94803719ac6..d94f3ec787a 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -128,35 +128,6 @@ science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.") (license license:bsd-3))) -(define-public domainfinder - (package - (name "domainfinder") - (version "2.0.5") - (source - (origin - (method url-fetch) - (uri (string-append "https://bitbucket.org/khinsen/" - "domainfinder/downloads/DomainFinder-" - version ".tar.gz")) - (sha256 - (base32 - "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr")))) - (build-system python-build-system) - (inputs - (list python2-mmtk)) - (arguments - `(#:python ,python-2 - ;; No test suite - #:tests? #f)) - (home-page "http://dirac.cnrs-orleans.fr/DomainFinder.html") - (synopsis "Analysis of dynamical domains in proteins") - (description "DomainFinder is an interactive program for the determination -and characterization of dynamical domains in proteins. It can infer dynamical -domains by comparing two protein structures, or from normal mode analysis on a -single structure. The software is currently not actively maintained and works -only with Python 2 and NumPy < 1.9.") - (license license:cecill-c))) - (define-public inchi (package (name "inchi") From 99d5c9b54afb78579b6a8f2e431195e7ca8cb1e5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:42:26 -0400 Subject: [PATCH 0811/1394] gnu: Remove nmoldyn. * gnu/packages/chemistry.scm (nmoldyn): Delete variable. --- gnu/packages/chemistry.scm | 60 -------------------------------------- 1 file changed, 60 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index d94f3ec787a..e5b63095853 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -306,66 +306,6 @@ staged, and output files collected using a standard interface.") (define with-numpy-1.8 (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8)))) -(define-public nmoldyn - (package - (name "nmoldyn") - (version "3.0.11") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/khinsen/nMOLDYN3") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r")))) - (build-system python-build-system) - (inputs - (list (with-numpy-1.8 python2-matplotlib) python2-scientific netcdf - gv)) - (propagated-inputs - (list python2-mmtk)) - (arguments - `(#:python ,python-2 - #:tests? #f ; No test suite - #:phases - (modify-phases %standard-phases - (add-before 'build 'create-linux2-directory - (lambda _ - (mkdir-p "nMOLDYN/linux2"))) - (add-before 'build 'change-PDF-viewer - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "nMOLDYN/Preferences.py" - ;; Set the paths for external executables, substituting - ;; gv for acroread. - ;; There is also vmd_path, but VMD is not free software - ;; and Guix contains currently no free molecular viewer that - ;; could be substituted. - (("PREFERENCES\\['acroread_path'\\] = ''") - (format #f "PREFERENCES['acroread_path'] = '~a'" - (which "gv"))) - (("PREFERENCES\\['ncdump_path'\\] = ''") - (format #f "PREFERENCES['ncdump_path'] = '~a'" - (which "ncdump"))) - (("PREFERENCES\\['ncgen_path'\\] = ''") - (format #f "PREFERENCES['ncgen_path'] = '~a'" - (which "ncgen3"))) - (("PREFERENCES\\['task_manager_path'\\] = ''") - (format #f "PREFERENCES['task_manager_path'] = '~a'" - (which "task_manager"))) - ;; Show documentation as PDF - (("PREFERENCES\\['documentation_style'\\] = 'html'") - "PREFERENCES['documentation_style'] = 'pdf'") )))))) - (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN.html") - (synopsis "Analysis software for Molecular Dynamics trajectories") - (description "nMOLDYN is an interactive analysis program for Molecular Dynamics -simulations. It is especially designed for the computation and decomposition of -neutron scattering spectra, but also computes other quantities. The software -is currently not actively maintained and works only with Python 2 and -NumPy < 1.9.") - (license license:cecill))) - (define-public tng (package (name "tng") From 466d81aae4386ed4601fc44bd408268dca4859e5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:42:29 -0400 Subject: [PATCH 0812/1394] gnu: Remove python2-neo4j-driver. * gnu/packages/databases.scm (python2-neo4j-driver): Delete variable. --- gnu/packages/databases.scm | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index a161e299072..7e3b9f110a1 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3674,27 +3674,6 @@ managers for automatically closing connections.") (description "This package implements async database support for Python.") (license license:bsd-3))) -(define-public python2-neo4j-driver - (package - (name "python2-neo4j-driver") - ;; NOTE: When upgrading to 1.5.0, please add a python3 variant. - (version "1.4.0") - (source (origin - (method url-fetch) - (uri (pypi-uri "neo4j-driver" version)) - (sha256 - (base32 - "011r1vh182p8mm83d8dz9rfnc3l7rf7fd00cyrbyfzi71jmc4g98")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) - (home-page "https://neo4j.com/developer/python/") - (synopsis "Neo4j driver code written in Python") - (description "This package provides the Neo4j Python driver that connects -to the database using Neo4j's binary protocol. It aims to be minimal, while -being idiomatic to Python.") - (license license:asl2.0))) - (define-public python2-py2neo (package (name "python2-py2neo") From 1aab8a5114a57fc131fe22ad8d62a6426b7792fc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:42:33 -0400 Subject: [PATCH 0813/1394] gnu: Remove python2-redis. * gnu/packages/databases.scm (python2-redis): Delete variable. --- gnu/packages/databases.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 7e3b9f110a1..e485b95b9c3 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -4020,9 +4020,6 @@ reasonable substitute.") "This package provides a Python interface to the Redis key-value store.") (license license:expat))) -(define-public python2-redis - (package-with-python2 python-redis)) - (define-public python-rq (package (name "python-rq") From 5ed4cfb924518a83a7e02f27fb77b8a295d15ae3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:42:37 -0400 Subject: [PATCH 0814/1394] gnu: Remove python2-trollius-redis. * gnu/packages/databases.scm (python2-trollius-redis): Delete variable. --- gnu/packages/databases.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index e485b95b9c3..7592572be9c 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -4117,9 +4117,6 @@ is designed to have a low barrier to entry.") Redis protocol.") (license license:bsd-2))) -(define-public python2-trollius-redis - (package-with-python2 python-trollius-redis)) - (define-public python-sqlparse (package (name "python-sqlparse") From 80963d9b0f95d03bddc4f55174e80b9f11c04abc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:42:40 -0400 Subject: [PATCH 0815/1394] gnu: Remove python2-peewee. * gnu/packages/databases.scm (python2-peewee): Delete variable. --- gnu/packages/databases.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 7592572be9c..4ff18ce628b 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2877,9 +2877,6 @@ support for sqlite, mysql and postgresql. If you already have a database, you can autogenerate peewee models using @code{pwiz}, a model generator.") (license license:expat))) -(define-public python2-peewee - (package-with-python2 python-peewee)) - (define-public python-pypika-tortoise (package (name "python-pypika-tortoise") From f503181ffbd30629c28398328e3c724d7a5e40b4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:42:44 -0400 Subject: [PATCH 0816/1394] gnu: Remove python2-ccm. * gnu/packages/databases.scm (python2-ccm): Delete variable. --- gnu/packages/databases.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 4ff18ce628b..f6b0c60ae42 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3311,9 +3311,6 @@ local Cassandra clusters. It creates, launches and removes Cassandra clusters on localhost.") (license license:asl2.0))) -(define-public python2-ccm - (package-with-python2 python-ccm)) - (define-public python2-pysqlite (package (name "python2-pysqlite") From 3ad04860d58d703a220e62651c09d90e4e1a363d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:42:47 -0400 Subject: [PATCH 0817/1394] gnu: Remove python2-apsw. * gnu/packages/databases.scm (python2-apsw): Delete variable. --- gnu/packages/databases.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index f6b0c60ae42..64ca0db19d0 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3609,9 +3609,6 @@ pysqlite it focuses on being a minimal layer over SQLite attempting just to translate the complete SQLite API into Python.") (license license:zlib))) -(define-public python2-apsw - (package-with-python2 python-apsw)) - (define-public python-aiosqlite (package (name "python-aiosqlite") From 25e4ddd84911d8ec16a22fc0ec6f4c66523c9af7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:42:58 -0400 Subject: [PATCH 0818/1394] gnu: Remove python2-py2neo. * gnu/packages/databases.scm (python2-py2neo): Delete variable. --- gnu/packages/databases.scm | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 64ca0db19d0..4f7e2d92ec5 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3665,27 +3665,6 @@ managers for automatically closing connections.") (description "This package implements async database support for Python.") (license license:bsd-3))) -(define-public python2-py2neo - (package - (name "python2-py2neo") - (version "3.1.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "py2neo" version)) - (sha256 - (base32 - "1f1q95vqcvlc3nsc33p841swnjdcjazddlq2dzi3qfnjqjrajxw1")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) - (home-page "https://py2neo.org") - (synopsis "Library and toolkit for working with Neo4j in Python") - (description "This package provides a client library and toolkit for -working with Neo4j from within Python applications and from the command -line. The core library has no external dependencies and has been carefully -designed to be easy and intuitive to use.") - (license license:asl2.0))) - (define-public python-psycopg2 (package (name "python-psycopg2") From e9121c2dda090fcb4f2ba5948ca10c8bafd85e7f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:43:01 -0400 Subject: [PATCH 0819/1394] gnu: Remove python2-pyodbc-c. * gnu/packages/databases.scm (python2-pyodbc-c): Delete variable. --- gnu/packages/databases.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 4f7e2d92ec5..f720938e7e9 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3092,9 +3092,6 @@ development.") for ODBC.") (license (license:x11-style "file://LICENSE.TXT")))) -(define-public python2-pyodbc-c - (package-with-python2 python-pyodbc-c)) - (define-public python-pyodbc (package (name "python-pyodbc") From bef8185d0880c79fc245e672497bd1e7e0c197b0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:43:05 -0400 Subject: [PATCH 0820/1394] gnu: Remove python2-pymysql. * gnu/packages/databases.scm (python2-pymysql): Delete variable. --- gnu/packages/databases.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index f720938e7e9..d1ea99fe84e 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1526,9 +1526,6 @@ CSV, DB3, iXF, SQLite, MS-SQL or MySQL to PostgreSQL.") Most public APIs are compatible with @command{mysqlclient} and MySQLdb.") (license license:expat))) -(define-public python2-pymysql - (package-with-python2 python-pymysql)) - (define-public qdbm (package (name "qdbm") From 716b5bd9d94d7e0f62c1345d16cbc2f008ad279f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 13:43:08 -0400 Subject: [PATCH 0821/1394] gnu: Remove python2-hiredis. * gnu/packages/databases.scm (python2-hiredis): Delete variable. --- gnu/packages/databases.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index d1ea99fe84e..9c46a5a9d24 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3895,9 +3895,6 @@ for Python. The design goals are: parsing code in hiredis. It primarily speeds up parsing of multi bulk replies.") (license license:bsd-3))) -(define-public python2-hiredis - (package-with-python2 python-hiredis)) - (define-public python-aioredis (package (name "python-aioredis") From dc514a51648afeae24d60d340e4c93934e807c5e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 14:06:36 -0400 Subject: [PATCH 0822/1394] gnu: Remove python2-pytest-pep8. * gnu/packages/check.scm (python2-pytest-pep8): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index ce5feca0205..9172888751b 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2399,9 +2399,6 @@ a Pytest test execution.") (description "Pytest plugin for checking PEP8 compliance.") (license license:expat))) -(define-public python2-pytest-pep8 - (package-with-python2 python-pytest-pep8)) - (define-public python-pytest-perf (package (name "python-pytest-perf") From 1c865e8e1c89db58fd6f55ae2c63029dad8e14b3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:07:26 -0400 Subject: [PATCH 0823/1394] gnu: Remove python2-scikit-learn. * gnu/packages/machine-learning.scm (python2-scikit-learn): Delete variable. (python-scikit-learn)[properties]: Remove the python2-variant property. --- gnu/packages/machine-learning.scm | 47 ------------------------------- 1 file changed, 47 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 38973423451..02cd6b31aad 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1128,55 +1128,8 @@ computing environments.") (description "Scikit-learn provides simple and efficient tools for data mining and data analysis.") - (properties `((python2-variant . ,(delay python2-scikit-learn)))) (license license:bsd-3))) -;; scikit-learn 0.22 and later only supports Python 3, so we stick with -;; an older version here. -(define-public python2-scikit-learn - (let ((base (package-with-python2 (strip-python2-variant python-scikit-learn)))) - (package - (inherit base) - (version "0.20.4") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/scikit-learn/scikit-learn") - (commit version))) - (file-name (git-file-name "python-scikit-learn" version)) - (sha256 - (base32 - "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj")))) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'build 'build-ext - (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace"))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - ;; Restrict OpenBLAS threads to prevent segfaults while testing! - (setenv "OPENBLAS_NUM_THREADS" "1") - - ;; Some tests require write access to $HOME. - (setenv "HOME" "/tmp") - - (invoke "pytest" "sklearn" "-m" "not network" - "-k" - (string-append - ;; This test tries to access the internet. - "not test_load_boston_alternative" - ;; This test fails for unknown reasons - " and not test_rank_deficient_design")))))))) - (inputs - (list openblas)) - (native-inputs - (list python2-pytest python2-pandas ;for tests - python2-cython)) - (propagated-inputs - (list python2-numpy python2-scipy python2-joblib))))) - (define-public python-threadpoolctl (package (name "python-threadpoolctl") From 1db80805914347ca964c1357fa0e38665ea4bddb Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:08:04 -0400 Subject: [PATCH 0824/1394] gnu: ocrodjvu: Use a Python 3 compatible fork. * gnu/packages/djvu.scm (ocrodjvu)[source]: Update URL to Python 3 fork. [inputs]: Use new style. Remove python2-subprocess32. Replace all other Python 2 inputs by their Python 3 equivalent. Add python-future and python-regex. [arguments]: Use gexps, and adjust accordingly, using this-package-input and search-input-file. --- gnu/packages/djvu.scm | 166 +++++++++++++++++++++--------------------- 1 file changed, 85 insertions(+), 81 deletions(-) diff --git a/gnu/packages/djvu.scm b/gnu/packages/djvu.scm index 07c77f318ed..0fc2f6dfb9c 100644 --- a/gnu/packages/djvu.scm +++ b/gnu/packages/djvu.scm @@ -24,6 +24,7 @@ #:use-module (guix utils) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix build-system python) @@ -398,85 +399,88 @@ and background layers of images, which can then be encoded into a DjVu file.") (license license:gpl2))) (define-public ocrodjvu - (package - (name "ocrodjvu") - (version "0.12") - (source - (origin - (method url-fetch) - (uri (string-append - "https://github.com/jwilk/ocrodjvu/releases/download/" version - "/ocrodjvu-" version ".tar.xz")) - (sha256 - (base32 "09w9rqr7z2jd5kwp178zz2yrsc82mxs7gksipg92znxzgzhmw2ng")))) - (build-system gnu-build-system) - (native-inputs - (list libxml2 python2-nose python2-pillow)) - (inputs - `(("djvulibre" ,djvulibre) - ("ocrad" ,ocrad) - ("python" ,python-2) - ("python2-djvulibre" ,python2-djvulibre) - ("python2-html5lib" ,python2-html5lib) - ("python2-lxml" ,python2-lxml) - ("python2-pyicu" ,python2-pyicu) - ("python2-subprocess32" ,python2-subprocess32) - ("tesseract-ocr" ,tesseract-ocr))) - (arguments - `(#:modules ((guix build gnu-build-system) - ((guix build python-build-system) #:prefix python:) - (guix build utils)) - #:imported-modules (,@%gnu-build-system-modules - (guix build python-build-system)) - #:test-target "test" - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-before 'check 'disable-failing-test - (lambda _ - (substitute* "tests/test_ipc.py" - ;; test_wait_signal gets stuck forever - (("yield self\\._test_signal, name") - "return True") - ;; test_path fails to find a file it should have created - (("path = os\\.getenv\\('PATH'\\)\\.split\\(':'\\)") - "return True")) - ;; Disable tests with tesseract. They can't work without - ;; the language files that must downloaded by the final user - ;; as they are not packaged in Guix. - (substitute* "tests/ocrodjvu/test.py" - (("engines = stdout\\.getvalue\\(\\)\\.splitlines\\(\\)") - "engines = ['ocrad']")) - (substitute* "tests/ocrodjvu/test_integration.py" - (("engines = 'tesseract', 'cuneiform', 'gocr', 'ocrad'") - "engines = 'ocrad'")))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (invoke "make" - "DESTDIR=" - (string-append "PREFIX=" out) - "install")))) - (add-after 'install 'wrap-python - (assoc-ref python:%standard-phases 'wrap)) - (add-after 'wrap-python 'wrap-path - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (djvulibre (assoc-ref inputs "djvulibre")) - (ocrad (assoc-ref inputs "ocrad")) - (tesseract (assoc-ref inputs "tesseract-ocr"))) - (for-each (lambda (file) - (wrap-program (string-append out "/bin/" file) - `("PATH" ":" prefix - (,(string-append djvulibre "/bin:" - ocrad "/bin:" - tesseract "/bin"))))) - '("djvu2hocr" - "hocr2djvused" - "ocrodjvu")))))))) - (synopsis "Program to perform OCR on DjVu files") - (description - "@code{ocrodjvu} is a wrapper for OCR systems, that allows you to perform + (let ((revision "0") + (commit "0dd3364462fc77d5674b4457fcc8230835323c30")) + (package + (name "ocrodjvu") + (version (git-version "0.12" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + ;; Use the following fork repository, as upstream + ;; doesn't seem too concerned with Python 3 + ;; compatibility. + (url "https://github.com/rmast/ocrodjvu") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0x64hg9ysrk8sismxb4jgk0sq7r9j90v2i9765xhmxpiy6f0lpni")))) + (build-system gnu-build-system) + (native-inputs + (list libxml2 python-nose python-pillow)) + (inputs + (list djvulibre + ocrad + python-djvulibre + python-future + python-html5lib + python-lxml + python-pyicu + python-regex + python-wrapper + tesseract-ocr)) + (arguments + (list + #:modules '((guix build gnu-build-system) + ((guix build python-build-system) #:prefix python:) + (guix build utils)) + #:imported-modules `(,@%gnu-build-system-modules + (guix build python-build-system)) + #:test-target "test" + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-before 'check 'disable-failing-test + (lambda _ + (substitute* "tests/test_ipc.py" + ;; test_wait_signal gets stuck forever + (("yield self\\._test_signal, name") + "return True") + ;; test_path fails to find a file it should have created + (("path = os\\.getenv\\('PATH'\\)\\.split\\(':'\\)") + "return True")) + ;; Disable tests with tesseract. They can't work without + ;; the language files that must downloaded by the final user + ;; as they are not packaged in Guix. + (substitute* "tests/ocrodjvu/test.py" + (("engines = stdout\\.getvalue\\(\\)\\.splitlines\\(\\)") + "engines = ['ocrad']")) + (substitute* "tests/ocrodjvu/test_integration.py" + (("engines = 'tesseract', 'cuneiform', 'gocr', 'ocrad'") + "engines = 'ocrad'")))) + (replace 'install + (lambda _ + (invoke "make" "install" + "DESTDIR=" (string-append "PREFIX=" #$output)))) + (add-after 'install 'wrap-python + (assoc-ref python:%standard-phases 'wrap)) + (add-after 'wrap-python 'wrap-path + (lambda* (#:key outputs #:allow-other-keys) + (for-each (lambda (file) + (wrap-program (search-input-file outputs file) + `("PATH" ":" prefix + (,(string-append + #$(this-package-input "djvulibre") "/bin:" + #$(this-package-input "ocrad") "/bin:" + #$(this-package-input "tesseract-ocr") + "/bin"))))) + '("bin/djvu2hocr" + "bin/hocr2djvused" + "bin/ocrodjvu"))))))) + (synopsis "Program to perform OCR on DjVu files") + (description + "@code{ocrodjvu} is a wrapper for OCR systems, that allows you to perform OCR on DjVu files.") - (home-page "https://jwilk.net/software/ocrodjvu") - (license license:gpl2))) + (home-page "https://jwilk.net/software/ocrodjvu") + (license license:gpl2)))) From b3c7d69fa0369ada0e501b093eb36565c161eea6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:09:20 -0400 Subject: [PATCH 0825/1394] gnu: Remove python2-pandas. * gnu/packages/python-science.scm (python2-pandas): Delete variable. (python-pandas): Delete related python2-variant property. --- gnu/packages/python-science.scm | 98 --------------------------------- 1 file changed, 98 deletions(-) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 5fbb7fd1c82..0b3547f552f 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -489,106 +489,8 @@ structures designed to make working with structured (tabular, multidimensional, potentially heterogeneous) and time series data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python.") - (properties `((python2-variant . ,(delay python2-pandas)))) (license license:bsd-3))) -;; Pandas 0.24.x are the last versions that support Python 2. -(define-public python2-pandas - (let ((pandas (package-with-python2 - (strip-python2-variant python-pandas)))) - (package - (inherit pandas) - (version "0.24.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "pandas" version)) - (sha256 - (base32 - "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Adjust for renamed error message in Python 2.7.17. Taken - ;; from . - (substitute* "pandas/io/parsers.py" - (("if 'NULL byte' in msg:") - "if 'NULL byte' in msg or 'line contains NUL' in msg:")))))) - (arguments - `(#:modules ((guix build utils) - (guix build python-build-system) - (ice-9 ftw) - (srfi srfi-26)) - #:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-which - (lambda* (#:key inputs #:allow-other-keys) - (let ((which (assoc-ref inputs "which"))) - (substitute* "pandas/io/clipboard/__init__.py" - (("^CHECK_CMD = .*") - (string-append "CHECK_CMD = \"" which "\"\n")))))) - (replace 'check - (lambda _ - (let ((build-directory - (string-append - (getcwd) "/build/" - (car (scandir "build" - (cut string-prefix? "lib." <>)))))) - ;; Disable the "strict data files" option which causes - ;; the build to error out if required data files are - ;; not available (as is the case with PyPI archives). - (substitute* "setup.cfg" - (("addopts = --strict-data-files") "addopts = ")) - (with-directory-excursion build-directory - ;; Delete tests that require "moto" which is not yet - ;; in Guix. - (for-each delete-file - '("pandas/tests/io/conftest.py" - "pandas/tests/io/json/test_compression.py" - "pandas/tests/io/parser/test_network.py" - "pandas/tests/io/test_parquet.py")) - (invoke "pytest" "-vv" "pandas" "--skip-slow" - "--skip-network" "-k" - ;; XXX: Due to the deleted tests above. - "not test_read_s3_jsonl")))))))) - (propagated-inputs - (list python2-numpy python2-openpyxl python2-pytz python2-dateutil - python2-xlrd)) - (inputs - (list which)) - (native-inputs - (list python2-cython - python2-beautifulsoup4 - python2-lxml - python2-html5lib - python2-nose - python2-pytest - python2-pytest-mock))))) - -(define-public python2-pyflow - (package - (name "python2-pyflow") - (version "1.1.20") - (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/Illumina/pyflow/releases/download/v" - version "/pyflow-" version ".tar.gz")) - (sha256 - (base32 - "1bvfvviw58cndyn862qnv9nj3d9cd3a0dm4vc4sd9vwq8a6z1riv")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; There is no test suite. - ;; There is no official Python 3-compatible version and upstream is - ;; dead. See https://github.com/Illumina/pyflow/issues/20. - #:python ,python-2)) - (home-page "https://illumina.github.io/pyflow/") - (synopsis "Tool to manage tasks in a task dependency graph") - (description "This package is a Python module to manage tasks in the -context of a task dependency graph. It has some similarities to make.") - (license license:bsd-2))) - (define-public python-pythran (package (name "python-pythran") From 46ef39b4be81076f11f37507667eb42786c4727f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:02:27 -0400 Subject: [PATCH 0826/1394] gnu: Remove python2-html5lib. * gnu/packages/python-web.scm (python2-html5lib): Delete variable. (python-html5lib-0.9, python2-html5lib-0.9): Likewise. --- gnu/packages/python-web.scm | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index b4a2bc365b7..7feac5955f2 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1326,25 +1326,6 @@ storage.") and written in Python.") (license license:expat))) -(define-public python2-html5lib - (package-with-python2 python-html5lib)) - -;; Needed for python-bleach, a dependency of python-notebook -(define-public python-html5lib-0.9 - (package - (inherit python-html5lib) - (version "0.999") - (source - (origin - (method url-fetch) - (uri (pypi-uri "html5lib" version)) - (sha256 - (base32 - "17n4zfsj6ynmbwdwviywmj8r6nzr3xvfx2zs0xhndmvm51z7z263")))))) - -(define-public python2-html5lib-0.9 - (package-with-python2 python-html5lib-0.9)) - (define-public python-html5-parser (package (name "python-html5-parser") From 32ec89285fdf36fd55c46b797b468c8c20f7c666 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:13:22 -0400 Subject: [PATCH 0827/1394] gnu: Remove python2-statsmodels. * gnu/packages/statistics.scm (python2-statsmodels): Delete variable. --- gnu/packages/statistics.scm | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5e6e9ba8371..7f543b16e7c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2082,27 +2082,6 @@ statistical computations including descriptive statistics and estimation and inference for statistical models.") (license license:bsd-3))) -(define-public python2-statsmodels - (let ((stats (package-with-python2 python-statsmodels))) - (package/inherit stats - ;; Version 0.11.1 and later does not work with Python 2. It may build - ;; fine but loading modules fails. - (version "0.9.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "statsmodels" version)) - (sha256 - (base32 - "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4")))) - (propagated-inputs - `(("python2-pytz" ,python2-pytz) - ("python2-numpy" ,python2-numpy) - ("python2-scipy" ,python2-scipy) - ("python2-pandas" ,python2-pandas) - ("python2-patsy" ,python2-patsy) - ("python2-matplotlib" ,python2-matplotlib)))))) - (define-public r-coda (package (name "r-coda") From 7ebb6b7b2b0806c605c88f80811a633cf153c2e5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 14:45:22 -0400 Subject: [PATCH 0828/1394] gnu: Remove python2-pytest-cache. * gnu/packages/check.scm (python2-pytest-cache): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 9172888751b..69644aefece 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2059,9 +2059,6 @@ the last py.test invocation.") (home-page "https://bitbucket.org/hpk42/pytest-cache/") (license license:expat))) -(define-public python2-pytest-cache - (package-with-python2 python-pytest-cache)) - (define-public python-pytest-localserver (package (name "python-pytest-localserver") From 0837d0aaf199f4826614f588342b871825273c25 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:31:50 -0400 Subject: [PATCH 0829/1394] gnu: Remove python2-fastlmm. * gnu/packages/machine-learning.scm (python2-fastlmm): Delete variable. --- gnu/packages/machine-learning.scm | 32 ------------------------------- 1 file changed, 32 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 02cd6b31aad..7b377c7d351 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1415,38 +1415,6 @@ such as online, hashing, allreduce, reductions, learning2search, active, and interactive learning.") (license license:bsd-3))) -(define-public python2-fastlmm - (package - (name "python2-fastlmm") - (version "0.2.21") - (source - (origin - (method url-fetch) - (uri (pypi-uri "fastlmm" version ".zip")) - (sha256 - (base32 - "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; some test files are missing - #:python ,python-2)) ; only Python 2.7 is supported - (propagated-inputs - (list python2-numpy - python2-scipy - python2-matplotlib - python2-pandas - python2-scikit-learn - python2-pysnptools)) - (native-inputs - (list unzip python2-cython python2-mock python2-nose)) - (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/") - (synopsis "Perform genome-wide association studies on large data sets") - (description - "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed -Models, is a program for performing both single-SNP and SNP-set genome-wide -association studies (GWAS) on extremely large data sets.") - (license license:asl2.0))) - (define-public python-hyperopt (package (name "python-hyperopt") From 55fc0947d484f13dec89a4897b9313c8079b1d98 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:32:48 -0400 Subject: [PATCH 0830/1394] gnu: Remove python2-parameterized. * gnu/packages/check.scm (python2-parameterized): Delete variable. * gnu/packages/patches/python2-parameterized-docstring-test.patch: Delete file. * gnu/local.mk (dist_patch_DATA): De-register it. --- gnu/local.mk | 1 - gnu/packages/check.scm | 11 ----------- .../python2-parameterized-docstring-test.patch | 18 ------------------ 3 files changed, 30 deletions(-) delete mode 100644 gnu/packages/patches/python2-parameterized-docstring-test.patch diff --git a/gnu/local.mk b/gnu/local.mk index 93b4902151d..3452b75e3bf 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1705,7 +1705,6 @@ dist_patch_DATA = \ %D%/packages/patches/python-mox3-python3.6-compat.patch \ %D%/packages/patches/python-typing-inspect-fix.patch \ %D%/packages/patches/python-packaging-test-arch.patch \ - %D%/packages/patches/python2-parameterized-docstring-test.patch \ %D%/packages/patches/python-paste-remove-timing-test.patch \ %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch \ %D%/packages/patches/python-pycrypto-time-clock.patch \ diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 69644aefece..197205a47e9 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -818,19 +818,8 @@ but it works for any C/C++ project.") (description "Parameterized is a Python library that aims to fix parameterized testing for every Python test framework. It supports nose, py.test, and unittest.") - (properties `((python2-variant . ,(delay python2-parameterized)))) (license license:bsd-2))) -(define-public python2-parameterized - (let ((base (package-with-python2 (strip-python2-variant - python-parameterized)))) - (package/inherit - base - (source - (origin - (inherit (package-source base)) - (patches (search-patches "python2-parameterized-docstring-test.patch"))))))) - (define-public python-minimock (package (name "python-minimock") diff --git a/gnu/packages/patches/python2-parameterized-docstring-test.patch b/gnu/packages/patches/python2-parameterized-docstring-test.patch deleted file mode 100644 index 14691e19044..00000000000 --- a/gnu/packages/patches/python2-parameterized-docstring-test.patch +++ /dev/null @@ -1,18 +0,0 @@ -Skip unicode docstring test, required when running on Python 2. - -See . - ---- a/parameterized/test.py -+++ b/parameterized/test.py -@@ -284,11 +284,6 @@ - " More" %(foo, ) - ) - -- @parameterized.expand([param("foo")]) -- def test_unicode_docstring(self, foo): -- u"""Döcumentation.""" -- self._assert_docstring(u"Döcumentation [with foo=%r]." %(foo, )) -- - @parameterized.expand([param("foo", )]) - def test_default_values_get_correct_value(self, foo, bar=12): - """Documentation""" From e7a41b15cee67739546d743670af266035d71036 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:32:52 -0400 Subject: [PATCH 0831/1394] gnu: Remove python2-pytest-warnings. * gnu/packages/check.scm (python2-pytest-warnings): Delete variable. --- gnu/packages/check.scm | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 197205a47e9..421b9bf2027 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2598,14 +2598,7 @@ recognize TestCases.") "Python-pytest-warnings is a pytest plugin to list Python warnings in pytest report.") (license license:expat) - (properties `((python2-variant . ,(delay python2-pytest-warnings)) - ;; This package is part of pytest as of version 3.1.0. - (superseded . ,python-pytest))))) - -(define-public python2-pytest-warnings - (package (inherit (package-with-python2 - (strip-python2-variant python-pytest-warnings))) - (properties `((superseded . ,python2-pytest))))) + (properties `((superseded unquote python-pytest))))) (define-public python-pytest-capturelog (package From d76de71dd6c451cef19a9477b8a8b417bf916f49 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:33:11 -0400 Subject: [PATCH 0832/1394] gnu: Remove python2-pyodbc. * gnu/packages/databases.scm (python2-pyodbc): Delete variable. --- gnu/packages/databases.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 9c46a5a9d24..c5480419558 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3111,9 +3111,6 @@ for ODBC.") for ODBC.") (license (license:x11-style "file:///LICENSE.TXT")))) -(define-public python2-pyodbc - (package-with-python2 python-pyodbc)) - (define-public mdbtools (package (name "mdbtools") From 9384d5de3c72d7d362c272b229ec951845160552 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:33:15 -0400 Subject: [PATCH 0833/1394] gnu: Remove python2-pickleshare. * gnu/packages/databases.scm (python2-pickleshare): Delete variable. --- gnu/packages/databases.scm | 9 --------- 1 file changed, 9 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index c5480419558..f90a1b6c747 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3546,17 +3546,8 @@ value in database is immediately visible to other processes accessing the same database. Concurrency is possible because the values are stored in separate files. Hence the “database” is a directory where all files are governed by PickleShare.") - (properties `((python2-variant . ,(delay python2-pickleshare)))) (license license:expat))) -(define-public python2-pickleshare - (let ((pickleshare (package-with-python2 - (strip-python2-variant python-pickleshare)))) - (package (inherit pickleshare) - (propagated-inputs (modify-inputs (package-propagated-inputs - pickleshare) - (prepend python2-pathlib2)))))) - (define-public python-apsw (package (name "python-apsw") From d9e54dfd4c60791b923ae309e1fb0ac635502c01 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:33:23 -0400 Subject: [PATCH 0834/1394] gnu: Remove djvusmooth. * gnu/packages/djvu.scm (djvusmooth): Delete variable. --- gnu/packages/djvu.scm | 40 ---------------------------------------- 1 file changed, 40 deletions(-) diff --git a/gnu/packages/djvu.scm b/gnu/packages/djvu.scm index 0fc2f6dfb9c..9c834bcfba1 100644 --- a/gnu/packages/djvu.scm +++ b/gnu/packages/djvu.scm @@ -291,46 +291,6 @@ and white.") (home-page "https://sourceforge.net/projects/minidjvu/") (license license:gpl2))) -(define-public djvusmooth - (package - (name "djvusmooth") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (string-append - "https://github.com/jwilk/djvusmooth/releases/download/" version - "/djvusmooth-" version ".tar.gz")) - (sha256 - (base32 "0z403cklvxzz0qaczgv83ax0nknrd9h8micp04j9kjfdxk2sgval")))) - (build-system python-build-system) - (inputs - (list djvulibre python2-djvulibre python2-subprocess32 - python2-wxpython)) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "lib/djvused.py" - (("djvused_path = 'djvused'") - (string-append "djvused_path = '" - (assoc-ref inputs "djvulibre") - "/bin/djvused'")))))))) - (synopsis "Graphical editor for DjVu documents") - (description - "@code{djvusmooth} is a graphical editor for DjVu_ documents. -It is able to: -@itemize -@item edit document metadata, -@item edit document outline (bookmarks), -@item add, remove or edit hyperlinks, -@item correct occasional errors in the hidden text layer. -@end itemize\n") - (home-page "https://jwilk.net/software/djvusmooth") - (license license:gpl2))) - (define-public didjvu (package (name "didjvu") From 19aa16d4a2f4f8b36f5bf9be3f3078e63cc1dbed Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:33:26 -0400 Subject: [PATCH 0835/1394] gnu: Remove omnitux. * gnu/packages/education.scm (omnitux): Delete variable. --- gnu/packages/education.scm | 100 ------------------------------------- 1 file changed, 100 deletions(-) diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 213c8f717b6..07843142f4a 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -679,106 +679,6 @@ used both with interactive whiteboards or in a dual-screen setup with a pen-tablet display and a beamer.") (license license:gpl3)))) -(define-public omnitux - (package - (name "omnitux") - (version "1.2.1") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/omnitux/omnitux/" - "v" version "/omnitux-" version ".tar.bz2")) - (sha256 - (base32 "1wmmmbzmxd0blhn00d4g91xwavnab143a31ca3i8hrqgzh6qz9w6")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Remove pre-compiled .pyc files from source. - (for-each delete-file (find-files "bin" "\\.pyc$")) - #t)))) - (build-system python-build-system) - (inputs - (list python2-pygame python2-pygtk)) - (arguments - `(#:tests? #f ;no test - #:python ,python-2 - #:phases - (modify-phases %standard-phases - (delete 'build) ;no setup.py - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (share (string-append out "/share")) - (data (string-append share "/omnitux"))) - ;; Install documentation. - (let ((doc (string-append share "/doc/" ,name "-" ,version))) - (for-each (lambda (f) (install-file f doc)) - '("LICENSE.txt" "README.txt"))) - ;; Install data. - (install-file "omnitux.sh" data) - (for-each (lambda (d) - (copy-recursively d (string-append data "/" d))) - '("bin" "data")) - ;; Install the launcher. - (let* ((bin (string-append out "/bin")) - (script (string-append bin "/omnitux")) - (bash (search-input-file %build-inputs "/bin/bash")) - (python (search-input-file %build-inputs - "/bin/python2"))) - (mkdir-p bin) - (with-output-to-file script - (lambda () - (format #t "#!~a~%" bash) - (format #t - "cd ~a; ~a menu.py~%" - (string-append data "/bin") - python))) - (chmod script #o755)) - ;; Install icon and desktop file. - (let ((pixmaps (string-append share "/pixmaps"))) - (install-file "data/default/icons/Omnitux_logo.svg" pixmaps)) - (let ((apps (string-append out "/share/applications"))) - (mkdir-p apps) - (with-output-to-file (string-append apps "/omnitux.desktop") - (lambda _ - (format #t - "[Desktop Entry]~@ - Name=Omnitux~@ - GenericName=Omnitux - Comment=An educational game based on multimedia elements.~@ - Comment[fr]=Un jeu ludo-éducatif basé sur des éléments multimédias.~@ - Exec=~a/bin/omnitux~@ - Type=Application~@ - Categories=Game;Education;~@ - Terminal=false~@ - Icon=Omnitux_logo.svg~@" - out)))) - #t)))))) - (home-page "http://omnitux.sourceforge.net/") - (synopsis "Educational activities based on multimedia elements") - (description "The project aims to provide various educational -activities around multimedia elements (images, sounds, texts). Types -of activities include: -@itemize -@item associations, -@item items to place on a map or a schema, -@item counting activities, -@item puzzles, -@item card faces to remember, -@item find differences between two pictures, -@item ... -@end itemize - -Activities are available in English, French, German, Polish, -Portuguese, Spanish and Italian.") - ;; Project's license is GPL3+, but multimedia elements are - ;; released under various licenses. - (license (list license:gpl3+ - license:gpl2+ - license:cc-by-sa2.0 - license:cc-by-sa3.0 - license:public-domain)))) - (define-public fet (package (name "fet") From 6d9044b3c895f842a241f485364544eb73579f4a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:33:30 -0400 Subject: [PATCH 0836/1394] gnu: Remove childsplay. * gnu/packages/education.scm (childsplay): Delete variable. --- gnu/packages/education.scm | 103 ------------------------------------- 1 file changed, 103 deletions(-) diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 07843142f4a..3b9c01c786b 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -445,109 +445,6 @@ specialized device.") (home-page "https://bipede.fr/contrib/") (license license:gpl3))) -(define-public childsplay - (package - (name "childsplay") - (version "3.4") - (source (origin - (method url-fetch) - (uri (string-append - "mirror://sourceforge/schoolsplay/" - "childsplay-" version ".tgz")) - (sha256 - (base32 - "0z7yp2swjnbz51vn2zyfnjn40jq38l5mbh15yafmx1z3vn2z1m77")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:tests? #f - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'unbundle-dejavu-font - (lambda* (#:key inputs #:allow-other-keys) - (let* ((dejavu-dir - (string-append (assoc-ref inputs "font-dejavu") - "/share/fonts/truetype")) - (dejavu-font - (string-append dejavu-dir - "/DejaVuSansCondensed-Bold.ttf"))) - (substitute* "SPConstants.py" - (("^(TTF(BOLD)? = ).*" _ prefix) - (string-append prefix "'" dejavu-font "'\n"))) - (for-each (lambda (f) (delete-file f)) - (find-files "lib/SPData" "DejaVu")) - #t))) - (delete 'build) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (pixmaps (string-append out "/share/pixmaps")) - (share (string-append out "/share/childsplay")) - (doc (string-append out "/share/doc/" ,name "-",version))) - ;; Install icon. - (install-file "lib/SPData/themes/childsplay/logo_cp.svg" pixmaps) - ;; Install data. - (mkdir-p share) - (for-each (lambda (f) - (copy-recursively f (string-append share "/" f))) - '("alphabet-sounds" "lib" "locale" "SPWidgets")) - (for-each (lambda (f) (install-file f share)) - (find-files "." "\\.(py|dev|db)$")) - ;; Install documentation. - (mkdir-p doc) - (copy-recursively "docs" doc) - #t))) - (add-after 'install 'create-executable - (lambda* (#:key outputs inputs #:allow-other-keys) - (let* ((python (search-input-file inputs "/bin/python")) - (out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (executable (string-append bin "/childsplay"))) - (mkdir-p bin) - (call-with-output-file executable - (lambda (file) - (format file - "~a ~a" - python - (string-append out "/share/childsplay/childsplay.py")))) - (chmod executable #o555) - #t))) - (add-after 'install 'create-desktop-file - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (applications (string-append out "/share/applications"))) - (mkdir-p applications) - (call-with-output-file - (string-append applications "/childsplay.desktop") - (lambda (file) - (format file - "[Desktop Entry]~@ - Name=Childsplay~@ - Comment=Suite of educational games for young children~@ - Comment[ca]=Conjunt de jocs educatius per a xiquets~@ - Comment[es]=Conjunto de juegos educativos para niños~@ - Comment[de]=Sammlung mit lehrreichen Spielen für kleine Kinder~@ - Exec=~a/bin/childsplay~@ - Terminal=false~@ - Icon=logo_cp.svg~@ - Type=Application~@ - Categories=Application;Game;Education;KidsGame;~@ - Keywords=suite;children;games;young;educational;~%" - out))) - #t)))))) - (inputs - `(("font-dejavu" ,font-dejavu) - ("pygame" ,python2-pygame) - ("sqlalchemy" ,python2-sqlalchemy))) - (synopsis "Suite of educational games for young children") - (description "Childsplay is a collection of educational activities -for young children. Childsplay can be used at home, kindergartens and -pre-schools. Childsplay is a fun and safe way to let young children -use the computer and at the same time teach them a little math, -letters of the alphabet, spelling, eye-hand coordination, etc.") - (home-page "http://www.schoolsplay.org") - (license license:gpl3+))) - (define-public openboard ;; The last release builds from qtwebkit, which is planned for removal in ;; Guix, so use the latest commit of the 1.7-dev branch, which builds with From 766af488846fdb9ba44641a15758b46d4ea2fb0d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:33:33 -0400 Subject: [PATCH 0837/1394] gnu: Remove python2-capstone. * gnu/packages/engineering.scm (python2-capstone): Delete variable. --- gnu/packages/engineering.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index dc902ef40f3..6b11fc54f04 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -1647,9 +1647,6 @@ bindings for Python, Java, OCaml and more.") (string-append "'" (assoc-ref %build-inputs "capstone") "/lib',\n"))) #t))))))) -(define-public python2-capstone - (package-with-python2 python-capstone)) - (define-public python-esptool-3.0 (package From a512c65503772837f2b9a061917d6ccaac645a10 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:33:40 -0400 Subject: [PATCH 0838/1394] gnu: Remove lekha. * gnu/packages/enlightenment.scm (lekha): Delete variable. --- gnu/packages/enlightenment.scm | 28 ---------------------------- 1 file changed, 28 deletions(-) diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index 6a02ab1ca4b..7be6304a5ee 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -483,34 +483,6 @@ and in creating applications based on the Enlightenment Foundation Library suite license:gpl2 ; edi license:gpl3)))) ; data/extra/examples/images/mono-runtime.png -(define-public lekha - (package - (name "lekha") - (version "0.2.1") - (source (origin - (method url-fetch) - (uri (pypi-uri "Lekha" version)) - (sha256 - (base32 - "0zr6i74ik58pbzrd7r9l7sawqbdv0r2c1a9927qkqzwga27x8j15")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; no test target - #:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-data-location - (lambda _ (substitute* "setup.py" - (("'/usr/")"'")) - #t))))) - (propagated-inputs - (list python2-efl python2-pypdf2 python2-pyxdg)) - (synopsis "Simple PDF viewer") - (description - "Simple PDF viewer based on the Enlightenment Foundation Libraries.") - (home-page "https://github.com/kaihu/lekha") - (license license:gpl3+))) - (define-public ephoto (package (name "ephoto") From 50491574a6ae5d3abe84f6cec94acc35f398bafd Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:33:43 -0400 Subject: [PATCH 0839/1394] gnu: Remove python2-stdnum. * gnu/packages/finance.scm (python2-stdnum): Delete variable. --- gnu/packages/finance.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 09b979899dd..d45cb42f094 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -1230,9 +1230,6 @@ The module also includes implementations of the Verhoeff, Luhn and family of ISO/IEC 7064 check digit algorithms.") (license license:lgpl2.1+))) -(define-public python2-stdnum - (package-with-python2 python-stdnum)) - (define-public python-duniterpy (package (name "python-duniterpy") From 6ad2c39af863f7c559f2d4bf1cb33cef6f14b82d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:33:47 -0400 Subject: [PATCH 0840/1394] gnu: Remove python2-ledgerblue. * gnu/packages/finance.scm (python2-ledgerblue): Delete variable. --- gnu/packages/finance.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index d45cb42f094..9ad046b2488 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -978,9 +978,6 @@ of Bitcoin BIP-0039.") Ledger Blue/Nano S.") (license license:asl2.0))) -(define-public python2-ledgerblue - (package-with-python2 python-ledgerblue)) - (define-public python-btchip-python (package (name "python-btchip-python") From c9a21c421641562a9a77a880eb118e4dc4675f7f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:33:52 -0400 Subject: [PATCH 0841/1394] gnu: Remove python2-keepkey. * gnu/packages/finance.scm (python2-keepkey): Delete variable. --- gnu/packages/finance.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 9ad046b2488..d528f2662d3 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -1085,9 +1085,6 @@ TREZOR Hardware Wallet.") the KeepKey Hardware Wallet.") (license license:lgpl3))) -(define-public python2-keepkey - (package-with-python2 python-keepkey)) - (define-public ledger-agent (package (name "ledger-agent") From 910ce808850323f1cfbbcbbbf133705bf1149d98 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:33:55 -0400 Subject: [PATCH 0842/1394] gnu: nototools: Update to 0.2.16. * gnu/packages/fontutils.scm (nototools): Update to 0.2.16. [arguments]: Remove python argument. [phases]: New argument. [native-inputs]: New field. [propagated-inputs]: Remove python2-booleanoperations, python2-defcon, python2-fonttools, python2-pillow, python2-pyclipper, and python2-ufolib. Add python-afdko. --- gnu/packages/fontutils.scm | 28 ++++++++++++++++------------ 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm index 444d1635cba..7c03109be53 100644 --- a/gnu/packages/fontutils.scm +++ b/gnu/packages/fontutils.scm @@ -1525,27 +1525,31 @@ UFO3 as described by the UFO font format.") (define-public nototools (package (name "nototools") - (version "20170925") + (version "0.2.16") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/googlei18n/nototools") - (commit "v2017-09-25-tooling-for-phase3-update"))) + (url "https://github.com/googlefonts/nototools") + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "03nzvcvwmrhfrcjhg218q2f3hfrm3vlivp4rk19sc397kh3hisiz")))) + "14rrdamkmhrykff8ln07fq9cm8zwj3k113lzwjcy0lgz23g51jyl")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) - (propagated-inputs - (list python2-booleanoperations - python2-defcon - python2-fonttools - python2-pillow - python2-pyclipper - python2-ufolib)) + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'pretend-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (with-directory-excursion "tests" + (invoke "./run_tests"))))))) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-afdko)) (home-page "https://github.com/googlei18n/nototools") (synopsis "Noto fonts support tools and scripts") (description From da52f45208f052c50ae482d1c9d95c43c81cf72d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:34:09 -0400 Subject: [PATCH 0843/1394] gnu: Remove python2-tmx. * gnu/packages/game-development.scm (python2-tmx): Delete variable. --- gnu/packages/game-development.scm | 8 -------- 1 file changed, 8 deletions(-) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index daeeec42cb5..d8725e837c4 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -407,14 +407,6 @@ levels.") ;; under the CC0 license. license:cc0)))) -(define-public python2-tmx - (let ((python2-tmx (package-with-python2 python-tmx))) - (package - (inherit python2-tmx) - (propagated-inputs - (modify-inputs (package-propagated-inputs python2-tmx) - (prepend python2-pathlib)))))) - (define-public python-xsge (package (name "python-xsge") From 9f1bd63fb5b6916f07d454ffde27cd3a66c95bb5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:34:16 -0400 Subject: [PATCH 0844/1394] gnu: renpy: Build with Python 3. * gnu/packages/game-development.scm (renpy)[python]: Delete argument. [phases]: Delete trailing #t. [propagated-inputs]: Update the inputs to their Python 3 counterparts. [native-inputs]: Likewise. --- gnu/packages/game-development.scm | 197 ++---------------------------- 1 file changed, 10 insertions(+), 187 deletions(-) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index d8725e837c4..961b396ea7d 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -1263,9 +1263,9 @@ developed mainly for Ren'py.") (define-public python2-pygame-sdl2 (package-with-python2 python-pygame-sdl2)) -(define-public python2-renpy +(define-public renpy (package - (name "python2-renpy") + (name "renpy") (version "7.4.11") (source (origin @@ -1284,8 +1284,7 @@ developed mainly for Ren'py.") #t)))) (build-system python-build-system) (arguments - `(#:tests? #f ; Ren'py doesn't seem to package tests - #:python ,python-2 + `(#:tests? #f ; Ren'py doesn't seem to package tests #:phases (modify-phases %standard-phases (add-after 'unpack 'fix-commands @@ -1293,8 +1292,7 @@ developed mainly for Ren'py.") (substitute* "renpy/editor.py" (("xdg-open") (string-append (assoc-ref inputs "xdg-utils") - "/bin/xdg-open"))) - #t)) + "/bin/xdg-open"))))) (add-after 'unpack 'fix-include-paths (lambda* (#:key inputs #:allow-other-keys) (substitute* "module/setup.py" @@ -1305,8 +1303,7 @@ developed mainly for Ren'py.") (setenv "RENPY_CYTHON" (search-input-file (or native-inputs inputs) "/bin/cython")) - (setenv "RENPY_DEPS_INSTALL" (string-join (map cdr inputs) ":")) - #t)) + (setenv "RENPY_DEPS_INSTALL" (string-join (map cdr inputs) ":")))) (replace 'build (lambda* (#:key inputs outputs #:allow-other-keys #:rest args) ;; The "module" subdirectory contains a python (really cython) @@ -1316,8 +1313,7 @@ developed mainly for Ren'py.") (apply (assoc-ref %standard-phases 'build) args)) ;; The above only builds the cython modules, but nothing else, ;; so we do that here. - (invoke "python" "-m" "compileall" "renpy") - #t)) + (invoke "python" "-m" "compileall" "renpy"))) (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys #:rest args) ;; Again, we have to wrap the module installation. @@ -1332,8 +1328,9 @@ developed mainly for Ren'py.") (apply (assoc-ref %standard-phases 'install) args)) (copy-recursively "renpy" (string-append out site "/renpy")) - (delete-file-recursively (string-append out site "/renpy/common"))) - #t))))) + (delete-file-recursively (string-append out site + "/renpy/common")))))))) + (native-inputs (list python-cython)) (inputs (list ffmpeg freetype @@ -1342,11 +1339,7 @@ developed mainly for Ren'py.") libpng (sdl-union (list sdl2 sdl2-image sdl2-mixer sdl2-ttf)) xdg-utils)) - (propagated-inputs - `(("python2-future" ,python2-future) - ("python2-pygame" ,python2-pygame-sdl2))) - (native-inputs - (list python2-cython)) + (propagated-inputs (list python-future python-pygame-sdl2)) (home-page "https://www.renpy.org/") (synopsis "Ren'py python module") (description "This package contains the shared libraries and Python modules @@ -1355,176 +1348,6 @@ the launcher and common Ren'py code provided by the @code{renpy} package and are only used to bootstrap it.") (license license:expat))) -(define-public renpy - (package - (inherit python2-renpy) - (name "renpy") - (build-system python-build-system) - (arguments - `(#:tests? #f ; see python2-renpy - #:python ,python-2 - #:modules ((srfi srfi-1) - (guix build python-build-system) - (guix build utils)) - #:imported-modules ((srfi srfi-1) ,@%python-build-system-modules) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-commands - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* "launcher/game/choose_directory.rpy" - (("/usr/bin/python") - (string-append (assoc-ref inputs "python2") - "/bin/python2"))) - (substitute* "launcher/game/front_page.rpy" - (("xdg-open") - (string-append (assoc-ref inputs "xdg-utils") - "/bin/xdg-open"))) - (substitute* "launcher/game/project.rpy" - (("cmd = \\[ executable, \"-EO\", sys.argv\\[0\\] \\]") - (string-append "cmd = [ \"" (assoc-ref outputs "out") - "/bin/renpy\" ]")) - ;; Projects are still created in the usual style, so we need - ;; to adjust the path. - (("cmd.append\\(self.path\\)") - "cmd.append(self.path + \"/game\")")) - #t)) - (add-after 'unpack 'drop-game-from-paths - (lambda _ - (substitute* (list "launcher/game/gui7.rpy" - "launcher/game/gui7/images.py") - ((", \"game\",") ",")) - #t)) - (add-before 'build 'start-xserver - (lambda* (#:key inputs native-inputs #:allow-other-keys) - (let ((xorg-server (assoc-ref (or native-inputs inputs) - "xorg-server"))) - (setenv "HOME" (getcwd)) - (system (format #f "~a/bin/Xvfb :1 &" xorg-server)) - (setenv "DISPLAY" ":1") - #t))) - (replace 'build - (lambda _ - (invoke "python" "renpy.py" "launcher" "quit") - (invoke "python" "renpy.py" "the_question" "quit") - (invoke "python" "renpy.py" "tutorial" "quit") - #t)) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Here we install our custom renpy program. - ;; After finishing this step, "out" will have the following: - ;; |-- bin/renpy - ;; `-- share/renpy ; i.e. path_to_renpy_base() - ;; |-- common - ;; `-- gui - ;; - ;; Note that common shares the source files that would be installed - ;; by python2-renpy (which are instead deleted from that package), - ;; but also contains their byte-compiled versions. - ;; On other systems, renpy_base would point to site-packages or - ;; even somewhere in /opt. - ;; The former approach is not as straightforward as it seems - ;; -- it causes renpy to load files twice for some weird reason -- - ;; and the latter is impossible on Guix. Hence the detour through - ;; share/renpy and the custom renpy program. - ;; - ;; As a convention, other games should be installed as - ;; subdirectories of share/renpy in their respective outputs as - ;; well. This differs from the traditional layout, which is - ;; roughly the following: - ;; `-- Super Awesome Game - ;; |-- game ; <- the folder we actually want - ;; |-- lib ; compiled renpy module and dependencies - ;; |-- renpy ; yet another copy of Ren'py's code - ;; | |-- common ; the common folder from above - ;; | `-- ... ; Python code (source + compiled) - ;; |-- Super Awesome Game.py - ;; `-- Super Awesome Game.sh - (let* ((out (assoc-ref outputs "out")) - (bin/renpy (string-append out "/bin/renpy"))) - (copy-recursively "renpy/common" - (string-append out "/share/renpy/common")) - (copy-recursively "gui" - (string-append out "/share/renpy/gui")) - - (mkdir-p (string-append out "/bin")) - (copy-file (assoc-ref inputs "renpy.in") bin/renpy) - (substitute* bin/renpy - (("@PYTHON@") (search-input-file inputs "bin/python2")) - (("@RENPY_BASE@") (string-append out "/share/renpy"))) - (chmod bin/renpy #o755)))) - - (add-after 'install 'install-games - (lambda* (#:key outputs #:allow-other-keys) - (define renpy (assoc-ref outputs "out")) - ;; TODO: We should offer a renpy-build-system to make the - ;; installation of Ren'py games easier. - (define* (install-renpy-game #:key output game name (renpy renpy) - #:allow-other-keys) - (let* ((name (or name (basename game))) - (launcher (string-append output "/bin/renpy-" name)) - (share (string-append output "/share/renpy/" name))) - (copy-recursively (string-append game "/game") share) - (mkdir-p (string-append output "/bin")) - (with-output-to-file launcher - (lambda () - (format #t - "#!~a~%~a ~a \"$@\"" - (which "bash") - (string-append renpy "/bin/renpy") - share))) - (chmod launcher #o755))) - - (install-renpy-game #:output (assoc-ref outputs "out") - #:game "launcher") - - (install-renpy-game #:output (assoc-ref outputs "the-question") - #:game "the_question" - #:name "the-question") - - (install-renpy-game #:output (assoc-ref outputs "tutorial") - #:game "tutorial") - #t)) - (replace 'wrap - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (site (string-append "/lib/python" - (python-version - (assoc-ref inputs "python")) - "/site-packages"))) - (wrap-program (string-append out "/bin/renpy") - `("GUIX_PYTHONPATH" = - (,@(delete-duplicates - (map - (lambda (store-path) - (string-append store-path site)) - (cons (assoc-ref outputs "out") - (map cdr - (filter - (lambda (input) - (string-prefix? "python2" (car input))) - inputs)))))))) - #t)))))) - (inputs - `(("renpy.in" ,(search-auxiliary-file "renpy/renpy.in")) - ("python2-renpy" ,python2-renpy) - ("python2-tkinter" ,python-2 "tk") - ("python2" ,python-2) ; for ‘fix-commands’ and ‘wrap’ - ("xdg-utils" ,xdg-utils))) - (propagated-inputs '()) - (native-inputs - (list xorg-server-for-tests)) - (outputs - (list "out" "tutorial" "the-question")) - (home-page "https://www.renpy.org/") - (synopsis "Visual Novel Engine") - (description "Ren'Py is a visual novel engine that helps you use words, -images, and sounds to tell interactive stories that run on computers and -mobile devices. These can be both visual novels and life simulation games. -The easy to learn script language allows anyone to efficiently write large -visual novels, while its Python scripting is enough for complex simulation -games.") - (license license:expat))) - (define-public python-pyxel (package (name "python-pyxel") From b7da08a4f9920f6aa703c9727b74644c4268763b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:34:19 -0400 Subject: [PATCH 0845/1394] gnu: Remove slingshot. * gnu/packages/games.scm (slingshot): Delete variable. --- gnu/packages/games.scm | 27 --------------------------- 1 file changed, 27 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 3e4369f4743..76f1e5df867 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -8682,33 +8682,6 @@ the net. There can be 1 to 8 balls in game. Once one ball touches the ground, the set ends and all balls are served again.") (license license:gpl3+))) -(define-public slingshot - (package - (name "slingshot") - (version "0.9") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ryanakca/slingshot") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "19m8b6nsi786bc6gmkp185mwri3r5y249gjmqd5qsc23nnfhgrs1")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) - (inputs - (list python2-pygame)) - (home-page "https://github.com/ryanakca/slingshot") - (synopsis "Simple 2D shooting strategy game set in space") - (description "Slingshot is a two-dimensional strategy game where two -players attempt to shoot one another through a section of space populated by -planets. The main feature of the game is that the shots, once fired, are -affected by the gravity of the planets.") - (license license:gpl2+))) - (define-public 4dtris (package (name "4dtris") From 14129029e26bbe18e6a63311447575e81e0e451f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:34:26 -0400 Subject: [PATCH 0846/1394] gnu: Remove python2-gpg. * gnu/packages/gnupg.scm (python2-gpg): Delete variable. --- gnu/packages/gnupg.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index cde7427d078..58a5c443186 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -532,9 +532,6 @@ cryptographic library. It is developed in the GPGME source code, and then distributed separately.") (license license:lgpl2.1+))) -(define-public python2-gpg - (package-with-python2 python-gpg)) - (define-public python-pygpgme (package (name "python-pygpgme") From 9d3c37b2c98093fd6c6c1fc0f8e698b6850c49ef Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:34:29 -0400 Subject: [PATCH 0847/1394] gnu: Remove python2-pygpgme. * gnu/packages/gnupg.scm (python2-pygpgme): Delete variable. --- gnu/packages/gnupg.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 58a5c443186..02a7c8d9426 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -567,9 +567,6 @@ distributed separately.") decrypt messages using the OpenPGP format by making use of GPGME.") (license license:lgpl2.1+))) -(define-public python2-pygpgme - (package-with-python2 python-pygpgme)) - (define-public python-gnupg (package (name "python-gnupg") From 5a2079594f8049447c09af21e27d977bafe2c92d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:34:33 -0400 Subject: [PATCH 0848/1394] gnu: pius: Update to 3.0.0. * gnu/packages/gnupg.scm (pius): Update to 3.0.0. [arguments]: Delete tests? and python arguments. [phases]{set-gpg-file-name}: Streamline. [description]: Spell key signing as two words. Mark commands with Texinfo markup. --- gnu/packages/gnupg.scm | 65 +++++++++++++++++++----------------------- 1 file changed, 30 insertions(+), 35 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 02a7c8d9426..c9b233c1e45 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2021 Maxime Devos ;;; Copyright © 2021 Nikita Domnitskii ;;; Copyright © 2021 Aleksandr Vityazev +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -638,44 +639,38 @@ signing, decryption, verification, and key-listing parsing.") (define-public pius (package - (name "pius") - (version "2.2.7") - (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/jaymzh/pius/releases/download/v" - version "/pius-" version ".tar.bz2")) - (sha256 - (base32 - "1nsl7czicv95j0gfz4s82ys3g3h2mwr6cq3ilid8bpz3iy7z4ipy")))) - (build-system python-build-system) - (inputs `(("perl" ,perl) ; for 'pius-party-worksheet' - ("gpg" ,gnupg) - ("python-six" ,python2-six))) - (arguments - `(#:tests? #f - #:python ,python-2 ; uses the Python 2 'print' syntax - #:phases - (modify-phases %standard-phases - (add-before - 'build 'set-gpg-file-name - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((gpg (search-input-file inputs "/bin/gpg"))) + (name "pius") + (version "3.0.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/jaymzh/pius/releases/download/v" + version "/pius-" version ".tar.bz2")) + (sha256 + (base32 + "11fhmfvr0avxl222rv43wjd2xjbpxrsmcl8xwmn0nvf1rw95v9fn")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'set-gpg-file-name + (lambda* (#:key inputs #:allow-other-keys) (substitute* "libpius/constants.py" - (("/usr/bin/gpg2") gpg)) - #t)))))) - (synopsis "Programs to simplify GnuPG key signing") - (description - "Pius (PGP Individual UID Signer) helps attendees of PGP keysigning + (("/usr/bin/gpg2") + (search-input-file inputs "bin/gpg")))))))) + (inputs (list perl ;for 'pius-party-worksheet' + gnupg)) + (synopsis "Programs to simplify GnuPG key signing") + (description + "Pius (PGP Individual UID Signer) helps attendees of PGP key signing parties. It is the main utility and makes it possible to quickly and easily sign each UID on a set of PGP keys. It is designed to take the pain out of -the sign-all-the-keys part of PGP Keysigning Party while adding security -to the process. - -pius-keyring-mgr and pius-party-worksheet help organisers of -PGP keysigning parties.") - (license license:gpl2) - (home-page "https://www.phildev.net/pius/index.shtml"))) +the sign-all-the-keys part of PGP key signing parties while adding security to +the process. The @command{pius-keyring-mgr} and +@command{pius-party-worksheet} commands help organizers of PGP key signing +parties.") + (license license:gpl2) + (home-page "https://www.phildev.net/pius/index.shtml"))) (define-public signing-party (package From 98b0ac0a77f9b72f58d5280776cbcce031e807aa Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:34:40 -0400 Subject: [PATCH 0849/1394] gnu: Remove python2-pydot. * gnu/packages/graphviz.scm (python2-pydot): Delete variable. --- gnu/packages/graphviz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm index dfbb28a8a92..2a99c0988e9 100644 --- a/gnu/packages/graphviz.scm +++ b/gnu/packages/graphviz.scm @@ -403,9 +403,6 @@ can be used either as a standalone application, or as a Python library.") graphs in Graphviz's DOT language, written in pure Python.") (license license:expat))) -(define-public python2-pydot - (package-with-python2 python-pydot)) - (define-public dot2tex (package (name "dot2tex") From 454987fcb215b1c0a9cc971f3d28debb2f352f63 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:34:43 -0400 Subject: [PATCH 0850/1394] gnu: dot2tex: Update to 2.11.3. * gnu/packages/graphviz.scm (dot2tex): Update to 2.11.3. [arguments]: Remove python argument. [phases]: New argument. [native-inputs]: New field. [inputs]: Move texlive-latex-preview to... [propagated-inputs]: ... here. Replace python2-pyparsing with python-parsing. Add texlive-bin, texlive-amsmath, texlive-latex-geometry, texlive-latex-graphics, texlive-latex-base, texlive-latex-xkeyval, texlive-pgf, texlive-pstricks and texlive-xcolor. --- gnu/packages/graphviz.scm | 30 ++++++++++++++++++++++++++---- 1 file changed, 26 insertions(+), 4 deletions(-) diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm index 2a99c0988e9..f2fd90e6161 100644 --- a/gnu/packages/graphviz.scm +++ b/gnu/packages/graphviz.scm @@ -415,11 +415,33 @@ graphs in Graphviz's DOT language, written in pure Python.") "1kp77wiv7b5qib82i3y3sn9r49rym43aaqm5aw1bwnzfbbq2m6i9")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) - (inputs - (list texlive-latex-preview graphviz)) + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "tests" + ;; The test_semicolon test fails for unknown reason + ;; (see: + ;; https://github.com/kjellmf/dot2tex/issues/94). + "-k" "not test_semicolon"))))))) + (native-inputs (list python-pytest)) + (inputs (list graphviz)) (propagated-inputs - (list python2-pyparsing)) + (list python-pyparsing + ;; These TeX dependencies are propagated to make it easier to build + ;; the resulting generated TeX files, which \usepackage them. + texlive-bin + texlive-amsmath + texlive-latex-geometry + texlive-latex-graphics + texlive-latex-base + texlive-latex-preview + texlive-latex-xkeyval + texlive-pgf + texlive-pstricks + texlive-xcolor)) (home-page "https://github.com/kjellmf/dot2tex") (synopsis "Graphviz to LaTeX converter") (description From 5fb6ad86bc973ccdb565bb95f00b07e09da00c8d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:34:52 -0400 Subject: [PATCH 0851/1394] gnu: Remove h-client. * gnu/packages/hardware.scm (h-client): Delete variable. --- gnu/packages/hardware.scm | 36 ------------------------------------ 1 file changed, 36 deletions(-) diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm index 38bc3881b98..946cd9aba41 100644 --- a/gnu/packages/hardware.scm +++ b/gnu/packages/hardware.scm @@ -375,42 +375,6 @@ through the Display Data Channel Command Interface (@dfn{DDC/CI}) protocol.") human-readable format and checks if it conforms to the standards.") (license license:expat)))) -(define-public h-client - (let ((version "0.0a0") - (revision 138)) - (package - (name "h-client") - (version (string-append version "-" (number->string revision))) - (source - (origin - (method svn-fetch) - (uri - (svn-reference - (url "https://svn.savannah.nongnu.org/svn/h-client/trunk/h-client") - (revision revision))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1pdd2qhyaa5vh7z4rkpwjlby1flkwhzmp8zlglalx5y5sv95l4kp")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - ;; Tests depends on /etc/os-release which does not exist in the - ;; build container. - #:tests? #f)) - (inputs - (list python-2 python2-pycurl python2-pygtk pciutils usbutils)) - (synopsis "Graphical client for the h-node hardware database -project") - (description - "The h-node project (https://www.h-node.org) aims to build a database of -hardware that works with fully free operating systems. -h-client is a GTK+ graphical client that is able to retrieves information on -the hardware inside the computer it's running on, and on peripherals connected -to it, and help you submit that information to the h-node project along with -whether the hardware works with a fully free operating system or not.") - (home-page "https://savannah.nongnu.org/projects/h-client/") - (license license:gpl3+)))) - (define-public headsetcontrol (package (name "headsetcontrol") From f2a579f8cb90313e73a40d7317b835c0fe29ea3e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:34:57 -0400 Subject: [PATCH 0852/1394] gnu: Remove python2-iso3166. * gnu/packages/iso-codes.scm (python2-iso3166): Delete variable. --- gnu/packages/iso-codes.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/iso-codes.scm b/gnu/packages/iso-codes.scm index b2cfd3434c4..b567c0e0294 100644 --- a/gnu/packages/iso-codes.scm +++ b/gnu/packages/iso-codes.scm @@ -115,6 +115,3 @@ groups.") (synopsis "Self-contained ISO 3166-1 country definitions") (description "This package provides the ISO 3166-1 country definitions.") (license license:expat))) - -(define-public python2-iso3166 - (package-with-python2 python-iso3166)) From 0082e6523fe729a462ea1e1c9f0d081cfda5c27e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:35:00 -0400 Subject: [PATCH 0853/1394] gnu: Remove python2-iso639. * gnu/packages/iso-codes.scm (python2-iso639): Delete variable. --- gnu/packages/iso-codes.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/iso-codes.scm b/gnu/packages/iso-codes.scm index b567c0e0294..c34911fe9b9 100644 --- a/gnu/packages/iso-codes.scm +++ b/gnu/packages/iso-codes.scm @@ -96,9 +96,6 @@ that is concerned with representation of names for languages and language groups.") (license license:agpl3+))) -(define-public python2-iso639 - (package-with-python2 python-iso639)) - (define-public python-iso3166 (package (name "python-iso3166") From 420052723ee68e33a9bea15e4662d50e9540ff9c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:35:03 -0400 Subject: [PATCH 0854/1394] gnu: Remove key-mon. * gnu/packages/key-mon.scm (key-mon): Delete variable. --- gnu/packages/key-mon.scm | 25 ------------------------- 1 file changed, 25 deletions(-) diff --git a/gnu/packages/key-mon.scm b/gnu/packages/key-mon.scm index e7b549d1841..d70dd0cd48b 100644 --- a/gnu/packages/key-mon.scm +++ b/gnu/packages/key-mon.scm @@ -26,28 +26,3 @@ #:use-module (gnu packages gtk) #:use-module (gnu packages gnome) #:use-module (guix build-system python)) - -(define-public key-mon - (package - (name "key-mon") - (version "1.17") - (source (origin - (method url-fetch) - (uri (string-append - "http://key-mon.googlecode.com/files/key-mon-" - version ".tar.gz")) - (sha256 - (base32 - "1liz0dxcqmchbnl1xhlxkqm3gh76wz9jxdxn9pa7dy77fnrjkl5q")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ;uses the Python 2 'print' syntax - #:tests? #f)) ;no tests - (inputs - (list python2-xlib python2-pygtk python2-rsvg)) - (home-page "https://code.google.com/p/key-mon") - (synopsis "Show keyboard and mouse status") - (description - "The key-mon utility displays the current keyboard and mouse status. -This is useful for teaching and screencasts.") - (license asl2.0))) From df29eb6500651e3d8fcee3b3f53d2ce1bddf5327 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:35:07 -0400 Subject: [PATCH 0855/1394] gnu: Remove python2-tegaki-recognize. * gnu/packages/language.scm (python2-tegaki-recognize): Delete variable. --- gnu/packages/language.scm | 52 --------------------------------------- 1 file changed, 52 deletions(-) diff --git a/gnu/packages/language.scm b/gnu/packages/language.scm index 6a0f1af2fa9..ce7646b7ad8 100644 --- a/gnu/packages/language.scm +++ b/gnu/packages/language.scm @@ -1006,58 +1006,6 @@ suitable for both the desktop and mobile devices.") ;; under gpl2+. Therefore, the combined work is licensed under gpl3+. (license license:gpl3+))) -(define-public python2-tegaki-recognize - (let ((commit "eceec69fe651d0733c8c8752dae569d2283d0f3c") - (revision "1")) - (package - (inherit python2-tegaki-tools) - (name "python2-tegaki-recognize") - ;; version copied from - (version (git-version "0.3.1" revision commit)) - (source - (origin - ;; We use GIT-FETCH because 'tegaki-recognize.desktop.in' and - ;; 'tegaki-recognize.in' are missing in the tarball. - (method git-fetch) - (uri (git-reference - (url "https://github.com/tegaki/tegaki") - (commit commit))) - (sha256 - (base32 - "09mw2if9p885phbgah5f95q3fwy7s5b46qlmpxqyzfcnj6g7afr5")) - (file-name (git-file-name name version)) - (modules `((guix build utils) - (ice-9 ftw) - (srfi srfi-26) - ,@remove-pre-compiled-files-modules)) - (snippet - `(begin - ;; remove unnecessary files with potentially different license - (for-each delete-file-recursively - (scandir "." - (negate (cut member <> '("tegaki-recognize" - "." ".."))))) - ,(remove-pre-compiled-files "pyc") - #t)))) - (arguments - (substitute-keyword-arguments (package-arguments python2-tegaki-tools) - ((#:phases _) - `(modify-phases %standard-phases - (add-after 'unpack 'chdir - (lambda _ - (chdir "tegaki-recognize") - #t)) - ;; 'setup.py' script does not support one of the Python build - ;; system's default flags, "--single-version-externally-managed" - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (invoke "python" "setup.py" "install" - (string-append "--prefix=" (assoc-ref outputs "out")) - "--root=/") - #t)))))) - (synopsis "Chinese and Japanese Handwriting Recognition (Main program)") - (license license:gpl2+)))) - (define-public tegaki-zinnia-japanese (package (inherit python2-tegaki-wagomu) From 3f48117a8ba90515e760470797b78dd7363d283e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:35:26 -0400 Subject: [PATCH 0856/1394] gnu: Remove python2-pyusb. * gnu/packages/libusb.scm (python2-pyusb): Delete variable. --- gnu/packages/libusb.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/libusb.scm b/gnu/packages/libusb.scm index 01771dffca1..8c34956feeb 100644 --- a/gnu/packages/libusb.scm +++ b/gnu/packages/libusb.scm @@ -300,9 +300,6 @@ wrapper for accessing libusb-1.0.") "PyUSB aims to be an easy to use Python module to access USB devices.") (license license:bsd-3))) -(define-public python2-pyusb - (package-with-python2 python-pyusb)) - (define-public python-capablerobot-usbhub (package (name "python-capablerobot-usbhub") From 9a550ba8c997d3577194eca22fd218a30cdfad90 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:35:30 -0400 Subject: [PATCH 0857/1394] gnu: Remove python2-autograd. * gnu/packages/machine-learning.scm (python2-autograd): Delete variable. --- gnu/packages/machine-learning.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 7b377c7d351..509b9c7cdd0 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1326,9 +1326,6 @@ forward-mode differentiation, and the two can be composed arbitrarily. The main intended application of Autograd is gradient-based optimization.") (license license:expat)))) -(define-public python2-autograd - (package-with-python2 python-autograd)) - (define-public lightgbm (package (name "lightgbm") From 7c443f915864f160cdfd72018566c14e4bdc2ca0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:35:33 -0400 Subject: [PATCH 0858/1394] gnu: getmail: Deprecate with getmail6. * gnu/packages/mail.scm (getmail): Mark as deprecated in favor of... (getmail6): ... this new package. --- gnu/packages/mail.scm | 45 ++++++++++++++++++++++--------------------- 1 file changed, 23 insertions(+), 22 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index c0b43f7c7fa..80bef35ac22 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -32,7 +32,7 @@ ;;; Copyright © 2020 Vincent Legoll ;;; Copyright © 2020 Justus Winter ;;; Copyright © 2020 Eric Brown -;;; Copyright © 2020, 2021 Maxim Cournoyer +;;; Copyright © 2020, 2021, 2022 Maxim Cournoyer ;;; Copyright © 2020 Michael Rohleder ;;; Copyright © 2020, 2021 Alexey Abramov ;;; Copyright © 2020 Tim Gesthuizen @@ -40,7 +40,6 @@ ;;; Copyright © 2020 Oleg Pykhalov ;;; Copyright © 2020 B. Wilson ;;; Copyright © 2020 divoplade -;;; Copyright © 2021 Maxim Cournoyer ;;; Copyright © 2021 Xinglu Chen ;;; Copyright © 2021 Benoit Joly ;;; Copyright © 2021 Morgan Smith @@ -1551,31 +1550,33 @@ minimum information necessary to bring replicas up to date regardless of which pairs have previously synchronized.") (license license:gpl2+))) ; with OpenSSL libcrypto exception -(define-public getmail +(define-public getmail6 (package - (name "getmail") - (version "5.16") - (source - (origin - (method url-fetch) - (uri (string-append "https://pyropus.ca/software/getmail/old-versions/" - "getmail-" version ".tar.gz")) - (sha256 - (base32 "1yk7lrndbfsrbdxikwzdqvadryqsldalxdn3a184dg4sxzmgis3a")))) + (name "getmail6") + (version "6.18.6") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/getmail6/getmail6") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "08a5yw6ll1kmd1ardj8rzhsw4wl48zzdc87g5lh4p5snv8w2m4ja")))) (build-system python-build-system) - (arguments - (list #:tests? #f ; no tests - #:python python-2)) - (home-page "https://pyropus.ca/software/getmail/") + (arguments (list #:tests? #f)) ;tests require docker + (home-page "https://github.com/getmail6/getmail6") (synopsis "Mail retriever") (description - "A flexible, extensible mail retrieval system with support for -POP3, IMAP4, SSL variants of both, maildirs, mboxrd files, external MDAs, -arbitrary message filtering, single-user and domain-mailboxes, and many other -useful features.") + "A flexible, extensible mail retrieval system with support for POP3, +IMAP4, SSL variants of both, maildirs, mboxrd files, external MDAs, arbitrary +message filtering, single-user and domain-mailboxes, and many other useful +features. This is a fork derived from getmali 5.14, aimed at Python 3 +compatibility.") + (license license:gpl2+))) ;see docs/COPYING - ;; License is specified in file '__init__.py'. - (license license:gpl2))) +(define-public getmail + (deprecated-package "getmail" getmail6)) (define-public libetpan (package From 310cf098510546b94e87b57520ebed4436320a4e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:35:39 -0400 Subject: [PATCH 0859/1394] gnu: Remove python2-mailmanclient. * gnu/packages/mail.scm (python2-mailmanclient): Delete variable. --- gnu/packages/mail.scm | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 80bef35ac22..7dcc1973138 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -3366,25 +3366,8 @@ filtering, digest delivery, and more.") (description "The mailmanclient library provides official Python bindings for the GNU Mailman 3 REST API.") - (properties `((python2-variant . ,(delay python2-mailmanclient)))) (license license:lgpl3+))) -;; This is the last version which supports Python-2. -(define-public python2-mailmanclient - (let ((base (package-with-python2 - (strip-python2-variant python-mailmanclient)))) - (package - (inherit base) - (version "3.1.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "mailmanclient" version)) - (sha256 - (base32 - "0fdfs5g3pf30v2i7w18pdkv9xnfxmfcv66mzv56dck0a1igq07m3")))) - (propagated-inputs - (list python2-six python2-httplib2))))) (define-public mlmmj (package From e89a1fc62aa154b9c57a54be624caf0ade608166 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:35:46 -0400 Subject: [PATCH 0860/1394] gnu: Remove python2-musicbrainzngs. * gnu/packages/music.scm (python2-musicbrainzngs): Delete variable. --- gnu/packages/music.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 8183ac942e1..47c38678ea6 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3679,9 +3679,6 @@ MusicBrainz database.") ;; 'musicbrainzngs/compat.py' is ISC licensed. (license (list license:bsd-2 license:isc)))) -(define-public python2-musicbrainzngs - (package-with-python2 python-musicbrainzngs)) - (define-public python-isrcsubmit (package (name "python-isrcsubmit") From ded6dbcb49e50ff8d26e091d8d3081bf07539809 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:35:50 -0400 Subject: [PATCH 0861/1394] gnu: Remove python2-pyechonest. * gnu/packages/music.scm (python2-pyechonest): Delete variable. --- gnu/packages/music.scm | 33 --------------------------------- 1 file changed, 33 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 47c38678ea6..ff5dc1aeb1e 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3700,39 +3700,6 @@ Standard Recording Code} (ISRCs) from audio CDs and submit them to @url{https://musicbrainz.org/, MusicBrainz}.") (license license:gpl3+))) -(define-public python2-pyechonest - (package - (name "python2-pyechonest") - (version "9.0.0") - (source (origin - (method url-fetch) - (uri (pypi-uri "pyechonest" version)) - (sha256 - (base32 - "1584nira3rkiman9dm81kdshihmkj21s8navndz2l8spnjwb790x")))) - (build-system python-build-system) - (arguments - `(;; Python 3 is not supported: - ;; https://github.com/echonest/pyechonest/issues/42 - #:python ,python-2)) - (home-page "https://github.com/echonest/pyechonest") - (synopsis "Python interface to The Echo Nest APIs") - (description "Pyechonest is a Python library for the Echo Nest API. With -Pyechonest you have Python access to the entire set of API methods including: - -@enumerate -@item artist - search for artists by name, description, or attribute, and get -back detailed information about any artist including audio, similar artists, -blogs, familiarity, hotttnesss, news, reviews, urls and video. -@item song - search songs by artist, title, description, or attribute (tempo, -duration, etc) and get detailed information back about each song, such as -hotttnesss, audio_summary, or tracks. -@item track - upload a track to the Echo Nest and receive summary information -about the track including key, duration, mode, tempo, time signature along with -detailed track info including timbre, pitch, rhythm and loudness information. -@end enumerate\n") - (license license:bsd-3))) - (define-public python-pylast (package (name "python-pylast") From a240fef7076677858ff41d3abf4c8d7830108427 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:35:54 -0400 Subject: [PATCH 0862/1394] gnu: Remove mloop. * gnu/packages/music.scm (mloop): Delete variable. --- gnu/packages/music.scm | 39 --------------------------------------- 1 file changed, 39 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index ff5dc1aeb1e..1d07993416f 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -5555,45 +5555,6 @@ with error and volume history, and advanced features.") ;; are under LGPL2.1. (license (list license:gpl2+ license:lgpl2.1)))) -(define-public mloop - (let ((commit "adebff98b0b4dc5872a03acb82e89c77cb29c127") - (revision "0")) - (package - (name "mloop") - (version (git-version "0.0.1" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "http://git.fuzzle.org/mloop") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "175gxvg5slq0bllcx1c381rjlq3xpxww8c3kpiw5i2kfr4m52myz")))) - (build-system waf-build-system) - (arguments - `(#:python ,python-2 - #:tests? #f)) ; no "check" target - (inputs - (list jack-1 ncurses)) - (native-inputs - (list pkg-config)) - (home-page "https://fuzzle.org/~petern/mloop.html") - (synopsis "Live MIDI looper") - (description "mloop is a live MIDI looping system, using jack-midi. -Loops are recorded, optionally with beat quantization, and can then be played -back, either once or looping. A 'note cache' system is implemented to -remember which notes are pressed and their velocities. This allows for a loop -to start off with the currently pressed notes, making seamless loops much -easier to perform. Features include: - -@itemize -@item Quantisation; end a loop on a beat exactly. -@item Delayed recording; wait for a MIDI event before starting a loop record. -@item Adjust tempo; Playback speed of loops can be adjusted on the fly. -@end itemize\n") - (license license:gpl2)))) - (define-public pragha (package (name "pragha") From e3205452db72a25eb130a9b1a5db151ecfbdc416 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:35:57 -0400 Subject: [PATCH 0863/1394] gnu: Remove gtklick. * gnu/packages/music.scm (gtklick): Delete variable. --- gnu/packages/music.scm | 46 ------------------------------------------ 1 file changed, 46 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 1d07993416f..dc341949059 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -1274,52 +1274,6 @@ standalone program which is able to download cover art, lyrics, photos, biographies, reviews and more.") (license license:lgpl3+))) -(define-public gtklick - (package - (name "gtklick") - (version "0.6.4") - (source (origin - (method url-fetch) - (uri (string-append "http://das.nasophon.de/download/gtklick-" - version ".tar.gz")) - (sha256 - (base32 - "0dq1km6njnzsqdqyf6wzir9g733z0mc9vmxfg2383k3c2a2di6bp")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; no tests - #:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-before 'build 'add-sitedirs - ;; .pth files are not automatically interpreted unless the - ;; directories containing them are added as "sites". The directories - ;; are then added to those in the PYTHONPATH. This is required for - ;; the operation of pygtk. - (lambda _ - (substitute* "gtklick/gtklick.py" - (("import pygtk") - "import pygtk, site, sys -for path in [path for path in sys.path if 'site-packages' in path]: site.addsitedir(path)")))) - (add-after 'unpack 'inject-store-path-to-klick - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "gtklick/klick_backend.py" - (("KLICK_PATH = 'klick'") - (string-append "KLICK_PATH = '" - (assoc-ref inputs "klick") - "/bin/klick'"))) - #t))))) - (inputs - (list klick python2-pyliblo python2-pygtk)) - (native-inputs - `(("gettext" ,gettext-minimal))) - (home-page "http://das.nasophon.de/gtklick/") - (synopsis "Simple metronome with an easy-to-use graphical interface") - (description - "Gtklick is a simple metronome with an easy-to-use graphical user -interface. It is implemented as a frontend to @code{klick}.") - (license license:gpl2+))) - (define-public lingot (package (name "lingot") From 9bdab23f22204941426f354a43155564531c539f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:36:12 -0400 Subject: [PATCH 0864/1394] gnu: Remove python2-ipy. * gnu/packages/networking.scm (python2-ipy): Delete variable. --- gnu/packages/networking.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 2d1cb50f4ad..bfa956149dc 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2622,9 +2622,6 @@ handling for most notations in use for IPv4 and IPv6 addresses and networks.") (license license:bsd-3))) -(define-public python2-ipy - (package-with-python2 python-ipy)) - (define-public speedtest-cli (package (name "speedtest-cli") From eb1b193379ee23b43ef7a3bb90d718df5c6c7d24 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:36:22 -0400 Subject: [PATCH 0865/1394] gnu: Remove sala. * gnu/packages/password-utils.scm (sala): Delete variable. --- gnu/packages/password-utils.scm | 27 --------------------------- 1 file changed, 27 deletions(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 1891a2cf099..348afb5af4e 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -1035,33 +1035,6 @@ of the box are Windows LM hashes, plus lots of other hashes and ciphers. This is the community-enhanced, \"jumbo\" version of John the Ripper.") (license license:gpl2+)))) -(define-public sala - (package - (name "sala") - (version "1.3") - (source - (origin - (method url-fetch) - (uri (pypi-uri "sala" version)) - (sha256 - (base32 - "13qgmc3i2a0cqp8jqrfl93lnphfagb32pgfikc1gza2a14asxzi8")))) - (build-system python-build-system) - (arguments - ;; Sala is supposed to work with Python 3.2 or higher, - ;; but it doesn't work with Python 3.6. Better stick - ;; to Python 2, which works fine. - `(#:python ,python-2)) - (propagated-inputs - (list gnupg pwgen)) - (home-page "http://www.digip.org/sala/") - (synopsis "Encrypted plaintext password store") - (description - "Store passwords and other bits of sensitive plain-text information -to encrypted files on a directory hierarchy. The information is protected -by GnuPG's symmetrical encryption.") - (license license:expat))) - (define-public fpm2 (package (name "fpm2") From 77afe03cf9e90f597571b4181f620da0997e84af Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 2 May 2022 00:38:02 -0400 Subject: [PATCH 0866/1394] gnu: Add python-jstyleson. * gnu/packages/python-web.scm (python-jstyleson): New variable. --- gnu/packages/python-web.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 7feac5955f2..cb52db3bbdb 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -7368,3 +7368,22 @@ scraping framework, used to crawl websites and extract structured data from their pages. It can be used for a wide range of purposes, from data mining to monitoring and automated testing.") (license license:bsd-3))) + +(define-public python-jstyleson + (package + (name "python-jstyleson") + (version "0.0.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "jstyleson" version)) + (sha256 + (base32 "13ihw6jqwkg3ai4xb83kw39pvh73b2wg6ld3wvj5jaasn7rh6038")))) + (build-system python-build-system) + (arguments (list #:tests? #f)) ;no tests in pypi release + (home-page "https://github.com/linjackson78/jstyleson") + (synopsis "JSON parser supporting js-style comments") + (description "@code{jstyleson} is a Python library to parse JSON. +Contrary to the standard Python @code{json} library, it understands js-style +comments. Trailing comma is also supported.") + (license license:expat))) From 32ffbb16e8cbb9c5416274320a56885c45a88ebf Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 2 May 2022 00:39:09 -0400 Subject: [PATCH 0867/1394] gnu: Add python-html-text. * gnu/packages/python-web.scm (python-html-text): New variable. --- gnu/packages/python-web.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index cb52db3bbdb..00fe560a360 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -7387,3 +7387,25 @@ mining to monitoring and automated testing.") Contrary to the standard Python @code{json} library, it understands js-style comments. Trailing comma is also supported.") (license license:expat))) + +(define-public python-html-text + (package + (name "python-html-text") + (version "0.5.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "html_text" version)) + (sha256 + (base32 "1v9x171l3bmyayc1144nrkn9410lp4lhlrrjii54j7b5f2xipmmg")))) + (build-system python-build-system) + (native-inputs (list python-pytest)) + (propagated-inputs (list python-lxml)) + (home-page "https://github.com/TeamHG-Memex/html-text") + (synopsis "Extract text from HTML") + (description "HTML to Text is a Python library for extract text from HTML. +Contrary to other solution such as LXML or Beautiful Soup, the text extracted +with @code{html_text} does not contain elements such as JavaScript or inline +styles not normally visible to users. It also normalizes white space +characters in a smarter, more visually pleasing style.") + (license license:expat))) From c5dd41afc6659b96c86efea512ee7ecc0bbf6604 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 2 May 2022 00:47:24 -0400 Subject: [PATCH 0868/1394] gnu: Add python-mf2py. * gnu/packages/python-web.scm (python-mf2py): New variable. --- gnu/packages/python-web.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 00fe560a360..59828d7473c 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -7409,3 +7409,35 @@ with @code{html_text} does not contain elements such as JavaScript or inline styles not normally visible to users. It also normalizes white space characters in a smarter, more visually pleasing style.") (license license:expat))) + +(define-public python-mf2py + (package + (name "python-mf2py") + (version "1.1.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/microformats/mf2py") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00pzfc5sl6ywlcr6f2k37n3f2bb7w488p2k95ixzjwx6w3yh747n")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "test"))))))) + (native-inputs (list python-pytest)) + (propagated-inputs + (list python-beautifulsoup4 python-html5lib python-requests)) + (home-page "https://github.com/microformats/mf2py") + (synopsis "Python Microformats2 parser") + (description "This Python library provides a Microformats2 parser +implementing the full Microformats2 (mf2) specification, including backward +compatibility with Microformats1 (mf1).") + (license license:expat))) From 0999af5b42540f2d5f4b52c65a7e350f071d2f3c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 3 May 2022 15:55:35 -0400 Subject: [PATCH 0869/1394] gnu: Add python-pyrdfa3. * gnu/packages/rdf.scm (python-pyrdfa3): New variable. --- gnu/packages/rdf.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm index 826330585df..6712c2c237a 100644 --- a/gnu/packages/rdf.scm +++ b/gnu/packages/rdf.scm @@ -471,6 +471,43 @@ RDF data that can also be queried for Triple Patterns. This package provides a C++ library as well as various command-line tools to to work with HDT.") (license license:lgpl2.1+))) +(define-public python-pyrdfa3 + (package + (name "python-pyrdfa3") + (version "3.5.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pyRdfa3" version)) + (sha256 + (base32 "1biif5lav3gswkhjzq882s4rgxzmvwsy5gb9dxdk9pw75fln6xhm")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f ;no test suite + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-python-3-issues + (lambda _ + ;; Delete files that appear to be versions for older Pythons; + ;; they fail to byte compile (see: + ;; https://github.com/RDFLib/pyrdfa3/issues/41). + (with-directory-excursion "pyRdfaExtras/serializers" + (for-each delete-file + (list "prettyXMLserializer_3.py" + "prettyXMLserializer_3_2.py"))) + ;; See https://github.com/RDFLib/pyrdfa3/issues/42. + (substitute* "pyRdfaExtras/__init__.py" + (("from StringIO import StringIO") + "from io import StringIO"))))))) + (propagated-inputs (list python-html5lib python-rdflib)) + (home-page "https://www.w3.org/2012/pyRdfa/") + (synopsis "RDFa Python distiller/parser library") + (description "This library can extract RDFa 1.1 from (X)HTML, SVG, or XML. +It can produce serialized versions of the extracted graph, or an RDFLib +Graph.") + (license license:bsd-3))) + (define-public python-sparqlwrapper (package (name "python-sparqlwrapper") From 4820a23521727091d0085e5b381aa5c44ebd2ecb Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 3 May 2022 16:05:36 -0400 Subject: [PATCH 0870/1394] gnu: Add python-extruct. * gnu/packages/python-web.scm (python-extruct): New variable. --- gnu/packages/python-web.scm | 47 +++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 59828d7473c..427994e22b6 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -97,6 +97,7 @@ #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) + #:use-module (gnu packages rdf) #:use-module (gnu packages rpc) #:use-module (gnu packages serialization) #:use-module (gnu packages sphinx) @@ -7441,3 +7442,49 @@ characters in a smarter, more visually pleasing style.") implementing the full Microformats2 (mf2) specification, including backward compatibility with Microformats1 (mf1).") (license license:expat))) + +(define-public python-extruct + (package + (name "python-extruct") + (version "0.13.0") + (source (origin + (method git-fetch) ;for tests + (uri (git-reference + (url "https://github.com/scrapinghub/extruct") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "075zldf3dqcc429z1vk2ngbmv034bnlyk6arh3rh30jbsvz9pzl5")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "tests"))))))) + (native-inputs (list python-pytest)) + (propagated-inputs + (list python-html-text + python-jstyleson + python-lxml + python-mf2py + python-pyrdfa3 + python-rdflib + python-rdflib-jsonld + python-w3lib)) + (home-page "https://github.com/scrapinghub/extruct") + (synopsis "Extract embedded metadata from HTML markup") + (description "@code{extruct} is a Python library for extracting embedded +metadata from HTML markup. Currently, extruct supports: +@itemize +@item W3C's HTML Microdata +@item embedded JSON-LD +@item Microformat via mf2py +@item Facebook's Open Graph +@item (experimental) RDFa via rdflib +@item Dublin Core Metadata (DC-HTML-2003) +@end itemize") + (license license:bsd-3))) From 421d09a1d3784e69239ac27294fa252e005a3fad Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 3 May 2022 17:14:48 -0400 Subject: [PATCH 0871/1394] gnu: Add python-scrape-schema-recipe. * gnu/packages/nutrition.scm (python-scrape-schema-recipe): New variable. --- gnu/packages/nutrition.scm | 44 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/nutrition.scm b/gnu/packages/nutrition.scm index f936c2651b8..8176ded9e1f 100644 --- a/gnu/packages/nutrition.scm +++ b/gnu/packages/nutrition.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2020 Efraim Flashner +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -20,19 +21,62 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages nutrition) + #:use-module (guix download) #:use-module (guix packages) #:use-module (guix licenses) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix build-system python) #:use-module (gnu packages) + #:use-module (gnu packages check) #:use-module (gnu packages databases) #:use-module (gnu packages gtk) #:use-module (gnu packages glib) #:use-module (gnu packages image) #:use-module (gnu packages python) + #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages time) #:use-module (gnu packages xml)) +(define-public python-scrape-schema-recipe + (package + (name "python-scrape-schema-recipe") + (version "0.2.0") + ;; The PyPI archive lacks a VERSION file as well as the test suite. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/micahcochran/scrape-schema-recipe") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "044c6qwhb4c710ksgiw29cd0qcp84h1m4y8yr2g4c8vdlm3kkqh5")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (substitute* "test_scrape.py" + (("DISABLE_NETWORK_TESTS = False") + "DISABLE_NETWORK_TESTS = True")) + (invoke "pytest" "-vv"))))))) + (native-inputs (list python-pytest)) + (propagated-inputs + (list python-extruct + python-importlib-resources + python-isodate + python-requests)) + (home-page "https://github.com/micahcochran/scrape-schema-recipe") + (synopsis "HTML Recipe format extractor") + (description "This tool extracts cooking recipe from HTML structured data +in the @url{https://schema.org/Recipe} format.") + (license asl2.0))) + (define-public gourmet (package (name "gourmet") From cfc02804fc5808647630c2fd75402887923168c8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:36:15 -0400 Subject: [PATCH 0872/1394] gnu: gourmet: Update to 0.17.4-0-8af29c8 and enable tests. * gnu/packages/patches/gourmet-sqlalchemy-compat.patch: Add file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/nutrition.scm (gourmet): Update to 0.17.4-0-8af29c8. [source]: Apply patch. [python]: Delete argument. [tests?]: Likewise. [phases]{prepare-x}: New phase. {check}: New phase override. {install-dekstop-file-and-icons}: New phase. [native-inputs]: Delete python2-distutils-extra, intltool and python2-pygtk. Add python-dogtail, python-pytest, python-selenium and xorg-server-for-tests. [inputs]: Delete python2-pygtk, python2-sqlalchemy, python2-lxml, python2-pillow and python2-elib.intl. Add gtk+, python-argcomplete, python-beautifulsoup4, python-gst, python-keyring, python-lxml, python-pillow, python-pycairo, python-pyenchant, python-pygobject, python-requests, python-scrape-schema-recipe, python-sqlalchemy. --- gnu/local.mk | 1 + gnu/packages/nutrition.scm | 120 ++++++++++++------ .../patches/gourmet-sqlalchemy-compat.patch | 18 +++ 3 files changed, 98 insertions(+), 41 deletions(-) create mode 100644 gnu/packages/patches/gourmet-sqlalchemy-compat.patch diff --git a/gnu/local.mk b/gnu/local.mk index 3452b75e3bf..1a0b998de33 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1214,6 +1214,7 @@ dist_patch_DATA = \ %D%/packages/patches/go-github-com-urfave-cli-fix-tests.patch \ %D%/packages/patches/go-github-com-urfave-cli-v2-fix-tests.patch \ %D%/packages/patches/go-skip-gc-test.patch \ + %D%/packages/patches/gourmet-sqlalchemy-compat.patch \ %D%/packages/patches/gpaste-fix-paths.patch \ %D%/packages/patches/gpm-glibc-2.26.patch \ %D%/packages/patches/gpodder-disable-updater.patch \ diff --git a/gnu/packages/nutrition.scm b/gnu/packages/nutrition.scm index 8176ded9e1f..90a70753de8 100644 --- a/gnu/packages/nutrition.scm +++ b/gnu/packages/nutrition.scm @@ -30,13 +30,17 @@ #:use-module (gnu packages) #:use-module (gnu packages check) #:use-module (gnu packages databases) - #:use-module (gnu packages gtk) + #:use-module (gnu packages enchant) #:use-module (gnu packages glib) + #:use-module (gnu packages gtk) + #:use-module (gnu packages gstreamer) #:use-module (gnu packages image) #:use-module (gnu packages python) + #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages time) + #:use-module (gnu packages xorg) #:use-module (gnu packages xml)) (define-public python-scrape-schema-recipe @@ -78,46 +82,80 @@ in the @url{https://schema.org/Recipe} format.") (license asl2.0))) (define-public gourmet - (package - (name "gourmet") - (version "0.17.4") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/thinkle/gourmet") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "09a2zk140l4babwdj8pwcgl9v7rvwff9cn7h3ppfhm3yvsgkrx07")))) - (build-system python-build-system) - (native-inputs - `(("distutils-extra" ,python2-distutils-extra) - ("intltool" ,intltool) - ("python-pygtk" ,python2-pygtk))) ;for tests - ;; TODO: Add python-reportlab and/or python-poppler for printing/pdf - ;; export, and python-beautifulsoup for web import plugin. - (inputs - `(("pygtk" ,python2-pygtk) - ("sqlalchemy" ,python2-sqlalchemy) - ("python-lxml" ,python2-lxml) - ("python-pillow" ,python2-pillow) - ("elib.intl" ,python2-elib.intl))) - (arguments - `(#:python ,python-2 ;exception and print syntax - #:tests? #f ;tests look bitrotted - #:phases - (modify-phases %standard-phases - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (invoke "python" "setup.py" "install" "--prefix" - (assoc-ref outputs "out"))))))) - (home-page "https://thinkle.github.io/gourmet/") - (synopsis "Recipe organizer") - (description - "Gourmet Recipe Manager is a recipe organizer that allows you to collect, + ;; Use the latest commit to gain Python 3 support. + (let ((revision "0") + (commit "8af29c8ded24528030e5ae2ea3461f61c1e5a575")) + (package + (name "gourmet") + (version (git-version "0.17.4" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/thinkle/gourmet") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "08fbw6zp32ws6w9czwy2sqc9c9izlkglsskshj2114d0l79z4gj8")) + (patches (search-patches "gourmet-sqlalchemy-compat.patch")))) + (build-system python-build-system) + (arguments + (list + #:modules `((guix build utils) + (guix build python-build-system) + (ice-9 ftw) + (srfi srfi-26)) + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'prepare-x + ;; Both the tests and the sanity-check phase need an X server to + ;; succeed. + (lambda _ + (system "Xvfb &") + (setenv "DISPLAY" ":0"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") ;needed by tests + (apply invoke "pytest" "-vv" + ;; XXX: This is needed because some tests in deeper + ;; directories or otherwise discovered by Pytest are + ;; broken. + (map (cut string-append "gourmet/tests/" <>) + (scandir "gourmet/tests" + (cut string-prefix? "test_" <>))))))) + (add-after 'install 'install-dekstop-file-and-icons + (lambda _ + (define share (string-append #$output "/share")) + (install-file ".flatpak/io.github.thinkle.Gourmet.desktop" + (string-append share "/applications")) + (install-file ".flatpak/io.github.thinkle.Gourmet.svg" + (string-append share "/icons/Gourmet"))))))) + (native-inputs + (list python-dogtail + python-pytest + python-selenium + xorg-server-for-tests)) + (inputs + (list gtk+ + python-argcomplete + python-beautifulsoup4 + python-gst + python-keyring + python-lxml + python-pillow + python-pycairo + python-pyenchant + python-pygobject + python-requests + python-scrape-schema-recipe + python-sqlalchemy)) + (home-page "https://thinkle.github.io/gourmet/") + (synopsis "Recipe organizer") + (description + "Gourmet Recipe Manager is a recipe organizer that allows you to collect, search, organize, and browse your recipes. Gourmet can also generate shopping lists and calculate nutritional information. It imports Mealmaster, MasterCook and KRecipe files and exports PDFs, webpages, and other formats.") - (license gpl2+))) + (license gpl2+)))) diff --git a/gnu/packages/patches/gourmet-sqlalchemy-compat.patch b/gnu/packages/patches/gourmet-sqlalchemy-compat.patch new file mode 100644 index 00000000000..d0cdf9e5a79 --- /dev/null +++ b/gnu/packages/patches/gourmet-sqlalchemy-compat.patch @@ -0,0 +1,18 @@ +diff --git a/gourmet/backends/db.py b/gourmet/backends/db.py +index faa6a57a..7e6d2bc6 100644 +--- a/gourmet/backends/db.py ++++ b/gourmet/backends/db.py +@@ -773,9 +773,11 @@ class RecData (Pluggable): + """Return the number of rows in table that match criteria + """ + if criteria: +- return table.count(*make_simple_select_arg(criteria,table)).execute().fetchone()[0] ++ return sqlalchemy.select( ++ sqlalchemy.func.count(criteria)).select_from(table).scalar() + else: +- return table.count().execute().fetchone()[0] ++ return sqlalchemy.select( ++ sqlalchemy.func.count()).select_from(table).scalar() + + def fetch_join (self, table1, table2, col1, col2, + column_names=None, sort_by=[], **criteria): From 312295d881031fa02b43930620bf833268b7eea3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:36:25 -0400 Subject: [PATCH 0873/1394] gnu: Remove patches. * gnu/packages/patchutils.scm (patches): Delete variable. --- gnu/packages/patchutils.scm | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/gnu/packages/patchutils.scm b/gnu/packages/patchutils.scm index 856413d83cd..fdbcb8e1e13 100644 --- a/gnu/packages/patchutils.scm +++ b/gnu/packages/patchutils.scm @@ -186,35 +186,6 @@ refreshed, and more.") 'syntax highlighting' for various patch formats.") (license gpl2+))) -(define-public patches - (let ((commit "ef1b8a7d954b82ed4af3a08fd63d2085d19090ef")) - (package - (name "patches") - (home-page "https://github.com/stefanha/patches") - (version (string-append "0.0-1." (string-take commit 7))) - (source (origin - (method git-fetch) - (uri (git-reference - (url home-page) - (commit commit))) - (sha256 - (base32 - "11rdmhv0l1s8nqb20ywmw2zqizczch2p62qf9apyx5wqgxlnjshk")) - (file-name (string-append name "-"version "-checkout")))) - (build-system python-build-system) - (inputs (list python2-notmuch)) - (arguments - `(#:tests? #f ;no "test" target - #:python ,python-2)) ;not compatible with Python 3 - (synopsis "Patch tracking tool") - (description - "@code{Patches} is a patch-tracking tool initially written for the QEMU -project. It provides commands that build a database of patches from a mailing -list, and commands that can search that database. It allows users to track -the status of a patch, apply patches, and search for patches---all that from -the command-line or from Emacs via its Notmuch integration.") - (license gpl2+)))) - (define-public vbindiff (package (name "vbindiff") From 48e18ab4aaea80bebaa5a6c014abbda7439733f6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:36:29 -0400 Subject: [PATCH 0874/1394] gnu: impressive: Update to 0.13.1. * gnu/packages/pdf.scm (impressive): Update to 0.13.1. [inputs]: Move below arguments field. Adjust to use Python 3 packages. [python]: Delete argument. [phases]: Use gexps. {install}: Use search-input-file and this-package-input. Make command executable. --- gnu/packages/pdf.scm | 55 +++++++++++++++++++++----------------------- 1 file changed, 26 insertions(+), 29 deletions(-) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 1f5c1b3005c..e2aa13526f0 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -1052,7 +1052,7 @@ vector formats.") (define-public impressive (package (name "impressive") - (version "0.12.1") + (version "0.13.1") (source (origin (method url-fetch) (uri (string-append @@ -1060,36 +1060,33 @@ vector formats.") version "/Impressive-" version ".tar.gz")) (sha256 (base32 - "1r7ihv41awnlnlry1kymb8fka053wdhzibfwcarn78rr3vs338vl")))) + "0d1d2jxfl9vmy4swcdz660xd4wx91w1i3n07k522pccapwxig294")))) (build-system python-build-system) - - ;; TODO: Add dependency on pdftk. - (inputs (list python2-pygame python2-pillow sdl xpdf)) - (arguments - `(#:python ,python-2 - #:phases (modify-phases %standard-phases - (delete 'build) - (delete 'configure) - (delete 'check) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; There's no 'setup.py' so install things manually. - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (man1 (string-append out "/share/man/man1")) - (sdl (assoc-ref inputs "sdl")) - (xpdf (assoc-ref inputs "xpdf"))) - (mkdir-p bin) - (copy-file "impressive.py" - (string-append bin "/impressive")) - (wrap-program (string-append bin "/impressive") - `("LIBRARY_PATH" ":" prefix ;for ctypes - (,(string-append sdl "/lib"))) - `("PATH" ":" prefix ;for pdftoppm - (,(string-append xpdf "/bin")))) - (install-file "impressive.1" man1) - #t)))))) + (list + #:phases + #~(modify-phases %standard-phases + (delete 'build) + (delete 'configure) + (delete 'check) + (replace 'install + (lambda* (#:key inputs #:allow-other-keys) + ;; There's no 'setup.py' so install things manually. + (let* ((bin (string-append #$output "/bin")) + (impressive (string-append bin "/impressive")) + (man1 (string-append #$output "/share/man/man1"))) + (mkdir-p bin) + (copy-file "impressive.py" impressive) + (chmod impressive #o755) + (wrap-program (string-append bin "/impressive") + `("LIBRARY_PATH" ":" prefix ;for ctypes + (,(string-append #$(this-package-input "sdl") + "/lib"))) + `("PATH" ":" prefix ;for pdftoppm + (,(search-input-file inputs "bin/xpdf")))) + (install-file "impressive.1" man1))))))) + ;; TODO: Add dependency on pdftk. + (inputs (list python-pygame python-pillow sdl xpdf)) (home-page "http://impressive.sourceforge.net") (synopsis "PDF presentation tool with visual effects") (description From aae86d4ddc342bc5950607e000e5f78d314606e5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:36:35 -0400 Subject: [PATCH 0875/1394] gnu: Remove python2-pypdf2. * gnu/packages/pdf.scm (python2-pypdf2): Delete variable. --- gnu/packages/pdf.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index e2aa13526f0..baafafcf4af 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -1240,9 +1240,6 @@ manipulation in memory. It is therefore a useful tool for websites that manage or manipulate PDFs.") (license license:bsd-3))) -(define-public python2-pypdf2 - (package-with-python2 python-pypdf2)) - (define-public python2-pypdf (package (name "python2-pypdf") From 914adf88adc82b694490c5d20279054fedd4e4d2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:36:39 -0400 Subject: [PATCH 0876/1394] gnu: Remove python2-reportlab. * gnu/packages/pdf.scm (python2-reportlab): Delete variable. --- gnu/packages/pdf.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index baafafcf4af..5da1e96e980 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -1046,9 +1046,6 @@ of rich PDF documents, and also creation of charts in a variety of bitmap and vector formats.") (license license:bsd-3))) -(define-public python2-reportlab - (package-with-python2 python-reportlab)) - (define-public impressive (package (name "impressive") From 7f50d105c767a47aa2e2e86c0d6e084f890b73fb Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:36:46 -0400 Subject: [PATCH 0877/1394] gnu: Remove pulseaudio-dlna. * gnu/packages/pulseaudio.scm (pulseaudio-dlna): Delete variable. --- gnu/packages/pulseaudio.scm | 52 ------------------------------------- 1 file changed, 52 deletions(-) diff --git a/gnu/packages/pulseaudio.scm b/gnu/packages/pulseaudio.scm index fe028b5202a..559dc752883 100644 --- a/gnu/packages/pulseaudio.scm +++ b/gnu/packages/pulseaudio.scm @@ -367,58 +367,6 @@ sinks.") curses-style interfaces.") (license l:expat))) -(define-public pulseaudio-dlna - ;; The last release was in 2016; use a more recent commit. - (let ((commit "4472928dd23f274193f14289f59daec411023ab0") - (revision "1")) - (package - (name "pulseaudio-dlna") - (version (git-version "0.5.2" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/masmu/pulseaudio-dlna") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1dfn7036vrq49kxv4an7rayypnm5dlawsf02pfsldw877hzdamqk")))) - (build-system python-build-system) - (arguments `(#:python ,python-2)) - (inputs - (list python2-chardet - python2-dbus - python2-docopt - python2-futures - python2-pygobject - python2-lxml - python2-netifaces - python2-notify2 - python2-protobuf - python2-psutil - python2-requests - python2-pyroute2 - python2-setproctitle - python2-zeroconf)) - (home-page "https://github.com/masmu/pulseaudio-dlna") - (synopsis "Stream audio to DLNA/UPnP and Chromecast devices") - (description "This lightweight streaming server brings DLNA/UPnP and -Chromecast support to PulseAudio. It can stream your current PulseAudio -playback to different UPnP devices (UPnP Media Renderers, including Sonos -devices and some Smart TVs) or Chromecasts in your network. You should also -install one or more of the following packages alongside pulseaudio-dlna: - -@itemize -@item ffmpeg - transcoding support for multiple codecs -@item flac - FLAC transcoding support -@item lame - MP3 transcoding support -@item opus-tools - Opus transcoding support -@item sox - WAV transcoding support -@item vorbis-tools - Vorbis transcoding support -@end itemize") - (license l:gpl3+)))) - (define-public pamixer (package (name "pamixer") From a13fb725f144a1546deba189a53e995932837da9 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:37:00 -0400 Subject: [PATCH 0878/1394] gnu: Remove python2-lz4. * gnu/packages/python-compression.scm (python2-lz4): Delete variable. --- gnu/packages/python-compression.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index e7f008e1128..38e66ec64c7 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -260,9 +260,6 @@ by Yann Collet. The project contains bindings for the LZ4 block format and the LZ4 frame format.") (license license:bsd-3))) -(define-public python2-lz4 - (package-with-python2 python-lz4)) - (define-public python-lzstring (package (name "python-lzstring") From 20935ba9f41d1567f80f4f0387755b449b1d8bb0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:37:04 -0400 Subject: [PATCH 0879/1394] gnu: Remove python2-lzstring. * gnu/packages/python-compression.scm (python2-lzstring): Delete variable. --- gnu/packages/python-compression.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 38e66ec64c7..3bcab200916 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -279,9 +279,6 @@ the LZ4 frame format.") (description "Lz-string is a string compressor library for Python.") (license license:expat))) -(define-public python2-lzstring - (package-with-python2 python-lzstring)) - (define-public bitshuffle (package (name "bitshuffle") From 592428a10d04d9da7a9085ffc69179cf1e794c7e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:37:07 -0400 Subject: [PATCH 0880/1394] gnu: Remove python2-lzo. * gnu/packages/python-compression.scm (python2-lzo): Delete variable. --- gnu/packages/python-compression.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 3bcab200916..7847a3e20e8 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -227,9 +227,6 @@ the LZO library from your Python scripts thereby compressing ordinary Python strings.") (license license:gpl2+))) -(define-public python2-lzo - (package-with-python2 python-lzo)) - (define-public python-lz4 (package (name "python-lz4") From 8ec7e1de69a8683a0d1611cac1059cae4592ba03 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:37:14 -0400 Subject: [PATCH 0881/1394] gnu: Remove python2-service-identity. * gnu/packages/python-crypto.scm (python2-service-identity): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 0bdcc693acb..201d5d8a53a 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -1320,9 +1320,6 @@ service_identity implements RFC 6125 fully and plans to add other relevant RFCs too.") (license license:expat))) -(define-public python2-service-identity - (package-with-python2 python-service-identity)) - (define-public python-hkdf (package (name "python-hkdf") From a7b67fdb0f83411e72d86d61a6b54dcfdf189b92 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:37:23 -0400 Subject: [PATCH 0882/1394] gnu: Remove python2-ed25519. * gnu/packages/python-crypto.scm (python2-ed25519): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 201d5d8a53a..208a749c09d 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -714,9 +714,6 @@ library.") (description "Ed25519 public-key signatures") (license license:expat))) -(define-public python2-ed25519 - (package-with-python2 python-ed25519)) - (define-public python-axolotl-curve25519 (package (name "python-axolotl-curve25519") From d76568317653a2ad05818d6095735e10153b0880 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:37:26 -0400 Subject: [PATCH 0883/1394] gnu: Remove python2-pycrypto. * gnu/packages/python-crypto.scm (python2-pycrypto): Delete variable. --- gnu/packages/python-crypto.scm | 9 --------- 1 file changed, 9 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 208a749c09d..4d148fd3d75 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -299,15 +299,6 @@ and RIPEMD160), and various encryption algorithms (AES, DES, RSA, ElGamal, etc.). The package is structured to make adding new modules easy.") (license license:public-domain))) -(define-public python2-pycrypto - (let ((pycrypto (package-with-python2 python-pycrypto))) - (package/inherit pycrypto - (inputs - `(("python" ,python-2) - ,@(alist-delete - "python" - (package-inputs pycrypto))))))) - (define-public python-kerberos (package (name "python-kerberos") From dad4d46545919b1815a511d8c071e78029227aa0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:37:35 -0400 Subject: [PATCH 0884/1394] gnu: Remove python2-axolotl-curve25519. * gnu/packages/python-crypto.scm (python2-axolotl-curve25519): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 4d148fd3d75..0a2686b9c93 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -726,9 +726,6 @@ python-axolotl.") (license (list license:gpl3 ; Most files license:bsd-3)))) ; curve/curve25519-donna.c -(define-public python2-axolotl-curve25519 - (package-with-python2 python-axolotl-curve25519)) - (define-public python-axolotl (package (name "python-axolotl") From d0d5f8fc09335898a840da3d47acbeb7c0da921c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:37:38 -0400 Subject: [PATCH 0885/1394] gnu: Remove python2-pyaes. * gnu/packages/python-crypto.scm (python2-pyaes): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 0a2686b9c93..9867f6842b1 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -799,9 +799,6 @@ AES block cipher algorithm and the common modes of operation (CBC, CFB, CTR, ECB and OFB).") (license license:expat))) -(define-public python2-pyaes - (package-with-python2 python-pyaes)) - (define-public python-asn1crypto (package (name "python-asn1crypto") From 522b18630dc4d25098d75eca9b5e2163a9541f40 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:37:45 -0400 Subject: [PATCH 0886/1394] gnu: Remove python2-slowaes. * gnu/packages/python-crypto.scm (python2-slowaes): Delete variable. --- gnu/packages/python-crypto.scm | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 9867f6842b1..0028b65f8b2 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -759,26 +759,6 @@ asynchronous messaging environments.") (define-public python2-axolotl (package-with-python2 python-axolotl)) -;; SlowAES isn't compatible with Python 3. -(define-public python2-slowaes - (package - (name "python2-slowaes") - (version "0.1a1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "slowaes" version)) - (sha256 - (base32 - "02dzajm83a7lqgxf6r3hgj64wfmcxz8gs4nvgxpvj5n19kjqlrc3")))) - (build-system python-build-system) - (arguments `(#:python ,python-2)) - (home-page "http://code.google.com/p/slowaes/") - (synopsis "Implementation of AES in Python") - (description "This package contains an implementation of AES in Python. -This implementation is slow (hence the project name) but still useful when -faster ones are not available.") - (license license:asl2.0))) (define-public python-pyaes (package From 08d11c8aee556e1bac6c32982aabc8711c11c3ca Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:37:48 -0400 Subject: [PATCH 0887/1394] gnu: Remove python2-josepy. * gnu/packages/python-crypto.scm (python2-josepy): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 0028b65f8b2..80e37aa13c7 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -938,9 +938,6 @@ Python.") protocol (Javascript Object Signing and Encryption).") (license license:asl2.0))) -(define-public python2-josepy - (package-with-python2 python-josepy)) - (define pycryptodome-unbundle-tomcrypt-snippet #~(begin ;; Unbundle libtomcrypt. From 56cfb65eb5acc3a87236344a24baaaad130e390d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:37:51 -0400 Subject: [PATCH 0888/1394] gnu: Remove python2-m2crypto. * gnu/packages/python-crypto.scm (python2-m2crypto): Delete variable. --- gnu/packages/python-crypto.scm | 8 -------- 1 file changed, 8 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 80e37aa13c7..3aa7327b0be 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -1087,16 +1087,8 @@ extensions to Python's httplib, urllib, and xmlrpclib; unforgeable HMAC'ing AuthCookies for web session management; FTP/TLS client and server; S/MIME; M2Crypto can also be used to provide TLS for Twisted. Smartcards supported through the Engine interface.") - (properties `((python2-variant . ,(delay python2-m2crypto)))) (license license:expat))) -(define-public python2-m2crypto - (let ((m2crypto (package-with-python2 - (strip-python2-variant python-m2crypto)))) - (package/inherit m2crypto - (propagated-inputs - `(("python2-typing" ,python2-typing)))))) - (define-public python-pykeepass (package (name "python-pykeepass") From 385fa1a3ed155591b07978c577ed55547319ba37 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:38:12 -0400 Subject: [PATCH 0889/1394] gnu: Remove python2-pycryptodome. * gnu/packages/python-crypto.scm (python2-pycryptodome): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 3aa7327b0be..502a809d293 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -1010,9 +1010,6 @@ PyCryptodome variants, the other being python-pycryptodomex.") (license (list license:bsd-2 license:public-domain)))) ; code inherited from PyCrypto -(define-public python2-pycryptodome - (package-with-python2 python-pycryptodome)) - (define-public python-pycryptodomex (package (inherit python-pycryptodome) (name "python-pycryptodomex") From b827d0f7b3b7ec00406f8aa0ca4abc9e36a8da83 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:38:22 -0400 Subject: [PATCH 0890/1394] gnu: Remove python2-weave. * gnu/packages/python-science.scm (python2-weave): Delete variable. --- gnu/packages/python-science.scm | 33 --------------------------------- 1 file changed, 33 deletions(-) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 0b3547f552f..ccff510ef62 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -180,39 +180,6 @@ routines such as routines for numerical integration and optimization.") perl which)))) -(define-public python2-weave - (package - (name "python2-weave") - (version "0.16.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "weave" version)) - (sha256 - (base32 "0jnm3584mfichgwgrd1gk5i42ll9c08nkw9716n947n4338f6ghs")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "nosetests" "-v" - "--exclude" - "test_(user|incorrect_ownership|char_fail|obj_fail)")))))) - (propagated-inputs - (list python2-numpy)) - (native-inputs - (list python2-nose)) - (home-page "https://www.scipy.org/") - (synopsis "Tools for including C/C++ code within Python code") - (description "Weave is the stand-alone version of the obsolete Scipy -submodule @code{scipy.weave}. It is Python 2.x only, and is provided for -users that need new versions of Scipy but have existing code that still -depends on @code{scipy.weave}. For new code, users are recommended to use -Cython.") - (license license:bsd-3))) - (define-public python-scikit-fuzzy (package (name "python-scikit-fuzzy") From c59edcc5ed822c8966443acf3eb9f63b1614dc27 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:38:29 -0400 Subject: [PATCH 0891/1394] gnu: Remove python2-oauth2client. * gnu/packages/python-web.scm (python2-oauth2client): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 427994e22b6..46d4ab105f0 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -3880,9 +3880,6 @@ users' sessions over extended periods of time.") library for Python") (license license:asl2.0))) -(define-public python2-oauth2client - (package-with-python2 python-oauth2client)) - (define-public python-flask-oidc (package (name "python-flask-oidc") From 7a9514eb059f9d7ef666e25be1825782a9eaf1a6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:38:49 -0400 Subject: [PATCH 0892/1394] gnu: Remove python2-zope-configuration. * gnu/packages/python-web.scm (python2-zope-configuration): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 46d4ab105f0..ce2dfffa693 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2385,9 +2385,6 @@ Markup Language.") (define-public python-zope-configuration-bootstrap (python-zope-bootstrap-package python-zope-configuration)) -(define-public python2-zope-configuration - (package-with-python2 python-zope-configuration)) - (define-public python-zope-copy (package (name "python-zope-copy") From e6ef574f2aed80b24fdaeda315f3a6d4b1903bb8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:38:52 -0400 Subject: [PATCH 0893/1394] gnu: Remove python2-sockjs-tornado. * gnu/packages/python-web.scm (python2-sockjs-tornado): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index ce2dfffa693..3e2fe276c19 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1160,9 +1160,6 @@ SockJS provides a low-latency, full-duplex, cross-domain communication channel between a web browser and web server.") (license license:expat))) -(define-public python2-sockjs-tornado - (package-with-python2 python-sockjs-tornado)) - (define-public python-flask-assets (package (name "python-flask-assets") From b63429583b6ad1460cbc249fd4a61aa3cb24ef95 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:38:58 -0400 Subject: [PATCH 0894/1394] gnu: Remove python2-zope-security. * gnu/packages/python-web.scm (python2-zope-security): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 3e2fe276c19..643cba6c770 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2539,9 +2539,6 @@ security policies on Python objects.") ("python-zope-proxy" ,python-zope-proxy-bootstrap) ("python-zope-schema" ,python-zope-schema))))) -(define-public python2-zope-security - (package-with-python2 python-zope-security)) - (define-public python-zope-component (package (name "python-zope-component") From 6944240e51c22d201d285a4ccb142b535239bd38 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:39:01 -0400 Subject: [PATCH 0895/1394] gnu: Remove python2-oauthlib. * gnu/packages/python-web.scm (python2-oauthlib): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 643cba6c770..f47ff351fff 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2966,9 +2966,6 @@ adapter for use with the Requests library.") OAuth request-signing logic.") (license license:bsd-3))) -(define-public python2-oauthlib - (package-with-python2 python-oauthlib)) - (define-public python-rauth (package (name "python-rauth") From 3ccf7ea236e0650f8b905df9f832bdde4b185ba9 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:39:13 -0400 Subject: [PATCH 0896/1394] gnu: Remove python2-rauth. * gnu/packages/python-web.scm (python2-rauth): Delete variable. --- gnu/packages/python-web.scm | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index f47ff351fff..3ae2e21f2cc 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2988,14 +2988,7 @@ OAuth request-signing logic.") "Rauth is a Python library for OAuth 1.0/a, 2.0, and Ofly. It also provides service wrappers for convenient connection initialization and authenticated session objects providing things like keep-alive.") - (license license:expat) - (properties `((python2-variant . ,(delay python2-rauth)))))) - -(define-public python2-rauth - (let ((base (package-with-python2 (strip-python2-variant python-rauth)))) - (package/inherit base - (native-inputs `(("python2-unittest2" ,python2-unittest2) - ,@(package-native-inputs base)))))) + (license license:expat))) (define-public python-unalix (package From 35caf03b1ea7385bad1b72ce20ee7df07a5f2227 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:39:18 -0400 Subject: [PATCH 0897/1394] gnu: Remove python2-betamax. * gnu/packages/python-web.scm (python2-betamax): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 3ae2e21f2cc..cc0061b0bf7 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -3518,9 +3518,6 @@ provide an easy-to-use Python interface for building OAuth1 and OAuth2 clients." replay them during future tests. It is designed to work with python-requests.") (license license:expat))) -(define-public python2-betamax - (package-with-python2 python-betamax)) - (define-public python-betamax-matchers (package (name "python-betamax-matchers") From 1e44359cc08dafce41c688effdf581e026d6aa4c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:39:30 -0400 Subject: [PATCH 0898/1394] gnu: Remove python2-pastedeploy. * gnu/packages/python-web.scm (python2-pastedeploy): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index cc0061b0bf7..38a0debca7b 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -3152,9 +3152,6 @@ Script provides commands to serve applications based on this configuration file.") (license license:expat))) -(define-public python2-pastedeploy - (package-with-python2 python-pastedeploy)) - (define-public python-webtest (package (name "python-webtest") From 4ed5bc1ca0269ca4e192007294eb6ea2e1207399 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:39:39 -0400 Subject: [PATCH 0899/1394] gnu: Remove python2-genshi. * gnu/packages/python-web.scm (python2-genshi): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 38a0debca7b..5969212b662 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -4026,9 +4026,6 @@ of components for parsing, generating, and processing HTML, XML or other textual content for output generation on the web.") (license license:bsd-3))) -(define-public python2-genshi - (package-with-python2 python-genshi)) - (define-public python-flask-principal (package (name "python-flask-principal") From 25a15e71e65b97f4b7ab9154411f42102beaab70 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:39:52 -0400 Subject: [PATCH 0900/1394] gnu: Remove python2-webob. * gnu/packages/python-web.scm (python2-webob): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 5969212b662..6b7585d10e3 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2126,9 +2126,6 @@ your Web app.") object to help create WSGI responses.") (license license:expat))) -(define-public python2-webob - (package-with-python2 python-webob)) - (define-public python-zope-event (package (name "python-zope-event") From b2515311f3b3700bf1ca3710796bb8b482688a73 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:39:57 -0400 Subject: [PATCH 0901/1394] gnu: Remove python2-readlike. * gnu/packages/python-xyz.scm (python2-readlike): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3ac9adee1ee..2d8fd4a86ae 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24939,9 +24939,6 @@ Currently, all stateless Readline commands are implemented. Yanking and history are not supported.") (license license:expat))) -(define-public python2-readlike - (package-with-python2 python-readlike)) - (define-public python-reparser (package (name "python-reparser") From a12716ed27581b7c5ceb5d20aa1d99c86803bc5d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:40:21 -0400 Subject: [PATCH 0902/1394] gnu: Remove python2-ipython-genutils. * gnu/packages/python-xyz.scm (python2-ipython-genutils): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2d8fd4a86ae..9c14a83d30f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8924,9 +8924,6 @@ packages will remove their dependency on this, and this package will go away.") (license license:bsd-3))) -(define-public python2-ipython-genutils - (package-with-python2 python-ipython-genutils)) - ;;; Variant used to break a cycle with python-ipykernel. (define-public python-ipyparallel-bootstrap (hidden-package From 39d627447c4b554f82ffeeade246ca79a8f1d7b5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:40:30 -0400 Subject: [PATCH 0903/1394] gnu: Remove python2-coloredlogs. * gnu/packages/python-xyz.scm (python2-coloredlogs): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9c14a83d30f..cd7705456f2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2512,9 +2512,6 @@ Python's logging module. The @code{ColoredFormatter} class inherits from messages in color.") (license license:expat))) -(define-public python2-coloredlogs - (package-with-python2 python-coloredlogs)) - (define-public python-editorconfig (package (name "python-editorconfig") From fdf3f8d6d0a0890066827f23147c1dac69c57d6a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:40:34 -0400 Subject: [PATCH 0904/1394] gnu: Remove python2-pythondialog. * gnu/packages/python-xyz.scm (python2-pythondialog): Delete variable. --- gnu/packages/python-xyz.scm | 57 ++++++++++++++----------------------- 1 file changed, 21 insertions(+), 36 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cd7705456f2..bfcbbd9fb7f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14540,48 +14540,33 @@ tasks. It includes single-command deployment for the Django Girls tutorial.") (package (name "python-pythondialog") (version "3.4.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pythondialog" version)) - (sha256 - (base32 - "1728ghsran47jczn9bhlnkvk5bvqmmbihabgif5h705b84r1272c")))) + (source (origin + (method url-fetch) + (uri (pypi-uri "pythondialog" version)) + (sha256 + (base32 + "1728ghsran47jczn9bhlnkvk5bvqmmbihabgif5h705b84r1272c")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-path - (lambda* (#:key inputs #:allow-other-keys) - (let* ((dialog (assoc-ref inputs "dialog"))) - ;; Since this library really wants to grovel the search path, we - ;; must hardcode dialog's store path into it. - (substitute* "dialog.py" - (("os.getenv\\(\"PATH\", \":/bin:/usr/bin\"\\)") - (string-append "os.getenv(\"PATH\") + \":" dialog "/bin\""))) - #t)))) - #:tests? #f)) ; no test suite - (propagated-inputs - (list dialog)) + `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-path + (lambda* (#:key inputs #:allow-other-keys) + (let* ((dialog (assoc-ref inputs "dialog"))) + (substitute* "dialog.py" + (("os.getenv\\(\"PATH\", \":/bin:/usr/bin\"\\)") (string-append + "os.getenv(\"PATH\") + \":" + dialog + "/bin\""))) + #t)))) + #:tests? #f)) + (propagated-inputs (list dialog)) (home-page "http://pythondialog.sourceforge.net/") (synopsis "Python interface to the UNIX dialog utility") - (description "A Python wrapper for the dialog utility. Its purpose is to + (description + "A Python wrapper for the dialog utility. Its purpose is to provide an easy to use, pythonic and comprehensive Python interface to dialog. This allows one to make simple text-mode user interfaces on Unix-like systems") - (license license:lgpl2.1) - (properties `((python2-variant . ,(delay python2-pythondialog)))))) - -(define-public python2-pythondialog - (let ((base (package-with-python2 (strip-python2-variant python-pythondialog)))) - (package - (inherit base) - (version (package-version python-pythondialog)) - (source (origin - (method url-fetch) - (uri (pypi-uri "python2-pythondialog" version)) - (sha256 - (base32 - "0d8k7lxk50imdyx85lv8j98i4c93a71iwpapnl1506rpkbm9qvd9"))))))) + (license license:lgpl2.1))) (define-public python-configobj (package From 66fc746068bc92bf992f30688f34144370b727bc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:40:40 -0400 Subject: [PATCH 0905/1394] gnu: Remove python2-straight-plugin. * gnu/packages/python-xyz.scm (python2-straight-plugin): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index bfcbbd9fb7f..80974120a8b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11844,9 +11844,6 @@ almost any existing Python modules, and an easy way for outside developers to add functionality and customization to your projects with their own plugins.") (license license:expat))) -(define-public python2-straight-plugin - (package-with-python2 python-straight-plugin)) - (define-public python-pysendfile (package (name "python-pysendfile") From c3f1148cf28b474b601e83b4d01ff888090c1450 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:40:44 -0400 Subject: [PATCH 0906/1394] gnu: Remove python2-enum. * gnu/packages/python-xyz.scm (python2-enum): Delete variable. --- gnu/packages/python-xyz.scm | 22 ---------------------- 1 file changed, 22 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 80974120a8b..ebfc8120676 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3016,28 +3016,6 @@ bug tracker.") (home-page "http://www.liquidx.net/pybugz/") (license license:gpl2))) -(define-public python2-enum - (package - (name "python2-enum") - (version "0.4.6") - (source (origin - (method url-fetch) - (uri (pypi-uri "enum" version)) - (sha256 - (base32 - "13lk3yrwj42vl30kw3c194f739nrfrdg64s6i0v2p636n4k8brsl")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) - (home-page "https://pypi.org/project/enum/") - (synopsis "Robust enumerated type support in Python") - (description - "This provides a module for robust enumerations in Python. It has -been superseded by the Python standard library and is provided only for -compatibility.") - ;; Choice of either license. - (license (list license:gpl3+ license:psfl)))) - (define-public python-enum34 (package (name "python-enum34") From 63a2d6b094fd041580aa1fee2b233be37d850742 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:40:50 -0400 Subject: [PATCH 0907/1394] gnu: Remove python2-uniseg. * gnu/packages/python-xyz.scm (python2-uniseg): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ebfc8120676..298f805a4e7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2096,9 +2096,6 @@ multiple Unicode code points, e.g. \"G\" + acute-accent) @end enumerate") (license license:expat))) -(define-public python2-uniseg - (package-with-python2 python-uniseg)) - (define-public python-humanfriendly (package (name "python-humanfriendly") From 2d9a73171cdacbec4bfbec326207265a5b45d8b6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:40:59 -0400 Subject: [PATCH 0908/1394] gnu: Remove python2-argcomplete. * gnu/packages/python-xyz.scm (python2-argcomplete): Delete variable. --- gnu/packages/python-xyz.scm | 17 +---------------- 1 file changed, 1 insertion(+), 16 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 298f805a4e7..5839b0d7dd8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19452,22 +19452,7 @@ JSON) codec.") particularly useful for programs with many options or sub-parsers that can dynamically suggest completions ; for example, when browsing resources over the network.") - (license license:asl2.0) - (properties `((python2-variant . ,(delay python2-argcomplete)))))) - -(define-public python2-argcomplete - (let ((variant (package-with-python2 - (strip-python2-variant python-argcomplete)))) - (package/inherit variant - (arguments - (substitute-keyword-arguments (package-arguments variant) - ((#:phases phases '%standard-phases) - `(modify-phases ,phases - (add-after 'unpack 'set-my-HOME - (lambda _ (setenv "HOME" "/tmp"))))))) - (native-inputs - `(("python2-importlib-metadata" ,python2-importlib-metadata) - ,@(package-native-inputs variant)))))) + (license license:asl2.0))) (define-public python-csscompressor (package From d96f7625e4b4998d68f55c7bed6218629a34de44 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:41:14 -0400 Subject: [PATCH 0909/1394] gnu: Remove python2-pkginfo. * gnu/packages/python-xyz.scm (python2-pkginfo): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5839b0d7dd8..599cf61839b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21913,9 +21913,6 @@ distribution, and the *.egg-info stored in a \"development checkout\" (e.g, created by running @code{python setup.py develop}).") (license license:expat))) -(define-public python2-pkginfo - (package-with-python2 python-pkginfo)) - (define-public python-twine (package (name "python-twine") From 03ecf0a3f4109c3b018c5659f1866042756d5619 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:41:17 -0400 Subject: [PATCH 0910/1394] gnu: Remove python2-mmtk. * gnu/packages/python-xyz.scm (python2-mmtk): Delete variable. --- gnu/packages/python-xyz.scm | 42 ------------------------------------- 1 file changed, 42 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 599cf61839b..38d84b3680e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22474,48 +22474,6 @@ domain-specific (e.g. netCDF and PDB support). The library is currently not actively maintained and works only with Python 2 and NumPy < 1.9.") (license license:cecill-c))) -(define-public python2-mmtk - (package - (name "python2-mmtk") - (version "2.7.12") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/khinsen/MMTK") - (commit (string-append "rel" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1fqwh3ba9jd42nigvn5shndgwb1zy7kh9520ncvqci7n8ffjr6p1")))) - (build-system python-build-system) - (native-inputs - (list netcdf)) - (propagated-inputs - `(("python-scientific" ,python2-scientific) - ("python-tkinter" ,python-2 "tk"))) - (arguments - `(#:python ,python-2 - #:tests? #f - #:phases - (modify-phases %standard-phases - (add-before 'build 'includes-from-scientific - (lambda* (#:key inputs #:allow-other-keys) - (mkdir-p "Include/Scientific") - (copy-recursively - (string-append - (assoc-ref inputs "python-scientific") - "/include/python2.7/Scientific") - "Include/Scientific")))))) - (home-page "http://dirac.cnrs-orleans.fr/MMTK") - (synopsis "Python library for molecular simulation") - (description "MMTK is a library for molecular simulations with an emphasis -on biomolecules. It provides widely used methods such as Molecular Dynamics -and normal mode analysis, but also basic routines for implementing new methods -for simulation and analysis. The library is currently not actively maintained -and works only with Python 2 and NumPy < 1.9.") - (license license:cecill-c))) - (define-public python-phonenumbers (package (name "python-phonenumbers") From ff4d3b7cb6372ff2c76010c30fe4b14d2805086d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:41:24 -0400 Subject: [PATCH 0911/1394] gnu: Remove python2-s3cmd. * gnu/packages/python-xyz.scm (python2-s3cmd): Delete variable. --- gnu/packages/python-xyz.scm | 37 ------------------------------------- 1 file changed, 37 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 38d84b3680e..6d6b030aea0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16834,43 +16834,6 @@ the same purpose: to provide Python bindings for libmagic.") (define-public python2-magic (package-with-python2 python-magic)) -(define-public python2-s3cmd - (package - (name "python2-s3cmd") - (version "1.6.1") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/s3tools/s3cmd/" version "/" - "s3cmd-" version ".tar.gz")) - (sha256 - (base32 - "0ki1rzhm5icvi9ry5jswi4b22yqwyj0d2wsqsgilwx6qhi7pjxa6")))) - (build-system python-build-system) - (arguments - ;; s3cmd is written for python2 only and contains no tests. - `(#:python ,python-2 - #:tests? #f)) - (propagated-inputs - (list python2-dateutil - ;; The python-file package also provides a magic.py module. - ;; This is an unfortunate state of affairs; however, s3cmd - ;; fails to install if it cannot find specifically the - ;; python-magic package. Thus we include it, instead of using - ;; python-file. Ironically, s3cmd sometimes works better - ;; without libmagic bindings at all: - ;; https://github.com/s3tools/s3cmd/issues/198 - python2-magic)) - (home-page "https://s3tools.org/s3cmd") - (synopsis "Command line tool for S3-compatible storage services") - (description - "S3cmd is a command line tool for uploading, retrieving and managing data -in storage services that are compatible with the Amazon Simple Storage -Service (S3) protocol, including S3 itself. It supports rsync-like backup, -GnuPG encryption, and more. It also supports management of Amazon's -CloudFront content delivery network.") - (license license:gpl2+))) - (define-public python-pkgconfig (package (name "python-pkgconfig") From ff6c3bace1677596ccf4fc87908ac8cdd904c91d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:41:27 -0400 Subject: [PATCH 0912/1394] gnu: Remove python2-clint. * gnu/packages/python-xyz.scm (python2-clint): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6d6b030aea0..cdd6d85d45e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15003,9 +15003,6 @@ command-line applications, including tools for colored and indented output, progress bar display, and pipes.") (license license:isc))) -(define-public python2-clint - (package-with-python2 python-clint)) - (define-public python-rply (package (name "python-rply") From fa94ed517368f9babc55375c758ea9e58b94bfcb Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:41:31 -0400 Subject: [PATCH 0913/1394] gnu: Remove python2-exif-read. * gnu/packages/python-xyz.scm (python2-exif-read): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cdd6d85d45e..286563ad9cc 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3538,9 +3538,6 @@ structure is left untouched.") files.") (license license:bsd-3))) -(define-public python2-exif-read - (package-with-python2 python-exif-read)) - (define-public python-pyld (package (name "python-pyld") From e75781ce7aabc96c1120680de8ff684c26b8a964 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:41:34 -0400 Subject: [PATCH 0914/1394] gnu: Remove python2-activepapers. * gnu/packages/python-xyz.scm (python2-activepapers): Delete variable. --- gnu/packages/python-xyz.scm | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 286563ad9cc..4e2d615c8d8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22290,25 +22290,8 @@ Time} values as well as an event scheduler.") combine data, code, and documentation in single-file packages, suitable for publication as supplementary material or on repositories such as figshare or Zenodo.") - (properties `((python2-variant . ,(delay python2-activepapers)))) (license license:bsd-3))) -(define-public python2-activepapers - (let ((base (package-with-python2 - (strip-python2-variant python-activepapers)))) - (package/inherit base - (arguments - (substitute-keyword-arguments (package-arguments base) - ((#:phases phases) - `(modify-phases ,phases - (delete 'delete-python2-code) - (add-after 'unpack 'delete-python3-code - (lambda _ - (for-each delete-file - '("lib/activepapers/builtins3.py" - "lib/activepapers/standardlib3.py" - "lib/activepapers/utility3.py"))))))))))) - (define-public python-semver (package (name "python-semver") From 61504ff725d8a2d3ce38a4333a60f893c848af15 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:41:43 -0400 Subject: [PATCH 0915/1394] gnu: Remove python2-argparse. * gnu/packages/python-xyz.scm (python2-argparse): Delete variable. --- gnu/packages/python-xyz.scm | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4e2d615c8d8..9e5d2581c8f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20465,27 +20465,6 @@ builds partial trees by inspecting living objects.") (define-public python2-mando (package-with-python2 python-mando)) -(define-public python2-argparse - (package - (name "python2-argparse") - (version "1.4.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "argparse" version)) - (sha256 - (base32 - "1r6nznp64j68ih1k537wms7h57nvppq0szmwsaf99n71bfjqkc32")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) - (home-page "https://github.com/ThomasWaldmann/argparse/") - (synopsis "Python command-line parsing library") - (description - "This package is mostly for people who want to have @code{argparse} on - older Pythons because it was not part of the standard library back then.") - (license license:psfl))) - (define-public python-mwclient (package (name "python-mwclient") From 54ca8f4c418b626eed17265ab4be8ad909c2a495 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:41:49 -0400 Subject: [PATCH 0916/1394] gnu: Remove python2-rencode. * gnu/packages/python-xyz.scm (python2-rencode): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9e5d2581c8f..30220bfc607 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21668,9 +21668,6 @@ complete rewrite in Cython to attempt to increase the performance over the pure Python module.") (license license:bsd-3))) -(define-public python2-rencode - (package-with-python2 python-rencode)) - (define-public python-xenon (package (name "python-xenon") From a00ab19763ff063225736f12ad63624c0a3bf550 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:41:53 -0400 Subject: [PATCH 0917/1394] gnu: Remove python2-parallel. * gnu/packages/python-xyz.scm (python2-parallel): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 30220bfc607..e6cbddcddeb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -28419,9 +28419,6 @@ heterogeneous and multi-platform clusters (including clusters running other applications with variable CPU loads).") (license license:bsd-3))) -(define-public python2-parallel - (package-with-python2 python-parallel)) - (define-public python-djvulibre (package (name "python-djvulibre") From de0ae971915e8e0c3733f0136ffba7b33a4bca1b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:42:00 -0400 Subject: [PATCH 0918/1394] gnu: Remove python2-colorspacious. * gnu/packages/python-xyz.scm (python2-colorspacious): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e6cbddcddeb..94d1c0a6247 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6582,9 +6582,6 @@ To address this and enable easy cycling over arbitrary @code{kwargs}, the convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.") (license license:expat))) -(define-public python2-colorspacious - (package-with-python2 python-colorspacious)) - (define-public python-proto-matcher (package (name "python-proto-matcher") From 8ac3ebf1b4924cb22da7e5048de9846493239081 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:42:14 -0400 Subject: [PATCH 0919/1394] gnu: Remove python2-mako. * gnu/packages/python-xyz.scm (python2-mako): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 94d1c0a6247..a6639dd46bb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15852,9 +15852,6 @@ of @acronym{REGEXPs, regular expressions}.") templates into Python modules.") (license license:expat))) -(define-public python2-mako - (package-with-python2 python-mako)) - (define-public python-waitress (package (name "python-waitress") From 2644fac20ee5bc7370186fadbd021b2395ca11b2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:42:18 -0400 Subject: [PATCH 0920/1394] gnu: Remove python2-polib. * gnu/packages/python-xyz.scm (python2-polib): Delete variable. --- gnu/packages/python-xyz.scm | 7 ------- 1 file changed, 7 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a6639dd46bb..bb20cfb52ba 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3114,13 +3114,6 @@ files. It can be used to create po files from scratch or to modify existing ones.") (license license:expat))) -(define-public python2-polib - (let ((base (package-with-python2 (strip-python2-variant python-polib)))) - (package/inherit base - (arguments `(,@(package-arguments base) - ;; Tests don't work with python2. - #:tests? #f))))) - (define-public python-polling2 (package (name "python-polling2") From 52abcbbdc03177f70b4a09946265866f402b1375 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:42:22 -0400 Subject: [PATCH 0921/1394] gnu: Remove python2-quex-0.67.3. * gnu/packages/python-xyz.scm (python2-quex-0.67.3): Delete variable. --- gnu/packages/python-xyz.scm | 42 ------------------------------------- 1 file changed, 42 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index bb20cfb52ba..3f16b211c2d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23094,48 +23094,6 @@ file system events on Linux.") (define-public python2-pyinotify (package-with-python2 python-pyinotify)) -;; Ada parser uses this version. -(define-public python2-quex-0.67.3 - (package - (name "python2-quex") - (version "0.67.3") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/quex/HISTORY/" - (version-major+minor version) - "/quex-" version ".zip")) - (sha256 - (base32 - "14gv8ll3ipqv4kyc2xiy891nrmjl4ic823zfyx8hassagyclyppw")))) - (build-system python-build-system) - (native-inputs - (list unzip)) - (arguments - `(#:python ,python-2 - #:tests? #f - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (share/quex (string-append out "/share/quex")) - (bin (string-append out "/bin"))) - (copy-recursively "." share/quex) - (mkdir-p bin) - (symlink (string-append share/quex "/quex-exe.py") - (string-append bin "/quex")) - #t)))))) - (native-search-paths - (list (search-path-specification - (variable "QUEX_PATH") - (files '("share/quex"))))) - (home-page "http://quex.sourceforge.net/") - (synopsis "Lexical analyzer generator in Python") - (description "@code{quex} is a lexical analyzer generator in Python.") - (license license:lgpl2.1+))) ; Non-military (define-public python2-quex (package (inherit python2-quex-0.67.3) From b199a48ef69d1d90d19b7f37763e19e05e1352da Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:42:41 -0400 Subject: [PATCH 0922/1394] gnu: Remove python2-netaddr. * gnu/packages/python-xyz.scm (python2-netaddr): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3f16b211c2d..f538d592983 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12195,9 +12195,6 @@ reading and writing MessagePack data.") and MAC network addresses.") (license license:bsd-3))) -(define-public python2-netaddr - (package-with-python2 python-netaddr)) - (define-public python2-pyroute2 (package (name "python2-pyroute2") From 714125fbd028946039ef93f42f0e396f954c3ecf Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:42:48 -0400 Subject: [PATCH 0923/1394] gnu: Remove python2-kivy. * gnu/packages/python-xyz.scm (python2-kivy): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f538d592983..6f798ff8e99 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18699,9 +18699,6 @@ multitouch applications.") Design spec without sacrificing ease of use or application performance.") (license license:expat))) -(define-public python2-kivy - (package-with-python2 python-kivy)) - (define-public python-binaryornot (package (name "python-binaryornot") From 2b612f1589beb4d5d99ff56f3d71adce55cdbacc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:42:54 -0400 Subject: [PATCH 0924/1394] gnu: Remove python2-kazoo. * gnu/packages/python-xyz.scm (python2-kazoo): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6f798ff8e99..cb4dd223837 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17446,9 +17446,6 @@ application service. It is designed to be easy to use and to avoid common programming errors.") (license license:asl2.0))) -(define-public python2-kazoo - (package-with-python2 python-kazoo)) - (define-public python-pykafka (package (name "python-pykafka") From 6a16599d391912ab8edaa605d34c5055c4b10bf0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:43:09 -0400 Subject: [PATCH 0925/1394] gnu: Remove python2-prompt-toolkit. * gnu/packages/python-xyz.scm (python2-prompt-toolkit): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cb4dd223837..1540cffce5e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18286,9 +18286,6 @@ scans through a file and detects issues.") (list python-wcwidth python-six python-pygments)) (properties '()))) -(define-public python2-prompt-toolkit - (package-with-python2 python-prompt-toolkit-2)) - (define-public python-prompt-toolkit-1 (package (inherit python-prompt-toolkit-2) (version "1.0.15") From a5581a11354b813bac186da74acdfdd98c01fe3e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:43:14 -0400 Subject: [PATCH 0926/1394] gnu: Remove python2-editor. * gnu/packages/python-xyz.scm (python2-editor): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1540cffce5e..8d4a0292578 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16348,9 +16348,6 @@ by providing an implementation of the PEP 3156 event-loop.") programmatically interfacing with your system's $EDITOR.") (license license:asl2.0))) -(define-public python2-editor - (package-with-python2 python-editor)) - (define-public python-multiprocessing-logging (package (name "python-multiprocessing-logging") From 38d6bfb6d611d069a5f615d1a4843e76705fed80 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:43:21 -0400 Subject: [PATCH 0927/1394] gnu: Remove python2-kitchen. * gnu/packages/python-xyz.scm (python2-kitchen): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8d4a0292578..891d7dbfe23 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3821,9 +3821,6 @@ cutting and pasting that code over and over.") ;; kitchen/pycompat25/defaultdict.py: license:psfl)))) -(define-public python2-kitchen - (package-with-python2 python-kitchen)) - (define-public python-roman (package (name "python-roman") From d8ca68f389a6189dca34bb47177ef1c5721438b7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:43:24 -0400 Subject: [PATCH 0928/1394] gnu: Remove python2-dns-lexicon. * gnu/packages/python-xyz.scm (python2-dns-lexicon): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 891d7dbfe23..d790f0c2331 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23881,9 +23881,6 @@ Python library. It was designed to be used in automation, specifically with Let's Encrypt.") (license license:expat))) -(define-public python2-dns-lexicon - (package-with-python2 python-dns-lexicon)) - (define-public python-cfgv (package (name "python-cfgv") From 9352fc5347fe77638ed001164a16a6efc80cde2c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:43:31 -0400 Subject: [PATCH 0929/1394] gnu: Remove python2-shedskin. * gnu/packages/python-xyz.scm (python2-shedskin): Delete variable. --- gnu/packages/python-xyz.scm | 38 ------------------------------------- 1 file changed, 38 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d790f0c2331..d1b2ed09bfb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16958,44 +16958,6 @@ respectively.") (define-public python2-cysignals (package-with-python2 python-cysignals)) -(define-public python2-shedskin - (package - (name "python2-shedskin") - (version "0.9.4") - (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/shedskin/shedskin/" - "releases/download/v" version - "/shedskin-" version ".tgz")) - (sha256 - (base32 - "0nzwrzgw1ga8rw6f0ryq7zr9kkiavd1cqz5hzxkcbicl1dk7kz41")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases (modify-phases %standard-phases - (add-after 'unpack 'fix-resulting-include-libs - (lambda* (#:key inputs #:allow-other-keys) - (let ((libgc (assoc-ref inputs "libgc")) - (pcre (assoc-ref inputs "pcre"))) - (substitute* "shedskin/makefile.py" - (("variable == 'CCFLAGS':[ ]*") - (string-append "variable == 'CCFLAGS':\n" - " line += ' -I " pcre "/include" - " -I " libgc "/include'")) - (("variable == 'LFLAGS':[ ]*") - (string-append "variable == 'LFLAGS':\n" - " line += ' -L" pcre "/lib" - " -L " libgc "/lib'"))) - #t)))))) - (inputs (list pcre libgc)) - (home-page "https://shedskin.github.io/") - (synopsis "Experimental Python-2 to C++ Compiler") - (description (string-append "This is an experimental compiler for a subset of -Python. It generates C++ code and a Makefile.")) - (license (list license:gpl3 license:bsd-3 license:expat)))) - (define-public python-rope (package (name "python-rope") From d09044194dfe64e3ab1dabbbcf98b5b5f5dabc74 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:43:38 -0400 Subject: [PATCH 0930/1394] gnu: Remove python2-unicodecsv. * gnu/packages/python-xyz.scm (python2-unicodecsv): Delete variable. --- gnu/packages/python-xyz.scm | 27 --------------------------- 1 file changed, 27 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d1b2ed09bfb..181e7a937d2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16600,33 +16600,6 @@ ambiguities (forward vs. backward slashes, etc.). encoding algorithms to do fuzzy string matching.") (license license:bsd-2))) -(define-public python2-unicodecsv - (package - (name "python2-unicodecsv") - (version "0.14.1") - (source (origin - (method git-fetch) - ;; The test suite is not included in the PyPi release. - ;; https://github.com/jdunck/python-unicodecsv/issues/19 - (uri (git-reference - (url "https://github.com/jdunck/python-unicodecsv") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "15hx2k41a2lpv4hcml9zp4cvlx1171mnb5s4s13xc1pxkq3vgdjy")))) - (build-system python-build-system) - (arguments - `(;; It supports Python 3, but Python 3 can already do Unicode CSV. - #:python ,python-2)) - (native-inputs - (list python2-unittest2)) - (home-page "https://github.com/jdunck/python-unicodecsv") - (synopsis "Unicode CSV module for Python 2") - (description "Unicodecsv is a drop-in replacement for Python 2.7's CSV -module, adding support for Unicode strings.") - (license license:bsd-2))) - (define-public python-pdfminer-six (package (name "python-pdfminer-six") From 77d25a62f271e47c343d62314d32b86ce0d1cede Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:43:41 -0400 Subject: [PATCH 0931/1394] gnu: Remove python2-cliapp. * gnu/packages/python-xyz.scm (python2-cliapp): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 181e7a937d2..c44b2934dde 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20033,9 +20033,6 @@ JSON) codec.") as parsing the command line for options, and iterating over input files.") (license license:gpl2+))) -(define-public python2-cliapp - (package-with-python2 python-cliapp)) - (define-public python-ttystatus (package (name "python-ttystatus") From 0202863b7692c9f2048829d093e7e15d808f6d92 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:43:51 -0400 Subject: [PATCH 0932/1394] gnu: Remove python2-text-unidecode. * gnu/packages/python-xyz.scm (python2-text-unidecode): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c44b2934dde..599354e18be 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3892,9 +3892,6 @@ memory usage and transliteration quality.") ;; The user can choose either license. (license (list license:clarified-artistic license:gpl2+)))) -(define-public python2-text-unidecode - (package-with-python2 python-text-unidecode)) - (define-public python-pyjwt (package (name "python-pyjwt") From 2841af8b9650f427b21e026aeca2def79aaa99ac Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:43:58 -0400 Subject: [PATCH 0933/1394] gnu: Remove python2-invoke. * gnu/packages/python-xyz.scm (python2-invoke): Delete variable. --- gnu/packages/python-xyz.scm | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 599354e18be..9b55cf3e7ce 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19865,19 +19865,6 @@ JSON) codec.") instead of servers and network commands.") (license license:bsd-3))) -(define-public python2-invoke - (let ((parent (package-with-python2 python-invoke))) - (package - (inherit parent) - (arguments - (substitute-keyword-arguments (package-arguments parent) - ((#:phases phases #t) - `(modify-phases ,phases - (delete 'delete-python2-code) - (add-after 'unpack 'delete-python3-code - (lambda _ - (delete-file-recursively "invoke/vendor/yaml3")))))))))) - (define-public python-automat (package (name "python-automat") From 5045ff299c484dbcf9752a5917065dfdc59ea188 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:44:04 -0400 Subject: [PATCH 0934/1394] gnu: Remove python2-validictory. * gnu/packages/python-xyz.scm (python2-validictory): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9b55cf3e7ce..2c1e745da64 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19168,9 +19168,6 @@ JSON) codec.") useful as a validator for JSON data.") (license license:expat))) -(define-public python2-validictory - (package-with-python2 python-validictory)) - (define-public python-pyelftools (package (name "python-pyelftools") From c93397ce1927ad9268f7cd0f6dd497b90625c4e4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:44:25 -0400 Subject: [PATCH 0935/1394] gnu: Remove python2-pycosat. * gnu/packages/python-xyz.scm (python2-pycosat): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2c1e745da64..9804c3751bf 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19745,9 +19745,6 @@ JSON) codec.") Problem} (SAT) solver.") (license license:expat))) -(define-public python2-pycosat - (package-with-python2 python-pycosat)) - (define-public python2-ruamel.ordereddict (package (name "python2-ruamel.ordereddict") From e44c586513f8b6dbccdeb0242dde019413a85ee8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:44:29 -0400 Subject: [PATCH 0936/1394] gnu: Remove python2-miniboa. * gnu/packages/python-xyz.scm (python2-miniboa): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9804c3751bf..b8af31ecaab 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3294,9 +3294,6 @@ matching them against a list of media-ranges.") server.") (license license:asl2.0))) -(define-public python2-miniboa - (package-with-python2 python-miniboa)) - (define-public python-pafy (package (name "python-pafy") From f24ad69f38b62b2bf6e2ad89973fc286942ed028 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:44:36 -0400 Subject: [PATCH 0937/1394] gnu: Remove python2-semver. * gnu/packages/python-xyz.scm (python2-semver): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b8af31ecaab..a08a6fa9026 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22170,9 +22170,6 @@ such as figshare or Zenodo.") @url{Semantic Versioning, http://semver.org/}.") (license license:bsd-3))) -(define-public python2-semver - (package-with-python2 python-semver)) - (define-public python-pyro4 (package (name "python-pyro4") From f5bf1eab9891a64129d11534526eaeb0caf081ae Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:44:40 -0400 Subject: [PATCH 0938/1394] gnu: Remove python2-configobj. * gnu/packages/python-xyz.scm (python2-configobj): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a08a6fa9026..75189927556 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14539,9 +14539,6 @@ config files.") (home-page "https://github.com/DiffSK/configobj") (license license:bsd-3))) -(define-public python2-configobj - (package-with-python2 python-configobj)) - (define-public python-configargparse (package (name "python-configargparse") From ce7fa258e5f354dbc1229c5634887af85c44bc09 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:44:44 -0400 Subject: [PATCH 0939/1394] gnu: Remove python2-verboselogs. * gnu/packages/python-xyz.scm (python2-verboselogs): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 75189927556..d477a74bcb7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2480,9 +2480,6 @@ some helpful Python 2 compatibility convenience methods.") add the log levels NOTICE, SPAM, SUCCESS and VERBOSE.") (license license:expat))) -(define-public python2-verboselogs - (package-with-python2 python-verboselogs)) - (define-public python-coloredlogs (package (name "python-coloredlogs") From e3bbddc406d66450505e67fd1bed291f0000ef85 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:44:48 -0400 Subject: [PATCH 0940/1394] gnu: Remove python2-glob2. * gnu/packages/python-xyz.scm (python2-glob2): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d477a74bcb7..47b02247d37 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23189,9 +23189,6 @@ on virtual file systems. Glob2 currently based on the glob code from Python 3.3.1.") (license license:bsd-2))) -(define-public python2-glob2 - (package-with-python2 python-glob2)) - (define-public python-gipc (package (name "python-gipc") From a969dd23c1eb2635c524dc83208de616e0371d3f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:44:52 -0400 Subject: [PATCH 0941/1394] gnu: Remove python2-funcy. * gnu/packages/python-xyz.scm (python2-funcy): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 47b02247d37..13d2dc0608e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22570,9 +22570,6 @@ Examples are: @end enumerate") (license license:bsd-3))) -(define-public python2-funcy - (package-with-python2 python-funcy)) - (define-public python-isoweek (package (name "python-isoweek") From 1351249e9625d3d02597b6665af26ca7d3eb6a99 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:44:56 -0400 Subject: [PATCH 0942/1394] gnu: Remove python2-phonenumbers. * gnu/packages/python-xyz.scm (python2-phonenumbers): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 13d2dc0608e..2bd2b1ef79b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22277,9 +22277,6 @@ not actively maintained and works only with Python 2 and NumPy < 1.9.") "This package provides a Python port of Google's libphonenumber library.") (license license:asl2.0))) -(define-public python2-phonenumbers - (package-with-python2 python-phonenumbers)) - (define-public python-heapdict (package (name "python-heapdict") From 08b026b3e3206dce0053c1998309859008d5458d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:45:00 -0400 Subject: [PATCH 0943/1394] gnu: Remove python2-tracing. * gnu/packages/python-xyz.scm (python2-tracing): Delete variable. --- gnu/packages/python-xyz.scm | 26 -------------------------- 1 file changed, 26 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2bd2b1ef79b..4900efee57e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20040,32 +20040,6 @@ JSON) codec.") (define-public python2-ttystatus (package-with-python2 python-ttystatus)) -(define-public python2-tracing - (package - (name "python2-tracing") - (version "0.10") - (source - (origin - (method url-fetch) - (uri (string-append - "http://git.liw.fi/cgi-bin/cgit/cgit.cgi/python-tracing/snapshot/tracing-" - version ".tar.gz")) - (sha256 - (base32 - "06cw4zg42fsvqy372vi2whj26w56vzg5axhzwdjc2bgwf03garbw")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) - (home-page "https://liw.fi/tracing/") - (synopsis "Python debug logging helper") - (description "@code{python2-tracing} is a python library for - logging debug messages. It provides a way to turn debugging messages - on and off, based on the filename they occur in. It is much faster - than using @code{logging.Filter} to accomplish the same thing, which - matters when code is run in production mode. The actual logging still - happens using the @code{logging} library.") - (license license:gpl3+))) - (define-public python-astroid (package (name "python-astroid") From 42aa6229eb2e63c8082a8e1fe7be34f3818da421 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:45:13 -0400 Subject: [PATCH 0944/1394] gnu: Remove python2-anyjson. * gnu/packages/python-xyz.scm (python2-anyjson): Delete variable. --- gnu/packages/python-xyz.scm | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4900efee57e..fcfd73ae165 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15953,17 +15953,7 @@ fast xml and html manipulation.") (description "Anyjson loads whichever is the fastest JSON module installed and provides a uniform API regardless of which JSON implementation is used.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python2-anyjson)))))) - -(define-public python2-anyjson - (let ((anyjson (package-with-python2 - (strip-python2-variant python-anyjson)))) - (package/inherit anyjson - (arguments `(;; Unlike the python 3 variant, we do run tests. See above! - #:tests? #t - ,@(package-arguments anyjson))) - (native-inputs `(("python2-nose" ,python2-nose)))))) + (license license:bsd-3))) (define-public python-amqp (package From 55383ea50bd6c2827712b64c2879105388cadcf4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:45:23 -0400 Subject: [PATCH 0945/1394] gnu: Remove python2-libarchive-c. * gnu/packages/python-xyz.scm (python2-libarchive-c): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index fcfd73ae165..4d16b16c566 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -13398,9 +13398,6 @@ access possibly compressed archives in many different formats. It uses Python's @code{ctypes} foreign function interface (FFI).") (license license:lgpl2.0+))) -(define-public python2-libarchive-c - (package-with-python2 python-libarchive-c)) - (define-public python-file (package/inherit file (name "python-file") From 1e6e65fc32a83d1515d63ef92f88bdedda69e5c8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:45:28 -0400 Subject: [PATCH 0946/1394] gnu: Remove python2-xopen. * gnu/packages/python-xyz.scm (python2-xopen): Delete variable. --- gnu/packages/python-xyz.scm | 7 ------- 1 file changed, 7 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4d16b16c566..3efdfe606aa 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19397,13 +19397,6 @@ JSON) codec.") possible on all supported Python versions.") (license license:expat))) -(define-public python2-xopen - (let ((base (package-with-python2 - (strip-python2-variant python-xopen)))) - (package/inherit base - (propagated-inputs `(("python2-bz2file" ,python2-bz2file) - ,@(package-propagated-inputs base)))))) - (define-public python-cheetah (package (name "python-cheetah") From f94f66b174d62cc9c829b7405ebf216fd4e9db71 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:45:35 -0400 Subject: [PATCH 0947/1394] gnu: Remove python2-quex. * gnu/packages/python-xyz.scm (python2-quex): Delete variable. --- gnu/packages/python-xyz.scm | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3efdfe606aa..0aa870dc06f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22923,19 +22923,6 @@ file system events on Linux.") (package-with-python2 python-pyinotify)) -(define-public python2-quex - (package (inherit python2-quex-0.67.3) - (name "python2-quex") - (version "0.68.1") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/quex/DOWNLOAD/quex-" version ".tar.gz")) - (sha256 - (base32 - "0svc9nla3b9145d6b7fb9dizx412l3difzqw0ilh9lz52nsixw8j")) - (file-name (string-append name "-" version ".tar.gz")))))) - (define-public python-more-itertools (package (name "python-more-itertools") From 72b519f4c935fdc150e567b034a2014f2fe4fe6b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:45:39 -0400 Subject: [PATCH 0948/1394] gnu: Remove python2-file. * gnu/packages/python-xyz.scm (python2-file): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0aa870dc06f..bd312c36a69 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -13430,9 +13430,6 @@ Note that this module and the @code{python-magic} module both provide a developed separately, both serve the same purpose: provide Python bindings for libmagic."))) -(define-public python2-file - (package-with-python2 python-file)) - (define-public python-pydevd ;; Use the latest commit, which includes cleanups that removes Python 2 ;; syntax that would fail to build. From 7a184a00aed417bb86237b76de2710b796352374 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:45:43 -0400 Subject: [PATCH 0949/1394] gnu: Remove python2-jsonrpclib-pelix. * gnu/packages/python-xyz.scm (python2-jsonrpclib-pelix): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index bd312c36a69..9155c74e9d0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21800,9 +21800,6 @@ version is a fork of jsonrpclib by Josh Marshall, usable with Pelix remote services.") (license license:asl2.0))) -(define-public python2-jsonrpclib-pelix - (package-with-python2 python-jsonrpclib-pelix)) - (define-public python-setuptools-scm-git-archive (package (name "python-setuptools-scm-git-archive") From d456a036db42ea04dc380af38601d797b52accff Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:45:46 -0400 Subject: [PATCH 0950/1394] gnu: Remove python2-munch. * gnu/packages/python-xyz.scm (python2-munch): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9155c74e9d0..6ed2732ce03 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6024,9 +6024,6 @@ Numeric.") objects.") (license license:expat))) -(define-public python2-munch - (package-with-python2 python-munch)) - (define-public python-colormath (package (name "python-colormath") From f3661413b2df2903c01c168da376eb18aa0988c0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:45:50 -0400 Subject: [PATCH 0951/1394] gnu: Remove python2-pycountry. * gnu/packages/python-xyz.scm (python2-pycountry): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6ed2732ce03..d920828939f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19683,9 +19683,6 @@ JSON) codec.") through a Python API.") (license license:lgpl2.1+))) -(define-public python2-pycountry - (package-with-python2 python-pycountry)) - (define-public python-pycosat (package (name "python-pycosat") From 8b3125c0692eadd232befd6c2648bf2ab4c57def Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:45:57 -0400 Subject: [PATCH 0952/1394] gnu: Remove python2-user-agents. * gnu/packages/python-xyz.scm (python2-user-agents): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d920828939f..04afc5131b3 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9737,9 +9737,6 @@ toolkit. Use it to build trees of widgets.") parsing (browser/HTTP) user agent strings.") (license license:expat))) -(define-public python2-user-agents - (package-with-python2 python-user-agents)) - (define-public python-pydbus (package (name "python-pydbus") From 72fe78ab85afb6522269bc4d294d882d98cd9d4f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:46:02 -0400 Subject: [PATCH 0953/1394] gnu: Remove python2-ratelimiter. * gnu/packages/python-xyz.scm (python2-ratelimiter): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 04afc5131b3..8ef36eb922b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21765,9 +21765,6 @@ interpreter when it prints a stack trace.") executed more than a given number of times during a given period.") (license license:asl2.0))) -(define-public python2-ratelimiter - (package-with-python2 python-ratelimiter)) - (define-public python-jsonrpclib-pelix (package (name "python-jsonrpclib-pelix") From 69655554e2b9c093195f857513dcb7c1102e25d6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:46:15 -0400 Subject: [PATCH 0954/1394] gnu: Remove python2-prettytable. * gnu/packages/python-xyz.scm (python2-prettytable): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8ef36eb922b..528063ae78f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12467,9 +12467,6 @@ independent alignment of columns (left or right justified or centred) and printing of sub-tables by specifying a row range.") (license license:bsd-3))) -(define-public python2-prettytable - (package-with-python2 python-prettytable)) - (define-public python-curio (package (name "python-curio") From 8f279ececf8e8cf89d70055331941b8b95fd43ad Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:46:18 -0400 Subject: [PATCH 0955/1394] gnu: Remove python2-jsonrpclib. * gnu/packages/python-xyz.scm (python2-jsonrpclib): Delete variable. --- gnu/packages/python-xyz.scm | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 528063ae78f..3598b86d157 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17385,29 +17385,6 @@ specified in POSIX.1-2001 and POSIX.1-2008.") (define-public python2-wcwidth (package-with-python2 python-wcwidth)) -(define-public python2-jsonrpclib - (package - (name "python2-jsonrpclib") - (version "0.1.7") - (source (origin - (method url-fetch) - (uri (pypi-uri "jsonrpclib" version)) - (sha256 - (base32 - "02vgirw2bcgvpcxhv5hf3yvvb4h5wzd1lpjx8na5psdmaffj6l3z")))) - (build-system python-build-system) - (arguments - `(#:tests? #f - #:python ,python-2)) - (home-page "https://github.com/joshmarshall/jsonrpclib/") - (synopsis "Implementation of JSON-RPC specification for Python") - (description - "This library is an implementation of the JSON-RPC specification. -It supports both the original 1.0 specification, as well as the -new (proposed) 2.0 spec, which includes batch submission, keyword arguments, -etc.") - (license license:asl2.0))) - (define-public python-chai (package (name "python-chai") From 20f94ed992f4d377021ae395f3e9c48a0d20685d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:46:24 -0400 Subject: [PATCH 0956/1394] gnu: Remove python2-translitcodec. * gnu/packages/python-xyz.scm (python2-translitcodec): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3598b86d157..a12dc2df50e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16174,9 +16174,6 @@ best-effort representations using smaller coded character sets (ASCII, ISO 8859, etc.).") (license license:expat))) -(define-public python2-translitcodec - (package-with-python2 python-translitcodec)) - (define-public python-anyqt (package (name "python-anyqt") From 4d235ef857b82ea2bcfd0ce5d45f85dcf760b4f2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:46:46 -0400 Subject: [PATCH 0957/1394] gnu: Remove python2-isoweek. * gnu/packages/python-xyz.scm (python2-isoweek): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a12dc2df50e..de31e9512d9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22494,9 +22494,6 @@ a notation for identifying weeks; yyyyWww (where the W is a literal). Week instances stringify to this form.") (license license:bsd-3))) -(define-public python2-isoweek - (package-with-python2 python-isoweek)) - (define-public python-pyzbar (package (name "python-pyzbar") From ece691528c39932cc27c7fbaed7dd9a390163933 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:46:53 -0400 Subject: [PATCH 0958/1394] gnu: Remove python2-tblib. * gnu/packages/python-xyz.scm (python2-tblib): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index de31e9512d9..d4e2f476530 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16977,9 +16977,6 @@ multiple processes (imagine multiprocessing, billiard, futures, celery etc). @end enumerate\n") (license license:bsd-3))) -(define-public python2-tblib - (package-with-python2 python-tblib)) - (define-public python-tftpy (package (name "python-tftpy") From 4ac9208922c7a50ba6c98e98ab90a1b875c94b71 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:46:56 -0400 Subject: [PATCH 0959/1394] gnu: Remove python2-smmap. * gnu/packages/python-xyz.scm (python2-smmap): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d4e2f476530..cc8c4c4c7eb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21315,9 +21315,6 @@ class ShellOutSSHClientTests")))) window memory map manager.") (license license:bsd-3))) -(define-public python2-smmap - (package-with-python2 python-smmap)) - (define-public python-regex (package (name "python-regex") From 87ef43f0152abc554584eb9137637d4467557a1b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 17:47:04 -0400 Subject: [PATCH 0960/1394] gnu: Remove python2-isort. * gnu/packages/python-xyz.scm (python2-isort): Delete variable. --- gnu/packages/python-xyz.scm | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cc8c4c4c7eb..939cef37bf2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20115,16 +20115,7 @@ builds partial trees by inspecting living objects.") imports alphabetically, and automatically separated into sections. It provides a command line utility, a python library and plugins for various editors.") - (license license:expat) - (properties `((python2-variant . ,(delay python2-isort)))))) - -(define-public python2-isort - (let ((base (package-with-python2 - (strip-python2-variant python-isort)))) - (package/inherit base - (native-inputs - `(("python2-futures" ,python2-futures) - ,@(package-native-inputs base)))))) + (license license:expat))) (define-public python2-backports-functools-lru-cache (package From f9cd6d905b2f02e5d7a236e7b39454da4d462468 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 20:59:02 -0400 Subject: [PATCH 0961/1394] gnu: non-session-manager: Supersede with new-session-manager. The new-session-manager project seems a more active fork (and the source of non-session-manager is no longer available from its project page). * gnu/packages/music.scm (non-sequencer): Mark as superseded with... (new-session-manager): ... this new package. (synthv1, drumkv1, samplv1, padthv1): Replace non-session-manager with new-session-manager. --- gnu/packages/music.scm | 37 ++++++++++++++++++++++++++++++++----- 1 file changed, 32 insertions(+), 5 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index dc341949059..27e2f437439 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -46,6 +46,7 @@ ;;; Copyright © 2021 Thomas Albers Raviola ;;; Copyright © 2022 Sughosha ;;; Copyright © 2022 Remco van 't Veer +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -1750,6 +1751,31 @@ Sequencer happens on-line, in real-time. Music can be composed live, while the transport is rolling.") (license license:gpl2+)))) +(define-public new-session-manager + (package + (name "new-session-manager") + (version "1.6.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jackaudio/new-session-manager") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ihngqbnc50izfy6x7nhgaah00byk8nl6n5smxbyb8fkhm2s8p21")))) + (build-system meson-build-system) + (native-inputs (list pkg-config)) + (inputs (list fltk jack-2 liblo libx11)) + (home-page "https://new-session-manager.jackaudio.org/") + (synopsis "Music production session management tool") + (description "New Session Manager (NSM) is a tool to assist music +production by grouping standalone programs into sessions. It can be used +create a session, or project, and add programs to it and then use commands to +save, start/stop, hide/show all programs at once, or individually. The +session can be interrupted and easily resumed at a later time.") + (license license:gpl3+))) + (define-public non-session-manager (package (inherit non-sequencer) (name "non-session-manager") @@ -1768,7 +1794,8 @@ transport is rolling.") "The Non Session Manager is an API and an implementation for audio session management. NSM clients use a well-specified OSC protocol to communicate with the session management daemon.") - (license license:gpl2+))) + (license license:gpl2+) + (properties `((superseded . ,new-session-manager))))) (define-public non-mixer (package (inherit non-sequencer) @@ -2255,7 +2282,7 @@ perform creative live mixes with digital music files.") (list jack-1 lv2 alsa-lib - non-session-manager + new-session-manager liblo qtbase-5)) (native-inputs @@ -2287,7 +2314,7 @@ oscillators and stereo effects.") lv2 libsndfile alsa-lib - non-session-manager + new-session-manager liblo qtbase-5)) (native-inputs @@ -2319,7 +2346,7 @@ effects.") lv2 libsndfile alsa-lib - non-session-manager + new-session-manager liblo qtbase-5)) (native-inputs @@ -2350,7 +2377,7 @@ effects.") (list jack-1 lv2 alsa-lib - non-session-manager + new-session-manager liblo fftwf qtbase-5)) From 15fb41cb49b7f2ccd28c27708da9c8724e8c4829 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:17:37 -0400 Subject: [PATCH 0962/1394] gnu: Remove python2-pyliblo. * gnu/packages/audio.scm (python2-pyliblo): Delete variable. --- gnu/packages/audio.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 136004425a1..844d4c63f39 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2594,9 +2594,6 @@ to send and receive OSC messages using a nice and simple Python API. Also included are the command line utilities @code{send_osc} and @code{dump_osc}.") (license license:lgpl2.1+))) -(define-public python2-pyliblo - (package-with-python2 python-pyliblo)) - (define-public python-soundfile (package (name "python-soundfile") From f7363b2479560961f66f2e1eaf055d681c19fce3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:18:09 -0400 Subject: [PATCH 0963/1394] gnu: Remove python2-nosexcover. * gnu/packages/check.scm (python2-nosexcover): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 421b9bf2027..5ba71753dd9 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2666,9 +2666,6 @@ It will honor all the options you pass to the Nose coverage plugin, especially -cover-package.") (license license:expat))) -(define-public python2-nosexcover - (package-with-python2 python-nosexcover)) - (define-public python-discover (package (name "python-discover") From 9f917c945eb4fd2478823d3c73f4a2db30be1b07 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:18:33 -0400 Subject: [PATCH 0964/1394] gnu: Remove python2-sqlalchemy. * gnu/packages/databases.scm (python2-sqlalchemy): Delete variable. --- gnu/packages/databases.scm | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index f90a1b6c747..7be109a6bcf 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3364,30 +3364,6 @@ designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language.") (license license:x11))) -(define-public python2-sqlalchemy - (let ((base (package-with-python2 python-sqlalchemy))) - (package - (inherit base) - (arguments - (substitute-keyword-arguments (package-arguments base) - ((#:phases phases) - #~(modify-phases #$phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-vv" - ;; The memory usage tests are very expensive and run in - ;; sequence; skip them. - "-k" - (string-append - "not test_memusage.py" - ;; This test fails with "AssertionError: Warnings - ;; were not seen [...]". - " and not test_fixture_five"))))))))) - ;; Do not use pytest-xdist, which is broken for Python 2. - (native-inputs (modify-inputs (package-native-inputs base) - (delete "python-pytest-xdist")))))) - (define-public python-sqlalchemy-stubs (package (name "python-sqlalchemy-stubs") From 8ca8ba17619e8d7852836d2bc76d9cc191833981 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:18:36 -0400 Subject: [PATCH 0965/1394] gnu: Remove python2-efl. * gnu/packages/enlightenment.scm (python2-efl): Delete variable. --- gnu/packages/enlightenment.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index 7be6304a5ee..12d5a56d6a0 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -439,9 +439,6 @@ embedded systems.") Libraries stack (eo, evas, ecore, edje, emotion, ethumb and elementary).") (license license:lgpl3))) -(define-public python2-efl - (package-with-python2 python-efl)) - (define-public edi (package (name "edi") From e19a8130c48966a587576e13cf0aa449275687f2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:18:39 -0400 Subject: [PATCH 0966/1394] gnu: Remove python2-mnemonic. * gnu/packages/finance.scm (python2-mnemonic): Delete variable. --- gnu/packages/finance.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index d528f2662d3..0f9a50045b9 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -950,9 +950,6 @@ settings.") of Bitcoin BIP-0039.") (license license:expat))) -(define-public python2-mnemonic - (package-with-python2 python-mnemonic)) - (define-public python-ledgerblue (package (name "python-ledgerblue") From 23435f257027e681362c62da8d2d07c15cd3af4c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:18:52 -0400 Subject: [PATCH 0967/1394] gnu: Remove python2-pygame. * gnu/packages/game-development.scm (python2-pygame): Delete variable. --- gnu/packages/game-development.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 961b396ea7d..b13d015ba42 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -1206,9 +1206,6 @@ to create fully featured games and multimedia programs in the python language.") license:public-domain license:lgpl2.1+)))) -(define-public python2-pygame - (package-with-python2 python-pygame)) - (define-public python-pygame-sdl2 (let ((real-version "2.1.0") (renpy-version "7.4.11")) From 7acc19900573ce14f6742fb86f1eadb29c6e3179 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:19:24 -0400 Subject: [PATCH 0968/1394] gnu: Remove python2-hidapi. * gnu/packages/libusb.scm (python2-hidapi): Delete variable. --- gnu/packages/libusb.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/libusb.scm b/gnu/packages/libusb.scm index 8c34956feeb..45cc2cda0de 100644 --- a/gnu/packages/libusb.scm +++ b/gnu/packages/libusb.scm @@ -621,6 +621,3 @@ HID-Class devices.") (license:non-copyleft "https://github.com/trezor/cython-hidapi/blob/master/LICENSE-orig.txt" "You are free to use cython-hidapi code for any purpose."))))) - -(define-public python2-hidapi - (package-with-python2 python-hidapi)) From e0c152e4a21aa70e6e40ffe09177fbc16b45f95d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:19:27 -0400 Subject: [PATCH 0969/1394] gnu: Remove python2-notmuch. * gnu/packages/mail.scm (python2-notmuch): Delete variable. --- gnu/packages/mail.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 7dcc1973138..f1af69faab8 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1482,9 +1482,6 @@ useful for email address completion.") and search library.") (license license:gpl3+))) -(define-public python2-notmuch - (package-with-python2 python-notmuch)) - (define-public python-notmuch2 (package (inherit python-notmuch) From c0587a5a9156c861a512ed224f1eeff26118c32f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:19:37 -0400 Subject: [PATCH 0970/1394] gnu: Remove python2-pypdf. * gnu/packages/pdf.scm (python2-pypdf): Delete variable. --- gnu/packages/pdf.scm | 22 ---------------------- 1 file changed, 22 deletions(-) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 5da1e96e980..a0c4b4dc152 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -1237,28 +1237,6 @@ manipulation in memory. It is therefore a useful tool for websites that manage or manipulate PDFs.") (license license:bsd-3))) -(define-public python2-pypdf - (package - (name "python2-pypdf") - (version "1.13") - (source (origin - (method url-fetch) - (uri (pypi-uri "pyPdf" version)) - (sha256 - (base32 - "0fqfvamir7k41w84c73rghzkiv891gdr17q5iz4hgbf6r71y9v9s")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; no tests - #:python ,python-2)) - (home-page "http://pybrary.net/pyPdf/") - (synopsis "Pure Python PDF toolkit") - (description "PyPDF2 is a pure Python PDF toolkit. - -Note: This module isn't maintained anymore. For new projects please use -python-pypdf2 instead.") - (license license:bsd-3))) - (define-public pdfarranger (package (name "pdfarranger") From 446e3b0ac0e64a1ee302e2767f61cccf7241d720 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:20:00 -0400 Subject: [PATCH 0971/1394] gnu: Remove python2-axolotl. * gnu/packages/python-crypto.scm (python2-axolotl): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 502a809d293..089dfdec382 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -756,9 +756,6 @@ is a ratcheting forward secrecy protocol that works in synchronous and asynchronous messaging environments.") (license license:gpl3))) -(define-public python2-axolotl - (package-with-python2 python-axolotl)) - (define-public python-pyaes (package From 7e27e99ea8a7b402591d741c430fdfc342eddef6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:20:16 -0400 Subject: [PATCH 0972/1394] gnu: Remove python2-ecpy. * gnu/packages/python-crypto.scm (python2-ecpy): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 089dfdec382..1eea11da989 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -900,9 +900,6 @@ of improving usability, security and speed.") Python.") (license license:asl2.0))) -(define-public python2-ecpy - (package-with-python2 python-ecpy)) - (define-public python-josepy (package (name "python-josepy") From 000663e05fad86ef4c94c7434d5e438ea3e05c0d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:20:20 -0400 Subject: [PATCH 0973/1394] gnu: Remove python2-ecdsa. * gnu/packages/python-crypto.scm (python2-ecdsa): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 1eea11da989..a270d0f78f2 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -261,9 +261,6 @@ messages, and verify the signatures. The keys and signatures are very short, making them easy to handle and incorporate into other protocols.") (license license:expat))) -(define-public python2-ecdsa - (package-with-python2 python-ecdsa)) - ;;; Pycrypto is abandoned upstream: ;;; ;;; https://github.com/dlitz/pycrypto/issues/173 From 9f97098f24a9d49ad51faa9eac1af0bb296e1bc1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:21:01 -0400 Subject: [PATCH 0974/1394] gnu: Remove python2-httplib2. * gnu/packages/python-web.scm (python2-httplib2): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 6b7585d10e3..f1655bbf851 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -811,9 +811,6 @@ over a different origin than that of the web application.") other HTTP libraries.") (license license:expat))) -(define-public python2-httplib2 - (package-with-python2 python-httplib2)) - (define-public httpie (package (name "httpie") From 1db8ff4b52edae3584ea108e8984ce135f2329db Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:21:10 -0400 Subject: [PATCH 0975/1394] gnu: Remove python2-zope-component. * gnu/packages/python-web.scm (python2-zope-component): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index f1655bbf851..79b7ab429e8 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2575,9 +2575,6 @@ facilities for defining, registering and looking up components.") (define-public python-zope-component-bootstrap (python-zope-bootstrap-package python-zope-component)) -(define-public python2-zope-component - (package-with-python2 python-zope-component)) - (define-public python-zope-deferredimport (package (name "python-zope-deferredimport") From 87c15103e6fc20137162ffa7d0306b150ff874b5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:21:15 -0400 Subject: [PATCH 0976/1394] gnu: Remove python2-zope-location. * gnu/packages/python-web.scm (python2-zope-location): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 79b7ab429e8..5374390cb14 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2489,9 +2489,6 @@ Zope3, which are are special objects that have a structural location.") (define-public python-zope-location-bootstrap (python-zope-bootstrap-package python-zope-location)) -(define-public python2-zope-location - (package-with-python2 python-zope-location)) - (define-public python-zope-security (package (name "python-zope-security") From 08b98d7ce38627ccf63279e708ade2344b52a077 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:21:22 -0400 Subject: [PATCH 0977/1394] gnu: Remove python2-random2. * gnu/packages/python-xyz.scm (python2-random2): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 939cef37bf2..8c3d4556a93 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18984,9 +18984,6 @@ JSON) codec.") between the different Python versions.") (license license:psfl))) -(define-public python2-random2 - (package-with-python2 python-random2)) - (define-public python-snowballstemmer (package (name "python-snowballstemmer") From 85fcfd59d439d1c480e1eb3cd4719ab8f718ae33 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:21:33 -0400 Subject: [PATCH 0978/1394] gnu: Remove python2-pynamecheap. * gnu/packages/python-xyz.scm (python2-pynamecheap): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8c3d4556a93..b8cdb326d84 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23613,9 +23613,6 @@ environments.") "PyNamecheap is a Namecheap API client in Python.") (license license:expat))) -(define-public python2-pynamecheap - (package-with-python2 python-pynamecheap)) - (define-public python-dns-lexicon (package (name "python-dns-lexicon") From 359d5ebf10a29fb7acffcd787ff46786f03dba56 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:21:37 -0400 Subject: [PATCH 0979/1394] gnu: Remove python2-reparser. * gnu/packages/python-xyz.scm (python2-reparser): Delete variable. --- gnu/packages/python-xyz.scm | 8 -------- 1 file changed, 8 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b8cdb326d84..1756b67953d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24447,14 +24447,6 @@ are not supported.") on regular expressions.") (license license:expat))) -(define-public python2-reparser - (let ((reparser (package-with-python2 - (strip-python2-variant python-reparser)))) - (package/inherit reparser - (propagated-inputs - `(("python2-enum34" ,python2-enum34) - ,@(package-propagated-inputs reparser)))))) - (define-public python-retrying (package (name "python-retrying") From 8f3d4178e7abe9747d0f50f9b3fadd2af31f1671 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:21:44 -0400 Subject: [PATCH 0980/1394] gnu: Remove python2-gyp. * gnu/packages/python-xyz.scm (python2-gyp): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1756b67953d..d42434bd876 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22374,9 +22374,6 @@ It can be used to generate XCode projects, Visual Studio projects, Ninja build files, and Makefiles.") (license license:bsd-3)))) -(define-public python2-gyp - (package-with-python2 python-gyp)) - (define-public python-whatever (package (name "python-whatever") From 83462e1f4cc303dbbd168392c8166b3b6e2dada0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:21:50 -0400 Subject: [PATCH 0981/1394] gnu: Remove python2-schema. * gnu/packages/python-xyz.scm (python2-schema): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d42434bd876..634f31baf4e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3773,9 +3773,6 @@ services or command-line parsing, converted from JSON/YAML (or something else) to Python data-types.") (license license:psfl))) -(define-public python2-schema - (package-with-python2 python-schema)) - (define-public python-schema-0.5 (package (inherit python-schema) (version "0.5.0") From 62aeb46d0d71053e7213fcd1dc4c428cb4503773 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:21:57 -0400 Subject: [PATCH 0982/1394] gnu: Remove python2-args. * gnu/packages/python-xyz.scm (python2-args): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 634f31baf4e..4a1c01dffa7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14923,9 +14923,6 @@ files for use with Python.") "This library provides a Python module to parse command-line arguments.") (license license:bsd-3))) -(define-public python2-args - (package-with-python2 python-args)) - (define-public python-clint (package (name "python-clint") From 2c7bdb3f250ea26c4b7f428a665fd6df538a47a0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:22:12 -0400 Subject: [PATCH 0983/1394] gnu: Remove python2-pip. * gnu/packages/python-xyz.scm (python2-pip): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4a1c01dffa7..880da9784d9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -13177,9 +13177,6 @@ responses, rather than doing any computation.") Python Package Index (PyPI).") (license license:expat))) -(define-public python2-pip - (package-with-python2 python-pip)) - ;;; Variant used to break a dependency cycle with ;;; python-pytest-perf-bootstrap. (define-public python-pip-run-bootstrap From b37fa3b15f2f8dc09553ec63753889684fa3e76d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:22:16 -0400 Subject: [PATCH 0984/1394] gnu: Remove python2-schedule. * gnu/packages/python-xyz.scm (python2-schedule): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 880da9784d9..41d137b5caa 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2744,9 +2744,6 @@ any other callable) periodically at pre-determined intervals using a simple, human-friendly syntax.") (license license:expat))) -(define-public python2-schedule - (package-with-python2 python-schedule)) - (define-public python-scour (package (name "python-scour") From 0769dda0201b6df61749ebefeb8c1a962228afc5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:22:19 -0400 Subject: [PATCH 0985/1394] gnu: Remove python2-ua-parser. * gnu/packages/python-xyz.scm (python2-ua-parser): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 41d137b5caa..bb279c089ac 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9705,9 +9705,6 @@ toolkit. Use it to build trees of widgets.") "@code{ua-parser} is a Python port of Browserscope's user agent parser.") (license license:asl2.0))) -(define-public python2-ua-parser - (package-with-python2 python-ua-parser)) - (define-public python-user-agents (package (name "python-user-agents") From 6e82d2fa0d5f250332e05e757843684c2475a44d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:22:23 -0400 Subject: [PATCH 0986/1394] gnu: Remove python2-xdo. * gnu/packages/python-xyz.scm (python2-xdo): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index bb279c089ac..2b91bc0be90 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15734,9 +15734,6 @@ input. (Note that this is mostly a legacy library; you may wish to look at python-xdo for newer bindings.)") (license license:bsd-3))) -(define-public python2-xdo - (package-with-python2 python-xdo)) - (define-public python-xdoctest (package (name "python-xdoctest") From 3ce963254b8349c85157e9fcecc8e8afbe4236ac Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:22:33 -0400 Subject: [PATCH 0987/1394] gnu: python-seaborn: Update to 0.11.2. * gnu/packages/python-xyz.scm (python-seaborn): Update to 0.11.2. --- gnu/packages/python-xyz.scm | 71 ++++++++++++++++--------------------- 1 file changed, 31 insertions(+), 40 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2b91bc0be90..7601f458835 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10349,48 +10349,39 @@ SVG, EPS, PNG and terminal output.") (package (name "python-seaborn") (version "0.11.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "seaborn" version)) - (sha256 - (base32 "1xpl3zb945sihsiwm9q1yyx84sakk1phcg0fprj6i0j0dllfjifg")) - (patches (search-patches "python-seaborn-kde-test.patch" - "python-seaborn-2690.patch")))) + (source (origin + (method url-fetch) + (uri (pypi-uri "seaborn" version)) + (sha256 + (base32 + "1xpl3zb945sihsiwm9q1yyx84sakk1phcg0fprj6i0j0dllfjifg")) + (patches (search-patches "python-seaborn-kde-test.patch" + "python-seaborn-2690.patch")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-more-tests - (lambda _ - (substitute* "seaborn/tests/test_distributions.py" - (("get_contour_color\\(ax\\.collections\\[0\\]\\)") - "get_contour_color(ax.collections[0])") - (("c\\.get_color\\(\\)") "get_contour_color(c)") - - ;; These three are borked and have been fixed upstream, but - ;; there's no simple patch we could apply here, so we just - ;; disable them. - (("def test_hue_ignores_cmap") - "def skip_test_hue_ignores_cmap") - (("def test_fill_artists") - "def skip_test_fill_artists") - (("def test_with_rug") - "def skip_test_with_rug")))) - (add-before 'check 'start-xserver - (lambda _ - ;; There must be a running X server and make check doesn't - ;; start one. Therefore we must do it. - (system "Xvfb :1 &") - (setenv "DISPLAY" ":1"))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "seaborn"))))))) - (propagated-inputs - (list python-pandas python-matplotlib python-numpy python-scipy)) - (native-inputs - (list python-pytest xorg-server-for-tests)) + `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-more-tests + (lambda _ + (substitute* "seaborn/tests/test_distributions.py" + (("get_contour_color\\(ax\\.collections\\[0\\]\\)") + "get_contour_color(ax.collections[0])") + (("c\\.get_color\\(\\)") "get_contour_color(c)") + (("def test_hue_ignores_cmap") + "def skip_test_hue_ignores_cmap") + (("def test_fill_artists") + "def skip_test_fill_artists") + (("def test_with_rug") "def skip_test_with_rug")))) + (add-before 'check 'start-xserver + (lambda _ + (system "Xvfb :1 &") + (setenv "DISPLAY" ":1"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "seaborn"))))))) + (propagated-inputs (list python-pandas python-matplotlib python-numpy + python-scipy)) + (native-inputs (list python-pytest xorg-server-for-tests)) (home-page "https://seaborn.pydata.org/") (synopsis "Statistical data visualization") (description From 08a63ca93e76ed6fde37024ff522effbfdf0766d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:22:37 -0400 Subject: [PATCH 0988/1394] gnu: Remove python2-zeroconf. * gnu/packages/python-xyz.scm (python2-zeroconf): Delete variable. --- gnu/packages/python-xyz.scm | 36 ------------------------------------ 1 file changed, 36 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7601f458835..821c330670d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -25069,42 +25069,6 @@ enumeration library in Python.") (Bonjour/Avahi compatible).") (license license:lgpl2.1+))) -(define-public python2-zeroconf - (package - (name "python2-zeroconf") - - ;; This is the last version that supports Python 2.x. - (version "0.19.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "zeroconf" version)) - (sha256 - (base32 - "0ykzg730n915qbrq9bn5pn06bv6rb5zawal4sqjyfnjjm66snkj3")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-requires - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "setup.py" - (("enum-compat") - "enum34")) - #t))))) - (native-inputs - `(("python2-six" ,python2-six) - ("python2-enum32" ,python2-enum34) - ("python2-netifaces" ,python2-netifaces) - ("python2-typing" ,python2-typing))) - (home-page "https://github.com/jstasiak/python-zeroconf") - (synopsis "Pure Python mDNS service discovery") - (description - "Pure Python multicast DNS (mDNS) service discovery library (Bonjour/Avahi -compatible).") - (license license:lgpl2.1+))) - (define-public python-bsddb3 (package (name "python-bsddb3") From 994f5a2843a7b5a4539e28ac71cdedb9a87c087a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:22:40 -0400 Subject: [PATCH 0989/1394] gnu: Remove python2-botocore. * gnu/packages/python-xyz.scm (python2-botocore): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 821c330670d..838c0b1001e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15626,9 +15626,6 @@ This software is unmaintained, and new projects should use @code{boto3} instead. interface to the Amazon Web Services (AWS) API.") (license license:asl2.0))) -(define-public python2-botocore - (package-with-python2 python-botocore)) - (define-public python-boto3 (package (name "python-boto3") From 76e08a34c8f0d5a49f36909ba7e247894b23ae8f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:22:43 -0400 Subject: [PATCH 0990/1394] gnu: Remove python2-email-validator. * gnu/packages/python-xyz.scm (python2-email-validator): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 838c0b1001e..996e2574e89 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17902,9 +17902,6 @@ simple, lightweight implementation.") "This library validates email address syntax and deliverability.") (license license:cc0))) -(define-public python2-email-validator - (package-with-python2 python-email-validator)) - (define-public python-ukpostcodeparser (package (name "python-ukpostcodeparser") From bb5a50d6a274bb2724ee365191bd6ab9083abd6b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:22:56 -0400 Subject: [PATCH 0991/1394] gnu: Remove python2-pyjwt. * gnu/packages/python-xyz.scm (python2-pyjwt): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 996e2574e89..4a2e3434a37 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3917,9 +3917,6 @@ memory usage and transliteration quality.") "PyJWT is a JSON Web Token implementation written in Python.") (license license:expat))) -(define-public python2-pyjwt - (package-with-python2 python-pyjwt)) - (define-public python-pymsgbox (package (name "python-pymsgbox") From 5ab8206491589e9e951498faba25de117c058ee8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:23:07 -0400 Subject: [PATCH 0992/1394] gnu: Remove python2-distutils-extra. * gnu/packages/python-xyz.scm (python2-distutils-extra): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4a2e3434a37..8188ff6333c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7234,9 +7234,6 @@ gettext support, themed icons, and scrollkeeper-based documentation into Python's distutils.") (license license:gpl2))) -(define-public python2-distutils-extra - (package-with-python2 python-distutils-extra)) - (define-public python2-elib.intl (package (name "python2-elib.intl") From 273ec2dc3b2c38a136cd7e184a625ea74b46ce88 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:23:11 -0400 Subject: [PATCH 0993/1394] gnu: Remove python2-schematics. * gnu/packages/python-xyz.scm (python2-schematics): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8188ff6333c..8bfc64a4d15 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18724,9 +18724,6 @@ JSON) codec.") (description "Python Data Structures for Humans.") (license license:bsd-3))) -(define-public python2-schematics - (package-with-python2 python-schematics)) - (define-public python-odfpy (package (name "python-odfpy") From 23936586f4dc1b4aa07cddc1ef4470811d1ec242 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:23:14 -0400 Subject: [PATCH 0994/1394] gnu: Remove python2-rsa. * gnu/packages/python-xyz.scm (python2-rsa): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8bfc64a4d15..3198a71e679 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15300,9 +15300,6 @@ library as well as on the command line.") (home-page "https://stuvel.eu/rsa") (license license:asl2.0))) -(define-public python2-rsa - (package-with-python2 python-rsa)) - (define-public python-pluggy (package (name "python-pluggy") From ae657ec626e58c095d072a4fdbef9b94f904e0ca Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:23:31 -0400 Subject: [PATCH 0995/1394] gnu: Remove python2-grako. * gnu/packages/python-xyz.scm (python2-grako): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3198a71e679..de65a8626e4 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8150,9 +8150,6 @@ Python language binding specification.") memoizing PEG/Packrat parser in Python.") (license license:bsd-3))) -(define-public python2-grako - (package-with-python2 python-grako)) - (define-public python-grandalf (package (name "python-grandalf") From accabb385a5539237047e98daa8f7753cf4d7234 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:23:38 -0400 Subject: [PATCH 0996/1394] gnu: Remove python2-whatever. * gnu/packages/python-xyz.scm (python2-whatever): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index de65a8626e4..db844c2b250 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22354,9 +22354,6 @@ files, and Makefiles.") functions by partial application of operators.") (license license:bsd-3))) -(define-public python2-whatever - (package-with-python2 python-whatever)) - (define-public python-funcy (package (name "python-funcy") From 1962c0dd71ad27e94d5159ff6a3eef5351de11d5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:23:50 -0400 Subject: [PATCH 0997/1394] gnu: Remove python2-blosc. * gnu/packages/python-xyz.scm (python2-blosc): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index db844c2b250..79f5b0efffb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24226,9 +24226,6 @@ regular-spaced values, etc. This Python package wraps the Blosc library.") (license license:bsd-3))) -(define-public python2-blosc - (package-with-python2 python-blosc)) - (define-public python-partd (package (name "python-partd") From 15e9d9aab3290bf560f3d93b5f084b09bf1bec21 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:24:02 -0400 Subject: [PATCH 0998/1394] gnu: Remove python2-xcffib. * gnu/packages/python-xyz.scm (python2-xcffib): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 79f5b0efffb..9c7569901e8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7974,9 +7974,6 @@ any machine that can run Python.") support for Python 3 and PyPy. It is based on cffi.") (license license:expat))) -(define-public python2-xcffib - (package-with-python2 python-xcffib)) - (define-public python-cairocffi (package (name "python-cairocffi") From 8084ae2e6abf382d42dc739d428a7f09db0f98a4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:24:05 -0400 Subject: [PATCH 0999/1394] gnu: Remove python2-pyev. * gnu/packages/python-xyz.scm (python2-pyev): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9c7569901e8..8549773944c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19114,9 +19114,6 @@ JSON) codec.") (description "Pyev provides a Python interface to libev.") (license license:gpl3))) -(define-public python2-pyev - (package-with-python2 python-pyev)) - (define-public python-imagesize (package (name "python-imagesize") From d9205205609a4cb3ec17fabe02f53193d2ba4eb4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:24:09 -0400 Subject: [PATCH 1000/1394] gnu: Remove python2-capturer. * gnu/packages/python-xyz.scm (python2-capturer): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8549773944c..dc82d71baae 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2424,9 +2424,6 @@ to the terminal in real time but is also available to the Python program for additional processing.") (license license:expat))) -(define-public python2-capturer - (package-with-python2 python-capturer)) - (define-public python-case (package (name "python-case") From c6f247617187e45ad7421b05a22e245ab65f4fd8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:24:15 -0400 Subject: [PATCH 1001/1394] gnu: Remove python2-drmaa. * gnu/packages/python-xyz.scm (python2-drmaa): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index dc82d71baae..db564e2d65e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8118,9 +8118,6 @@ submission and control. This package is an implementation of the DRMAA 1.0 Python language binding specification.") (license license:bsd-3))) -(define-public python2-drmaa - (package-with-python2 python-drmaa)) - (define-public python-grako (package (name "python-grako") From b2750c2172e493d65915706c9fd37b9a1bebd176 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:24:19 -0400 Subject: [PATCH 1002/1394] gnu: Remove python2-sympy. * gnu/packages/python-xyz.scm (python2-sympy): Delete variable. --- gnu/packages/python-xyz.scm | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index db564e2d65e..b268695b3c0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10547,17 +10547,6 @@ full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible.") (license license:bsd-3))) -(define-public python2-sympy - (package - (inherit (package-with-python2 python-sympy)) - (version "1.5.1") ; last release for python2 - (source - (origin - (method url-fetch) - (uri (pypi-uri "sympy" version)) - (sha256 - (base32 "0zjfbxlkazzh9z22gf62azrkipb2xw7mpzjz3wl1az9893bh2yfp")))))) - (define-public python-q (package (name "python-q") From 538eadceb27fe43324dab94fdd873b8cda787b56 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:24:22 -0400 Subject: [PATCH 1003/1394] gnu: Remove python2-pybugz. * gnu/packages/python-xyz.scm (python2-pybugz): Delete variable. --- gnu/packages/python-xyz.scm | 28 ---------------------------- 1 file changed, 28 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b268695b3c0..481e9f90c02 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2976,34 +2976,6 @@ commands.") "http://docs.python.org/2/license.html" "Like \"CWI LICENSE AGREEMENT FOR PYTHON 0.9.0 THROUGH 1.2\".")))) -(define-public python2-pybugz - (package - (name "python2-pybugz") - (version "0.6.11") - (source (origin - (method url-fetch) - (uri (string-append - "http://bits.liquidx.net/projects/pybugz/pybugz-" - version ".tar.gz")) - (sha256 - (base32 - "17ni00p08gp5lkxlrrcnvi3x09fmajnlbz4da03qcgl9q21ym4jd")) - (patches (search-patches "pybugz-stty.patch" - "pybugz-encode-error.patch")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; SyntaxError with Python 3 - #:tests? #f)) ; no 'test' sub-command - (propagated-inputs - `(("element-tree" ,python2-element-tree))) - (synopsis "Python and command-line interface to Bugzilla") - (description - "PyBugz is a Python library and command-line tool to query the Bugzilla -bug tracking system. It is meant as an aid to speed up interaction with the -bug tracker.") - (home-page "http://www.liquidx.net/pybugz/") - (license license:gpl2))) - (define-public python-enum34 (package (name "python-enum34") From 4dac0380f41220663ed27e148d6522ba10a3057d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:24:27 -0400 Subject: [PATCH 1004/1394] gnu: Remove python2-bz2file. * gnu/packages/python-xyz.scm (python2-bz2file): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 481e9f90c02..150579b2914 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16711,9 +16711,6 @@ standard library's @code{bz2} module, including features from the latest development version of CPython that are not available in older releases.") (license license:asl2.0))) -(define-public python2-bz2file - (package-with-python2 python-bz2file)) - (define-public python-future (package (name "python-future") From 627b81c15993e4622c2f8e05e56b1f8878bf534a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:24:40 -0400 Subject: [PATCH 1005/1394] gnu: Remove python2-ttystatus. * gnu/packages/python-xyz.scm (python2-ttystatus): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 150579b2914..1128817bead 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19868,9 +19868,6 @@ JSON) codec.") if it does not fit, and resized if the terminal size changes.") (license license:gpl3+))) -(define-public python2-ttystatus - (package-with-python2 python-ttystatus)) - (define-public python-astroid (package (name "python-astroid") From a1f4dcacb3821721522ddf6012fdd35ed349900c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:24:44 -0400 Subject: [PATCH 1006/1394] gnu: Remove python2-pystache. * gnu/packages/python-xyz.scm (python2-pystache): Delete variable. --- gnu/packages/python-xyz.scm | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1128817bead..6b54bf2f94f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4202,20 +4202,7 @@ templates. A format string can be provided to control the output.") (description "Pystache is a Python implementation of the framework agnostic, logic-free templating system Mustache.") - (license license:expat) - (properties `((python2-variant . ,(delay python2-pystache)))))) - -(define-public python2-pystache - (let ((base (package-with-python2 - (strip-python2-variant python-pystache)))) - (package/inherit base - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "python" "test_pystache.py"))))))))) + (license license:expat))) (define-public python-pystitcher (package From fc43de306371a52c0865d103a865daf14ae3c9ad Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:24:51 -0400 Subject: [PATCH 1007/1394] gnu: Remove python2-rply. * gnu/packages/python-xyz.scm (python2-rply): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6b54bf2f94f..b78a497cb5f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14884,9 +14884,6 @@ works with RPython. It is a more-or-less direct port of David Bazzley's PLY, with a new public API, and RPython support.") (license license:bsd-3))) -(define-public python2-rply - (package-with-python2 python-rply)) - (define-public python-hy (package (name "python-hy") From da2f9c95ab021c3db47e525b88a0f37772c04b45 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:24:55 -0400 Subject: [PATCH 1008/1394] gnu: Remove python2-serpent. * gnu/packages/python-xyz.scm (python2-serpent): Delete variable. --- gnu/packages/python-xyz.scm | 8 -------- 1 file changed, 8 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b78a497cb5f..2ef1e242484 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1903,16 +1903,8 @@ to rebuild the original object tree. Because only safe literals are encoded, it is safe to send serpent data to other machines, such as over the network.") - (properties `((python2-variant . ,(delay python2-serpent)))) (license license:expat))) -(define-public python2-serpent - (let ((base (package-with-python2 (strip-python2-variant python-serpent)))) - (package/inherit base - (propagated-inputs - `(("python-enum34" ,python2-enum34) - ,@(package-propagated-inputs base)))))) - (define-public python-setuptools (package (name "python-setuptools") From 04624f006f447b28319901d7f5d5858000ea8bf1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:25:11 -0400 Subject: [PATCH 1009/1394] gnu: Remove python2-incremental. * gnu/packages/python-xyz.scm (python2-incremental): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2ef1e242484..079b943c0e7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19618,9 +19618,6 @@ JSON) codec.") projects.") (license license:expat))) -(define-public python2-incremental - (package-with-python2 python-incremental)) - (define-public python-invoke (package (name "python-invoke") From ff1b08f7c49ad0d7029093847b7c697fee4a04ce Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:25:38 -0400 Subject: [PATCH 1010/1394] gnu: Remove python2-steadymark. * gnu/packages/python-xyz.scm (python2-steadymark): Delete variable. --- gnu/packages/python-xyz.scm | 37 ------------------------------------- 1 file changed, 37 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 079b943c0e7..3e9d53b7206 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20579,43 +20579,6 @@ while only declaring the test-specific fields.") (define-public python2-misaka (package-with-python2 python-misaka)) -(define-public python2-steadymark - ;; This is forced into being a python2 only variant - ;; due to its dependence on couleur that has no support - ;; for python3 - (package - (name "python2-steadymark") - (version "0.7.3") - (source - (origin - (method url-fetch) - (uri (pypi-uri "steadymark" version)) - (sha256 - (base32 - "1640i9g8dycql3cc8j0bky0jkzj0q39blfbp4lsgpkprkfgcdk8v")))) - (build-system python-build-system) - (native-inputs - (list python2-couleur python2-sure python2-misaka)) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-before 'build 'patch-setup-py - (lambda _ - ;; Update requirements from dependency==version - ;; to dependency>=version - (substitute* "setup.py" - (("==") ">=")) - #t))))) - (home-page "https://github.com/gabrielfalcao/steadymark") - (synopsis "Markdown-based test runner for python") - (description - "@code{Steadymark} allows documentation to be written in github-flavoured - markdown. The documentation may contain snippets of code surrounded by python - code blocks and @code{Steadymark} will find these snippets and run them, making - sure that there are no old malfunctional examples in the documentation examples.") - (license license:expat))) - (define-public python-jsonpointer (package (name "python-jsonpointer") From 34f6230b886866a50cdb0e0c06bfb7f605df04f3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:25:45 -0400 Subject: [PATCH 1011/1394] gnu: Remove python2-waitress. * gnu/packages/python-xyz.scm (python2-waitress): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3e9d53b7206..dc9ffa382df 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15717,9 +15717,6 @@ templates into Python modules.") server with very acceptable performance.") (license license:zpl2.1))) -(define-public python2-waitress - (package-with-python2 python-waitress)) - (define-public python-whichcraft (package (name "python-whichcraft") From 3fbcab1e38e42848175f7cd3583b76637f2f4d80 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:25:49 -0400 Subject: [PATCH 1012/1394] gnu: Remove python2-radon. * gnu/packages/python-xyz.scm (python2-radon): Delete variable. --- gnu/packages/python-xyz.scm | 9 --------- 1 file changed, 9 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index dc9ffa382df..4b32d406c35 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20481,17 +20481,8 @@ while only declaring the test-specific fields.") @item Halstead metrics (all of them) @item the Maintainability Index (a Visual Studio metric) @end itemize") - (properties `((python2-variant . ,(delay python2-radon)))) (license license:expat))) -(define-public python2-radon - (let ((base (package-with-python2 (strip-python2-variant python-radon)))) - (package/inherit base - (propagated-inputs - `(("python-configparser" ,python2-configparser) - ("python-future" ,python2-future) - ,@(package-propagated-inputs base)))))) - (define-public python-sure (package (name "python-sure") From 5bc038d2229d3f9059c28090f17108ee851f26bc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 21:25:58 -0400 Subject: [PATCH 1013/1394] gnu: Remove python2-mimeparse. * gnu/packages/python-xyz.scm (python2-mimeparse): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4b32d406c35..b13a7f17148 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3227,9 +3227,6 @@ documentation-related tools used by the Astropy project.") matching them against a list of media-ranges.") (license license:expat))) -(define-public python2-mimeparse - (package-with-python2 python-mimeparse)) - (define-public python-miniboa (package (name "python-miniboa") From 1143a16830c2e0ee5d8f95835d25b68843513114 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:18:17 -0400 Subject: [PATCH 1014/1394] gnu: Remove python2-coverage-test-runner. * gnu/packages/check.scm (python2-coverage-test-runner): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 5ba71753dd9..40c90a03f92 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2504,9 +2504,6 @@ unit tests and failing them if the unit test module does not exercise all statements in the module it tests.") (license license:gpl3+))) -(define-public python2-coverage-test-runner - (package-with-python2 python-coverage-test-runner)) - (define-public python-pylint (package (name "python-pylint") From 1a6eb0d6fec040d1de5664ccaf35c2051046bad5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:18:46 -0400 Subject: [PATCH 1015/1394] gnu: Remove python2-pygame-sdl2. * gnu/packages/game-development.scm (python2-pygame-sdl2): Delete variable. --- gnu/packages/game-development.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index b13d015ba42..4c1b97f0411 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -1257,9 +1257,6 @@ While it aims to be used as a drop-in replacement, it appears to be developed mainly for Ren'py.") (license (list license:lgpl2.1 license:zlib))))) -(define-public python2-pygame-sdl2 - (package-with-python2 python-pygame-sdl2)) - (define-public renpy (package (name "renpy") From cf03e0d290688d0620782b5e6109a17800d591c5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:19:21 -0400 Subject: [PATCH 1016/1394] gnu: Remove python2-protobuf. * gnu/packages/protobuf.scm (python2-protobuf): Delete variable. --- gnu/packages/protobuf.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm index d6cc03faf38..f66e3469b8a 100644 --- a/gnu/packages/protobuf.scm +++ b/gnu/packages/protobuf.scm @@ -285,9 +285,6 @@ language-neutral, platform-neutral extensible mechanism for serializing structured data.") (license license:expat))) -(define-public python2-protobuf - (package-with-python2 python-protobuf)) - ;; For tensorflow. (define-public python-protobuf-3.6 (package From b6cd6bee626fe87718817b657ddbc2b3afbb0204 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:20:35 -0400 Subject: [PATCH 1017/1394] gnu: Remove python2-zope-proxy. * gnu/packages/python-web.scm (python2-zope-proxy): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 5374390cb14..52bb55ac3e4 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2435,9 +2435,6 @@ brokering, etc.) for which the proxy is responsible.") (define-public python-zope-proxy-bootstrap (python-zope-bootstrap-package python-zope-proxy)) -(define-public python2-zope-proxy - (package-with-python2 python-zope-proxy)) - (define-public python-zope-hookable (package (name "python-zope-hookable") From 6b90432e79b9c49584099170d05dca2ccdc77bef Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:20:41 -0400 Subject: [PATCH 1018/1394] gnu: Remove python2-objgraph. * gnu/packages/python-xyz.scm (python2-objgraph): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b13a7f17148..fa326cb2f7c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16928,9 +16928,6 @@ are synchronized with data exchanges on \"channels\".") graphviz.") (license license:expat))) -(define-public python2-objgraph - (package-with-python2 python-objgraph)) - (define-public python-gevent (package (name "python-gevent") From 87bd8bd1dd88c4c4683275f99e67d1b54e6f79c1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:20:54 -0400 Subject: [PATCH 1019/1394] gnu: Remove python2-yapf. * gnu/packages/python-xyz.scm (python2-yapf): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index fa326cb2f7c..0adfbfca44f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22119,9 +22119,6 @@ takes the code and reformats it to the best formatting that conforms to the style guide, even if the original code didn't violate the style guide.") (license license:asl2.0))) -(define-public python2-yapf - (package-with-python2 python-yapf)) - (define-public python-yq (package (name "python-yq") From 8b9bda873dc11ff6b73888c1745c15e9618b1778 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:21:01 -0400 Subject: [PATCH 1020/1394] gnu: Remove python2-misaka. * gnu/packages/python-xyz.scm (python2-misaka): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0adfbfca44f..b109662ec3e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20558,9 +20558,6 @@ while only declaring the test-specific fields.") renderers (e.g. man pages or LaTeX).") (license license:expat))) -(define-public python2-misaka - (package-with-python2 python-misaka)) - (define-public python-jsonpointer (package (name "python-jsonpointer") From 9c054861a1aa4d02af55182ec0b40ea02d89bfdf Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:21:11 -0400 Subject: [PATCH 1021/1394] gnu: Remove python2-mpmath. * gnu/packages/python-xyz.scm (python2-mpmath): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b109662ec3e..fa3cc12c441 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10391,9 +10391,6 @@ Python's float/complex types and math/cmath modules, but also does much more advanced mathematics.") (license license:bsd-3))) -(define-public python2-mpmath - (package-with-python2 python-mpmath)) - (define-public python-bigfloat (package (name "python-bigfloat") From 5571221cb665e96dbf7a79459e317c582a1cf0b3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:21:18 -0400 Subject: [PATCH 1022/1394] gnu: Remove python2-binaryornot. * gnu/packages/python-xyz.scm (python2-binaryornot): Delete variable. --- gnu/packages/python-xyz.scm | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index fa3cc12c441..fc2806a22f1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18451,15 +18451,7 @@ Design spec without sacrificing ease of use or application performance.") (synopsis "Package to check if a file is binary or text") (description "Ultra-lightweight pure Python package to check if a file is binary or text.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python2-binaryornot)))))) - -(define-public python2-binaryornot - (let ((base (package-with-python2 (strip-python2-variant python-binaryornot)))) - (package/inherit base - (propagated-inputs - `(("python2-enum34" ,python2-enum34) - ,@(package-propagated-inputs base)))))) + (license license:bsd-3))) (define-public binwalk (package From 46de9d31619af0cf71a12f33847788705e640fa1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:21:31 -0400 Subject: [PATCH 1023/1394] gnu: Remove python2-cheetah. * gnu/packages/python-xyz.scm (python2-cheetah): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index fc2806a22f1..995f5aaf03d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19269,9 +19269,6 @@ JSON) codec.") @end enumerate") (license (license:x11-style "file://LICENSE")))) -(define-public python2-cheetah - (package-with-python2 python-cheetah)) - (define-public python-dulwich (package (name "python-dulwich") From f243080d73ae74e658a77dd637d4e69bb2326e4d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:21:35 -0400 Subject: [PATCH 1024/1394] gnu: Remove python2-ruamel.ordereddict. * gnu/packages/python-xyz.scm (python2-ruamel.ordereddict): Delete variable. --- gnu/packages/python-xyz.scm | 34 ---------------------------------- 1 file changed, 34 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 995f5aaf03d..e9e38dc92ef 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19520,40 +19520,6 @@ JSON) codec.") Problem} (SAT) solver.") (license license:expat))) -(define-public python2-ruamel.ordereddict - (package - (name "python2-ruamel.ordereddict") - (version "0.4.9") - (source - (origin - (method url-fetch) - (uri (pypi-uri "ruamel.ordereddict" version)) - (sha256 - (base32 - "1xmkl8v9l9inm2pyxgc1fm5005yxm7fkd5gv74q7lj1iy5qc8n3h")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (delete 'check) - (add-after 'install 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" "test/testordereddict.py")))))) - (home-page "https://bitbucket.org/ruamel/ordereddict") - (synopsis "Version of dict that keeps keys in insertion order") - (description - "This is an implementation of an ordered dictionary with @dfn{Key - Insertion Order} (KIO: updates of values do not affect the position of the - key), @dfn{Key Value Insertion Order} (KVIO, an existing key's position is - removed and put at the back). The standard library module @code{OrderedDict}, - implemented later, implements a subset of @code{ordereddict} functionality. - Sorted dictionaries are also provided. Currently only with @dfn{Key Sorted - Order} (KSO, no sorting function can be specified, but a transform can be - specified to apply on the key before comparison (e.g. @code{string.lower})).") - (license license:expat))) - (define-public python-pypeg2 (package (name "python-pypeg2") From 7f7716a0e7074bc53e1ab0e79067e7cbd0929cb2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:21:47 -0400 Subject: [PATCH 1025/1394] gnu: Remove python2-blinker. * gnu/packages/python-xyz.scm (python2-blinker): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e9e38dc92ef..8682c11437b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5523,9 +5523,6 @@ enable formatting of partial files.") interested parties to subscribe to events, or \"signals\".") (license license:expat))) -(define-public python2-blinker - (package-with-python2 python-blinker)) - (define-public pelican (package (name "pelican") From 5b93a4325a286a65ff5efb4ffd887c9959b63b72 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:21:53 -0400 Subject: [PATCH 1026/1394] gnu: Remove python2-termcolor. * gnu/packages/python-xyz.scm (python2-termcolor): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8682c11437b..b2ddec4b177 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -13222,9 +13222,6 @@ a hash value.") "This package provides ANSII Color formatting for output in terminals.") (license license:expat))) -(define-public python2-termcolor - (package-with-python2 python-termcolor)) - (define-public python-terminaltables (package (name "python-terminaltables") From f0713c6fe7b484e6321156d74014969a23e95516 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:22:06 -0400 Subject: [PATCH 1027/1394] gnu: Remove python2-booleanoperations. * gnu/packages/python-xyz.scm (python2-booleanoperations): Delete variable. --- gnu/packages/python-xyz.scm | 25 ------------------------- 1 file changed, 25 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b2ddec4b177..a7b03b0e469 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21626,31 +21626,6 @@ Angus Johnson's polygon clipping Clipper library (ver. 6.4.2).") (define-public python2-pyclipper (package-with-python2 python-pyclipper)) -(define-public python2-booleanoperations - (package - (name "python2-booleanoperations") - (version "0.7.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "booleanOperations" version ".zip")) - (sha256 - (base32 - "1hw42fazdpvsn77glx96hwsj9l17mvx37sc5707s08y5w6fx16mn")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) - (native-inputs - (list unzip python2-pytest python2-pytest-runner)) - (propagated-inputs - (list python2-fonttools python2-pyclipper python2-ufolib)) - (home-page "https://github.com/typemytype/booleanOperations") - (synopsis "Boolean operations on paths") - (description - "BooleanOperations provides a Python library that enables -boolean operations on paths.") - (license license:expat))) - (define-public python-tempdir (package (name "python-tempdir") From 754d176b07fd3536e139751a63b41d865285ea71 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:22:12 -0400 Subject: [PATCH 1028/1394] gnu: Remove python2-dirsync. * gnu/packages/python-xyz.scm (python2-dirsync): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a7b03b0e469..48bce48b836 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20153,9 +20153,6 @@ point is the point of maximum curvature.") (description "Advanced directory tree synchronisation tool.") (license license:expat))) -(define-public python2-dirsync - (package-with-python2 python-dirsync)) - (define-public python-levenshtein (package (name "python-levenshtein") From 30ea94bae1a3e57dd78dea0cdd3f01105ce1dbac Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:22:16 -0400 Subject: [PATCH 1029/1394] gnu: Remove python2-rfc3986. * gnu/packages/python-xyz.scm (python2-rfc3986): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 48bce48b836..71a6d310c7e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20594,9 +20594,6 @@ while only declaring the test-specific fields.") which adds support for zone identifiers to IPv6 addresses.") (license license:asl2.0))) -(define-public python2-rfc3986 - (package-with-python2 python-rfc3986)) - (define-public python-rfc3987 (package (name "python-rfc3987") From d33297e7d6ce99bbc828d0b0a07a6e2221a18973 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:22:24 -0400 Subject: [PATCH 1030/1394] gnu: Remove python2-feedgenerator. * gnu/packages/python-xyz.scm (python2-feedgenerator): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 71a6d310c7e..445b5cd02be 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5259,9 +5259,6 @@ public key files.") which can produce feeds in RSS 2.0, RSS 0.91, and Atom formats.") (license license:bsd-3))) -(define-public python2-feedgenerator - (package-with-python2 python-feedgenerator)) - (define-public python-lsp-jsonrpc (package (name "python-lsp-jsonrpc") From 81db76247cb105768b01bbbf42696ff76a27ac00 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:22:27 -0400 Subject: [PATCH 1031/1394] gnu: Remove python2-ipaddr. * gnu/packages/python-xyz.scm (python2-ipaddr): Delete variable. --- gnu/packages/python-xyz.scm | 28 ---------------------------- 1 file changed, 28 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 445b5cd02be..967aa2b4105 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12824,34 +12824,6 @@ codecs (e.g. BER, PER, UPER, XER) as well as limited C source code generating for OER and UPER.") (license license:expat))) -(define-public python2-ipaddr - (package - (name "python2-ipaddr") - (version "2.1.11") - (source - (origin - (method url-fetch) - (uri (pypi-uri "ipaddr" version)) - (sha256 - (base32 "1dwq3ngsapjc93fw61rp17fvzggmab5x1drjzvd4y4q0i255nm8v")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ;version 2 only - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ (invoke "python" "ipaddr_test.py")))))) - (home-page "https://github.com/google/ipaddr-py") - (synopsis "IP address manipulation library") - (description - "Ipaddr is a Python@tie{}2 library for creating and manupilating IPv4 and -IPv6 addresses and networks. - -For new implementations you may prefer to use the standard module -@code{ipaddress}, which was introduced in Python 3.3 and backported to older -versions of Python.") - (license license:asl2.0))) - (define-public python-idna (package (name "python-idna") From 2ab90fcf3aa6a33cad2126eb3c251d8856ffde3e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:22:31 -0400 Subject: [PATCH 1032/1394] gnu: Remove python2-autopep8. * gnu/packages/python-xyz.scm (python2-autopep8): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 967aa2b4105..e72449ae008 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7114,9 +7114,6 @@ by pycodestyle.") (license (license:non-copyleft "https://github.com/hhatto/autopep8/blob/master/LICENSE")))) -(define-public python2-autopep8 - (package-with-python2 python-autopep8)) - (define-public python-distlib (package (name "python-distlib") From 9d6953aa5d08b137d47d9730d328a29317e9bccc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:22:43 -0400 Subject: [PATCH 1033/1394] gnu: Remove python2-humanfriendly. * gnu/packages/python-xyz.scm (python2-humanfriendly): Delete variable. --- gnu/packages/python-xyz.scm | 9 --------- 1 file changed, 9 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e72449ae008..ebe975073e5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2111,17 +2111,8 @@ text interfaces more user-friendly. It includes tools to parse and format numbers, file sizes, and timespans, timers for long-running operations, menus to allow the user to choose from a list of options, and terminal interaction helpers.") - (properties `((python2-variant . ,(delay python2-humanfriendly)))) (license license:expat))) -(define-public python2-humanfriendly - (let ((base (package-with-python2 - (strip-python2-variant python-humanfriendly)))) - (package/inherit base - (propagated-inputs - `(("python2-monotonic" ,python2-monotonic) - ,@(package-propagated-inputs base)))))) - (define-public python-textparser (package (name "python-textparser") From a8c28b8391dc6cf307ee3a1a3362fc77f9ef2349 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:22:52 -0400 Subject: [PATCH 1034/1394] gnu: Remove python2-consul. * gnu/packages/python-xyz.scm (python2-consul): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ebe975073e5..29d3309648d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18546,9 +18546,6 @@ JSON) codec.") discovery, monitoring and configuration.") (license license:expat))) -(define-public python2-consul - (package-with-python2 python-consul)) - (define-public python-schematics (package (name "python-schematics") From 41e7bfb458909b13413edcaaf8f4fd913fa58ecb Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:22:56 -0400 Subject: [PATCH 1035/1394] gnu: Remove python2-flex. * gnu/packages/python-xyz.scm (python2-flex): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 29d3309648d..cba4a76af80 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20794,9 +20794,6 @@ while only declaring the test-specific fields.") (description "@code{flex} can be used to validate Swagger schemata.") (license license:bsd-3))) -(define-public python2-flex - (package-with-python2 python-flex)) - (define-public python-marshmallow (package (name "python-marshmallow") From fc90a42f5f11cbe082369732feb773cf4ac4be0d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:23:02 -0400 Subject: [PATCH 1036/1394] gnu: Remove python2-numexpr. * gnu/packages/python-xyz.scm (python2-numexpr): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cba4a76af80..c7628d010bb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6418,9 +6418,6 @@ computations, most specially if they are not memory-bounded (e.g. those using transcendental functions).") (license license:expat))) -(define-public python2-numexpr - (package-with-python2 python-numexpr)) - (define-public python-cycler (package (name "python-cycler") From 9e1ee95c1751f97f987f9200d9434b61ea038e9a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:23:06 -0400 Subject: [PATCH 1037/1394] gnu: Remove python2-texttable. * gnu/packages/python-xyz.scm (python2-texttable): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c7628d010bb..e589cb154f6 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14504,9 +14504,6 @@ the standard library.") tables.") (license license:expat))) -(define-public python2-texttable - (package-with-python2 python-texttable)) - (define-public python-atomicwrites (package (name "python-atomicwrites") From 3cf21db34a34b38af993302c61a80f9f4c5b224f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:23:12 -0400 Subject: [PATCH 1038/1394] gnu: Remove python2-simplegeneric. * gnu/packages/python-xyz.scm (python2-simplegeneric): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e589cb154f6..b79b99be620 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8743,9 +8743,6 @@ e.g. @code{pickle.dump()} and other generic functions found in the Python standard library.") (license license:zpl2.1))) -(define-public python2-simplegeneric - (package-with-python2 python-simplegeneric)) - (define-public python-ipython-genutils ;; TODO: This package is retired, check if can be removed, see description. (package From 1d8b2a07d920ffabb06a802e44d2d2c9574dc73d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:25:06 -0400 Subject: [PATCH 1039/1394] gnu: Remove python2-dnspython-1.16. * gnu/packages/python-xyz.scm (python2-dnspython-1.16): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b79b99be620..4027a63d887 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17684,9 +17684,6 @@ It supports TSIG authenticated messages and EDNS0.") "1yaw7irazy42n0kdhlk7wyg8ki34rxcnc5xbc1wfwy245b0wbxab")))) (native-inputs '()))) -(define-public python2-dnspython-1.16 - (package-with-python2 python-dnspython-1.16)) - (define-public python-py3dns (package (name "python-py3dns") From c4a9b0b03b0cb4e5637bb2688dfbb2cdc344354f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:28:05 -0400 Subject: [PATCH 1040/1394] gnu: Remove python2-zope-schema. * gnu/packages/python-web.scm (python2-zope-schema): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 52bb55ac3e4..f0729ce4cc9 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2348,9 +2348,6 @@ internationalized messages within program source text.") defining data schemas.") (license license:zpl2.1))) -(define-public python2-zope-schema - (package-with-python2 python-zope-schema)) - (define-public python-zope-configuration (package (name "python-zope-configuration") From 4a37995b04c7dbd46b40be5d342145b825b098e5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:28:27 -0400 Subject: [PATCH 1041/1394] gnu: Remove python2-pyclipper. * gnu/packages/python-xyz.scm (python2-pyclipper): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4027a63d887..a8b10994705 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21556,9 +21556,6 @@ Rust Python extensions implemented with @code{PyO3} or @code{rust-cpython}.") Angus Johnson's polygon clipping Clipper library (ver. 6.4.2).") (license license:expat))) -(define-public python2-pyclipper - (package-with-python2 python-pyclipper)) - (define-public python-tempdir (package (name "python-tempdir") From 90e2ad11c7220327779c78672fea80421b179237 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:35:25 -0400 Subject: [PATCH 1042/1394] gnu: Remove ptpython-2. * gnu/packages/python-xyz.scm (ptpython-2): Delete variable. (ptpython)[properties]: Delete field. --- gnu/packages/python-xyz.scm | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a8b10994705..b6a61f5e08c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18033,13 +18033,7 @@ as well.") It supports syntax highlighting, multiline editing, autocompletion, mouse, color schemes, bracketed paste, Vi and Emacs keybindings, Chinese characters etc.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay ptpython-2)))))) - -(define-public ptpython-2 - (let ((base (package-with-python2 (strip-python2-variant ptpython)))) - (package/inherit base - (name "ptpython2")))) + (license license:bsd-3))) (define-public python-easyprocess (package From 60d41d55eb33241330d2ab8bc159a6e20865f3f6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:38:54 -0400 Subject: [PATCH 1043/1394] gnu: Remove python2-locket. * gnu/packages/python-xyz.scm (python2-locket): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b6a61f5e08c..3f3a9bf3648 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23892,9 +23892,6 @@ data.") they use the same path.") (license license:bsd-2))) -(define-public python2-locket - (package-with-python2 python-locket)) - (define-public python-blosc (package (name "python-blosc") From 176f6ae5a1fabfca78812acb83320ebc47617ebf Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:38:54 -0400 Subject: [PATCH 1044/1394] gnu: Remove python2-zope-i18nmessageid. * gnu/packages/python-web.scm (python2-zope-i18nmessageid): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index f0729ce4cc9..905c4d8fc91 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2313,9 +2313,6 @@ tests.") internationalized messages within program source text.") (license license:zpl2.1))) -(define-public python2-zope-i18nmessageid - (package-with-python2 python-zope-i18nmessageid)) - (define-public python-zope-schema (package (name "python-zope-schema") From 089caa19c78fd27034bb7bd29b83fc24fb452444 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:38:58 -0400 Subject: [PATCH 1045/1394] gnu: Remove python2-jsonpatch. * gnu/packages/python-xyz.scm (python2-jsonpatch): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3f3a9bf3648..0888662ec20 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20482,9 +20482,6 @@ while only declaring the test-specific fields.") applying JSON Patches according to RFC 6902.") (license license:bsd-3))) -(define-public python2-jsonpatch - (package-with-python2 python-jsonpatch)) - (define-public python-jsonpatch-0.4 (package (inherit python-jsonpatch) (name "python-jsonpatch") From c83f305075878bfd4e29949b94e82bd2eda99263 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:39:16 -0400 Subject: [PATCH 1046/1394] gnu: Remove python2-ansi2html. * gnu/packages/python-xyz.scm (python2-ansi2html): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0888662ec20..7628e918f08 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19347,9 +19347,6 @@ JSON) codec.") converting text with ANSI color codes to HTML or LaTeX.") (license license:gpl3+))) -(define-public python2-ansi2html - (package-with-python2 python-ansi2html)) - (define-public python-easy-ansi (package (name "python-easy-ansi") From c76c7556cdf8b1cdd98d4b7a7e8144d419a92212 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:44:33 -0400 Subject: [PATCH 1047/1394] gnu: Remove python-prompt-toolkit-1. * gnu/packages/python-xyz.scm (python-prompt-toolkit-1): Delete variable. (python2-prompt-toolkit-1): Likewise. --- gnu/packages/python-xyz.scm | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7628e918f08..5d633919ab5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17956,20 +17956,6 @@ scans through a file and detects issues.") (list python-wcwidth python-six python-pygments)) (properties '()))) -(define-public python-prompt-toolkit-1 - (package (inherit python-prompt-toolkit-2) - (version "1.0.15") - (source - (origin - (method url-fetch) - (uri (pypi-uri "prompt_toolkit" version ".tar.gz")) - (sha256 - (base32 - "05v9h5nydljwpj5nm8n804ms0glajwfy1zagrzqrg91wk3qqi1c5")))))) - -(define-public python2-prompt-toolkit-1 - (package-with-python2 python-prompt-toolkit-1)) - (define-public python-jedi (package (name "python-jedi") From f5c3588726f664adbf849df4b09cdc8fbffecc2f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:48:24 -0400 Subject: [PATCH 1048/1394] gnu: Remove python2-zope-testrunner. * gnu/packages/python-web.scm (python2-zope-testrunner): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 905c4d8fc91..4eccfcb29f1 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2288,9 +2288,6 @@ tests.") ("python-zope-exceptions" ,python-zope-exceptions-bootstrap))) (properties `((hidden? . #t))))) -(define-public python2-zope-testrunner - (package-with-python2 python-zope-testrunner)) - (define-public python-zope-i18nmessageid (package (name "python-zope-i18nmessageid") From 0d21cf9f565f9dd7843fd0a12ce0c1724439a7a0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:48:51 -0400 Subject: [PATCH 1049/1394] gnu: Remove python2-xlib. * gnu/packages/python-xyz.scm (python2-xlib): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5d633919ab5..e502626ddd9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10528,9 +10528,6 @@ X client library for Python programs. It is useful to implement low-level X clients. It is written entirely in Python.") (license license:gpl2+))) -(define-public python2-xlib - (package-with-python2 python-xlib)) - (define-public python-singledispatch (package (name "python-singledispatch") From b05d8d8bf30b08b2e20a65ded0194ad448483cad Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:48:55 -0400 Subject: [PATCH 1050/1394] gnu: Remove python2-pysnptools. * gnu/packages/python-xyz.scm (python2-pysnptools): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e502626ddd9..b9cb3343d1d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6849,9 +6849,6 @@ those files. It can also efficiently manipulate ranges of integers using set operators such as union, intersection, and difference.") (license license:asl2.0))) -(define-public python2-pysnptools - (package-with-python2 python-pysnptools)) - (define-public python-pykdtree (package (name "python-pykdtree") From 3598e53ec934fb97ca70acec1ee6cb2b937b88a7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:48:59 -0400 Subject: [PATCH 1051/1394] gnu: Remove python2-qrcode. * gnu/packages/python-xyz.scm (python2-qrcode): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b9cb3343d1d..4d397fefae5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19280,9 +19280,6 @@ JSON) codec.") console.") (license license:bsd-3))) -(define-public python2-qrcode - (package-with-python2 python-qrcode)) - (define-public python-rst2ansi (package (name "python-rst2ansi") From 487177f00eb961733af567350b2772bfeb69c7c6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:49:03 -0400 Subject: [PATCH 1052/1394] gnu: Remove python2-tabulate. * gnu/packages/python-xyz.scm (python2-tabulate): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4d397fefae5..d5abea46f4a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17113,9 +17113,6 @@ It uses LR parsing and does extensive error checking.") data in Python.") (license license:expat))) -(define-public python2-tabulate - (package-with-python2 python-tabulate)) - (define-public python-kazoo (package (name "python-kazoo") From 8c85b4ed8fc1fa4f4ab6dce7e492da4858a56e1d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:49:06 -0400 Subject: [PATCH 1053/1394] gnu: Remove python2-markdown. * gnu/packages/python-xyz.scm (python2-markdown): Delete variable. --- gnu/packages/python-xyz.scm | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d5abea46f4a..cbaae6c1a7e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11448,21 +11448,8 @@ Python.") Markdown. The library features international input, various Markdown extensions, and several HTML output formats. A command line wrapper markdown_py is also provided to convert Markdown files to HTML.") - (properties `((python2-variant . ,(delay python2-markdown)))) (license license:bsd-3))) -;; Markdown 3.2 dropped support for Python 2. -(define-public python2-markdown - (let ((base (package-with-python2 (strip-python2-variant python-markdown)))) - (package - (inherit base) - (version "3.1.1") - (source (origin - (method url-fetch) - (uri (pypi-uri "Markdown" version)) - (sha256 - (base32 - "0yhylk4ffqqs7x086fav4pnfsl1021v7lghznzkififprmmqfl1f"))))))) (define-public python-ptyprocess (package From 90dd2a406db42309e87048ede38601c0af8e6612 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:51:31 -0400 Subject: [PATCH 1054/1394] gnu: Remove python2-jsonpatch-0.4. * gnu/packages/python-xyz.scm (python2-jsonpatch-0.4): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cbaae6c1a7e..972828c0c49 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20455,9 +20455,6 @@ while only declaring the test-specific fields.") (base32 "1fq02y57kinyknxjcav0slcb0k9mwdffqw2hnlhdkpj7palh2mwk")))))) -(define-public python2-jsonpatch-0.4 - (package-with-python2 python-jsonpatch-0.4)) - (define-public python-rfc3986 (package (name "python-rfc3986") From 7ced2152d520e4858c31537e06ab2ba0a07a7569 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:52:22 -0400 Subject: [PATCH 1055/1394] gnu: Remove python2-pytest-xdist. * gnu/packages/check.scm (python2-pytest-xdist): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 40c90a03f92..224c7e62e70 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -1476,9 +1476,6 @@ program code to a remote location, executes there, and then syncs the result back.") (license license:expat))) -(define-public python2-pytest-xdist - (package-with-python2 python-pytest-xdist)) - (define-public python-pytest-xdist-next (package/inherit python-pytest-xdist (name "python-pytest-xdist") From 3db04d3051fc4e9c139dd1585e71e218819dd2f6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:54:14 -0400 Subject: [PATCH 1056/1394] gnu: Remove python2-zope-exceptions. * gnu/packages/python-web.scm (python2-zope-exceptions): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 4eccfcb29f1..18722b842ac 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2224,9 +2224,6 @@ that have uses outside of the Zope framework.") (define-public python-zope-exceptions-bootstrap (python-zope-bootstrap-package python-zope-exceptions)) -(define-public python2-zope-exceptions - (package-with-python2 python-zope-exceptions)) - (define-public python-zope-testing (package (name "python-zope-testing") From 25632fa151c0a630ed82c3e63bda51eb0160a337 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:54:53 -0400 Subject: [PATCH 1057/1394] gnu: Remove python2-netifaces. * gnu/packages/python-xyz.scm (python2-netifaces): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 972828c0c49..12fd7ddebb1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9848,9 +9848,6 @@ some are not yet implemented).") interfaces in an easy and portable manner.") (license license:expat))) -(define-public python2-netifaces - (package-with-python2 python-netifaces)) - (define-public python-networkx (package (name "python-networkx") From 451681e2244b314afd24d7c80f6cf452a7d2778f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:54:56 -0400 Subject: [PATCH 1058/1394] gnu: Remove python2-pyinotify. * gnu/packages/python-xyz.scm (python2-pyinotify): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 12fd7ddebb1..e1acb9defb6 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22446,9 +22446,6 @@ interpreter. bpython's main features are file system events on Linux.") (license license:expat))) -(define-public python2-pyinotify - (package-with-python2 python-pyinotify)) - (define-public python-more-itertools (package From 8e25d494a17e5a5dfa4591081686d6d394beaa4c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:55:11 -0400 Subject: [PATCH 1059/1394] gnu: Remove python2-msgpack. * gnu/packages/python-xyz.scm (python2-msgpack): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e1acb9defb6..80c6dcb5e75 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12006,9 +12006,6 @@ reading and writing MessagePack data.") ((".fromstring\\(") ".frombytes(")) #t)))))))) -(define-public python2-msgpack - (package-with-python2 python-msgpack)) - (define-public python-netaddr (package (name "python-netaddr") From 5dce1d8b40cebd87ddaa2153828898a0264aa6fd Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:55:14 -0400 Subject: [PATCH 1060/1394] gnu: Remove python2-element-tree. * gnu/packages/python-xyz.scm (python2-element-tree): Delete variable. --- gnu/packages/python-xyz.scm | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 80c6dcb5e75..30f0ad7c38c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2935,30 +2935,6 @@ system is highly configurable via command line options and embedded commands.") (license license:lgpl2.1+))) -(define-public python2-element-tree - (package - (name "python2-element-tree") - (version "1.2.6") - (source (origin - (method url-fetch) - (uri (string-append - "http://effbot.org/media/downloads/elementtree-" - version "-20050316.tar.gz")) - (sha256 - (base32 - "016bphqnlg0l4vslahhw4r0aanw95bpypy65r1i1acyb2wj5z7dj")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; seems to be part of Python 3 - #:tests? #f)) ; no 'test' sub-command - (synopsis "Toolkit for XML processing in Python") - (description - "ElementTree is a Python library supporting lightweight XML processing.") - (home-page "https://effbot.org/zone/element-index.htm") - (license (license:x11-style - "http://docs.python.org/2/license.html" - "Like \"CWI LICENSE AGREEMENT FOR PYTHON 0.9.0 THROUGH 1.2\".")))) - (define-public python-enum34 (package (name "python-enum34") From 37e8d6cd9ccafdca912bf11f74f029e07e7a2012 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:55:18 -0400 Subject: [PATCH 1061/1394] gnu: Remove python2-joblib. * gnu/packages/python-xyz.scm (python2-joblib): Delete variable. --- gnu/packages/python-xyz.scm | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 30f0ad7c38c..f205acc2123 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4219,17 +4219,6 @@ and lazy re-evaluation (memoize pattern), easy simple parallel computing logging and tracing of the execution.") (license license:bsd-3))) -;; Newer versions of joblib don't support Python 2. -(define-public python2-joblib - (package - (inherit (package-with-python2 python-joblib)) - (version "0.14.1") - (source (origin - (method url-fetch) - (uri (pypi-uri "joblib" version)) - (sha256 - (base32 - "1j464w137w6s367gl697j1l63g52akydrxgv4czlck36ynjfwc06")))))) (define-public python-daemon (package From ca01fd0084d0d76670209ea9bac3df18f397488a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:55:32 -0400 Subject: [PATCH 1062/1394] gnu: Remove python2-cram. * gnu/packages/python-xyz.scm (python2-cram): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f205acc2123..081a455d042 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11501,9 +11501,6 @@ command and compares the command output in the test with the command’s actual output.") (license license:gpl2+))) -(define-public python2-cram - (package-with-python2 python-cram)) - (define-public python-crccheck (package (name "python-crccheck") From ce6d29988816bb9e0c5f8da775405527f22f2e63 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:55:45 -0400 Subject: [PATCH 1063/1394] gnu: Remove python2-cloudpickle. * gnu/packages/python-xyz.scm (python2-cloudpickle): Delete variable. --- gnu/packages/python-xyz.scm | 22 ---------------------- 1 file changed, 22 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 081a455d042..ed0c6d22fbe 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23754,30 +23754,8 @@ supported by the default pickle module from the Python standard library. It is especially useful for cluster computing where Python expressions are shipped over the network to execute on remote hosts, possibly close to the data.") - (properties `((python2-variant . ,(delay python2-cloudpickle)))) (license license:bsd-3))) -(define-public python2-cloudpickle - (let ((base (package-with-python2 (strip-python2-variant python-cloudpickle)))) - (package/inherit base - (version "1.3.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "cloudpickle" version)) - (sha256 - (base32 - "0lx7gy9clp427qwcm7b23zdsldpr03gy3vxxhyi8fpbhwz859brq")))) - (native-inputs - `(;; For tests. - ("python-mock" ,python2-mock) - ("python-psutil" ,python2-psutil) - ("python-pytest" ,python2-pytest) - ("python-tornado" ,python2-tornado))) - (propagated-inputs - `(("python-futures" ,python2-futures) - ,@(package-propagated-inputs base)))))) - (define-public python-locket (package (name "python-locket") From eccb33c210e364b2c29c08a148e19f1801310888 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:59:09 -0400 Subject: [PATCH 1064/1394] gnu: Remove python2-tornado. * gnu/packages/python-web.scm (python2-tornado): Delete variable. (python-tornado)[properties]: Delete field. --- gnu/packages/python-web.scm | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 18722b842ac..cc444cf488e 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1985,8 +1985,7 @@ originally developed at FriendFeed. By using non-blocking network I/O, Tornado can scale to tens of thousands of open connections, making it ideal for long polling, WebSockets, and other applications that require a long-lived connection to each user.") - (license license:asl2.0) - (properties `((python2-variant . ,(delay python2-tornado)))))) + (license license:asl2.0))) (define-public python-tornado-6 (package @@ -2019,16 +2018,6 @@ for long polling, WebSockets, and other applications that require a long-lived connection to each user.") (license license:asl2.0))) -(define-public python2-tornado - (let ((tornado (package-with-python2 (strip-python2-variant python-tornado)))) - (package/inherit tornado - (propagated-inputs - `(("python2-backport-ssl-match-hostname" - ,python2-backport-ssl-match-hostname) - ("python2-backports-abc" ,python2-backports-abc) - ("python2-singledispatch" ,python2-singledispatch) - ,@(package-propagated-inputs tornado)))))) - (define-public python-tornado-http-auth (package (name "python-tornado-http-auth") From 7287f835234f3087ce7f467517a1e55679683050 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:59:34 -0400 Subject: [PATCH 1065/1394] gnu: Remove python2-zope-interface. * gnu/packages/python-web.scm (python2-zope-interface): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index cc444cf488e..e24b691abdf 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2159,9 +2159,6 @@ interfaces\" for Python. Interfaces are a mechanism for labeling objects as conforming to a given API or contract.") (license license:zpl2.1))) -(define-public python2-zope-interface - (package-with-python2 python-zope-interface)) - (define-public python-zope-exceptions (package (name "python-zope-exceptions") From 79884ad0da33455c9f2779800427015d47324e41 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:59:41 -0400 Subject: [PATCH 1066/1394] gnu: Remove python2-tldextract. * gnu/packages/python-xyz.scm (python2-tldextract): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ed0c6d22fbe..57371a3bca8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23069,9 +23069,6 @@ the public ICANN TLDs and their exceptions. It can optionally support the Public Suffix List's private domains as well.") (license license:bsd-3))) -(define-public python2-tldextract - (package-with-python2 python-tldextract)) - (define-public python-tldr (package (name "python-tldr") From be3db968b39b21bae0d24a6ff3457c7f5beabb87 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:59:45 -0400 Subject: [PATCH 1067/1394] gnu: Remove python2-notify2. * gnu/packages/python-xyz.scm (python2-notify2): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 57371a3bca8..231c0adeb9a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9698,9 +9698,6 @@ the GObject Introspection bindings to libnotify for non-GTK applications.") (license (list license:bsd-2 license:lgpl2.1+)))) -(define-public python2-notify2 - (package-with-python2 python-notify2)) - ;; beautifulsoup4 has a totally different namespace than 3.x, ;; and pypi seems to put it under its own name, so I guess we should too (define-public python-beautifulsoup4 From 7d42c04f09804e8df9f277a13a7b1154cf0e3b3f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:59:48 -0400 Subject: [PATCH 1068/1394] gnu: Remove python2-pydiff. * gnu/packages/python-xyz.scm (python2-pydiff): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 231c0adeb9a..e5817d63b4c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21097,9 +21097,6 @@ version of @code{SocksiPy} with bug fixes and extra features.") ignoring formatting changes.") (license license:expat))) -(define-public python2-pydiff - (package-with-python2 python-pydiff)) - (define-public python-pydub (package (name "python-pydub") From 2dc5af1fc9e4f851d99e496deca4214cab700659 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:59:52 -0400 Subject: [PATCH 1069/1394] gnu: Remove python2-parso. * gnu/packages/python-xyz.scm (python2-parso): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e5817d63b4c..bb5ca24cdb9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22526,9 +22526,6 @@ round-trip parsing for different Python versions (in multiple Python versions). Parso is also able to list multiple syntax errors in your Python file.") (license license:expat))) -(define-public python2-parso - (package-with-python2 python-parso)) - (define-public python-async-generator (package (name "python-async-generator") From 3893e94b369302afcbcbadbb1d77dd2ee985ac98 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 22:59:58 -0400 Subject: [PATCH 1070/1394] gnu: Remove python2-vcversioner. * gnu/packages/python-xyz.scm (python2-vcversioner): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index bb5ca24cdb9..f4fbba3a4fd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3590,9 +3590,6 @@ version numbers.") (home-page "https://github.com/habnabit/vcversioner") (license license:isc))) -(define-public python2-vcversioner - (package-with-python2 python-vcversioner)) - (define-public python-jdcal (package (name "python-jdcal") From f137896cfda05ec3a6dc9251cb9cc885e601cafd Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:00:02 -0400 Subject: [PATCH 1071/1394] gnu: Remove python2-extras. * gnu/packages/python-xyz.scm (python2-extras): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f4fbba3a4fd..ef20e461280 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3165,9 +3165,6 @@ documentation-related tools used by the Astropy project.") "Extras is a set of extensions to the Python standard library.") (license license:expat))) -(define-public python2-extras - (package-with-python2 python-extras)) - (define-public python-mimeparse (package (name "python-mimeparse") From 979af29d5c3db3b3a9671b122ccbbbec2a9e6c9f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:00:09 -0400 Subject: [PATCH 1072/1394] gnu: Remove python2-inflection. * gnu/packages/python-xyz.scm (python2-inflection): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ef20e461280..7cc84e53685 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17157,9 +17157,6 @@ and pluralizes English words, and transforms strings from CamelCase to underscored string.") (license license:expat))) -(define-public python2-inflection - (package-with-python2 python-inflection)) - (define-public python-pylev (package (name "python-pylev") From ff70ce499bd391ddd4e09dc9186754ddde885cb7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:00:34 -0400 Subject: [PATCH 1073/1394] gnu: Remove python2-execnet. * gnu/packages/python-xyz.scm (python2-execnet): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7cc84e53685..d0b9c0201ea 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14652,9 +14652,6 @@ minimal and fast API targeting the following uses: (home-page "https://codespeak.net/execnet/") (license license:expat))) -(define-public python2-execnet - (package-with-python2 python-execnet)) - (define-public python-icalendar (package (name "python-icalendar") From 552076fddf9363fde88cfc4bec9d70d79ca589a2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:00:43 -0400 Subject: [PATCH 1074/1394] gnu: Remove python2-scientific. * gnu/packages/python-xyz.scm (python2-scientific): Delete variable. --- gnu/packages/python-xyz.scm | 39 ------------------------------------- 1 file changed, 39 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d0b9c0201ea..34a41cfec2e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21652,45 +21652,6 @@ longer maintained. New projects should use Pyro4 instead, which is the new Pyro version that is actively developed.") (license license:expat))) -(define-public python2-scientific - (package - (name "python2-scientific") - (version "2.9.4") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/khinsen/ScientificPython") - (commit (string-append "rel" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "16l48aj9fps9r7jyk8gpxppwrv0fqvlc13sayxskz28r5s6sjwbl")))) - (build-system python-build-system) - (inputs - (list netcdf)) - (propagated-inputs - (list python2-numpy-1.8 python2-pyro)) - (arguments - ;; ScientificPython is not compatible with Python 3 - `(#:python ,python-2 - #:tests? #f ; No test suite - #:phases - (modify-phases %standard-phases - (replace 'build - (lambda* (#:key inputs #:allow-other-keys) - (invoke "python" "setup.py" "build" - (string-append "--netcdf_prefix=" - (assoc-ref inputs "netcdf")))))))) - (home-page "http://dirac.cnrs-orleans.fr/ScientificPython") - (synopsis "Python modules for scientific computing") - (description "ScientificPython is a collection of Python modules that are -useful for scientific computing. Most modules are rather general (Geometry, -physical units, automatic derivatives, ...) whereas others are more -domain-specific (e.g. netCDF and PDB support). The library is currently -not actively maintained and works only with Python 2 and NumPy < 1.9.") - (license license:cecill-c))) - (define-public python-phonenumbers (package (name "python-phonenumbers") From 9549a466b89377b0f965e63b7133e2f411321953 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:00:47 -0400 Subject: [PATCH 1075/1394] gnu: Remove python2-automat. * gnu/packages/python-xyz.scm (python2-automat): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 34a41cfec2e..321ff5703ec 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19461,9 +19461,6 @@ JSON) codec.") transducers).") (license license:expat))) -(define-public python2-automat - (package-with-python2 python-automat)) - (define-public python-m2r (package (name "python-m2r") From a38349bc66efbb9f24213510ee0bf6240c673d90 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:00:54 -0400 Subject: [PATCH 1076/1394] gnu: Remove python2-mando. * gnu/packages/python-xyz.scm (python2-mando): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 321ff5703ec..67b485a480f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19867,9 +19867,6 @@ builds partial trees by inspecting living objects.") applications in seconds while maintaining all the flexibility.") (license license:expat))) -(define-public python2-mando - (package-with-python2 python-mando)) - (define-public python-mwclient (package (name "python-mwclient") From 9d9855f6b839d2cba9e537a06255c15656f4059f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:00:58 -0400 Subject: [PATCH 1077/1394] gnu: Remove python2-pexpect. * gnu/packages/python-xyz.scm (python2-pexpect): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 67b485a480f..3025300a8e1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8222,9 +8222,6 @@ Pexpect works like Don Libes’ Expect. Pexpect allows your script to spawn a child application and control it as if a human were typing commands.") (license license:isc))) -(define-public python2-pexpect - (package-with-python2 python-pexpect)) - (define-public python-setuptools-scm (package (name "python-setuptools-scm") From 5afc4b537e70ad969f9e240a51c0cefab2db91cc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:01:01 -0400 Subject: [PATCH 1078/1394] gnu: Remove python2-couleur. * gnu/packages/python-xyz.scm (python2-couleur): Delete variable. --- gnu/packages/python-xyz.scm | 26 -------------------------- 1 file changed, 26 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3025300a8e1..b831c864d11 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20272,32 +20272,6 @@ while only declaring the test-specific fields.") (define-public python2-sure (package-with-python2 python-sure)) -(define-public python2-couleur - ;; This package does not seem to support python3 at all, hence, - ;; only the python2 variant definition is provided. - (package - (name "python2-couleur") - (version "0.6.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "couleur" version)) - (sha256 - (base32 - "1qqaxyqz74wvid0cr119dhcwz0h0if5b5by44zl49pd5z65v58k1")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) - (home-page "https://github.com/gabrielfalcao/couleur") - (synopsis - "ANSI terminal tool for python, colored shell and other handy fancy features") - (description - "@code{Couleur} provides python programs a way to use the ANSI features in a unix - terminal such as coloured output in the shell, overwriting output, indentation, etc.") - ;; README.md says ASL2.0, but all source code headers are LGPL3+. - ;; https://github.com/gabrielfalcao/couleur/issues/11 - (license license:lgpl3+))) - (define-public python-misaka (package (name "python-misaka") From 15558b09beed1ff84464384706ee2c8fd18913c0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:01:05 -0400 Subject: [PATCH 1079/1394] gnu: Remove python2-dogtail. * gnu/packages/python-xyz.scm (python2-dogtail): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b831c864d11..0623e4fdd33 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2902,9 +2902,6 @@ applications. dogtail scripts are written in Python and executed like any other Python program.") (license license:gpl2+))) -(define-public python2-dogtail - (package-with-python2 python-dogtail)) - (define-public python-empy (package (name "python-empy") From 5478ffa1ba8dee7548fe558fca18cfa742e22c6e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:01:08 -0400 Subject: [PATCH 1080/1394] gnu: Remove python2-magic. * gnu/packages/python-xyz.scm (python2-magic): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0623e4fdd33..c41eaae45f0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16474,9 +16474,6 @@ modules, which are different and were developed separately, both serve the same purpose: to provide Python bindings for libmagic.") (license license:expat))) -(define-public python2-magic - (package-with-python2 python-magic)) - (define-public python-pkgconfig (package (name "python-pkgconfig") From e0996a01534c7a5c1c0cc7afdc29d07134b47a54 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:01:21 -0400 Subject: [PATCH 1081/1394] gnu: Remove python2-fusepy. * gnu/packages/python-xyz.scm (python2-fusepy): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c41eaae45f0..dddc463228f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22662,9 +22662,6 @@ commit, but it also includes some other useful statistics.") MacFUSE. The binding is created using the standard @code{ctypes} library.") (license license:isc))) -(define-public python2-fusepy - (package-with-python2 python-fusepy)) - (define-public python-fusepyng (package (name "python-fusepyng") From 05f8ac96551bf7eb257721b4ee8d94505d9cc6f6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:01:24 -0400 Subject: [PATCH 1082/1394] gnu: Remove python2-wrapt. * gnu/packages/python-xyz.scm (python2-wrapt): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index dddc463228f..cf203245927 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12032,9 +12032,6 @@ Supported netlink families and protocols include: wrappers and decorator functions.") (license license:bsd-2))) -(define-public python2-wrapt - (package-with-python2 python-wrapt)) - (define-public python-commentjson (package (name "python-commentjson") From e6e55d7efb25f48cd90da2331c232076af542658 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:01:37 -0400 Subject: [PATCH 1083/1394] gnu: Remove python2-pyasn1-modules. * gnu/packages/python-xyz.scm (python2-pyasn1-modules): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cf203245927..5edeef44f0c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12678,9 +12678,6 @@ suitable for a wide range of protocols based on the ASN.1 specification.") implementations of ASN.1-based codecs and protocols.") (license license:bsd-3))) -(define-public python2-pyasn1-modules - (package-with-python2 python-pyasn1-modules)) - (define-public python-ipaddress (package (name "python-ipaddress") From c80cd05540493c06abebbbcb86ce1dbe278cfc88 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:01:57 -0400 Subject: [PATCH 1084/1394] gnu: Remove python2-xlrd. * gnu/packages/python-xyz.scm (python2-xlrd): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5edeef44f0c..ce12ac2ded2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12185,9 +12185,6 @@ spreadsheets using Microsoft Excel proprietary file formats @samp{.xls} and Unicode-aware. It is not intended as an end-user tool.") (license license:bsd-3))) -(define-public python2-xlrd - (package-with-python2 python-xlrd)) - ;;; Note: this package is unmaintained since 2018 (archived on GitHub). (define-public python-xlwt (package From fc06b4cbd699776042bf5ba59b17861f65e95c3a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:02:03 -0400 Subject: [PATCH 1085/1394] gnu: Remove python2-h5py. * gnu/packages/python-xyz.scm (python2-h5py): Delete variable. --- gnu/packages/python-xyz.scm | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ce12ac2ded2..c4c62fa50fb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1523,21 +1523,7 @@ HDF5 library from Python. The low-level interface is intended to be a complete wrapping of the HDF5 API, while the high-level component supports access to HDF5 files, datasets and groups using established Python and NumPy concepts.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python2-h5py)))))) - -(define-public python2-h5py - (let ((base (package-with-python2 (strip-python2-variant python-h5py)))) - (package - (inherit base) - (version "2.10.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "h5py" version)) - (sha256 - (base32 - "0baipzv8n93m0dq0riyi8rfhzrjrfrfh8zqhszzp1j2xjac2fhc4"))))))) + (license license:bsd-3))) (define-public python-hnswlib (package From b5891dab65e853e12382167b1126756fe3de96b7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:02:11 -0400 Subject: [PATCH 1086/1394] gnu: Remove python2-colorama. * gnu/packages/python-xyz.scm (python2-colorama): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c4c62fa50fb..d7cd2dbcaf0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14944,9 +14944,6 @@ text.") (home-page "https://pypi.org/project/colorama/") (license license:bsd-3))) -(define-public python2-colorama - (package-with-python2 python-colorama)) - ;; awscli and botocore do not accept version 0.4.4 (define-public python-colorama-for-awscli (package From dd10d66a4c06f4affc209637cc7b006c60de5a74 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:02:15 -0400 Subject: [PATCH 1087/1394] gnu: Remove python2-flake8-polyfill. * gnu/packages/python-xyz.scm (python2-flake8-polyfill): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d7cd2dbcaf0..cf26c2d4aeb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11162,9 +11162,6 @@ unnecessary plus operators for explicit string literal concatenation.") plugins that intend to support Flake8 2.x and 3.x simultaneously.") (license license:expat))) -(define-public python2-flake8-polyfill - (package-with-python2 python-flake8-polyfill)) - (define-public python-flake8-print (package (name "python-flake8-print") From 7f3aec372a6122ad06d3f8ac620e101891a6f4c3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:02:24 -0400 Subject: [PATCH 1088/1394] gnu: Remove python2-elib.intl. * gnu/packages/python-xyz.scm (python2-elib.intl): Delete variable. --- gnu/packages/python-xyz.scm | 28 ---------------------------- 1 file changed, 28 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cf26c2d4aeb..93100f6366d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7097,34 +7097,6 @@ gettext support, themed icons, and scrollkeeper-based documentation into Python's distutils.") (license license:gpl2))) -(define-public python2-elib.intl - (package - (name "python2-elib.intl") - (version "0.0.3") - (source - (origin - ;; This project doesn't tag releases or publish tarballs, so we take - ;; source from a (semi-arbitrary, i.e. latest as of now) git commit. - (method git-fetch) - (uri (git-reference - (url "https://github.com/dieterv/elib.intl") - (commit "d09997cfef"))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "0y7vzff9xgbnaay7m0va1arl6g68ncwrvbgwl7jqlclsahzzb09d")))) - (build-system python-build-system) - (arguments - ;; incompatible with Python 3 (exception syntax) - `(#:python ,python-2 - #:tests? #f)) - (home-page "https://github.com/dieterv/elib.intl") - (synopsis "Enhanced internationalization for Python") - (description - "The elib.intl module provides enhanced internationalization (I18N) -services for your Python modules and applications.") - (license license:lgpl3+))) - (define-public python-olefile (package (name "python-olefile") From 25ed723d5e0ebbbad84271ed9b6cf723cc67cff6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:02:44 -0400 Subject: [PATCH 1089/1394] gnu: Remove python2-pyroute2. * gnu/packages/python-xyz.scm (python2-pyroute2): Delete variable. --- gnu/packages/python-xyz.scm | 35 ----------------------------------- 1 file changed, 35 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 93100f6366d..b5356102451 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11928,41 +11928,6 @@ reading and writing MessagePack data.") and MAC network addresses.") (license license:bsd-3))) -(define-public python2-pyroute2 - (package - (name "python2-pyroute2") - (version "0.5.6") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pyroute2" version)) - (sha256 - (base32 - "1gmz4r1w0yzj6fjjypnalmfyy0lnfznydyn62gi3wk50j5hhxbny")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) ;Python 3.x is not supported - (home-page "https://github.com/svinota/pyroute2") - (synopsis "Python netlink library") - (description - "Pyroute2 is a pure Python netlink library with minimal dependencies. -Supported netlink families and protocols include: -@itemize -@item rtnl, network settings - addresses, routes, traffic controls -@item nfnetlink - netfilter API: ipset, nftables, ... -@item ipq - simplest userspace packet filtering, iptables QUEUE target -@item devlink - manage and monitor devlink-enabled hardware -@item generic - generic netlink families - @itemize - @item nl80211 - wireless functions API (basic support) - @item taskstats - extended process statistics - @item acpi_events - ACPI events monitoring - @item thermal_events - thermal events monitoring - @item VFS_DQUOT - disk quota events monitoring - @end itemize -@end itemize") - (license license:gpl2+))) - (define-public python-wrapt (package (name "python-wrapt") From 16ccac5a1b43300e1dacdbc6cb02390633a80cc4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:02:47 -0400 Subject: [PATCH 1090/1394] gnu: Remove python2-psutil. * gnu/packages/python-xyz.scm (python2-psutil): Delete variable. --- gnu/packages/python-xyz.scm | 8 -------- 1 file changed, 8 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b5356102451..0637ca81b26 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1118,16 +1118,8 @@ profiling and limiting process resources and management of running processes. It implements many functionalities offered by command line tools such as: ps, top, lsof, netstat, ifconfig, who, df, kill, free, nice, ionice, iostat, iotop, uptime, pidof, tty, taskset, pmap.") - (properties `((python2-variant . ,(delay python2-psutil)))) (license license:bsd-3))) -(define-public python2-psutil - (let ((base (package-with-python2 (strip-python2-variant python-psutil)))) - (package/inherit base - (propagated-inputs - `(("python2-enum34" ,python2-enum34) ;optional - ,@(package-propagated-inputs base)))))) - (define-public python-shapely (package (name "python-shapely") From 3143a4166eefb7c870154625fa680561f09e838a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:02:54 -0400 Subject: [PATCH 1091/1394] gnu: Remove python2-tempdir. * gnu/packages/python-xyz.scm (python2-tempdir): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0637ca81b26..b2d74108d23 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21322,9 +21322,6 @@ deleted with all their contents when they are no longer needed. It is particularly convenient for use in tests.") (license license:expat))) -(define-public python2-tempdir - (package-with-python2 python-tempdir)) - (define-public python-tempora (package (name "python-tempora") From 061d33df7304e08125b91a3ae8e53ab56575296c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:02:58 -0400 Subject: [PATCH 1092/1394] gnu: Remove python2-djvulibre. * gnu/packages/python-xyz.scm (python2-djvulibre): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b2d74108d23..f0c71d07267 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -27400,9 +27400,6 @@ applications with variable CPU loads).") (home-page "https://jwilk.net/software/python-djvulibre") (license license:gpl2))) -(define-public python2-djvulibre - (package-with-python2 python-djvulibre)) - (define-public python-versioneer (package (name "python-versioneer") From c8638b6db6437eb4ed323a1ae411eb21b5c79b8c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:03:17 -0400 Subject: [PATCH 1093/1394] gnu: Remove python2-urwidtrees. * gnu/packages/python-xyz.scm (python2-urwidtrees): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f0c71d07267..161042124a5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9486,9 +9486,6 @@ distance between two or more sequences by many algorithms.") toolkit. Use it to build trees of widgets.") (license license:gpl3+))) -(define-public python2-urwidtrees - (package-with-python2 python-urwidtrees)) - (define-public python-ua-parser (package (name "python-ua-parser") From d0d907dff8e6684d0d15e4567757fb3c41ae6564 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:03:30 -0400 Subject: [PATCH 1094/1394] gnu: Remove python2-clyent. * gnu/packages/python-xyz.scm (python2-clyent): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 161042124a5..a4392bcd157 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1242,9 +1242,6 @@ and function call return values in a human-readable way.") by @code{binstar}, @code{binstar-build}, and @code{chalmers}.") (license license:bsd-3))) -(define-public python2-clyent - (package-with-python2 python-clyent)) - (define-public python-babel (package (name "python-babel") From 745be53c5f6bdbd221e6e3f33e04e5016b7c7c15 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:03:36 -0400 Subject: [PATCH 1095/1394] gnu: Remove python2-constantly. * gnu/packages/python-xyz.scm (python2-constantly): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a4392bcd157..99c3e8d1acd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19388,9 +19388,6 @@ JSON) codec.") and bit flag values.") (license license:expat))) -(define-public python2-constantly - (package-with-python2 python-constantly)) - (define-public python-attrs (package (name "python-attrs") From 9702e5f26cf4bac6ceb909c271d39c6889e52663 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:03:42 -0400 Subject: [PATCH 1096/1394] gnu: Remove python2-pep517. * gnu/packages/python-xyz.scm (python2-pep517): Delete variable. --- gnu/packages/python-xyz.scm | 31 ++++++++----------------------- 1 file changed, 8 insertions(+), 23 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 99c3e8d1acd..a6b36ea44a0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10807,30 +10807,15 @@ plugin for flake8 to check PEP-8 naming conventions.") (inherit python-pep517-bootstrap) (name "python-pep517") (arguments - '(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (delete-file "pytest.ini") - ;; This test tries to connect to the internet - (delete-file "tests/test_meta.py") - (if tests? - (invoke "pytest") - #t)))))) - (native-inputs - (list python-mock python-pytest python-testpath)) - (properties `((python2-variant . ,(delay python2-pep517)))))) + '(#:phases (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (delete-file "pytest.ini") + (delete-file "tests/test_meta.py") + (if tests? + (invoke "pytest") #t)))))) + (native-inputs (list python-mock python-pytest python-testpath)))) -;; Skip the tests so we don't create a cyclical dependency with pytest. -(define-public python2-pep517 - (let ((base (package-with-python2 - (strip-python2-variant python-pep517)))) - (package/inherit base - (name "python2-pep517") - (arguments - `(#:tests? #f - ,@(package-arguments base))) - (native-inputs `())))) (define-public python-pep621 (package From 5f33d83bf820e3284c1cc72686bd041033ffa4d6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:03:45 -0400 Subject: [PATCH 1097/1394] gnu: Remove python2-q. * gnu/packages/python-xyz.scm (python2-q): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a6b36ea44a0..eb543ac5b6a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10376,9 +10376,6 @@ provides convenient short API for print out of values, tracebacks, and falling into the Python interpreter.") (license license:asl2.0))) -(define-public python2-q - (package-with-python2 python-q)) - (define-public python-xlib (package (name "python-xlib") From 27bdd10b92bee9db0e590e46eec42757478bedc4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:03:51 -0400 Subject: [PATCH 1098/1394] gnu: Remove python2-rst.linker. * gnu/packages/python-xyz.scm (python2-rst.linker): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index eb543ac5b6a..ff905a09eb6 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5125,9 +5125,6 @@ reStructuredText external reference or timestamps. It's primary purpose is to augment the changelog, but it can be used for other documents, too.") (license license:expat))) -(define-public python2-rst.linker - (package-with-python2 python-rst.linker)) - (define-public python-sshpubkeys (package (name "python-sshpubkeys") From f64aac1e4ae04d00de88736b92349c8361e4995e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:03:54 -0400 Subject: [PATCH 1099/1394] gnu: Remove python2-pathlib. * gnu/packages/python-xyz.scm (python2-pathlib): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ff905a09eb6..7f00cefe2a1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16093,9 +16093,6 @@ standard library module. This module (python-pathlib) isn't maintained anymore.") (license license:expat))) -(define-public python2-pathlib - (package-with-python2 python-pathlib)) - (define-public python2-pathlib2 (package (name "python2-pathlib2") From b95b97530565cd6a604c03089b54f5f328a54e28 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:04:10 -0400 Subject: [PATCH 1100/1394] gnu: Remove python2-whoosh. * gnu/packages/python-xyz.scm (python2-whoosh): Delete variable. --- gnu/packages/python-xyz.scm | 8 -------- 1 file changed, 8 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7f00cefe2a1..5b4861266b8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16007,14 +16007,6 @@ useful for solving the Assignment Problem.") checking library.") (license license:bsd-2))) -(define-public python2-whoosh - (let ((whoosh (package-with-python2 (strip-python2-variant python-whoosh)))) - (package/inherit whoosh - (propagated-inputs - `(("python2-backport-ssl-match-hostname" - ,python2-backport-ssl-match-hostname) - ,@(package-propagated-inputs whoosh)))))) - (define-public python-codespell (package (name "python-codespell") From ddd1154db6c4384339d510cf4cfb853eeefec37a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:04:19 -0400 Subject: [PATCH 1101/1394] gnu: Remove python2-openpyxl. * gnu/packages/python-xyz.scm (python2-openpyxl): Delete variable. --- gnu/packages/python-xyz.scm | 29 ++++------------------------- 1 file changed, 4 insertions(+), 25 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5b4861266b8..2f2c960656b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2565,37 +2565,16 @@ of @code{xmlfile}.") (replace 'check (lambda _ (invoke "pytest")))))) - (native-inputs - ;; For the test suite. - (list python-lxml python-pillow python-pytest)) - (propagated-inputs - (list python-et-xmlfile python-jdcal)) + (native-inputs (list python-lxml python-pillow python-pytest)) + (propagated-inputs (list python-et-xmlfile python-jdcal)) (home-page "https://openpyxl.readthedocs.io") (synopsis "Python library to read/write Excel 2010 XLSX/XLSM files") - (description "This Python library allows reading and writing to the Excel XLSX, XLSM, + (description + "This Python library allows reading and writing to the Excel XLSX, XLSM, XLTX and XLTM file formats that are defined by the Office Open XML (OOXML) standard.") - (properties `((python2-variant . ,(delay python2-openpyxl)))) (license license:expat))) -(define-public python2-openpyxl - (let ((base (package-with-python2 - (strip-python2-variant python-openpyxl)))) - (package - (inherit base) - ;; This is the latest version that has python2 support - (version "2.6.4") - (source - (origin - (method url-fetch) - (uri (pypi-uri "openpyxl" version)) - (sha256 - (base32 - "1qzjj8nwj4dn0mhq1j64f136afiqqb81lvqiikipz3g1g0b80lqx")))) - (arguments - `(#:python ,python-2 - #:tests? #f))))) ; No test suite. - (define-public python-eventlet (package (name "python-eventlet") From 76cebcc03dd563aca4c62ac74f14512a3c0fd18e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:04:25 -0400 Subject: [PATCH 1102/1394] gnu: Remove python2-validate-email. * gnu/packages/python-xyz.scm (python2-validate-email): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2f2c960656b..e694ba0febe 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20437,9 +20437,6 @@ while only declaring the test-specific fields.") address is valid and really exists.") (license license:lgpl3+))) -(define-public python2-validate-email - (package-with-python2 python-validate-email)) - (define-public python-flex (package (name "python-flex") From abb9adfff89d33415b53ef758e6323bc1de46330 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:04:36 -0400 Subject: [PATCH 1103/1394] gnu: Remove python2-setproctitle. * gnu/packages/python-xyz.scm (python2-setproctitle): Delete variable. --- gnu/packages/python-xyz.scm | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e694ba0febe..cd60cd201dd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18580,15 +18580,7 @@ JSON) codec.") example when a master process is forked: changing the children's title allows identifying the task each process is busy with. The technique is used by PostgreSQL and the OpenSSH Server for example.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python2-setproctitle)))))) - -(define-public python2-setproctitle - (let ((base (package-with-python2 - (strip-python2-variant python-setproctitle)))) - (package/inherit base - (native-inputs `(("python2-nose" ,python2-nose) - ,@(package-native-inputs base)))))) + (license license:bsd-3))) (define-public python-validictory (package From 748f3ef4834364df041f6b385caa615af8889a58 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:04:44 -0400 Subject: [PATCH 1104/1394] gnu: Remove python2-fuzzywuzzy. * gnu/packages/python-xyz.scm (python2-fuzzywuzzy): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cd60cd201dd..ca0d483e346 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -25610,9 +25610,6 @@ custom PNG processing.") sequences.") (license license:gpl2))) -(define-public python2-fuzzywuzzy - (package-with-python2 python-fuzzywuzzy)) - (define-public python-block-tracing (package (name "python-block-tracing") From 4087be253b2b60c5bc73ebf6a931a03e8e5041b2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:05:33 -0400 Subject: [PATCH 1105/1394] gnu: Remove python2-schema-0.5. * gnu/packages/python-xyz.scm (python2-schema-0.5): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ca0d483e346..9f00dbc889a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3651,9 +3651,6 @@ something else) to Python data-types.") (base32 "10zqvpaky51kgb8nd42bk7jwl8cn2zvayxjpdc1wwmpybj92x67s")))))) -(define-public python2-schema-0.5 - (package-with-python2 python-schema-0.5)) - (define-public python-kitchen (package (name "python-kitchen") From eb6d69ff1656f8d98c96c0f2d40f2b52466527c1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:07:04 -0400 Subject: [PATCH 1106/1394] gnu: Remove python2-graphviz. * gnu/packages/graphviz.scm (python2-graphviz): Delete variable. --- gnu/packages/graphviz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm index f2fd90e6161..68d0741957d 100644 --- a/gnu/packages/graphviz.scm +++ b/gnu/packages/graphviz.scm @@ -208,9 +208,6 @@ interfaces for other technical domains.") visualization tool suite.") (license license:expat))) -(define-public python2-graphviz - (package-with-python2 python-graphviz)) - (define-public python-pygraphviz (package (name "python-pygraphviz") From 61a775f38542c3da48b6a440da85191c0c9890d7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:07:32 -0400 Subject: [PATCH 1107/1394] gnu: Remove python2-wheel. * gnu/packages/python-build.scm (python2-wheel): Delete variable. --- gnu/packages/python-build.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-build.scm b/gnu/packages/python-build.scm index eb291c2c864..e3b160bc85c 100644 --- a/gnu/packages/python-build.scm +++ b/gnu/packages/python-build.scm @@ -68,9 +68,6 @@ scripts to their final locations) at any later time. Wheel files can be installed with a newer @code{pip} or with wheel's own command line utility.") (license license:expat))) -(define-public python2-wheel - (package-with-python2 python-wheel)) - ;;; XXX: Not really at home, but this seems the best place to prevent circular ;;; module dependencies. (define-public python-toml From 6de507f5c931886f475d98b63fe6e786e403461f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:08:05 -0400 Subject: [PATCH 1108/1394] gnu: Remove python2-zope-testing. * gnu/packages/python-web.scm (python2-zope-testing): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index e24b691abdf..3edeef68a4f 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2228,9 +2228,6 @@ that have uses outside of the Zope framework.") forms, HTTP servers, regular expressions, and more.") (license license:zpl2.1))) -(define-public python2-zope-testing - (package-with-python2 python-zope-testing)) - (define-public python-zope-testrunner (package (name "python-zope-testrunner") From a03c2d9c7b6a1fa0c81c020f7140c16be1509db7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:08:09 -0400 Subject: [PATCH 1109/1394] gnu: Remove python2-zope-event. * gnu/packages/python-web.scm (python2-zope-event): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 3edeef68a4f..4151d77d2dd 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2132,9 +2132,6 @@ is a simple event-dispatching system on which more sophisticated event dispatching systems can be built.") (license license:zpl2.1))) -(define-public python2-zope-event - (package-with-python2 python-zope-event)) - (define-public python-zope-interface (package (name "python-zope-interface") From 4d7ae91d3e92723b123b2a56d9638cd556fedade Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:08:24 -0400 Subject: [PATCH 1110/1394] gnu: Remove python2-responses. * gnu/packages/python-web.scm (python2-responses): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 4151d77d2dd..a50f071debf 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -3260,9 +3260,6 @@ Python.") library.") (license license:asl2.0))) -(define-public python2-responses - (package-with-python2 python-responses)) - (define-public python-grequests (package (name "python-grequests") From 810f12114a33dad2b833ea90a59935138d6b8252 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:08:40 -0400 Subject: [PATCH 1111/1394] gnu: Remove python2-pyro. * gnu/packages/python-xyz.scm (python2-pyro): Delete variable. --- gnu/packages/python-xyz.scm | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9f00dbc889a..6b2e2331656 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21403,35 +21403,6 @@ other over the network. You can just use normal Python method calls to call objects on other machines, also known as remote procedure calls (RPC).") (license license:expat))) -(define-public python2-pyro - (package - (name "python2-pyro") - (version "3.16") - (source - (origin - (method url-fetch) - (uri (pypi-uri "Pyro" version)) - (file-name (string-append "Pyro-" version ".tar.gz")) - (sha256 - (base32 - "0y75wzdqbjy565rpxaxscav4j8xg060sa90lnmb7aypgaf251v8v")))) - (build-system python-build-system) - (arguments - ;; Pyro is not compatible with Python 3 - `(#:python ,python-2 - ;; Pyro has no test cases for automatic execution - #:tests? #f)) - (home-page "https://pythonhosted.org/Pyro/") - (synopsis "Distributed object manager for Python") - (description "Pyro is a Distributed Object Technology system -written in Python that is designed to be easy to use. It resembles -Java's Remote Method Invocation (RMI). It has less similarity to CORBA, -which is a system and language independent Distributed Object Technology -and has much more to offer than Pyro or RMI. Pyro 3.x is no -longer maintained. New projects should use Pyro4 instead, which -is the new Pyro version that is actively developed.") - (license license:expat))) - (define-public python-phonenumbers (package (name "python-phonenumbers") From 53ef4cc4048817656506b06c53b6e9fee196361a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:08:44 -0400 Subject: [PATCH 1112/1394] gnu: Remove python2-lazy-object-proxy. * gnu/packages/python-xyz.scm (python2-lazy-object-proxy): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6b2e2331656..11f24330674 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17382,9 +17382,6 @@ inspection of types defined in the Python standard typing module.") until the object is actually required, and caches the result of said call.") (license license:bsd-2))) -(define-public python2-lazy-object-proxy - (package-with-python2 python-lazy-object-proxy)) - (define-public python-dnspython (package (name "python-dnspython") From 242d07cad01b267792b9f39b2002e80975401c7f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:08:59 -0400 Subject: [PATCH 1113/1394] gnu: Remove python2-astor. * gnu/packages/python-xyz.scm (python2-astor): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 11f24330674..0ff7913538d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23776,9 +23776,6 @@ of Python libraries for building Python applications.") source via the Abstract Syntax Tree.") (license license:bsd-3))) -(define-public python2-astor - (package-with-python2 python-astor)) - (define-public python-astunparse (package (name "python-astunparse") From 01bbf6fd67e2c609f5630362a1e895c2c5ea863b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:09:03 -0400 Subject: [PATCH 1114/1394] gnu: Remove python2-requests-file. * gnu/packages/python-xyz.scm (python2-requests-file): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0ff7913538d..a2d1ef9b318 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22688,9 +22688,6 @@ and corruption checks.") library to allow local file system access via @code{file://} URLs.") (license license:asl2.0))) -(define-public python2-requests-file - (package-with-python2 python-requests-file)) - (define-public python-identify (package (name "python-identify") From 6b3cd3c779a6181cbb0a99098ab05bb859ec6b85 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:09:29 -0400 Subject: [PATCH 1115/1394] gnu: Remove python2-backports-abc. * gnu/packages/python-xyz.scm (python2-backports-abc): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a2d1ef9b318..8b12d9b913e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10431,9 +10431,6 @@ low-level X clients. It is written entirely in Python.") @code{collections.abc} module in Python-3.5.") (license license:psfl))) -(define-public python2-backports-abc - (package-with-python2 python-backports-abc)) - (define-public python-backports-csv (package (name "python-backports-csv") From fb081632a33e1fa70ea9ace25881fe2147f962aa Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:09:46 -0400 Subject: [PATCH 1116/1394] gnu: Remove python2-singledispatch. * gnu/packages/python-xyz.scm (python2-singledispatch): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8b12d9b913e..e22ff9dc9e0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10408,9 +10408,6 @@ low-level X clients. It is written entirely in Python.") 2.6-3.3.") (license license:expat))) -(define-public python2-singledispatch - (package-with-python2 python-singledispatch)) - ;; the python- version can be removed with python-3.5 (define-public python-backports-abc (package From a5071d3ab93c545a1e3c827de559e8fc30934ed0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:10:03 -0400 Subject: [PATCH 1117/1394] gnu: Remove python2-waf. * gnu/packages/python-xyz.scm (python2-waf): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e22ff9dc9e0..30c2540dd9e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10529,9 +10529,6 @@ so it might be a tiny bit slower.") applications.") (license license:bsd-3))) -(define-public python2-waf - (package-with-python2 python-waf)) - (define-public python-pyzmq (package (name "python-pyzmq") From cff40b61c2639e657b9ad0e6438a0e8bca6dd5ce Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:10:12 -0400 Subject: [PATCH 1118/1394] gnu: Remove python2-pyrsistent. * gnu/packages/python-xyz.scm (python2-pyrsistent): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 30c2540dd9e..7da5570a908 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3373,9 +3373,6 @@ new copy of the structure containing the requested updates. The original structure is left untouched.") (license license:expat))) -(define-public python2-pyrsistent - (package-with-python2 python-pyrsistent)) - (define-public python-exif-read (package (name "python-exif-read") From 09fb006f8694aa6aec493e01efa65296545d6713 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:10:28 -0400 Subject: [PATCH 1119/1394] gnu: Remove python2-sure. * gnu/packages/python-xyz.scm (python2-sure): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7da5570a908..3c4f2815ed3 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20075,9 +20075,6 @@ while only declaring the test-specific fields.") Sure is heavily inspired by @code{RSpec Expectations} and @code{should.js}.") (license license:gpl3+))) -(define-public python2-sure - (package-with-python2 python-sure)) - (define-public python-misaka (package (name "python-misaka") From a5815cc1bb59d028bfa4bacb65b735df8d5367ab Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:10:36 -0400 Subject: [PATCH 1120/1394] gnu: Remove python2-attrs. * gnu/packages/python-xyz.scm (python2-attrs): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3c4f2815ed3..3f62b0f3b2c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19336,9 +19336,6 @@ JSON) codec.") protocols.") (license license:expat))) -(define-public python2-attrs - (package-with-python2 python-attrs)) - (define-public python-attrs-bootstrap (package (inherit python-attrs) From b8859d30b7453621a53520fb93421d7ceccb87ee Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:10:41 -0400 Subject: [PATCH 1121/1394] gnu: Remove python2-pkgconfig. * gnu/packages/python-xyz.scm (python2-pkgconfig): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3f62b0f3b2c..6c1cc590356 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16336,9 +16336,6 @@ check if a package meets certain version requirements, query CFLAGS and LDFLAGS and parse the output to build extensions with setup.py.") (license license:expat))) -(define-public python2-pkgconfig - (package-with-python2 python-pkgconfig)) - (define-public python-bz2file (package (name "python-bz2file") From 9b0da239eb58f0649d6db2641b05922579882df8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:10:44 -0400 Subject: [PATCH 1122/1394] gnu: Remove python2-pbkdf2. * gnu/packages/python-xyz.scm (python2-pbkdf2): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6c1cc590356..5ff4491d3f5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18976,9 +18976,6 @@ JSON) codec.") a file-like object from which an arbitrarily-sized key can be read.") (license license:expat))) -(define-public python2-pbkdf2 - (package-with-python2 python-pbkdf2)) - (define-public python-qrcode (package (name "python-qrcode") From c3a8ee49bc924fdeec6b5258c573e93231e2d0bd Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:11:02 -0400 Subject: [PATCH 1123/1394] gnu: Remove python2-pylzma. * gnu/packages/python-xyz.scm (python2-pylzma): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5ff4491d3f5..1342bb10a84 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24207,9 +24207,6 @@ access the system cron automatically and simply using a direct API.") by Igor Pavlov.") (license license:lgpl2.1+))) -(define-public python2-pylzma - (package-with-python2 python-pylzma)) - (define-public python-ifaddr (package (name "python-ifaddr") From 08063afd31562f71b7b3e12c270ab46230fa9b6a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:11:08 -0400 Subject: [PATCH 1124/1394] gnu: Remove python2-futures. * gnu/packages/python-xyz.scm (python2-futures): Delete variable. --- gnu/packages/python-xyz.scm | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1342bb10a84..7d8eb7c2ea8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14687,35 +14687,6 @@ in threaded applications. It includes timeout support from Python 3.3 but otherwise matches 3.2’s API.") (license license:psfl))) -(define-public python2-futures - (package - (name "python2-futures") - (version "3.2.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "futures" version)) - (sha256 - (base32 - "0rdjmmsab550kxsssdq49jcniz77zlkpw4pvi9hvib3lsskjmh4y")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "python" "test_futures.py") - #t))))) - (home-page "https://github.com/agronholm/pythonfutures") - (synopsis - "Backport of the concurrent.futures package from Python 3.2") - (description - "The concurrent.futures module provides a high-level interface for -asynchronously executing callables. This package backports the -concurrent.futures package from Python 3.2") - (license license:bsd-3))) - (define-public python-promise (package (name "python-promise") From 0438c799af9190fe1c9b9323a50990668e7f06b6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:11:15 -0400 Subject: [PATCH 1125/1394] gnu: Remove python2-et-xmlfile. * gnu/packages/python-xyz.scm (python2-et-xmlfile): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7d8eb7c2ea8..41fd1efe311 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2541,9 +2541,6 @@ from @code{lxml}. It aims to provide a low memory, compatible implementation of @code{xmlfile}.") (license license:expat))) -(define-public python2-et-xmlfile - (package-with-python2 python-et-xmlfile)) - (define-public python-openpyxl (package (name "python-openpyxl") From 3beeb2a8191f3982ba7032879cb68881d689bc28 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:11:24 -0400 Subject: [PATCH 1126/1394] gnu: Remove python2-m2r. * gnu/packages/python-xyz.scm (python2-m2r): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 41fd1efe311..b7b04f2445d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19250,9 +19250,6 @@ JSON) codec.") reST format.") (license license:expat))) -(define-public python2-m2r - (package-with-python2 python-m2r)) - (define-public python-constantly (package (name "python-constantly") From 85af3513d7ce18c4d34e8e661ebe96d6790fda28 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:11:34 -0400 Subject: [PATCH 1127/1394] gnu: Remove python2-jdcal. * gnu/packages/python-xyz.scm (python2-jdcal): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b7b04f2445d..a6e2eeaf435 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3557,9 +3557,6 @@ version numbers.") between Julian dates and Gregorian dates.") (license license:bsd-2))) -(define-public python2-jdcal - (package-with-python2 python-jdcal)) - (define-public python-jsondiff (package (name "python-jsondiff") From b684e7c82771fd249daa82bac3ff64f5c13ec10f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:11:53 -0400 Subject: [PATCH 1128/1394] gnu: Remove python2-rfc3987. * gnu/packages/python-xyz.scm (python2-rfc3987): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a6e2eeaf435..896d26f7db0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20162,9 +20162,6 @@ while only declaring the test-specific fields.") validation of URIs (see RFC 3986) and IRIs (see RFC 3987).") (license license:gpl3+))) -(define-public python2-rfc3987 - (package-with-python2 python-rfc3987)) - ;; The latest commit contains fixes for building with both python3 and python2. (define-public python-rfc6555 (let ((commit "1a181b432312731f6742a5eb558dae4761d32361") From 9c4efa2f1148a0ed1ff9e50b19f48567c4859f94 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:12:14 -0400 Subject: [PATCH 1129/1394] gnu: Remove python2-jsonpointer. * gnu/packages/python-xyz.scm (python2-jsonpointer): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 896d26f7db0..557997a0d80 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20075,9 +20075,6 @@ while only declaring the test-specific fields.") by path in a JSON document (see RFC 6901).") (license license:bsd-3))) -(define-public python2-jsonpointer - (package-with-python2 python-jsonpointer)) - (define-public python-jsonpatch (package (name "python-jsonpatch") From 862f56e8cb07df8c919ca641de9604294621efa4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:12:17 -0400 Subject: [PATCH 1130/1394] gnu: Remove python2-semantic-version. * gnu/packages/python-xyz.scm (python2-semantic-version): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 557997a0d80..5d9a714dc00 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1852,9 +1852,6 @@ the version levels, and check whether any given string is a proper semantic version identifier.") (license license:bsd-3))) -(define-public python2-semantic-version - (package-with-python2 python-semantic-version)) - (define-public python-serpent (package (name "python-serpent") From 2f049c3ac40a56631b6de740f8ae729114420a82 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:12:26 -0400 Subject: [PATCH 1131/1394] gnu: Remove python2-stemming. * gnu/packages/python-xyz.scm (python2-stemming): Delete variable. --- gnu/packages/python-xyz.scm | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5d9a714dc00..b1918cd2996 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19794,29 +19794,6 @@ point is the point of maximum curvature.") (define-public python2-scandir (package-with-python2 python-scandir)) -(define-public python2-stemming - (package - (name "python2-stemming") - (version "1.0.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "stemming" version)) - (sha256 - (base32 "0ldwa24gnnxhniv0fhygkpc2mwgd93q10ag8rvzayv6hw418frsr")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) - (home-page "https://bitbucket.org/mchaput/stemming/overview") - (synopsis "Python implementations of various stemming algorithms") - (description - "Python implementations of the Porter, Porter2, Paice-Husk, and Lovins - stemming algorithms for English. These implementations are straightforward and - efficient, unlike some Python versions of the same algorithms available on the - Web. This package is an extraction of the stemming code included in the Whoosh - search engine.") - (license license:public-domain))) - (define-public python-factory-boy (package (name "python-factory-boy") From 722fb58519fbd40fc1d4fabb7eb3845950ce7414 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:12:29 -0400 Subject: [PATCH 1132/1394] gnu: Remove python2-pep8. * gnu/packages/python-xyz.scm (python2-pep8): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b1918cd2996..bb502df4b37 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10727,9 +10727,6 @@ application monitoring and error tracking software.") PEP 8.") (license license:expat))) -(define-public python2-pep8 - (package-with-python2 python-pep8)) - (define-public python-pep8-naming (package (name "python-pep8-naming") From 764e195c784d634be95013e866c3aaa5836c257c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:12:36 -0400 Subject: [PATCH 1133/1394] gnu: Remove python2-regex. * gnu/packages/python-xyz.scm (python2-regex): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index bb502df4b37..2b5dbb79abb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20588,9 +20588,6 @@ compatible with the standard @code{re} module, but offers additional functionality like full case-folding for case-insensitive matches in Unicode.") (license license:psfl))) -(define-public python2-regex - (package-with-python2 python-regex)) - (define-public python-pyopengl (package (name "python-pyopengl") From 9075726baa293f8ed9cbd602c0eabe84fb77a22b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:12:45 -0400 Subject: [PATCH 1134/1394] gnu: Remove python2-socksipy-branch. * gnu/packages/python-xyz.scm (python2-socksipy-branch): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2b5dbb79abb..31f8ac2a395 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6815,9 +6815,6 @@ branch created by Mario Vilas to address some open issues, as the original project seems to have been abandoned circa 2007.") (license license:bsd-3))) -(define-public python2-socksipy-branch - (package-with-python2 python-socksipy-branch)) - (define-public python-socksipychain (package (name "python-socksipychain") From 3cf5dfe72ca44f20ecee8837178de141a39fdab2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:12:58 -0400 Subject: [PATCH 1135/1394] gnu: Remove python2-setuptools-scm-git-archive. * gnu/packages/python-xyz.scm (python2-setuptools-scm-git-archive): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 31f8ac2a395..5cc9674499c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21025,9 +21025,6 @@ setuptools_scm, which supports obtaining versions from git archives that belong to tagged versions.") (license license:expat))) -(define-public python2-setuptools-scm-git-archive - (package-with-python2 python-setuptools-scm-git-archive)) - (define-public python-setuptools-git (package (name "python-setuptools-git") From 68f71a2bfded463ceb4bb57a6ba9f7e5d0aea6a1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:13:09 -0400 Subject: [PATCH 1136/1394] gnu: Remove python2-ukpostcodeparser. * gnu/packages/python-xyz.scm (python2-ukpostcodeparser): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5cc9674499c..e678e95ae7e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17461,9 +17461,6 @@ simple, lightweight implementation.") parsing UK postcodes.") (license license:expat))) -(define-public python2-ukpostcodeparser - (package-with-python2 python-ukpostcodeparser)) - (define-public python-faker (package (name "python-faker") From 59a04f3229ebff19bc2c6bcc0b8626ed0db55803 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:13:13 -0400 Subject: [PATCH 1137/1394] gnu: Remove python2-pyld. * gnu/packages/python-xyz.scm (python2-pyld): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e678e95ae7e..865dd80b10d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3403,9 +3403,6 @@ files.") "PyLD is an implementation of the JSON-LD specification.") (license license:bsd-3))) -(define-public python2-pyld - (package-with-python2 python-pyld)) - (define-public python-cli-helpers (package (name "python-cli-helpers") From c7353caca5ff7dc5e7e76ec5d164535d7b08425e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:13:25 -0400 Subject: [PATCH 1138/1394] gnu: Remove python2-mechanize. * gnu/packages/python-xyz.scm (python2-mechanize): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 865dd80b10d..5f8ba8855bc 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2720,9 +2720,6 @@ lossless but can be tweaked for more aggressive cleaning.") after Andy Lester’s Perl module WWW::Mechanize.") (license license:bsd-3))) -(define-public python2-mechanize - (package-with-python2 python-mechanize)) - (define-public python-simpleaudio (package (name "python-simpleaudio") From 059365b96904c788d06a995d61d9e00d40a44963 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:13:31 -0400 Subject: [PATCH 1139/1394] gnu: Remove python2-parse-type. * gnu/packages/python-xyz.scm (python2-parse-type): Delete variable. --- gnu/packages/python-xyz.scm | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5f8ba8855bc..66cfbb77f6a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2922,20 +2922,9 @@ backported for previous versions of Python from 2.4 to 3.3.") (native-inputs (list python-pytest)) (home-page "https://github.com/jenisys/parse_type") (synopsis "Extended parse module") - (description - "Parse_type extends the python parse module.") - (properties - `((python2-variant . ,(delay python2-parse-type)))) + (description "Parse_type extends the python parse module.") (license license:bsd-3))) -(define-public python2-parse-type - (let ((base (package-with-python2 - (strip-python2-variant python-parse-type)))) - (package/inherit base - (propagated-inputs - `(("python2-enum34" ,python2-enum34) - ,@(package-propagated-inputs base)))))) - (define-public python-parse (package (name "python-parse") From 4392bf589f0a654f71e245794bcafc1351f28943 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:13:42 -0400 Subject: [PATCH 1140/1394] gnu: Remove python2-ptyprocess. * gnu/packages/python-xyz.scm (python2-ptyprocess): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 66cfbb77f6a..c45f8ef4361 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11276,9 +11276,6 @@ markdown_py is also provided to convert Markdown files to HTML.") pseudo terminal (pty), and interact with both the process and its pty.") (license license:isc))) -(define-public python2-ptyprocess - (package-with-python2 python-ptyprocess)) - (define-public python-cram (package (name "python-cram") From 87465a718a3cd0bf3b73d254eb2b281173bd78c8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:13:49 -0400 Subject: [PATCH 1141/1394] gnu: Remove python2-flake8. * gnu/packages/python-xyz.scm (python2-flake8): Delete variable. --- gnu/packages/python-xyz.scm | 35 ++++++++++------------------------- 1 file changed, 10 insertions(+), 25 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c45f8ef4361..b38ecc69081 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10862,35 +10862,20 @@ cyclomatic complexity of Python source code.") "0y732h02n2aih8gzyfj4bbhg4jgahyv84mjwfindk2g6w45rka0s")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-v")))))) - (propagated-inputs - (list python-pycodestyle python-entrypoints python-pyflakes - python-mccabe)) - (native-inputs - (list python-mock python-pytest)) + `(#:phases (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-v")))))) + (propagated-inputs (list python-pycodestyle python-entrypoints + python-pyflakes python-mccabe)) + (native-inputs (list python-mock python-pytest)) (home-page "https://gitlab.com/pycqa/flake8") - (synopsis - "The modular source code checker: pep8, pyflakes and co") + (synopsis "The modular source code checker: pep8, pyflakes and co") (description - "Flake8 is a wrapper around PyFlakes, pep8 and python-mccabe.") - (properties `((python2-variant . ,(delay python2-flake8)))) + "Flake8 is a wrapper around PyFlakes, pep8 and python-mccabe.") (license license:expat))) -(define-public python2-flake8 - (let ((base (package-with-python2 (strip-python2-variant python-flake8)))) - (package/inherit base - (propagated-inputs - `(("python2-configparser" ,python2-configparser) - ("python2-enum34" ,python2-enum34) - ("python2-functools32" ,python2-functools32) - ("python2-typing" ,python2-typing) - ,@(package-propagated-inputs base)))))) - (define-public python-flake8-3.8 (package (inherit python-flake8) From b1f059ddf63de4db7aa1391ac6b91b31692d9e4b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:13:58 -0400 Subject: [PATCH 1142/1394] gnu: Remove python2-virtualenv. * gnu/packages/python-xyz.scm (python2-virtualenv): Delete variable. --- gnu/packages/python-xyz.scm | 8 -------- 1 file changed, 8 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b38ecc69081..6aacb472dff 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3937,14 +3937,6 @@ e.g. filters, callbacks and errbacks can all be promises.") "Virtualenv is a tool to create isolated Python environments.") (license license:expat))) -(define-public python2-virtualenv - (let ((base (package-with-python2 (strip-python2-variant python-virtualenv)))) - (package - (inherit base) - (propagated-inputs - (modify-inputs (package-propagated-inputs base) - (prepend python2-contextlib2)))))) - (define-public python-markupsafe (package (name "python-markupsafe") From a53d1098dc6b70c721fddc619de9c41106503d2b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:13 -0400 Subject: [PATCH 1143/1394] gnu: Remove python2-pyasn1. * gnu/packages/python-xyz.scm (python2-pyasn1): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6aacb472dff..402b1b9871b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12442,9 +12442,6 @@ primary use case is APIs defined before keyword-only parameters existed.") suitable for a wide range of protocols based on the ASN.1 specification.") (license license:bsd-2))) -(define-public python2-pyasn1 - (package-with-python2 python-pyasn1)) - (define-public python-pyasn1-modules (package (name "python-pyasn1-modules") From 2f870e1b13b83d35711cc6e03174386f7cd5a97f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:16 -0400 Subject: [PATCH 1144/1394] gnu: Remove chirp. * gnu/packages/radio.scm (chirp): Delete variable. --- gnu/packages/radio.scm | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 1d8167553f7..31d2b0f6255 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -430,30 +430,6 @@ controls for certain tuners which may be paired with an audio device.") "This package provides RTL-SDR devices support to the SoapySDR library.") (license license:expat))) -(define-public chirp - (package - (name "chirp") - (version "20220118") - (source - (origin - (method url-fetch) - (uri (string-append "https://trac.chirp.danplanet.com/chirp_daily/daily-" - version "/chirp-daily-" version ".tar.gz")) - (sha256 - (base32 "0q2ifmprxqqxnww8fx8fjmm2lv9vdv6xzsk1ysa27fb290vgyawn")))) - (build-system python-build-system) - (inputs - (list python2-libxml2 python2-pygtk python2-pyserial)) - (arguments - `(#:python ,python-2)) - (home-page "https://chirp.danplanet.com") - (synopsis "Cross-radio programming tool") - (description "Chirp is a cross-radio programming tool. It supports a -growing list of radios across several manufacturers and allows transferring of -memory contents between them.") - (license (list license:gpl3+ - license:lgpl3+)))) ; chirp/elib_intl.py - (define-public aptdec ;; No release since 2013, use commit directly. (let ((commit "51405971fd4e97714d1e987269e49c6edfe4e0da") From 0dbeb5d2f9676e48cc3a167406192cf0e52efc6f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:19 -0400 Subject: [PATCH 1145/1394] gnu: Remove python2-rdflib. * gnu/packages/rdf.scm (python2-rdflib): Delete variable. --- gnu/packages/rdf.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm index 6712c2c237a..03aecd1ee5f 100644 --- a/gnu/packages/rdf.scm +++ b/gnu/packages/rdf.scm @@ -399,9 +399,6 @@ powerful language for representing information.") ;; and this package is only transitional. (arguments '(#:tests? #f)))) -(define-public python2-rdflib - (package-with-python2 python-rdflib-5)) - ;; Note: This package is only needed for rdflib < 6.0; supersede when ;; the above are removed. (define-public python-rdflib-jsonld From a4210881a87439252e188bb3cccee739b32626e5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:23 -0400 Subject: [PATCH 1146/1394] gnu: Remove python2-gmpy2. * gnu/packages/sagemath.scm (python2-gmpy2): Delete variable. --- gnu/packages/sagemath.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index b603a2f151d..e8a021e91b4 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -101,9 +101,6 @@ but it can be used independently.") libraries GMO, MPFR and MPC.") (license license:lgpl3+))) -(define-public python2-gmpy2 - (package-with-python2 python-gmpy2)) - (define-public cliquer (package (name "cliquer") From 8f2eb654cdc8ba10b602245d8126bbdd27d61930 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:26 -0400 Subject: [PATCH 1147/1394] gnu: Remove python2-cypari2. * gnu/packages/sagemath.scm (python2-cypari2): Delete variable. --- gnu/packages/sagemath.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index e8a021e91b4..7f76f8912bf 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -69,9 +69,6 @@ PARI/GP. It has been spun off from the SageMath mathematics software system, but it can be used independently.") (license license:gpl2+))) -(define-public python2-cypari2 - (package-with-python2 python-cypari2)) - ;; The stable version of the following package is not young enough to be ;; used with Sage, since it does not support cython; so we use a beta ;; release. From b11719f12b7e4865bd434b33e8c6df84aaa87067 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:30 -0400 Subject: [PATCH 1148/1394] gnu: Remove python2-pyscard. * gnu/packages/security-token.scm (python2-pyscard): Delete variable. --- gnu/packages/security-token.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm index 2cc1fa38c06..74ea57137f4 100644 --- a/gnu/packages/security-token.scm +++ b/gnu/packages/security-token.scm @@ -446,9 +446,6 @@ aware applications in Python. The smart card module is built on top of the PCSC API Python wrapper module.") (license license:lgpl2.1+))) -(define-public python2-pyscard - (package-with-python2 python-pyscard)) - (define-public yubikey-oath-dmenu (package (name "yubikey-oath-dmenu") From 082a6f41c46ffaf97ca9a1707200e971f5ca11bd Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:39 -0400 Subject: [PATCH 1149/1394] gnu: Remove python2-patsy. * gnu/packages/statistics.scm (python2-patsy): Delete variable. --- gnu/packages/statistics.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7f543b16e7c..6e18fc3f4d8 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2033,9 +2033,6 @@ building design matrices.") ;; and is covered by the PSFL. (license (list license:bsd-2 license:psfl)))) -(define-public python2-patsy - (package-with-python2 python-patsy)) - (define-public python-statsmodels (package (name "python-statsmodels") From 5a601e8f2b7598afabe5752a25395cef6af30701 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:42 -0400 Subject: [PATCH 1150/1394] gnu: Remove rawdog. * gnu/packages/syndication.scm (rawdog): Delete variable. --- gnu/packages/syndication.scm | 25 ------------------------- 1 file changed, 25 deletions(-) diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm index 20929aa7ade..6eb88afb8f8 100644 --- a/gnu/packages/syndication.scm +++ b/gnu/packages/syndication.scm @@ -491,31 +491,6 @@ a simple interface that makes it easy to organize and browse feeds.") (license (list license:expat license:gpl3+)))) ; tuir/packages/praw -(define-public rawdog - (package - (name "rawdog") - (version "2.23") - (source - (origin - (method url-fetch) - (uri (string-append "https://offog.org/files/rawdog-" - version ".tar.gz")) - (sha256 - (base32 - "18nyg19mwxyqdnykplkqmzb4n27vvrhvp639zai8f81gg9vdbsjp")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2.7)) - (inputs - (list python2-feedparser python2-pytidylib)) - (home-page "https://offog.org/code/rawdog/") - (synopsis "RSS Aggregator Without Delusions Of Grandeur") - (description - "@command{rawdog} is a feed aggregator, capable of producing a personal -\"river of news\" or a public \"planet\" page. It supports all common feed -formats, including all versions of RSS and Atom.") - (license license:gpl2+))) - (define-public gfeeds (package (name "gfeeds") From 59e5142d4f3866ee4ec8ad1ad9d4b5fb2f860459 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:45 -0400 Subject: [PATCH 1151/1394] gnu: Remove python2-pyte. * gnu/packages/terminals.scm (python2-pyte): Delete variable. --- gnu/packages/terminals.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index 83e0e463774..be9f1a0e2a1 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -1063,9 +1063,6 @@ pyte is a fork of vt102, which was an incomplete pure Python implementation of VT100 terminal.") (license license:lgpl3+))) -(define-public python2-pyte - (package-with-python2 python-pyte)) - (define-public python-blessings (package (name "python-blessings") From 42e78fb0a10e4c0fd7c8fbaf40153c0413de98ce Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:48 -0400 Subject: [PATCH 1152/1394] gnu: Remove python2-blessings. * gnu/packages/terminals.scm (python2-blessings): Delete variable. --- gnu/packages/terminals.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index be9f1a0e2a1..4ad21fd05a1 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -1091,9 +1091,6 @@ avoids styling altogether when the output is redirected to something other than a terminal.") (license license:expat))) -(define-public python2-blessings - (package-with-python2 python-blessings)) - (define-public python-curtsies (package (name "python-curtsies") From 96254cbd02b9f4d24bbfff6b6027862ce5e3d193 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:52 -0400 Subject: [PATCH 1153/1394] gnu: Remove virtaal. * gnu/packages/text-editors.scm (virtaal): Delete variable. --- gnu/packages/text-editors.scm | 36 ----------------------------------- 1 file changed, 36 deletions(-) diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index 7cbad042c92..cb86a907ffe 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -1132,42 +1132,6 @@ systems that displays its buffer(s) as a hex dump. The user interface is kept similar to vi/ex.") (license license:bsd-3))) -(define-public virtaal - (package - (name "virtaal") - (version "0.7.1") - (source (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/translate/Virtaal/" - version "/virtaal-" version ".tar.bz2")) - (sha256 - (base32 - "0cyimjp3191qlmw6n0ipqdr9xr0cq4f6dqvz4rl9q31h6l3kywf9")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:use-setuptools? #f - #:tests? #f ;; Failing tests - #:phases - (modify-phases %standard-phases - (add-before 'build 'configure - (lambda* (#:key outputs #:allow-other-keys) - ;; Set data file path to absolute store path. - (substitute* "virtaal/common/pan_app.py" - (("file_discovery\\.get_abs_data_filename.*") - (string-append "os.path.join('" - (assoc-ref outputs "out") - "/share', *path_parts)")))))))) - (inputs - (list python2-lxml python2-pygtk python2-simplejson - python2-translate-toolkit python2-pycurl)) - (synopsis "Graphical translation tool") - (description "Virtaal is a powerful yet simple translation tool with an -uncluttered user interface. It supports a multitude of translation formats -provided by the Translate Toolkit, including XLIFF and PO.") - (home-page "https://virtaal.translatehouse.org/") - (license license:gpl2+))) - (define-public tree-sitter (package (name "tree-sitter") From 041c048119f13e40527ccc20a0819fce4c8663a9 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:14:58 -0400 Subject: [PATCH 1154/1394] gnu: Remove python2-monotonic. * gnu/packages/time.scm (python2-monotonic): Delete variable. --- gnu/packages/time.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index ca5e462680f..496177323e7 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -436,9 +436,6 @@ ISO 8601 dates, time and duration.") value (in fractional seconds) of a clock which never goes backwards.") (license asl2.0))) -(define-public python2-monotonic - (package-with-python2 python-monotonic)) - (define-public python-pyrfc3339 (package (name "python-pyrfc3339") From 17143c8c4d31a70349262976326bb1017ebee40b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:15:02 -0400 Subject: [PATCH 1155/1394] gnu: Remove python2-parsedatetime. * gnu/packages/time.scm (python2-parsedatetime): Delete variable. --- gnu/packages/time.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index 496177323e7..7d1e296176b 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -294,9 +294,6 @@ datetime module, available in Python 2.3+.") "Parse human-readable date/time text.") (license asl2.0))) -(define-public python2-parsedatetime - (package-with-python2 python-parsedatetime)) - (define-public python-ciso8601 (package (name "python-ciso8601") From 1e3beb327d54832192cbf2bb12e00def2ba30625 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:15:11 -0400 Subject: [PATCH 1156/1394] gnu: Remove python2-aniso8601. * gnu/packages/time.scm (python2-aniso8601): Delete variable. --- gnu/packages/time.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index 7d1e296176b..779b6cb495f 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -515,9 +515,6 @@ datetime type.") "This package contains a library for parsing ISO 8601 datetime strings.") (license bsd-3))) -(define-public python2-aniso8601 - (package-with-python2 python-aniso8601)) - (define-public datefudge (package (name "datefudge") From 391251a74ca230555277055e2ae23c59ee49116b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:16:57 -0400 Subject: [PATCH 1157/1394] gnu: Remove python2-tzdata. * gnu/packages/time.scm (python2-tzdata): Delete variable. --- gnu/packages/time.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index 779b6cb495f..9f41f352bb1 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -119,9 +119,6 @@ expressions.") "This library provides a timezone database for Python.") (license expat))) -(define-public python2-tzdata - (package-with-python2 python-pytzdata)) - (define-public python-pytz (package (name "python-pytz") From 75f49c4cc126be6f93c2ed5fd0c54c1deb8d213d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:26:20 -0400 Subject: [PATCH 1158/1394] gnu: Remove python2-defcon. * gnu/packages/fontutils.scm (python2-defcon): Delete variable. --- gnu/packages/fontutils.scm | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm index 7c03109be53..1c824a9100e 100644 --- a/gnu/packages/fontutils.scm +++ b/gnu/packages/fontutils.scm @@ -1504,24 +1504,6 @@ UFO3 as described by the UFO font format.") (modify-inputs (package-propagated-inputs python-defcon-bootstrap) (replace "python-fontpens-bootstrap" python-fontpens)))))) -(define-public python2-defcon - (package - (inherit python-defcon) - (name "python2-defcon") - (version "0.3.5") - (source (origin - (method url-fetch) - (uri (pypi-uri "defcon" version ".zip")) - (sha256 - (base32 - "03jlm2gy9lvbwj68kfdm43yaddwd634jwkdg4wf0jxx2s8mwbg22")))) - (arguments - `(#:python ,python-2)) - (native-inputs - (list unzip python2-pytest python2-pytest-runner)) - (propagated-inputs - (list python2-fonttools python2-ufolib)))) - (define-public nototools (package (name "nototools") From a5e29cd838f8c4e0cbe8de79a5205def563ef579 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:31:00 -0400 Subject: [PATCH 1159/1394] gnu: Remove gess. * gnu/packages/bioinformatics.scm (gess): Delete variable. --- gnu/packages/bioinformatics.scm | 66 --------------------------------- 1 file changed, 66 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 40c060b2dc3..32a9a8d5269 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8984,72 +8984,6 @@ adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files.") (license license:gpl3+))) -(define-public gess - (package - (name "gess") - (version "1.0") - (source (origin - (method url-fetch) - (uri (string-append "http://compbio.uthscsa.edu/" - "GESS_Web/files/" - "gess-" version ".src.tar.gz")) - (sha256 - (base32 - "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; no tests - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((python (assoc-ref inputs "python")) - (out (assoc-ref outputs "out")) - (bin (string-append out "/bin/")) - (target (string-append - out "/lib/python" - ,(version-major+minor - (package-version python)) - "/site-packages/gess/"))) - (mkdir-p target) - (copy-recursively "." target) - ;; Make GESS.py executable - (chmod (string-append target "GESS.py") #o555) - ;; Add Python shebang to the top and make Matplotlib - ;; usable. - (substitute* (string-append target "GESS.py") - (("\"\"\"Description:" line) - (string-append "#!" (which "python") " -import matplotlib -matplotlib.use('Agg') -" line))) - ;; Make sure GESS has all modules in its path - (wrap-script (string-append target "GESS.py") - #:guile (search-input-file inputs "bin/guile") - `("GUIX_PYTHONPATH" ":" = (,target ,(getenv "GUIX_PYTHONPATH")))) - (mkdir-p bin) - (symlink (string-append target "GESS.py") - (string-append bin "GESS.py")) - #t)))))) - (inputs - `(("python" ,python-2) - ("python2-pysam" ,python2-pysam) - ("python2-scipy" ,python2-scipy) - ("python2-numpy" ,python2-numpy) - ("python2-networkx" ,python2-networkx) - ("python2-biopython" ,python2-biopython) - ("guile" ,guile-3.0))) ; for the script wrapper - (home-page "https://compbio.uthscsa.edu/GESS_Web/") - (synopsis "Detect exon-skipping events from raw RNA-seq data") - (description - "GESS is an implementation of a novel computational method to detect de -novo exon-skipping events directly from raw RNA-seq data without the prior -knowledge of gene annotation information. GESS stands for the graph-based -exon-skipping scanner detection scheme.") - (license license:bsd-3))) - (define-public phylip (package (name "phylip") From 955e7d628d6759e8be0d5fb2d8ca9ab4c99a54bf Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:33:43 -0400 Subject: [PATCH 1160/1394] gnu: Remove find-circ. * gnu/packages/bioinformatics.scm (find-circ): Delete variable. --- gnu/packages/bioinformatics.scm | 50 --------------------------------- 1 file changed, 50 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 32a9a8d5269..e8823fed7a3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11677,56 +11677,6 @@ conversions, region filtering, FASTA sequence extraction and more.") (license (list license:expat license:artistic2.0))))) -(define-public find-circ - ;; The last release was in 2015. The license was clarified in 2017, so we - ;; take the latest commit. - (let ((commit "8655dca54970fcf7e92e22fbf57e1188724dda7d") - (revision "1")) - (package - (name "find-circ") - (version (git-version "1.2" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/marvin-jens/find_circ") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0p77pbqbclqr4srms34y1b9b4njybfpjiknc11ki84f3p8skb3cg")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; there are none - #:phases - ;; There is no actual build system. - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (path (getenv "GUIX_PYTHONPATH"))) - (for-each (lambda (script) - (install-file script bin) - (wrap-program (string-append bin "/" script) - `("GUIX_PYTHONPATH" ":" prefix (,path)))) - '("cmp_bed.py" - "find_circ.py" - "maxlength.py" - "merge_bed.py" - "unmapped2anchors.py"))) - #t))))) - (inputs - (list python-2 python2-pysam python2-numpy)) - (home-page "https://github.com/marvin-jens/find_circ") - (synopsis "circRNA detection from RNA-seq reads") - (description "This package provides tools to detect head-to-tail -spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) -in RNA-seq data.") - (license license:gpl3)))) - (define-public fit-sne (package (name "fit-sne") From 4f18b13436f52c107e66056a9dd3a13bb99c8030 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:35:12 -0400 Subject: [PATCH 1161/1394] gnu: Remove python2-matplotlib. * gnu/packages/python-xyz.scm (python2-matplotlib): Delete variable. * tests/profiles.scm ("package->manifest-entry, search paths"): Use python 3 matplotlib in test. --- gnu/packages/python-xyz.scm | 48 +------------------------------------ tests/profiles.scm | 2 +- 2 files changed, 2 insertions(+), 48 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 402b1b9871b..8981ca0e474 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6518,53 +6518,7 @@ quality figures in a variety of hardcopy formats and interactive environments across platforms. Matplotlib can be used in Python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.") - (license license:psfl) - (properties `((python2-variant . ,(delay python2-matplotlib)))))) - -(define-public python2-matplotlib - (let ((matplotlib (package-with-python2 - (strip-python2-variant python-matplotlib)))) - (package/inherit matplotlib - (version "2.2.5") - (source - (origin - (method url-fetch) - (uri (pypi-uri "matplotlib" version)) - (sha256 - (base32 - "1sk05fdai9rw35l983rw2ymvz0nafs7szs7yz4nxrpyr1j27l0x3")))) - (arguments - (substitute-keyword-arguments (package-arguments matplotlib) - ((#:phases phases) - #~(modify-phases #$phases - (add-after 'install 'create-init-file - (lambda _ - (with-output-to-file - (string-append - #$output - "/lib/python2.7/site-packages/mpl_toolkits/__init__.py") - (lambda _ (display ""))))) - (delete 'fix-and-disable-failing-tests) - (delete 'check))))) ; These tests weren't run the the past. - (native-inputs - `(("pkg-config" ,pkg-config))) - (propagated-inputs - `(("gobject-introspection" ,gobject-introspection) - ("python2-backports-functools-lru-cache" ,python2-backports-functools-lru-cache) - ("python2-certifi" ,python2-certifi) - ("python2-cycler" ,python2-cycler) - ("python2-dateutil" ,python2-dateutil) - ("python2-functools32" ,python2-functools32) - ("python2-kiwisolver" ,python2-kiwisolver) - ("python2-numpy" ,python2-numpy) - ("python2-pillow" ,python2-pillow) - ("python2-pycairo" ,python2-pycairo) - ("python2-pygobject-2" ,python2-pygobject-2) - ("python2-pyparsing" ,python2-pyparsing) - ("python2-pytz" ,python2-pytz) - ("python2-six" ,python2-six) - ("python2-subprocess32" ,python2-subprocess32) - ("python2-tkinter" ,python-2 "tk")))))) + (license license:psfl))) (define-public python-matplotlib-documentation (package diff --git a/tests/profiles.scm b/tests/profiles.scm index d59d75985fa..7418b7470f2 100644 --- a/tests/profiles.scm +++ b/tests/profiles.scm @@ -471,7 +471,7 @@ (test-assert "package->manifest-entry, search paths" ;; See . - (let ((mpl (@ (gnu packages python-xyz) python2-matplotlib))) + (let ((mpl (@ (gnu packages python-xyz) python-matplotlib))) (lset= eq? (package-transitive-native-search-paths mpl) (manifest-entry-search-paths From 5ab0cbd0f1e0fa7cca3052a51f032460fb3bb17c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:37:03 -0400 Subject: [PATCH 1162/1394] gnu: Remove python2-numpy. * gnu/packages/python-xyz.scm (python2-numpy): Delete variable. (python2-numpy-1.8): Likewise. (python-numpy)[properties]: Delete field. * gnu/packages/maths.scm (flann): Delete comment. * gnu/packages/chemistry.scm (with-numpy-1.8): Delete procedure. --- gnu/packages/chemistry.scm | 3 -- gnu/packages/maths.scm | 1 - gnu/packages/python-xyz.scm | 69 ------------------------------------- 3 files changed, 73 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index e5b63095853..735d599d2d6 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -303,9 +303,6 @@ with templates to facilitate the execution of the program. Input files can be staged, and output files collected using a standard interface.") (license license:bsd-3))) -(define with-numpy-1.8 - (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8)))) - (define-public tng (package (name "tng") diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 16faf1ec18a..9cecf5cc408 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5366,7 +5366,6 @@ in finite element programs.") ;; Disable it for now. ;;("octave" ,octave-cli) ("python" ,python-2) ; print syntax - ;; ("python2-numpy" ,python2-numpy) ; only required for the tests ("zlib" ,zlib))) (arguments `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8981ca0e474..df27279e6d0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5614,7 +5614,6 @@ with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities.") - (properties `((python2-variant . ,(delay python2-numpy)))) (license license:bsd-3))) (define-public python-numpy-next @@ -5726,74 +5725,6 @@ capabilities.") (description "This package provides the complete NumPy documentation in the Texinfo, HTML, and PDF formats."))) -;; Numpy 1.16.x are the last versions that support Python 2. -(define-public python2-numpy - (let ((numpy (package-with-python2 - (strip-python2-variant python-numpy)))) - (package - (inherit numpy) - (name "python2-numpy") - (version "1.16.5") - (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/numpy/numpy/releases/download/v" - version "/numpy-" version ".tar.gz")) - (sha256 - (base32 - "0lg1cycxzi4rvvrd5zxinpdz0ni792fpx6xjd75z1923zcac8qrb")))) - (arguments - (substitute-keyword-arguments (package-arguments numpy) - ((#:phases phases) - #~(modify-phases #$phases - (add-after 'unpack 'delete-failing-tests - (lambda _ - ;; There's just one failing test here. - (delete-file "numpy/linalg/tests/test_linalg.py") - ;; ...and this one depends on the previous one. - (delete-file "numpy/matrixlib/tests/test_matrix_linalg.py"))) - (replace 'check - ;; Older versions don't cope well with the extra Pytest - ;; options, so remove them. - (lambda* (#:key tests? outputs inputs #:allow-other-keys) - (when tests? - (invoke "./runtests.py" "-vv" "--no-build" "--mode=fast" - "-j" (number->string (parallel-job-count)))))))))) - (native-inputs - (list python2-cython python2-pytest gfortran))))) - -;; NOTE: NumPy 1.8 is packaged only for Python 2 because it is of -;; interest only for legacy code going back to NumPy's predecessor -;; Numeric. -(define-public python2-numpy-1.8 - (package - (inherit python2-numpy) - (version "1.8.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/numpy/numpy") - (commit (string-append "v" version)))) - (file-name (git-file-name "numpy" version)) - (sha256 - (base32 - "0ikgi15rsqwbkfsjjxrwh40lqyal2wvyp3923y6w6ch3dcr82sfk")))) - (arguments (substitute-keyword-arguments (package-arguments python2-numpy) - ((#:tests? _ #f) #f) ;disable tests - ((#:phases phases) - #~(modify-phases #$phases - (delete 'delete-failing-tests))))) - (native-inputs '()) - (description "NumPy is the fundamental package for scientific computing -with Python. It contains among other things: a powerful N-dimensional array -object, sophisticated (broadcasting) functions, tools for integrating C/C++ -and Fortran code, useful linear algebra, Fourier transform, and random number -capabilities. Version 1.8 is the last one to contain the numpy.oldnumeric API -that includes the compatibility layer numpy.oldnumeric with NumPy's predecessor -Numeric.") - (license license:bsd-3))) - (define-public python-munch (package (name "python-munch") From 30413f1180de483b99e757d5b5c21ed775b1fc29 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:40:51 -0400 Subject: [PATCH 1163/1394] gnu: Remove python2-scipy. * gnu/packages/python-science.scm (python2-scipy): Delete variable. (python-scipy)[properties]: Delete field. --- gnu/packages/python-science.scm | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index ccff510ef62..855fe9a72c7 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -154,32 +154,8 @@ atlas_libs = openblas~%" #$(this-package-input "openblas")))))) (description "The SciPy library is one of the core packages that make up the SciPy stack. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.") - (properties `((python2-variant . ,(delay python2-scipy)))) (license license:bsd-3))) -;; Version 1.2.2 is the last version to support Python 2 -(define-public python2-scipy - (package - (inherit (package-with-python2 - (strip-python2-variant python-scipy))) - (version "1.2.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "scipy" version)) - (sha256 - (base32 - "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4")))) - (native-inputs - (list python2-cython - python2-pytest - python2-sphinx - python2-numpydoc - gfortran-7 - gcc-7 - perl - which)))) - (define-public python-scikit-fuzzy (package (name "python-scikit-fuzzy") From d2d222ddc2ab233bf039e9bdb98ffd348a100c5c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:41:12 -0400 Subject: [PATCH 1164/1394] gnu: Remove python2-numpydoc. * gnu/packages/python-xyz.scm (python2-numpydoc): Delete variable. (python-numpy)[properties]: Delete field. --- gnu/packages/python-xyz.scm | 20 +------------------- 1 file changed, 1 insertion(+), 19 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index df27279e6d0..aad5dabe187 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6170,25 +6170,7 @@ parse and apply unified diffs. It has features such as: (home-page "https://pypi.org/project/numpydoc/") (synopsis "Numpy's Sphinx extensions") (description "Sphinx extension to support docstrings in Numpy format.") - (license license:bsd-2) - (properties `((python2-variant . ,(delay python2-numpydoc)))))) - -(define-public python2-numpydoc - (let ((base (package-with-python2 - (strip-python2-variant python-numpydoc)))) - (package/inherit base - ;; This is the last version to support Python 2 - (version "0.9.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "numpydoc" version)) - (sha256 - (base32 - "09x6l1a4dcvj7001bvcmcayg1nwqwhaxlwbp6kzj9qrk57lqx3z0")))) - (propagated-inputs - `(("python2-jinja2" ,python2-jinja2) - ,@(package-propagated-inputs base)))))) + (license license:bsd-2))) (define-public python-numexpr (package From 6792b0b6cde37a56dd77b9a0830eebd6ab57cf99 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:44:05 -0400 Subject: [PATCH 1165/1394] gnu: Remove python2-pysam. * gnu/packages/bioinformatics.scm (python2-pysam): Delete variable. --- gnu/packages/bioinformatics.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e8823fed7a3..9b302475941 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2241,9 +2241,6 @@ SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It also includes an interface for tabix.") (license license:expat))) -(define-public python2-pysam - (package-with-python2 python-pysam)) - (define-public python-twobitreader (package (name "python-twobitreader") From aa8ec684ab43fe5c348c20ea3f7a151af3eb8ffe Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:44:39 -0400 Subject: [PATCH 1166/1394] gnu: Remove python2-ufolib. * gnu/packages/fontutils.scm (python2-ufolib): Delete variable. --- gnu/packages/fontutils.scm | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm index 1c824a9100e..712517c6853 100644 --- a/gnu/packages/fontutils.scm +++ b/gnu/packages/fontutils.scm @@ -1442,30 +1442,6 @@ other support classes. Where useful and possible, ufoLib2 tries to be API-compatible with defcon.") (license license:asl2.0))) -(define-public python2-ufolib - (package - (name "python2-ufolib") - (version "2.1.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "ufoLib" version ".zip")) - (sha256 - (base32 "07qy6mx7z0wi9a30lc2hj5i9q1gnz1n8l40dmjz2c19mj9s6mz9l")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) - (propagated-inputs - (list python2-fonttools)) - (native-inputs - (list unzip python2-pytest python2-pytest-runner)) - (home-page "https://github.com/unified-font-object/ufoLib") - (synopsis "Low-level UFO reader and writer") - (description - "UfoLib reads and writes Unified Font Object (UFO) -files. UFO is a file format that stores fonts source files.") - (license license:bsd-3))) - ;;; A variant used to break a cycle between python-fontpens and ;;; python-fontparts. (define-public python-defcon-bootstrap From 8824061544976e6113e5ae83ad55787662f6974e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:45:08 -0400 Subject: [PATCH 1167/1394] gnu: Remove python2-kiwisolver. * gnu/packages/maths.scm (python2-kiwisolver): Delete variable. --- gnu/packages/maths.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 9cecf5cc408..54ea2af5155 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3336,9 +3336,6 @@ Cassowary solver with typical use cases gaining a 40x improvement. Memory savings are consistently > 5x.") (license license:bsd-3))) -(define-public python2-kiwisolver - (package-with-python2 python-kiwisolver)) - (define-public slepc (package (name "slepc") From 26f5764071e606658a8b244bb2cc1d1724cd5481 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:45:39 -0400 Subject: [PATCH 1168/1394] gnu: Remove python2-cookies. * gnu/packages/python-web.scm (python2-cookies): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index a50f071debf..2950a095eb4 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -3232,9 +3232,6 @@ Python.") (home-page "https://gitlab.com/sashahart/cookies") (license license:expat))) -(define-public python2-cookies - (package-with-python2 python-cookies)) - (define-public python-responses (package (name "python-responses") From c427de65313f5875c0fc2b5af41d16a346e70214 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:45:48 -0400 Subject: [PATCH 1169/1394] gnu: Remove python2-pycurl. * gnu/packages/python-web.scm (python2-pycurl): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 2950a095eb4..f4302e0108f 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1414,9 +1414,6 @@ high-speed transfers via libcurl and frequently outperforms alternatives.") ;; under the terms of LGPLv2.1+ or Expat. (license (list license:lgpl2.1+ license:expat)))) -(define-public python2-pycurl - (package-with-python2 python-pycurl)) - (define-public python-webencodings (package (name "python-webencodings") From 0d74e94f1023091a6fec4626212147233ccf6c7b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:46:02 -0400 Subject: [PATCH 1170/1394] gnu: Remove python2-cleo. * gnu/packages/python-xyz.scm (python2-cleo): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index aad5dabe187..3341330fe7c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16789,9 +16789,6 @@ Wikipedia code samples at docstring and colored output.") (license license:expat))) -(define-public python2-cleo - (package-with-python2 python-cleo)) - (define-public python-tomlkit (package (name "python-tomlkit") From c75c1e811e6e602f30bdd2da1e32e93cedb074e7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:46:12 -0400 Subject: [PATCH 1171/1394] gnu: Remove python2-entrypoints. * gnu/packages/python-xyz.scm (python2-entrypoints): Delete variable. --- gnu/packages/python-xyz.scm | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3341330fe7c..9b6d3eb5696 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -13250,15 +13250,7 @@ objects with some common interface. The most common examples are @code{console_scripts} entry points, which define shell commands by identifying a Python function to run. The @code{entrypoints} module contains functions to find and load entry points.") - (license license:expat) - (properties `((python2-variant . ,(delay python2-entrypoints)))))) - -(define-public python2-entrypoints - (package - (inherit (package-with-python2 - (strip-python2-variant python-entrypoints))) - (propagated-inputs - (list python2-configparser)))) + (license license:expat))) (define-public python-epc (package From bec1c898917d571cc099bda20472bac4377fb22a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:46:33 -0400 Subject: [PATCH 1172/1394] gnu: Remove python2-mccabe. * gnu/packages/python-xyz.scm (python2-mccabe): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- guix/lint.scm | 20 ++++++++++---------- 2 files changed, 10 insertions(+), 13 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9b6d3eb5696..76fe4d61581 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10706,9 +10706,6 @@ file (e.g. @file{PKG-INFO}).") cyclomatic complexity of Python source code.") (license license:expat))) -(define-public python2-mccabe - (package-with-python2 python-mccabe)) - (define-public python-flake8 (package (name "python-flake8") diff --git a/guix/lint.scm b/guix/lint.scm index 375f189335c..aa16efe6dbb 100644 --- a/guix/lint.scm +++ b/guix/lint.scm @@ -494,16 +494,16 @@ of a package, and INPUT-NAMES, a list of package specifications such as "m4" "qttools" "yasm" "nasm" "fasm" - "python-coverage" "python2-coverage" - "python-cython" "python2-cython" - "python-docutils" "python2-docutils" - "python-mock" "python2-mock" - "python-nose" "python2-nose" - "python-pbr" "python2-pbr" - "python-pytest" "python2-pytest" - "python-pytest-cov" "python2-pytest-cov" - "python-setuptools-scm" "python2-setuptools-scm" - "python-sphinx" "python2-sphinx" + "python-coverage" + "python-cython" + "python-docutils" + "python-mock" + "python-nose" + "python-pbr" + "python-pytest" + "python-pytest-cov" + "python-setuptools-scm" + "python-sphinx" "scdoc" "swig" "qmake" From 6ce91100d6c778af97c12c74de44381dbb4da823 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:46:44 -0400 Subject: [PATCH 1173/1394] gnu: Remove python2-networkx. * gnu/packages/python-xyz.scm (python2-networkx): Delete variable. --- gnu/packages/python-xyz.scm | 32 ++++++-------------------------- 1 file changed, 6 insertions(+), 26 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 76fe4d61581..b1044fb5408 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9559,37 +9559,17 @@ interfaces in an easy and portable manner.") (lambda* (#:key tests? #:allow-other-keys) (if tests? (invoke "pytest" "-vv" "--pyargs" "networkx") - (format #t "test suite not run~%")) - #t))))) - ;; python-decorator is needed at runtime. - (propagated-inputs - (list python-decorator)) - (native-inputs - (list python-pytest)) + (format #t "test suite not run~%")) #t))))) + (propagated-inputs (list python-decorator)) + (native-inputs (list python-pytest)) (home-page "https://networkx.github.io/") - (synopsis "Python module for creating and manipulating graphs and networks") + (synopsis + "Python module for creating and manipulating graphs and networks") (description - "NetworkX is a Python package for the creation, manipulation, and study + "NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.") - (properties `((python2-variant . ,(delay python2-networkx)))) (license license:bsd-3))) -;; NetworkX 2.2 is the last version with support for Python 2. -(define-public python2-networkx - (let ((base (package-with-python2 (strip-python2-variant python-networkx)))) - (package - (inherit base) - (version "2.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "networkx" version ".zip")) - (sha256 - (base32 - "12swxb15299v9vqjsq4z8rgh5sdhvpx497xwnhpnb0gynrx6zra5")))) - (arguments - `(#:python ,python-2)) - (native-inputs - (list python2-nose unzip))))) (define-public python-datrie (package From 674c7b765a19c3da6cff639639c01ea4111936a7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:46:51 -0400 Subject: [PATCH 1174/1394] gnu: Remove python2-pycodestyle. * gnu/packages/python-xyz.scm (python2-pycodestyle): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b1044fb5408..e47d1ca8bff 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6710,9 +6710,6 @@ Python code against some of the style conventions in @url{http://www.python.org/dev/peps/pep-0008/,PEP 8}.") (license license:expat))) -(define-public python2-pycodestyle - (package-with-python2 python-pycodestyle)) - (define-public python-pycodestyle-2.6 (package (inherit python-pycodestyle) From c0a8ddc36d6ca8df9486159dd0f66b40ece66a0d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:47:00 -0400 Subject: [PATCH 1175/1394] gnu: Remove python2-pyserial. * gnu/packages/python-xyz.scm (python2-pyserial): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e47d1ca8bff..3e43add7892 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17620,9 +17620,6 @@ as well.") and/or Xon/Xoff. The port is accessed in RAW mode.") (license license:bsd-3))) -(define-public python2-pyserial - (package-with-python2 python-pyserial)) - (define-public python-pyserial-asyncio (package (name "python-pyserial-asyncio") From 2f7eee37b946ec726bdefa97a1d0a622090b2cb5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:47:23 -0400 Subject: [PATCH 1176/1394] gnu: Remove python2-cycler. * gnu/packages/python-xyz.scm (python2-cycler): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3e43add7892..cbd463459cd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6225,9 +6225,6 @@ To address this and enable easy cycling over arbitrary @code{kwargs}, the @code{Cycler} class was developed.") (license license:bsd-3))) -(define-public python2-cycler - (package-with-python2 python-cycler)) - (define-public python-colorspacious (package (name "python-colorspacious") From ffec658a72bf1053842d9237b939c86779f497da Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:47:34 -0400 Subject: [PATCH 1177/1394] gnu: Remove python2-future. * gnu/packages/python-xyz.scm (python2-future): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cbd463459cd..5c8bf5412d1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16140,9 +16140,6 @@ Python 3. It allows you to use a single, clean Python 3.x-compatible codebase to support both Python 2 and Python 3 with minimal overhead.") (license license:expat))) -(define-public python2-future - (package-with-python2 python-future)) - (define-public python-cysignals (package (name "python-cysignals") From 4c17f2b3fe209296ba6f1f9dabde9d3a4b0ce7c0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:47:43 -0400 Subject: [PATCH 1178/1394] gnu: Remove python2-mistune. * gnu/packages/python-xyz.scm (python2-mistune): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5c8bf5412d1..72868cd4826 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11024,9 +11024,6 @@ It also removes useless @code{pass} statements.") Python.") (license license:bsd-3))) -(define-public python2-mistune - (package-with-python2 python-mistune)) - ;; 2.0 is not released yet, but some packages have started using it. (define-public python-mistune-next (package From 4a2e05d1483e9775cb11daaeb236609d45c49690 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:47:46 -0400 Subject: [PATCH 1179/1394] gnu: Remove python2-cysignals. * gnu/packages/python-xyz.scm (python2-cysignals): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 72868cd4826..158caca68c9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16177,9 +16177,6 @@ for mixed Cython/Python code or external C libraries and pure Cython code, respectively.") (license license:lgpl3+))) -(define-public python2-cysignals - (package-with-python2 python-cysignals)) - (define-public python-rope (package (name "python-rope") From f283842e3c9125b7d8f1d356509e6c92d810cd4d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:48:21 -0400 Subject: [PATCH 1180/1394] gnu: Remove python2-pytidylib. * gnu/packages/python-xyz.scm (python2-pytidylib): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 158caca68c9..9b04da8acd7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -26152,9 +26152,6 @@ be necessary when using @code{cmd}.") allows you, from Python code, to “fix” invalid (X)HTML markup.") (license license:expat))) -(define-public python2-pytidylib - (package-with-python2 python-pytidylib)) - (define-public python-mujson (package (name "python-mujson") From 6ce1f74c9a91de93951a480baa2b33d3d2ce6317 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 30 Apr 2022 00:06:55 -0400 Subject: [PATCH 1181/1394] gnu: Remove python2-sphinx. * gnu/packages/sphinx.scm (python2-sphinx): Delete variable. (python-sphinx)[properties]: Delete field. --- gnu/packages/sphinx.scm | 49 +---------------------------------------- 1 file changed, 1 insertion(+), 48 deletions(-) diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 93f174217a6..2c4eb09d040 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -146,54 +146,7 @@ (description "Sphinx is a tool that makes it easy to create documentation for Python projects or other documents consisting of multiple reStructuredText sources.") - (license license:bsd-2) - (properties `((python2-variant . ,(delay python2-sphinx)))))) - -;; Sphinx 2 does not support Python 2, so we stick with this older version here. -(define-public python2-sphinx - (let ((base (package-with-python2 (strip-python2-variant python-sphinx)))) - (package - (inherit base) - (version "1.7.7") - (source (origin - (method url-fetch) - (uri (pypi-uri "Sphinx" version)) - (sha256 - (base32 - "0pkkbfj7cl157q550gcs45am5y78ps0h7q6455d64s1zmw01jlvi")))) - (arguments - (substitute-keyword-arguments (package-arguments base) - ((#:phases phases) - `(modify-phases ,phases - (add-before 'check 'disable-broken-tests - (lambda _ - (for-each delete-file - ;; These tests are broken when using Python2: - ;; . - '("tests/test_api_translator.py" - "tests/test_setup_command.py" - ;; Websupport is provided by a separate package - "tests/test_websupport.py" - ;; This one fails for unknown reasons. - "tests/test_correct_year.py")))))))) - (native-inputs (modify-inputs (package-native-inputs base) - (prepend python2-mock python2-enum34))) - ;; Sphinx 2 has some dependencies that do not support Python 2, so - ;; we keep our own propagated-inputs here instead of inheriting. - (propagated-inputs - (list python2-pytz - python2-typing - python2-imagesize - python2-sphinx-alabaster-theme - python2-babel - python2-snowballstemmer - python2-docutils-0.14 - python2-jinja2 - python2-packaging - python2-pygments - python2-requests - python2-six - python2-sphinxcontrib-websupport))))) + (license license:bsd-2))) (define-public python-sphinxcontrib-apidoc (package From 5bd5443ededb922cbbd74e3b271770ca4ddc6bf5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:48:33 -0400 Subject: [PATCH 1182/1394] gnu: Remove python2-docutils. * gnu/packages/python-xyz.scm (python2-docutils): Delete variable. (python2-docutils-0.14): Likewise. --- gnu/packages/python-xyz.scm | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9b04da8acd7..6a796b92adc 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4310,9 +4310,6 @@ via commands such as @command{rst2man}, as well as supporting Python code.") ;; licensed under the PFSL, BSD 2-clause, and GPLv3+ licenses. (license (list license:public-domain license:psfl license:bsd-2 license:gpl3+)))) -(define-public python2-docutils - (package-with-python2 python-docutils)) - ;; awscli refuses to be built with docutils < 0.16. (define-public python-docutils-0.15 (package @@ -4327,18 +4324,6 @@ via commands such as @command{rst2man}, as well as supporting Python code.") ;; tests contain Python 2 syntax. (arguments '(#:tests? #false)))) -;; python2-sphinx fails its test suite with newer versions. -(define-public python2-docutils-0.14 - (package - (inherit python2-docutils) - (version "0.14") - (source (origin - (method url-fetch) - (uri (pypi-uri "docutils" version)) - (sha256 - (base32 - "0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji")))))) - (define-public python-restructuredtext-lint (package (name "python-restructuredtext-lint") From 787e582c47f4de3bb8dea14a2041c272d8240d0f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:49:25 -0400 Subject: [PATCH 1183/1394] gnu: Remove python2-translate-toolkit. * gnu/packages/python-xyz.scm (python2-translate-toolkit): Delete variable. --- gnu/packages/python-xyz.scm | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6a796b92adc..dba156eaa8e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19605,18 +19605,6 @@ while only declaring the test-specific fields.") several utilities, as well as an API for building localization tools.") (license license:gpl2+))) -;; Required for virtaal, newer versions do not build with python2 -(define-public python2-translate-toolkit - (package-with-python2 - (package - (inherit python-translate-toolkit) - (version "2.1.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "translate-toolkit" version ".tar.bz2")) - (sha256 - (base32 "1vlkwrg83vb17jc36pmwh2b7jphwf390lz0jw8hakcg16qhwypvq"))))))) (define-public python-packaging (package/inherit python-packaging-bootstrap From 64c86457db9dceafc3453967e9f6c6fec776ab13 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:49:31 -0400 Subject: [PATCH 1184/1394] gnu: Remove python2-subprocess32. * gnu/packages/python-xyz.scm (python2-subprocess32): Delete variable. * gnu/packages/patches/python2-subprocess32-disable-input-test.patch: Delete file. * gnu/local.mk (dist_patch_DATA): De-register it. --- gnu/local.mk | 1 - ...hon2-subprocess32-disable-input-test.patch | 18 --------- gnu/packages/python-xyz.scm | 37 ------------------- 3 files changed, 56 deletions(-) delete mode 100644 gnu/packages/patches/python2-subprocess32-disable-input-test.patch diff --git a/gnu/local.mk b/gnu/local.mk index 1a0b998de33..a4d5235be67 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1721,7 +1721,6 @@ dist_patch_DATA = \ %D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \ %D%/packages/patches/python-seaborn-kde-test.patch \ %D%/packages/patches/python-seaborn-2690.patch \ - %D%/packages/patches/python2-subprocess32-disable-input-test.patch \ %D%/packages/patches/python-unittest2-python3-compat.patch \ %D%/packages/patches/python-unittest2-remove-argparse.patch \ %D%/packages/patches/python-versioneer-guix-support.patch \ diff --git a/gnu/packages/patches/python2-subprocess32-disable-input-test.patch b/gnu/packages/patches/python2-subprocess32-disable-input-test.patch deleted file mode 100644 index 05b4eef1ba2..00000000000 --- a/gnu/packages/patches/python2-subprocess32-disable-input-test.patch +++ /dev/null @@ -1,18 +0,0 @@ -This test tries to send a KeyboardInterrupt, which does -not work in the build environment. - ---- a/test_subprocess32.py 2017-03-06 22:21:49.334045485 +0100 -+++ b/test_subprocess32.py 2017-03-06 22:22:02.490439949 +0100 -@@ -1299,12 +1299,6 @@ - getattr(p, method)(*args) - return p - -- def test_send_signal(self): -- p = self._kill_process('send_signal', signal.SIGINT) -- _, stderr = p.communicate() -- self.assertIn('KeyboardInterrupt', stderr) -- self.assertNotEqual(p.wait(), 0) -- - def test_kill(self): - p = self._kill_process('kill') - _, stderr = p.communicate() diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index dba156eaa8e..31c597a8593 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14401,43 +14401,6 @@ to the Python ecosystem.") 3.2.3 for use with older versions of Python and PyPy.") (license license:expat))) -(define-public python2-subprocess32 - (package - (name "python2-subprocess32") - (version "3.2.7") - (source (origin - (method url-fetch) - (uri (pypi-uri "subprocess32" version)) - (sha256 - (base32 - "14350dhhlhyz5gqzi3lihn9m6lvskx5mcb20srx1kgsk9i50li8y")) - (patches - (search-patches "python2-subprocess32-disable-input-test.patch")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - ;; The test suite fails with Python > 2.7.13: - ;; import test.support - ;; ImportError: No module named support - #:tests? #f - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-/bin/sh - (lambda _ - (substitute* '("subprocess32.py" - "test_subprocess32.py") - (("/bin/sh") (which "sh"))) - #t))))) - (home-page "https://github.com/google/python-subprocess32") - (synopsis "Backport of the subprocess module from Python 3.2") - (description - "This is a backport of the @code{subprocess} standard library module -from Python 3.2 and 3.3 for use on Python 2. It includes bugfixes and some -new features. On POSIX systems it is guaranteed to be reliable when used -in threaded applications. It includes timeout support from Python 3.3 but -otherwise matches 3.2’s API.") - (license license:psfl))) - (define-public python-promise (package (name "python-promise") From ff37995afc60de2412b60fd88b7a3a2025194a71 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:49:35 -0400 Subject: [PATCH 1185/1394] gnu: Remove python2-pyflakes. * gnu/packages/python-xyz.scm (python2-pyflakes): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 31c597a8593..26c39d0f6d4 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10629,9 +10629,6 @@ file (e.g. @file{PKG-INFO}).") "Pyflakes statically checks Python source code for common errors.") (license license:expat))) -(define-public python2-pyflakes - (package-with-python2 python-pyflakes)) - (define-public python-pyflakes-2.2 (package (inherit python-pyflakes) From 89f3f16a8435145cbc75d040441a498e6497873a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:49:41 -0400 Subject: [PATCH 1186/1394] gnu: Remove python2-pympler. * gnu/packages/python-xyz.scm (python2-pympler): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 26c39d0f6d4..2255d0c0822 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3822,9 +3822,6 @@ A web profiling frontend exposes process statistics, garbage visualisation and class tracker statistics.") (license license:asl2.0))) -(define-public python2-pympler - (package-with-python2 python-pympler)) - (define-public python-itsdangerous (package (name "python-itsdangerous") From 9257f235f09ce9da68b4329ee1ad888eb8e40f52 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:49:57 -0400 Subject: [PATCH 1187/1394] gnu: Remove python2-isodate. * gnu/packages/time.scm (python2-isodate): Delete variable. --- gnu/packages/time.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index 9f41f352bb1..2930d1f3a7c 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -378,9 +378,6 @@ under several distributions that's hard or impossible to figure out.") ISO 8601 dates, time and duration.") (license bsd-3))) -(define-public python2-isodate - (package-with-python2 python-isodate)) - (define-public python-iso8601 (package (name "python-iso8601") From 74f9e518c674e25ff4598c8887461bb26bbfb8ac Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:50:02 -0400 Subject: [PATCH 1188/1394] gnu: Remove python2-pyrfc3339. * gnu/packages/time.scm (python2-pyrfc3339): Delete variable. --- gnu/packages/time.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index 2930d1f3a7c..4ff7b889ac4 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -449,9 +449,6 @@ value (in fractional seconds) of a clock which never goes backwards.") timestamps.") (license expat))) -(define-public python2-pyrfc3339 - (package-with-python2 python-pyrfc3339)) - (define-public python-arrow (package (name "python-arrow") From 139d78581f74721ae9bb4cd473d5d54da8042730 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:50:13 -0400 Subject: [PATCH 1189/1394] gnu: Remove youtube-dl-gui. * gnu/packages/video.scm (youtube-dl-gui): Delete variable. --- gnu/packages/video.scm | 97 ------------------------------------------ 1 file changed, 97 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index bddfbf1128a..d10382a7382 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2528,103 +2528,6 @@ original project.") (properties '((release-monitoring-url . "https://pypi.org/project/yt-dlp/"))) (home-page "https://github.com/yt-dlp/yt-dlp"))) -(define-public youtube-dl-gui - (package - (name "youtube-dl-gui") - (version "0.4") - (source - (origin - (method url-fetch) - (uri (pypi-uri "Youtube-DLG" version)) - (sha256 - (base32 - "1bvq2wyn6az59vpdy04dh68fs8m2qzz948xhphibbcpwpcdk00cd")))) - (build-system python-build-system) - (arguments - ;; In Guix, wxpython has not yet been packaged for Python 3. - `(#:python ,python-2 - ;; This package has no tests. - #:tests? #f - #:phases - (modify-phases %standard-phases - (add-before 'build 'patch-source - (lambda* (#:key inputs #:allow-other-keys) - ;; The youtube-dl-gui program lets you configure options. Some of - ;; them are problematic, so we change their defaults. - (substitute* "youtube_dl_gui/optionsmanager.py" - ;; When this is true, the builder process will try (and fail) to - ;; write logs to the builder user's home directory. - (("'enable_log': True") "'enable_log': False") - ;; This determines which youtube-dl program youtube-dl-gui will - ;; run. If we don't set this, then youtube-dl-gui might download - ;; an arbitrary copy from the Internet into the user's home - ;; directory and run it, so let's make sure youtube-dl-gui uses - ;; the youtube-dl from the inputs by default. - (("'youtubedl_path': self.config_path") - (string-append "'youtubedl_path': '" - (assoc-ref inputs "youtube-dl") - "/bin'")) - ;; When this is True, when youtube-dl-gui is finished downloading - ;; a file, it will try (and possibly fail) to open the directory - ;; containing the downloaded file. This can fail because it - ;; assumes that xdg-open is in PATH. Unfortunately, simply - ;; adding xdg-utils to the propagated inputs is not enough to - ;; make this work, so for now we set the default to False. - (("'open_dl_dir': True") "'open_dl_dir': False")) - ;; The youtube-dl program from the inputs is actually a wrapper - ;; script written in bash, so attempting to invoke it as a python - ;; script will fail. - (substitute* "youtube_dl_gui/downloaders.py" - (("cmd = \\['python', self\\.youtubedl_path\\]") - "cmd = [self.youtubedl_path]")) - ;; Use relative paths for installing data files so youtube-dl-gui - ;; installs the files relative to its prefix in the store, rather - ;; than relative to /. Also, instead of installing data files into - ;; $prefix/usr/share, install them into $prefix/share for - ;; consistency (see: (standards) Directory Variables). - (substitute* "setup.py" - (("= '/usr/share") "= 'share")) - ;; Update get_locale_file() so it finds the installed localization - ;; files. - (substitute* "youtube_dl_gui/utils.py" - (("os\\.path\\.join\\('/usr', 'share'") - (string-append "os.path.join('" - (assoc-ref %outputs "out") - "', 'share'"))) - #t)) - (add-after 'install 'create-desktop-file - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (applications (string-append out "/share/applications"))) - (mkdir-p applications) - (call-with-output-file - (string-append applications "/youtube-dl-gui.desktop") - (lambda (file) - (format - file - "[Desktop Entry]~@ - Name=Youtube-dl GUI~@ - Comment=Graphical interface to download video with youtube-dl~@ - Exec=youtube-dl-gui~@ - TryExec=youtube-dl-gui~@ - Terminal=false~@ - Icon=youtube-dl-gui~@ - Type=Application~@ - Categories=AudioVideo;Audio;Video;Network~%"))) - #t)))))) - (native-inputs - (list gettext-minimal)) - (inputs - (list python2-twodict python2-wxpython youtube-dl)) - (home-page "https://github.com/MrS0m30n3/youtube-dl-gui") - (synopsis - "GUI (Graphical User Interface) for @command{youtube-dl}") - (description - "Youtube-dlG is a GUI (Graphical User Interface) for -@command{youtube-dl}. You can use it to download videos from YouTube and any -other site that youtube-dl supports.") - (license license:unlicense))) - (define-public you-get (package (name "you-get") From 1475672e5fdb6ca534762f373f0183b225d303d6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 5 May 2022 08:18:57 -0400 Subject: [PATCH 1190/1394] gnu: Add python-avocado-framework. * gnu/packages/python-check.scm (python-avocado-framework): New variable. --- gnu/packages/python-check.scm | 82 +++++++++++++++++++++++++++++++++++ 1 file changed, 82 insertions(+) diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index d788935caa1..0803d6fed2e 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -33,9 +33,14 @@ (define-module (gnu packages python-check) #:use-module (gnu packages) + #:use-module (gnu packages admin) + #:use-module (gnu packages base) + #:use-module (gnu packages bash) #:use-module (gnu packages check) + #:use-module (gnu packages docker) #:use-module (gnu packages django) #:use-module (gnu packages openstack) + #:use-module (gnu packages perl) #:use-module (gnu packages python-build) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) @@ -2102,6 +2107,83 @@ The purpose of this package is to provide an easy way to test asynchronous HTTP requests.") (license license:expat))) +(define-public python-avocado-framework + (package + (name "python-avocado-framework") + (version "96.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "avocado-framework" version)) + (sha256 + (base32 "0zhz6423p0b5gqx2mvg7dmq8m9gbsay7wqjdwzirlwcg2v3rcz0m")))) + (build-system python-build-system) + (arguments + (list + ;; The test suite hangs, due to a serious bug in Python/Avocado (see: + ;; https://github.com/avocado-framework/avocado/issues/4935). + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda* (#:key native-inputs inputs #:allow-other-keys) + ;; These are runtime dependencies (inputs). + (substitute* "avocado/plugins/spawners/podman.py" + (("default='/usr/bin/podman'") + "default='podman'")) + (substitute* "avocado/utils/podman.py" + (("\"/usr/bin/env\", \"python3\"") + (format #f "~s" (search-input-file inputs "bin/python")))) + (substitute* "avocado/utils/memory.py" + (("\"sync\"") + (format #f "~s" (search-input-file inputs "bin/sync"))) + (("/bin/sh") + (search-input-file inputs "bin/sh"))) + ;; Batch process the tests modules with less care; if something + ;; is wrong, the test suite will fail. These are tests + ;; dependencies (native inputs). + (substitute* (find-files "selftests" "\\.py$") + (("#!/usr/bin/env") + (string-append "#!" (search-input-file (or native-inputs inputs) + "bin/env"))) + (("/bin/(false|true|sh|sleep|sudo)" _ name) + (search-input-file (or native-inputs inputs) + (string-append "bin/" name)))))) + (add-after 'unpack 'remove-broken-entrypoints + ;; The avocado-external-runner entry point fails to load, the + ;; 'scripts' top level package not being found (see: + ;; https://github.com/avocado-framework/avocado/issues/5370). + (lambda _ + (substitute* "setup.py" + (("'avocado-external-runner = scripts.external_runner:main'.*") + "")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") + (setenv "PYTHONPATH" (getcwd)) + (invoke "./selftests/check.py" "--skip" "static-checks"))))))) + (native-inputs (list bash-minimal coreutils-minimal perl sudo)) + (inputs (list bash-minimal coreutils-minimal)) + (home-page "https://avocado-framework.github.io/") + (synopsis "Tools and libraries to help with automated testing") + (description "Avocado is a set of tools and libraries to help with +automated testing, i.e. a test framework. Native tests are written in Python +and they follow the unittest pattern, but any executable can serve as a +test. The following output formats are supported: +@table @asis +@item xUnit +an XML format that contains test results in a structured form, and are used by +other test automation projects, such as Jenkins. +@item JSON +a widely used data exchange format. The JSON Avocado plugin outputs job +information, similarly to the xunit output plugin. +@item TAP +Provides the basic TAP (Test Anything Protocol) results. Unlike most existing +Avocado machine readable outputs this one is streamlined (per test results). +@end table") + (license license:gpl2))) ;some files are under GPLv2 only + (define-public python-parameterizedtestcase (package (name "python-parameterizedtestcase") From 99c68135469e53eace92877f7279b4175ef80c8b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 5 May 2022 08:29:10 -0400 Subject: [PATCH 1191/1394] gnu: python-pygments: Update to 2.12.0. * gnu/packages/python-xyz.scm (python-pygments): Update to 2.12.0. (python2-pygments): Delete variable. --- gnu/packages/python-xyz.scm | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2255d0c0822..5b210bc4d91 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4438,21 +4438,7 @@ text styles of documentation.") (synopsis "Syntax highlighting") (description "Pygments is a syntax highlighting package written in Python.") - (license license:bsd-2) - (properties `((python2-variant . ,(delay python2-pygments)))))) - -;; Pygments 2.6 and later does not support Python 2. -(define-public python2-pygments - (let ((base (package-with-python2 (strip-python2-variant python-pygments)))) - (package - (inherit base) - (version "2.5.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "Pygments" version)) - (sha256 - (base32 - "1zmhnswy0wxfn0xprs9aqsvx2c3kmzfn2wx14q8cv3vpkxdamj4q"))))))) + (license license:bsd-2))) (define-public python-pygments-github-lexers (package From 6d398096e23dc940437c990c86f7043c78a77f8f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 5 May 2022 08:34:23 -0400 Subject: [PATCH 1192/1394] gnu: python-urwid-readline: Update to 0.13. * gnu/packages/python-xyz.scm (python-urwid-readline): Update to 0.13. Re-indent propagated-inputs and native-inputs. [phases]: Delete trailing #t. {check}: Invoke pytest directly, with increased verbosity. --- gnu/packages/python-xyz.scm | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5b210bc4d91..80cdf159280 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9150,7 +9150,7 @@ features useful for text console applications.") (define-public python-urwid-readline (package (name "python-urwid-readline") - (version "0.12") + (version "0.13") (source (origin (method git-fetch) @@ -9160,7 +9160,7 @@ features useful for text console applications.") (file-name (git-file-name name version)) (sha256 (base32 - "0sq5qgxj7gcfww3ww7idr87isnmp0hi36n241b3q395x1zafdv22")))) + "0y9k86p31mlr9rwnrbljvfgl183r5j60yaj0r3scljn1m0mlg8qg")))) (build-system python-build-system) (arguments `(#:phases @@ -9168,12 +9168,9 @@ features useful for text console applications.") (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? - (invoke "python" "-m" "pytest")) - #t))))) - (propagated-inputs - (list python-urwid)) - (native-inputs - (list python-pytest)) + (invoke "pytest" "-vv"))))))) + (propagated-inputs (list python-urwid)) + (native-inputs (list python-pytest)) (home-page "https://github.com/rr-/urwid_readline") (synopsis "Text input widget for urwid that supports readline shortcuts") (description From 5daac1a797240f643827baf31272e85c422d8595 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 5 May 2022 13:21:41 -0400 Subject: [PATCH 1193/1394] gnu: Add python-qemu-qmp. * gnu/packages/virtualization.scm (python-qemu-qmp): New variable. --- gnu/packages/virtualization.scm | 46 ++++++++++++++++++++++++++++++++- 1 file changed, 45 insertions(+), 1 deletion(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 60dc0e75889..9a6791627b0 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -15,7 +15,7 @@ ;;; Copyright © 2020, 2021 Brice Waegeneire ;;; Copyright © 2020 Mathieu Othacehe ;;; Copyright © 2020, 2021 Marius Bakke -;;; Copyright © 2020, 2021 Maxim Cournoyer +;;; Copyright © 2020, 2021, 2022 Maxim Cournoyer ;;; Copyright © 2020 Brett Gilio ;;; Copyright © 2021 Leo Famulari ;;; Copyright © 2021 Pierre Langlois @@ -1655,6 +1655,50 @@ mainly implemented in user space.") ;; LGPLv2.1. (license (list license:gpl2 license:lgpl2.1)))) +(define-public python-qemu-qmp + (package + (name "python-qemu-qmp") + (version "0.0.0a0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "qemu.qmp" version)) + (sha256 + (base32 "1rpsbiwvngij6fjcc5cx1azcc4dxmm080crr31wc7jrm7i61p7c2")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; The Avocado test runner insists on writing stuff to HOME. + (setenv "HOME" "/tmp") + ;; The mypy tests fail (see: + ;; https://gitlab.com/jsnow/qemu.qmp/-/issues/1). + (delete-file "tests/mypy.sh") + (invoke "avocado" "--show=all" "run" "tests"))))))) + (native-inputs + (list python-avocado-framework + python-setuptools-scm + python-flake8 + python-isort + python-pylint)) + (propagated-inputs + (list python-pygments + python-urwid + python-urwid-readline)) + (home-page "https://gitlab.com/jsnow/qemu.qmp") + (synopsis "QEMU Monitor Protocol Python library") + (description "@code{emu.qmp} is a +@url{https://gitlab.com/qemu-project/qemu/-/blob/master/docs/interop/qmp-intro.txt, +QEMU Monitor Protocol (QMP)} library written in Python. It is used to send +QMP messages to running QEMU emulators. It can be used to communicate with +QEMU emulators, the QEMU Guest Agent (QGA), the QEMU Storage Daemon (QSD), or +any other utility or application that speaks QMP.") + (license license:gpl2+))) + (define-public qmpbackup (package (name "qmpbackup") From 8f49a084bafc150822c636959576b17ae0df806e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:50:17 -0400 Subject: [PATCH 1194/1394] gnu: qmpbackup: Update to 0.23. * gnu/packages/virtualization.scm (qmpbackup): Update to 0.23. [inputs]: Add python-qemu-qmp. [python]: Delete argument. [tests?]: New argument. --- gnu/packages/virtualization.scm | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 9a6791627b0..b522b9d4743 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -1702,23 +1702,24 @@ any other utility or application that speaks QMP.") (define-public qmpbackup (package (name "qmpbackup") - (version "0.2") + (version "0.23") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/abbbi/qmpbackup") - (commit version))) + (url "https://github.com/abbbi/qmpbackup") + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "0swhp5byz44brhyis1a39p11fyn9q84xz5q6v2fah29r7d71kmmx")))) + "0x9v81z0b2qr2y6m46rfnl4kl5jnixsdrl1c790iwl6pq9kzzvzg")))) (build-system python-build-system) - (arguments - `(#:python ,python-2)) + ;; The test suite requires to download a 241 MiB QEMU image; skip it. + (arguments (list #:tests? #f)) + (inputs (list python-qemu-qmp)) (home-page "https://github.com/abbbi/qmpbackup") (synopsis "Backup and restore QEMU machines") - (description "qmpbackup is designed to create and restore full and -incremental backups of running QEMU virtual machines via QMP, the QEMU + (description "@command{qmpbackup} is designed to create and restore full +and incremental backups of running QEMU virtual machines via QMP, the QEMU Machine Protocol.") (license license:gpl3+))) From aea5860747abda4a8d161adf9105ec59cde25169 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:50:20 -0400 Subject: [PATCH 1195/1394] gnu: Remove python2-feedparser. * gnu/packages/web.scm (python2-feedparser): Delete variable. --- gnu/packages/web.scm | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 4723d218d40..fb5d3dab9a8 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4652,30 +4652,6 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (license (list license:bsd-2 ; source code license:freebsd-doc)))) ; documentation -(define-public python2-feedparser - (package - (name "python2-feedparser") - (version "5.2.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "feedparser" version ".tar.bz2")) - (sha256 - (base32 - "00hb4qg2am06g81mygfi1jsbx8830024jm45g6qp9g8fr6am91yf")))) - (build-system python-build-system) - (arguments - `(#:tests? #f - #:python ,python-2)) - (home-page - "https://github.com/kurtmckee/feedparser") - (synopsis "Parse feeds in Python") - (description - "Universal feed parser which handles RSS 0.9x, RSS 1.0, RSS 2.0, -CDF, Atom 0.3, and Atom 1.0 feeds.") - (license (list license:bsd-2 ; source code - license:freebsd-doc)))) ; documentation - (define-public guix-data-service (let ((commit "198b6ef719745a48918e703990d1e846ffcd65b0") (revision "31")) From bbbfe095fb167cb56b1fd9a20bf50bf53a0cdaf5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:50:23 -0400 Subject: [PATCH 1196/1394] gnu: Remove python2-clf. * gnu/packages/web.scm (python2-clf): Delete variable. --- gnu/packages/web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index fb5d3dab9a8..8c74f742f6e 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6354,9 +6354,6 @@ internetarchive python module for programmatic access to archive.org.") snippets on @url{https://commandlinefu.com}.") (license license:expat)))) -(define-public python2-clf - (package-with-python2 python-clf)) - (define-public rss-bridge (package (name "rss-bridge") From edac21bfc78ffea85f4dac7206e5e7cd621bba19 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:50:26 -0400 Subject: [PATCH 1197/1394] gnu: Remove wicd. The last release is from 2017, stuck on Python 2. * gnu/packages/wicd.scm: Delete file. * gnu/packages/patches/wicd-bitrate-none-fix.patch: Delete file. * gnu/packages/patches/wicd-get-selected-profile-fix.patch: Likewise. * gnu/packages/patches/wicd-urwid-1.3.patch: Likewise. * gnu/packages/patches/wicd-wpa2-ttls.patch: Likewise. * gnu/local.mk: De-register them. * gnu/services/networking.scm: Remove wicd service... * doc/guix.texi: ... and its documentation. * gnu/system/linux-container.scm (containerized-operating-system) : Remove wicd-service-type. --- doc/guix.texi | 14 -- gnu/local.mk | 5 - .../patches/wicd-bitrate-none-fix.patch | 24 --- .../wicd-get-selected-profile-fix.patch | 16 -- gnu/packages/patches/wicd-urwid-1.3.patch | 18 -- gnu/packages/patches/wicd-wpa2-ttls.patch | 38 ---- gnu/packages/wicd.scm | 197 ------------------ gnu/services/networking.scm | 62 ------ gnu/system/linux-container.scm | 3 +- 9 files changed, 1 insertion(+), 376 deletions(-) delete mode 100644 gnu/packages/patches/wicd-bitrate-none-fix.patch delete mode 100644 gnu/packages/patches/wicd-get-selected-profile-fix.patch delete mode 100644 gnu/packages/patches/wicd-urwid-1.3.patch delete mode 100644 gnu/packages/patches/wicd-wpa2-ttls.patch delete mode 100644 gnu/packages/wicd.scm diff --git a/doc/guix.texi b/doc/guix.texi index 88e009fe7c3..2bfff7c2ff9 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -18659,20 +18659,6 @@ List of additional command-line arguments to pass to the daemon. @end table @end deftp -@cindex wicd -@cindex wireless -@cindex WiFi -@cindex network management -@deffn {Scheme Procedure} wicd-service [#:wicd @var{wicd}] -Return a service that runs @url{https://launchpad.net/wicd,Wicd}, a network -management daemon that aims to simplify wired and wireless networking. - -This service adds the @var{wicd} package to the global profile, providing -several commands to interact with the daemon and configure networking: -@command{wicd-client}, a graphical user interface, and the @command{wicd-cli} -and @command{wicd-curses} user interfaces. -@end deffn - @cindex ModemManager Some networking devices such as modems require special care, and this is what the services below focus on. diff --git a/gnu/local.mk b/gnu/local.mk index a4d5235be67..7a030283a70 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -612,7 +612,6 @@ GNU_SYSTEM_MODULES = \ %D%/packages/web-browsers.scm \ %D%/packages/webkit.scm \ %D%/packages/wget.scm \ - %D%/packages/wicd.scm \ %D%/packages/wine.scm \ %D%/packages/wireservice.scm \ %D%/packages/wm.scm \ @@ -1941,10 +1940,6 @@ dist_patch_DATA = \ %D%/packages/patches/webkitgtk-adjust-bubblewrap-paths.patch \ %D%/packages/patches/webrtc-audio-processing-big-endian.patch \ %D%/packages/patches/websocketpp-fix-for-cmake-3.15.patch \ - %D%/packages/patches/wicd-bitrate-none-fix.patch \ - %D%/packages/patches/wicd-get-selected-profile-fix.patch \ - %D%/packages/patches/wicd-urwid-1.3.patch \ - %D%/packages/patches/wicd-wpa2-ttls.patch \ %D%/packages/patches/widelands-add-missing-map-include.patch \ %D%/packages/patches/widelands-system-wide_minizip.patch \ %D%/packages/patches/wmctrl-64-fix.patch \ diff --git a/gnu/packages/patches/wicd-bitrate-none-fix.patch b/gnu/packages/patches/wicd-bitrate-none-fix.patch deleted file mode 100644 index 1809b7217d4..00000000000 --- a/gnu/packages/patches/wicd-bitrate-none-fix.patch +++ /dev/null @@ -1,24 +0,0 @@ -Fix copied from https://bugs.launchpad.net/wicd/+bug/1432423/comments/1 - ---- wicd-1.7.3/curses/netentry_curses.py 1969-12-31 19:00:00.000000000 -0500 -+++ wicd-1.7.3/curses/netentry_curses.py 2015-08-11 23:26:19.999999649 -0400 -@@ -538,11 +538,16 @@ - self.bitrates = wireless.GetAvailableBitrates() - self.bitrates.append('auto') - self.bitrate_combo.set_list(self.bitrates) -+ -+ # bitrate property is sometimes None -+ chosen_bitrate = wireless.GetWirelessProperty(networkID, 'bitrate') -+ if chosen_bitrate not in self.bitrates: -+ chosen_bitrate = 'auto' -+ - self.bitrate_combo.set_focus( -- self.bitrates.index( -- wireless.GetWirelessProperty(networkID, 'bitrate') -- ) -+ self.bitrates.index(chosen_bitrate) - ) -+ - self.allow_lower_bitrates_chkbox.set_state( - to_bool(self.format_entry(networkID, 'allow_lower_bitrates')) - ) diff --git a/gnu/packages/patches/wicd-get-selected-profile-fix.patch b/gnu/packages/patches/wicd-get-selected-profile-fix.patch deleted file mode 100644 index 3042a87308b..00000000000 --- a/gnu/packages/patches/wicd-get-selected-profile-fix.patch +++ /dev/null @@ -1,16 +0,0 @@ -Fix copied from https://bugs.launchpad.net/wicd/+bug/1421918/comments/2 - ---- wicd-1.7.3/curses/wicd-curses.py 2014-12-21 16:57:33 +0000 -+++ wicd-1.7.3/curses/wicd-curses.py 2015-02-24 23:41:01 +0000 -@@ -532,7 +532,10 @@ - def get_selected_profile(self): - """Get the selected wired profile""" - loc = self.get_focus()[1] -- return self.theList[loc] -+ if len(self.theList) > loc: -+ return self.theList[loc] -+ else: -+ return self.theList[-1] - - - class AdHocDialog(Dialog2): diff --git a/gnu/packages/patches/wicd-urwid-1.3.patch b/gnu/packages/patches/wicd-urwid-1.3.patch deleted file mode 100644 index 1dc47f869b0..00000000000 --- a/gnu/packages/patches/wicd-urwid-1.3.patch +++ /dev/null @@ -1,18 +0,0 @@ -Update the wicd-curses client to work with urwid-1.3. Based on a patch from: -http://technik.blogbasis.net/wicd-curses-fix-fuer-attributeerror-screen-object-no-attribute-get_input_nonblocking-04-12-2014 - ---- wicd-1.7.3/curses/wicd-curses.py.orig 2014-12-21 14:40:46.000000000 -0500 -+++ wicd-1.7.3/curses/wicd-curses.py 2015-02-05 23:41:17.530901204 -0500 -@@ -1153,9 +1153,10 @@ - if not ui._started: - return False - -- input_data = ui.get_input_nonblocking() -+ ui.set_input_timeouts(max_wait=0) -+ input_data = ui.get_input() - # Resolve any "alarms" in the waiting -- self.handle_keys(input_data[1]) -+ self.handle_keys(input_data) - - # Update the screen - canvas = self.frame.render((self.size), True) diff --git a/gnu/packages/patches/wicd-wpa2-ttls.patch b/gnu/packages/patches/wicd-wpa2-ttls.patch deleted file mode 100644 index 9d80ee7ed2c..00000000000 --- a/gnu/packages/patches/wicd-wpa2-ttls.patch +++ /dev/null @@ -1,38 +0,0 @@ -Add a template for WPA2-TTLS, which is notably used by Eduroam. - ---- a/encryption/templates/active -+++ b/encryption/templates/active -@@ -4,6 +4,7 @@ wpa-psk - wpa-psk-hex - wpa2-leap - wpa2-peap -+wpa2-ttls - wep-hex - wep-passphrase - wep-shared -diff --git a/encryption/templates/wpa2-ttls b/encryption/templates/wpa2-ttls -new file mode 100644 -index 0000000..4f66a1e ---- /dev/null -+++ b/encryption/templates/wpa2-ttls -@@ -0,0 +1,20 @@ -+name = WPA2-TTLS (used notably by Eduroam) -+author = various contributors -+version = 1 -+require identity *Identity anonymous_identity *Anonymous_identity password *Password ca_cert *Path_to_CA_Cert -+protected password *Password -+----- -+ctrl_interface=/var/run/wpa_supplicant -+network={ -+ ssid="$_ESSID" -+ scan_ssid=$_SCAN -+ proto=WPA2 -+ key_mgmt=WPA-EAP -+ group=CCMP TKIP -+ eap=TTLS -+ identity="$_IDENTITY" -+ password="$_PASSWORD" -+ anonymous_identity="$_ANONYMOUS_IDENTITY" -+ ca_cert="$_CA_CERT" -+ phase2="auth=PAP" -+} diff --git a/gnu/packages/wicd.scm b/gnu/packages/wicd.scm deleted file mode 100644 index 073d4404798..00000000000 --- a/gnu/packages/wicd.scm +++ /dev/null @@ -1,197 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015 Mark H Weaver -;;; Copyright © 2015 Pierre-Antoine Rault -;;; Copyright © 2015 Andreas Enge -;;; Copyright © 2016 Ludovic Courtès -;;; -;;; This file is part of GNU Guix. -;;; -;;; GNU Guix is free software; you can redistribute it and/or modify it -;;; under the terms of the GNU General Public License as published by -;;; the Free Software Foundation; either version 3 of the License, or (at -;;; your option) any later version. -;;; -;;; GNU Guix is distributed in the hope that it will be useful, but -;;; WITHOUT ANY WARRANTY; without even the implied warranty of -;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -;;; GNU General Public License for more details. -;;; -;;; You should have received a copy of the GNU General Public License -;;; along with GNU Guix. If not, see . - -(define-module (gnu packages wicd) - #:use-module (guix packages) - #:use-module (guix download) - #:use-module (guix build-system python) - #:use-module (guix licenses) - #:use-module (guix utils) - #:use-module (gnu packages) - #:use-module (gnu packages glib) - #:use-module (gnu packages gtk) - #:use-module (gnu packages gnome) - #:use-module (gnu packages gettext) - #:use-module (gnu packages linux) - #:use-module (gnu packages admin) - #:use-module (gnu packages python) - #:use-module (gnu packages python-xyz)) - -(define-public wicd - (package - (name "wicd") - (version "1.7.4") - (source - (origin - (method url-fetch) - (uri (string-append "https://launchpad.net/wicd/" - (version-major+minor version) "/" version - "/+download/wicd-" version ".tar.gz")) - (sha256 - (base32 "0qpbwwsrqdp40mm3a8djpn2d055rxxspdhwijwsdnws700a9d637")) - (patches (search-patches - "wicd-bitrate-none-fix.patch" - "wicd-get-selected-profile-fix.patch" - "wicd-urwid-1.3.patch" - "wicd-wpa2-ttls.patch")))) - (build-system python-build-system) - (native-inputs `(("gettext" ,gettext-minimal))) - (inputs `(("dbus-glib" ,dbus-glib) - ("python2-dbus" ,python2-dbus) - ("python2-pygtk" ,python2-pygtk) - ("python2-urwid" ,python2-urwid) - ("python2-babel" ,python2-babel) - ("wireless-tools" ,wireless-tools) - ("wpa-supplicant" ,wpa-supplicant) - ("net-tools" ,net-tools) - ("isc-dhcp" ,isc-dhcp) - ("iproute" ,iproute) - ("hicolor-icon-theme" ,hicolor-icon-theme))) - (arguments - `(#:python ,python-2 - #:tests? #f ; test suite requires networking - ;; wicd directly extends distutils command classes, - ;; we can't easily make setup.py use setuptools. - #:use-setuptools? #f - #:phases - (modify-phases %standard-phases - (add-before 'build 'configure - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (python (assoc-ref inputs "python"))) - (define (which* cmd) - (cond ((string=? cmd "ping") - "/run/setuid-programs/ping") - ((which cmd) - => identity) - (else - (format (current-error-port) - "WARNING: Unable to find absolute path for ~s~%" - cmd) - #f))) - (substitute* "setup.py" - ;; The handling of unrecognized distros in setup.py is - ;; broken. Work around the problem. - (("\\('init=', " all) - (string-append "#" all)) - ;; Inhibit attempts to install in /var or /etc. - (("\\(wpath\\.(log|etc|networks|.*scripts), " all) - (string-append "#" all))) - - ;; Patch references to subprograms with absolute pathnames. - (substitute* "wicd/wnettools.py" - (("(misc\\.Run\\(\\[?[\"'])([^\"' ]*)" all pre cmd) - (string-append pre (which* cmd))) - (("(self\\._find_program_path|misc\\.find_path)\\([\"']([^\"']*)[\"']\\)" - all dummy cmd) - (let ((pathname (which* cmd))) - (if pathname - (string-append "'" pathname "'") - "None"))) - (("([\"'])(ifconfig|route|wpa_cli|wpa_supplicant|iwconfig|iwpriv|iwlist|ping)" - all open-quote cmd) - (string-append open-quote (which* cmd)))) - - ;; setup.py cannot cope without LANG - (setenv "LANG" "C") - - (let ((params - (list - (string-append "--python=" python "/bin/python") - "--no-install-init" - "--no-install-docs" - "--no-install-acpi" - "--no-install-pmutils" - "--no-install-kde" - "--no-install-gnome-shell-extensions" - - ;; Don't pass --distro= despite setup.py's complaints. - ;; Guix isn't recognised, and if it ever would be we'd - ;; rather ask upstream to follow standards instead. - - "--wicdgroup=netdev" - "--loggroup=root" - "--logperms=0640" - - ;; XXX setup.py configure asks us to pass --init=, - ;; but if we do it says "no such option 'init'". - ;; (string-append "--init=" out "/etc/init.d") - - (string-append "--initfile=" out "/etc/init.d/wicd") - (string-append "--lib=" out "/lib/wicd") - (string-append "--share=" out "/share/wicd") - - "--etc=/etc/wicd" - "--scripts=/etc/wicd/scripts" - "--pmutils=/etc/pm-utils/sleep.d" - - (string-append "--encryption=" - out "/etc/encryption/templates") - (string-append "--bin=" out "/bin") - (string-append "--sbin=" out "/sbin") - (string-append "--daemon=" out "/share/wicd/daemon") - (string-append "--backends=" out "/share/wicd/backends") - (string-append "--curses=" out "/share/wicd/curses") - (string-append "--gtk=" out "/share/wicd/gtk") - (string-append "--cli=" out "/share/wicd/cli") - (string-append "--gnome-shell-extensions=" - out "/share/gnome-shell-extensions") - (string-append "--icons=" out "/share/icons/hicolor") - (string-append "--pixmaps=" out "/share/pixmaps") - (string-append "--images=" out "/share/icons") - (string-append "--dbus=" out "/etc/dbus-1/system.d") - (string-append "--dbus-service=" - out "/share/dbus-1/system-services") - (string-append "--systemd=" out "/lib/systemd/system") - (string-append "--logrotate=" out "/etc/logrotate.d") - (string-append "--desktop=" out "/share/applications") - (string-append "--translations=" out "/share/locale") - (string-append "--autostart=" out "/etc/xdg/autostart") - (string-append "--docdir=" out "/share/doc/wicd") - (string-append "--mandir=" out "/share/man") - (string-append "--kdedir=" out "/share/autostart")))) - (format #t - "running ~s with command ~s and parameters ~s~%" - "python setup.py" "configure" params) - (apply invoke "python" "setup.py" "configure" params))))) - (add-after 'install 'post-install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - ;; wicd's installer tries to put dhclient.conf.template.default - ;; in /etc/wicd/other, which is not available in the build - ;; environment, so here we install it manually in the output - ;; directory. - (let ((dest-dir (string-append out "/etc/wicd")) - (name "dhclient.conf.template.default")) - (install-file (string-append "other/" name) dest-dir)) - - ;; Copy index.theme from hicolor-icon-theme. This is needed to - ;; allow wicd-gtk to find its icons. - (let ((hicolor (assoc-ref inputs "hicolor-icon-theme")) - (name "/share/icons/hicolor/index.theme")) - (install-file (string-append hicolor name) - (string-append out "/share/icons/hicolor"))) - #t)))))) - (synopsis "Network connection manager") - (description "Wicd is a network manager that aims to simplify wired and -wireless networking.") - (home-page "https://launchpad.net/wicd") - (license gpl2+))) diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index d8fe638940f..90b93175108 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -57,7 +57,6 @@ #:use-module (gnu packages messaging) #:use-module (gnu packages networking) #:use-module (gnu packages ntp) - #:use-module (gnu packages wicd) #:use-module (gnu packages gnome) #:use-module (gnu packages ipfs) #:use-module (gnu build linux-container) @@ -130,9 +129,6 @@ tor-hidden-service tor-service-type - wicd-service-type - wicd-service - network-manager-configuration network-manager-configuration? network-manager-configuration-dns @@ -1092,64 +1088,6 @@ project's documentation} for more information." (service tor-hidden-service-type (hidden-service name mapping))) - -;;; -;;; Wicd. -;;; - -(define %wicd-activation - ;; Activation gexp for Wicd. - #~(begin - (use-modules (guix build utils)) - - (mkdir-p "/etc/wicd") - (let ((file-name "/etc/wicd/dhclient.conf.template.default")) - (unless (file-exists? file-name) - (copy-file (string-append #$wicd file-name) - file-name))) - - ;; Wicd invokes 'wpa_supplicant', which needs this directory for its - ;; named socket files. - (mkdir-p "/var/run/wpa_supplicant") - (chmod "/var/run/wpa_supplicant" #o750))) - -(define (wicd-shepherd-service wicd) - "Return a shepherd service for WICD." - (list (shepherd-service - (documentation "Run the Wicd network manager.") - (provision '(networking)) - (requirement '(user-processes dbus-system loopback)) - (start #~(make-forkexec-constructor - (list (string-append #$wicd "/sbin/wicd") - "--no-daemon"))) - (stop #~(make-kill-destructor))))) - -(define wicd-service-type - (service-type (name 'wicd) - (extensions - (list (service-extension shepherd-root-service-type - wicd-shepherd-service) - (service-extension dbus-root-service-type - list) - (service-extension activation-service-type - (const %wicd-activation)) - - ;; Add Wicd to the global profile. - (service-extension profile-service-type list))) - (description - "Run @url{https://launchpad.net/wicd,Wicd}, a network -management daemon that aims to simplify wired and wireless networking."))) - -(define* (wicd-service #:key (wicd wicd)) - "Return a service that runs @url{https://launchpad.net/wicd,Wicd}, a network -management daemon that aims to simplify wired and wireless networking. - -This service adds the @var{wicd} package to the global profile, providing -several commands to interact with the daemon and configure networking: -@command{wicd-client}, a graphical user interface, and the @command{wicd-cli} -and @command{wicd-curses} user interfaces." - (service wicd-service-type wicd)) - ;;; ;;; ModemManager diff --git a/gnu/system/linux-container.scm b/gnu/system/linux-container.scm index eeb0f68c026..24077e347a0 100644 --- a/gnu/system/linux-container.scm +++ b/gnu/system/linux-container.scm @@ -129,8 +129,7 @@ containerized OS. EXTRA-FILE-SYSTEMS is a list of file systems to add to OS." static-networking-service-type dhcp-client-service-type network-manager-service-type - connman-service-type - wicd-service-type) + connman-service-type) (list)))) (define services-to-add From 261f030340e03f85439afc9e56cc4e73955333b9 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:50:30 -0400 Subject: [PATCH 1198/1394] gnu: Remove python2-i3-py. * gnu/packages/wm.scm (python2-i3-py): Delete variable. --- gnu/packages/wm.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 83b75ca9b8c..3f203d83511 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -545,9 +545,6 @@ kinds of messages to i3, select the affected containers, filter results and subscribe to events.") (license license:gpl3+))) -(define-public python2-i3-py - (package-with-python2 python-i3-py)) - (define-public qtile (package (name "qtile") From f162273a2cb730526785ca5edd55b52c82a2ea91 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:50:38 -0400 Subject: [PATCH 1199/1394] gnu: Remove python2-pyxb. * gnu/packages/xml.scm (python2-pyxb): Delete variable. --- gnu/packages/xml.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index ecc19a7eb84..6dbcf67d8c1 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -1119,9 +1119,6 @@ code for classes that correspond to data structures defined by XMLSchema.") license:gpl2 ; bundled jquery in doc is dual MIT/GPL2 license:psfl)))) ; pyxb/utils/activestate.py -(define-public python2-pyxb - (package-with-python2 python-pyxb)) - (define-public xmlto (package (name "xmlto") From 709c0244e45ddfd19cfb318ab63a04c220b33eb7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 29 Apr 2022 23:50:41 -0400 Subject: [PATCH 1200/1394] gnu: xlsx2csv: Update to 0.7.8. * gnu/packages/xml.scm (xlsx2csv): Update to 0.7.8. [python]: Delete argument. --- gnu/packages/xml.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 6dbcf67d8c1..a9bf07de96b 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -27,7 +27,7 @@ ;;; Copyright © 2020 Brett Gilio ;;; Copyright © 2020 Pierre Langlois ;;; Copyright © 2021 Michael Rohleder -;;; Copyright © 2021 Maxim Cournoyer +;;; Copyright © 2021, 2022 Maxim Cournoyer ;;; Copyright © 2021 Julien Lepiller ;;; Copyright © 2021 Felix Gruber ;;; Copyright © 2021 Guillaume Le Vaillant @@ -1421,7 +1421,7 @@ elements to their parents (define-public xlsx2csv (package (name "xlsx2csv") - (version "0.7.4") + (version "0.7.8") (source (origin (method git-fetch) @@ -1430,17 +1430,17 @@ elements to their parents (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "168dm6p7w6pvgd87yb9hcxv9y0liv6mxgril202nfva68cp8y939")))) + (base32 "1p10571295f8zw1lsma8k5z07hrk9aspar0lsz8zpgjl7v35zcq7")))) (build-system python-build-system) (arguments - `(#:python ,python-2 ; use python-2 for the test script - #:phases + `(#:phases (modify-phases %standard-phases (replace 'check (lambda _ (substitute* "test/run" ;; Run tests with `python' only. - (("^(PYTHON_VERSIONS = ).*" all m) (string-append m "['']"))) + (("^(PYTHON_VERSIONS = ).*" all m) + (string-append m "['']"))) (invoke "test/run")))))) (home-page "https://github.com/dilshod/xlsx2csv") (synopsis "XLSX to CSV converter") From 1c142bb829ef24b43297b4492b865a642c06920d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 30 Apr 2022 00:15:22 -0400 Subject: [PATCH 1201/1394] gnu: Remove python2-pyatspi. * gnu/packages/gnome.scm (python2-pyatspi): Delete variable. --- gnu/packages/gnome.scm | 8 -------- 1 file changed, 8 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 81b74a2497c..f9613df00b4 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -10446,14 +10446,6 @@ accessibility infrastructure.") (license license:lgpl2.0) (properties '((upstream-name . "pyatspi"))))) -(define-public python2-pyatspi - (package/inherit python-pyatspi - (name "python2-pyatspi") - (inputs - `(("python" ,python-2))) - (propagated-inputs - `(("python-pygobject" ,python2-pygobject))))) - (define-public orca (package (name "orca") From 984a04210a21e6b124e76ff33636c7d74d623ca5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 30 Apr 2022 00:15:39 -0400 Subject: [PATCH 1202/1394] gnu: Remove python2-rsvg. * gnu/packages/gnome.scm (python2-rsvg): Delete variable. --- gnu/packages/gnome.scm | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index f9613df00b4..0cb46b48a5b 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4766,35 +4766,6 @@ commercial X servers. It is useful for creating XKB-related software (layout indicators etc).") (license license:lgpl2.0+))) -(define-public python2-rsvg - ;; XXX: This is actually a subset of gnome-python-desktop. - (package - (name "python2-rsvg") - (version "2.32.0") - (source - (origin - (method url-fetch) - (uri (string-append - "mirror://gnome/sources/gnome-python-desktop/2.32/gnome-python-desktop-" - version ".tar.bz2")) - (sha256 - (base32 - "1s8f9rns9v7qlwjv9qh9lr8crp88dpzfm45hj47zc3ivpy0dbnq9")))) - (build-system gnu-build-system) - (native-inputs - (list pkg-config)) - (inputs - (list python-2 python2-pygtk librsvg)) - (home-page "https://www.gnome.org") - (synopsis "Python bindings to librsvg") - (description - "This package provides Python bindings to librsvg, the SVG rendering -library.") - - ;; This is the license of the rsvg bindings. The license of each module - ;; of gnome-python-desktop is given in 'COPYING'. - (license license:lgpl2.1+))) - (define-public glib-networking (package (name "glib-networking") From 8ab2f519d42b2221b53e0a9ecc57a86548969309 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 30 Apr 2022 00:52:53 -0400 Subject: [PATCH 1203/1394] gnu: solfege: Update to 3.23.5pre2. * gnu/packages/music.scm (solfege): Update to 3.23.5pre2. [source]: Use git. [arguments]: Use gexps. Remove trailing #t. [phases]{patch-python-shebangs, wrap-program}: Use search-file-input. {fix-version}: New phase. [inputs]: Use new style. Remove python-2 and python2-pygtk. Add python-wrapper and python-pygobject. [native-inputs]: Add autoconf and automake. Use latest texinfo. --- gnu/packages/music.scm | 127 +++++++++++++++++++++++------------------ 1 file changed, 70 insertions(+), 57 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 27e2f437439..756e1ca45ba 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2008,72 +2008,85 @@ Key features include: (define-public solfege (package (name "solfege") - (version "3.22.2") + (version "3.23.5pre2") (source (origin - (method url-fetch) - (uri (string-append - "mirror://gnu/solfege/solfege-" - version ".tar.xz")) + (method git-fetch) + (uri (git-reference + (url "https://git.savannah.gnu.org/git/solfege.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1w25rxdbj907nsx285k9nm480pvy12w3yknfh4n1dfv17cwy072i")))) + "1lmzp4kn0xh58yc8gzriz1i34g5qaa2xxrxzpmr7v9jyk19dqmcm")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; xmllint attempts to download DTD - #:test-target "test" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-configuration - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "default.config" - (("/usr/bin/aplay") "aplay") - (("/usr/bin/timidity") "timidity") - (("/usr/bin/mpg123") "mpg123") - (("/usr/bin/ogg123") "ogg123")))) - (add-before 'build 'patch-python-shebangs - (lambda _ - ;; Two python scripts begin with a Unicode BOM, so patch-shebang - ;; has no effect. - (substitute* '("solfege/parsetree.py" - "solfege/presetup.py") - (("#!/usr/bin/python") (string-append "#!" (which "python")))))) - (add-before 'build 'add-sitedirs - ;; .pth files are not automatically interpreted unless the - ;; directories containing them are added as "sites". The directories - ;; are then added to those in the PYTHONPATH. This is required for - ;; the operation of pygtk and pygobject. - (lambda _ - (substitute* "run-solfege.py" - (("import os") - "import os, site -for path in [path for path in sys.path if 'site-packages' in path]: site.addsitedir(path)")) - #t)) - (add-before 'build 'adjust-config-file-prefix - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "run-solfege.py" - (("prefix = os.path.*$") - (string-append "prefix = " (assoc-ref outputs "out")))) - #t)) - (add-after 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Make sure 'solfege' runs with the correct PYTHONPATH. - (let* ((out (assoc-ref outputs "out")) - (path (getenv "GUIX_PYTHONPATH"))) - (wrap-program (string-append out "/bin/solfege") - `("GUIX_PYTHONPATH" ":" prefix (,path)))) - #t))))) + (list + #:tests? #f ;xmllint attempts to download DTD + #:test-target "test" + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-version + (lambda _ + (substitute* "autogen.sh" + (("python3 -c \"import tools.*create_versions_file.*") + (string-append "echo \"version_info = '" + #$version "' > solfege/_version.py\"\n"))) + (substitute* "Makefile.in" + (("\\$\\(PYTHON) -c \"import tools.*create_versions_file.*") + "true\n")) + (substitute* "solfege/buildinfo.py.in" + (("from solfege._version import version_info") + "version_info = {'git_sha': 'N/A'}")))) + (add-after 'unpack 'fix-configuration + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "default.config" + (("/usr/bin/aplay") "aplay") + (("/usr/bin/timidity") "timidity") + (("/usr/bin/mpg123") "mpg123") + (("/usr/bin/ogg123") "ogg123")))) + (add-before 'build 'patch-python-shebangs + (lambda* (#:key inputs #:allow-other-keys) + ;; Two python scripts begin with a Unicode BOM, so patch-shebang + ;; has no effect. + (substitute* '("solfege/parsetree.py" + "solfege/presetup.py") + (("#!/usr/bin/python") + (string-append "#!" search-input-file inputs "bin/python"))))) + (add-before 'build 'add-sitedirs + ;; .pth files are not automatically interpreted unless the + ;; directories containing them are added as "sites". The + ;; directories are then added to those in the PYTHONPATH. This is + ;; required for the operation of pygtk and pygobject. + (lambda _ + (substitute* "run-solfege.py" + (("import os") + "import os, site +for path in [path for path in sys.path if 'site-packages' in path]: site.addsitedir(path)")))) + (add-before 'build 'adjust-config-file-prefix + (lambda _ + (substitute* "run-solfege.py" + (("prefix = os.path.*$") + (string-append "prefix = " #$output))))) + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure 'solfege' runs with the correct PYTHONPATH. + (let ((path (getenv "GUIX_PYTHONPATH"))) + (wrap-program (search-input-file outputs "bin/solfege") + `("GUIX_PYTHONPATH" ":" prefix (,path))))))))) (inputs - `(("python" ,python-2) - ("pygtk" ,python2-pygtk) - ("gettext" ,gettext-minimal) - ("gtk" ,gtk+) - ("lilypond" ,lilypond))) + (list python-wrapper + python-pygobject + gettext-minimal + gtk+ + lilypond)) (native-inputs - (list pkg-config + (list autoconf + automake + pkg-config txt2man - libxml2 ; for tests + libxml2 ; for tests ghostscript - texinfo-5)) + texinfo)) (home-page "https://www.gnu.org/software/solfege/") (synopsis "Ear training") (description From 60965e70ed41c2086352f11ad3eedd69b59aec44 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 30 Apr 2022 10:32:34 -0400 Subject: [PATCH 1204/1394] gnu: dosage: Remove python2 inputs. * gnu/packages/python-xyz.scm (dosage)[propagated-inputs]: Remove python2-backports-functools-lru-cache and python2-backports-shutil-get-terminal-size. --- gnu/packages/python-xyz.scm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 80cdf159280..f605d146c4a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2492,9 +2492,7 @@ files are easily readable and they work nicely with version control systems.") "0vmxgn9wd3j80hp4gr5iq06jrl4gryz5zgfdd2ah30d12sfcfig0")))) (build-system python-build-system) (propagated-inputs - (list python2-backports-functools-lru-cache - python2-backports-shutil-get-terminal-size - python-cached-property + (list python-cached-property python-colorama python-imagesize python-importlib-metadata From 6c80abe0977907441df2603a00f0be2fcc4e04f0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 00:00:23 -0400 Subject: [PATCH 1205/1394] gnu: Remove python2-pytest-mock. * gnu/packages/check.scm (python2-pytest-mock): Delete variable. (python-pytest-mock)[properties]: Delete field. --- gnu/packages/check.scm | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 224c7e62e70..8b77bf77ce4 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -1401,29 +1401,8 @@ around the patching API provided by the @code{mock} package, but with the benefit of not having to worry about undoing patches at the end of a test. The mocker fixture has the same API as @code{mock.patch}, supporting the same arguments.") - (properties `((python2-variant . ,(delay python2-pytest-mock)))) (license license:expat))) -(define-public python2-pytest-mock - (let ((base (package-with-python2 - (strip-python2-variant python-pytest-mock)))) - (package/inherit base - (version "1.10.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pytest-mock" version)) - (sha256 - (base32 - "1i5mg3ff1qk0wqfcxfz60hwy3q5dskdp36i10ckigkzffg8hc3ad")))) - (arguments - `(#:python ,python-2)) - (native-inputs - `(("python2-setuptools-scm" ,python2-setuptools-scm))) - (propagated-inputs - `(("python2-mock" ,python2-mock) - ("python2-pytest" ,python2-pytest)))))) - (define-public python-pytest-xdist (package (name "python-pytest-xdist") From c339c84f0f22c2e83dcf69bab6697ce034cdefda Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 00:02:41 -0400 Subject: [PATCH 1206/1394] gnu: Remove python2-backports-shutil-get-terminal-size. * gnu/packages/python-xyz.scm (python2-backports-shutil-get-terminal-size): Delete variable. --- gnu/packages/python-xyz.scm | 30 ------------------------------ 1 file changed, 30 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f605d146c4a..b5bebb98c3e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10223,36 +10223,6 @@ Python 2 and Python 3.") ;; module "backports". (delete 'sanity-check)))))) -(define-public python2-backports-shutil-get-terminal-size - (package - (name "python2-backports-shutil-get-terminal-size") - (version "1.0.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "backports.shutil_get_terminal_size" version)) - (sha256 - (base32 - "107cmn7g3jnbkp826zlj8rrj19fam301qvaqf0f3905f5217lgki")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "py.test" "-v")))))) - (native-inputs - (list python2-pytest)) - (home-page "https://github.com/chrippa/backports.shutil_get_terminal_size") - (synopsis "Backport of Python 3.3's @code{shutil.get_terminal_size}") - (description - "This package provides a backport of the @code{get_terminal_size -function} from Python 3.3's @code{shutil}. -Unlike the original version it is written in pure Python rather than C, -so it might be a tiny bit slower.") - (license license:expat))) - (define-public python-waf (package (name "python-waf") From faefd4d1db6ba84931e8201171555b004d0fc65c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 01:18:08 -0400 Subject: [PATCH 1207/1394] gnu: libappindicator: Update to 12.10.1-0-298. * gnu/packages/freedesktop.scm (libappindicator): Update to 12.10.1-0-298. [source]: Fetch from bazaar and remove snippet. [native-inputs]: Add autoconf, automake, at-spi2-core, gnome-common, gobject-introspection, gtk-doc, libtool, vala and which. [inputs]: Delete libindicator, python-2, python2-pygtk, python2-pygobject-2 and vala. [phases]{fix-paths}: Only patch tests/Makefile.in. Use search-input-file. --- gnu/packages/freedesktop.scm | 134 +++++++++++++++-------------------- 1 file changed, 58 insertions(+), 76 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index f4b63cefe66..c94cacbbfff 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -27,7 +27,7 @@ ;;; Copyright © 2021 Robby Zambito ;;; Copyright © 2021 Maxime Devos ;;; Copyright © 2021 John Kehayias -;;; Copyright © 2021 Maxim Cournoyer +;;; Copyright © 2021, 2021 Maxim Cournoyer ;;; Copyright © 2022 Daniel Meißner ;;; ;;; This file is part of GNU Guix. @@ -46,12 +46,13 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages freedesktop) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix utils) - #:use-module (guix packages) + #:use-module (guix bzr-download) #:use-module (guix download) #:use-module (guix gexp) #:use-module (guix git-download) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix utils) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system meson) @@ -2172,80 +2173,61 @@ useful with system integration.") (license license:gpl3))) (define-public libappindicator - (package - (name "libappindicator") - (version "12.10.0") - (source - (origin - (method url-fetch) - (uri (string-append - "https://launchpad.net/libappindicator/" - (version-major+minor version) "/" version - "/+download/libappindicator-" version ".tar.gz")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Fix 'multiple definitions' error from GCC 10 - (substitute* "bindings/python/appindicatormodule.c" - (("^#include " all) - (string-append "#define NO_IMPORT_PYGOBJECT\n" all))))) - (sha256 - (base32 - "17xlqd60v0zllrxp8bgq3k5a1jkj0svkqn8rzllcyjh8k0gpr46m")))) - (build-system gnu-build-system) - (native-inputs - `(("dbus-test-runner" ,dbus-test-runner) - ("glib:bin" ,glib "bin") - ("gobject-introspection" ,gobject-introspection) - ("pkg-config" ,pkg-config) - ("xvfb" ,xorg-server-for-tests))) - (inputs - `(("dbus-glib" ,dbus-glib) - ("libindicator" ,libindicator) - ("python@2" ,python-2) - ("python2-pygtk" ,python2-pygtk) - ("python2-pygobject-2" ,python2-pygobject-2) - ;; ("mono" ,mono) ; requires non-packaged gapi - ("vala" ,vala))) - (propagated-inputs - (list gtk+ libdbusmenu)) - (arguments - ;; FIXME: do not hardcode gtk version - `(#:configure-flags '("--with-gtk=3") - #:make-flags '("CFLAGS=-Wno-error") - #:tests? #f ; One test does not pass (it succeeds when it should fail). - #:phases - (modify-phases %standard-phases - (add-before 'configure 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "docs/reference/Makefile.in" - (("/bin/sh") (which "sh"))) - (substitute* "tests/Makefile.in" - (("/bin/sh") (which "sh")) - (("#!/bin/bash") (string-append "#!" (which "bash"))) - (("/usr") (string-append (assoc-ref inputs "dbus-test-runner")))) - (substitute* "bindings/python/Makefile.in" - (("-lappindicator") "-lappindicator3")) - #t)) - (add-after 'unpack 'fix-codegen-path - (lambda _ - (substitute* "configure" - (("PYGTK_CODEGEN=.*") "PYGTK_CODEGEN=pygtk-codegen-2.0\n")) - #t)) - (add-after 'build 'build-bindings - (lambda _ - (invoke "make" "-C" "bindings/python") - #t)) - (add-after 'install 'install-bindings - (lambda _ - (invoke "make" "-C" "bindings/python" "install") - #t))))) - (home-page "https://launchpad.net/libappindicator") - (synopsis "Allow applications to export a menu into the Unity menu bar") - (description "A library to allow applications to export a menu, originally + ;; Use the latest commit as the latest official release from 2012 uses + ;; Python 2. + (let ((revision "0") + ;; Corresponds to the 12.10.1+20.10.20200706.1-0ubuntu1 tag. + (bazaar-revision "298")) + (package + (name "libappindicator") + (version (string-append "12.10.1-" revision "-" bazaar-revision)) + (source (origin + (method bzr-fetch) + (uri (bzr-reference + (url "lp:libappindicator") + (revision bazaar-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0jkc1xdsa7r71vrr2l7wgkarvzvwrpwn0m8m4ipaqlzfa5d45n3a")))) + (build-system gnu-build-system) + (native-inputs + (list autoconf + automake + at-spi2-core + dbus-test-runner + `(,glib "bin") + gnome-common + gobject-introspection + gtk-doc + libtool + pkg-config + vala + which + xorg-server-for-tests)) + (inputs + (list dbus-glib)) + (propagated-inputs + (list gtk+ libdbusmenu)) + (arguments + `(#:configure-flags '("--with-gtk=3") + #:make-flags '("CFLAGS=-Wno-error") + #:tests? #f ; One test does not pass (it succeeds when it should fail). + #:phases + (modify-phases %standard-phases + (add-before 'configure 'fix-paths + (lambda* (#:key native-inputs inputs #:allow-other-keys) + (substitute* "tests/Makefile.in" + (("/bin/sh") (which "sh")) + (("/bin/bash") (which "bash")) + (("/usr/(share/dbus-test-runner/session.conf)" _ tail) + (search-input-file (or native-inputs inputs) tail)))))))) + (home-page "https://launchpad.net/libappindicator") + (synopsis "Allow applications to export a menu into the Unity menu bar") + (description "A library to allow applications to export a menu, originally into the Unity menu bar. Based on KSNI, it also works in KDE and will fallback to generic Systray support if none of those are available.") - (license license:lgpl2.1+))) + (license license:lgpl2.1+)))) (define-public libportal (package From 8d71e5b2a5b5f5e6ca49e10a65384c298437b401 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 01:27:04 -0400 Subject: [PATCH 1208/1394] gnu: gimp: Drop Python 2 support. * gnu/packages/gimp.scm (gimp)[inputs]: Delete python-2 and python2-pygtk. [configure-flags]: Use gexps. Add "--disable-python". [phases]: Delete argument. [inputs, native-inputs]: Use new style. --- gnu/packages/gimp.scm | 104 ++++++++++++++++++------------------------ 1 file changed, 45 insertions(+), 59 deletions(-) diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm index 0ad75de700a..2cf0a2b2d43 100644 --- a/gnu/packages/gimp.scm +++ b/gnu/packages/gimp.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2020 Marius Bakke ;;; Copyright © 2020 Michael Rohleder ;;; Copyright © 2021 Vinicius Monego +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -27,6 +28,7 @@ (define-module (gnu packages gimp) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix utils) #:use-module ((guix licenses) #:prefix license:) @@ -297,71 +299,55 @@ buffers.") (base32 "1p375gaw2daip6aiv1icrlpws5m1my5kalxkxrvl4zgdfsm5v0c8")))) (build-system gnu-build-system) (outputs '("out" - "doc")) ; 9 MiB of gtk-doc HTML + "doc")) ; 9 MiB of gtk-doc HTML (arguments - '(#:configure-flags - (list (string-append "--with-html-dir=" - (assoc-ref %outputs "doc") - "/share/gtk-doc/html") + (list + #:configure-flags + #~(list (string-append "--with-html-dir=" #$output "/share/gtk-doc/html") - ;; Prevent the build system from running 'gtk-update-icon-cache' - ;; which is not needed during the build because Guix runs it at - ;; profile creation time. - "ac_cv_path_GTK_UPDATE_ICON_CACHE=true" + ;; Prevent the build system from running 'gtk-update-icon-cache' + ;; which is not needed during the build because Guix runs it at + ;; profile creation time. + "ac_cv_path_GTK_UPDATE_ICON_CACHE=true" - ;; Disable automatic network request on startup to check for - ;; version updates. - "--disable-check-update" + ;; Disable automatic network request on startup to check for + ;; version updates. + "--disable-check-update" - ;; ./configure requests not to annoy upstream with packaging bugs. - "--with-bug-report-url=https://bugs.gnu.org/guix") - #:phases - (modify-phases %standard-phases - (add-after 'install 'install-sitecustomize.py - ;; Install 'sitecustomize.py' into gimp's python directory to - ;; add pygobject and pygtk to pygimp's search path. - (lambda* (#:key outputs #:allow-other-keys) - (let* ((pythonpath (getenv "GUIX_PYTHONPATH")) - (out (assoc-ref outputs "out")) - (sitecustomize.py - (string-append - out "/lib/gimp/2.0/python/sitecustomize.py"))) - (call-with-output-file sitecustomize.py - (lambda (port) - (format port "import site~%") - (format port "for dir in '~a'.split(':'):~%" pythonpath) - (format port " site.addsitedir(dir)~%"))))))))) + ;; Only Python 2 is supported; disable it. + "--disable-python" + + ;; ./configure requests not to annoy upstream with packaging bugs. + "--with-bug-report-url=https://bugs.gnu.org/guix"))) (inputs - `(("atk" ,atk) - ("babl" ,babl) - ("gegl" ,gegl) - ("gexiv2" ,gexiv2) - ("glib" ,glib) - ("glib-networking" ,glib-networking) - ("gtk+" ,gtk+-2) - ("libjpeg" ,libjpeg-turbo) - ("libmypaint" ,libmypaint) - ("libtiff" ,libtiff) - ("libwebp" ,libwebp) - ("mypaint-brushes" ,mypaint-brushes-1.3) - ("exif" ,libexif) ; optional, EXIF + XMP support - ("ghostscript" ,ghostscript) ; optional, EPS + PS support - ("lcms" ,lcms) ; optional, color management - ("libheif" ,libheif) ; optional, HEIF + AVIF support - ("libmng" ,libmng) ; optional, MNG support - ("librsvg" ,librsvg) ; optional, SVG support - ("libxcursor" ,libxcursor) ; optional, Mouse Cursor support - ("openexr" ,openexr-2) ; optional, EXR support - ("openjpeg" ,openjpeg) ; optional, JPEG 2000 support - ("poppler" ,poppler) ; optional, PDF support - ("poppler-data" ,poppler-data) ; optional, PDF support - ("python" ,python-2) ; optional, Python support - ("python2-pygtk" ,python2-pygtk))) ; optional, Python support + (list atk + babl + gegl + gexiv2 + glib + glib-networking + gtk+-2 + libjpeg-turbo + libmypaint + libtiff + libwebp + mypaint-brushes-1.3 + libexif ;optional, EXIF + XMP support + ghostscript ;optional, EPS + PS support + lcms ;optional, color management + libheif ;optional, HEIF + AVIF support + libmng ;optional, MNG support + librsvg ;optional, SVG support + libxcursor ;optional, Mouse Cursor support + openexr-2 ;optional, EXR support + openjpeg ;optional, JPEG 2000 support + poppler ;optional, PDF support + poppler-data)) ;optional, PDF support (native-inputs - `(("desktop-file-utils" ,desktop-file-utils) - ("glib:bin" ,glib "bin") ; for glib-compile-resources and gdbus-codegen - ("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list desktop-file-utils + `(,glib "bin") ;for glib-compile-resources and gdbus-codegen + intltool + pkg-config)) (home-page "https://www.gimp.org") (synopsis "GNU Image Manipulation Program") (description From 5f2c56e739d03ba418dadb7f4dcb0bfb5f7ffd38 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 01:27:46 -0400 Subject: [PATCH 1209/1394] gnu: glimpse: Drop Python 2 support. * gnu/packages/gimp.scm (glimpse)[source]: Fix indentation. [arguments]: Use gexps. [phases]{install-sitecustomize}: Delete phase. [native-inputs]: Use new style. [inputs]: Use new style. Delete python-2 and python2-pygtk. --- gnu/packages/gimp.scm | 104 +++++++++++++++++------------------------- 1 file changed, 43 insertions(+), 61 deletions(-) diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm index 2cf0a2b2d43..1bf396670e8 100644 --- a/gnu/packages/gimp.scm +++ b/gnu/packages/gimp.scm @@ -581,79 +581,61 @@ transferring the style of an image.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/glimpse-editor/Glimpse") - (commit (string-append "v" version)))) + (url "https://github.com/glimpse-editor/Glimpse") + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0drngj2xqzxfaag6pc4xjffiw003n4y43x5rb5bf4ziv1ac51dm9")))) (build-system gnu-build-system) (outputs '("out" - "doc")) ; 9 MiB of gtk-doc HTML + "doc")) ; 9 MiB of gtk-doc HTML (arguments - '(#:configure-flags - (list (string-append "--with-html-dir=" - (assoc-ref %outputs "doc") - "/share/gtk-doc/html") - "--enable-gtk-doc" + (list + #:configure-flags + #~(list + (string-append "--with-html-dir=" #$output "/share/gtk-doc/html") + "--enable-gtk-doc" - ;; Prevent the build system from running 'gtk-update-icon-cache' - ;; which is not needed during the build because Guix runs it at - ;; profile creation time. - "ac_cv_path_GTK_UPDATE_ICON_CACHE=true" + ;; Prevent the build system from running 'gtk-update-icon-cache' + ;; which is not needed during the build because Guix runs it at + ;; profile creation time. + "ac_cv_path_GTK_UPDATE_ICON_CACHE=true" - ;; Disable automatic network request on startup to check for - ;; version updates. - "--disable-check-update" + ;; Disable automatic network request on startup to check for + ;; version updates. + "--disable-check-update" - ;; ./configure requests not to annoy upstream with packaging bugs. - "--with-bug-report-url=https://bugs.gnu.org/guix") - #:phases - (modify-phases %standard-phases - (add-after 'install 'install-sitecustomize.py - ;; Install 'sitecustomize.py' into glimpse's python directory to - ;; add pygobject and pygtk to pygimp's search path. - (lambda* (#:key outputs #:allow-other-keys) - (let* ((pythonpath (getenv "GUIX_PYTHONPATH")) - (out (assoc-ref outputs "out")) - (sitecustomize.py - (string-append - out "/lib/glimpse/2.0/python/sitecustomize.py"))) - (call-with-output-file sitecustomize.py - (lambda (port) - (format port "import site~%") - (format port "for dir in '~a'.split(':'):~%" pythonpath) - (format port " site.addsitedir(dir)~%"))))))))) + ;; ./configure requests not to annoy upstream with packaging bugs. + "--with-bug-report-url=https://bugs.gnu.org/guix"))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gtk-doc" ,gtk-doc) - ("intltool" ,intltool) - ("libtool" ,libtool) - ("libxslt" ,libxslt) ; for xsltproc - ("pkg-config" ,pkg-config) - ("glib:bin" ,glib "bin"))) ; for gdbus-codegen + (list autoconf + automake + gtk-doc + intltool + libtool + libxslt ;for xsltproc + pkg-config + `(,glib "bin"))) ;for gdbus-codegen (inputs - `(("babl" ,babl) - ("glib" ,glib) - ("glib-networking" ,glib-networking) - ("libtiff" ,libtiff) - ("libwebp" ,libwebp) - ("libjpeg" ,libjpeg-turbo) - ("atk" ,atk) - ("gexiv2" ,gexiv2) - ("gtk+" ,gtk+-2) - ("libmypaint" ,libmypaint) - ("mypaint-brushes" ,mypaint-brushes-1.3) - ("exif" ,libexif) ; optional, EXIF + XMP support - ("lcms" ,lcms) ; optional, color management - ("librsvg" ,librsvg) ; optional, SVG support - ("libxcursor" ,libxcursor) ; optional, Mouse Cursor support - ("poppler" ,poppler) ; optional, PDF support - ("poppler-data" ,poppler-data) - ("python" ,python-2) ; optional, Python support - ("python2-pygtk" ,python2-pygtk) ; optional, Python support - ("gegl" ,gegl-for-glimpse))) ; XXX see comment in gegl-for-glimpse + (list babl + glib + glib-networking + libtiff + libwebp + libjpeg-turbo + atk + gexiv2 + gtk+-2 + libmypaint + mypaint-brushes-1.3 + libexif ;optional, EXIF + XMP support + lcms ;optional, color management + librsvg ;optional, SVG support + libxcursor ;optional, Mouse Cursor support + poppler ;optional, PDF support + poppler-data + gegl-for-glimpse)) ;XXX see comment in gegl-for-glimpse (home-page "https://glimpse-editor.github.io/") (synopsis "Glimpse Image Editor") (description "The Glimpse Image Editor is an application for image From 166350036ca82cdad6f385215da4dc80a97c2ffe Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 01:35:52 -0400 Subject: [PATCH 1210/1394] gnu: keybinder: Replace with keybinder-3.0. * gnu/packages/wm.scm (keybinder): Replace definition with that of keybinder-3.0. (keybinder-3.0): New deprecated alias. --- gnu/packages/wm.scm | 34 ++++++---------------------------- 1 file changed, 6 insertions(+), 28 deletions(-) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 3f203d83511..123e6ca7e7a 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -53,6 +53,7 @@ ;;; Copyright © 2022 Jai Vetrivelan ;;; Copyright © 2022 Daniel Meißner ;;; Copyright © 2022 Pier-Hugues Pellerin +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -1240,39 +1241,13 @@ all of them. Currently supported window managers include: (define-public keybinder (package (name "keybinder") - (version "0.3.1") - (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/kupferlauncher/keybinder" - "/releases/download/v" version "/keybinder-" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0h52hj3ay8mfhwvmfxbxlfyq74hifdk8wxgxp7fr4iy6189hg7w7")))) - (build-system gnu-build-system) - (inputs - (list python-2 gtk+-2)) - (native-inputs - (list python2-pygtk gtk-doc pkg-config)) - (synopsis "Library for registering global keyboard shortcuts") - (description - "Keybinder is a library for registering global keyboard shortcuts. -Keybinder works with GTK-based applications using the X Window System.") - (home-page "https://github.com/kupferlauncher/keybinder") - (license license:gpl2+))) - -(define-public keybinder-3.0 - (package - (name "keybinder-3.0") (version "0.3.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/kupferlauncher/keybinder" - "/releases/download/" name "-v" version "/" name "-" - version ".tar.gz")) + "/releases/download/" name "-3.0-v" version "/" + name "-3.0-" version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 @@ -1289,6 +1264,9 @@ Keybinder works with GTK-based applications using the X Window System.") (home-page "https://github.com/kupferlauncher/keybinder") (license license:x11))) +(define-public keybinder-3.0 + (deprecated-package "keybinder-3.0" keybinder)) + (define-public spectrwm (package (name "spectrwm") From ed3c97f53ef5d60f103b93d15ccce5db052bfad1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:40:37 -0400 Subject: [PATCH 1211/1394] gnu: language: Remove tegaki packages. As they only support Python 2 and appear to be unmaintained. * gnu/packages/language.scm (python2-tegaki-wagomu): (python2-tegaki-python, python2-tegaki-pygtk, python2-tegaki-tools) (tegaki-zinnia-japanese, tegaki-zinnia-japanese-light) (tegaki-zinnia-japanese-kyoiku, tegaki-zinnia-japanese-joyo) (tegaki-zinnia-simplified-chinese, tegaki-zinnia-simplified-chinese-light) (tegaki-zinnia-traditional-chinese, tegaki-zinnia-traditional-chinese-light) (tegaki-wagomu-japanese, tegaki-wagomu-japanese-kyoiku) (tegaki-wagomu-japanese-joyo, tegaki-wagomu-simplified-chinese) (tegaki-wagomu-traditional-chinese): Delete variables. --- gnu/packages/language.scm | 385 -------------------------------------- 1 file changed, 385 deletions(-) diff --git a/gnu/packages/language.scm b/gnu/packages/language.scm index ce7646b7ad8..61c9e682ed3 100644 --- a/gnu/packages/language.scm +++ b/gnu/packages/language.scm @@ -855,391 +855,6 @@ extensions in EXTS." (srfi srfi-1) (srfi srfi-26))) -(define-public python2-tegaki-wagomu - (package - (name "python2-tegaki-wagomu") - (version "0.3.1") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri "tegaki-wagomu" version)) - (sha256 - (base32 - "1pzdiq4zy1nyylaj9i6v2h4h0r05klahskzpafpp367p4rysi1x9")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "pyc")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; only Python 2 is supported - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-recognizer - (lambda* (#:key inputs #:allow-other-keys) - ;; fix missing module and function - (substitute* "tegakiwagomu.py" - (("import Results,") - "import ") - (("def _recognize") - "def recognize") - (("Results\\(candidates\\)") - "candidates")) - #t))))) - (inputs - (list glib)) - (native-inputs - (list pkg-config swig)) - (home-page "https://tegaki.github.io/") - (synopsis - "Chinese and Japanese Handwriting Recognition (Recognition engine)") - (description - "Tegaki is an ongoing project which aims to develop a free and open-source -modern implementation of handwriting recognition software, specifically -designed for Chinese (simplified and traditional) and Japanese, and that is -suitable for both the desktop and mobile devices.") - (license license:gpl2+))) ; all files - -(define-public python2-tegaki-python - (package - (inherit python2-tegaki-wagomu) - (name "python2-tegaki-python") - (version "0.3.1") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri "tegaki-python" version)) - (sha256 - (base32 - "0x93k7pw9nh0ywd97pr8pm7jv3f94nw044i5k0zvzhdpsjqvak7p")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "pyc")))) - (arguments - (substitute-keyword-arguments (package-arguments python2-tegaki-wagomu) - ((#:phases _) - `(modify-phases %standard-phases - (add-after 'unpack 'pre-configure - (lambda* (#:key inputs #:allow-other-keys) - ;; Always convert string to unicode to avoid the following error - ;; when running "tegaki-build" in python2-tegaki-tools: - ;; - ;; sqlite3.ProgrammingError: You must not use 8-bit bytestrings - ;; unless you use a text_factory that can interpret 8-bit - ;; bytestrings (like text_factory = str). - ;; It is highly recommended that you instead just switch your - ;; application to Unicode strings. - (substitute* "tegaki/charcol.py" - (("sqlite3.OptimizedUnicode") - "lambda s: unicode(s, 'utf-8')")) - (substitute* "tegaki/engine.py" - (("/usr(/local)?") - (assoc-ref inputs "python2-tegaki-wagomu"))) - #t)))))) - ;; override inherited inputs - (inputs '()) - (native-inputs '()) - (propagated-inputs - (list python2-tegaki-wagomu python2-zinnia)) - (synopsis - "Chinese and Japanese Handwriting Recognition (Base python library)") - (license (list license:gpl2+ ; all files except... - license:bsd-3 ; dictutils.py - license:zpl2.1)))) ; minjson.py - -(define-public python2-tegaki-pygtk - (package - (inherit python2-tegaki-wagomu) - (name "python2-tegaki-pygtk") - (version "0.3.1") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri "tegaki-pygtk" version)) - (sha256 - (base32 - "1cip0azxhjdj2dg2z85cp1z3lz4qwx3w1j7z4xmcm7npapmsaqs2")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "pyc")))) - (arguments - (substitute-keyword-arguments (package-arguments python2-tegaki-wagomu) - ((#:phases _) - `(modify-phases %standard-phases - (add-after 'unpack 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "tegakigtk/fakekey.py" - (("libX11.so.6" so) - (search-input-file inputs - (string-append "/lib/" so))) - (("libXtst.so.6" so) - (search-input-file inputs - (string-append "/lib/" so)))))))))) - (inputs ; required for sending key strokes - (list libx11 libxtst)) - (native-inputs '()) ; override inherited inputs - (propagated-inputs - (list python2-pygtk python2-tegaki-python)) - (synopsis "Chinese and Japanese Handwriting Recognition (Base UI library)") - (license license:gpl2+))) - -(define-public python2-tegaki-tools - (package - (inherit python2-tegaki-wagomu) - (name "python2-tegaki-tools") - (version "0.3.1") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri "tegaki-tools" version)) - (sha256 - (base32 - "0xxv97ggh2jgldw3r7y59lv3fhz733r6l7mdn6nh4m0gvb0ja971")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "pyc")))) - (arguments - (substitute-keyword-arguments (package-arguments python2-tegaki-wagomu) - ((#:phases _) '%standard-phases))) - (inputs - (list python2-tegaki-pygtk)) - ;; override inherited inputs - (native-inputs '()) - (propagated-inputs '()) - (synopsis "Chinese and Japanese Handwriting Recognition (Advanced tools)") - ;; Files in gifenc/ are licensed under gpl3+ while other files are licensed - ;; under gpl2+. Therefore, the combined work is licensed under gpl3+. - (license license:gpl3+))) - -(define-public tegaki-zinnia-japanese - (package - (inherit python2-tegaki-wagomu) - (name "tegaki-zinnia-japanese") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "1nmg9acxhcqly9gwkyb9m0hpy76fll91ywk4b1q4xms0ajxip1h7")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; no tests - #:phases - (modify-phases %standard-phases - (replace 'configure - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "Makefile" - (("/usr/local") - (assoc-ref outputs "out"))) - #t))))) - ;; override inherited inputs - (inputs '()) - (native-inputs - (list python2-tegaki-tools)) - (propagated-inputs '()) - (native-search-paths - (list (search-path-specification - (variable "TEGAKI_MODEL_PATH") - (files '("share/tegaki/models"))))) - (synopsis "Chinese and Japanese Handwriting Recognition (Model)") - (license license:lgpl2.1))) - -(define-public tegaki-zinnia-japanese-light - (package - (inherit tegaki-zinnia-japanese) - (name "tegaki-zinnia-japanese-light") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "0x0fs29ylqzxd6xvg51h7rigpbisd7q8v11df425ib2j792yfyf8")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (license license:lgpl2.1))) - -(define-public tegaki-zinnia-japanese-kyoiku - (package - (inherit tegaki-zinnia-japanese) - (name "tegaki-zinnia-japanese-kyoiku") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "0am94bcpmbzplxdnwn9gk15sgaizvcfhmv13mk14jjvx3419cvvx")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (license license:lgpl2.1))) - -(define-public tegaki-zinnia-japanese-joyo - (package - (inherit tegaki-zinnia-japanese) - (name "tegaki-zinnia-japanese-joyo") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "1v0j40lzdyiz01ayws0b8r7fsdy2mr32658382kz4wyk883wzx2z")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (license license:lgpl2.1))) - -(define-public tegaki-zinnia-simplified-chinese - (package - (inherit tegaki-zinnia-japanese) - (name "tegaki-zinnia-simplified-chinese") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "18wq0jccv7lpnrfnzspyc110d6pj2v1i21xcx4fmgzz1lnln3fs5")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (license license:lgpl2.1))) - -(define-public tegaki-zinnia-simplified-chinese-light - (package - (inherit tegaki-zinnia-japanese) - (name "tegaki-zinnia-simplified-chinese-light") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "0v24yf0w0p03lb7fyx128a75mwzad166bigvlbrzqnad789qg1sr")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (license license:lgpl2.1))) - -(define-public tegaki-zinnia-traditional-chinese - (package - (inherit tegaki-zinnia-japanese) - (name "tegaki-zinnia-traditional-chinese") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "140nlp6hynrai2svs5670jjfw1za6ayflhyj2dl0bzsfgbk3447l")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (license license:lgpl2.1))) - -(define-public tegaki-zinnia-traditional-chinese-light - (package - (inherit tegaki-zinnia-japanese) - (name "tegaki-zinnia-traditional-chinese-light") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "1m6yk6a57vs9wg5y50qciwi1ahhmklp2mgsjysbj4mnyzv6yhcr2")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (license license:lgpl2.1))) - -(define-public tegaki-wagomu-japanese - (package - (inherit tegaki-zinnia-japanese) - (name "tegaki-wagomu-japanese") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "0flj5id8xwsn7csrrzqz9prdikswnwm2wms0as2vzdpxzph1az4k")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (license license:lgpl2.1))) - -(define-public tegaki-wagomu-japanese-kyoiku - (package - (inherit tegaki-zinnia-japanese) - (name "tegaki-wagomu-japanese-kyoiku") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "0v8crfh8rdf6ndp16g52s5jlrrlwh73xp38zjn5i9dlacx8kfqg1")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (license license:lgpl2.1))) - -(define-public tegaki-wagomu-japanese-joyo - (package - (inherit tegaki-zinnia-japanese) - (name "tegaki-wagomu-japanese-joyo") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "0wk8shpr963zp328g991qs6abpnacq4242003m687z2d6yp7nph2")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (license license:lgpl2.1))) - -(define-public tegaki-wagomu-simplified-chinese - (package - (inherit tegaki-zinnia-japanese) - (name "tegaki-wagomu-simplified-chinese") - (version "0.3") - (source - (origin - (method url-fetch) - (uri (tegaki-release-uri name version "zip")) - (sha256 - (base32 - "0wqprynigqxqxv128i1smh81gxvmjj056d9qpznxa3n9f5ymlbj6")) - (modules remove-pre-compiled-files-modules) - (snippet (remove-pre-compiled-files "model")))) - (license license:lgpl2.1))) - -;;; Upstream does not provide the source for tegaki-wagomu-traditional-chinese. -;;; Therefore, we use the source for tegaki-zinnia-traditional-chinese and -;;; patch the Makefile accordingly. -(define-public tegaki-wagomu-traditional-chinese - (package - (inherit tegaki-zinnia-traditional-chinese) - (name "tegaki-wagomu-traditional-chinese") - (arguments - (substitute-keyword-arguments - (package-arguments tegaki-zinnia-traditional-chinese) - ((#:phases phases '%standard-phases) - `(modify-phases ,phases - (replace 'configure - (lambda args - (let ((configure (assq-ref ,phases 'configure))) - (apply configure args)) - (substitute* "Makefile" - (("zinnia") "wagomu")) - #t)))))) - (license license:lgpl2.1))) - (define-public link-grammar (package (name "link-grammar") From 1c09ed37211d983d04e626d736df8f69f504630d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 01:38:27 -0400 Subject: [PATCH 1212/1394] gnu: Remove python2-pygtk. * gnu/packages/gtk.scm (python2-pygtk): Delete variable. --- gnu/packages/gtk.scm | 70 -------------------------------------------- 1 file changed, 70 deletions(-) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index af695d118b9..2518b987560 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -1940,76 +1940,6 @@ printing and other features typical of a source code editor.") ;; Dual-licensed under LGPL 2.1 or Mozilla Public License 1.1 (license (list license:lgpl2.1 license:mpl1.1))))) -(define-public python2-pygtk - (package - (name "python2-pygtk") - (version "2.24.0") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://gnome/sources" - "/pygtk/" (version-major+minor version) - "/pygtk-" version ".tar.bz2")) - (sha256 - (base32 - "04k942gn8vl95kwf0qskkv6npclfm31d78ljkrkgyqxxcni1w76d")))) - (build-system gnu-build-system) - (outputs '("out" - "doc")) ;13 MiB of gtk-doc HTML - (native-inputs - (list pkg-config)) - (inputs - `(("python" ,python-2) - - ;; XXX: The package fails to build with the latest Pango (propagated - ;; from GTK+2), so we provide it with this older version. - ("pango" ,pango-1.42) - - ("libglade" ,libglade) - ("glib" ,glib))) - (propagated-inputs - `(("python-pycairo" ,python2-pycairo) ;loaded at runtime - ("python-pygobject" ,python2-pygobject-2) ;referenced in pc file - ("gtk+" ,gtk+-2))) - (arguments - `(#:tests? #f - #:phases (modify-phases %standard-phases - (add-before 'configure 'set-gtk-doc-directory - (lambda* (#:key outputs #:allow-other-keys) - ;; Install documentation to "doc". - (let ((doc (assoc-ref outputs "doc"))) - (substitute* "docs/Makefile.in" - (("TARGET_DIR = \\$\\(datadir\\)") - (string-append "TARGET_DIR = " doc)))))) - (add-after 'configure 'fix-codegen - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "pygtk-codegen-2.0" - (("^prefix=.*$") - (string-append - "prefix=" - (assoc-ref inputs "python-pygobject") "\n"))))) - (add-after 'install 'install-pth - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; pygtk's modules are stored in a subdirectory of - ;; python's site-packages directory. Add a .pth file so - ;; that python will add that subdirectory to its module - ;; search path. - (let* ((out (assoc-ref outputs "out")) - (site (string-append out "/lib/python" - ,(version-major+minor - (package-version python-2)) - "/site-packages"))) - (call-with-output-file (string-append site "/pygtk.pth") - (lambda (port) - (format port "gtk-2.0~%"))))))))) - (home-page "http://www.pygtk.org/") - (synopsis "Python bindings for GTK+") - (description - "PyGTK allows you to write full featured GTK programs in Python. It is -targeted at GTK 2.x, and can be used in conjunction with gnome-python to -write GNOME applications.") - (license license:lgpl2.1+))) - (define-public perl-cairo (package (name "perl-cairo") From fa4800461458e44196d9399b7880a69730933966 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 01:39:47 -0400 Subject: [PATCH 1213/1394] gnu: Remove python2-pytest-runner. * gnu/packages/check.scm (python2-pytest-runner): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 8b77bf77ce4..a4e505d4943 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -1327,9 +1327,6 @@ Python's @code{random.seed}.") @file{setup.py} files can use to run tests.") (license license:expat))) -(define-public python2-pytest-runner - (package-with-python2 python-pytest-runner)) - (define-public python-pytest-lazy-fixture (package (name "python-pytest-lazy-fixture") From 26876b66001a1dc45ee6d05015fddd7f5a88676e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:20:05 -0400 Subject: [PATCH 1214/1394] gnu: lightdm: Update to 1.30.0-0.b7fc321. * gnu/packages/display-managers.scm (lightdm): Update to 1.30.0-0.b7fc321. [source]: Use git. [configure-flags]: Add CFLAGS=-Wno-error=missing-prototypes. [phases]: Delete trailing #t. {fix-paths}: Use search-input-file. [inputs]: Add coreutils. [native-inputs]: Use new style. Replace python-2 by python-wrapper and python2-pygobject by python-pygobject. Add autoconf, automake, gtk-doc, libtool, which and yelp-tools. --- gnu/packages/display-managers.scm | 143 +++++++++++++++++------------- 1 file changed, 81 insertions(+), 62 deletions(-) diff --git a/gnu/packages/display-managers.scm b/gnu/packages/display-managers.scm index 80aad1af5d4..d567f7d3feb 100644 --- a/gnu/packages/display-managers.scm +++ b/gnu/packages/display-managers.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2021 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2021 Efraim Flashner ;;; Copyright © 2021 Petr Hodina +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -41,7 +42,9 @@ #:use-module (guix utils) #:use-module (guix gexp) #:use-module (gnu packages) + #:use-module (gnu packages autotools) #:use-module (gnu packages admin) + #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) @@ -252,70 +255,86 @@ experience for your users, your family and yourself") (license license:gpl3+))) (define-public lightdm - (package - (name "lightdm") - (version "1.30.0") - (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/CanonicalLtd/lightdm/releases/download/" - version "/lightdm-" version ".tar.xz")) - (sha256 - (base32 - "158zb2d0v1309a8v19hh32y4yj3v6yg4yg6m0l7v59d3a2b7f651")))) - (build-system gnu-build-system) - (arguments - '(#:parallel-tests? #f ; fails when run in parallel - #:configure-flags - (list "--localstatedir=/var") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-paths - (lambda _ - (substitute* "src/shared-data-manager.c" - (("/bin/rm") (which "rm"))) - (substitute* '("data/users.conf" - "common/user-list.c") - (("/bin/false") (which "false")) - (("/usr/sbin/nologin") (which "nologin"))) - (substitute* "src/seat.c" - (("/bin/sh") (which "sh"))) - #t)) - (add-before 'check 'pre-check - ;; Run test-suite under a dbus session. - (lambda* (#:key inputs #:allow-other-keys) - (wrap-program "tests/src/test-python-greeter" - `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH"))) - `("GI_TYPELIB_PATH" ":" prefix (,(getenv "GI_TYPELIB_PATH")))) + ;; Use the latest commit, as the current official release doesn't build with + ;; glib >= 2.33. + (let ((revision "0") + (commit "b7fc3214cbaed09c73e963847443a0d648dfd896")) + (package + (name "lightdm") + (version (git-version "1.30.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/canonical/lightdm") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0378jacazpmdgdjkiilk3mbikz3iysb4s9q40hg9zv4yngwsix1m")))) + (build-system gnu-build-system) + (arguments + '(#:parallel-tests? #f ; fails when run in parallel + #:configure-flags + (list "--localstatedir=/var" + ;; Otherwise the test suite fails on such a warning. + "CFLAGS=-Wno-error=missing-prototypes") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/shared-data-manager.c" + (("/bin/rm") + (search-input-file inputs "bin/rm"))) + (substitute* '("data/users.conf" + "common/user-list.c") + (("/bin/false") + (search-input-file inputs "bin/false")) + (("/usr/sbin/nologin") + (search-input-file inputs "sbin/nologin"))) + (substitute* "src/seat.c" + (("/bin/sh") + (search-input-file inputs "bin/sh"))))) + (add-before 'check 'pre-check + ;; Run test-suite under a dbus session. + (lambda _ + (wrap-program "tests/src/test-python-greeter" + `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH"))) + `("GI_TYPELIB_PATH" ":" prefix (,(getenv "GI_TYPELIB_PATH")))) - ;; Avoid printing locale warnings, which trip up the text - ;; matching tests. - (unsetenv "LC_ALL") - #t))))) - (inputs - (list audit - linux-pam - shadow ;for sbin/nologin - libgcrypt - libxcb)) - (native-inputs - `(("gobject-introspection" ,gobject-introspection) - ("pkg-config" ,pkg-config) - ("itstool" ,itstool) - ("intltool" ,intltool) - ("vala" ,vala) ;for Vala bindings - ;; For tests - ("dbus" ,dbus) - ("python" ,python-2) - ("python-pygobject" ,python2-pygobject))) - ;; Required by liblightdm-gobject-1.pc. - (propagated-inputs - (list glib libx11 libxklavier)) - (home-page "https://www.freedesktop.org/wiki/Software/LightDM/") - (synopsis "Lightweight display manager") - (description "The Light Display Manager (LightDM) is a cross-desktop + ;; Avoid printing locale warnings, which trip up the text + ;; matching tests. + (unsetenv "LC_ALL")))))) + (inputs + (list audit + coreutils ;for cross-compilation + linux-pam + shadow ;for sbin/nologin + libgcrypt + libxcb)) + (native-inputs + (list autoconf + automake + gobject-introspection + gtk-doc + pkg-config + itstool + intltool + libtool + vala ;for Vala bindings + ;; For tests + dbus + ;; python-wrapper + ;; python-pygobject + which + yelp-tools)) + ;; Required by liblightdm-gobject-1.pc. + (propagated-inputs + (list glib libx11 libxklavier)) + (home-page "https://www.freedesktop.org/wiki/Software/LightDM/") + (synopsis "Lightweight display manager") + (description "The Light Display Manager (LightDM) is a cross-desktop display manager which supports different greeters.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public lightdm-gtk-greeter (package From 88a77bdda15cd915481de02655987489853786c3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:26:52 -0400 Subject: [PATCH 1215/1394] gnu: Remove python2-pygobject. * gnu/packages/glib.scm (python2-pygobject, python2-pygobject-2): Delete variables. (python-pygobject)[properties]: Delete field. * gnu/packages/patches/python2-pygobject-2-deprecation.patch: Delete file. * gnu/local.mk (dist_patch_DATA): De-register it. * gnu/packages/gnome.scm (libsecret): Remove commented Python 2 inputs. --- gnu/local.mk | 1 - gnu/packages/glib.scm | 70 +------------------ gnu/packages/gnome.scm | 7 -- .../python2-pygobject-2-deprecation.patch | 39 ----------- 4 files changed, 1 insertion(+), 116 deletions(-) delete mode 100644 gnu/packages/patches/python2-pygobject-2-deprecation.patch diff --git a/gnu/local.mk b/gnu/local.mk index 7a030283a70..b54c1fbefe2 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1710,7 +1710,6 @@ dist_patch_DATA = \ %D%/packages/patches/python-pycrypto-time-clock.patch \ %D%/packages/patches/python-pyan3-fix-absolute-path-bug.patch \ %D%/packages/patches/python-pyan3-fix-positional-arguments.patch \ - %D%/packages/patches/python2-pygobject-2-deprecation.patch \ %D%/packages/patches/python-pygpgme-fix-pinentry-tests.patch \ %D%/packages/patches/python-pytorch-runpath.patch \ %D%/packages/patches/python-pytorch-system-libraries.patch \ diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index 30e5433776c..09d5a03555d 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -816,44 +816,6 @@ useful for C++.") (modify-inputs (package-propagated-inputs glibmm) (replace "libsigc++" libsigc++-2))))) -(define-public python2-pygobject-2 - (package - (name "python2-pygobject") - ;; This was the last version to declare the 2.0 platform number, i.e. its - ;; pkg-config files were named pygobject-2.0.pc - (version "2.28.7") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://gnome/sources/pygobject/" - (version-major+minor version) - "/pygobject-" version ".tar.xz")) - (sha256 - (base32 - "0nkam61rsn7y3wik3vw46wk5q2cjfh2iph57hl9m39rc8jijb7dv")) - (patches (search-patches "python2-pygobject-2-deprecation.patch")))) - (build-system gnu-build-system) - (native-inputs - `(("which" ,which) - ("glib-bin" ,glib "bin") ;for tests: glib-compile-schemas - ("pkg-config" ,pkg-config) - ("dbus" ,dbus))) ;for tests - (inputs - `(("python" ,python-2) - ("glib" ,glib) - ("python2-pycairo" ,python2-pycairo) - ("gobject-introspection" ,gobject-introspection))) - (propagated-inputs - (list libffi)) ;mentioned in pygobject-2.0.pc - (arguments - `(#:tests? #f ;segfaults during tests - #:configure-flags '("LIBS=-lcairo-gobject"))) - (home-page "https://pypi.org/project/PyGObject/") - (synopsis "Python bindings for GObject") - (description - "Python bindings for GLib, GObject, and GIO.") - (license license:lgpl2.1+))) - (define-public python-pygobject (package (name "python-pygobject") @@ -902,37 +864,7 @@ useful for C++.") (synopsis "Python bindings for GObject") (description "Python bindings for GLib, GObject, and GIO.") - (license license:lgpl2.1+) - (properties `((python2-variant . ,(delay python2-pygobject)))))) - -(define-public python2-pygobject - (let ((base (strip-python2-variant python-pygobject))) - (package/inherit base - (name "python2-pygobject") - - ;; Note: We use python-build-system here, because Meson only supports - ;; Python 3, and needs PYTHONPATH etc set up correctly, which makes it - ;; difficult to use for Python 2 projects. - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'delete-broken-tests - (lambda _ - ;; FIXME: this test freezes and times out. - (delete-file "tests/test_mainloop.py") - ;; FIXME: this test fails with this kind of error: - ;; AssertionError: != -Date: Sat, 13 Aug 2011 04:13:28 -0400 -Subject: remove references to deprecated GI_INFO_TYPE_ERROR_DOMAIN - - -diff --git a/gi/pygi-info.c b/gi/pygi-info.c -index 8729e25..007b609 100644 ---- a/gi/pygi-info.c -+++ b/gi/pygi-info.c -@@ -165,9 +165,6 @@ _pygi_info_new (GIBaseInfo *info) - case GI_INFO_TYPE_CONSTANT: - type = &PyGIConstantInfo_Type; - break; -- case GI_INFO_TYPE_ERROR_DOMAIN: -- type = &PyGIErrorDomainInfo_Type; -- break; - case GI_INFO_TYPE_UNION: - type = &PyGIUnionInfo_Type; - break; -@@ -484,7 +481,6 @@ _pygi_g_type_info_size (GITypeInfo *type_info) - case GI_INFO_TYPE_INVALID: - case GI_INFO_TYPE_FUNCTION: - case GI_INFO_TYPE_CONSTANT: -- case GI_INFO_TYPE_ERROR_DOMAIN: - case GI_INFO_TYPE_VALUE: - case GI_INFO_TYPE_SIGNAL: - case GI_INFO_TYPE_PROPERTY: -@@ -863,7 +859,6 @@ pygi_g_struct_info_is_simple (GIStructInfo *struct_info) - case GI_INFO_TYPE_INVALID: - case GI_INFO_TYPE_FUNCTION: - case GI_INFO_TYPE_CONSTANT: -- case GI_INFO_TYPE_ERROR_DOMAIN: - case GI_INFO_TYPE_VALUE: - case GI_INFO_TYPE_SIGNAL: - case GI_INFO_TYPE_PROPERTY: --- -cgit v0.10.1 - From 4e7d6a2dbe74f32fc22bfb2e7a3bbaab7c18cc79 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:32:06 -0400 Subject: [PATCH 1216/1394] gnu: Remove python2-pytest. * gnu/packages/check.scm (python2-pytest): Delete variable. (python-pytest)[properties]: Delete field. (python-pytest-bootstrap): Do no strip python2-variant from parent. (python2-pytest-bootstrap): Delete variable. --- gnu/packages/check.scm | 66 ++---------------------------------------- 1 file changed, 3 insertions(+), 63 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index a4e505d4943..0618ddbd039 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -1026,77 +1026,17 @@ standard library.") "Pytest is a testing tool that provides auto-discovery of test modules and functions, detailed info on failing assert statements, modular fixtures, and many external plugins.") - (license license:expat) - (properties `((python2-variant . ,(delay python2-pytest)))))) + (license license:expat))) (define-public python-pytest-6 python-pytest) -;; Pytest 4.x are the last versions that support Python 2. -(define-public python2-pytest - (package - (inherit (strip-python2-variant python-pytest)) - (name "python2-pytest") - (version "4.6.11") - (source (origin - (method url-fetch) - (uri (pypi-uri "pytest" version)) - (sha256 - (base32 - "0ls3pqr86xgif6bphsb6wrww9r2vc7p7a2naq8zcq8115wwq5yjh")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - ,@(package-arguments python-pytest))) - (propagated-inputs - `(("python-atomicwrites" ,python2-atomicwrites) - ("python-attrs" ,python2-attrs-bootstrap) - ("python-funcsigs" ,python2-funcsigs) - ("python-importlib-metadata" ,python2-importlib-metadata-bootstrap) - ("python-more-itertools" ,python2-more-itertools) - ("python-packaging" ,python2-packaging-bootstrap) - ("python-pathlib2" ,python2-pathlib2) - ("python-pluggy" ,python2-pluggy) - ("python-py" ,python2-py) - ("python-six" ,python2-six-bootstrap) - ("python-wcwidth" ,python2-wcwidth))) - (native-inputs - `(("bash" ,bash) ;tests require 'compgen' - ("python-hypothesis" ,python2-hypothesis) - ("python-nose" ,python2-nose) - ("python-mock" ,python2-mock) - ("python-pytest" ,python2-pytest-bootstrap) - ("python-setuptools-scm" ,python2-setuptools-scm))))) - (define-public python-pytest-bootstrap (package - (inherit (strip-python2-variant python-pytest)) + (inherit python-pytest) (name "python-pytest-bootstrap") (native-inputs (list python-iniconfig python-setuptools-scm python-toml)) - (arguments `(#:tests? #f)) - (properties `((python2-variant . ,(delay python2-pytest-bootstrap)))))) - -(define-public python2-pytest-bootstrap - (hidden-package - (package/inherit - python2-pytest - (name "python2-pytest-bootstrap") - (arguments - (substitute-keyword-arguments (package-arguments python2-pytest) - ((#:tests? _ #f) #f))) - (native-inputs - `(("python-setuptools-scm" ,python2-setuptools-scm))) - (propagated-inputs - `(("python-atomicwrites" ,python2-atomicwrites) - ("python-attrs" ,python2-attrs-bootstrap) - ("python-funcsigs" ,python2-funcsigs-bootstrap) - ("python-importlib-metadata" ,python2-importlib-metadata-bootstrap) - ("python-more-itertools" ,python2-more-itertools) - ("python-packaging" ,python2-packaging-bootstrap) - ("python-pathlib2" ,python2-pathlib2-bootstrap) - ("python-pluggy" ,python2-pluggy-bootstrap) - ("python-py" ,python2-py) - ("python-wcwidth" ,python2-wcwidth)))))) + (arguments `(#:tests? #f)))) (define-public python-pytest-assume (package From cdbfe93f164c1621be4e0e0558c3529ff0c720c8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 30 Apr 2022 00:11:11 -0400 Subject: [PATCH 1217/1394] gnu: Remove python2-pluggy. * gnu/packages/python-xyz.scm (python2-pluggy): Delete variable. (python2-pluggy-bootstrap): Likewise. (python-pluggy)[properties]: Delete field. --- gnu/packages/python-xyz.scm | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b5bebb98c3e..74d0e4379ce 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14565,31 +14565,8 @@ library as well as on the command line.") (description "Pluggy is an extraction of the plugin manager as used by Pytest but stripped of Pytest specific details.") (home-page "https://pypi.org/project/pluggy/") - (properties `((python2-variant . ,(delay python2-pluggy)))) (license license:expat))) -(define-public python2-pluggy - (let ((base (package-with-python2 (strip-python2-variant - python-pluggy)))) - (package/inherit - base - (propagated-inputs - `(("python-importlib-metadata" ,python2-importlib-metadata)))))) - -;; This package requires python2-importlib-metadata, but that package -;; ends up needing python2-pluggy via python2-pytest, so we need this -;; variant to solve the circular dependency. -(define-public python2-pluggy-bootstrap - (hidden-package - (package/inherit - python2-pluggy - (name "python2-pluggy-bootstrap") - (arguments - `(#:tests? #f - ,@(package-arguments python2-pluggy))) - (propagated-inputs - `(("python-importlib-metadata" ,python2-importlib-metadata-bootstrap)))))) - (define-public python-plumbum (package (name "python-plumbum") From 0e406da6a07dbafbc4422294956878057508131a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:46:27 -0400 Subject: [PATCH 1218/1394] gnu: Remove python2-pycairo. * gnu/packages/gtk.scm (python2-pycairo): Delete variable. --- gnu/packages/gtk.scm | 19 +------------------ 1 file changed, 1 insertion(+), 18 deletions(-) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 2518b987560..a15d2be1a65 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -1919,26 +1919,9 @@ printing and other features typical of a source code editor.") (synopsis "Python bindings for cairo") (description "Pycairo is a set of Python bindings for the Cairo graphics library.") - (license license:lgpl3+) - (properties `((python2-variant . ,(delay python2-pycairo)))))) + (license license:lgpl3+))) ;; Pycairo no longer supports Python 2 since version 1.19.0, so we stick -;; with this older version here. -(define-public python2-pycairo - (let ((pycairo (package-with-python2 - (strip-python2-variant python-pycairo)))) - (package - (inherit pycairo) - (version "1.18.2") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/pygobject/pycairo/releases" - "/download/v" version "/pycairo-" version ".tar.gz")) - (sha256 - (base32 - "0cb5n4r4nl0k1g90b1gz9iyk4lp7hi03db98i1p52a870bym7f6w")))) - ;; Dual-licensed under LGPL 2.1 or Mozilla Public License 1.1 - (license (list license:lgpl2.1 license:mpl1.1))))) (define-public perl-cairo (package From 2d51db54bd9abafd7777012e94e8f4c21dff8aa1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:46:34 -0400 Subject: [PATCH 1219/1394] gnu: Remove python2-zinnia. * gnu/packages/ocr.scm (python2-zinnia): Delete variable. --- gnu/packages/ocr.scm | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/gnu/packages/ocr.scm b/gnu/packages/ocr.scm index 190bed27255..cc0f84d55c0 100644 --- a/gnu/packages/ocr.scm +++ b/gnu/packages/ocr.scm @@ -240,21 +240,4 @@ that allows us to create any hand-written recognition systems with low-cost.") license:x11 ; 'install-sh' license:public-domain))))) ; 'install-sh' -;;; python 2 bindings, license under the same terms as zinnia -(define-public python2-zinnia - (package - (inherit zinnia) - (name "python2-zinnia") - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; CObject API is used, it was removed in Python 3.2 - #:tests? #f ; avoid circular dependency on tegaki-zinnia-japanese - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'chdir - (lambda _ - (chdir "zinnia/python") - #t))))) - (inputs - (list zinnia)))) From 7720afd99ae389cca36bca51abe7ba6b500fb190 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:47:04 -0400 Subject: [PATCH 1220/1394] gnu: Remove python2-requests. * gnu/packages/python-web.scm (python2-requests): Delete variable. --- gnu/packages/python-web.scm | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index f4302e0108f..398f2891dd5 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2723,17 +2723,7 @@ APIs.") (description "Requests is a Python HTTP client library. It aims to be easier to use than Python’s urllib2 library.") - (license license:asl2.0) - (properties `((python2-variant . ,(delay python2-requests)))))) - -(define-public python2-requests - (let ((base (package-with-python2 (strip-python2-variant python-requests)))) - (package - (inherit base) - ;; The python-charset-normalizer dependency is necessary on Python 3 - ;; only. - (propagated-inputs (modify-inputs (package-propagated-inputs base) - (delete "python-charset-normalizer")))))) + (license license:asl2.0))) (define-public python-requests-unixsocket (package From 89ffe2297fd00e498b94466d3477c8833d116bb7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:47:09 -0400 Subject: [PATCH 1221/1394] gnu: Remove python2-bottle. * gnu/packages/python-web.scm (python2-bottle): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 398f2891dd5..24aebe765a4 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -4147,9 +4147,6 @@ addon modules.") (description "@code{python-bottle} is a WSGI framework for small web-applications.") (license license:expat))) -(define-public python2-bottle - (package-with-python2 python-bottle)) - (define-public python-wtforms (package (name "python-wtforms") From 191207aae237bb7a797dc29a8935c79f71dd8b71 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:47:37 -0400 Subject: [PATCH 1222/1394] gnu: Remove python2-docopt. * gnu/packages/python-xyz.scm (python2-docopt): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 74d0e4379ce..b3af73a99e5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -13712,9 +13712,6 @@ programmatically with command-line parsers like @code{getopt} and @code{argparse}.") (license license:expat))) -(define-public python2-docopt - (package-with-python2 python-docopt)) - (define-public python-pythonanywhere (package (name "python-pythonanywhere") From 2d9550cf6a1e84a334aed1af04a1832d530b2f06 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:47:54 -0400 Subject: [PATCH 1223/1394] gnu: Remove python2-decorator. * gnu/packages/python-xyz.scm (python2-decorator): Delete variable. --- gnu/packages/python-xyz.scm | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b3af73a99e5..8197201aedc 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7661,21 +7661,8 @@ PNG, PostScript, PDF, and SVG file output.") for the average programmer, and to popularize decorators usage giving examples of useful decorators, such as memoize, tracing, redirecting_stdout, locked, etc. The core of this module is a decorator factory.") - (license license:expat) - (properties `((python2-variant . ,(delay python2-decorator)))))) + (license license:expat))) -;; Version 5 does not support Python 2 -(define-public python2-decorator - (package - (inherit (package-with-python2 - (strip-python2-variant python-decorator))) - (version "4.3.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "decorator" version)) - (sha256 - (base32 "0308djallnh00v112y5b7nadl657ysmkp6vc8xn51d6yzc9zm7n3")))))) (define-public python-drmaa (package From f3412d78c5931f233d3280d02de2ee72ac5557bf Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:48:06 -0400 Subject: [PATCH 1224/1394] gnu: Remove python2-beautifulsoup4. * gnu/packages/python-xyz.scm (python2-beautifulsoup4): Delete variable. --- gnu/packages/python-xyz.scm | 17 +---------------- 1 file changed, 1 insertion(+), 16 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8197201aedc..9fe692ef886 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9400,22 +9400,7 @@ screen-scraping projects. It offers Pythonic idioms for navigating, searching, and modifying a parse tree, providing a toolkit for dissecting a document and extracting what you need. It automatically converts incoming documents to Unicode and outgoing documents to UTF-8.") - (license license:expat) - (properties `((python2-variant . ,(delay python2-beautifulsoup4)))))) - -(define-public python2-beautifulsoup4 - (let ((base (package-with-python2 - (strip-python2-variant python-beautifulsoup4)))) - (package/inherit base - (version "4.9.3") ;last version to support Python 2 - (source - (origin - (method url-fetch) - (uri (pypi-uri "beautifulsoup4" version)) - (sha256 - (base32 - "09gbd49mwz86k572r1231x2rdp82p42zlnw0bz9b9mfi58r9wwl4")))) - (arguments `(#:python ,python-2))))) + (license license:expat))) (define-public python-soupsieve (package From 1630806fa8431d212ce2ee79f55e73dca920e08d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:48:25 -0400 Subject: [PATCH 1225/1394] gnu: Remove python2-clikit. * gnu/packages/python-xyz.scm (python2-clikit): Delete variable. --- gnu/packages/python-xyz.scm | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9fe692ef886..04b9a2e8a4f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16699,18 +16699,8 @@ useful to combine multiple data objects as one.") (description "CliKit is a group of utilities to build testable command line interfaces.") - (properties `((python2-variant . ,(delay python2-clikit)))) (license license:expat))) -(define-public python2-clikit - (let ((base (package-with-python2 (strip-python2-variant python-clikit)))) - (package/inherit - base - (propagated-inputs - `(("python-enum34" ,python2-enum34) - ("python-typing" ,python2-typing) - ,@(package-propagated-inputs base)))))) - (define-public python-msgpack-python (package (name "python-msgpack-python") From 9374dbf3ee650e9daf6ffba3df10c54892f05b2e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:48:32 -0400 Subject: [PATCH 1226/1394] gnu: Remove python2-funcsigs-bootstrap. * gnu/packages/python-xyz.scm (python2-funcsigs-bootstrap): Delete variable. --- gnu/packages/python-xyz.scm | 9 --------- 1 file changed, 9 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 04b9a2e8a4f..50e5879b0c2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3219,15 +3219,6 @@ port forwards using @acronym{UPnP, Universal Plug and Play}.") "Backport of @code{funcsigs} which was introduced in Python 3.3.") (license license:asl2.0))) -(define-public python2-funcsigs-bootstrap - (package - (inherit python2-funcsigs) - (name "python2-funcsigs-bootstrap") - (native-inputs `()) - (arguments - `(#:tests? #f - ,@(package-arguments python2-funcsigs))))) - (define-public python-py (package (name "python-py") From e8a4b28581a6b1c92b79a6a8ca06381ee65c454d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:48:38 -0400 Subject: [PATCH 1227/1394] gnu: Remove python2-snowballstemmer. * gnu/packages/python-xyz.scm (python2-snowballstemmer): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 50e5879b0c2..c76ab8878cd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18050,9 +18050,6 @@ JSON) codec.") English stemmer.") (license license:bsd-3))) -(define-public python2-snowballstemmer - (package-with-python2 python-snowballstemmer)) - (define-public python-setproctitle (package (name "python-setproctitle") From 01dff5c377e6c22c6b8311f05dc5d4e385551545 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:48:54 -0400 Subject: [PATCH 1228/1394] gnu: Remove python2-packaging. * gnu/packages/python-xyz.scm (python2-packaging): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c76ab8878cd..5c061ae3b4a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19465,9 +19465,6 @@ while only declaring the test-specific fields.") ;; licenses. (license (list license:asl2.0 license:bsd-2)))) -(define-public python2-packaging - (package-with-python2 python-packaging)) - ;; TODO(staging): merge with python-packaging-bootstrap. (define-public python-packaging-next (package From a3f8802a90b85a6794e0c49790c6aabae81cc4e3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:48:57 -0400 Subject: [PATCH 1229/1394] gnu: Remove python2-backpack. * gnu/packages/python-xyz.scm (python2-backpack): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5c061ae3b4a..b4ca9ea7b6c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17150,9 +17150,6 @@ environment variables in YAML files.") collections of data.") (license license:expat))) -(define-public python2-backpack - (package-with-python2 python-backpack)) - (define-public python-prompt-toolkit (package (name "python-prompt-toolkit") From b3aefaf48bb7544613b0b070c3a48f8e37e6c5b6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:49:04 -0400 Subject: [PATCH 1230/1394] gnu: Remove python2-urwid. * gnu/packages/python-xyz.scm (python2-urwid): Delete variable. --- gnu/packages/python-xyz.scm | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b4ca9ea7b6c..c8c30bcfda4 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9106,23 +9106,8 @@ computing.") (description "Urwid is a curses-based UI/widget library for Python. It includes many features useful for text console applications.") - (properties `((python2-variant . ,(delay python2-urwid)))) (license license:lgpl2.1+))) -(define-public python2-urwid - (let ((base (package-with-python2 - (strip-python2-variant python-urwid)))) - (package - (inherit base) - (version "2.1.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "urwid" version)) - (sha256 - (base32 - "11ndnhxd41m13darf5s0c6bafdpkzq1l6mfb04wbzdmyc1hg75h8"))))))) - (define-public python-urwid-readline (package (name "python-urwid-readline") From 1fc39b25bcb0812e4a3d36879d866ceaef30c2e9 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:49:10 -0400 Subject: [PATCH 1231/1394] gnu: Remove python2-diff-match-patch. * gnu/packages/python-xyz.scm (python2-diff-match-patch): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c8c30bcfda4..8ebbb1edc59 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19272,9 +19272,6 @@ point is the point of maximum curvature.") perform the operations required for synchronizing plain text.") (license license:asl2.0))) -(define-public python2-diff-match-patch - (package-with-python2 python-diff-match-patch)) - (define-public python-dirsync (package (name "python-dirsync") From a8c87c9f06462a110913f0bf0dee7c011deb4889 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:49:15 -0400 Subject: [PATCH 1232/1394] gnu: Remove python2-jinja2. * gnu/packages/python-xyz.scm (python2-jinja2): Delete variable. --- gnu/packages/python-xyz.scm | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8ebbb1edc59..2337f4c3f58 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3991,22 +3991,8 @@ for Python.") (description "Jinja2 is a small but fast and easy to use stand-alone template engine written in pure Python.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python2-jinja2)))))) + (license license:bsd-3))) -;; Version 2.11.3 is the last to support Python 2. -(define-public python2-jinja2 - (package - (inherit (package-with-python2 - (strip-python2-variant python-jinja2))) - (version "2.11.3") - (source - (origin - (method url-fetch) - (uri (pypi-uri "Jinja2" version)) - (sha256 - (base32 - "1iiklf3wns67y5lfcacxma5vxfpb7h2a67xbghs01s0avqrq9md6")))))) (define-public python-jinja2-time (package From 29618c72d5441fda71237e50d266cb33050b60cd Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:49:35 -0400 Subject: [PATCH 1233/1394] gnu: Remove python2-twodict. * gnu/packages/python-xyz.scm (python2-twodict): Delete variable. --- gnu/packages/python-xyz.scm | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2337f4c3f58..c6c63ebab0b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -505,21 +505,6 @@ remembers the order in which the items were inserted and supports almost all the features of the Python's built-in dict.") (license license:unlicense))) -(define-public python2-twodict - (package - (inherit python-twodict) - (name "python2-twodict") - (version "1.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "twodict" version)) - (sha256 - (base32 "0ifv7dv18jn2lg0a3l6zdlvmmlda2ivixfjbsda58a2ay6kxznr0")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)))) - (define-public python-argopt (package (name "python-argopt") From de39a426bda295bd9a9075c53683fc208cdb6154 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:49:38 -0400 Subject: [PATCH 1234/1394] gnu: Remove python2-vobject. * gnu/packages/python-xyz.scm (python2-vobject): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c6c63ebab0b..c2f911549b9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15450,9 +15450,6 @@ way.") (home-page "https://eventable.github.io/vobject/") (license license:asl2.0))) -(define-public python2-vobject - (package-with-python2 python-vobject)) - (define-public python-munkres (package (name "python-munkres") From 4e9bacaaf3bd5c6759d14e0ee4312b19344678ef Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:50:50 -0400 Subject: [PATCH 1235/1394] gnu: Remove python2-pastel. * gnu/packages/graphics.scm (python2-pastel): Delete variable. --- gnu/packages/graphics.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index e966a82dbb0..4b07061fa1b 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -1593,9 +1593,6 @@ rendering @acronym{SVG, Scalable Vector Graphics}.") your terminal.") (license license:expat))) -(define-public python2-pastel - (package-with-python2 python-pastel)) - (define-public fgallery (package (name "fgallery") From c0e3ba2904f5fbaa105d54f4a5a920e04caff629 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:51:20 -0400 Subject: [PATCH 1236/1394] gnu: Remove python2-webencodings. * gnu/packages/python-web.scm (python2-webencodings): Delete variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 24aebe765a4..d5132670d5a 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1452,9 +1452,6 @@ BOM detection, but the actual implementation for encoders and decoders is Python’s.") (license license:bsd-3))) -(define-public python2-webencodings - (package-with-python2 python-webencodings)) - (define-public python-openapi-schema-validator (package (name "python-openapi-schema-validator") From eb13c73ce271c8566a7a4fafdbc00d2997dd3740 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:51:23 -0400 Subject: [PATCH 1237/1394] gnu: Remove python2-urllib3. * gnu/packages/python-web.scm (python2-urllib3): Delete variable. --- gnu/packages/python-web.scm | 9 --------- 1 file changed, 9 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index d5132670d5a..b0454b6f819 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2983,17 +2983,8 @@ addon for removing tracking fields from URLs.") "Urllib3 supports features left out of urllib and urllib2 libraries. It can reuse the same socket connection for multiple requests, it can POST files, supports url redirection and retries, and also gzip and deflate decoding.") - (properties `((python2-variant . ,(delay python2-urllib3)))) (license license:expat))) -(define-public python2-urllib3 - (let ((base (package-with-python2 (strip-python2-variant python-urllib3)))) - (package/inherit - base - (propagated-inputs - `(("python-ipaddress" ,python2-ipaddress) - ,@(package-propagated-inputs base)))))) - (define-public awscli (package ;; Note: updating awscli typically requires updating botocore as well. From e9d63dbd23c7fe5754dfc1a906a4521e33f80277 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:51:31 -0400 Subject: [PATCH 1238/1394] gnu: Remove python2-markupsafe. * gnu/packages/python-xyz.scm (python2-markupsafe): Delete variable. --- gnu/packages/python-xyz.scm | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c2f911549b9..ba71259c26b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3933,22 +3933,8 @@ e.g. filters, callbacks and errbacks can all be promises.") (description "Markupsafe provides an XML/HTML/XHTML markup safe string implementation for Python.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python2-markupsafe)))))) + (license license:bsd-3))) -;; Version 1.1.1 is the last to support Python 2. -(define-public python2-markupsafe - (package - (inherit (package-with-python2 - (strip-python2-variant python-markupsafe))) - (version "1.1.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "MarkupSafe" version)) - (sha256 - (base32 - "0sqipg4fk7xbixqd8kq6rlkxj664d157bdwbh93farcphf92x1r9")))))) (define-public python-jinja2 (package From 3dd350f5277358bb42aa32a22f3eeb1667e17ab1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:51:40 -0400 Subject: [PATCH 1239/1394] gnu: Remove python2-chardet. * gnu/packages/python-xyz.scm (python2-chardet): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ba71259c26b..97a81980a5a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -13559,9 +13559,6 @@ simulation, statistical modeling, machine learning and much more.") automatically detect a wide range of file encodings.") (license license:lgpl2.1+))) -(define-public python2-chardet - (package-with-python2 python-chardet)) - (define-public python-charset-normalizer (package (name "python-charset-normalizer") From 8577f93ba3eb076bfb0d437db506f6e44629a64b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:51:46 -0400 Subject: [PATCH 1240/1394] gnu: Remove python2-imagesize. * gnu/packages/python-xyz.scm (python2-imagesize): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 97a81980a5a..b7acb78f9e3 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18151,9 +18151,6 @@ JSON) codec.") PNG, JPEG, JPEG2000 and GIF files in pure Python.") (license license:expat))) -(define-public python2-imagesize - (package-with-python2 python-imagesize)) - (define-public python-termstyle (package (name "python-termstyle") From 8710fb9462912b733a5eee1609318be7e73075fa Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:51:54 -0400 Subject: [PATCH 1241/1394] gnu: Remove python2-babel. * gnu/packages/python-xyz.scm (python2-babel): Delete variable. --- gnu/packages/python-xyz.scm | 33 --------------------------------- 1 file changed, 33 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b7acb78f9e3..b03091668fc 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1259,39 +1259,6 @@ access to various locale display names, localized number and date formatting, etc.") (license license:bsd-3))) -(define-public python2-babel - (package - (name "python2-babel") - (version "2.9.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "Babel" version)) - (sha256 - (base32 - "018yg7g2pa6vjixx1nx41cfispgfi0azzp0a1chlycbj8jsil0ys")))) - (build-system python-build-system) - (native-inputs - (list python2-freezegun python2-pytest tzdata-for-tests)) - (propagated-inputs - (list python2-pytz)) - (arguments - `(#:python ,python-2 - #:phases (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "pytest" "-vv")))))) - (home-page "https://babel.pocoo.org/") - (synopsis - "Tools for internationalizing Python applications") - (description - "Babel is composed of two major parts: -- tools to build and work with gettext message catalogs -- a Python interface to the CLDR (Common Locale Data Repository), providing -access to various locale display names, localized number and date formatting, -etc.") - (license license:bsd-3))) - (define-public python2-backport-ssl-match-hostname (package (name "python2-backport-ssl-match-hostname") From 139b97b65e0817e91bced3aa326781b014849f14 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:51:57 -0400 Subject: [PATCH 1242/1394] gnu: Remove python2-levenshtein. * gnu/packages/python-xyz.scm (python2-levenshtein): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b03091668fc..038f54ec741 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19231,9 +19231,6 @@ point is the point of maximum curvature.") It supports both normal and Unicode strings.") (license license:gpl2+))) -(define-public python2-levenshtein - (package-with-python2 python-levenshtein)) - (define-public python-scandir (package (name "python-scandir") From d6c43683cf6ea671c6702d0c49b4854ace8b2db5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:52:08 -0400 Subject: [PATCH 1243/1394] gnu: Remove python2-pyaml. * gnu/packages/python-xyz.scm (python2-pyaml): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 038f54ec741..ae7c51a5a9c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17010,9 +17010,6 @@ addresses, and phone numbers.") YAML-serialized data.") (license license:wtfpl2))) -(define-public python2-pyaml - (package-with-python2 python-pyaml)) - (define-public python-pyyaml-env-tag (package (name "python-pyyaml-env-tag") From 3bf50750fcf4630bb1f7e1cc447cb0dd420fbab3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:52:49 -0400 Subject: [PATCH 1244/1394] gnu: Remove python2-simplejson. * gnu/packages/python-xyz.scm (python2-simplejson): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ae7c51a5a9c..3a2cd2c1b2d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2724,9 +2724,6 @@ the optional C extension for speedups. Simplejson is also supported on Python 3.3+.") (license license:x11))) -(define-public python2-simplejson - (package-with-python2 python-simplejson)) - (define-public python-pyicu (package From 42333736e05161d29aac60b6a810f56160987057 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:52:52 -0400 Subject: [PATCH 1245/1394] gnu: Remove python2-pylev. * gnu/packages/python-xyz.scm (python2-pylev): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3a2cd2c1b2d..667e2ceaf79 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16447,9 +16447,6 @@ Wikipedia code samples at @url{http://en.wikipedia.org/wiki/Levenshtein_distance}.") (license license:bsd-3))) -(define-public python2-pylev - (package-with-python2 python-pylev)) - (define-public python-cleo (package (name "python-cleo") From 018c96f0c780b1605923c427a3b6f6a0600669cf Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:53:06 -0400 Subject: [PATCH 1246/1394] gnu: Remove python2-soupsieve. * gnu/packages/python-xyz.scm (python2-soupsieve): Delete variable. --- gnu/packages/python-xyz.scm | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 667e2ceaf79..9ba7e9ce76d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9328,25 +9328,8 @@ Soup 4. It aims to provide selecting, matching, and filtering using modern CSS selectors. Soup Sieve currently provides selectors from the CSS level 1 specifications up through the latest CSS level 4 drafts and beyond (though some are not yet implemented).") - (properties `((python2-variant . ,(delay python2-soupsieve)))) (license license:expat))) -;; This is the last version that supports python-2 -(define-public python2-soupsieve - (let ((base (package-with-python2 (strip-python2-variant python-soupsieve)))) - (package - (inherit base) - (version "1.9.6") - (source - (origin - (method url-fetch) - (uri (pypi-uri "soupsieve" version)) - (sha256 - (base32 - "1apgqxngi1216h1cyvrvj9gy3wf45mh1lz4n76j26jf3k36bm1br")))) - (propagated-inputs - (modify-inputs (package-propagated-inputs base) - (prepend python2-backports-functools-lru-cache)))))) (define-public python-netifaces (package From 677ed5345309e64b5f7c3425b67cc8cd97dabc87 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:53:19 -0400 Subject: [PATCH 1247/1394] gnu: Remove python2-atomicwrites. * gnu/packages/python-xyz.scm (python2-atomicwrites): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9ba7e9ce76d..875ef1753c1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -13823,9 +13823,6 @@ for atomic file system operations.") (home-page "https://github.com/untitaker/python-atomicwrites") (license license:expat))) -(define-public python2-atomicwrites - (package-with-python2 python-atomicwrites)) - (define-public python-atomicwrites-1.4 (package (inherit python-atomicwrites) From 46933e2b7e222f12313237e2601054036f7c8641 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:53:43 -0400 Subject: [PATCH 1248/1394] gnu: Remove python2-importlib-metadata. * gnu/packages/python-xyz.scm (python2-importlib-metadata): Delete variable. (python2-importlib-metadata-bootstrap): Likewise. --- gnu/packages/python-xyz.scm | 44 ------------------------------------- 1 file changed, 44 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 875ef1753c1..577f6d3ce23 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8012,52 +8012,8 @@ its top-level name. This functionality intends to replace most uses of @code{pkg_resources} entry point API and metadata API. Along with @code{importlib.resources} in Python 3.7 and newer, this can eliminate the need to use the older and less efficient @code{pkg_resources} package.") - (properties `((python2-variant . ,(delay python2-importlib-metadata)))) (license license:asl2.0))) -(define-public python2-importlib-metadata - (let ((base (package-with-python2 (strip-python2-variant - python-importlib-metadata)))) - (package/inherit base - (name "python2-importlib-metadata") - (version "1.5.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "importlib_metadata" version)) - (sha256 - (base32 - "00ikdj4gjhankdljnz7g5ggak4k9lql2926x0x117ir9j2lv7x86")))) - (arguments (substitute-keyword-arguments (package-arguments base) - ((#:phases phases) ;reset standard phases - #~%standard-phases))) - (native-inputs - `(("python-setuptools-scm" ,python2-setuptools-scm) - ("python-pyfakefs" ,python2-pyfakefs-bootstrap) - ("python-packaging" ,python2-packaging-bootstrap))) - (propagated-inputs - `(("python-configparser" ,python2-configparser) - ("python-contextlib2" ,python2-contextlib2) - ("python-importlib-resources" ,python2-importlib-resources) - ("python-pathlib2" ,python2-pathlib2) - ,@(package-propagated-inputs base)))))) - -;; This package is used by python2-pytest, and thus must not depend on it. -(define-public python2-importlib-metadata-bootstrap - (hidden-package - (package/inherit - python2-importlib-metadata - (name "python2-importlib-metadata-bootstrap") - (arguments - `(#:tests? #f - ,@(package-arguments python2-importlib-metadata))) - (propagated-inputs - `(("python-zipp" ,python2-zipp-bootstrap) - ("python-pathlib2" ,python2-pathlib2-bootstrap) - ("python-configparser" ,python2-configparser) - ("python-contextlib2" ,python2-contextlib2-bootstrap) - ("python-importlib-resources" ,python2-importlib-resources-bootstrap)))))) - (define-public python-importmagic (package (name "python-importmagic") From 80e3ab8d1ee13ab24c29be03c66f6ec6c3b72ec2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:53:51 -0400 Subject: [PATCH 1249/1394] gnu: Remove python2-pyicu. * gnu/packages/python-xyz.scm (python2-pyicu): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 577f6d3ce23..7478d29065e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2747,9 +2747,6 @@ Python 3.3+.") "PyICU is a python extension wrapping the ICU C++ API.") (license license:x11))) -(define-public python2-pyicu - (package-with-python2 python-pyicu)) - (define-public python-dogtail (package (name "python-dogtail") From ba8ab7a48153b6fc784f93804339bf82aacb4b15 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:53:55 -0400 Subject: [PATCH 1250/1394] gnu: Remove python2-sphinx-alabaster-theme. * gnu/packages/sphinx.scm (python2-sphinx-alabaster-theme): Delete variable. --- gnu/packages/sphinx.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 2c4eb09d040..197e2da4645 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -631,9 +631,6 @@ introspection of @code{zope.interface} instances in code.") theme for the Sphinx documentation system. It's the default theme of Sphinx.") (license license:bsd-3))) -(define-public python2-sphinx-alabaster-theme - (package-with-python2 python-sphinx-alabaster-theme)) - (define-public python-sphinx-argparse (package (name "python-sphinx-argparse") From 1a6b88192dba4aae27bc56f848f2ec42fa3d2eb5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:53:58 -0400 Subject: [PATCH 1251/1394] gnu: Remove python2-sphinxcontrib-websupport. * gnu/packages/sphinx.scm (python2-sphinxcontrib-websupport): Delete variable. --- gnu/packages/sphinx.scm | 26 +++----------------------- 1 file changed, 3 insertions(+), 23 deletions(-) diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 197e2da4645..1ae6be40ca5 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -470,32 +470,12 @@ builder does not support SVG images natively (e.g. LaTeX).") `(#:tests? #f)) (home-page "https://sphinx-doc.org/") (synopsis "Sphinx API for web applications") - (description "This package provides a Python API to easily integrate + (description + "This package provides a Python API to easily integrate Sphinx documentation into your web application. It provides tools to integrate Sphinx documents in web templates and to handle searches.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python2-sphinxcontrib-websupport)))))) + (license license:bsd-3))) -;; 1.1.2 is the last version to support Python 2. -(define-public python2-sphinxcontrib-websupport - (package - (inherit (package-with-python2 - (strip-python2-variant python-sphinxcontrib-websupport))) - (version "1.1.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "sphinxcontrib-websupport" version)) - (sha256 - (base32 - "1z7fqra0xm1cdp8vvp80fcvnjlywym7bzz80m0liq7fz1zxvw08m")))) - (arguments - `(#:tests? #f - #:python ,python-2 - #:phases - (modify-phases %standard-phases - (delete 'sanity-check)))) - (propagated-inputs - (list python2-six)))) (define-public python-sphinx-gallery (package From 0f3cd86c67f767b7931871546bbac441483d0a1b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 02:54:11 -0400 Subject: [PATCH 1252/1394] gnu: Remove python2-wxpython. * gnu/packages/wxwidgets.scm (python2-wxpython): Delete variable. --- gnu/packages/wxwidgets.scm | 73 -------------------------------------- 1 file changed, 73 deletions(-) diff --git a/gnu/packages/wxwidgets.scm b/gnu/packages/wxwidgets.scm index ca1b33081d1..4d2fd73cee4 100644 --- a/gnu/packages/wxwidgets.scm +++ b/gnu/packages/wxwidgets.scm @@ -265,79 +265,6 @@ library. In most cases, wxPython uses the native widgets on each platform to provide a 100% native look and feel for the application.") (license l:wxwindows3.1+))) -(define-public python2-wxpython - (package - (name "python2-wxpython") - (version "3.0.2.0") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/wxpython/wxPython/" - version "/wxPython-src-" version ".tar.bz2")) - (sha256 - (base32 - "0qfzx3sqx4mwxv99sfybhsij4b5pc03ricl73h4vhkzazgjjjhfm")) - (modules '((guix build utils))) - (snippet - '(begin - (lambda (folder) - (delete-file-recursively (string-append "src/" folder)) - '("expat" "jpeg" "png" "tiff" "zlib" "msw" "osx" "msdos")) - (substitute* '("wxPython/setup.py") - ;; setup.py tries to keep its own license the same as wxwidget's - ;; license (which it expects under $WXWIN/docs). - (("'preamble.txt', 'licence.txt', 'licendoc.txt', 'lgpl.txt'") - "")) - #t)))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:tests? #f ; tests fail - ;; wxPython directly extends distutils command classes, - ;; we can't easily make setup.py use setuptools. - #:use-setuptools? #f - #:configure-flags (list "WXPORT=gtk2" - "UNICODE=1") - #:phases - (modify-phases %standard-phases - (add-before 'build 'chdir - (lambda _ - (chdir "wxPython") - #t)) - (add-after 'chdir 'set-wx-out-dir - (lambda* (#:key outputs #:allow-other-keys) - ;; By default, install phase tries to copy the wxPython headers in - ;; gnu/store/...-wxwidgets-3.0.2 , which it can't, so they are - ;; redirected to the output directory by setting WXPREFIX. - (substitute* "config.py" - (("= getWxConfigValue\\('--prefix'\\)") - (string-append "= '" (assoc-ref outputs "out") "'"))) - (substitute* "wx/build/config.py" - (("= getWxConfigValue\\('--prefix'\\)") - (string-append "= '" (assoc-ref outputs "out") "'"))) - #t)) - (add-after 'set-wx-out-dir 'setenv - (lambda* (#:key inputs outputs #:allow-other-keys) - (setenv "WXWIN" (assoc-ref inputs "wxwidgets")) - (use-modules (ice-9 popen) (ice-9 rdelim)) - (let ((port (open-pipe* OPEN_READ - (search-input-file inputs - "/bin/wx-config") - "--cppflags"))) - (setenv "CPPFLAGS" (read-string port)) - (close-pipe port)) - #t))))) - (native-inputs - (list mesa ; for glcanvas - pkg-config)) - (inputs - `(("gtk+" ,gtk+-2) ; for wxPython/src/helpers.cpp - ("wxwidgets" ,wxwidgets-gtk2))) - (synopsis "Python 2 Bindings for wxWidgets") - (description "@code{wxpython} provides Python 2 bindings for wxWidgets.") - (home-page "https://wxpython.org/") - (license (package-license wxwidgets)))) - (define-public wxsvg (package (name "wxsvg") From d0d694355c2eacc66e0f89b3a4940d9a8c6694d7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:06:34 -0400 Subject: [PATCH 1253/1394] gnu: Remove python2-freezegun. * gnu/packages/check.scm (python2-freezegun): Delete variable. --- gnu/packages/check.scm | 31 ------------------------------- 1 file changed, 31 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 0618ddbd039..be67b20d768 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2794,37 +2794,6 @@ create data based on random numbers and yet remain repeatable.") time by mocking the datetime module.") (license license:asl2.0))) -(define-public python2-freezegun - (package - (name "python2-freezegun") - (version "0.3.14") - (source - (origin - (method url-fetch) - (uri (pypi-uri "freezegun" version)) - (sha256 - (base32 "0al75mk829j1izxi760b7yjnknjihyfhp2mvi5qiyrxb9cpxwqk2")))) - (build-system python-build-system) - (native-inputs - (list python2-mock python2-pytest)) - (propagated-inputs - (list python2-six python2-dateutil)) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - ;; The tests are normally executed via `make test`, but the PyPi - ;; package does not include the Makefile. - (replace 'check - (lambda _ - (invoke "pytest" "-vv")))))) - (home-page "https://github.com/spulec/freezegun") - (synopsis "Test utility for mocking the datetime module") - (description - "FreezeGun is a library that allows your python tests to travel through -time by mocking the datetime module.") - (license license:asl2.0))) - (define-public python-flexmock (package (name "python-flexmock") From 987861f79dcafcf6f7c0a9cd99357997b63d5222 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:07:02 -0400 Subject: [PATCH 1254/1394] gnu: Remove python2-packaging-bootstrap. * gnu/packages/python-build.scm (python2-packaging-bootstrap): Delete variable. --- gnu/packages/python-build.scm | 21 ++------------------- 1 file changed, 2 insertions(+), 19 deletions(-) diff --git a/gnu/packages/python-build.scm b/gnu/packages/python-build.scm index e3b160bc85c..3fb01199a88 100644 --- a/gnu/packages/python-build.scm +++ b/gnu/packages/python-build.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2016 Leo Famulari ;;; Copyright © 2020 Marius Bakke ;;; Copyright © 2020 Tanguy Le Carrour -;;; Copyright © 2018, 2021 Maxim Cournoyer +;;; Copyright © 2018, 2021, 2022 Maxim Cournoyer ;;; Copyright © 2021 Tobias Geerinckx-Rice ;;; Copyright © 2021, 2022 Ricardo Wurmus ;;; @@ -306,24 +306,7 @@ information.") ;; *either* of the licenses found in LICENSE.APACHE or LICENSE.BSD. ;; Contributions to this software is made under the terms of *both* these ;; licenses. - (license (list license:asl2.0 license:bsd-2)) - (properties `((python2-variant . ,(delay python2-packaging-bootstrap)))))) - -(define-public python2-packaging-bootstrap - (let ((base (package-with-python2 - (strip-python2-variant python-packaging-bootstrap)))) - (package/inherit base - (version "20.0") ;last version with Python 2 support - (source - (origin - (method url-fetch) - (uri (pypi-uri "packaging" version)) - ;; XXX: The URL in the patch file is wrong, it should be - ;; . - (patches (search-patches "python-packaging-test-arch.patch")) - (sha256 - (base32 - "1y2ip3a4ykkpgnwgn85j6hkspcl0cg3mzms97f40mk57vwqq67gy"))))))) + (license (list license:asl2.0 license:bsd-2)))) ;;; The name 'python-pypa-build' is chosen rather than 'python-build' to avoid ;;; a name clash with python-build from (guix build-system python). From e38618c50de8b1a8c6bcf606e09435429b49601d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:07:09 -0400 Subject: [PATCH 1255/1394] gnu: Remove python2-zipp. * gnu/packages/python-compression.scm (python2-zipp): Delete variable. (python2-zipp-bootstrap): Likewise. --- gnu/packages/python-compression.scm | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 7847a3e20e8..edfa974a716 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -383,31 +383,8 @@ install: libbitshuffle.so (description "This package provides a @code{pathlib}-compatible @code{Zipfile} object wrapper. It provides a backport of the @code{Path} object.") - (properties `((python2-variant . ,(delay python2-zipp)))) (license license:expat))) -(define-public python2-zipp - (let ((base (package-with-python2 (strip-python2-variant python-zipp)))) - (package/inherit - base - (native-inputs - `(("python-contextlib2" ,python2-contextlib2) - ("python-pathlib2" ,python2-pathlib2) - ("python-unittest2" ,python2-unittest2) - ,@(package-native-inputs base)))))) - -;; This package is used to bootstrap pytest, via importlib-metadata. -(define-public python2-zipp-bootstrap - (hidden-package - (package/inherit - python2-zipp - (name "python2-zipp-bootstrap") - (arguments - `(#:tests? #f - ,@(package-arguments python2-zipp))) - (native-inputs - `(("python-setuptools-scm" ,python2-setuptools-scm)))))) - (define-public python-zopfli (package (name "python-zopfli") From bf4cddbf6abd6f13c7dbfd89f8509f24ae2f8cae Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:07:18 -0400 Subject: [PATCH 1256/1394] gnu: Remove python2-certifi. * gnu/packages/python-crypto.scm (python2-certifi): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index a270d0f78f2..5938ff7e036 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -437,9 +437,6 @@ for example, for recording or replaying web content.") is used by the Requests library to verify HTTPS requests.") (license license:asl2.0))) -(define-public python2-certifi - (package-with-python2 python-certifi)) - (define-public python-cryptography-vectors (package (name "python-cryptography-vectors") From 843904d6430c0b1e5a5a863cd0bd5e836cf8f73c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:07:25 -0400 Subject: [PATCH 1257/1394] gnu: Remove python2-pyopenssl. * gnu/packages/python-crypto.scm (python2-pyopenssl): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 5938ff7e036..406e5b685a0 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -679,9 +679,6 @@ message digests and key derivation functions.") library.") (license license:asl2.0))) -(define-public python2-pyopenssl - (package-with-python2 python-pyopenssl)) - (define-public python-ed25519 (package (name "python-ed25519") From 9bf8cc112cbc9fb3936cc8cfb0693cc67602749b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:07:49 -0400 Subject: [PATCH 1258/1394] gnu: Remove python2-unidecode. * gnu/packages/python-xyz.scm (python2-unidecode): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7478d29065e..c515954b486 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3622,9 +3622,6 @@ machine identifiers from human-readable Unicode strings that should still be somewhat intelligible.") (license license:gpl2+))) -(define-public python2-unidecode - (package-with-python2 python-unidecode)) - (define-public python-text-unidecode (package (name "python-text-unidecode") From f14f81e497c0d93ac9e9bf145e2b7df54da94617 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:07:53 -0400 Subject: [PATCH 1259/1394] gnu: Remove python2-configparser. * gnu/packages/python-xyz.scm (python2-configparser): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c515954b486..cb18fec8302 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18943,9 +18943,6 @@ builds partial trees by inspecting living objects.") in other versions.") (license license:expat))) -(define-public python2-configparser - (package-with-python2 python-configparser)) - (define-public python-iniconfig (package (name "python-iniconfig") From ca7117a9ddc6a62c0ccd0d23112a632db0d9c2d7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:08:15 -0400 Subject: [PATCH 1260/1394] gnu: Remove python2-importlib-resources. * gnu/packages/python-xyz.scm (python2-importlib-resources): Delete variable. (python2-importlib-resources-bootstrap): Likewise. (python-importlib-resources)[properties]: Delete field. --- gnu/packages/python-xyz.scm | 57 ++++--------------------------------- 1 file changed, 6 insertions(+), 51 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cb18fec8302..a3c525b2f1e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7899,66 +7899,21 @@ older Python versions.") (package (name "python-importlib-resources") (version "3.0.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "importlib_resources" version)) - (sha256 - (base32 - "1hq626mx5jl9zfl0wdrjkxsnh8qd98fqv322n68b9251xjk4bxqr")))) - (build-system python-build-system) - (native-inputs - (list python-setuptools-scm python-toml)) - (home-page "http://importlib-resources.readthedocs.io/") - (synopsis "Read resources from Python packages") - (description - "@code{importlib_resources} is a backport of Python 3's standard library -@code{importlib.resources} module for Python 2.7, and Python 3.") - (properties `((python2-variant . ,(delay python2-importlib-resources)))) - (license license:asl2.0))) - -(define-public python2-importlib-resources - (package - (name "python2-importlib-resources") - (version "1.0.2") (source (origin (method url-fetch) (uri (pypi-uri "importlib_resources" version)) (sha256 (base32 - "0y3hg12iby1qyaspnbisz4s4vxax7syikk3skznwqizqyv89y9yk")))) + "1hq626mx5jl9zfl0wdrjkxsnh8qd98fqv322n68b9251xjk4bxqr")))) (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases (modify-phases %standard-phases - ;; The build system tests for python-wheel, but it is - ;; not required for Guix nor the test suite. Just drop - ;; it to make bootstrapping pytest easier. - (add-after 'unpack 'drop-wheel-dependency - (lambda _ - (substitute* "setup.cfg" - (("^[[:blank:]]+wheel") - "")) - #t))))) - (propagated-inputs - (list python2-pathlib2 python2-typing)) - (home-page "https://gitlab.com/python-devs/importlib_resources") - (synopsis "Backport of @code{importlib.resources} from Python 3.7") + (native-inputs (list python-setuptools-scm python-toml)) + (home-page "http://importlib-resources.readthedocs.io/") + (synopsis "Read resources from Python packages") (description - "This package provides an implementation of @code{importlib.resources} -for older versions of Python.") + "@code{importlib_resources} is a backport of Python 3's standard library +@code{importlib.resources} module for Python 2.7, and Python 3.") (license license:asl2.0))) -;; For importlib-metadata-bootstrap below. -(define-public python2-importlib-resources-bootstrap - (hidden-package - (package/inherit - python2-importlib-resources - (name "python2-importlib-resources-bootstrap") - (propagated-inputs - `(("python-pathlib2-bootstrap" ,python2-pathlib2-bootstrap) - ("python-typing" ,python2-typing)))))) - (define-public python-importlib-metadata (package (name "python-importlib-metadata") From 5f973da340d149b07f8a1401c9fa77aa45f02621 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:08:37 -0400 Subject: [PATCH 1261/1394] gnu: Remove python2-pysocks. * gnu/packages/python-xyz.scm (python2-pysocks): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a3c525b2f1e..b47096d5cea 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20072,9 +20072,6 @@ requirements is not met.") version of @code{SocksiPy} with bug fixes and extra features.") (license license:bsd-3))) -(define-public python2-pysocks - (package-with-python2 python-pysocks)) - (define-public python-pydiff (package (name "python-pydiff") From 6d22dc676a4e1ad9d5aea7a47f95a1242ada957a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:08:52 -0400 Subject: [PATCH 1262/1394] gnu: Remove python2-backports-functools-lru-cache. * gnu/packages/python-xyz.scm (python2-backports-functools-lru-cache): Delete variable. --- gnu/packages/python-xyz.scm | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b47096d5cea..aa9b33165b1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18854,29 +18854,6 @@ builds partial trees by inspecting living objects.") editors.") (license license:expat))) -(define-public python2-backports-functools-lru-cache - (package - (name "python2-backports-functools-lru-cache") - (version "1.6.1") - (source - (origin - (method url-fetch) - ;; only the pypi tarballs contain the necessary metadata - (uri (pypi-uri "backports.functools_lru_cache" version)) - (sha256 - (base32 - "0jidrkk2w6bhjm197plxiaxrav64mgcrign0bfyr7md2ilc5zplg")))) - (build-system python-build-system) - (native-inputs - (list python2-setuptools-scm)) - (arguments - `(#:python ,python-2)) - (home-page "https://github.com/jaraco/backports.functools_lru_cache") - (synopsis "Backport of functools.lru_cache from Python 3.3") - (description "@code{python2-backports-functools-lru-cache} is a backport - of @code{functools.lru_cache} from python 3.3.") - (license license:expat))) - (define-public python-configparser (package (name "python-configparser") From 5df79d1ea84a27afce5487eef888e7371739a519 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:14:17 -0400 Subject: [PATCH 1263/1394] gnu: Remove python2-flaky. * gnu/packages/check.scm (python2-flaky): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index be67b20d768..29388ffab64 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2838,9 +2838,6 @@ those tests or marking them to @code{@@skip}, they can be automatically retried.") (license license:asl2.0))) -(define-public python2-flaky - (package-with-python2 python-flaky)) - (define-public python-pyhamcrest (package (name "python-pyhamcrest") From 9c74e5d566e52d5271d7bdcf7d31ed46df5e944a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:14:50 -0400 Subject: [PATCH 1264/1394] gnu: Remove python2-cryptography. * gnu/packages/python-crypto.scm (python2-cryptography): Delete variable. (python-cryptography)[properties]: Delete field. --- gnu/packages/python-crypto.scm | 21 +-------------------- 1 file changed, 1 insertion(+), 20 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 406e5b685a0..c91a247c099 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -488,26 +488,7 @@ library” for Python. The package includes both high level recipes, and low level interfaces to common cryptographic algorithms such as symmetric ciphers, message digests and key derivation functions.") ;; Distributed under either BSD-3 or ASL2.0 - (license (list license:bsd-3 license:asl2.0)) - (properties `((python2-variant . ,(delay python2-cryptography)))))) - -(define-public python2-cryptography - (let ((crypto (package-with-python2 - (strip-python2-variant python-cryptography)))) - (package/inherit crypto - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - ;; The sanity-check attempts attempts to import the non-existent - ;; modules "_openssl" and "_padding". - (delete 'sanity-check)))) - (propagated-inputs - `(("python2-ipaddress" ,python2-ipaddress) - ("python2-backport-ssl-match-hostname" - ,python2-backport-ssl-match-hostname) - ("python2-enum34" ,python2-enum34) - ,@(package-propagated-inputs crypto)))))) + (license (list license:bsd-3 license:asl2.0)))) ;; TODO: Make this the default in the next staging cycle. (define-public python-cryptography-vectors-next From 206c05deadb3113632b759bd613d80c246d72122 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:15:05 -0400 Subject: [PATCH 1265/1394] gnu: Remove python2-pathlib2. * gnu/packages/python-xyz.scm (python2-pathlib2): Delete variable. (python2-pathlib2-bootstrap): Likewise. --- gnu/packages/python-xyz.scm | 47 ------------------------------------- 1 file changed, 47 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index aa9b33165b1..3a92429b96d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15401,53 +15401,6 @@ standard library module. This module (python-pathlib) isn't maintained anymore.") (license license:expat))) -(define-public python2-pathlib2 - (package - (name "python2-pathlib2") - (version "2.3.5") - (source (origin - (method url-fetch) - (uri (pypi-uri "pathlib2" version)) - (sha256 - (base32 - "0s4qa8c082fdkb17izh4mfgwrjd1n5pya18wvrbwqdvvb5xs9nbc")))) - (build-system python-build-system) - ;; We only need the the Python 2 variant, since for Python 3 our minimum - ;; version is 3.4 which already includes this package as part of the - ;; standard library. - (arguments - `(#:python ,python-2)) - (propagated-inputs - (list python2-scandir python2-six)) - (home-page "https://pypi.org/project/pathlib2/") - (synopsis "Object-oriented file system paths - backport of standard -pathlib module") - (description "The goal of pathlib2 is to provide a backport of standard -pathlib module which tracks the standard library module, so all the newest -features of the standard pathlib can be used also on older Python versions. - -Pathlib offers a set of classes to handle file system paths. It offers the -following advantages over using string objects: - -@enumerate -@item No more cumbersome use of os and os.path functions. Everything can -be done easily through operators, attribute accesses, and method calls. -@item Embodies the semantics of different path types. For example, -comparing Windows paths ignores casing. -@item Well-defined semantics, eliminating any inconsistencies or -ambiguities (forward vs. backward slashes, etc.). -@end enumerate") - (license license:expat))) - -(define-public python2-pathlib2-bootstrap - (hidden-package - (package - (inherit python2-pathlib2) - (name "python2-pathlib2-bootstrap") - (propagated-inputs - `(("python2-scandir" ,python2-scandir) - ("python2-six" ,python2-six-bootstrap)))))) - (define-public python-jellyfish (package (name "python-jellyfish") From 405a7b3f47d54ce794b6bf1506547bb722e6d46e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:15:11 -0400 Subject: [PATCH 1266/1394] gnu: Remove python2-typing. * gnu/packages/python-xyz.scm (python2-typing): Delete variable. --- gnu/packages/python-xyz.scm | 22 ---------------------- 1 file changed, 22 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3a92429b96d..b67dbaad918 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21087,28 +21087,6 @@ Python 3.6+ type hints.") with PEP 484 argument (and return) type annotations.") (license license:expat))) -(define-public python2-typing - (package - (name "python2-typing") - (version "3.10.0.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "typing" version)) - (sha256 - (base32 "0c5il4d68fd4qrm5k3dps70j0xz0n5krj6lhwn9vzpal3whsvd0k")))) - (build-system python-build-system) - (arguments (list #:python python-2)) - (home-page "https://docs.python.org/3/library/typing.html") - (synopsis "Type hints for Python") - (description "This is a backport of the standard library @code{typing} -module to Python versions older than 3.5. Typing defines a standard notation -for Python function and variable type annotations. The notation can be used -for documenting code in a concise, standard format, and it has been designed -to also be used by static and runtime type checkers, static analyzers, IDEs -and other tools.") - (license license:psfl))) - (define-public python-typing-extensions (package (name "python-typing-extensions") From dd915ae36952f31ecf68b9b72c6e630b5abfd75d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:15:29 -0400 Subject: [PATCH 1267/1394] gnu: Remove python2-contextlib2. * gnu/packages/python-xyz.scm (python2-contextlib2): Delete variable. (python2-contextlib2-bootstrap): Likewise. --- gnu/packages/python-xyz.scm | 26 -------------------------- 1 file changed, 26 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b67dbaad918..1568ed486d4 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -13656,34 +13656,8 @@ connection pool.") provides utilities for common tasks involving decorators and context managers. It also contains additional features that are not part of the standard library.") - (properties `((python2-variant . ,(delay python2-contextlib2)))) (license license:psfl))) -(define-public python2-contextlib2 - (let ((base (package-with-python2 - (strip-python2-variant python-contextlib2)))) - (package/inherit base - (arguments - (substitute-keyword-arguments (package-arguments base) - ((#:phases phases) - `(modify-phases ,phases - (replace 'check - (lambda _ (invoke "python" "test_contextlib2.py" "-v"))))))) - (native-inputs - `(("python2-unittest2" ,python2-unittest2)))))) - -;; This package is used by python2-pytest via python2-importlib-metadata, -;; and thus can not depend on python-unittest2 (which depends on pytest). -(define-public python2-contextlib2-bootstrap - (hidden-package - (package/inherit - python2-contextlib2 - (name "python2-contextlib2-bootstrap") - (arguments - `(#:tests? #f - ,@(package-arguments python2-contextlib2))) - (native-inputs '())))) - (define-public python-texttable (package (name "python-texttable") From dd722fc950ab7df501537254d0800c8ecbbd98a5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:16:15 -0400 Subject: [PATCH 1268/1394] gnu: Remove python2-dateutil. * gnu/packages/time.scm (python2-dateutil): Delete variable. --- gnu/packages/time.scm | 40 ---------------------------------------- 1 file changed, 40 deletions(-) diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index 4ff7b889ac4..314ffcc18f4 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -229,46 +229,6 @@ datetime module, available in Python 2.3+.") ;; BSD-3 still; but all new code is dual licensed (the user can choose). (license (list bsd-3 asl2.0)))) -(define-public python2-dateutil - (package - (name "python2-dateutil") - (version "2.8.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "python-dateutil" version)) - (sha256 - (base32 - "11iy7m4bp2lgfkcl0r6xzf34bvk7ppjmsyn2ygfikbi72v6cl8q1")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases (modify-phases %standard-phases - (replace 'check - (lambda _ - ;; Delete tests that depend on "freezegun" to avoid a - ;; circular dependency. - (delete-file "dateutil/test/test_utils.py") - (delete-file "dateutil/test/test_rrule.py") - - ;; XXX: Fails to get timezone from /etc/localtime. - (delete-file "dateutil/test/test_tz.py") - - (invoke "pytest" "-vv")))))) - (native-inputs - (list python2-pytest python2-pytest-cov python2-setuptools-scm)) - (propagated-inputs - (list python2-six)) - (home-page "https://dateutil.readthedocs.io/en/stable/") - (synopsis "Extensions to the standard datetime module") - (description - "The dateutil module provides powerful extensions to the standard -datetime module, available in Python 2.3+.") - ;; The license was changed from the three-clause BSD license to a dual - ;; Apache 2.0/BSD-3 variant at 2017-12-01. Some code is only available as - ;; BSD-3 still; but all new code is dual licensed (the user can choose). - (license (list bsd-3 asl2.0)))) - (define-public python-parsedatetime (package (name "python-parsedatetime") From 1924d8237d7574c62042fa0f60bffcee84f0f580 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:19:17 -0400 Subject: [PATCH 1269/1394] gnu: Remove python2-coverage. * gnu/packages/check.scm (python2-coverage): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 29388ffab64..90b83496579 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -1790,9 +1790,6 @@ library to determine which lines are executable, and which have been executed.") (license license:bsd-3))) -(define-public python2-coverage - (package-with-python2 python-coverage)) - (define-public python-pytest-asyncio (package (name "python-pytest-asyncio") From 5e6cc60122bc482c2e6825ce645238637a41026d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:19:35 -0400 Subject: [PATCH 1270/1394] gnu: Remove python2-cffi. * gnu/packages/libffi.scm (python2-cffi): Delete variable. --- gnu/packages/libffi.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/libffi.scm b/gnu/packages/libffi.scm index 2efec07e1d9..701feeb7736 100644 --- a/gnu/packages/libffi.scm +++ b/gnu/packages/libffi.scm @@ -152,9 +152,6 @@ conversions for values passed between the two languages.") (sha256 (base32 "0m3rz2pqfmyfagx0bhj2jlbr2h58j3wr3cyv1agxkhlnm1k0s3wj")))))) -(define-public python2-cffi - (package-with-python2 python-cffi)) - (define-public python-cffi-documentation (package (name "python-cffi-documentation") From 6efcb2463f3a4efded106b81e4a70efc9e8a958b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:19:45 -0400 Subject: [PATCH 1271/1394] gnu: Remove python2-cryptography-vectors. * gnu/packages/python-crypto.scm (python2-cryptography-vectors): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index c91a247c099..18b55ba403b 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -456,9 +456,6 @@ is used by the Requests library to verify HTTPS requests.") ;; Distributed under either BSD-3 or ASL2.0 (license (list license:bsd-3 license:asl2.0)))) -(define-public python2-cryptography-vectors - (package-with-python2 python-cryptography-vectors)) - (define-public python-cryptography (package (name "python-cryptography") From dcf62928b7608d28d699e523696e70b1da73a0fc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:19:49 -0400 Subject: [PATCH 1272/1394] gnu: Remove python2-asn1crypto. * gnu/packages/python-crypto.scm (python2-asn1crypto): Delete variable. --- gnu/packages/python-crypto.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 18b55ba403b..753f6bb5031 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -772,9 +772,6 @@ for private keys, public keys, certificates, CRL, OCSP, CMS, PKCS#3, PKCS#7, PKCS#8, PKCS#12, PKCS#5, X.509 and TSP.") (license license:expat))) -(define-public python2-asn1crypto - (package-with-python2 python-asn1crypto)) - (define-public python-pynacl (package (name "python-pynacl") From 6bafe76c351c375746b69ff30657c2295d4a4cfa Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:19:54 -0400 Subject: [PATCH 1273/1394] gnu: Remove python2-ipaddress. * gnu/packages/python-xyz.scm (python2-ipaddress): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1568ed486d4..56a8edc8643 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12004,9 +12004,6 @@ implementations of ASN.1-based codecs and protocols.") IPv6 addresses and networks.") (license license:psfl))) -(define-public python2-ipaddress - (package-with-python2 python-ipaddress)) - (define-public python-asn1tools (package (name "python-asn1tools") From c7f95514c25bcdd8e6c9c7a105428ed007c1ac37 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:19:58 -0400 Subject: [PATCH 1274/1394] gnu: Remove python2-scandir. * gnu/packages/python-xyz.scm (python2-scandir): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 56a8edc8643..a370e5e0957 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19033,9 +19033,6 @@ point is the point of maximum curvature.") This package is part of the Python standard library since version 3.5.") (license license:bsd-3))) -(define-public python2-scandir - (package-with-python2 python-scandir)) - (define-public python-factory-boy (package (name "python-factory-boy") From 4687f296e35f9e763dd56078d93990c7d545803e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:20:13 -0400 Subject: [PATCH 1275/1394] gnu: Remove python2-backport-ssl-match-hostname. * gnu/packages/python-xyz.scm (python2-backport-ssl-match-hostname): Delete variable. --- gnu/packages/python-xyz.scm | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a370e5e0957..88c882eafa6 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1259,30 +1259,6 @@ access to various locale display names, localized number and date formatting, etc.") (license license:bsd-3))) -(define-public python2-backport-ssl-match-hostname - (package - (name "python2-backport-ssl-match-hostname") - (version "3.5.0.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "backports.ssl_match_hostname" version)) - (sha256 - (base32 - "1wndipik52cyqy0677zdgp90i435pmvwd89cz98lm7ri0y3xjajh")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:tests? #f)) ; no test target - (home-page "https://bitbucket.org/brandon/backports.ssl_match_hostname") - (synopsis "Backport of ssl.match_hostname() function from Python 3.5") - (description - "This backport brings the ssl.match_hostname() function to users of -earlier versions of Python. The function checks the hostname in the -certificate returned by the server to which a connection has been established, -and verifies that it matches the intended target hostname.") - (license license:psfl))) - (define-public python-bidict (package (name "python-bidict") From afdf9e409017a14505c5a463cfd7c87e06c5ef78 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:20:49 -0400 Subject: [PATCH 1276/1394] gnu: Remove python2-idna. * gnu/packages/python-xyz.scm (python2-idna): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 88c882eafa6..9974263a4e8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12026,9 +12026,6 @@ the Python standard library but currently only supports the older 2003 specification.") (license license:bsd-4))) -(define-public python2-idna - (package-with-python2 python-idna)) - (define-public python-libsass (package (name "python-libsass") From cd78abdbe7b26e8e31b5918760f2b2b3948008dc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:21:01 -0400 Subject: [PATCH 1277/1394] gnu: Remove python2-pretend. * gnu/packages/python-xyz.scm (python2-pretend): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9974263a4e8..31b8791d5a4 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12195,9 +12195,6 @@ fakes, or doubles. Basically, a stub is an object that returns pre-canned responses, rather than doing any computation.") (license license:bsd-3))) -(define-public python2-pretend - (package-with-python2 python-pretend)) - (define-public python-pip (package (name "python-pip") From 69e5efbcaf3be1822fd7ba9ece9842da0c0c95a4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:21:09 -0400 Subject: [PATCH 1278/1394] gnu: Remove python2-pytz. * gnu/packages/time.scm (python2-pytz): Delete variable. --- gnu/packages/time.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index 314ffcc18f4..4aba10e01ec 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -140,9 +140,6 @@ higher. It also solves the issue of ambiguous times at the end of daylight saving time. Almost all of the Olson timezones are supported.") (license expat))) -(define-public python2-pytz - (package-with-python2 python-pytz)) - (define-public python-pendulum (package (name "python-pendulum") From 979f6b6e1d33164ca3790f01d51101e17335b207 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 1 May 2022 03:21:12 -0400 Subject: [PATCH 1279/1394] gnu: Remove python2-iso8601. * gnu/packages/time.scm (python2-iso8601): Delete variable. --- gnu/packages/time.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index 4aba10e01ec..185bb682f68 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -361,9 +361,6 @@ ISO 8601 dates, time and duration.") @code{2007-01-14T20:34:22+00:00}) into @code{datetime} objects.") (license expat))) -(define-public python2-iso8601 - (package-with-python2 python-iso8601)) - (define-public python-monotonic (package (name "python-monotonic") From 9022934059f0159007b3eda737d97971eaa39bc1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 5 May 2022 22:48:30 -0400 Subject: [PATCH 1280/1394] gnu: Remove python2-seaborn. * gnu/packages/python-xyz.scm (python2-seaborn): Delete variable. --- gnu/packages/python-xyz.scm | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 31b8791d5a4..3e8d10d8bcd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9653,21 +9653,8 @@ SVG, EPS, PNG and terminal output.") graphics in Python. It is built on top of matplotlib and tightly integrated with the PyData stack, including support for numpy and pandas data structures and statistical routines from scipy and statsmodels.") - (properties `((python2-variant . ,(delay python2-seaborn)))) (license license:bsd-3))) -;; 0.9.1 is the last release with support for Python 2. -(define-public python2-seaborn - (let ((base (package-with-python2 (strip-python2-variant python-seaborn)))) - (package - (inherit base) - (version "0.9.1") - (source (origin - (method url-fetch) - (uri (pypi-uri "seaborn" version)) - (sha256 - (base32 - "1bjnshjz4d6z3vrwfwall1a3yh8h3a1h47c3fg7458x9426alcys"))))))) (define-public python-session-info (package From e3b18cfbb7751397ab273bb503b7e19c20c5d2e7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 15 May 2022 22:41:27 -0400 Subject: [PATCH 1281/1394] gnu: python-gamera: Update to 4.0.0. * gnu/packages/python-xyz.scm (python2-gamera): Rename to... (python-gamera): ... this. Update to 4.0.0. [python]: Delete argument. [phases]{check}: New override. [native-inputs]: Add python-pytest. --- gnu/packages/python-xyz.scm | 34 +++++++++++++++++++++++++--------- 1 file changed, 25 insertions(+), 9 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3e8d10d8bcd..74b927eab24 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -26357,17 +26357,17 @@ error-prone \"update the embedded version string\" step from your release process.") (license license:public-domain))) -(define-public python2-gamera +(define-public python-gamera (package - (name "python2-gamera") - (version "3.4.4") + (name "python-gamera") + (version "4.0.0") (source (origin (method url-fetch) (uri (string-append "https://gamera.informatik.hsnr.de/download/" "gamera-" version ".tar.gz")) (sha256 - (base32 "1g4y1kxk1hmxfsiz682hbxvwryqilnb21ci509m559yp7hcliiyy")) + (base32 "0fhlwbvpm3k54n4aa1y6qd348jqrb54ak9p0ic16drx7f07dsq05")) (modules '((guix build utils))) (snippet '(begin @@ -26377,17 +26377,33 @@ process.") "src/libtiff" "src/zlib-1.2.8")))))) (build-system python-build-system) - (inputs - (list libpng libtiff zlib)) (arguments - `(#:python ,python-2 - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'disable-wx-support (lambda _ (substitute* "setup.py" (("no_wx = False") - "no_wx = True"))))))) + "no_wx = True")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Some tests require a writable HOME directory and test + ;; directory. + (setenv "HOME" "/tmp") + (mkdir "tests/tmp") ;the code assumes this directory exists + ;; (for-each make-file-writable (find-files "tests")) + (with-directory-excursion "tests" + (invoke "pytest" "-vv" + ;; This test causes gamera/gendoc.py to be loaded, + ;; which fails due to the missing docutils, pygments + ;; and silvercity (very old, unpackaged) libraries. + "--ignore" "test_plugins.py" + ;; This test triggers a segfault (see: + ;; https://github.com/hsnr-gamera/gamera-4/issues/47). + "--ignore" "test_rle.py")))))))) + (native-inputs (list python-pytest)) + (inputs (list libpng libtiff zlib)) (synopsis "Framework for building document analysis applications") (description "Gamera is a toolkit for building document image recognition systems.") From 89f9678126e7dbcd3b1f96694fdf96778d9b5979 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 15 May 2022 22:52:12 -0400 Subject: [PATCH 1282/1394] gnu: didjvu: Switch to a Python 3 compatible fork. * gnu/packages/djvu.scm (didjvu)[source]: Switch to a Python 3 compatible fork. [native-inputs, inputs]: Move below arguments field. Use new style. Replace the Python 2 inputs by their Python 3 equivalents. --- gnu/packages/djvu.scm | 131 +++++++++++++++++++++--------------------- 1 file changed, 67 insertions(+), 64 deletions(-) diff --git a/gnu/packages/djvu.scm b/gnu/packages/djvu.scm index 9c834bcfba1..f27dc70b70e 100644 --- a/gnu/packages/djvu.scm +++ b/gnu/packages/djvu.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2020 Nicolas Goaziou ;;; Copyright © 2020 Tobias Geerinckx-Rice ;;; Copyright © 2020, 2021 Guillaume Le Vaillant +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -292,71 +293,73 @@ and white.") (license license:gpl2))) (define-public didjvu - (package - (name "didjvu") - (version "0.9") - (source - (origin - (method url-fetch) - (uri (string-append - "https://github.com/jwilk/didjvu/releases/download/" version - "/didjvu-" version ".tar.gz")) - (sha256 - (base32 "0xyrnk8d2khi7q1zr28gjkjq6frz4mkb5jdl8821yzf12k7c8pbv")))) - (build-system gnu-build-system) - (native-inputs - (list python2-nose)) - (inputs - `(("djvulibre" ,djvulibre) - ("minidjvu" ,minidjvu) - ("python" ,python-2) - ("python2-gamera" ,python2-gamera) - ("python2-pillow" ,python2-pillow))) - (arguments - `(#:modules ((guix build gnu-build-system) - ((guix build python-build-system) #:prefix python:) - (guix build utils)) - #:imported-modules (,@%gnu-build-system-modules - (guix build python-build-system)) - #:test-target "test" - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-before 'check 'disable-failing-test - (lambda _ - (substitute* "tests/test_ipc.py" - ;; test_wait_signal gets stuck forever - (("yield self\\._test_signal, name") - "return True") - ;; test_path fails to find a file it should have created - (("path = os\\.getenv\\('PATH'\\)\\.split\\(':'\\)") - "return True")) - (substitute* "tests/test_timestamp.py" - ;; test_timezones fails with: - ;; '2009-12-18T21:25:14Z' != '2009-12-18T22:25:14+01:00' - (("@fork_isolation") - "return True")))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (invoke "make" - "DESTDIR=" - (string-append "PREFIX=" out) - "install")))) - (add-after 'install 'wrap-python - (assoc-ref python:%standard-phases 'wrap)) - (add-after 'wrap-python 'wrap-path - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (djvulibre (assoc-ref inputs "djvulibre"))) - (wrap-program (string-append out "/bin/didjvu") - `("PATH" ":" prefix (,(string-append djvulibre "/bin")))))))))) - (synopsis "DjVu encoder with foreground/background separation") - (description - "@code{didjvu} uses the @code{Gamera} framework to separate the foreground + (let ((revision "0") + (commit "c792d61e85fbe5b6e678bc7d686b0208717c587b")) + (package + (name "didjvu") + (version (git-version "0.9" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/FriedrichFroebel/didjvu") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "09lwfwirmfl93062i2rvdcrgwp9fj95ny07059bxq7dl6z0z35qj")))) + (build-system gnu-build-system) + (arguments + `(#:modules ((guix build gnu-build-system) + ((guix build python-build-system) #:prefix python:) + (guix build utils)) + #:imported-modules (,@%gnu-build-system-modules + (guix build python-build-system)) + #:test-target "test" + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'check 'disable-failing-test + (lambda _ + (substitute* "tests/test_ipc.py" + ;; test_wait_signal gets stuck forever + (("yield self\\._test_signal, name") + "return True") + ;; test_path fails to find a file it should have created + (("path = os\\.getenv\\('PATH'\\)\\.split\\(':'\\)") + "return True")) + (substitute* "tests/test_timestamp.py" + ;; test_timezones fails with: + ;; '2009-12-18T21:25:14Z' != '2009-12-18T22:25:14+01:00' + (("@fork_isolation") + "return True")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (invoke "make" + "DESTDIR=" + (string-append "PREFIX=" out) + "install")))) + (add-after 'install 'wrap-python + (assoc-ref python:%standard-phases 'wrap)) + (add-after 'wrap-python 'wrap-path + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (djvulibre (assoc-ref inputs "djvulibre"))) + (wrap-program (string-append out "/bin/didjvu") + `("PATH" ":" prefix (,(string-append djvulibre "/bin")))))))))) + (native-inputs (list python-nose)) + (inputs + (list djvulibre + minidjvu + python-gamera + python-pillow + python-wrapper)) + (synopsis "DjVu encoder with foreground/background separation") + (description + "@code{didjvu} uses the @code{Gamera} framework to separate the foreground and background layers of images, which can then be encoded into a DjVu file.") - (home-page "https://jwilk.net/software/didjvu") - (license license:gpl2))) + (home-page "https://jwilk.net/software/didjvu") + (license license:gpl2)))) (define-public ocrodjvu (let ((revision "0") From 493ee41adaeaddc7e750eb16290cc2f43e842684 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 5 May 2022 22:57:19 -0400 Subject: [PATCH 1283/1394] gnu: Remove python2-pillow. * gnu/packages/python-xyz.scm (python2-pillow): Delete variable. --- gnu/packages/python-xyz.scm | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 74b927eab24..12ac929c510 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6862,24 +6862,6 @@ a general image processing tool.") "http://www.pythonware.com/products/pil/license.htm" "The PIL Software License")))) -(define-public python2-pillow - (package-with-python2 - (package - (inherit (strip-python2-variant python-pillow)) - ;; Version 6 is the last series with Python 2 support. - (version "6.2.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "Pillow" version)) - (sha256 - (base32 - "0l5rv8jkdrb5q846v60v03mcq64yrhklidjkgwv6s1pda71g17yv")))) - (arguments - (substitute-keyword-arguments (package-arguments python-pillow) - ;; FIXME: One of the tests is failing. - ((#:tests? _ #f) #f)))))) - (define-public python-pillow-2.9 (package (inherit python-pillow) From dba760f78cc831f6415d3c81a8a88d00183c7aee Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 5 May 2022 22:57:22 -0400 Subject: [PATCH 1284/1394] gnu: python-pillow: Update to 9.0.0. * gnu/packages/python-xyz.scm (python-pillow): Update to 9.0.0. --- gnu/packages/python-xyz.scm | 71 +++++++++++++++++-------------------- 1 file changed, 32 insertions(+), 39 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 12ac929c510..3c30886cd84 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6808,45 +6808,39 @@ retrieve text and metadata from PDFs as well as merge entire files together.") (package (name "python-pillow") (version "9.0.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "Pillow" version)) - (sha256 - (base32 - "0gjry0yqryd2678sm47jhdnbghzxn5wk8pgyaqwr4qi7x5ijjvpf")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file-recursively "src/thirdparty"))))) + (source (origin + (method url-fetch) + (uri (pypi-uri "Pillow" version)) + (sha256 + (base32 + "0gjry0yqryd2678sm47jhdnbghzxn5wk8pgyaqwr4qi7x5ijjvpf")) + (modules '((guix build utils))) + (snippet '(begin + (delete-file-recursively "src/thirdparty"))))) (build-system python-build-system) - (native-inputs - (list python-pytest)) - (inputs - (list freetype - lcms - libjpeg-turbo - libtiff - libwebp - openjpeg - zlib)) - (propagated-inputs - (list python-olefile)) + (native-inputs (list python-pytest)) + (inputs (list freetype + lcms + libjpeg-turbo + libtiff + libwebp + openjpeg + zlib)) + (propagated-inputs (list python-olefile)) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-ldconfig - (lambda _ - (substitute* "setup.py" - (("\\['/sbin/ldconfig', '-p'\\]") "['true']")))) - (replace 'check - (lambda* (#:key outputs inputs tests? #:allow-other-keys) - (when tests? - (setenv "HOME" (getcwd)) - ;; Make installed package available for running the tests. - (add-installed-pythonpath inputs outputs) - (invoke "python" "selftest.py" "--installed") - (invoke "python" "-m" "pytest" "-vv"))))))) + `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-ldconfig + (lambda _ + (substitute* "setup.py" + (("\\['/sbin/ldconfig', '-p'\\]") "['true']")))) + (replace 'check + (lambda* (#:key outputs inputs tests? #:allow-other-keys) + (when tests? + (setenv "HOME" + (getcwd)) + (add-installed-pythonpath inputs outputs) + (invoke "python" "selftest.py" "--installed") + (invoke "python" "-m" "pytest" "-vv"))))))) (home-page "https://python-pillow.org") (synopsis "Fork of the Python Imaging Library") (description @@ -6856,8 +6850,7 @@ efficient internal representation, and fairly powerful image processing capabilities. The core image library is designed for fast access to data stored in a few basic pixel formats. It should provide a solid foundation for a general image processing tool.") - (properties `((python2-variant . ,(delay python2-pillow)) - (cpe-name . "pillow"))) + (properties `((cpe-name . "pillow"))) (license (license:x11-style "http://www.pythonware.com/products/pil/license.htm" "The PIL Software License")))) From 030e5793d64984910c61000bac17577141004fef Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 5 May 2022 23:01:03 -0400 Subject: [PATCH 1285/1394] gnu: Remove python2-olefile. * gnu/packages/python-xyz.scm (python2-olefile): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3c30886cd84..1f72d1a2849 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6750,9 +6750,6 @@ Storage or Compound Document, Microsoft Office). It is an improved version of the OleFileIO module from PIL, the Python Image Library.") (license license:bsd-3))) -(define-public python2-olefile - (package-with-python2 python-olefile)) - (define-public python-pypdf3 (package (name "python-pypdf3") From 553c009d7415288fff4ab758d906449c4c18ef69 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 5 May 2022 23:41:25 -0400 Subject: [PATCH 1286/1394] gnu: pypy3: Rename to pypy and modernize definition. * gnu/packages/python.scm (pypy3): Deprecate in favor of... (pypy): ... this renamed package. [native-inputs, inputs]: Move after arguments, use new style and sort. [native-inputs]: Remove python2-hypothesis. [phases]: Adjust to use gexps, with search-input-file and this-package-input. --- gnu/packages/python.scm | 272 ++++++++++++++++++++-------------------- 1 file changed, 135 insertions(+), 137 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 3bc3346c215..bcaf06977c4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -743,9 +743,9 @@ compatible with normal Python as possible to allow you to transfer code with ease from the desktop to a microcontroller or embedded system.") (license license:expat))) -(define-public pypy3 +(define-public pypy (package - (name "pypy3") + (name "pypy") (version "7.3.5") (source (origin (method url-fetch) @@ -755,148 +755,144 @@ ease from the desktop to a microcontroller or embedded system.") (base32 "18lrdmpcczlbk3cfarkgwqdmilrybz56i1dafk8dkjlyk90gw86r")))) (build-system gnu-build-system) + (arguments + (list + #:tests? #f ;FIXME: 43 out of 364 tests are failing + #:modules '((ice-9 ftw) (ice-9 match) + (guix build utils) (guix build gnu-build-system)) + #:disallowed-references (list nss-certs) + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("rpython/rlib/clibffi.py") + ;; find_library does not work for libc + (("ctypes\\.util\\.find_library\\('c'\\)") "'libc.so'")) + (substitute* '("lib_pypy/cffi/_pycparser/ply/cpp.py") + ;; Make reproducible (XXX: unused?) + (("time\\.localtime\\(\\)") "time.gmtime(0)")) + (substitute* '("pypy/module/sys/version.py") + ;; Make reproducible + (("t\\.gmtime\\(\\)") "t.gmtime(0)")) + (substitute* '("lib_pypy/_tkinter/tklib_build.py") + ;; Link to versioned libtcl and libtk + (("linklibs = \\['tcl', 'tk'\\]") + "linklibs = ['tcl8.6', 'tk8.6']") + (("incdirs = \\[\\]") + (string-append + "incdirs = ['" + #$(this-package-input "tcl") "/include', '" + #$(this-package-input "tk") "/include']"))) + (substitute* '("lib_pypy/_curses_build.py") + ;; Find curses + (("/usr/local") + #$(this-package-input "ncurses"))) + (substitute* '("lib_pypy/_dbm.py") + ;; Use gdbm compat library, so we don’t need to pull + ;; in bdb. + (("ctypes.util.find_library\\('db'\\)") + (format #f "~s" (search-input-file + inputs "lib/libgdbm_compat.so")))) + (substitute* '("lib_pypy/_sqlite3_build.py") + ;; Always use search paths + (("sys\\.platform\\.startswith\\('freebsd'\\)") "True") + ;; Find sqlite3 + (("/usr/local") (assoc-ref inputs "sqlite")) + (("libname = 'sqlite3'") + (format #f "libname = ~s" + (search-input-file inputs "lib/libsqlite3.so.0")))) + (substitute* '("lib-python/3/subprocess.py") + ;; Fix shell path + (("/bin/sh") + (search-input-file inputs "/bin/sh"))) + (substitute* '("lib-python/3/distutils/unixccompiler.py") + ;; gcc-toolchain does not provide symlink cc -> gcc + (("\"cc\"") "\"gcc\"")))) + (add-after 'unpack 'set-source-file-times-to-1980 + ;; copied from python package, required by zip testcase + (lambda _ + (let ((circa-1980 (* 10 366 24 60 60))) + (ftw "." (lambda (file stat flag) + (utime file circa-1980 circa-1980) + #t))))) + (replace 'build + (lambda _ + (with-directory-excursion "pypy/goal" + ;; Build with jit optimization. + (invoke "python2" + "../../rpython/bin/rpython" + (string-append "--make-jobs=" + (number->string (parallel-job-count))) + "-Ojit" + "targetpypystandalone" + "--allworkingmodules")) + ;; Build c modules and package everything, so tests work. + (with-directory-excursion "pypy/tool/release" + (invoke "python2" "package.py" + "--archive-name" "pypy-dist" + "--builddir" (getcwd))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (if tests? + (begin + (setenv "HOME" "/tmp") ; test_with_pip tries to + ; access ~/.cache/pip + ;; Run library tests only (no interpreter unit tests). + ;; This is what Gentoo does. + (invoke "python" "pypy/test_all.py" + "--pypy=pypy/tool/release/pypy-dist/bin/pypy3" + "lib-python")) + (format #t "test suite not run~%")))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((bin-pypy3 (string-append #$output "/bin/pypy3")) + (shebang-match-python "#!.+/bin/python") + (shebang-pypy3 (string-append "#!" bin-pypy3)) + (dist-dir "pypy/tool/release/pypy-dist")) + (with-directory-excursion dist-dir + ;; Delete test data. + (for-each + (lambda (x) + (delete-file-recursively (string-append + "lib-python/3/" x))) + '("tkinter/test" + "test" + "sqlite3/test" + "lib2to3/tests" + "idlelib/idle_test" + "distutils/tests" + "ctypes/test" + "unittest/test")) + ;; Patch shebang referencing python. + (substitute* '("lib-python/3/cgi.py" + "lib-python/3/encodings/rot_13.py") + ((shebang-match-python) shebang-pypy3)) + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* '("lib_pypy/_md5.py" + "lib_pypy/_sha1.py") + ((shebang-match-python) shebang-pypy3)))) + (copy-recursively dist-dir out))))))) (native-inputs - `(("python-2" ,python-2) - ("pkg-config" ,pkg-config) - ("tar" ,tar) ; Required for package.py - ("python2-pycparser" ,python2-pycparser) - ("python2-hypothesis" ,python2-hypothesis) - ("nss-certs" ,nss-certs) ; For ssl tests - ("gzip" ,gzip))) + (list gzip + nss-certs ; For ssl tests + pkg-config + python-2 + python2-pycparser + tar)) ; Required for package.py (inputs - (list libffi - zlib + (list bzip2 + expat + gdbm + glibc + libffi ncurses openssl - expat - bzip2 sqlite - gdbm tcl tk - glibc - xz)) ; liblzma - (arguments - `(#:tests? #f ;FIXME: 43 out of 364 tests are failing - #:modules ((ice-9 ftw) (ice-9 match) - (guix build utils) (guix build gnu-build-system)) - #:disallowed-references (,nss-certs) - #:phases (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'patch-source - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* '("rpython/rlib/clibffi.py") - ;; find_library does not work for libc - (("ctypes\\.util\\.find_library\\('c'\\)") "'libc.so'")) - (substitute* '("lib_pypy/cffi/_pycparser/ply/cpp.py") - ;; Make reproducible (XXX: unused?) - (("time\\.localtime\\(\\)") "time.gmtime(0)")) - (substitute* '("pypy/module/sys/version.py") - ;; Make reproducible - (("t\\.gmtime\\(\\)") "t.gmtime(0)")) - (substitute* '("lib_pypy/_tkinter/tklib_build.py") - ;; Link to versioned libtcl and libtk - (("linklibs = \\['tcl', 'tk'\\]") - "linklibs = ['tcl8.6', 'tk8.6']") - (("incdirs = \\[\\]") - (string-append "incdirs = ['" - (assoc-ref inputs "tcl") - "/include', '" - (assoc-ref inputs "tk") - "/include']"))) - (substitute* '("lib_pypy/_curses_build.py") - ;; Find curses - (("/usr/local") (assoc-ref inputs "ncurses"))) - (substitute* '("lib_pypy/_dbm.py") - ;; Use gdbm compat library, so we don’t need to pull - ;; in bdb. - (("ctypes.util.find_library\\('db'\\)") - (format #f "'~a/lib/libgdbm_compat.so'" - (assoc-ref inputs "gdbm")))) - (substitute* '("lib_pypy/_sqlite3_build.py") - ;; Always use search paths - (("sys\\.platform\\.startswith\\('freebsd'\\)") "True") - ;; Find sqlite3 - (("/usr/local") (assoc-ref inputs "sqlite")) - (("libname = 'sqlite3'") - (string-append "libname = '" - (assoc-ref inputs "sqlite") - "/lib/libsqlite3.so.0'"))) - (substitute* '("lib-python/3/subprocess.py") - ;; Fix shell path - (("/bin/sh") - (search-input-file inputs "/bin/sh"))) - (substitute* '("lib-python/3/distutils/unixccompiler.py") - ;; gcc-toolchain does not provide symlink cc -> gcc - (("\"cc\"") "\"gcc\"")))) - (add-after - 'unpack 'set-source-file-times-to-1980 - ;; copied from python package, required by zip testcase - (lambda _ - (let ((circa-1980 (* 10 366 24 60 60))) - (ftw "." (lambda (file stat flag) - (utime file circa-1980 circa-1980) - #t))))) - (replace 'build - (lambda* (#:key inputs #:allow-other-keys) - (with-directory-excursion "pypy/goal" - ;; Build with jit optimization. - (invoke "python2" - "../../rpython/bin/rpython" - (string-append "--make-jobs=" - (number->string (parallel-job-count))) - "-Ojit" - "targetpypystandalone" - "--allworkingmodules")) - ;; Build c modules and package everything, so tests work. - (with-directory-excursion "pypy/tool/release" - (invoke "python2" "package.py" - "--archive-name" "pypy-dist" - "--builddir" (getcwd))))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (if tests? - (begin - (setenv "HOME" "/tmp") ; test_with_pip tries to - ; access ~/.cache/pip - ;; Run library tests only (no interpreter unit - ;; tests). This is what Gentoo does. - (invoke - "python2" - "pypy/test_all.py" - "--pypy=pypy/tool/release/pypy-dist/bin/pypy3" - "lib-python")) - (format #t "test suite not run~%")))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin-pypy3 (string-append out "/bin/pypy3")) - (shebang-match-python "#!.+/bin/python") - (shebang-pypy3 (string-append "#!" bin-pypy3)) - (dist-dir "pypy/tool/release/pypy-dist")) - (with-directory-excursion dist-dir - ;; Delete test data. - (for-each - (lambda (x) - (delete-file-recursively (string-append - "lib-python/3/" x))) - '("tkinter/test" - "test" - "sqlite3/test" - "lib2to3/tests" - "idlelib/idle_test" - "distutils/tests" - "ctypes/test" - "unittest/test")) - ;; Patch shebang referencing python2 - (substitute* '("lib-python/3/cgi.py" - "lib-python/3/encodings/rot_13.py") - ((shebang-match-python) shebang-pypy3)) - (with-fluids ((%default-port-encoding "ISO-8859-1")) - (substitute* '("lib_pypy/_md5.py" - "lib_pypy/_sha1.py") - ((shebang-match-python) shebang-pypy3)))) - (copy-recursively dist-dir out))))))) + xz + zlib)) (home-page "https://www.pypy.org/") (synopsis "Python implementation with just-in-time compilation") (description "PyPy is a faster, alternative implementation of the Python @@ -910,3 +906,5 @@ Python code natively, including C extensions.") (license:non-copyleft "http://www.unicode.org/copyright.html"))))) +(define-public pypy3 + (deprecated-package "pypy3" pypy)) From 6a778b47052d27e4edb242c32fccd9339c7d5a12 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 6 May 2022 00:03:20 -0400 Subject: [PATCH 1287/1394] gnu: python-fastbencode: Build C extensions. * gnu/packages/python-xyz.scm (python-fastbencode) [source]: Delete pre-generated C source files in snippet. [native-inputs]: Add python-cython. --- gnu/packages/python-xyz.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1f72d1a2849..2c141b104ce 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12663,9 +12663,13 @@ JSON Reference and JSON Pointer.") (origin (method url-fetch) (uri (pypi-uri "fastbencode" version)) + (modules '((guix build utils))) + ;; Delete pre-generated Cython C files. + (snippet '(for-each delete-file (find-files "." "\\.c$"))) (sha256 (base32 "1r66w3vpmvfmssshjpgqaj2m14c8p94nymr96mwn61idajz9mg5n")))) (build-system python-build-system) + (native-inputs (list python-cython)) (home-page "https://github.com/breezy-team/fastbencode") (synopsis "Python Bencode (de)serializer with optional fast C extensions") (description From 9377be6a4816c92e13be34c8d3291895a96db757 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 6 May 2022 00:37:38 -0400 Subject: [PATCH 1288/1394] gnu: Add python-lazr-uri. * gnu/packages/python-web.scm (python-lazr-uri): New variable. --- gnu/packages/python-web.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index b0454b6f819..76d9642616c 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -109,6 +109,24 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (srfi srfi-1)) +(define-public python-lazr-uri + (package + (name "python-lazr-uri") + (version "1.0.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "lazr.uri" version)) + (sha256 + (base32 "0r44rw0bj5mayhqwfwj1dnrjgzj1lrh7ishiddd1vygnrczqa9jh")))) + (build-system python-build-system) + (native-inputs (list python-zope-testrunner)) + (home-page "https://launchpad.net/lazr.uri") + (synopsis "Python URI manipulation library") + (description "This Python package provides a self-contained, easily +reusable library for parsing, manipulating, and generating URIs.") + (license license:lgpl3))) + (define-public python-prawcore (package (name "python-prawcore") From 5e25aeee162d88fd2a7c9254a3b3df1783e1b69b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 6 May 2022 00:41:39 -0400 Subject: [PATCH 1289/1394] gnu: Add python-wadllib. * gnu/packages/python-web.scm (python-wadllib): New variable. --- gnu/packages/python-web.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 76d9642616c..d6f068f6077 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -7394,3 +7394,21 @@ metadata from HTML markup. Currently, extruct supports: @item Dublin Core Metadata (DC-HTML-2003) @end itemize") (license license:bsd-3))) + +(define-public python-wadllib + (package + (name "python-wadllib") + (version "1.3.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "wadllib" version)) + (sha256 + (base32 "1z65crvdsjxh9nahz1g6q021ijmv85ixmq88l96d61qh5imavndc")))) + (build-system python-build-system) + (propagated-inputs (list python-lazr-uri)) + (home-page "https://launchpad.net/wadllib") + (synopsis "Web Application Description Language (WADL) navigation library") + (description "The @code{wadllib} Python library allows navigating HTTP +resources using Web Application Description Language (WADL) files as guides.") + (license license:lgpl3))) From f880fc7b88f25f9cca59dffabd9de6dd0ab24fc9 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 10 May 2022 01:05:48 -0400 Subject: [PATCH 1290/1394] gnu: Add python-lazr-restfulclient. * gnu/packages/python-web.scm (python-lazr-restfulclient): New variable. --- gnu/packages/python-web.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index d6f068f6077..47ba88882f6 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -109,6 +109,31 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (srfi srfi-1)) +(define-public python-lazr-restfulclient + (package + (name "python-lazr-restfulclient") + (version "0.14.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "lazr.restfulclient" version)) + (sha256 + (base32 "11yhlqmdf2cqbdfzn8gdmzvmcivh4fflr18zf412sflvfjrdc3xz")))) + (build-system python-build-system) + ;; Disable the test suite to avoid the lazr.authentication requirement, + ;; which requires the ancient 'oauth', a Python 2 only library. + (arguments (list #:tests? #f)) + (propagated-inputs + (list python-distro + python-httplib2 + python-oauthlib + python-wadllib)) + (home-page "https://launchpad.net/lazr.restfulclient") + (synopsis "Web client Python library extending wadlib") + (description "This package provides a programmable client library that +adds functionality on top of @code{wadlib}.") + (license license:lgpl3+))) + (define-public python-lazr-uri (package (name "python-lazr-uri") From dad15bdb26edbdf7b80519a2e7d0edf4e1efcd5f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 10 May 2022 01:05:59 -0400 Subject: [PATCH 1291/1394] gnu: Add python-launchpadlib. * gnu/packages/python-web.scm (python-launchpadlib): New variable. --- gnu/packages/python-web.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 47ba88882f6..bfbae3ce074 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -134,6 +134,35 @@ adds functionality on top of @code{wadlib}.") (license license:lgpl3+))) +(define-public python-launchpadlib + (package + (name "python-launchpadlib") + (version "1.10.16") + (source + (origin + (method url-fetch) + (uri (pypi-uri "launchpadlib" version)) + (sha256 + (base32 "106aixwchwyb100wlf4cnj1vgsi2d7x40ps8xv8az27r6qwv3x0d")))) + (build-system python-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-before 'check 'set-home + (lambda _ + ;; Tests require a writable home. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list python-httplib2 + python-keyring + python-lazr-restfulclient + python-lazr-uri)) + (native-inputs (list python-mock python-testresources python-wadllib)) + (home-page "https://help.launchpad.net/API/launchpadlib") + (synopsis "Python client library for Launchpad's web service") + (description "@code{launchpadlib} is a Python library that allows +scripting Launchpad via its the web service API.") + (license license:lgpl3+))) + (define-public python-lazr-uri (package (name "python-lazr-uri") From dc71b4f1c65c9f3244f96aaf69b9218825361eda Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 6 May 2022 00:09:29 -0400 Subject: [PATCH 1292/1394] gnu: breezy: Update to 3.2.2. * gnu/packages/patches/breezy-fix-gio.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/version-control.scm (breezy): Update to 3.2.2. [source]{snippet}: Delete pre-generated cythonized C files. {patches}: Apply patch. [tests?]: Disable tests. [phases]{patch-test-shebangs, check}: New phase and override. [native-inputs]: Add nano, python-cython, python-docutils, and python-testrepository. [inputs]: Use new style. Add python-launchpadlib and python-pygobject. [description]: Adjust Bazaar URL. --- gnu/local.mk | 1 + gnu/packages/patches/breezy-fix-gio.patch | 338 ++++++++++++++++++++++ gnu/packages/version-control.scm | 64 +++- 3 files changed, 388 insertions(+), 15 deletions(-) create mode 100644 gnu/packages/patches/breezy-fix-gio.patch diff --git a/gnu/local.mk b/gnu/local.mk index b54c1fbefe2..513216183d9 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -916,6 +916,7 @@ dist_patch_DATA = \ %D%/packages/patches/bloomberg-bde-cmake-module-path.patch \ %D%/packages/patches/bloomberg-bde-tools-fix-install-path.patch \ %D%/packages/patches/bpftrace-disable-bfd-disasm.patch \ + %D%/packages/patches/breezy-fix-gio.patch \ %D%/packages/patches/byobu-writable-status.patch \ %D%/packages/patches/bubblewrap-fix-locale-in-tests.patch \ %D%/packages/patches/cabal-install-base16-bytestring1.0.patch \ diff --git a/gnu/packages/patches/breezy-fix-gio.patch b/gnu/packages/patches/breezy-fix-gio.patch new file mode 100644 index 00000000000..f70e761555f --- /dev/null +++ b/gnu/packages/patches/breezy-fix-gio.patch @@ -0,0 +1,338 @@ +This patch combines https://code.launchpad.net/~jelmer/brz/enable-gio/+merge/419150 +and https://bazaar.launchpad.net/~jelmer/brz/fix-gio/revision/7570. + +=== modified file 'breezy/transport/gio_transport.py' +--- a/breezy/transport/gio_transport.py 2022-04-09 12:17:41 +0000 ++++ b/breezy/transport/gio_transport.py 2022-04-09 12:33:51 +0000 +@@ -52,11 +52,7 @@ + from ..tests.test_server import TestServer + + try: +- import glib +-except ImportError as e: +- raise errors.DependencyNotPresent('glib', e) +-try: +- import gio ++ from gi.repository import Gio as gio + except ImportError as e: + raise errors.DependencyNotPresent('gio', e) + + +@@ -57,6 +57,9 @@ + raise errors.DependencyNotPresent('gio', e) + + ++from gi.repository.GLib import GError ++ ++ + class GioLocalURLServer(TestServer): + """A pretend server for local transports, using file:// urls. + +@@ -81,7 +84,7 @@ + def __init__(self, transport, relpath): + FileStream.__init__(self, transport, relpath) + self.gio_file = transport._get_GIO(relpath) +- self.stream = self.gio_file.create() ++ self.stream = self.gio_file.create(0, None) + + def _close(self): + self.stream.close() +@@ -90,7 +93,7 @@ + try: + # Using pump_string_file seems to make things crash + osutils.pumpfile(BytesIO(bytes), self.stream) +- except gio.Error as e: ++ except GError as e: + # self.transport._translate_gio_error(e,self.relpath) + raise errors.BzrError(str(e)) + +@@ -98,12 +101,12 @@ + class GioStatResult(object): + + def __init__(self, f): +- info = f.query_info('standard::size,standard::type') ++ info = f.query_info('standard::size,standard::type', 0, None) + self.st_size = info.get_size() + type = info.get_file_type() +- if (type == gio.FILE_TYPE_REGULAR): ++ if type == gio.FileType.REGULAR: + self.st_mode = stat.S_IFREG +- elif type == gio.FILE_TYPE_DIRECTORY: ++ elif type == gio.FileType.DIRECTORY: + self.st_mode = stat.S_IFDIR + + +@@ -122,7 +125,7 @@ + user, netloc = netloc.rsplit('@', 1) + # Seems it is not possible to list supported backends for GIO + # so a hardcoded list it is then. +- gio_backends = ['dav', 'file', 'ftp', 'obex', 'sftp', 'ssh', 'smb'] ++ gio_backends = ['dav', 'file', 'ftp', 'obex', 'sftp', 'ssh', 'smb', 'http'] + if scheme not in gio_backends: + raise urlutils.InvalidURL(base, + extra="GIO support is only available for " + +@@ -138,13 +141,10 @@ + _from_transport=_from_transport) + + def _relpath_to_url(self, relpath): +- full_url = urlutils.join(self.url, relpath) +- if isinstance(full_url, str): +- raise urlutils.InvalidURL(full_url) +- return full_url ++ return urlutils.join(self.url, relpath) + + def _get_GIO(self, relpath): +- """Return the ftplib.GIO instance for this object.""" ++ """Return the GIO instance for this object.""" + # Ensures that a connection is established + connection = self._get_connection() + if connection is None: +@@ -152,7 +152,7 @@ + connection, credentials = self._create_connection() + self._set_connection(connection, credentials) + fileurl = self._relpath_to_url(relpath) +- file = gio.File(fileurl) ++ file = gio.File.new_for_uri(fileurl) + return file + + def _auth_cb(self, op, message, default_user, default_domain, flags): +@@ -197,7 +197,7 @@ + try: + obj.mount_enclosing_volume_finish(res) + self.loop.quit() +- except gio.Error as e: ++ except GError as e: + self.loop.quit() + raise errors.BzrError( + "Failed to mount the given location: " + str(e)) +@@ -209,12 +209,12 @@ + user, password = credentials + + try: +- connection = gio.File(self.url) ++ connection = gio.File.new_for_uri(self.url) + mount = None + try: + mount = connection.find_enclosing_mount() +- except gio.Error as e: +- if (e.code == gio.ERROR_NOT_MOUNTED): ++ except GError as e: ++ if e.code == gio.IOErrorEnum.NOT_MOUNTED: + self.loop = glib.MainLoop() + ui.ui_factory.show_message('Mounting %s using GIO' % + self.url) +@@ -227,7 +227,7 @@ + m = connection.mount_enclosing_volume(op, + self._mount_done_cb) + self.loop.run() +- except gio.Error as e: ++ except GError as e: + raise errors.TransportError(msg="Error setting up connection:" + " %s" % str(e), orig_error=e) + return connection, (user, password) +@@ -257,8 +257,8 @@ + if stat.S_ISREG(st.st_mode) or stat.S_ISDIR(st.st_mode): + return True + return False +- except gio.Error as e: +- if e.code == gio.ERROR_NOT_FOUND: ++ except GError as e: ++ if e.code == gio.IOErrorEnum.NOT_FOUND: + return False + else: + self._translate_gio_error(e, relpath) +@@ -281,10 +281,10 @@ + buf = fin.read() + fin.close() + return BytesIO(buf) +- except gio.Error as e: ++ except GError as e: + # If we get a not mounted here it might mean + # that a bad path has been entered (or that mount failed) +- if (e.code == gio.ERROR_NOT_MOUNTED): ++ if e.code == gio.IOErrorEnum.NOT_MOUNTED: + raise errors.PathError(relpath, + extra='Failed to get file, make sure the path is correct. ' + + str(e)) +@@ -307,19 +307,19 @@ + closed = True + try: + f = self._get_GIO(tmppath) +- fout = f.create() ++ fout = f.create(0, None) + closed = False + length = self._pump(fp, fout) + fout.close() + closed = True + self.stat(tmppath) + dest = self._get_GIO(relpath) +- f.move(dest, flags=gio.FILE_COPY_OVERWRITE) ++ f.move(dest, flags=gio.FileCopyFlags.OVERWRITE) + f = None + if mode is not None: + self._setmode(relpath, mode) + return length +- except gio.Error as e: ++ except GError as e: + self._translate_gio_error(e, relpath) + finally: + if not closed and fout is not None: +@@ -335,7 +335,7 @@ + f = self._get_GIO(relpath) + f.make_directory() + self._setmode(relpath, mode) +- except gio.Error as e: ++ except GError as e: + self._translate_gio_error(e, relpath) + + def open_write_stream(self, relpath, mode=None): +@@ -369,14 +369,11 @@ + f.delete() + else: + raise errors.NotADirectory(relpath) +- except gio.Error as e: ++ except GError as e: + self._translate_gio_error(e, relpath) + except errors.NotADirectory as e: + # just pass it forward + raise e +- except Exception as e: +- mutter('failed to rmdir %s: %s' % (relpath, e)) +- raise errors.PathError(relpath) + + def append_file(self, relpath, file, mode=None): + """Append the text in the file-like object into the final +@@ -392,7 +389,7 @@ + result = 0 + fo = self._get_GIO(tmppath) + fi = self._get_GIO(relpath) +- fout = fo.create() ++ fout = fo.create(0, None) + try: + info = GioStatResult(fi) + result = info.st_size +@@ -400,11 +397,11 @@ + self._pump(fin, fout) + fin.close() + # This separate except is to catch and ignore the +- # gio.ERROR_NOT_FOUND for the already existing file. ++ # gio.IOErrorEnum.NOT_FOUND for the already existing file. + # It is valid to open a non-existing file for append. + # This is caused by the broken gio append_to... +- except gio.Error as e: +- if e.code != gio.ERROR_NOT_FOUND: ++ except GError as e: ++ if e.code != gio.IOErrorEnum.NOT_FOUND: + self._translate_gio_error(e, relpath) + length = self._pump(file, fout) + fout.close() +@@ -413,9 +410,11 @@ + raise errors.BzrError("Failed to append size after " + "(%d) is not original (%d) + written (%d) total (%d)" % + (info.st_size, result, length, result + length)) +- fo.move(fi, flags=gio.FILE_COPY_OVERWRITE) ++ fo.move( ++ fi, flags=gio.FileCopyFlags.OVERWRITE, cancellable=None, ++ progress_callback=None) + return result +- except gio.Error as e: ++ except GError as e: + self._translate_gio_error(e, relpath) + + def _setmode(self, relpath, mode): +@@ -429,8 +428,8 @@ + try: + f = self._get_GIO(relpath) + f.set_attribute_uint32(gio.FILE_ATTRIBUTE_UNIX_MODE, mode) +- except gio.Error as e: +- if e.code == gio.ERROR_NOT_SUPPORTED: ++ except GError as e: ++ if e.code == gio.IOErrorEnum.NOT_SUPPORTED: + # Command probably not available on this server + mutter("GIO Could not set permissions to %s on %s. %s", + oct(mode), self._remote_path(relpath), str(e)) +@@ -444,8 +443,8 @@ + mutter("GIO move (rename): %s => %s", rel_from, rel_to) + f = self._get_GIO(rel_from) + t = self._get_GIO(rel_to) +- f.move(t) +- except gio.Error as e: ++ f.move(t, flags=0, cancellable=None, progress_callback=None) ++ except GError as e: + self._translate_gio_error(e, rel_from) + + def move(self, rel_from, rel_to): +@@ -455,8 +454,8 @@ + mutter("GIO move: %s => %s", rel_from, rel_to) + f = self._get_GIO(rel_from) + t = self._get_GIO(rel_to) +- f.move(t, flags=gio.FILE_COPY_OVERWRITE) +- except gio.Error as e: ++ f.move(t, flags=gio.FileCopyFlags.OVERWRITE) ++ except GError as e: + self._translate_gio_error(e, relfrom) + + def delete(self, relpath): +@@ -466,7 +465,7 @@ + mutter("GIO delete: %s", relpath) + f = self._get_GIO(relpath) + f.delete() +- except gio.Error as e: ++ except GError as e: + self._translate_gio_error(e, relpath) + + def external_url(self): +@@ -489,11 +488,11 @@ + try: + entries = [] + f = self._get_GIO(relpath) +- children = f.enumerate_children(gio.FILE_ATTRIBUTE_STANDARD_NAME) ++ children = f.enumerate_children(gio.FILE_ATTRIBUTE_STANDARD_NAME, 0, None) + for child in children: + entries.append(urlutils.escape(child.get_name())) + return entries +- except gio.Error as e: ++ except GError as e: + self._translate_gio_error(e, relpath) + + def iter_files_recursive(self): +@@ -519,7 +518,7 @@ + mutter("GIO stat: %s", relpath) + f = self._get_GIO(relpath) + return GioStatResult(f) +- except gio.Error as e: ++ except GError as e: + self._translate_gio_error(e, relpath, extra='error w/ stat') + + def lock_read(self, relpath): +@@ -556,21 +555,21 @@ + mutter("GIO Error: %s %s" % (str(err), path)) + if extra is None: + extra = str(err) +- if err.code == gio.ERROR_NOT_FOUND: ++ if err.code == gio.IOErrorEnum.NOT_FOUND: + raise errors.NoSuchFile(path, extra=extra) +- elif err.code == gio.ERROR_EXISTS: ++ elif err.code == gio.IOErrorEnum.EXISTS: + raise errors.FileExists(path, extra=extra) +- elif err.code == gio.ERROR_NOT_DIRECTORY: ++ elif err.code == gio.IOErrorEnum.NOT_DIRECTORY: + raise errors.NotADirectory(path, extra=extra) +- elif err.code == gio.ERROR_NOT_EMPTY: ++ elif err.code == gio.IOErrorEnum.NOT_EMPTY: + raise errors.DirectoryNotEmpty(path, extra=extra) +- elif err.code == gio.ERROR_BUSY: ++ elif err.code == gio.IOErrorEnum.BUSY: + raise errors.ResourceBusy(path, extra=extra) +- elif err.code == gio.ERROR_PERMISSION_DENIED: ++ elif err.code == gio.IOErrorEnum.PERMISSION_DENIED: + raise errors.PermissionDenied(path, extra=extra) +- elif err.code == gio.ERROR_HOST_NOT_FOUND: ++ elif err.code == gio.IOErrorEnum.HOST_NOT_FOUND: + raise errors.PathError(path, extra=extra) +- elif err.code == gio.ERROR_IS_DIRECTORY: ++ elif err.code == gio.IOErrorEnum.IS_DIRECTORY: + raise errors.PathError(path, extra=extra) + else: + mutter('unable to understand error for path: %s: %s', path, err) + diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 30d15919abe..7351d966004 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -187,29 +187,63 @@ as well as the classic centralized workflow.") (uri (string-append "https://launchpad.net/brz/" (version-major+minor version) "/" version "/+download/breezy-" version ".tar.gz")) + (modules '((guix build utils))) + ;; Delete pre-generated Cython C files. + (snippet '(for-each delete-file (find-files "." "\\pyx.c$"))) (sha256 - (base32 "1md4b6ajawf5h50fqizmjj0g833ihc674dh7fn0mvl4d412nwyhq")))) + (base32 + "1md4b6ajawf5h50fqizmjj0g833ihc674dh7fn0mvl4d412nwyhq")) + (patches (search-patches "breezy-fix-gio.patch")))) (build-system python-build-system) - ;; TODO: Maybe regenerate C files with Cython? - (inputs - `(("gettext" ,gettext-minimal) - ("python-configobj" ,python-configobj) - ("python-dulwich" ,python-dulwich) - ("python-fastbencode" ,python-fastbencode) - ("python-fastimport" ,python-fastimport) - ("python-paramiko" ,python-paramiko) - ("python-patiencediff" ,python-patiencediff) - ("python-pycryptodome" ,python-pycryptodome) - ("python-pygpgme" ,python-pygpgme))) (arguments - `(#:tests? #f)) ; no tests in release tarball + (list + #:tests? #f ;FIXME: the test suite hangs + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-test-shebangs + (lambda _ + (substitute* (append (find-files "breezy/bzr/tests") + (find-files "breezy/tests")) + (("#!/bin/sh") + (format #f "#!~a" (which "sh")))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; The test_read_bundle tests fails with "TypeError: a + ;; bytes-like object is required, not '_ResultTuple'" (see: + ;; https://bugs.launchpad.net/brz/+bug/1968415/comments/4). + (substitute* "breezy/bzr/tests/__init__.py" + (("'test_read_bundle'," all) + (string-append "# " all))) + (setenv "BZR_EDITOR" "nano") + (setenv "HOME" "/tmp") + (invoke "testr" "init") + (invoke "testr" "run"))))))) + (native-inputs + (list nano ;for tests + python-cython + python-docutils + python-subunit + python-testrepository)) + (inputs + (list gettext-minimal + python-configobj + python-dulwich + python-fastbencode + python-fastimport + python-launchpadlib + python-paramiko + python-patiencediff + python-pycryptodome + python-pygobject + python-pygpgme)) (home-page "https://www.breezy-vcs.org/") (synopsis "Decentralized revision control system") (description "Breezy (@command{brz}) is a decentralized revision control system. By default, Breezy provides support for both the -@uref{https://www.bazaar-vcs.org, Bazaar} and @uref{https://www.git-scm.com, -Git} file formats. Breezy is backwards compatible with Bazaar's disk format +@uref{https://bazaar.canonical.com/, Bazaar} and @uref{https://www.git-scm.com, +Git} file formats. Breezy is backwabrds compatible with Bazaar's disk format and protocols. One of the key differences with Bazaar is that Breezy runs on Python 3.3 and later, rather than on Python 2.") (license license:gpl2+))) From be672f1f7f0cda28823ef4a4260f39bc845cbabe Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Wed, 11 May 2022 02:03:36 -0400 Subject: [PATCH 1293/1394] gnu: bazaar: Obsolete with breezy. * gnu/packages/version-control.scm (bazaar): Deprecate package. * guix/build/bzr.scm (bzr-fetch): Adjust to use breezy; delete trailing #t. * guix/bzr-download.scm (bzr-package): Replace bazaar by breezy. --- gnu/packages/version-control.scm | 41 +++----------------------------- guix/build/bzr.scm | 8 +++---- guix/bzr-download.scm | 6 ++--- 3 files changed, 9 insertions(+), 46 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 7351d966004..a43382e94fa 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -139,44 +139,6 @@ #:use-module (ice-9 match) #:use-module (srfi srfi-1)) -(define-public bazaar - (package - (name "bazaar") - (version "2.7.0") - (source - (origin - (method url-fetch) - (uri (string-append "https://launchpad.net/bzr/" - (version-major+minor version) "/" version - "/+download/bzr-" version ".tar.gz")) - (patches (search-patches "bazaar-CVE-2017-14176.patch")) - (sha256 - (base32 - "1cysix5k3wa6y7jjck3ckq3abls4gvz570s0v0hxv805nwki4i8d")))) - (build-system python-build-system) - (inputs - ;; Note: 'tools/packaging/lp-upload-release' and 'tools/weavemerge.sh' - ;; require Zsh. - `(("gettext" ,gettext-minimal))) - (arguments - `(#:tests? #f ; no test target - #:python ,python-2 ; Python 3 apparently not yet supported, see - ; https://answers.launchpad.net/bzr/+question/229048 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-mandir - (lambda _ - (substitute* "setup.py" - (("man/man1") "share/man/man1")) - #t))))) - (home-page "https://gnu.org/software/bazaar") - (synopsis "Version control system supporting both distributed and centralized workflows") - (description - "GNU Bazaar is a version control system that allows you to record -changes to project files over time. It supports both a distributed workflow -as well as the classic centralized workflow.") - (license license:gpl2+))) - (define-public breezy (package (name "breezy") @@ -248,6 +210,9 @@ and protocols. One of the key differences with Bazaar is that Breezy runs on Python 3.3 and later, rather than on Python 2.") (license license:gpl2+))) +(define-public bazaar + (deprecated-package "bazaar" breezy)) + (define git-cross-configure-flags '("ac_cv_fread_reads_directories=yes" "ac_cv_snprintf_returns_bogus=no" diff --git a/guix/build/bzr.scm b/guix/build/bzr.scm index 86ee11391d1..a0f5e15880c 100644 --- a/guix/build/bzr.scm +++ b/guix/build/bzr.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2018 Maxim Cournoyer +;;; Copyright © 2018, 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -28,7 +28,7 @@ ;;; Code: (define* (bzr-fetch url revision directory - #:key (bzr-command "bzr")) + #:key (bzr-command "brz")) "Fetch REVISION from URL into DIRECTORY. REVISION must be a valid Bazaar revision identifier. Return #t on success, else throw an exception." ;; Do not attempt to write .bzr.log to $HOME, which doesn't exist. @@ -37,8 +37,6 @@ revision identifier. Return #t on success, else throw an exception." (invoke bzr-command "-Ossl.cert_reqs=none" "checkout" "--lightweight" "-r" revision url directory) (with-directory-excursion directory - (begin - (delete-file-recursively ".bzr") - #t))) + (delete-file-recursively ".bzr"))) ;;; bzr.scm ends here diff --git a/guix/bzr-download.scm b/guix/bzr-download.scm index 010e0decff8..d97f84838e1 100644 --- a/guix/bzr-download.scm +++ b/guix/bzr-download.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017 Maxim Cournoyer +;;; Copyright © 2017, 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -48,7 +48,7 @@ (define (bzr-package) "Return the default Bazaar package." (let ((distro (resolve-interface '(gnu packages version-control)))) - (module-ref distro 'bazaar))) + (module-ref distro 'breezy))) (define* (bzr-fetch ref hash-algo hash #:optional name @@ -64,7 +64,7 @@ HASH-ALGO (a symbol). Use NAME as the file name, or a generic name if #f." (use-modules (guix build bzr)) (bzr-fetch (getenv "bzr url") (getenv "bzr reference") #$output - #:bzr-command (string-append #+bzr "/bin/bzr"))))) + #:bzr-command (string-append #+bzr "/bin/brz"))))) (mlet %store-monad ((guile (package->derivation guile system))) (gexp->derivation (or name "bzr-branch") build From a3605b59c6b0cb4595f5f05e9167518ba2a6923c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 15:39:44 -0400 Subject: [PATCH 1294/1394] gnu: icecat: Remove obsolete Python 2 dependencies. * gnu/packages/gnuzilla.scm (icecat)[native-inputs]: Remove python-2 and python2-pysqlite. Replace python by python-wrapper. --- gnu/packages/gnuzilla.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 4728b5e3475..006191c9bd2 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -17,7 +17,7 @@ ;;; Copyright © 2020 Marius Bakke ;;; Copyright © 2021 Brice Waegeneire ;;; Copyright © 2021 Maxime Devos -;;; Copyright © 2021 Maxim Cournoyer +;;; Copyright © 2021, 2022 Maxim Cournoyer ;;; Copyright © 2021 Baptiste Strazzul ;;; ;;; This file is part of GNU Guix. @@ -974,9 +974,7 @@ in C/C++.") ("clang" ,clang-11) ("perl" ,perl) ("node" ,node) - ("python" ,python) - ("python-2" ,python-2) - ("python2-pysqlite" ,python2-pysqlite) + ("python" ,python-wrapper) ("yasm" ,yasm) ("nasm" ,nasm) ; XXX FIXME: only needed on x86_64 and i686 ("pkg-config" ,pkg-config) From 7aa0e310fa01e5a11624bd5cc8418f6e0fe32a67 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 16:13:10 -0400 Subject: [PATCH 1295/1394] gnu: icecat: Modernize package definition. * gnu/packages/gnuzilla.scm (icecat)[inputs, native-inputs]: Use new style. [configure-flags, phases]: Use gexps. --- gnu/packages/gnuzilla.scm | 748 +++++++++++++++++++------------------- 1 file changed, 367 insertions(+), 381 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 006191c9bd2..8f1e8fe6475 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -904,160 +904,156 @@ in C/C++.") (source icecat-source) (build-system gnu-build-system) (inputs - `(("alsa-lib" ,alsa-lib) - ("bzip2" ,bzip2) - ("cups" ,cups) - ("dbus-glib" ,dbus-glib) - ("gdk-pixbuf" ,gdk-pixbuf) - ("glib" ,glib) - ("gtk+" ,gtk+) - ("gtk+-2" ,gtk+-2) - ;; UNBUNDLE-ME! ("graphite2" ,graphite2) - ("cairo" ,cairo) - ("pango" ,pango) - ("freetype" ,freetype) - ("font-dejavu" ,font-dejavu) - ;; UNBUNDLE-ME! ("harfbuzz" ,harfbuzz) - ("libcanberra" ,libcanberra) - ("libgnome" ,libgnome) - ("libjpeg-turbo" ,libjpeg-turbo) - ("libpng-apng" ,libpng-apng) - ;; UNBUNDLE-ME! ("libogg" ,libogg) - ;; UNBUNDLE-ME! ("libtheora" ,libtheora) ; wants theora-1.2, not yet released - ;; UNBUNDLE-ME! ("libvorbis" ,libvorbis) - ("libxft" ,libxft) - ("libevent" ,libevent) - ("libxinerama" ,libxinerama) - ("libxscrnsaver" ,libxscrnsaver) - ("libxcomposite" ,libxcomposite) - ("libxt" ,libxt) - ("libffi" ,libffi) - ("ffmpeg" ,ffmpeg) - ("libvpx" ,libvpx) - ("icu4c" ,icu4c) - ("pixman" ,pixman) - ("pulseaudio" ,pulseaudio) - ("mesa" ,mesa) - ("pciutils" ,pciutils) - ("mit-krb5" ,mit-krb5) - ("hunspell" ,hunspell) - ("libnotify" ,libnotify) - ;; See - ;; and related comments in the 'remove-bundled-libraries' phase. - ;; UNBUNDLE-ME! ("nspr" ,nspr) - ;; UNBUNDLE-ME! ("nss" ,nss) - ("shared-mime-info" ,shared-mime-info) - ("sqlite" ,sqlite) - ("eudev" ,eudev) - ("unzip" ,unzip) - ("zip" ,zip) - ("zlib" ,zlib))) + (list alsa-lib + bzip2 + cups + dbus-glib + gdk-pixbuf + glib + gtk+ + gtk+-2 + ;; UNBUNDLE-ME! graphite2 + cairo + pango + freetype + font-dejavu + ;; UNBUNDLE-ME! harfbuzz + libcanberra + libgnome + libjpeg-turbo + libpng-apng + ;; UNBUNDLE-ME! libogg + ;; UNBUNDLE-ME! libtheora ; wants theora-1.2, not yet released + ;; UNBUNDLE-ME! libvorbis + libxft + libevent + libxinerama + libxscrnsaver + libxcomposite + libxt + libffi + ffmpeg + libvpx + icu4c + pixman + pulseaudio + mesa + pciutils + mit-krb5 + hunspell + libnotify + ;; See + ;; and related comments in the 'remove-bundled-libraries' phase. + ;; UNBUNDLE-ME! nspr + ;; UNBUNDLE-ME! nss + shared-mime-info + sqlite + eudev + unzip + zip + zlib)) (native-inputs ;; The following patches are specific to the Guix packaging of IceCat, ;; and therefore we prefer to leave them out of 'source', which should be ;; a tarball suitable for compilation on any system that IceCat supports. ;; (Bug fixes and security fixes, however, should go in 'source'). - `(;; XXX TODO: Adapt these patches to IceCat 91. - ;; ("icecat-avoid-bundled-libraries.patch" - ;; ,(search-patch "icecat-avoid-bundled-libraries.patch")) - ;; ("icecat-use-system-graphite2+harfbuzz.patch" - ;; ,(search-patch "icecat-use-system-graphite2+harfbuzz.patch")) - ;; ("icecat-use-system-media-libs.patch" - ;; ,(search-patch "icecat-use-system-media-libs.patch")) - - ("patch" ,(canonical-package patch)) - - ("rust" ,rust) - ("cargo" ,rust "cargo") - ("rust-cbindgen" ,rust-cbindgen-0.19) - ("llvm" ,llvm-11) - ("clang" ,clang-11) - ("perl" ,perl) - ("node" ,node) - ("python" ,python-wrapper) - ("yasm" ,yasm) - ("nasm" ,nasm) ; XXX FIXME: only needed on x86_64 and i686 - ("pkg-config" ,pkg-config) - ("m4" ,m4) - ("which" ,which))) + (list + ;; XXX TODO: Adapt these patches to IceCat 91. + ;; ("icecat-avoid-bundled-libraries.patch" + ;; ,(search-patch "icecat-avoid-bundled-libraries.patch")) + ;; ("icecat-use-system-graphite2+harfbuzz.patch" + ;; ,(search-patch "icecat-use-system-graphite2+harfbuzz.patch")) + ;; ("icecat-use-system-media-libs.patch" + ;; ,(search-patch "icecat-use-system-media-libs.patch")) + rust + `(,rust "cargo") + rust-cbindgen-0.19 + llvm-11 + clang-11 + perl + node + python-wrapper + yasm + nasm ; XXX FIXME: only needed on x86_64 and i686 + pkg-config + m4 + which)) (arguments - `(#:tests? #f ;not worth the cost + (list + #:tests? #f ;not worth the cost - ;; Some dynamic lib was determined at runtime, so rpath check may fail. - #:validate-runpath? #f + ;; Some dynamic lib was determined at runtime, so rpath check may fail. + #:validate-runpath? #f - #:configure-flags `("--enable-application=browser" - "--with-distribution-id=org.gnu" - "--enable-geckodriver" - ;; Do not require addons in the global app or - ;; system directories to be signed by Mozilla. - "--with-unsigned-addon-scopes=app,system" - "--allow-addon-sideload" + #:configure-flags + #~(list + "--enable-application=browser" + "--with-distribution-id=org.gnu" + "--enable-geckodriver" + ;; Do not require addons in the global app or system directories to + ;; be signed by Mozilla. + "--with-unsigned-addon-scopes=app,system" + "--allow-addon-sideload" - "--enable-pulseaudio" + "--enable-pulseaudio" - "--disable-tests" - "--disable-updater" - "--disable-crashreporter" - "--disable-eme" + "--disable-tests" + "--disable-updater" + "--disable-crashreporter" + "--disable-eme" - ;; Building with debugging symbols takes ~5GiB, so - ;; disable it. - "--disable-debug" - "--disable-debug-symbols" + ;; Building with debugging symbols takes ~5GiB, so disable it. + "--disable-debug" + "--disable-debug-symbols" - "--enable-rust-simd" - "--enable-release" - "--enable-optimize" - "--enable-strip" - "--disable-elf-hack" + "--enable-rust-simd" + "--enable-release" + "--enable-optimize" + "--enable-strip" + "--disable-elf-hack" - ;; Clang is needed to build Stylo, Mozilla's new - ;; CSS engine. We must specify the clang paths - ;; manually, because otherwise the Mozilla build - ;; system looks in the directories returned by - ;; llvm-config --bindir and llvm-config --libdir, - ;; which return paths in the llvm package where - ;; clang is not found. - ,(string-append "--with-clang-path=" - (assoc-ref %build-inputs "clang") - "/bin/clang") - ,(string-append "--with-libclang-path=" - (assoc-ref %build-inputs "clang") - "/lib") + ;; Clang is needed to build Stylo, Mozilla's new CSS engine. We must + ;; specify the clang paths manually, because otherwise the Mozilla + ;; build system looks in the directories returned by llvm-config + ;; --bindir and llvm-config --libdir, which return paths in the llvm + ;; package where clang is not found. + (string-append "--with-clang-path=" + (search-input-file %build-inputs "bin/clang")) + (string-append "--with-libclang-path=" + (dirname (search-input-file %build-inputs + "lib/libclang.so"))) - ;; Hack to work around missing - ;; "unofficial" branding in icecat. - "--enable-official-branding" + ;; Hack to work around missing "unofficial" branding in icecat. + "--enable-official-branding" - ;; Avoid bundled libraries. - "--with-system-jpeg" ; must be libjpeg-turbo - "--with-system-png" ; must be libpng-apng - "--with-system-zlib" - ;; UNBUNDLE-ME! "--with-system-bz2" - ;; UNBUNDLE-ME! "--with-system-libevent" - ;; UNBUNDLE-ME! "--with-system-ogg" - ;; UNBUNDLE-ME! "--with-system-vorbis" - ;; UNBUNDLE-ME! "--with-system-theora" ; wants theora-1.2, not yet released - ;; UNBUNDLE-ME! "--with-system-libvpx" - "--with-system-icu" + ;; Avoid bundled libraries. + "--with-system-jpeg" ;must be libjpeg-turbo + "--with-system-png" ;must be libpng-apng + "--with-system-zlib" + ;; UNBUNDLE-ME! "--with-system-bz2" + ;; UNBUNDLE-ME! "--with-system-libevent" + ;; UNBUNDLE-ME! "--with-system-ogg" + ;; UNBUNDLE-ME! "--with-system-vorbis" + ;; UNBUNDLE-ME! "--with-system-theora" ; wants theora-1.2, not yet released + ;; UNBUNDLE-ME! "--with-system-libvpx" + "--with-system-icu" - ;; See - ;; and related comments in the - ;; 'remove-bundled-libraries' phase below. - ;; UNBUNDLE-ME! "--with-system-nspr" - ;; UNBUNDLE-ME! "--with-system-nss" + ;; See + ;; and related comments in the + ;; 'remove-bundled-libraries' phase below. + ;; UNBUNDLE-ME! "--with-system-nspr" + ;; UNBUNDLE-ME! "--with-system-nss" - ;; UNBUNDLE-ME! "--with-system-harfbuzz" - ;; UNBUNDLE-ME! "--with-system-graphite2" - "--enable-system-pixman" - "--enable-system-ffi" - ;; UNBUNDLE-ME! "--enable-system-sqlite" - ) + ;; UNBUNDLE-ME! "--with-system-harfbuzz" + ;; UNBUNDLE-ME! "--with-system-graphite2" + "--enable-system-pixman" + "--enable-system-ffi" + ;; UNBUNDLE-ME! "--enable-system-sqlite" + ) - #:imported-modules ,%cargo-utils-modules ;for `generate-all-checksums' + #:imported-modules %cargo-utils-modules ;for `generate-all-checksums' - #:modules ((ice-9 ftw) + #:modules `((ice-9 ftw) (ice-9 match) (srfi srfi-1) (srfi srfi-26) @@ -1066,257 +1062,247 @@ in C/C++.") (guix elf) (guix build gremlin) ,@%gnu-build-system-modules) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'apply-guix-specific-patches - (lambda* (#:key inputs native-inputs #:allow-other-keys) - (let ((patch (string-append (assoc-ref (or native-inputs inputs) - "patch") - "/bin/patch"))) - (for-each (match-lambda - ((label . file) - (when (and (string-prefix? "icecat-" label) - (string-suffix? ".patch" label)) - (format #t "applying '~a'...~%" file) - (invoke patch "--force" "--no-backup-if-mismatch" - "-p1" "--input" file)))) - (or native-inputs inputs))))) - (add-after 'apply-guix-specific-patches 'remove-bundled-libraries - (lambda _ - ;; Remove bundled libraries that we don't use, since they may - ;; contain unpatched security flaws, they waste disk space and - ;; memory, and may cause confusion. - (for-each (lambda (file) - (format #t "deleting '~a'...~%" file) - (delete-file-recursively file)) - '(;; FIXME: Removing the bundled icu breaks configure. - ;; * The bundled icu headers are used in some places. - ;; * The version number is taken from the bundled copy. - ;;"intl/icu" - ;; - ;; FIXME: A script from the bundled nspr is used. - ;;"nsprpub" - ;; - ;; FIXME: With the update to IceCat 60, using system NSS - ;; broke certificate validation. See - ;; . For now, we use - ;; the bundled NSPR and NSS. TODO: Investigate, - ;; and try to unbundle these libraries again. - ;; UNBUNDLE-ME! "security/nss" - ;; - ;; TODO: Use more system media libraries. See: - ;; - ;; * libtheora: esr60 wants v1.2, not yet released. - ;; * soundtouch: avoiding the bundled library would - ;; result in some loss of functionality. There's - ;; also an issue with exception handling - ;; configuration. It seems that this is needed in - ;; some moz.build: - ;; DEFINES['ST_NO_EXCEPTION_HANDLING'] = 1 - ;; * libopus - ;; * speex - ;; - "modules/freetype2" - ;; "media/libjpeg" ; needed for now, because media/libjpeg/moz.build is referenced from config/external/moz.build - ;; UNBUNDLE-ME! "modules/zlib" - ;; UNBUNDLE-ME! "ipc/chromium/src/third_party/libevent" - ;; UNBUNDLE-ME! "media/libvpx" - ;; UNBUNDLE-ME! "media/libogg" - ;; UNBUNDLE-ME! "media/libvorbis" - ;; UNBUNDLE-ME! "media/libtheora" ; wants theora-1.2, not yet released - ;; UNBUNDLE-ME! "media/libtremor" - ;; UNBUNDLE-ME! "gfx/harfbuzz" - ;; UNBUNDLE-ME! "gfx/graphite2" - "js/src/ctypes/libffi" - ;; UNBUNDLE-ME! "db/sqlite3" - )))) - (add-after 'remove-bundled-libraries 'fix-ffmpeg-runtime-linker - (lambda* (#:key inputs #:allow-other-keys) - (let* ((ffmpeg (assoc-ref inputs "ffmpeg")) - (libavcodec (string-append ffmpeg "/lib/libavcodec.so"))) - ;; Arrange to load libavcodec.so by its absolute file name. - (substitute* "dom/media/platforms/ffmpeg/FFmpegRuntimeLinker.cpp" - (("libavcodec\\.so") - libavcodec))))) - (add-after 'fix-ffmpeg-runtime-linker 'build-sandbox-whitelist - (lambda* (#:key inputs #:allow-other-keys) - (define (runpath-of lib) - (call-with-input-file lib - (compose elf-dynamic-info-runpath - elf-dynamic-info - parse-elf - get-bytevector-all))) - (define (runpaths-of-input label) - (let* ((dir (string-append (assoc-ref inputs label) "/lib")) - (libs (find-files dir "\\.so$"))) - (append-map runpath-of libs))) - ;; Populate the sandbox read-path whitelist as needed by ffmpeg. - (let* ((whitelist - (map (cut string-append <> "/") - (delete-duplicates - `(,(string-append (assoc-ref inputs "shared-mime-info") - "/share/mime") - ,(string-append (assoc-ref inputs "font-dejavu") - "/share/fonts") - "/run/current-system/profile/share/fonts" - ,@(append-map runpaths-of-input - '("mesa" "ffmpeg")))))) - (whitelist-string (string-join whitelist ",")) - (port (open-file "browser/app/profile/icecat.js" "a"))) - (format #t "setting 'security.sandbox.content.read_path_whitelist' to '~a'~%" - whitelist-string) - (format port "~%pref(\"security.sandbox.content.read_path_whitelist\", ~S);~%" - whitelist-string) - (close-output-port port)))) - (add-after 'patch-source-shebangs 'patch-cargo-checksums - (lambda _ - (use-modules (guix build cargo-utils)) - (let ((null-hash "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855")) - (for-each (lambda (file) - (format #t "patching checksums in ~a~%" file) - (substitute* file - (("^checksum = \".*\"") - (string-append "checksum = \"" null-hash "\"")))) - (find-files "." "Cargo.lock$")) - (for-each generate-all-checksums - '("services" - "js" - "third_party/rust" - "dom/media" - "dom/webauthn" - "toolkit" - "gfx" - "storage" - "modules" - "xpcom/rust" - "media" - "mozglue/static/rust" - "netwerk" - "remote" - "intl" - "servo" - "security/manager/ssl" - "build"))))) - (delete 'bootstrap) - (replace 'configure - ;; configure does not work followed by both "SHELL=..." and - ;; "CONFIG_SHELL=..."; set environment variables instead - (lambda* (#:key outputs configure-flags #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bash (which "bash")) - (abs-srcdir (getcwd)) - (flags `(,(string-append "--prefix=" out) - ,(string-append "--with-l10n-base=" - abs-srcdir "/l10n") - ,@configure-flags))) - (setenv "SHELL" bash) - (setenv "CONFIG_SHELL" bash) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'apply-guix-specific-patches + (lambda* (#:key inputs native-inputs #:allow-other-keys) + (let ((patch (search-input-file inputs "bin/patch"))) + (for-each (match-lambda + ((label . file) + (when (and (string-prefix? "icecat-" label) + (string-suffix? ".patch" label)) + (format #t "applying '~a'...~%" file) + (invoke patch "--force" "--no-backup-if-mismatch" + "-p1" "--input" file)))) + (or native-inputs inputs))))) + (add-after 'apply-guix-specific-patches 'remove-bundled-libraries + (lambda _ + ;; Remove bundled libraries that we don't use, since they may + ;; contain unpatched security flaws, they waste disk space and + ;; memory, and may cause confusion. + (for-each (lambda (file) + (format #t "deleting '~a'...~%" file) + (delete-file-recursively file)) + '( ;; FIXME: Removing the bundled icu breaks configure. + ;; * The bundled icu headers are used in some places. + ;; * The version number is taken from the bundled copy. + ;;"intl/icu" + ;; + ;; FIXME: A script from the bundled nspr is used. + ;;"nsprpub" + ;; + ;; FIXME: With the update to IceCat 60, using system NSS + ;; broke certificate validation. See + ;; . For now, we use + ;; the bundled NSPR and NSS. TODO: Investigate, + ;; and try to unbundle these libraries again. + ;; UNBUNDLE-ME! "security/nss" + ;; + ;; TODO: Use more system media libraries. See: + ;; + ;; * libtheora: esr60 wants v1.2, not yet released. + ;; * soundtouch: avoiding the bundled library would + ;; result in some loss of functionality. There's + ;; also an issue with exception handling + ;; configuration. It seems that this is needed in + ;; some moz.build: + ;; DEFINES['ST_NO_EXCEPTION_HANDLING'] = 1 + ;; * libopus + ;; * speex + ;; + "modules/freetype2" + ;; "media/libjpeg" ; needed for now, because media/libjpeg/moz.build is referenced from config/external/moz.build + ;; UNBUNDLE-ME! "modules/zlib" + ;; UNBUNDLE-ME! "ipc/chromium/src/third_party/libevent" + ;; UNBUNDLE-ME! "media/libvpx" + ;; UNBUNDLE-ME! "media/libogg" + ;; UNBUNDLE-ME! "media/libvorbis" + ;; UNBUNDLE-ME! "media/libtheora" ; wants theora-1.2, not yet released + ;; UNBUNDLE-ME! "media/libtremor" + ;; UNBUNDLE-ME! "gfx/harfbuzz" + ;; UNBUNDLE-ME! "gfx/graphite2" + "js/src/ctypes/libffi" + ;; UNBUNDLE-ME! "db/sqlite3" + )))) + (add-after 'remove-bundled-libraries 'fix-ffmpeg-runtime-linker + (lambda* (#:key inputs #:allow-other-keys) + ;; Arrange to load libavcodec.so by its absolute file name. + (substitute* "dom/media/platforms/ffmpeg/FFmpegRuntimeLinker.cpp" + (("libavcodec\\.so") + (search-input-file inputs "lib/libavcodec.so"))))) + (add-after 'fix-ffmpeg-runtime-linker 'build-sandbox-whitelist + (lambda* (#:key inputs #:allow-other-keys) + (define (runpath-of lib) + (call-with-input-file lib + (compose elf-dynamic-info-runpath + elf-dynamic-info + parse-elf + get-bytevector-all))) + (define (runpaths-of-input label) + (let* ((dir (string-append (assoc-ref inputs label) "/lib")) + (libs (find-files dir "\\.so$"))) + (append-map runpath-of libs))) + ;; Populate the sandbox read-path whitelist as needed by ffmpeg. + (let* ((whitelist + (map (cut string-append <> "/") + (delete-duplicates + `(,(string-append (assoc-ref inputs "shared-mime-info") + "/share/mime") + ,(string-append (assoc-ref inputs "font-dejavu") + "/share/fonts") + "/run/current-system/profile/share/fonts" + ,@(append-map runpaths-of-input + '("mesa" "ffmpeg")))))) + (whitelist-string (string-join whitelist ",")) + (port (open-file "browser/app/profile/icecat.js" "a"))) + (format #t "setting 'security.sandbox.content.read_path_whitelist' to '~a'~%" + whitelist-string) + (format port "~%pref(\"security.sandbox.content.read_path_whitelist\", ~S);~%" + whitelist-string) + (close-output-port port)))) + (add-after 'patch-source-shebangs 'patch-cargo-checksums + (lambda _ + (use-modules (guix build cargo-utils)) + (let ((null-hash "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855")) + (for-each (lambda (file) + (format #t "patching checksums in ~a~%" file) + (substitute* file + (("^checksum = \".*\"") + (string-append "checksum = \"" null-hash "\"")))) + (find-files "." "Cargo.lock$")) + (for-each generate-all-checksums + '("services" + "js" + "third_party/rust" + "dom/media" + "dom/webauthn" + "toolkit" + "gfx" + "storage" + "modules" + "xpcom/rust" + "media" + "mozglue/static/rust" + "netwerk" + "remote" + "intl" + "servo" + "security/manager/ssl" + "build"))))) + (delete 'bootstrap) + (replace 'configure + ;; configure does not work followed by both "SHELL=..." and + ;; "CONFIG_SHELL=..."; set environment variables instead + (lambda* (#:key outputs configure-flags #:allow-other-keys) + (let* ((bash (which "bash")) + (abs-srcdir (getcwd)) + (flags `(,(string-append "--prefix=" #$output) + ,(string-append "--with-l10n-base=" + abs-srcdir "/l10n") + ,@configure-flags))) + (setenv "SHELL" bash) + (setenv "CONFIG_SHELL" bash) - (setenv "AR" "llvm-ar") - (setenv "NM" "llvm-nm") - (setenv "CC" "clang") - (setenv "CXX" "clang++") - (setenv "LDFLAGS" (string-append "-Wl,-rpath=" - (assoc-ref outputs "out") - "/lib/icecat")) + (setenv "AR" "llvm-ar") + (setenv "NM" "llvm-nm") + (setenv "CC" "clang") + (setenv "CXX" "clang++") + (setenv "LDFLAGS" (string-append "-Wl,-rpath=" + #$output "/lib/icecat")) - (setenv "MACH_USE_SYSTEM_PYTHON" "1") - (setenv "MOZ_NOSPAM" "1") - (setenv "MOZ_BUILD_DATE" ,%icecat-build-id) ; avoid timestamp + (setenv "MACH_USE_SYSTEM_PYTHON" "1") + (setenv "MOZ_NOSPAM" "1") + (setenv "MOZ_BUILD_DATE" #$%icecat-build-id) ; avoid timestamp - (format #t "build directory: ~s~%" (getcwd)) - (format #t "configure flags: ~s~%" flags) + (format #t "build directory: ~s~%" (getcwd)) + (format #t "configure flags: ~s~%" flags) - (call-with-output-file "mozconfig" - (lambda (out) - (for-each (lambda (flag) - (format out "ac_add_options ~a\n" flag)) - flags))) + (call-with-output-file "mozconfig" + (lambda (port) + (for-each (lambda (flag) + (format port "ac_add_options ~a\n" flag)) + flags))) - (invoke "./mach" "configure")))) - (replace 'build - (lambda* (#:key (make-flags '()) (parallel-build? #t) - #:allow-other-keys) - (apply invoke "./mach" "build" - ;; mach will use parallel build if possible by default - `(,@(if parallel-build? - '() - '("-j1")) - ,@make-flags)))) - (add-after 'build 'neutralise-store-references - (lambda _ - ;; Mangle the store references to compilers & other build tools in - ;; about:buildconfig, reducing IceCat's closure by 1 GiB on x86-64. - (let* ((obj-dir (match (scandir "." (cut string-prefix? "obj-" <>)) - ((dir) dir))) - (file (string-append - obj-dir - "/dist/bin/chrome/toolkit/content/global/buildconfig.html"))) - (substitute* file - (("[0-9a-df-np-sv-z]{32}" hash) - (string-append (string-take hash 8) - "" - (string-drop hash 8))))))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (invoke "./mach" "install") - ;; The geckodriver binary is not installed by the above, for some - ;; reason. Use 'find-files' to avoid having to deal with the - ;; system/architecture-specific file name. - (install-file (first (find-files "." "geckodriver")) - (string-append (assoc-ref outputs "out") "/bin")))) - (add-after 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib")) - (gtk (assoc-ref inputs "gtk+")) - (gtk-share (string-append gtk "/share")) - (ld-libs (map (lambda (label) - (string-append (assoc-ref inputs label) - "/lib")) - '("libpng-apng" - "libxscrnsaver" - "mesa" - "pciutils" - "mit-krb5" - "eudev" - "pulseaudio" - ;; For the integration of native notifications - "libnotify")))) - (wrap-program (car (find-files lib "^icecat$")) - `("XDG_DATA_DIRS" prefix (,gtk-share)) - ;; The following line is commented out because the icecat - ;; package on guix has been observed to be unstable when - ;; using wayland, and the bundled extensions stop working. - ;; `("MOZ_ENABLE_WAYLAND" = ("1")) - `("LD_LIBRARY_PATH" prefix ,ld-libs))))) - (add-after 'wrap-program 'install-desktop-entry - (lambda* (#:key outputs #:allow-other-keys) - ;; Install the '.desktop' file. - (let* ((desktop-file "taskcluster/docker/icecat-snap/icecat.desktop") - (out (assoc-ref outputs "out")) - (applications (string-append out "/share/applications"))) - (substitute* desktop-file - (("^Exec=icecat") (string-append "Exec=" out "/bin/icecat")) - (("IceCat") "GNU IceCat") - (("Icon=.*") "Icon=icecat\n") - (("NewWindow") "new-window") - (("NewPrivateWindow") "new-private-window")) - (install-file desktop-file applications)))) - (add-after 'install-desktop-entry 'install-icons - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (with-directory-excursion "browser/branding/official" - (for-each - (lambda (file) - (let* ((size (string-filter char-numeric? file)) - (icons (string-append out "/share/icons/hicolor/" - size "x" size "/apps"))) - (mkdir-p icons) - (copy-file file (string-append icons "/icecat.png")))) - '("default16.png" "default22.png" "default24.png" - "default32.png" "default48.png" "content/icon64.png" - "mozicon128.png" "default256.png"))))))))) + (invoke "./mach" "configure")))) + (replace 'build + (lambda* (#:key (make-flags '()) (parallel-build? #t) + #:allow-other-keys) + (apply invoke "./mach" "build" + ;; mach will use parallel build if possible by default + `(,@(if parallel-build? + '() + '("-j1")) + ,@make-flags)))) + (add-after 'build 'neutralise-store-references + (lambda _ + ;; Mangle the store references to compilers & other build tools in + ;; about:buildconfig, reducing IceCat's closure by 1 GiB on x86-64. + (let* ((obj-dir (match (scandir "." (cut string-prefix? "obj-" <>)) + ((dir) dir))) + (file (string-append + obj-dir + "/dist/bin/chrome/toolkit/content/global/buildconfig.html"))) + (substitute* file + (("[0-9a-df-np-sv-z]{32}" hash) + (string-append (string-take hash 8) + "" + (string-drop hash 8))))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (invoke "./mach" "install") + ;; The geckodriver binary is not installed by the above, for some + ;; reason. Use 'find-files' to avoid having to deal with the + ;; system/architecture-specific file name. + (install-file (first (find-files "." "geckodriver")) + (string-append #$output "/bin")))) + (add-after 'install 'wrap-program + (lambda* (#:key inputs #:allow-other-keys) + (let* ((lib (string-append #$output "/lib")) + (gtk #$(this-package-input "gtk+")) + (gtk-share (string-append gtk "/share")) + (ld-libs '#$(map (lambda (label) + (file-append (this-package-input label) "/lib")) + '("libpng-apng" + "libxscrnsaver" + "mesa" + "pciutils" + "mit-krb5" + "eudev" + "pulseaudio" + ;; For the integration of native notifications + "libnotify")))) + (wrap-program (car (find-files lib "^icecat$")) + `("XDG_DATA_DIRS" prefix (,gtk-share)) + ;; The following line is commented out because the icecat + ;; package on guix has been observed to be unstable when + ;; using wayland, and the bundled extensions stop working. + ;; `("MOZ_ENABLE_WAYLAND" = ("1")) + `("LD_LIBRARY_PATH" prefix ,ld-libs))))) + (add-after 'wrap-program 'install-desktop-entry + (lambda _ + ;; Install the '.desktop' file. + (let* ((desktop-file "taskcluster/docker/icecat-snap/icecat.desktop") + (applications (string-append #$output "/share/applications"))) + (substitute* desktop-file + (("^Exec=icecat") (string-append "Exec=" #$output "/bin/icecat")) + (("IceCat") "GNU IceCat") + (("Icon=.*") "Icon=icecat\n") + (("NewWindow") "new-window") + (("NewPrivateWindow") "new-private-window")) + (install-file desktop-file applications)))) + (add-after 'install-desktop-entry 'install-icons + (lambda _ + (with-directory-excursion "browser/branding/official" + (for-each + (lambda (file) + (let* ((size (string-filter char-numeric? file)) + (icons (string-append #$output "/share/icons/hicolor/" + size "x" size "/apps"))) + (mkdir-p icons) + (copy-file file (string-append icons "/icecat.png")))) + '("default16.png" "default22.png" "default24.png" + "default32.png" "default48.png" "content/icon64.png" + "mozicon128.png" "default256.png")))))))) (home-page "https://www.gnu.org/software/gnuzilla/") (synopsis "Entirely free browser derived from Mozilla Firefox") (description From 4d7bb37981d5d1e639cbd7837cddc76c45271de2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 16:40:49 -0400 Subject: [PATCH 1296/1394] gnu: Remove fraggenescan. * gnu/packages/bioinformatics.scm (fraggenescan): Delete variable. --- gnu/packages/bioinformatics.scm | 90 --------------------------------- 1 file changed, 90 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9b302475941..3223d6eea8a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3660,96 +3660,6 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.") (license license:bsd-3))) -(define-public fraggenescan - (package - (name "fraggenescan") - (version "1.30") - (source - (origin - (method url-fetch) - (uri - (string-append "mirror://sourceforge/fraggenescan/" - "FragGeneScan" version ".tar.gz")) - (sha256 - (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj")))) - (build-system gnu-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (delete 'configure) - (add-before 'build 'patch-paths - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (string-append (assoc-ref outputs "out"))) - (share (string-append out "/share/fraggenescan/"))) - (substitute* "run_FragGeneScan.pl" - (("system\\(\"rm") - (string-append "system(\"" (which "rm"))) - (("system\\(\"mv") - (string-append "system(\"" (which "mv"))) - (("\\\"awk") (string-append "\"" (which "awk"))) - ;; This script and other programs expect the training files - ;; to be in the non-standard location bin/train/XXX. Change - ;; this to be share/fraggenescan/train/XXX instead. - (("^\\$train.file = \\$dir.*") - (string-append "$train_file = \"" - share - "train/\".$FGS_train_file;"))) - (substitute* "run_hmm.c" - (("^ strcat\\(train_dir, \\\"train/\\\"\\);") - (string-append " strcpy(train_dir, \"" share "/train/\");")))) - #t)) - (replace 'build - (lambda _ - (invoke "make" "clean") - (invoke "make" "fgs") - #t)) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (string-append (assoc-ref outputs "out"))) - (bin (string-append out "/bin/")) - (share (string-append out "/share/fraggenescan/train"))) - (install-file "run_FragGeneScan.pl" bin) - (install-file "FragGeneScan" bin) - (copy-recursively "train" share)) - #t)) - (delete 'check) - (add-after 'install 'post-install-check - ;; In lieu of 'make check', run one of the examples and check the - ;; output files gets created. - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (string-append (assoc-ref outputs "out"))) - (bin (string-append out "/bin/")) - (frag (string-append bin "run_FragGeneScan.pl"))) - ;; Test complete genome. - (invoke frag - "-genome=./example/NC_000913.fna" - "-out=./test2" - "-complete=1" - "-train=complete") - (unless (and (file-exists? "test2.faa") - (file-exists? "test2.ffn") - (file-exists? "test2.gff") - (file-exists? "test2.out")) - (error "Expected files do not exist.")) - ;; Test incomplete sequences. - (invoke frag - "-genome=./example/NC_000913-fgs.ffn" - "-out=out" - "-complete=0" - "-train=454_30") - #t)))))) - (inputs - `(("perl" ,perl) - ("python" ,python-2))) ;not compatible with python 3. - (home-page "https://sourceforge.net/projects/fraggenescan/") - (synopsis "Finds potentially fragmented genes in short reads") - (description - "FragGeneScan is a program for predicting bacterial and archaeal genes in -short and error-prone DNA sequencing reads. It can also be applied to predict -genes in incomplete assemblies or complete genomes.") - ;; GPL3+ according to private correspondense with the authors. - (license license:gpl3+))) - (define-public fxtract (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) (package From 7cd3a88f27b4d90b18cba1dd1fd1e1b9cc4c8f8e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 17:01:08 -0400 Subject: [PATCH 1297/1394] gnu: Remove python2-pysqlite. * gnu/packages/databases.scm (python2-pysqlite): Delete variable. --- gnu/packages/databases.scm | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 7be109a6bcf..cd5045ed125 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3302,30 +3302,6 @@ local Cassandra clusters. It creates, launches and removes Cassandra clusters on localhost.") (license license:asl2.0))) -(define-public python2-pysqlite - (package - (name "python2-pysqlite") - (version "2.8.3") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pysqlite" version)) - (sha256 - (base32 - "1424gwq9sil2ffmnizk60q36vydkv8rxs6m7xs987kz8cdc37lqp")))) - (build-system python-build-system) - (inputs - (list sqlite)) - (arguments - `(#:python ,python-2 ; incompatible with Python 3 - #:tests? #f)) ; no test target - (home-page "https://github.com/ghaering/pysqlite") - (synopsis "SQLite bindings for Python") - (description - "Pysqlite provides SQLite bindings for Python that comply to the -Database API 2.0T.") - (license license:zlib))) - (define-public python-sqlalchemy (package (name "python-sqlalchemy") From a9e9d9f41ce4c82098c27f14e98d13afb6b53b97 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 20:14:06 -0400 Subject: [PATCH 1298/1394] gnu: lvtk: Update to 1.2.0-0.a73feab. * gnu/packages/audio.scm (lvtk): Update to 1.2.0-0.a73feab. [python]: Delete argument. [configure-flags]: Likewise. [inputs]: Replace gtkmm-2 by gtkmm. [license]: Change license to isc. --- gnu/packages/audio.scm | 56 ++++++++++++++++++++---------------------- 1 file changed, 26 insertions(+), 30 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 844d4c63f39..1ba93afdfb6 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2016–2022 Tobias Geerinckx-Rice ;;; Copyright © 2018, 2020 Oleg Pykhalov ;;; Copyright © 2018 okapi -;;; Copyright © 2018, 2020 Maxim Cournoyer +;;; Copyright © 2018, 2020, 2022 Maxim Cournoyer ;;; Copyright © 2018 Clément Lassieur ;;; Copyright © 2018 Brett Gilio ;;; Copyright © 2018, 2019 Marius Bakke @@ -2801,37 +2801,33 @@ software.") (description "An LV2 port of the mda EPiano VSTi."))) (define-public lvtk - (package - (name "lvtk") - (version "1.2.0") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/lvtk/lvtk") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1b01zvzl70ana6l1kn8fgyr7msnn3c7x61cgw7fdpp50322352p8")))) - (build-system waf-build-system) - (arguments - `(#:tests? #f ; no check target - #:python ,python-2 - #:configure-flags - (list (string-append "--boost-includes=" - (assoc-ref %build-inputs "boost") - "/include")))) - (inputs - (list boost gtkmm-2 lv2)) - (native-inputs - (list pkg-config)) - (home-page "https://github.com/lvtk/lvtk") - (synopsis "C++ libraries for LV2 plugins") - (description - "The LV2 Toolkit (LVTK) contains libraries that wrap the LV2 C API and + ;; Use the latest commit, as the latest release was made in 2014 and depends + ;; on Python 2. + (let ((commit "a73feabe772f9650aa071e6a4df660e549ab7c48") + (revision "0")) + (package + (name "lvtk") + (version (git-version "1.2.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/lvtk/lvtk") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0scmv8b4jlm88d21dqqchjy98wb93zclc9x960h213gdi871vsaj")))) + (build-system waf-build-system) + (arguments (list #:tests? #f)) ;no check target + (inputs (list boost gtkmm lv2)) + (native-inputs (list pkg-config)) + (home-page "https://github.com/lvtk/lvtk") + (synopsis "C++ libraries for LV2 plugins") + (description + "The LV2 Toolkit (LVTK) contains libraries that wrap the LV2 C API and extensions into easy to use C++ classes. It is the successor of lv2-c++-tools.") - (license license:gpl3+))) + (license license:isc)))) (define-public openal (package From 953a5ea59d7b2b436773f318cc687f03c52b3185 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 20:38:53 -0400 Subject: [PATCH 1299/1394] gnu: jalv: Use Python 3. * gnu/packages/audio.scm (jalv)[python]: Delete argument. [inputs]: Use new style. {gtk+-2}: Delete input. {gtk+}: Replace with... {gtk}: ... this. {gtkmm-2}: Replace with... {gtkmm}: ... this. --- gnu/packages/audio.scm | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 1ba93afdfb6..94979a3500f 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2306,17 +2306,15 @@ synchronous execution of all clients, and low latency operation.") "05lycfq0f06zjp5xqvzjz9hx9kmqx72yng1lghh76hv63dw43lcj")))) (build-system waf-build-system) (arguments - `(#:tests? #f ; no check target - #:python ,python-2)) + `(#:tests? #f)) ; no check target (inputs - `(("lv2" ,lv2) - ("lilv" ,lilv) - ("suil" ,suil) - ("gtk2" ,gtk+-2) - ("gtk3" ,gtk+) - ("gtkmm" ,gtkmm-2) - ("qtbase" ,qtbase-5) - ("jack" ,jack-1))) + (list lv2 + lilv + suil + gtk + gtkmm + qtbase-5 + jack-1)) (native-inputs (list pkg-config)) (home-page "https://drobilla.net/software/jalv/") From eb36a550e369d1fb0324af3c501070ae6e3b0462 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 20:45:16 -0400 Subject: [PATCH 1300/1394] gnu: aubio: Use Python 3. * gnu/packages/audio.scm (aubio)[python]: Delete argument. --- gnu/packages/audio.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 94979a3500f..01f809d5e98 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -617,8 +617,7 @@ Filter) modules follow the convention of 1V / Octave.") "--enable-jack" "--enable-sndfile" "--enable-samplerate" - "--enable-avcodec") - #:python ,python-2)) + "--enable-avcodec"))) (inputs (list jack-1 libsndfile libsamplerate fftwf ffmpeg)) ; for libavcodec (native-inputs From 0b85c365a2a569a6a87facc420fe8bee52652994 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 20:47:18 -0400 Subject: [PATCH 1301/1394] gnu: Remove python2-mock. * gnu/packages/check.scm (python2-mock): Delete variable. (python-mock)[properties]: Delete field. --- gnu/packages/check.scm | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 90b83496579..0e2417c4003 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -862,18 +862,8 @@ doctest.") of your system under test with mock objects and make assertions about how they have been used. This library is now part of Python (since Python 3.3), available via the @code{unittest.mock} module.") - (properties `((python2-variant . ,(delay python2-mock)))) (license license:expat))) -(define-public python2-mock - (let ((base (package-with-python2 - (strip-python2-variant python-mock)))) - (package/inherit base - (propagated-inputs - `(("python2-functools32" ,python2-functools32) - ("python2-funcsigs" ,python2-funcsigs) - ,@(package-propagated-inputs base)))))) - ;;; This package is unmaintained (see the note at the top of doc/index.rst). (define-public python-nose (package From fe136c39bf26599814fabcb87407f8f747ff73e4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 20:48:14 -0400 Subject: [PATCH 1302/1394] gnu: Remove python2-hypothesis. * gnu/packages/check.scm (python2-hypothesis): Delete variable. (python-hypothesis)[properties]: Delete field. --- gnu/packages/check.scm | 19 +------------------ 1 file changed, 1 insertion(+), 18 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 0e2417c4003..05192af76a9 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2062,8 +2062,7 @@ much larger range of examples than you would ever want to write by hand. It’s based on the Haskell library, Quickcheck, and is designed to integrate seamlessly into your existing Python unit testing work flow.") (home-page "https://github.com/HypothesisWorks/hypothesis") - (license license:mpl2.0) - (properties `((python2-variant . ,(delay python2-hypothesis)))))) + (license license:mpl2.0))) ;;; TODO: Make the default python-hypothesis in the next rebuild cycle. (define-public python-hypothesis-next @@ -2080,22 +2079,6 @@ seamlessly into your existing Python unit testing work flow.") (modify-inputs (package-propagated-inputs python-hypothesis) (append python-pytest))))) ;to satisfy the sanity-check phase -;; This is the last version of Hypothesis that supports Python 2. -(define-public python2-hypothesis - (let ((hypothesis (package-with-python2 - (strip-python2-variant python-hypothesis)))) - (package (inherit hypothesis) - (version "4.57.1") - (source (origin - (method url-fetch) - (uri (pypi-uri "hypothesis" version)) - (sha256 - (base32 - "183gpxbfcdhdqzlahkji5a71n6lmvgqsbkcb0ihqad51n2j6jhrw")))) - (propagated-inputs - (modify-inputs (package-propagated-inputs hypothesis) - (prepend python2-enum34)))))) - (define-public python-hypothesmith (package (name "python-hypothesmith") From 26d35cb40d32d9717160051851a1308365849656 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 20:49:02 -0400 Subject: [PATCH 1303/1394] gnu: Remove python2-functools32. * gnu/packages/python-xyz.scm (python2-functools32): Delete variable. --- gnu/packages/python-xyz.scm | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2c141b104ce..a157f67e78f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -13975,29 +13975,6 @@ functional subset of Python—Syntactic macro metaprogramming with full access to the Python ecosystem.") (license license:asl2.0))) -(define-public python2-functools32 - (package - (name "python2-functools32") - (version "3.2.3-2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "functools32" version)) - (sha256 - (base32 - "0v8ya0b58x47wp216n1zamimv4iw57cxz3xxhzix52jkw3xks9gn")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:tests? #f)) ; no test target - (home-page "https://github.com/MiCHiLU/python-functools32") - (synopsis - "Backport of the functools module from Python 3.2.3") - (description - "This package is a backport of the @code{functools} module from Python -3.2.3 for use with older versions of Python and PyPy.") - (license license:expat))) - (define-public python-promise (package (name "python-promise") From c71ab167f2ebfa0200c4e9bcc21e34adca26d053 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 20:54:21 -0400 Subject: [PATCH 1304/1394] gnu: Remove python2-funcsigs. * gnu/packages/python-xyz.scm (python2-funcsigs): Delete variable. --- gnu/packages/python-xyz.scm | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a157f67e78f..66ef65fdbd5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3120,27 +3120,6 @@ port forwards using @acronym{UPnP, Universal Plug and Play}.") (home-page "http://miniupnp.free.fr") (license license:bsd-3))) -(define-public python2-funcsigs - (package - (name "python2-funcsigs") - (version "1.0.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "funcsigs" version)) - (sha256 - (base32 - "0l4g5818ffyfmfs1a924811azhjj8ax9xd1cffr1mzd3ycn0zfx7")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) - (native-inputs - (list python2-unittest2)) - (home-page "http://funcsigs.readthedocs.org") - (synopsis "Python function signatures from PEP362") - (description - "Backport of @code{funcsigs} which was introduced in Python 3.3.") - (license license:asl2.0))) - (define-public python-py (package (name "python-py") From 8a60b34e2b65e8f4a35422bd5a34e1695e222a24 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 20:54:46 -0400 Subject: [PATCH 1305/1394] gnu: Remove python2-sortedcontainers. * gnu/packages/python-xyz.scm (python2-sortedcontainers): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 66ef65fdbd5..2ad95ff251b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22362,9 +22362,6 @@ that is accessible to other projects developed in Cython.") pure-Python.") (license license:asl2.0))) -(define-public python2-sortedcontainers - (package-with-python2 python-sortedcontainers)) - (define python-cloudpickle-testpkg (package (name "python-cloudpickle-testpkg") From f07cfa3c9ad1709be05216422672dbdb601c53d7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 20:56:24 -0400 Subject: [PATCH 1306/1394] gnu: Remove python2-unittest2. * gnu/packages/check.scm (python2-unittest2): Delete variable. --- gnu/packages/check.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 05192af76a9..471150c4df1 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -953,9 +953,6 @@ interfaces and processes.") standard library.") (license license:psfl))) -(define-public python2-unittest2 - (package-with-python2 python-unittest2)) - (define-public python-pytest (package (name "python-pytest") From 22e269f566ea31e339b6afe3ce80000e88735a5c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 20:58:25 -0400 Subject: [PATCH 1307/1394] gnu: Remove python2-traceback2. * gnu/packages/python-xyz.scm (python2-traceback2): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2ad95ff251b..fea173baa2c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20060,9 +20060,6 @@ stack traces of Python programs. It exactly mimics the behavior of the Python interpreter when it prints a stack trace.") (license license:psfl))) -(define-public python2-traceback2 - (package-with-python2 python-traceback2)) - (define-public python-ratelimiter (package (name "python-ratelimiter") From ceee9eb31276b5758155377e1f59a78c7030c543 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 20:58:47 -0400 Subject: [PATCH 1308/1394] gnu: Remove python2-linecache2. * gnu/packages/python-xyz.scm (python2-linecache2): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index fea173baa2c..3c4d9f73b7b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20029,9 +20029,6 @@ attempting to optimize internally, using a cache, the common case where many lines are read from a single file.") (license license:psfl))) -(define-public python2-linecache2 - (package-with-python2 python-linecache2)) - (define-public python-traceback2 (package (name "python-traceback2") From 00dff2c76853980a70079fe682d184bb6ef16b03 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 11:55:30 -0400 Subject: [PATCH 1309/1394] gnu: Remove beast. * gnu/packages/music.scm (beast): Delete variable. --- gnu/packages/music.scm | 42 ------------------------------------------ 1 file changed, 42 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 756e1ca45ba..b3989e11f9b 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2507,48 +2507,6 @@ modification devices that brought world-wide fame to the names and products of Laurens Hammond and Don Leslie.") (license license:gpl2+))) -(define-public beast - (package - (name "beast") - (version "0.10.0") - (source (origin - (method url-fetch) - (uri (string-append "https://testbit.eu/pub/dists/beast/beast-" - version ".tar.xz")) - (sha256 - (base32 - "1jzzmfwssklzw8fvvil04n8csc0zm99fnd9p2xa7c0xchg37lvhn")))) - (build-system gnu-build-system) - (arguments - '(#:parallel-build? #f)) ; Race conditions cause build failures - (inputs - `(("rapicorn" ,rapicorn) - ("guile" ,guile-1.8) - ("python" ,python-2) - ("libgnomecanvas" ,libgnomecanvas) - ("libogg" ,libogg) - ("libmad" ,libmad) - ("flac" ,flac) - ("alsa-lib" ,alsa-lib) - ("libvorbis" ,libvorbis) - ("gettext" ,gettext-minimal))) - (native-inputs - `(("pkg-config" ,pkg-config) - ("glib:bin" ,glib "bin") - ("cython" ,python2-cython) - ("perl" ,perl) - ("perl-xml-parser" ,perl-xml-parser))) - (home-page "https://testbit.eu/wiki/Beast_Home") - (synopsis "Music composition and modular synthesis environment") - (description - "Beast is a music composition and modular synthesis application. It -supports a wide range of standards in the field, such as MIDI, various audio -file formats and LADSPA modules. It allows for multitrack editing, real-time -synthesis, 32bit audio rendering, precise timing down to sample granularity, -on-demand and partial loading of wave files, on the fly decoding, stereo -mixing, FFT scopes, MIDI automation and full scriptability in Scheme.") - (license license:gpl3+))) - (define-public bristol (package (name "bristol") From aad73bb58edd03d448cc0c9c4fd209eda7976ec4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 21:40:30 -0400 Subject: [PATCH 1310/1394] gnu: Remove rapicorn. * gnu/packages/graphics.scm (rapicorn): Delete variable. * gnu/packages/patches/rapicorn-isnan.patch: Remove patch. * gnu/local.mk (dist_patch_DATA): De-register it. --- gnu/local.mk | 1 - gnu/packages/graphics.scm | 67 ----------------- gnu/packages/patches/rapicorn-isnan.patch | 87 ----------------------- 3 files changed, 155 deletions(-) delete mode 100644 gnu/packages/patches/rapicorn-isnan.patch diff --git a/gnu/local.mk b/gnu/local.mk index 513216183d9..1286bdddb56 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1747,7 +1747,6 @@ dist_patch_DATA = \ %D%/packages/patches/ragel-char-signedness.patch \ %D%/packages/patches/randomjungle-disable-static-build.patch \ %D%/packages/patches/range-v3-build-with-gcc10.patch \ - %D%/packages/patches/rapicorn-isnan.patch \ %D%/packages/patches/rapidjson-gcc-compat.patch \ %D%/packages/patches/raptor2-heap-overflow.patch \ %D%/packages/patches/ratpoints-sturm_and_rp_private.patch \ diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 4b07061fa1b..64286bf68d4 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -1361,73 +1361,6 @@ realistic reflections, shading, perspective and other effects.") (home-page "http://www.povray.org/") (license license:agpl3+))) -(define-public rapicorn - (package - (name "rapicorn") - (version "16.0.0") - (source (origin - (method url-fetch) - (uri (string-append "https://testbit.eu/pub/dists/rapicorn/" - "rapicorn-" version ".tar.xz")) - (sha256 - (base32 - "1y51yjrpsihas1jy905m9p3r8iiyhq6bwi2690c564i5dnix1f9d")) - (patches (search-patches "rapicorn-isnan.patch")))) - (build-system gnu-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-tests - (lambda _ - ;; Our grep does not support perl regular expressions. - (substitute* "taptool.sh" - (("grep -P") "grep -E")) - ;; Disable path tests because we cannot access /bin or /sbin. - (substitute* "rcore/tests/multitest.cc" - (("TCMP \\(Path::equals \\(\"/bin\"") "//")) - #t)) - (add-before 'check 'pre-check - (lambda _ - ;; The test suite requires a running X server (with DISPLAY - ;; number 99 or higher). - (system "Xvfb :99 &") - (setenv "DISPLAY" ":99") - #t)) - (add-after 'unpack 'replace-fhs-paths - (lambda _ - (substitute* (cons "Makefile.decl" - (find-files "." "^Makefile\\.in$")) - (("/bin/ls") (which "ls")) - (("/usr/bin/env") (which "env"))) - #t))))) - ;; These libraries are listed in the "Required" section of the pkg-config - ;; file. - (propagated-inputs - (list librsvg cairo pango libxml2 python2-enum34)) - (inputs - `(("gdk-pixbuf" ,gdk-pixbuf) - ("libpng" ,libpng-1.2) - ("readline" ,readline) - ("libcroco" ,libcroco) - ("python" ,python-2) - ("cython" ,python2-cython))) - (native-inputs - `(("pandoc" ,pandoc) - ("bison" ,bison) - ("flex" ,flex) - ("doxygen" ,doxygen) - ("graphviz" ,graphviz) - ("intltool" ,intltool) - ("pkg-config" ,pkg-config) - ("xvfb" ,xorg-server-for-tests))) - (home-page "https://rapicorn.testbit.org/") - (synopsis "Toolkit for rapid development of user interfaces") - (description - "Rapicorn is a toolkit for rapid development of user interfaces in C++ -and Python. The user interface is designed in a declarative markup language -and is connected to the programming logic using data bindings and commands.") - (license license:mpl2.0))) - (define-public ctl (package (name "ctl") diff --git a/gnu/packages/patches/rapicorn-isnan.patch b/gnu/packages/patches/rapicorn-isnan.patch deleted file mode 100644 index b0e7819e64b..00000000000 --- a/gnu/packages/patches/rapicorn-isnan.patch +++ /dev/null @@ -1,87 +0,0 @@ -From e0c8341b3e4e13778bcde00d477e461ea8e94306 Mon Sep 17 00:00:00 2001 -From: Stefan Westerfeld -Date: Fri, 22 Apr 2016 18:03:37 +0200 -Subject: [PATCH 031/176] RCORE: compile fixes for KUbuntu 16.04/gcc - 5.3.1-14ubuntu2 - -Rapicorn uses isnan(...) and isinf(...) from cmath.h, however on KUbuntu 16.04 -it should use std::isnan(...) and std::isinf(...) instead. Patch below. - -Acked-by: Tim Janik ---- - rcore/strings.cc | 10 +++++----- - rcore/tests/benchrcore.cc | 4 ++-- - rcore/tests/strings.cc | 4 ++-- - 3 files changed, 9 insertions(+), 9 deletions(-) - -diff --git a/rcore/strings.cc b/rcore/strings.cc -index d5b0216..8b3bc3f 100644 ---- a/rcore/strings.cc -+++ b/rcore/strings.cc -@@ -437,7 +437,7 @@ static long double - libc_strtold (const char *nptr, char **endptr) - { - const long double result = strtold (nptr, endptr); -- if (isnan (result) && std::signbit (result) == 0) -+ if (std::isnan (result) && std::signbit (result) == 0) - { - const char *p = nptr; - while (isspace (*p)) -@@ -500,9 +500,9 @@ string_to_double (const char *dblstring, const char **endptr) - String - string_from_float (float value) - { -- if (isnan (value)) -+ if (std::isnan (value)) - return std::signbit (value) ? "-NaN" : "+NaN"; -- if (isinf (value)) -+ if (std::isinf (value)) - return std::signbit (value) ? "-Infinity" : "+Infinity"; - return string_format ("%.7g", value); - } -@@ -511,9 +511,9 @@ string_from_float (float value) - String - string_from_double (double value) - { -- if (isnan (value)) -+ if (std::isnan (value)) - return std::signbit (value) ? "-NaN" : "+NaN"; -- if (isinf (value)) -+ if (std::isinf (value)) - return std::signbit (value) ? "-Infinity" : "+Infinity"; - return string_format ("%.17g", value); - } -diff --git a/rcore/tests/benchrcore.cc b/rcore/tests/benchrcore.cc -index 3899a08..12fde16 100644 ---- a/rcore/tests/benchrcore.cc -+++ b/rcore/tests/benchrcore.cc -@@ -188,8 +188,8 @@ test_random_numbers() - const double rf = random_frange (989617512, 9876547656); - TASSERT (rf >= 989617512 && rf < 9876547656); - } -- TASSERT (isnan (random_frange (NAN, 1))); -- TASSERT (isnan (random_frange (0, NAN))); -+ TASSERT (std::isnan (random_frange (NAN, 1))); -+ TASSERT (std::isnan (random_frange (0, NAN))); - #if 0 // example penalty paid in random_int64() - size_t i, j = 0; - for (i = 0; i < 100; i++) -diff --git a/rcore/tests/strings.cc b/rcore/tests/strings.cc -index 468a6e6..dae3e3d 100644 ---- a/rcore/tests/strings.cc -+++ b/rcore/tests/strings.cc -@@ -311,9 +311,9 @@ string_conversions (void) - TCMP (string_to_double ("-0.5"), ==, -0.5); - double tfloat; - tfloat = string_to_double ("+NAN"); -- assert (isnan (tfloat) && std::signbit (tfloat) == 0); -+ assert (std::isnan (tfloat) && std::signbit (tfloat) == 0); - tfloat = string_to_double ("-NAN"); -- assert (isnan (tfloat) && std::signbit (tfloat) == 1); -+ assert (std::isnan (tfloat) && std::signbit (tfloat) == 1); - TCMP (string_capitalize ("fOO bar"), ==, "Foo Bar"); - TCMP (string_capitalize ("foo BAR BAZ", 2), ==, "Foo Bar BAZ"); - } --- -2.9.1 - From 3b50b327f7cf3226a0e37bc6afa1e921c9c075f7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 21:40:57 -0400 Subject: [PATCH 1311/1394] gnu: Remove libpng-1.2. * gnu/packages/image.scm (libpng-1.2): Delete variable. --- gnu/packages/image.scm | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index d45a14ec14e..a4370b10ca9 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -239,25 +239,6 @@ APNG patch provides APNG support to libpng.") (home-page "https://sourceforge.net/projects/libpng-apng/") (license license:zlib))) -(define-public libpng-1.2 - (package - (inherit libpng) - (version "1.2.59") - (source - (origin - (method url-fetch) - (uri (list (string-append "mirror://sourceforge/libpng/libpng12/" - version "/libpng-" version ".tar.xz") - (string-append - "ftp://ftp.simplesystems.org/pub/libpng/png/src" - "/libpng12/libpng-" version ".tar.xz") - (string-append - "ftp://ftp.simplesystems.org/pub/libpng/png/src/history" - "/libpng12/libpng-" version ".tar.xz"))) - (sha256 - (base32 - "1izw9ybm27llk8531w6h4jp4rk2rxy2s9vil16nwik5dp0amyqxl")))))) - (define-public pngcrush (package (name "pngcrush") From 098372a81e61f92bab4439c9bbaf43a73e1649b3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 21:41:34 -0400 Subject: [PATCH 1312/1394] gnu: Remove boost-with-python2. * gnu/packages/boost.scm (boost-with-python2): Delete variable. --- gnu/packages/boost.scm | 7 ------- 1 file changed, 7 deletions(-) diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm index b53b1f42576..ca320c37fb0 100644 --- a/gnu/packages/boost.scm +++ b/gnu/packages/boost.scm @@ -278,13 +278,6 @@ across a broad spectrum of applications.") (define-public boost-with-python3 (deprecated-package "boost-with-python3" boost)) -(define-public boost-with-python2 - (package/inherit boost - (name "boost-python2") - (native-inputs - `(("python" ,python-2) - ,@(alist-delete "python" (package-native-inputs boost)))))) - (define-public boost-static (package (inherit boost) From ec822034d9fb0cb97be04342bed399489bef1b0a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 21:49:16 -0400 Subject: [PATCH 1313/1394] gnu: john-the-ripper-jumbo: Use Python 3. * gnu/packages/password-utils.scm (john-the-ripper-jumbot): [inputs]: Use new style and replace python-2 by python-wrapper. [phases]{install}: Delete trailing #t. --- gnu/packages/password-utils.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 348afb5af4e..127cfdf7aa1 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -33,6 +33,7 @@ ;;; Copyright © 2021 Xinglu Chen ;;; Copyright © 2020 Hartmut Goebel ;;; Copyright © 2021 David Dashyan +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -951,13 +952,13 @@ between hosts and entries in the password store.") (native-inputs (list perl)) (inputs - `(("gmp" ,gmp) - ("libpcap" ,libpcap) - ("nss" ,nss) - ("openssl" ,openssl) - ("python" ,python-2) ; For "python" and "python2" shebangs - ("ruby" ,ruby) ; For genincstats.rb - ("zlib" ,zlib))) + (list gmp + libpcap + nss + openssl + python-wrapper + ruby ; For genincstats.rb + zlib)) (arguments `(#:configure-flags (list "--with-systemwide" @@ -1018,8 +1019,7 @@ between hosts and entries in the password store.") (find-files "." "(.*\\.chr|.*\\.lst)") (find-files "." ".*\\.conf"))) (copy-recursively "rules" (string-append datadir "/rules"))) - (copy-recursively "../doc" docdir) - #t))) + (copy-recursively "../doc" docdir)))) (delete 'check) ; Tests need installed .conf files; move after install (add-after 'install 'check (lambda args From 5551922a24350d525046afd1d58ed2449946edde Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 21:50:51 -0400 Subject: [PATCH 1314/1394] gnu: Remove python2-enum34. * gnu/packages/python-xyz.scm (python2-enum34): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3c4d9f73b7b..9307adb536f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2816,9 +2816,6 @@ commands.") backported for previous versions of Python from 2.4 to 3.3.") (license license:bsd-3))) -(define-public python2-enum34 - (package-with-python2 python-enum34)) - (define-public python-parse-type (package (name "python-parse-type") From 17375266ea2e94726bf3d28c1d4fb3899c115377 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 21:52:31 -0400 Subject: [PATCH 1315/1394] gnu: Remove python2-appdirs. * gnu/packages/python-xyz.scm (python2-appdirs): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9307adb536f..33137bf050b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11095,9 +11095,6 @@ provided that can be used to do various manipulations with LilyPond files.") should be stored on various operating systems.") (license license:expat))) -(define-public python2-appdirs - (package-with-python2 python-appdirs)) - (define-public python-gorilla (package (name "python-gorilla") From 607e48ba3ccb038e2fa4b956cb62ce628cdc8cd0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 12 May 2022 23:43:39 -0400 Subject: [PATCH 1316/1394] gnu: Add vtk-7. * gnu/packages/image-processing.scm: (vtk-7): New variable. * gnu/packages/patches/vtk-7-gcc-10-compat.patch: New patch. * gnu/packages/patches/vtk-7-hdf5-compat.patch: Likewise. * gnu/packages/patches/vtk-7-python-compat.patch: Likewise. * gnu/local.mk (dist_patch_DATA): Register them. --- gnu/local.mk | 3 ++ gnu/packages/image-processing.scm | 22 +++++++++++ .../patches/vtk-7-gcc-10-compat.patch | 14 +++++++ gnu/packages/patches/vtk-7-hdf5-compat.patch | 38 +++++++++++++++++++ .../patches/vtk-7-python-compat.patch | 16 ++++++++ 5 files changed, 93 insertions(+) create mode 100644 gnu/packages/patches/vtk-7-gcc-10-compat.patch create mode 100644 gnu/packages/patches/vtk-7-hdf5-compat.patch create mode 100644 gnu/packages/patches/vtk-7-python-compat.patch diff --git a/gnu/local.mk b/gnu/local.mk index 1286bdddb56..0cd874dae7d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1935,6 +1935,9 @@ dist_patch_DATA = \ %D%/packages/patches/vte-CVE-2012-2738-pt1.patch \ %D%/packages/patches/vte-CVE-2012-2738-pt2.patch \ %D%/packages/patches/vtk-fix-freetypetools-build-failure.patch \ + %D%/packages/patches/vtk-7-gcc-10-compat.patch \ + %D%/packages/patches/vtk-7-hdf5-compat.patch \ + %D%/packages/patches/vtk-7-python-compat.patch \ %D%/packages/patches/warsow-qfusion-fix-bool-return-type.patch \ %D%/packages/patches/webkitgtk-adjust-bubblewrap-paths.patch \ %D%/packages/patches/webrtc-audio-processing-big-endian.patch \ diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index 1995f71cc2a..08aeaed202c 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -407,6 +407,28 @@ a suite of 3D interaction widgets, supports parallel processing, and integrates with various databases on GUI toolkits such as Qt and Tk.") (license license:bsd-3))) +(define-public vtk-7 + (package + (inherit vtk) + (version "7.1.1") + (source (origin + (method url-fetch) + (uri (string-append "https://vtk.org/files/release/" + (version-major+minor version) + "/VTK-" version ".tar.gz")) + (sha256 + (base32 + "0nm7xwwj7rnsxjdv2ssviys8nhci4n9iiiqm2y14s520hl2dsp1d")) + (patches (search-patches "vtk-7-python-compat.patch" + "vtk-7-hdf5-compat.patch" + "vtk-7-gcc-10-compat.patch")))) + (arguments + (substitute-keyword-arguments (package-arguments vtk) + ((#:configure-flags flags) + ;; Otherwise, the build would fail with: "error: invalid conversion + ;; from ‘const char*’ to ‘char*’ [-fpermissive]". + `(cons "-DCMAKE_CXX_FLAGS=-fpermissive" ,flags)))))) + ;; itksnap needs an older variant of VTK. (define-public vtk-6 (package (inherit vtk) diff --git a/gnu/packages/patches/vtk-7-gcc-10-compat.patch b/gnu/packages/patches/vtk-7-gcc-10-compat.patch new file mode 100644 index 00000000000..50f9f6cca3a --- /dev/null +++ b/gnu/packages/patches/vtk-7-gcc-10-compat.patch @@ -0,0 +1,14 @@ +Retrieved from +https://sources.debian.org/src/vtk7/7.1.1%2Bdfsg2-10.1/debian/patches/. + +--- a/CMake/VTKGenerateExportHeader.cmake ++++ b/CMake/VTKGenerateExportHeader.cmake +@@ -174,7 +174,7 @@ + execute_process(COMMAND ${CMAKE_C_COMPILER} --version + OUTPUT_VARIABLE _gcc_version_info + ERROR_VARIABLE _gcc_version_info) +- string(REGEX MATCH "[3-9]\\.[0-9]\\.[0-9]*" ++ string(REGEX MATCH "[0-9]*\\.[0-9]\\.[0-9]*" + _gcc_version "${_gcc_version_info}") + # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the + # patch level, handle this here: diff --git a/gnu/packages/patches/vtk-7-hdf5-compat.patch b/gnu/packages/patches/vtk-7-hdf5-compat.patch new file mode 100644 index 00000000000..1f3c0c7be42 --- /dev/null +++ b/gnu/packages/patches/vtk-7-hdf5-compat.patch @@ -0,0 +1,38 @@ +Description: The H5FD_class_t struct gained an extra member in 1.10 +Bug-Debian: https://bugs.debian.org/846372 +Author: Iain Lane +--- a/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx ++++ b/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfH5Driver.cxx +@@ -139,7 +139,11 @@ + #if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=8)) + static haddr_t H5FD_dsm_get_eoa(const H5FD_t *_file, H5FD_mem_t type); + static herr_t H5FD_dsm_set_eoa(H5FD_t *_file, H5FD_mem_t type, haddr_t addr); ++#if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=10)) ++static haddr_t H5FD_dsm_get_eof(const H5FD_t *_file, H5FD_mem_t type); ++#else + static haddr_t H5FD_dsm_get_eof(const H5FD_t *_file); ++#endif + #else + static haddr_t H5FD_dsm_get_eoa(H5FD_t *_file); + static herr_t H5FD_dsm_set_eoa(H5FD_t *_file, haddr_t addr); +@@ -155,6 +159,9 @@ + "dsm", /*name */ + MAXADDR, /*maxaddr */ + H5F_CLOSE_WEAK, /*fc_degree */ ++#if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=8)) ++ NULL, /* terminate */ ++#endif + NULL, /*sb_size */ + NULL, /*sb_encode */ + NULL, /*sb_decode */ +@@ -687,7 +694,9 @@ + *------------------------------------------------------------------------- + */ + static haddr_t +-#if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=8)) ++#if (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=10)) ++H5FD_dsm_get_eof(const H5FD_t *_file, H5FD_mem_t type) ++#elif (H5_VERS_MAJOR>1)||((H5_VERS_MAJOR==1)&&(H5_VERS_MINOR>=8)) + H5FD_dsm_get_eof(const H5FD_t *_file) + #else + H5FD_dsm_get_eof(H5FD_t *_file) diff --git a/gnu/packages/patches/vtk-7-python-compat.patch b/gnu/packages/patches/vtk-7-python-compat.patch new file mode 100644 index 00000000000..375624e4e26 --- /dev/null +++ b/gnu/packages/patches/vtk-7-python-compat.patch @@ -0,0 +1,16 @@ +Author: Gert Wollny +Description: Work around compile bug with python 3.7.1 +Debian-Bug: https://bugs.debian.org/914347 +diff --git a/Wrapping/PythonCore/vtkPythonArgs.cxx b/Wrapping/PythonCore/vtkPythonArgs.cxx +index 1b1e4b9..682f8b8 100644 +--- a/Wrapping/PythonCore/vtkPythonArgs.cxx ++++ b/Wrapping/PythonCore/vtkPythonArgs.cxx +@@ -102,7 +102,7 @@ bool vtkPythonGetStringValue(PyObject *o, T *&a, const char *exctext) + else if (PyUnicode_Check(o)) + { + #if PY_VERSION_HEX >= 0x03030000 +- a = PyUnicode_AsUTF8(o); ++ a = const_cast(PyUnicode_AsUTF8(o)); + return true; + #else + PyObject *s = _PyUnicode_AsDefaultEncodedString(o, NULL); From 887dec8a51604408214d28290ce857451dcd7192 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 01:25:05 -0400 Subject: [PATCH 1317/1394] gnu: itk-snap: Fix build. * gnu/packages/patches/itk-snap-alt-glibc-compat.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/image-processing.scm (itk-snap): Apply it. [phases]: Delete trailing #t. [inputs]: Use new style. Replace vtk-6 with vtk-7. --- gnu/local.mk | 1 + gnu/packages/image-processing.scm | 52 ++++++++----------- .../patches/itk-snap-alt-glibc-compat.patch | 22 ++++++++ 3 files changed, 46 insertions(+), 29 deletions(-) create mode 100644 gnu/packages/patches/itk-snap-alt-glibc-compat.patch diff --git a/gnu/local.mk b/gnu/local.mk index 0cd874dae7d..c4d774052b1 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1302,6 +1302,7 @@ dist_patch_DATA = \ %D%/packages/patches/ipxe-reproducible-geniso.patch \ %D%/packages/patches/irrlicht-use-system-libs.patch \ %D%/packages/patches/isl-0.11.1-aarch64-support.patch \ + %D%/packages/patches/itk-snap-alt-glibc-compat.patch \ %D%/packages/patches/json-c-0.13-CVE-2020-12762.patch \ %D%/packages/patches/json-c-0.12-CVE-2020-12762.patch \ %D%/packages/patches/jsoncpp-pkg-config-version.patch \ diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index 08aeaed202c..d0d80c08cf9 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -1032,7 +1032,8 @@ combine the information contained in both.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q")))) + (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q")) + (patches (search-patches "itk-snap-alt-glibc-compat.patch")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -1051,22 +1052,19 @@ combine the information contained in both.") (substitute* "CMakeLists.txt" (("install_qt5_executable\ \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)") - "")) - #t)) + "")))) (add-after 'unpack 'disable-gui-tests (lambda _ ;; The GUI tests just time out. (substitute* "CMakeLists.txt" ((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\ |RandomForest|RandomForestBailOut)") - "")) - #t)) + "")))) (add-after 'unpack 'make-reproducible (lambda _ (substitute* "CMakeLists.txt" (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)") - "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")")) - #t)) + "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")")))) (add-after 'unpack 'prepare-submodules (lambda* (#:key inputs #:allow-other-keys) (rmdir "Submodules/c3d") @@ -1077,19 +1075,16 @@ combine the information contained in both.") (("vcl_") "std::")) (rmdir "Submodules/greedy") (symlink (assoc-ref inputs "greedy-src") - "Submodules/greedy") - #t)) + "Submodules/greedy"))) (add-after 'unpack 'fix-includes (lambda _ (substitute* "GUI/Model/RegistrationModel.cxx" (("") - "")) - #t)) + "")))) (add-before 'check 'prepare-tests (lambda _ ;; Needed by at least one test. - (setenv "HOME" "/tmp") - #t)) + (setenv "HOME" "/tmp"))) (add-after 'install 'wrap-executable (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -1098,23 +1093,22 @@ combine the information contained in both.") ,(map (lambda (label) (string-append (assoc-ref inputs label) "/lib/qt5/plugins")) - '("qtbase" "qtdeclarative")))) - #t)))))) + '("qtbase" "qtdeclarative")))))))))) (inputs - `(("curl" ,curl) - ("fftw" ,fftw) - ("fftwf" ,fftwf) - ("glu" ,glu) - ("hdf5" ,hdf5) - ("mesa" ,mesa-opencl) - ;; This package does not build with either insight-toolkit 5.0.0 and - ;; not with 4.13. It really needs to be 4.12. - ("itk" ,insight-toolkit-4.12) - ("vtk" ,vtk-6) - ("qtbase" ,qtbase-5) - ("qtdeclarative" ,qtdeclarative) - ("vxl" ,vxl-1) - ("zlib" ,zlib))) + (list curl + fftw + fftwf + glu + hdf5 + mesa-opencl + ;; This package does not build with either insight-toolkit 5.0.0 + ;; and not with 4.13. It really needs to be 4.12. + insight-toolkit-4.12 + vtk-7 + qtbase-5 + qtdeclarative + vxl-1 + zlib)) (native-inputs `(("googletest" ,googletest) ("qttools" ,qttools) diff --git a/gnu/packages/patches/itk-snap-alt-glibc-compat.patch b/gnu/packages/patches/itk-snap-alt-glibc-compat.patch new file mode 100644 index 00000000000..764c5da2c22 --- /dev/null +++ b/gnu/packages/patches/itk-snap-alt-glibc-compat.patch @@ -0,0 +1,22 @@ +Retrieved from ALT Linux. +https://git.altlinux.org/tasks/273587/build/300/x86_64/srpm/itk-snap-3.8.0-alt6.src.rpm + +diff --git a/GUI/Qt/main.cxx b/GUI/Qt/main.cxx +index 576f7160..ceab92e6 100644 +--- a/GUI/Qt/main.cxx ++++ b/GUI/Qt/main.cxx +@@ -51,12 +51,13 @@ using namespace std; + #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__)) + + #include ++#include + #include + + void SegmentationFaultHandler(int sig) + { + cerr << "*************************************" << endl; +- cerr << "ITK-SNAP: " << sys_siglist[sig] << endl; ++ cerr << "ITK-SNAP: " << strsignal(sig) << " (" << sigabbrev_np(sig) << ")" << endl; + cerr << "BACKTRACE: " << endl; + void *array[50]; + int nsize = backtrace(array, 50); From 3e917d2e183a7e521bb08e2edac39881c587903b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 01:26:55 -0400 Subject: [PATCH 1318/1394] gnu: Remove vtk-6. * gnu/packages/image-processing.scm (vtk-6): Delete variable. --- gnu/packages/image-processing.scm | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index d0d80c08cf9..92ee7b84656 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -429,23 +429,6 @@ integrates with various databases on GUI toolkits such as Qt and Tk.") ;; from ‘const char*’ to ‘char*’ [-fpermissive]". `(cons "-DCMAKE_CXX_FLAGS=-fpermissive" ,flags)))))) -;; itksnap needs an older variant of VTK. -(define-public vtk-6 - (package (inherit vtk) - (version "6.3.0") - (source (origin - (method url-fetch) - (uri (string-append "https://vtk.org/files/release/" - (version-major+minor version) - "/VTK-" version ".tar.gz")) - (sha256 - (base32 - "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j")))) - (inputs - (modify-inputs (package-inputs vtk) - (replace "jsoncpp" jsoncpp-for-tensorflow) - (replace "python" python-2))))) ;fails to build with Python 3.9 - (define-public opencv (package (name "opencv") From 672eab90bbeb16e51322505739b14de6a8f1fa6d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 11:41:09 -0400 Subject: [PATCH 1319/1394] gnu: dcmtk: Update to 3.6.7 and build as a shared library. * gnu/packages/image-processing.scm (dcmtk): Update to 3.6.7. [arguments]: New field. --- gnu/packages/image-processing.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index 92ee7b84656..e725fe04f7b 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2021 Paul Garlick ;;; Copyright © 2021 Guillaume Le Vaillant ;;; Copyright © 2021 Ivan Gankevich +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -145,7 +146,7 @@ Magnetic Resonance Imaging.") (define-public dcmtk (package (name "dcmtk") - (version "3.6.6") + (version "3.6.7") (source (origin (method url-fetch) @@ -154,8 +155,11 @@ Magnetic Resonance Imaging.") "dcmtk" (string-join (string-split version #\.) "") "/dcmtk-" version ".tar.gz")) (sha256 - (base32 "13j5yf3p6qj3mr17d77r3kcqchf055hgvk1w15vmdr8f54mwcnb8")))) + (base32 "02kix73qhndgb56cmi5327666i6imp7hi17wwqp26q4d7s72jn3w")))) (build-system cmake-build-system) + (arguments + ;; By default, only static archives are built. + (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON"))) (inputs (list icu4c libjpeg-turbo From 54ef40a1f79d6d636ba26ac47f6dd0b84172dd0d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 11:47:19 -0400 Subject: [PATCH 1320/1394] gnu: mia: Update to 2.4.7. * gnu/packages/patches/mia-fix-boost-headers.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/image-processing.scm (mia): Update to 2.4.7. [source]: Apply patch. [configure-flags]: Use the more conventional OFF option value (instead of 0). [inputs]: Use new style. Replace python2-lxml by python-lxml. Replace vtk by vtk-7. [native-inputs]: Use new style. Replace python-2 with python-wrapper. --- gnu/local.mk | 1 + gnu/packages/image-processing.scm | 56 +- .../patches/mia-fix-boost-headers.patch | 479 ++++++++++++++++++ 3 files changed, 510 insertions(+), 26 deletions(-) create mode 100644 gnu/packages/patches/mia-fix-boost-headers.patch diff --git a/gnu/local.mk b/gnu/local.mk index c4d774052b1..83ee7e29303 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1492,6 +1492,7 @@ dist_patch_DATA = \ %D%/packages/patches/mesa-skip-tests.patch \ %D%/packages/patches/meson-allow-dirs-outside-of-prefix.patch \ %D%/packages/patches/mhash-keygen-test-segfault.patch \ + %D%/packages/patches/mia-fix-boost-headers.patch \ %D%/packages/patches/minetest-add-MINETEST_MOD_PATH.patch \ %D%/packages/patches/mingw-w64-6.0.0-gcc.patch \ %D%/packages/patches/mingw-w64-dlltool-temp-prefix.patch \ diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index e725fe04f7b..f4bf1724b44 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -185,7 +185,7 @@ licences similar to the Modified BSD licence.")))) (define-public mia (package (name "mia") - (version "2.4.6") + (version "2.4.7") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/mia/mia/" @@ -193,37 +193,41 @@ licences similar to the Modified BSD licence.")))) "/mia-" version ".tar.xz")) (sha256 (base32 - "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb")))) + "0qpcd3n26q52dpyibm11f5l6cgscdr54p2jish39gc3p1f5h3ws1")) + (patches (search-patches "mia-fix-boost-headers.patch")))) (build-system cmake-build-system) (arguments `(#:configure-flags - (list "-DMIA_CREATE_NIPYPE_INTERFACES=0" + (list "-DMIA_CREATE_NIPYPE_INTERFACES=OFF" "-DCMAKE_CXX_FLAGS=-fpermissive"))) (inputs - `(("boost" ,boost) - ("dcmtk" ,dcmtk) - ("doxygen" ,doxygen) - ("eigen" ,eigen) - ("fftw" ,fftw) - ("fftwf" ,fftwf) - ("gsl" ,gsl) - ("gts" ,gts) - ("hdf5" ,hdf5) - ("itpp" ,itpp) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libtiff" ,libtiff) - ("libxml" ,libxml2) - ("libxml++" ,libxml++) - ("maxflow" ,maxflow) - ("niftilib" ,niftilib) - ("nlopt" ,nlopt) - ("openexr" ,openexr-2) - ("python-lxml" ,python2-lxml) - ("vtk" ,vtk))) + (list boost + dcmtk + doxygen + eigen + fftw + fftwf + gsl + gts + hdf5 + itpp + libjpeg-turbo + libpng + libtiff + libxml2 + libxml++ + maxflow + niftilib + nlopt + openexr-2 + python-lxml + ;; The build fails when using the regular VTK (currently at version + ;; 9), with error "addons/vtk/vtkvf.cc:23:10: fatal error: + ;; vtkStructuredPointsReader.h: No such file or directory". + vtk-7)) (native-inputs - `(("pkg-config" ,pkg-config) - ("python" ,python-2))) + (list pkg-config + python-wrapper)) (home-page "http://mia.sourceforge.net") (synopsis "Toolkit for gray scale medical image analysis") (description "MIA provides a combination of command line tools, plug-ins, diff --git a/gnu/packages/patches/mia-fix-boost-headers.patch b/gnu/packages/patches/mia-fix-boost-headers.patch new file mode 100644 index 00000000000..158ab2afebb --- /dev/null +++ b/gnu/packages/patches/mia-fix-boost-headers.patch @@ -0,0 +1,479 @@ +Retrieved from Debian, and added a few "#include " +directives to fix the build. + +diff --git a/addons/hdf5/test_hdf5_3dimage.cc b/addons/hdf5/test_hdf5_3dimage.cc +index a7185618..7a398821 100644 +--- a/addons/hdf5/test_hdf5_3dimage.cc ++++ b/addons/hdf5/test_hdf5_3dimage.cc +@@ -23,7 +23,7 @@ + #include + + #include +-#include ++#include + + #include + +diff --git a/addons/hdf5/test_hdf5mia.cc b/addons/hdf5/test_hdf5mia.cc +index 3d62106e..8141be07 100644 +--- a/addons/hdf5/test_hdf5mia.cc ++++ b/addons/hdf5/test_hdf5mia.cc +@@ -23,7 +23,6 @@ + #include + + #include +-#include + #include + + #include +diff --git a/addons/nifti/test_niftiimage.cc b/addons/nifti/test_niftiimage.cc +index 8df3f0b5..840ae585 100644 +--- a/addons/nifti/test_niftiimage.cc ++++ b/addons/nifti/test_niftiimage.cc +@@ -23,8 +23,6 @@ + #include + + #include +-#include +- + + #include + #include +diff --git a/addons/vistaio/test_2dvistaio.cc b/addons/vistaio/test_2dvistaio.cc +index b3da29a0..9b1599dd 100644 +--- a/addons/vistaio/test_2dvistaio.cc ++++ b/addons/vistaio/test_2dvistaio.cc +@@ -23,8 +23,6 @@ + #include + + #include +-#include +- + + #include + #include +diff --git a/addons/vistaio/test_3dvistaio.cc b/addons/vistaio/test_3dvistaio.cc +index 93c007d0..c3ae1fdb 100644 +--- a/addons/vistaio/test_3dvistaio.cc ++++ b/addons/vistaio/test_3dvistaio.cc +@@ -23,8 +23,6 @@ + #include + + #include +-#include +- + + #include + #include +diff --git a/addons/vtk/test_vtkimage.cc b/addons/vtk/test_vtkimage.cc +index eaf96a6b..8212ef1d 100644 +--- a/addons/vtk/test_vtkimage.cc ++++ b/addons/vtk/test_vtkimage.cc +@@ -23,8 +23,6 @@ + #include + + #include +-#include +- + + #include + #include +diff --git a/mia/2d/creator/test_circle.cc b/mia/2d/creator/test_circle.cc +index 9784e05d..7ca4bab9 100644 +--- a/mia/2d/creator/test_circle.cc ++++ b/mia/2d/creator/test_circle.cc +@@ -21,8 +21,6 @@ + + #include + #include +-#include +- + #include + + using namespace mia; +diff --git a/mia/2d/filter/test_convert.cc b/mia/2d/filter/test_convert.cc +index 80304793..f40d295a 100644 +--- a/mia/2d/filter/test_convert.cc ++++ b/mia/2d/filter/test_convert.cc +@@ -25,7 +25,6 @@ + #include + + #include +-#include + #include + + +diff --git a/mia/2d/filter/test_morphological.cc b/mia/2d/filter/test_morphological.cc +index 2fc58583..9a004946 100644 +--- a/mia/2d/filter/test_morphological.cc ++++ b/mia/2d/filter/test_morphological.cc +@@ -20,7 +20,6 @@ + + #include + #include +-#include + #include + + namespace bmpl = boost::mpl; +diff --git a/mia/2d/filter/test_sortlabel.cc b/mia/2d/filter/test_sortlabel.cc +index 78464e1a..49c327e3 100644 +--- a/mia/2d/filter/test_sortlabel.cc ++++ b/mia/2d/filter/test_sortlabel.cc +@@ -23,7 +23,6 @@ + #include + + #include +-#include + namespace bmpl = boost::mpl; + + +diff --git a/mia/2d/filter/test_thinning.cc b/mia/2d/filter/test_thinning.cc +index 3ebb2cdc..8bc5b356 100644 +--- a/mia/2d/filter/test_thinning.cc ++++ b/mia/2d/filter/test_thinning.cc +@@ -21,7 +21,6 @@ + + #include + #include +-#include + #include + #include + +diff --git a/mia/2d/test_filter_cast.cc b/mia/2d/test_filter_cast.cc +index e806e14f..91c77398 100644 +--- a/mia/2d/test_filter_cast.cc ++++ b/mia/2d/test_filter_cast.cc +@@ -24,7 +24,7 @@ + #include + #include + +-#include ++#include + #include + #include + +diff --git a/mia/2d/test_image.cc b/mia/2d/test_image.cc +index c82dc59b..1f602510 100644 +--- a/mia/2d/test_image.cc ++++ b/mia/2d/test_image.cc +@@ -24,6 +24,7 @@ + #include + + #include ++#include + + #include + +diff --git a/mia/2d/test_interpol.cc b/mia/2d/test_interpol.cc +index d1f3703d..5caafccf 100644 +--- a/mia/2d/test_interpol.cc ++++ b/mia/2d/test_interpol.cc +@@ -23,7 +23,6 @@ + + #include + +-#include + #include + #include + +diff --git a/mia/3d/fifotestfixture.cc b/mia/3d/fifotestfixture.cc +index ab2e7c65..1b6e6bb4 100644 +--- a/mia/3d/fifotestfixture.cc ++++ b/mia/3d/fifotestfixture.cc +@@ -24,7 +24,7 @@ + + #include + #include +-#include ++#include + #include + #include + #include +diff --git a/mia/3d/filter/test_convert.cc b/mia/3d/filter/test_convert.cc +index e83032c1..dad9afaa 100644 +--- a/mia/3d/filter/test_convert.cc ++++ b/mia/3d/filter/test_convert.cc +@@ -20,7 +20,6 @@ + + #include + #include +-#include + #include + #include + #include +diff --git a/mia/3d/test_image.cc b/mia/3d/test_image.cc +index 18f71892..c21e0d20 100644 +--- a/mia/3d/test_image.cc ++++ b/mia/3d/test_image.cc +@@ -21,7 +21,8 @@ + #include + #include + #include +-#include ++#include ++#include + + #include + #include +diff --git a/mia/3d/test_imageio.cc b/mia/3d/test_imageio.cc +index 0640a668..7a6b5635 100644 +--- a/mia/3d/test_imageio.cc ++++ b/mia/3d/test_imageio.cc +@@ -20,7 +20,6 @@ + + #include + #include +-#include + #include + + #include +diff --git a/mia/core/splinekernel/test_bspline.cc b/mia/core/splinekernel/test_bspline.cc +index 54d6bda3..0abfe443 100644 +--- a/mia/core/splinekernel/test_bspline.cc ++++ b/mia/core/splinekernel/test_bspline.cc +@@ -23,8 +23,6 @@ + #include + #include + #include +-#include +- + + using namespace mia; + using namespace mia::bsplinekernel; +diff --git a/mia/core/test_cost.cc b/mia/core/test_cost.cc +index 70097b2e..305ca84d 100644 +--- a/mia/core/test_cost.cc ++++ b/mia/core/test_cost.cc +@@ -27,7 +27,7 @@ + #include + + #include +-#include ++#include + #include + + NS_MIA_USE +diff --git a/mia/core/test_cstplan.cc b/mia/core/test_cstplan.cc +index aa241d48..a9e5a0e3 100644 +--- a/mia/core/test_cstplan.cc ++++ b/mia/core/test_cstplan.cc +@@ -23,7 +23,7 @@ + + #include + #include +-#include ++#include + + #include + +diff --git a/mia/core/test_dictmap.cc b/mia/core/test_dictmap.cc +index a9217290..fd05fe30 100644 +--- a/mia/core/test_dictmap.cc ++++ b/mia/core/test_dictmap.cc +@@ -26,7 +26,7 @@ + + #include + #include +-#include ++#include + + #include + #include +diff --git a/mia/core/test_fifofilter.cc b/mia/core/test_fifofilter.cc +index 2a066f2e..6e2a385d 100644 +--- a/mia/core/test_fifofilter.cc ++++ b/mia/core/test_fifofilter.cc +@@ -27,7 +27,7 @@ + + #include + #include +-#include ++#include + + + #include +diff --git a/mia/core/test_gsl_matrix.cc b/mia/core/test_gsl_matrix.cc +index 4add5f7a..6d16353d 100644 +--- a/mia/core/test_gsl_matrix.cc ++++ b/mia/core/test_gsl_matrix.cc +@@ -25,7 +25,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_ALTERNATIVE_INIT_API + #include +-#include ++#include + #include + + #include +diff --git a/mia/core/test_gsl_matrix_vector_ops.cc b/mia/core/test_gsl_matrix_vector_ops.cc +index e5f7d7b9..217020f7 100644 +--- a/mia/core/test_gsl_matrix_vector_ops.cc ++++ b/mia/core/test_gsl_matrix_vector_ops.cc +@@ -28,7 +28,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_ALTERNATIVE_INIT_API + #include +-#include ++#include + + #include + #include +diff --git a/mia/core/test_gsl_multimin.cc b/mia/core/test_gsl_multimin.cc +index 5bbc434b..129f578a 100644 +--- a/mia/core/test_gsl_multimin.cc ++++ b/mia/core/test_gsl_multimin.cc +@@ -25,7 +25,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_ALTERNATIVE_INIT_API + #include +-#include ++#include + #include + + #include +diff --git a/mia/core/test_gsl_pca.cc b/mia/core/test_gsl_pca.cc +index 436b36b0..12942921 100644 +--- a/mia/core/test_gsl_pca.cc ++++ b/mia/core/test_gsl_pca.cc +@@ -27,7 +27,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_ALTERNATIVE_INIT_API + #include +-#include ++#include + + #include + +diff --git a/mia/core/test_gsl_vector.cc b/mia/core/test_gsl_vector.cc +index 541c88b8..ba91f159 100644 +--- a/mia/core/test_gsl_vector.cc ++++ b/mia/core/test_gsl_vector.cc +@@ -25,10 +25,9 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_ALTERNATIVE_INIT_API + #include +-#include ++#include + + #include +-#include + + #include + +diff --git a/mia/core/test_interpol.cc b/mia/core/test_interpol.cc +index 36669dc0..2dd5157d 100644 +--- a/mia/core/test_interpol.cc ++++ b/mia/core/test_interpol.cc +@@ -24,7 +24,7 @@ + #include + + #include +-#include ++#include + #include + #include + +diff --git a/mia/core/test_parameter.cc b/mia/core/test_parameter.cc +index ae9b4976..28ef2a80 100644 +--- a/mia/core/test_parameter.cc ++++ b/mia/core/test_parameter.cc +@@ -26,7 +26,7 @@ + + #include + #include +-#include ++#include + + #include + #include +diff --git a/mia/core/test_probmap.cc b/mia/core/test_probmap.cc +index 2dc6cb6c..38052681 100644 +--- a/mia/core/test_probmap.cc ++++ b/mia/core/test_probmap.cc +@@ -22,7 +22,7 @@ + + #include + #include +-#include ++#include + + #include + #include +diff --git a/mia/core/test_sqmin.cc b/mia/core/test_sqmin.cc +index f00b3b85..4a0b67b9 100644 +--- a/mia/core/test_sqmin.cc ++++ b/mia/core/test_sqmin.cc +@@ -23,7 +23,7 @@ + #define BOOST_TEST_DYN_LINK + #include + #include +-#include ++#include + + #include + +diff --git a/mia/internal/autotest.hh b/mia/internal/autotest.hh +index 419f6e8f..4458c0b2 100644 +--- a/mia/internal/autotest.hh ++++ b/mia/internal/autotest.hh +@@ -34,7 +34,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_NO_MAIN + #include +-#include ++#include + + #include + #include +diff --git a/mia/internal/plugintester.hh b/mia/internal/plugintester.hh +index 2d42b858..e632e5f7 100644 +--- a/mia/internal/plugintester.hh ++++ b/mia/internal/plugintester.hh +@@ -31,7 +31,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_NO_MAIN + #include +-#include ++#include + + #include + #include +diff --git a/mia/test/testhelpers.hh b/mia/test/testhelpers.hh +index 27f37e7f..68c213a6 100644 +--- a/mia/test/testhelpers.hh ++++ b/mia/test/testhelpers.hh +@@ -23,7 +23,7 @@ + + #include + #include +-#include ++#include + + namespace miatest + { +diff --git a/src/2dlerp.cc b/src/2dlerp.cc +index 4c7dde77..1e8801de 100644 +--- a/src/2dlerp.cc ++++ b/src/2dlerp.cc +@@ -25,7 +25,7 @@ + + #include + #include +-#include ++#include + + #include + #include +diff --git a/src/3dlerp.cc b/src/3dlerp.cc +index 6ee8dca0..2f1c1f3a 100644 +--- a/src/3dlerp.cc ++++ b/src/3dlerp.cc +@@ -24,7 +24,7 @@ + #define BOOST_TEST_NO_MAIN + #include + #include +-#include ++#include + + #include + #include From 41efd94c3e8dca19446906f69a7543abd9a0fa3e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 11:58:10 -0400 Subject: [PATCH 1321/1394] gnu: Remove python2-lxml. * gnu/packages/xml.scm (python2-lxml): Delete variable. --- gnu/packages/xml.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index a9bf07de96b..99cb02a09af 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -2541,9 +2541,6 @@ libxml2 and libxslt.") (base32 "090viyanaki4q7w7i000xl0qh4in52bkl3qal55sz2bbm8w3hqd1")))))) -(define-public python2-lxml - (package-with-python2 python-lxml)) - (define-public python-untangle ;; The latest tagged release is from 2014; use the latest commit. (let ((revision "1") From 2815b1963b26027e80b8db63b657d43b879482f2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 12:02:46 -0400 Subject: [PATCH 1322/1394] gnu: brasero: Remove obsolete gnome-doc-utils input. * gnu/packages/gnome.scm (brasero)[inputs]: Delete gnome-doc-utils. --- gnu/packages/gnome.scm | 1 - 1 file changed, 1 deletion(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index b2567844d88..78a52a64d54 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -332,7 +332,6 @@ (inputs (list dvd+rw-tools glib - gnome-doc-utils gstreamer gst-plugins-base gtk+ From 08c19564c4c345d458301b2f73610ec8ba2284f3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 13:12:17 -0400 Subject: [PATCH 1323/1394] gnu: libdbusmenu: Update to 16.04.0-496. * gnu/packages/gtk.scm (libdbusmenu): Update to 16.04.0-496. [source]: Fetch using Breezy. [arguments]: Use gexps. [phases]: Delete trailing #t. {remove-deprecated-gnome-common-macros}: New phase. {patch-paths}: Likewise. [inputs]: Use new style. [native-inputs]: Likewise. Replace gnome-doc-utils with gnome-common. Replace python-2 with python-wrapper. Add autoconf, automake, libtool, libxslt and which. --- gnu/packages/gtk.scm | 134 +++++++++++++++++++++++++------------------ 1 file changed, 78 insertions(+), 56 deletions(-) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index a15d2be1a65..64bac20f3d9 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -24,7 +24,7 @@ ;;; Copyright © 2019 Giacomo Leidi ;;; Copyright © 2020 Brendan Tildesley ;;; Copyright © 2020 Guillaume Le Vaillant -;;; Copyright © 2020, 2021 Maxim Cournoyer +;;; Copyright © 2020, 2021, 2022 Maxim Cournoyer ;;; Copyright © 2021 Leo Famulari ;;; Copyright © 2021 Simon Streit ;;; Copyright © 2021 Maxime Devos @@ -53,6 +53,7 @@ #:use-module (guix utils) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix bzr-download) #:use-module (guix git-download) #:use-module ((guix build utils) #:select (alist-replace)) #:use-module (guix build-system cmake) @@ -2544,64 +2545,85 @@ printed to standard output.") (license license:gpl3+))) (define-public libdbusmenu - (package - (name "libdbusmenu") - (version "16.04.0") - (source - (origin - (method url-fetch) - (uri (string-append "https://launchpad.net/libdbusmenu/" - (version-major+minor version) "/" version - "/+download/libdbusmenu-" version ".tar.gz")) - (sha256 - (base32 "12l7z8dhl917iy9h02sxmpclnhkdjryn08r8i4sr8l3lrlm4mk5r")))) - (build-system gnu-build-system) - (arguments - `(#:configure-flags - '("--sysconfdir=/etc" - "--localstatedir=/var" - ;; The shebang of the generated test files should be patched before - ;; enabling tests. - "--disable-tests") - #:make-flags - `(,(string-append "typelibdir=" (assoc-ref %outputs "out") - "/lib/girepository-1.0")) - #:phases - (modify-phases %standard-phases - (add-before 'configure 'do-not-treat-warnings-as-errors - (lambda _ - ;; Prevent the build from failing due to deprecation warnings - ;; from newer GLib and GTK versions. - (substitute* (find-files "." "^Makefile.in$") - ((" -Werror") - "")) - #t)) - (add-before 'configure 'set-environment - (lambda _ - (setenv "HAVE_VALGRIND_TRUE" "") - (setenv "HAVE_VALGRIND_FALSE" "#") - #t))))) - (inputs - `(("glib" ,glib) - ("gtk+" ,gtk+) - ("gtk+-2" ,gtk+-2))) - (native-inputs - `(("glib:bin" ,glib "bin") - ("gnome-doc-utils" ,gnome-doc-utils) - ("gobject-introspection" ,gobject-introspection) - ("intltool" ,intltool) - ("json-glib" ,json-glib) - ("pkg-config" ,pkg-config) - ("python" ,python-2) - ("vala" ,vala))) - (home-page "https://launchpad.net/libdbusmenu") - (synopsis "Library for passing menus over DBus") - (description "@code{libdbusmenu} passes a menu structure across DBus so + (let ((bzr-revision "496")) + (package + (name "libdbusmenu") + (version (string-append "16.04.0" "-" bzr-revision)) + (source + (origin + (method bzr-fetch) + (uri (bzr-reference + (url "lp:libdbusmenu") + (revision bzr-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1rnp86r8f2xjcbk6jjl6np1qdhc3d7fj1c3ggn0gbv2kksc8r1bx")))) + (build-system gnu-build-system) + (arguments + (list + #:configure-flags + #~(list "--sysconfdir=/etc" + "--localstatedir=/var" + ;; The shebang of the generated test files should be patched + ;; before enabling tests. + "--disable-tests") + #:make-flags + #~(list (string-append "typelibdir=" #$output "/lib/girepository-1.0")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-deprecated-gnome-common-macros + (lambda _ + ;; Adapted from a Debian patch to remove deprecated macros. + (substitute* "autogen.sh" + (("^USE_GNOME2_MACROS.*") "") + (("^USE_COMMON_DOC_BUILD.*") "")))) + (add-after 'unpack 'patch-paths + (lambda _ + (substitute* "libdbusmenu-glib/Makefile.am" + (("/bin/false") + "false") + ;; (("\\$\\(srcdir)/clean-namespaces.xslt") + ;; "clean-namespaces.xslt") + ))) + (add-before 'configure 'do-not-treat-warnings-as-errors + (lambda _ + ;; Prevent the build from failing due to deprecation warnings + ;; from newer GLib and GTK versions. + (substitute* (find-files "." "^Makefile.in$") + ((" -Werror") + "")))) + (add-before 'configure 'set-environment + (lambda _ + (setenv "HAVE_VALGRIND_TRUE" "") + (setenv "HAVE_VALGRIND_FALSE" "#")))))) + (inputs + (list glib + gtk+ + gtk+-2)) + (native-inputs + (list autoconf + automake + `(,glib "bin") + gobject-introspection + gnome-common + gtk-doc ;FIXME: propagate by gnome-common? + intltool + json-glib + libtool + libxslt + pkg-config + python-wrapper + which + vala)) + (home-page "https://launchpad.net/libdbusmenupython") + (synopsis "Library for passing menus over DBus") + (description "@code{libdbusmenu} passes a menu structure across DBus so that a program can create a menu simply without worrying about how it is displayed on the other side of the bus.") - ;; Dual-licensed under either LGPLv2.1 or LGPLv3. - (license (list license:lgpl2.1 license:lgpl3)))) + ;; Dual-licensed under either LGPLv2.1 or LGPLv3. + (license (list license:lgpl2.1 license:lgpl3))))) (define-public gtk-layer-shell (package From 209558948406f9ada66f2686a087a331b611a462 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 13:20:16 -0400 Subject: [PATCH 1324/1394] gnu: dico: Use Python 3. * gnu/packages/dico.scm (dico)[source]: Fix indentation. [phases]: Delete trailing #t. [inputs]: Use new style. Replace python-2 with python-wrapper. --- gnu/packages/dico.scm | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/gnu/packages/dico.scm b/gnu/packages/dico.scm index c7c19637263..dac61611d55 100644 --- a/gnu/packages/dico.scm +++ b/gnu/packages/dico.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2016, 2018 Efraim Flashner ;;; Copyright © 2018, 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2020 Vincent Legoll +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -41,12 +42,12 @@ (name "dico") (version "2.11") (source (origin - (method url-fetch) - (uri (string-append "mirror://gnu/dico/dico-" - version ".tar.xz")) - (sha256 - (base32 - "0nic4mggc0yhms130k7x4qp5k9c42fwg6n8hmk5cmynh6gi9h7xc")))) + (method url-fetch) + (uri (string-append "mirror://gnu/dico/dico-" + version ".tar.xz")) + (sha256 + (base32 + "0nic4mggc0yhms130k7x4qp5k9c42fwg6n8hmk5cmynh6gi9h7xc")))) (build-system gnu-build-system) (arguments '(#:configure-flags (list (string-append "--with-guile-site-dir=" %output @@ -59,23 +60,22 @@ ;; Guile is too talkative, which disturbs the test ;; infrastructure. Gag it. (setenv "GUILE_AUTO_COMPILE" "0") - (setenv "GUILE_WARN_DEPRECATED" "no") - #t)) + (setenv "GUILE_WARN_DEPRECATED" "no"))) (replace 'check (lambda _ ;; Test '71: append + dooffs + env' fails if $V is not 2. (invoke "make" "check" "V=2")))))) (native-inputs (list groff)) (inputs - `(("m4" ,m4) ;used at run time - ("pcre" ,pcre) - ("python" ,python-2) - ("guile" ,guile-2.2) - ("gsasl" ,gsasl) - ("readline" ,readline) - ("zlib" ,zlib) - ("wordnet" ,wordnet) - ("libltdl" ,libltdl))) + (list m4 ;used at run time + pcre + python-wrapper + guile-2.2 + gsasl + readline + zlib + wordnet + libltdl)) (home-page "https://www.gnu.org/software/dico/") (synopsis "Implementation of DICT server (RFC 2229)") (description @@ -84,4 +84,4 @@ RFC 2229 (DICT Server). It is able to access any database available, regardless of format, thanks to its modular structure. New modules may be written in C, Guile or Python. Dico also includes a command-line client, which may be used to query remote dictionary databases.") - (license gpl3+))) + (license gpl3+))) From 37240ead723e0eba13824e691239597f5bce7b3d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 13:28:10 -0400 Subject: [PATCH 1325/1394] gnu: lolcode-lci: Update to 0.11.2-0.6762b72. * gnu/packages/esolangs.scm (lolcode-lci): Update to 0.11.2-0.6762b72. [native-inputs]: Replace python-2 with python-wrapper. --- gnu/packages/esolangs.scm | 50 ++++++++++++++++++++++----------------- 1 file changed, 28 insertions(+), 22 deletions(-) diff --git a/gnu/packages/esolangs.scm b/gnu/packages/esolangs.scm index c37df58fe8b..81906dac15c 100644 --- a/gnu/packages/esolangs.scm +++ b/gnu/packages/esolangs.scm @@ -61,26 +61,32 @@ identified by unique ID codes).") (license license:gpl3))) (define-public lolcode-lci - (package - (name "lolcode-lci") - (version "0.11.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/justinmeza/lci") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0syw60b93iajgh91ffchirwwhm2kix2753ibx845kyrhzggmdh2l")))) - (build-system cmake-build-system) - (inputs - (list readline)) - (native-inputs - (list python-2)) ; for the tests - (synopsis "LOLCODE interpreter written in C") - (description - "@code{lci} is a LOLCODE interpreter written in C and is designed to be + ;; Use the latest commit as the last release is from 2014 with Python 2. + (let ((commit "6762b724361a4fb471345961b4750657783aeb3b") + (revision "0")) + (package + (name "lolcode-lci") + (version (git-version "0.11.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/justinmeza/lci") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0phqnqp7qvkn0kxkk5qsc76b9gxs932w4dy3jm96pmknh1q7h6kk")))) + (build-system cmake-build-system) + ;; The test suite is currently failing with Python 3 (see: + ;; https://github.com/justinmeza/lci/issues/75). + (arguments (list #:tests? #f)) + (inputs + (list readline)) + (native-inputs + (list python-wrapper)) ; for the tests + (synopsis "LOLCODE interpreter written in C") + (description + "@code{lci} is a LOLCODE interpreter written in C and is designed to be correct, portable, fast, and precisely documented. @enumerate @item correct: Every effort has been made to test lci's conformance to the @@ -90,8 +96,8 @@ to compile on a broad range of systems. @item fast: Much effort has gone into producing simple and efficient code whenever possible to the extent that the above points are not compromized. @end enumerate") - (home-page "http://lolcode.org/") - (license license:gpl3+))) + (home-page "http://lolcode.org/") + (license license:gpl3+)))) (define-public shakespeare-spl (package From d5c2d48f9e824e6d459575bdfd9ef6a5bf9d3780 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 13:30:19 -0400 Subject: [PATCH 1326/1394] gnu: Remove python2-libmpsse. * gnu/packages/embedded.scm (python2-libmpsse): Delete variable. --- gnu/packages/embedded.scm | 30 ------------------------------ 1 file changed, 30 deletions(-) diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm index 010f5b84d29..6a66fe4753a 100644 --- a/gnu/packages/embedded.scm +++ b/gnu/packages/embedded.scm @@ -1144,36 +1144,6 @@ MPSSE (Multi-Protocol Synchronous Serial Engine) adapter by FTDI that can do SPI, I2C, JTAG.") (license license:gpl2+))) -(define-public python2-libmpsse - (package - (inherit python-libmpsse) - (name "python2-libmpsse") - (arguments - (substitute-keyword-arguments (package-arguments python-libmpsse) - ((#:phases phases) - `(modify-phases ,phases - (replace 'set-environment-up - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((python (assoc-ref inputs "python"))) - (chdir "src") - (setenv "PYDEV" (string-append python - "/include/python" - ,(version-major+minor (package-version python-2)))) - #t))) - (replace 'install - (lambda* (#:key inputs outputs make-flags #:allow-other-keys #:rest args) - (let* ((out (assoc-ref outputs "out")) - (out-python (string-append out - "/lib/python" - ,(version-major+minor (package-version python-2)) - "/site-packages")) - (install (assoc-ref %standard-phases 'install))) - (install #:make-flags (cons (string-append "PYLIB=" out-python) - make-flags))))))))) - (inputs - (alist-replace "python" (list python-2) - (package-inputs python-libmpsse))))) - (define-public picprog (package (name "picprog") From 5fe7b6efbb93cadc22d39b26aa526870a682362c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 13:38:26 -0400 Subject: [PATCH 1327/1394] gnu: Remove gnome-doc-utils. * gnu/packages/gnome.scm (gnome-doc-utils): Delete variable. --- gnu/packages/gnome.scm | 31 ------------------------------- 1 file changed, 31 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 78a52a64d54..df95553d1ee 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -2226,37 +2226,6 @@ The gnome-about program helps find which version of GNOME is installed.") ; Some bits under the LGPL. (license license:gpl2+))) -(define-public gnome-doc-utils - (package - (name "gnome-doc-utils") - (version "0.20.10") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://gnome/sources/" name "/" - (version-major+minor version) "/" - name "-" version ".tar.xz")) - (sha256 - (base32 - "19n4x25ndzngaciiyd8dd6s2mf9gv6nv3wv27ggns2smm7zkj1nb")))) - (build-system gnu-build-system) - (native-inputs - (list intltool - docbook-xml-4.4 - python2-libxml2 - libxml2 - libxslt - pkg-config - python-2)) - (home-page "https://wiki.gnome.org/GnomeDocUtils") - (synopsis - "Documentation utilities for the Gnome project") - (description - "Gnome-doc-utils is a collection of documentation utilities for the -Gnome project. It includes xml2po tool which makes it easier to translate -and keep up to date translations of documentation.") - (license license:gpl2+))) ; xslt under lgpl - (define-public gnome-disk-utility (package (name "gnome-disk-utility") From 6fedf5c5b09a63ac5b63127c19044c53823d2094 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 13:44:51 -0400 Subject: [PATCH 1328/1394] gnu: gnome-keyring: Use Python 3. * gnu/packages/gnome.scm (libgnome-keyring)[source]: Fix indentation. [arguments]: Use gexps. [phases]{fix-docbook}: Delete phase. [native-inputs]: Use new style. Replaec python-2 with python-wrapper. Use current docbook-xml. Add libxml2. --- gnu/packages/gnome.scm | 83 +++++++++++++++++------------------------- 1 file changed, 33 insertions(+), 50 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index df95553d1ee..f33f3a26324 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -2477,61 +2477,44 @@ GNOME Desktop.") (name "gnome-keyring") (version "40.0") (source (origin - (method url-fetch) - (uri (string-append "mirror://gnome/sources/" name "/" - (version-major version) "/" - name "-" version ".tar.xz")) - (sha256 - (base32 - "0cdrlcw814zayhvlaxqs1sm9bqlfijlp22dzzd0g5zg2isq4vlm3")))) + (method url-fetch) + (uri (string-append "mirror://gnome/sources/" name "/" + (version-major version) "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "0cdrlcw814zayhvlaxqs1sm9bqlfijlp22dzzd0g5zg2isq4vlm3")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ;48 of 603 tests fail because /var/lib/dbus/machine-id does - ;not exist - #:configure-flags - (list - (string-append "--with-pkcs11-config=" - (assoc-ref %outputs "out") "/share/p11-kit/modules/") - (string-append "--with-pkcs11-modules=" - (assoc-ref %outputs "out") "/share/p11-kit/modules/")) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-/bin/sh-reference - (lambda _ - (substitute* "po/Makefile.in.in" - (("/bin/sh") (which "sh"))) - #t)) - (add-after 'unpack 'fix-docbook - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "docs/Makefile.am" - (("http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl") - (string-append (assoc-ref inputs "docbook-xsl") - "/xml/xsl/docbook-xsl-" - ,(package-version docbook-xsl) - "/manpages/docbook.xsl"))) - (setenv "XML_CATALOG_FILES" - (string-append (assoc-ref inputs "docbook-xml") - "/xml/dtd/docbook/catalog.xml")) - ;; Rerun the whole thing to avoid version mismatch ("This is - ;; Automake 1.15.1, but the definition used by this - ;; AM_INIT_AUTOMAKE comes from Automake 1.15."). Note: we don't - ;; use 'autoreconf' because it insists on running 'libtoolize'. - (invoke "autoconf") - (invoke "aclocal") - (invoke "automake" "-ac")))))) + (list + #:tests? #f ;48 of 603 tests fail because /var/lib/dbus/machine-id does + ;not exist + #:configure-flags + #~(list + (string-append "--with-pkcs11-config=" + #$output "/share/p11-kit/modules/") + (string-append "--with-pkcs11-modules=" + #$output "/share/p11-kit/modules/")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-/bin/sh-reference + (lambda _ + (substitute* "po/Makefile.in.in" + (("/bin/sh") (which "sh")))))))) (inputs (list libgcrypt linux-pam openssh dbus gcr)) (native-inputs - `(("pkg-config" ,pkg-config) - ("glib" ,glib "bin") - ("glib" ,glib) ; for m4 macros - ("python" ,python-2) ;for tests - ("intltool" ,intltool) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("libxslt" ,libxslt) ;for documentation - ("docbook-xml" ,docbook-xml-4.3) - ("docbook-xsl" ,docbook-xsl))) + (list pkg-config + `(,glib "bin") + glib ;for m4 macros + python-wrapper ;for tests + intltool + autoconf + automake + libxml2 ;for XML_CATALOG_FILES + libxslt ;for documentation + docbook-xml + docbook-xsl)) (propagated-inputs (list gcr)) (home-page "https://www.gnome.org") From affa792b5e48ac4f1355412338ef819f7a5088e0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 13:48:19 -0400 Subject: [PATCH 1329/1394] gnu: Remove python2-more-itertools. * gnu/packages/python-xyz.scm (python2-more-itertools): Delete variable. (python-jsonpatch)[properties]: Delete field. --- gnu/packages/python-xyz.scm | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 33137bf050b..2c081908f36 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21091,26 +21091,8 @@ file system events on Linux.") number of iterator building blocks inspired by constructs from APL, Haskell, and SML. @code{more-itertools} includes additional building blocks for working with iterables.") - (properties `((python2-variant . ,(delay python2-more-itertools)))) (license license:expat))) -;; The 5.x series are the last versions supporting Python 2.7. -(define-public python2-more-itertools - (package - (inherit python-more-itertools) - (name "python2-more-itertools") - (version "5.0.0") - (source (origin - (method url-fetch) - (uri (pypi-uri "more-itertools" version)) - (sha256 - (base32 - "1r12cm6mcdwdzz7d47a6g4l437xsvapdlgyhqay3i2nrlv03da9q")))) - (arguments - `(#:python ,python-2)) - (propagated-inputs - `(("python2-six" ,python2-six-bootstrap))))) - (define-public python-latexcodec (package (name "python-latexcodec") From fdf967e8fe0f4393d1788d0e103c6eb78d2aec86 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 13:48:50 -0400 Subject: [PATCH 1330/1394] gnu: Remove python2-tlsh. * gnu/packages/python-xyz.scm (python2-tlsh): Delete variable. --- gnu/packages/python-xyz.scm | 5 ----- 1 file changed, 5 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2c081908f36..5fa13f01a49 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12269,11 +12269,6 @@ of complexity; for example, a byte stream of identical bytes will not generate a hash value.") (license license:asl2.0))) -(define-public python2-tlsh - (package/inherit python-tlsh - (name "python2-tlsh") - (inputs `(("python" ,python-2))))) - (define-public python-termcolor (package (name "python-termcolor") From 0b478a5d701f4794e46794967055d9e11c8bdfb2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 13:50:14 -0400 Subject: [PATCH 1331/1394] gnu: Remove python2-lirc. * gnu/packages/lirc.scm (python2-lirc): Delete variable. (python-lirc)[properties]: Delete field. --- gnu/packages/lirc.scm | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) diff --git a/gnu/packages/lirc.scm b/gnu/packages/lirc.scm index 1b8e8e37bd8..5c89e83d7c3 100644 --- a/gnu/packages/lirc.scm +++ b/gnu/packages/lirc.scm @@ -133,17 +133,4 @@ on just one button press.") (home-page "https://github.com/tompreston/python-lirc") (synopsis "Python bindings for LIRC") (description "@code{lirc} is a Python module which provides LIRC bindings.") - (license license:gpl3) - (properties `((python2-variant . ,(delay python2-lirc))))))) - - (define-public python2-lirc - (let ((base (package-with-python2 (strip-python2-variant python-lirc)))) - (package/inherit base - (arguments - `(#:tests? #f ; the only tests that exist are human-interactive - #:phases - (modify-phases %standard-phases - (add-before 'build 'build-from-cython-files - (lambda _ (invoke "make" "py2")))))) - (native-inputs - `(("python2-cython" ,python2-cython)))))) + (license license:gpl3)))) From 425783b5dcec38842718829c9fe56741bbcfc567 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 13:50:50 -0400 Subject: [PATCH 1332/1394] gnu: Remove python2-cython. * gnu/packages/python-xyz.scm (python2-cython): Delete variable. (python-feedgenerator)[properties]: Delete field. --- gnu/packages/python-xyz.scm | 37 +------------------------------------ 1 file changed, 1 insertion(+), 36 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5fa13f01a49..e1627a960a2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5313,42 +5313,7 @@ provides additional functionality on the produced Mallard documents.") (description "Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language. It makes writing C extensions for Python as easy as Python itself.") - (license license:asl2.0) - (properties `((python2-variant . ,(delay python2-cython)))))) - -(define-public python2-cython - (let ((base (package-with-python2 (strip-python2-variant python-cython)))) - (package/inherit base - (name "python2-cython") - (inputs - `(("python-2" ,python-2))) ;this is not automatically changed - (arguments - (substitute-keyword-arguments (package-arguments base) - ((#:phases phases) - `(modify-phases ,phases - (add-before 'check 'adjust-test_embed - (lambda _ - (substitute* "runtests.py" - ;; test_embed goes great lengths to find the static libpythonX.Y.a - ;; so it can give the right -L flag to GCC when embedding static - ;; builds of Python. It is unaware that the Python "config" - ;; directory (where the static library lives) was renamed in - ;; Python 3, and falls back to sysconfig.get_config_var('LIBDIR'), - ;; which works fine, because that is where the shared library is. - ;; - ;; It also appears to be unaware that the Makefile in Demos/embed - ;; already unconditionally pass the static library location to GCC, - ;; after checking sysconfig.get_config_var('LIBPL). - ;; - ;; The effect is that the linker is unable to resolve libexpat - ;; symbols when building for Python 2, because neither the Python 2 - ;; shared library nor Expat is available. To fix it, we can either - ;; add Expat as an input and make it visible to the linker, or just - ;; prevent it from overriding the Python shared library location. - ;; The end result is identical, so we take the easy route. - ((" or libname not in os\\.listdir\\(libdir\\)") - "")) - #t))))))))) + (license license:asl2.0))) (define-public python-cython-3 (package From 5e25a69e6e3733ad8845d1b187940877deba7750 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 14:03:41 -0400 Subject: [PATCH 1333/1394] gnu: mozjs: Cleanup to only keep the last version. * gnu/packages/gnuzilla.scm (mozjs): Preserve only the metadata and otherwise update fields to use those of mozjs-78. [arguments]: Use gexps. [phases]: Delete trailing #t. [native-inputs]: Use new style. (mozjs-38, mozjs-52, mozjs-60, mozjs-78): Delete variables. * gnu/packages/patches/mozjs17-aarch64-support.patch * gnu/packages/patches/mozjs24-aarch64-support.patch * gnu/packages/patches/mozjs38-pkg-config-version.patch * gnu/packages/patches/mozjs38-shell-version.patch * gnu/packages/patches/mozjs38-tracelogger.patch * gnu/packages/patches/mozjs38-version-detection.patch * gnu/packages/patches/mozjs60-riscv64-support.patch: Delete patches. * gnu/local.mk (dist_patch_DATA): De-register them. * gnu/packages/games.scm (0ad): Adjust accordingly. * gnu/packages/gnome.scm (gjs): Likewise. * gnu/packages/polkit.scm (polkit-mozjs): Likewise. --- gnu/local.mk | 7 - gnu/packages/games.scm | 2 +- gnu/packages/gnome.scm | 2 +- gnu/packages/gnuzilla.scm | 555 +++------------- .../patches/mozjs17-aarch64-support.patch | 60 -- .../patches/mozjs24-aarch64-support.patch | 21 - .../patches/mozjs38-pkg-config-version.patch | 24 - .../patches/mozjs38-shell-version.patch | 67 -- .../patches/mozjs38-tracelogger.patch | 608 ------------------ .../patches/mozjs38-version-detection.patch | 180 ------ .../patches/mozjs60-riscv64-support.patch | 122 ---- gnu/packages/polkit.scm | 2 +- 12 files changed, 108 insertions(+), 1542 deletions(-) delete mode 100644 gnu/packages/patches/mozjs17-aarch64-support.patch delete mode 100644 gnu/packages/patches/mozjs24-aarch64-support.patch delete mode 100644 gnu/packages/patches/mozjs38-pkg-config-version.patch delete mode 100644 gnu/packages/patches/mozjs38-shell-version.patch delete mode 100644 gnu/packages/patches/mozjs38-tracelogger.patch delete mode 100644 gnu/packages/patches/mozjs38-version-detection.patch delete mode 100644 gnu/packages/patches/mozjs60-riscv64-support.patch diff --git a/gnu/local.mk b/gnu/local.mk index 83ee7e29303..947669459e4 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1509,13 +1509,6 @@ dist_patch_DATA = \ %D%/packages/patches/monero-use-system-miniupnpc.patch \ %D%/packages/patches/mono-mdoc-timestamping.patch \ %D%/packages/patches/mosaicatcher-unbundle-htslib.patch \ - %D%/packages/patches/mozjs17-aarch64-support.patch \ - %D%/packages/patches/mozjs24-aarch64-support.patch \ - %D%/packages/patches/mozjs38-pkg-config-version.patch \ - %D%/packages/patches/mozjs38-shell-version.patch \ - %D%/packages/patches/mozjs38-tracelogger.patch \ - %D%/packages/patches/mozjs38-version-detection.patch \ - %D%/packages/patches/mozjs60-riscv64-support.patch \ %D%/packages/patches/mrrescue-support-love-11.patch \ %D%/packages/patches/mtools-mformat-uninitialized.patch \ %D%/packages/patches/mumps-build-parallelism.patch \ diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 76f1e5df867..05bcdc9b989 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -6690,7 +6690,7 @@ fight against their plot and save his fellow rabbits from slavery.") libxcursor libxml2 miniupnpc - mozjs-78 + mozjs openal sdl2 wxwidgets diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index f33f3a26324..15d0d5f6a04 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -7203,7 +7203,7 @@ configuration program to choose applications starting on login.") ("xvfb" ,xorg-server-for-tests))) (propagated-inputs ;; These are all in the Requires.private field of gjs-1.0.pc. - (list cairo gobject-introspection mozjs-78)) + (list cairo gobject-introspection mozjs)) (inputs (list gtk+ readline)) (synopsis "Javascript bindings for GNOME") diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 8f1e8fe6475..0c64c44adf1 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -96,356 +96,6 @@ (define-public mozjs (package (name "mozjs") - (version "17.0.0") - (source (origin - (method url-fetch) - (uri (string-append - "https://ftp.mozilla.org/pub/mozilla.org/js/" - name version ".tar.gz")) - (sha256 - (base32 - "1fig2wf4f10v43mqx67y68z6h77sy900d1w0pz9qarrqx57rc7ij")) - (patches (search-patches "mozjs17-aarch64-support.patch")) - (modules '((guix build utils))) - (snippet - ;; Fix incompatibility with Perl 5.22+. - '(begin - (substitute* '("js/src/config/milestone.pl") - (("defined\\(@TEMPLATE_FILE)") "@TEMPLATE_FILE")) - #t)))) - (build-system gnu-build-system) - (native-inputs - `(("perl" ,perl) - ("pkg-config" ,pkg-config) - ("python" ,python-2))) - (propagated-inputs - (list nspr)) ; in the Requires.private field of mozjs-17.0.pc - (inputs - (list zlib)) - (arguments - `(;; XXX: parallel build fails, lacking: - ;; mkdir -p "system_wrapper_js/" - #:parallel-build? #f - #:make-flags '("CXXFLAGS=-fpermissive") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'delete-timedout-test - ;; This test times out on slower hardware. - (lambda _ - (delete-file "js/src/jit-test/tests/basic/bug698584.js") - #t)) - (add-before 'configure 'chdir - (lambda _ - (chdir "js/src") - #t)) - (replace 'configure - ;; configure fails if it is followed by SHELL and CONFIG_SHELL - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (setenv "SHELL" (which "sh")) - (setenv "CONFIG_SHELL" (which "sh")) - (invoke "./configure" (string-append "--prefix=" out) - ,@(if (string=? "aarch64-linux" - (%current-system)) - '("--host=aarch64-unknown-linux-gnu") - '())))))))) - (home-page - "https://developer.mozilla.org/en-US/docs/Mozilla/Projects/SpiderMonkey") - (synopsis "Mozilla javascript engine") - (description "SpiderMonkey is Mozilla's JavaScript engine written -in C/C++.") - (license license:mpl2.0))) ; and others for some files - -(define-public mozjs-24 - (package (inherit mozjs) - (name "mozjs") - (version "24.2.0") - (source (origin - (method url-fetch) - (uri (string-append - "https://ftp.mozilla.org/pub/mozilla.org/js/" - name "-" version ".tar.bz2")) - (sha256 - (base32 - "1n1phk8r3l8icqrrap4czplnylawa0ddc2cc4cgdz46x3lrkybz6")) - (modules '((guix build utils))) - (patches (search-patches "mozjs24-aarch64-support.patch")) - (snippet - ;; Fix incompatibility with Perl 5.22+. - '(begin - (substitute* '("js/src/config/milestone.pl") - (("defined\\(@TEMPLATE_FILE)") "@TEMPLATE_FILE")) - #t)))) - (arguments - (substitute-keyword-arguments (package-arguments mozjs) - ((#:phases phases) - `(modify-phases ,phases - (replace 'configure - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - ;; configure fails if it is followed by SHELL and CONFIG_SHELL - (setenv "SHELL" (which "sh")) - (setenv "CONFIG_SHELL" (which "sh")) - (invoke "./configure" - (string-append "--prefix=" out) - "--with-system-nspr" - "--enable-system-ffi" - "--enable-threadsafe" - ,@(if (string=? "aarch64-linux" - (%current-system)) - '("--host=aarch64-unknown-linux-gnu") - '()))))))))) - (inputs - (list libffi zlib)))) - -(define-public mozjs-38 - (package - (inherit mozjs) - (name "mozjs") - (version "38.2.1.rc0") - (source (origin - (method url-fetch) - (uri (string-append - "https://anduin.linuxfromscratch.org/BLFS/mozjs/" - name "-" version ".tar.bz2")) - (sha256 - (base32 - "0p4bmbpgkfsj54xschcny0a118jdrdgg0q29rwxigg3lh5slr681")) - (patches - (search-patches - ;; See https://bugzilla.mozilla.org/show_bug.cgi?id=1269317 for - ;; GCC 6 compatibility. - - "mozjs38-version-detection.patch" ; for 0ad - "mozjs38-tracelogger.patch" - - ;; See https://bugzilla.mozilla.org/show_bug.cgi?id=1339931. - "mozjs38-pkg-config-version.patch" - "mozjs38-shell-version.patch")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Fix incompatibility with sed 4.4. - (substitute* "js/src/configure" - (("\\^\\[:space:\\]") "^[[:space:]]")) - - ;; The headers are symlinks to files that are in /tmp, so they - ;; end up broken. Copy them instead. - (substitute* - "python/mozbuild/mozbuild/backend/recursivemake.py" - (("\\['dist_include'\\].add_symlink") - "['dist_include'].add_copy")) - - ;; Remove bundled libraries. - (for-each delete-file-recursively - '("intl" - "js/src/ctypes/libffi" - "js/src/ctypes/libffi-patches" - "modules/zlib")) - #t)))) - (arguments - `(;; XXX: parallel build fails, lacking: - ;; mkdir -p "system_wrapper_js/" - #:parallel-build? #f - ;; See https://bugzilla.mozilla.org/show_bug.cgi?id=1008470. - #:tests? #f - #:phases - (modify-phases %standard-phases - (replace 'configure - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (chdir "js/src") - (setenv "SHELL" (which "sh")) - (setenv "CONFIG_SHELL" (which "sh")) - (invoke "./configure" - (string-append "--prefix=" out) - "--enable-ctypes" - "--enable-gcgenerational" - "--enable-optimize" - "--enable-pie" - "--enable-readline" - "--enable-shared-js" - "--enable-system-ffi" - "--enable-threadsafe" - "--enable-xterm-updates" - "--with-system-icu" - "--with-system-nspr" - "--with-system-zlib" - - ;; Intl API requires bundled ICU. - "--without-intl-api"))))))) - (native-inputs - `(("perl" ,perl) - ("pkg-config" ,pkg-config) - ("python-2" ,python-2))) - (inputs - (list libffi readline icu4c zlib)))) - -(define-public mozjs-52 - ;; No releases yet at . - ;; While we could take a snapshot of the complete mozilla-esr52 repository at - ;; , - ;; we take the Debian version instead, because it is easier to work with. - (let ((commit "6507e63cc416fd7a3269e390efe712f8b56f374a") - (revision "1")) - (package (inherit mozjs-38) - (version (git-version "52.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://salsa.debian.org/gnome-team/mozjs52.git") - (commit commit))) - (file-name (git-file-name "mozjs" version)) - (sha256 - (base32 - "1ny0s53r8wn4byys87h784xrq1xg767akmfm6gqrbvrz57mlm3q2")))) - (arguments - `(#:tests? #f ; depends on repository metadata - #:configure-flags - '("--enable-ctypes" - "--enable-optimize" - "--enable-pie" - "--enable-readline" - "--enable-shared-js" - "--enable-system-ffi" - "--with-system-icu" - "--with-system-nspr" - "--with-system-zlib" - - ;; Intl API requires bundled ICU. - "--without-intl-api" - - ;; Without this gnome-shell will crash at runtime. - "--disable-jemalloc") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-and-chdir - (lambda* (#:key inputs #:allow-other-keys) - ;; This patch prevents a segfault when executing JS_Init(). - ;; The build does not fail without this patch, but the - ;; configure phase of the gjs package would fail. - ;; See https://bugzilla.mozilla.org/show_bug.cgi?id=1176787 - (make-file-writable "js/src/old-configure.in") - (make-file-writable "js/src/old-configure") - (make-file-writable "mozglue/build/moz.build") - (invoke "patch" "-p1" "--force" - "--input" "debian/patches/disable-mozglue.patch") - (invoke "touch" "js/src/configure") - (chdir "js/src") - #t)) - (replace 'configure - (lambda* (#:key inputs outputs configure-flags #:allow-other-keys) - ;; The configure script does not accept environment variables - ;; as arguments. - (let ((out (assoc-ref outputs "out"))) - (setenv "SHELL" (which "sh")) - (setenv "CONFIG_SHELL" (which "sh")) - (setenv "AUTOCONF" (which "autoconf")) - (apply invoke "./configure" - (cons (string-append "--prefix=" out) - configure-flags)))))))) - (native-inputs - (modify-inputs (package-native-inputs mozjs-38) - (prepend autoconf-2.13 automake)))))) - -(define-public mozjs-60 - ;; No releases yet at . - ;; While we could take a snapshot of the complete mozilla-esr60 repository at - ;; , - ;; we take the Debian version instead, because it is easier to work with. - (package - (inherit mozjs-38) - (version "60.2.3-4") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://salsa.debian.org/gnome-team/mozjs60.git") - (commit (string-append "debian/" version)))) - (file-name (git-file-name "mozjs" version)) - (sha256 - (base32 - "1xl6avsj9gkgma71p56jzs7nasc767k3n1frnmri5pad4rj94bij")) - (patches (search-patches "mozjs60-riscv64-support.patch")))) - (arguments - `(#:tests? #f ; FIXME: all tests pass, but then the check phase fails anyway. - #:test-target "check-jstests" - #:configure-flags - ,#~(quasiquote - ("--enable-ctypes" - "--enable-optimize" - "--enable-pie" - "--enable-readline" - "--enable-shared-js" - "--enable-system-ffi" - "--with-system-nspr" - #$@(if (%current-target-system) - #~(,(string-append "--with-nspr-prefix=" - #$(this-package-input "nspr"))) - #~()) - "--with-system-zlib" - "--with-system-icu" - "--with-intl-api" - ;; This is important because without it gjs will segfault during the - ;; configure phase. With jemalloc only the standalone mozjs console - ;; will work. - "--disable-jemalloc" - ;; Mozilla deviates from Autotools conventions due to historical - ;; reasons. - #$@(if (%current-target-system) - #~(#$(string-append - "--host=" - (nix-system->gnu-triplet (%current-system))) - #$(string-append "--target=" (%current-target-system))) - #~()))) - #:phases - (modify-phases %standard-phases - ;; Make sure pkg-config will be found. - ,@(if (%current-target-system) - `((add-before 'configure 'set-PKG-CONFIG - (lambda _ - (setenv "PKG_CONFIG" ,(pkg-config-for-target))))) - '()) - (replace 'configure - (lambda* (#:key inputs outputs configure-flags #:allow-other-keys) - ;; The configure script does not accept environment variables as - ;; arguments. It also must be run from a different directory, - ;; but not the root directory either. - (let ((out (assoc-ref outputs "out"))) - (mkdir "run-configure-from-here") - (chdir "run-configure-from-here") - (setenv "SHELL" (which "sh")) - (setenv "CONFIG_SHELL" (which "sh")) - (setenv "AUTOCONF" (which "autoconf")) - (apply invoke "../js/src/configure" - (cons (string-append "--prefix=" out) - configure-flags)) - #t))) - (add-after 'unpack 'update-config-scripts - (lambda* (#:key native-inputs inputs #:allow-other-keys) - (for-each (lambda (file) - (install-file - (search-input-file - (or native-inputs inputs) - (string-append "/bin/" file)) "build/autoconf")) - '("config.guess" "config.sub")))) - (add-after 'unpack 'disable-broken-tests - (lambda _ - ;; This test assumes that /bin exists and contains certain - ;; executables. - (delete-file "js/src/tests/shell/os.js") - #t))))) - (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("config" ,config) - ("which" ,which) - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("python" ,python-2))))) - -(define-public mozjs-78 - (package - (inherit mozjs-60) (version "78.15.0") (source (origin (method url-fetch) @@ -456,13 +106,16 @@ in C/C++.") (sha256 (base32 "0l91cxdc5v9fps79ckb1kid4gw6v5qng1jd9zvaacwaiv628shx4")))) + (build-system gnu-build-system) (arguments - `(#:imported-modules ,%cargo-utils-modules ;for `generate-all-checksums' - #:modules ((guix build cargo-utils) + (list + #:imported-modules %cargo-utils-modules ;for `generate-all-checksums' + #:modules `((guix build cargo-utils) ,@%gnu-build-system-modules) - #:test-target "check-jstests" - #:configure-flags - '(;; Disable debugging symbols to save space. + #:test-target "check-jstests" + #:configure-flags + #~(list + ;; Disable debugging symbols to save space. "--disable-debug" "--disable-debug-symbols" ;; This is important because without it gjs will segfault during the @@ -483,109 +136,111 @@ in C/C++.") "--with-system-nspr" "--with-system-zlib" "--with-intl-api") - #:phases - (modify-phases %standard-phases - (add-after 'patch-source-shebangs 'patch-cargo-checksums - (lambda _ - (let ((null-hash - "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855")) - (for-each (lambda (file) - (format #t "patching checksums in ~a~%" file) - (substitute* file - (("^checksum = \".*\"") - (string-append "checksum = \"" null-hash "\"")))) - (find-files "." "Cargo\\.lock$")) - (for-each generate-all-checksums - '("js" "third_party/rust")) - #t))) - (replace 'configure - (lambda* (#:key inputs outputs configure-flags #:allow-other-keys) - ;; The configure script does not accept environment variables as - ;; arguments. It also must be run from a different directory, - ;; but not the root directory either. - (let ((out (assoc-ref outputs "out"))) - (mkdir "run-configure-from-here") - (chdir "run-configure-from-here") - (setenv "SHELL" (which "sh")) - (setenv "CONFIG_SHELL" (which "sh")) - (setenv "AUTOCONF" (which "autoconf")) - (apply invoke "../js/src/configure" - (cons (string-append "--prefix=" out) - configure-flags)) - #t))) - (add-after 'unpack 'adjust-for-icu-68 - (lambda _ - (with-directory-excursion "js/src/tests" - ;; The test suite expects a lightly patched ICU 67. Since - ;; Guix is about to switch to ICU 68, massage the tests to - ;; work with that instead of patching ICU. Try removing this - ;; phase for newer versions of mozjs. + #:phases + #~(modify-phases %standard-phases + (add-after 'patch-source-shebangs 'patch-cargo-checksums + (lambda _ + (let ((null-hash + "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855")) + (for-each (lambda (file) + (format #t "patching checksums in ~a~%" file) + (substitute* file + (("^checksum = \".*\"") + (string-append "checksum = \"" null-hash "\"")))) + (find-files "." "Cargo\\.lock$")) + (for-each generate-all-checksums + '("js" "third_party/rust"))))) + (replace 'configure + (lambda* (#:key inputs configure-flags #:allow-other-keys) + ;; The configure script does not accept environment variables as + ;; arguments. It also must be run from a different directory, + ;; but not the root directory either. + (mkdir "run-configure-from-here") + (chdir "run-configure-from-here") + (setenv "SHELL" (which "sh")) + (setenv "CONFIG_SHELL" (which "sh")) + (setenv "AUTOCONF" (which "autoconf")) + (apply invoke "../js/src/configure" + (cons (string-append "--prefix=" #$output) + configure-flags)))) + (add-after 'unpack 'adjust-for-icu-68 + (lambda _ + (with-directory-excursion "js/src/tests" + ;; The test suite expects a lightly patched ICU 67. Since + ;; Guix is about to switch to ICU 68, massage the tests to + ;; work with that instead of patching ICU. Try removing this + ;; phase for newer versions of mozjs. - ;; These tests look up locale names and expects to get - ;; "GB" instead of "UK". - (substitute* "non262/Intl/DisplayNames/language.js" - (("Traditionell, GB") - "Traditionell, UK")) - (substitute* "non262/Intl/DisplayNames/region.js" - (("\"GB\": \"GB\"") - "\"GB\": \"UK\"")) + ;; These tests look up locale names and expects to get + ;; "GB" instead of "UK". + (substitute* "non262/Intl/DisplayNames/language.js" + (("Traditionell, GB") + "Traditionell, UK")) + (substitute* "non262/Intl/DisplayNames/region.js" + (("\"GB\": \"GB\"") + "\"GB\": \"UK\"")) - ;; XXX: Some localized time formats have changed, and - ;; substitution fails for accented characters, even though - ;; it works in the REPL(?). Just delete these for now. - (delete-file "non262/Intl/Date/toLocaleString_timeZone.js") - (delete-file "non262/Intl/Date/toLocaleDateString_timeZone.js") + ;; XXX: Some localized time formats have changed, and + ;; substitution fails for accented characters, even though + ;; it works in the REPL(?). Just delete these for now. + (delete-file "non262/Intl/Date/toLocaleString_timeZone.js") + (delete-file "non262/Intl/Date/toLocaleDateString_timeZone.js") - ;; Similarly, these get an unexpected "A" suffix when looking - ;; up a time in the "ar-MA-u-ca-islamicc" locale, which is - ;; tricky to substitute. - (delete-file "non262/Intl/DateTimeFormat/format_timeZone.js") - (delete-file "non262/Intl/DateTimeFormat/format.js") + ;; Similarly, these get an unexpected "A" suffix when looking + ;; up a time in the "ar-MA-u-ca-islamicc" locale, which is + ;; tricky to substitute. + (delete-file "non262/Intl/DateTimeFormat/format_timeZone.js") + (delete-file "non262/Intl/DateTimeFormat/format.js") - ;; This file compares a generated list of ICU locale names - ;; with actual lookups. Some have changed slightly, i.e. - ;; daf-Latn-ZZ -> daf-Latn-CI, so drop it for simplicity. - (delete-file "non262/Intl/Locale/likely-subtags-generated.js")) + ;; This file compares a generated list of ICU locale names + ;; with actual lookups. Some have changed slightly, i.e. + ;; daf-Latn-ZZ -> daf-Latn-CI, so drop it for simplicity. + (delete-file "non262/Intl/Locale/likely-subtags-generated.js")))) + (add-before 'check 'pre-check + (lambda _ + (with-directory-excursion "../js/src/tests" + (substitute* "shell/os.js" + ;; FIXME: Why does the killed process have an exit status? + ((".*killed process should not have exitStatus.*") + "")) - #t)) - (add-before 'check 'pre-check - (lambda _ - (with-directory-excursion "../js/src/tests" - (substitute* "shell/os.js" - ;; FIXME: Why does the killed process have an exit status? - ((".*killed process should not have exitStatus.*") - "")) + ;; XXX: Delete all tests that test time zone functionality, + ;; because the test suite uses /etc/localtime to figure out + ;; the offset from the hardware clock, which does not work + ;; in the build container. See . + (delete-file-recursively "non262/Date") + (delete-file "non262/Intl/DateTimeFormat/tz-environment-variable.js") - ;; XXX: Delete all tests that test time zone functionality, - ;; because the test suite uses /etc/localtime to figure out - ;; the offset from the hardware clock, which does not work - ;; in the build container. See . - (delete-file-recursively "non262/Date") - (delete-file "non262/Intl/DateTimeFormat/tz-environment-variable.js") - - (setenv "JSTESTS_EXTRA_ARGS" - (string-join - (list - ;; Do not run tests marked as "random". - "--exclude-random" - ;; Exclude web platform tests. - "--wpt=disabled" - ;; Respect the daemons configured number of jobs. - (string-append "--worker-count=" - (number->string (parallel-job-count))))))) - #t))))) + (setenv "JSTESTS_EXTRA_ARGS" + (string-join + (list + ;; Do not run tests marked as "random". + "--exclude-random" + ;; Exclude web platform tests. + "--wpt=disabled" + ;; Respect the daemons configured number of jobs. + (string-append "--worker-count=" + (number->string (parallel-job-count)))))))))))) (native-inputs - `(("autoconf" ,autoconf-2.13) - ("automake" ,automake) - ;; TODO(staging): Use the default LLVM in the next rebuild cycle. - ("llvm" ,llvm-9) ;for llvm-objdump - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("python" ,python-3) - ("rust" ,rust) - ("cargo" ,rust "cargo"))) + (list autoconf-2.13 + automake + ;; TODO(staging): Use the default LLVM in the next rebuild cycle. + llvm-9 ;for llvm-objdump + perl + pkg-config + python-3 + rust + `(,rust "cargo"))) (inputs - (list icu4c readline zlib)))) + (list icu4c readline zlib)) + (propagated-inputs + (list nspr)) ; in the Requires.private field of mozjs-*.pc + (home-page + "https://developer.mozilla.org/en-US/docs/Mozilla/Projects/SpiderMonkey") + (synopsis "Mozilla javascript engine") + (description "SpiderMonkey is Mozilla's JavaScript engine written +in C/C++.") + (license license:mpl2.0))) ; and others for some files (define mozilla-compare-locales (origin diff --git a/gnu/packages/patches/mozjs17-aarch64-support.patch b/gnu/packages/patches/mozjs17-aarch64-support.patch deleted file mode 100644 index 51e2e306d51..00000000000 --- a/gnu/packages/patches/mozjs17-aarch64-support.patch +++ /dev/null @@ -1,60 +0,0 @@ -https://build.opensuse.org/package/view_file/openSUSE:Factory/mozjs17/mozjs-aarch64-support.patch - -index c071c33..90764c3 100644 ---- a/js/src/assembler/jit/ExecutableAllocator.h -+++ b/js/src/assembler/jit/ExecutableAllocator.h -@@ -382,6 +382,12 @@ public: - { - reprotectRegion(start, size, Executable); - } -+#elif WTF_CPU_AARCH64 && WTF_PLATFORM_LINUX -+ static void cacheFlush(void* code, size_t size) -+ { -+ intptr_t end = reinterpret_cast(code) + size; -+ __builtin___clear_cache(reinterpret_cast(code), reinterpret_cast(end)); -+ } - #else - static void makeWritable(void*, size_t) {} - static void makeExecutable(void*, size_t) {} -diff --git a/js/src/assembler/wtf/Platform.h b/js/src/assembler/wtf/Platform.h -index 0c84896..e8763a7 100644 ---- a/js/src/assembler/wtf/Platform.h -+++ b/js/src/assembler/wtf/Platform.h -@@ -325,6 +325,10 @@ - #define WTF_THUMB_ARCH_VERSION 0 - #endif - -+/* CPU(AArch64) - 64-bit ARM */ -+#if defined(__aarch64__) -+#define WTF_CPU_AARCH64 1 -+#endif - - /* WTF_CPU_ARMV5_OR_LOWER - ARM instruction set v5 or earlier */ - /* On ARMv5 and below the natural alignment is required. -diff --git a/js/src/configure.in b/js/src/configure.in -index 15605b2..19fd704 100644 ---- a/js/src/configure.in -+++ b/js/src/configure.in -@@ -1121,6 +1121,10 @@ arm*) - CPU_ARCH=arm - ;; - -+aarch64) -+ CPU_ARCH=aarch64 -+ ;; -+ - mips|mipsel) - CPU_ARCH="mips" - ;; -diff --git a/mfbt/double-conversion/utils.h b/mfbt/double-conversion/utils.h -index 0eec2d9..fe26dab 100644 ---- a/mfbt/double-conversion/utils.h -+++ b/mfbt/double-conversion/utils.h -@@ -58,6 +58,7 @@ - defined(__mips__) || defined(__powerpc__) || \ - defined(__sparc__) || defined(__sparc) || defined(__s390__) || \ - defined(__SH4__) || defined(__alpha__) || \ -+ defined(__aarch64__) || \ - defined(_MIPS_ARCH_MIPS32R2) - #define DOUBLE_CONVERSION_CORRECT_DOUBLE_OPERATIONS 1 - #elif defined(_M_IX86) || defined(__i386__) || defined(__i386) diff --git a/gnu/packages/patches/mozjs24-aarch64-support.patch b/gnu/packages/patches/mozjs24-aarch64-support.patch deleted file mode 100644 index 9dca8e500c3..00000000000 --- a/gnu/packages/patches/mozjs24-aarch64-support.patch +++ /dev/null @@ -1,21 +0,0 @@ -This patch is sourced from Debian's mozjs24 patch set. - -Description: Add arm64 support -Author: Andreas Schwab -Origin: vendor, https://build.opensuse.org/package/view_file/openSUSE:Factory/mozjs17/mozjs-aarch64-support.patch -Forwarded: no -Last-Update: 2014-01-03 - -Index: b/mfbt/double-conversion/utils.h -=================================================================== ---- a/mfbt/double-conversion/utils.h -+++ b/mfbt/double-conversion/utils.h -@@ -58,7 +58,7 @@ - defined(__mips__) || defined(__powerpc__) || \ - defined(__sparc__) || defined(__sparc) || defined(__s390__) || \ - defined(__SH4__) || defined(__alpha__) || \ -- defined(_MIPS_ARCH_MIPS32R2) -+ defined(_MIPS_ARCH_MIPS32R2) || defined(__aarch64__) - #define DOUBLE_CONVERSION_CORRECT_DOUBLE_OPERATIONS 1 - #elif defined(_M_IX86) || defined(__i386__) || defined(__i386) - #if defined(_WIN32) diff --git a/gnu/packages/patches/mozjs38-pkg-config-version.patch b/gnu/packages/patches/mozjs38-pkg-config-version.patch deleted file mode 100644 index 49ff6f6f8d1..00000000000 --- a/gnu/packages/patches/mozjs38-pkg-config-version.patch +++ /dev/null @@ -1,24 +0,0 @@ -Taken from https://bug1339931.bmoattachments.org/attachment.cgi?id=8837770. - -Add major version to pkg-config filename. -Author: Rico Tzschichholz -Forwarded: no -Last-Update: 2015-05-04 - -Index: b/js/src/Makefile.in -=================================================================== ---- a/js/src/Makefile.in -+++ b/js/src/Makefile.in -@@ -214,10 +214,10 @@ - $(JS_CONFIG_NAME): js-config - cp $^ $@ - --$(LIBRARY_NAME).pc: js.pc -+$(JS_LIBRARY_NAME).pc: js.pc - cp $^ $@ - --install:: $(LIBRARY_NAME).pc -+install:: $(JS_LIBRARY_NAME).pc - $(SYSINSTALL) $^ $(DESTDIR)$(libdir)/pkgconfig - - install:: js-config.h diff --git a/gnu/packages/patches/mozjs38-shell-version.patch b/gnu/packages/patches/mozjs38-shell-version.patch deleted file mode 100644 index e7d3d19c852..00000000000 --- a/gnu/packages/patches/mozjs38-shell-version.patch +++ /dev/null @@ -1,67 +0,0 @@ -Taken from https://bug1339931.bmoattachments.org/attachment.cgi?id=8837771. - -# HG changeset patch -# Parent 4732a0e5d22bc7e5c1f1ace7a182d537d9cc2c6a -Add major version to shell and js-config filenames. -Author: Rico Tzschichholz -Forwarded: no -Last-Update: 2014-10-29 - ---- -diff --git a/js/src/configure b/js/src/configure ---- a/js/src/configure -+++ b/js/src/configure -@@ -1696,8 +1696,13 @@ - MOZJS_PATCH_VERSION=`echo $MOZILLA_VERSION | sed "s|^[0-9]*\.[0-9]*[^0-9]*||"` - IS_ALPHA=`echo $MOZILLA_VERSION | grep '[ab]'` - -+if test -n "$JS_STANDALONE"; then -+JS_SHELL_NAME=js$MOZJS_MAJOR_VERSION -+JS_CONFIG_NAME=js$MOZJS_MAJOR_VERSION-config -+else - JS_SHELL_NAME=js - JS_CONFIG_NAME=js-config -+fi - - - if test -n "$IS_ALPHA"; then - -diff --git a/js/src/configure.in b/js/src/configure.in ---- a/js/src/configure.in -+++ b/js/src/configure.in -@@ -234,16 +234,13 @@ MOZJS_MINOR_VERSION=`echo $MOZILLA_VERSI - MOZJS_PATCH_VERSION=`echo $MOZILLA_VERSION | sed "s|^[0-9]*\.[0-9]*[^0-9]*||"` - IS_ALPHA=`echo $MOZILLA_VERSION | grep '[ab]'` - --dnl XXX in a temporary bid to avoid developer anger at renaming files --dnl XXX before "js" symlinks exist, don't change names. --dnl --dnl if test -n "$JS_STANDALONE"; then --dnl JS_SHELL_NAME=js$MOZJS_MAJOR_VERSION --dnl JS_CONFIG_NAME=js$MOZJS_MAJOR_VERSION-config --dnl else -+if test -n "$JS_STANDALONE"; then -+JS_SHELL_NAME=js$MOZJS_MAJOR_VERSION -+JS_CONFIG_NAME=js$MOZJS_MAJOR_VERSION-config -+else - JS_SHELL_NAME=js - JS_CONFIG_NAME=js-config --dnl fi -+fi - - changequote([,]) - if test -n "$IS_ALPHA"; then - -diff -r 80a9e64d75f5 js/src/Makefile.in ---- a/js/src/Makefile.in Wed Jun 25 15:11:42 2014 +0200 -+++ b/js/src/Makefile.in Sat Jul 05 14:08:38 2014 +0200 -@@ -273,6 +273,9 @@ - SCRIPTS = $(JS_CONFIG_NAME) - SDK_BINARY = $(JS_CONFIG_NAME) - -+$(JS_CONFIG_NAME): js-config -+ cp $^ $@ -+ - $(JS_LIBRARY_NAME).pc: js.pc - cp $^ $@ - diff --git a/gnu/packages/patches/mozjs38-tracelogger.patch b/gnu/packages/patches/mozjs38-tracelogger.patch deleted file mode 100644 index 0375ec36cc3..00000000000 --- a/gnu/packages/patches/mozjs38-tracelogger.patch +++ /dev/null @@ -1,608 +0,0 @@ -Squashed version of several commits to fix the tracelogger. - -Taken from -https://github.com/GNOME/jhbuild/blob/master/patches/mozjs38-fix-tracelogger.patch. - -# === Fix the SM38 tracelogger === -# This patch is a squashed version of several patches that were adapted -# to fix failing hunks. -# -# Applied in the following order, they are: -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1223767 -# Assertion failure: i < size_, at js/src/vm/TraceLoggingTypes.h:210 -# Also fix stop-information to make reduce.py work correctly. -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1227914 -# Limit the memory tracelogger can take. -# This causes tracelogger to flush data to the disk regularly and prevents out of -# memory issues if a lot of data gets logged. -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1155618 -# Fix tracelogger destructor that touches possibly uninitialised hash table. -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1223636 -# Don't treat extraTextId as containing only extra ids. -# This fixes an assertion failure: id == nextTextId at js/src/vm/TraceLoggingGraph.cpp -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1227028 -# Fix when to keep the payload of a TraceLogger event. -# This fixes an assertion failure: textId < uint32_t(1 << 31) at js/src/vm/TraceLoggingGraph.h -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1266649 -# Handle failing to add to pointermap gracefully. -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1280648 -# Don't cache based on pointers to movable GC things. -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1224123 -# Fix the use of LastEntryId in tracelogger.h. -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1231170 -# Use size in debugger instead of the current id to track last logged item. -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1221844 -# Move TraceLogger_Invalidation to LOG_ITEM. -# Add some debug checks to logTimestamp. -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1255766 -# Also mark resizing of memory. -# * https://bugzilla.mozilla.org/show_bug.cgi?id=1259403 -# Only increase capacity by multiples of 2. -# Always make sure there are 3 free slots for events. -# === - -diff --git a/js/src/jit-test/tests/tracelogger/bug1231170.js b/js/src/jit-test/tests/tracelogger/bug1231170.js -new file mode 100644 -index 0000000..023e93e ---- /dev/null -+++ b/js/src/jit-test/tests/tracelogger/bug1231170.js -@@ -0,0 +1,3 @@ -+var du = new Debugger(); -+if (typeof du.drainTraceLogger === "function") -+ du.drainTraceLogger(); -diff --git a/js/src/jit-test/tests/tracelogger/bug1266649.js b/js/src/jit-test/tests/tracelogger/bug1266649.js -new file mode 100644 -index 0000000..81ae7ad ---- /dev/null -+++ b/js/src/jit-test/tests/tracelogger/bug1266649.js -@@ -0,0 +1,10 @@ -+ -+var du = new Debugger(); -+if (typeof du.setupTraceLogger === "function" && -+ typeof oomTest === 'function') -+{ -+ du.setupTraceLogger({ -+ Scripts: true -+ }) -+ oomTest(() => function(){}); -+} -diff --git a/js/src/jit/Ion.cpp b/js/src/jit/Ion.cpp -index 93e2fda..09049d6 100644 ---- a/js/src/jit/Ion.cpp -+++ b/js/src/jit/Ion.cpp -@@ -1055,6 +1055,8 @@ IonScript::Destroy(FreeOp* fop, IonScript* script) - - script->destroyCaches(); - script->unlinkFromRuntime(fop); -+ // Frees the potential event we have set. -+ script->traceLoggerScriptEvent_ = TraceLoggerEvent(); - fop->free_(script); - } - -diff --git a/js/src/vm/Debugger.cpp b/js/src/vm/Debugger.cpp -index 26262fd..af7f313 100644 ---- a/js/src/vm/Debugger.cpp -+++ b/js/src/vm/Debugger.cpp -@@ -369,10 +369,10 @@ Debugger::Debugger(JSContext* cx, NativeObject* dbg) - objects(cx), - environments(cx), - #ifdef NIGHTLY_BUILD -- traceLoggerLastDrainedId(0), -+ traceLoggerLastDrainedSize(0), - traceLoggerLastDrainedIteration(0), - #endif -- traceLoggerScriptedCallsLastDrainedId(0), -+ traceLoggerScriptedCallsLastDrainedSize(0), - traceLoggerScriptedCallsLastDrainedIteration(0) - { - assertSameCompartment(cx, dbg); -@@ -3907,9 +3907,9 @@ Debugger::drainTraceLogger(JSContext* cx, unsigned argc, Value* vp) - size_t num; - TraceLoggerThread* logger = TraceLoggerForMainThread(cx->runtime()); - bool lostEvents = logger->lostEvents(dbg->traceLoggerLastDrainedIteration, -- dbg->traceLoggerLastDrainedId); -+ dbg->traceLoggerLastDrainedSize); - EventEntry* events = logger->getEventsStartingAt(&dbg->traceLoggerLastDrainedIteration, -- &dbg->traceLoggerLastDrainedId, -+ &dbg->traceLoggerLastDrainedSize, - &num); - - RootedObject array(cx, NewDenseEmptyArray(cx)); -@@ -4002,10 +4002,10 @@ Debugger::drainTraceLoggerScriptCalls(JSContext* cx, unsigned argc, Value* vp) - size_t num; - TraceLoggerThread* logger = TraceLoggerForMainThread(cx->runtime()); - bool lostEvents = logger->lostEvents(dbg->traceLoggerScriptedCallsLastDrainedIteration, -- dbg->traceLoggerScriptedCallsLastDrainedId); -+ dbg->traceLoggerScriptedCallsLastDrainedSize); - EventEntry* events = logger->getEventsStartingAt( - &dbg->traceLoggerScriptedCallsLastDrainedIteration, -- &dbg->traceLoggerScriptedCallsLastDrainedId, -+ &dbg->traceLoggerScriptedCallsLastDrainedSize, - &num); - - RootedObject array(cx, NewDenseEmptyArray(cx)); -diff --git a/js/src/vm/Debugger.h b/js/src/vm/Debugger.h -index 8cac36a..c92d685 100644 ---- a/js/src/vm/Debugger.h -+++ b/js/src/vm/Debugger.h -@@ -314,10 +314,10 @@ class Debugger : private mozilla::LinkedListElement - * lost events. - */ - #ifdef NIGHTLY_BUILD -- uint32_t traceLoggerLastDrainedId; -+ uint32_t traceLoggerLastDrainedSize; - uint32_t traceLoggerLastDrainedIteration; - #endif -- uint32_t traceLoggerScriptedCallsLastDrainedId; -+ uint32_t traceLoggerScriptedCallsLastDrainedSize; - uint32_t traceLoggerScriptedCallsLastDrainedIteration; - - class FrameRange; -diff --git a/js/src/vm/TraceLogging.cpp b/js/src/vm/TraceLogging.cpp -index 6715b36..9766a6f 100644 ---- a/js/src/vm/TraceLogging.cpp -+++ b/js/src/vm/TraceLogging.cpp -@@ -131,7 +131,7 @@ TraceLoggerThread::init() - { - if (!pointerMap.init()) - return false; -- if (!extraTextId.init()) -+ if (!textIdPayloads.init()) - return false; - if (!events.init()) - return false; -@@ -185,10 +185,10 @@ TraceLoggerThread::~TraceLoggerThread() - graph = nullptr; - } - -- for (TextIdHashMap::Range r = extraTextId.all(); !r.empty(); r.popFront()) -- js_delete(r.front().value()); -- extraTextId.finish(); -- pointerMap.finish(); -+ if (textIdPayloads.initialized()) { -+ for (TextIdHashMap::Range r = textIdPayloads.all(); !r.empty(); r.popFront()) -+ js_delete(r.front().value()); -+ } - } - - bool -@@ -287,7 +287,7 @@ TraceLoggerThread::eventText(uint32_t id) - if (id < TraceLogger_Last) - return TLTextIdString(static_cast(id)); - -- TextIdHashMap::Ptr p = extraTextId.lookup(id); -+ TextIdHashMap::Ptr p = textIdPayloads.lookup(id); - MOZ_ASSERT(p); - - return p->value()->string(); -@@ -341,13 +341,15 @@ TraceLoggerThread::extractScriptDetails(uint32_t textId, const char** filename, - TraceLoggerEventPayload* - TraceLoggerThread::getOrCreateEventPayload(TraceLoggerTextId textId) - { -- TextIdHashMap::AddPtr p = extraTextId.lookupForAdd(textId); -- if (p) -+ TextIdHashMap::AddPtr p = textIdPayloads.lookupForAdd(textId); -+ if (p) { -+ MOZ_ASSERT(p->value()->textId() == textId); // Sanity check. - return p->value(); -+ } - - TraceLoggerEventPayload* payload = js_new(textId, (char*)nullptr); - -- if (!extraTextId.add(p, textId, payload)) -+ if (!textIdPayloads.add(p, textId, payload)) - return nullptr; - - return payload; -@@ -357,8 +359,10 @@ TraceLoggerEventPayload* - TraceLoggerThread::getOrCreateEventPayload(const char* text) - { - PointerHashMap::AddPtr p = pointerMap.lookupForAdd((const void*)text); -- if (p) -+ if (p) { -+ MOZ_ASSERT(p->value()->textId() < nextTextId); // Sanity check. - return p->value(); -+ } - - size_t len = strlen(text); - char* str = js_pod_malloc(len + 1); -@@ -369,7 +373,7 @@ TraceLoggerThread::getOrCreateEventPayload(const char* text) - MOZ_ASSERT(ret == len); - MOZ_ASSERT(strlen(str) == len); - -- uint32_t textId = extraTextId.count() + TraceLogger_Last; -+ uint32_t textId = nextTextId; - - TraceLoggerEventPayload* payload = js_new(textId, str); - if (!payload) { -@@ -377,17 +381,19 @@ TraceLoggerThread::getOrCreateEventPayload(const char* text) - return nullptr; - } - -- if (!extraTextId.putNew(textId, payload)) { -+ if (!textIdPayloads.putNew(textId, payload)) { - js_delete(payload); - return nullptr; - } - -- if (!pointerMap.add(p, text, payload)) -- return nullptr; -- - if (graph.get()) - graph->addTextId(textId, str); - -+ nextTextId++; -+ -+ if (!pointerMap.add(p, text, payload)) -+ return nullptr; -+ - return payload; - } - -@@ -407,9 +413,14 @@ TraceLoggerThread::getOrCreateEventPayload(TraceLoggerTextId type, const char* f - if (!traceLoggerState->isTextIdEnabled(type)) - return getOrCreateEventPayload(type); - -- PointerHashMap::AddPtr p = pointerMap.lookupForAdd(ptr); -- if (p) -- return p->value(); -+ PointerHashMap::AddPtr p; -+ if (ptr) { -+ p = pointerMap.lookupForAdd(ptr); -+ if (p) { -+ MOZ_ASSERT(p->value()->textId() < nextTextId); // Sanity check. -+ return p->value(); -+ } -+ } - - // Compute the length of the string to create. - size_t lenFilename = strlen(filename); -@@ -428,24 +439,28 @@ TraceLoggerThread::getOrCreateEventPayload(TraceLoggerTextId type, const char* f - MOZ_ASSERT(ret == len); - MOZ_ASSERT(strlen(str) == len); - -- uint32_t textId = extraTextId.count() + TraceLogger_Last; -+ uint32_t textId = nextTextId; - TraceLoggerEventPayload* payload = js_new(textId, str); - if (!payload) { - js_free(str); - return nullptr; - } - -- if (!extraTextId.putNew(textId, payload)) { -+ if (!textIdPayloads.putNew(textId, payload)) { - js_delete(payload); - return nullptr; - } - -- if (!pointerMap.add(p, ptr, payload)) -- return nullptr; -- - if (graph.get()) - graph->addTextId(textId, str); - -+ nextTextId++; -+ -+ if (ptr) { -+ if (!pointerMap.add(p, ptr, payload)) -+ return nullptr; -+ } -+ - return payload; - } - -@@ -453,14 +468,14 @@ TraceLoggerEventPayload* - TraceLoggerThread::getOrCreateEventPayload(TraceLoggerTextId type, JSScript* script) - { - return getOrCreateEventPayload(type, script->filename(), script->lineno(), script->column(), -- script); -+ nullptr); - } - - TraceLoggerEventPayload* - TraceLoggerThread::getOrCreateEventPayload(TraceLoggerTextId type, - const JS::ReadOnlyCompileOptions& script) - { -- return getOrCreateEventPayload(type, script.filename(), script.lineno, script.column, &script); -+ return getOrCreateEventPayload(type, script.filename(), script.lineno, script.column, nullptr); - } - - void -@@ -485,7 +500,7 @@ TraceLoggerThread::startEvent(uint32_t id) - if (!traceLoggerState->isTextIdEnabled(id)) - return; - -- logTimestamp(id); -+ log(id); - } - - void -@@ -510,7 +525,7 @@ TraceLoggerThread::stopEvent(uint32_t id) - if (!traceLoggerState->isTextIdEnabled(id)) - return; - -- logTimestamp(TraceLogger_Stop); -+ log(TraceLogger_Stop); - } - - void -@@ -522,23 +537,57 @@ TraceLoggerThread::logTimestamp(TraceLoggerTextId id) - void - TraceLoggerThread::logTimestamp(uint32_t id) - { -+ MOZ_ASSERT(id > TraceLogger_LastTreeItem && id < TraceLogger_Last); -+ log(id); -+} -+ -+void -+TraceLoggerThread::log(uint32_t id) -+{ - if (enabled == 0) - return; - - MOZ_ASSERT(traceLoggerState); -- if (!events.ensureSpaceBeforeAdd()) { -+ -+ // We request for 3 items to add, since if we don't have enough room -+ // we record the time it took to make more place. To log this information -+ // we need 2 extra free entries. -+ if (!events.hasSpaceForAdd(3)) { - uint64_t start = rdtsc() - traceLoggerState->startupTime; - -- if (graph.get()) -- graph->log(events); -+ if (!events.ensureSpaceBeforeAdd(3)) { -+ if (graph.get()) -+ graph->log(events); -+ -+ iteration_++; -+ events.clear(); -+ -+ // Remove the item in the pointerMap for which the payloads -+ // have no uses anymore -+ for (PointerHashMap::Enum e(pointerMap); !e.empty(); e.popFront()) { -+ if (e.front().value()->uses() != 0) -+ continue; -+ -+ TextIdHashMap::Ptr p = textIdPayloads.lookup(e.front().value()->textId()); -+ MOZ_ASSERT(p); -+ textIdPayloads.remove(p); -+ -+ e.removeFront(); -+ } - -- iteration_++; -- events.clear(); -+ // Free all payloads that have no uses anymore. -+ for (TextIdHashMap::Enum e(textIdPayloads); !e.empty(); e.popFront()) { -+ if (e.front().value()->uses() == 0) { -+ js_delete(e.front().value()); -+ e.removeFront(); -+ } -+ } -+ } - - // Log the time it took to flush the events as being from the - // Tracelogger. - if (graph.get()) { -- MOZ_ASSERT(events.capacity() > 2); -+ MOZ_ASSERT(events.hasSpaceForAdd(2)); - EventEntry& entryStart = events.pushUninitialized(); - entryStart.time = start; - entryStart.textId = TraceLogger_Internal; -@@ -548,13 +597,6 @@ TraceLoggerThread::logTimestamp(uint32_t id) - entryStop.textId = TraceLogger_Stop; - } - -- // Free all TextEvents that have no uses anymore. -- for (TextIdHashMap::Enum e(extraTextId); !e.empty(); e.popFront()) { -- if (e.front().value()->uses() == 0) { -- js_delete(e.front().value()); -- e.removeFront(); -- } -- } - } - - uint64_t time = rdtsc() - traceLoggerState->startupTime; -@@ -956,3 +998,16 @@ TraceLoggerEvent::~TraceLoggerEvent() - if (payload_) - payload_->release(); - } -+ -+TraceLoggerEvent& -+TraceLoggerEvent::operator=(const TraceLoggerEvent& other) -+{ -+ if (hasPayload()) -+ payload()->release(); -+ if (other.hasPayload()) -+ other.payload()->use(); -+ -+ payload_ = other.payload_; -+ -+ return *this; -+} -diff --git a/js/src/vm/TraceLogging.h b/js/src/vm/TraceLogging.h -index a124dcb..91a1eb0 100644 ---- a/js/src/vm/TraceLogging.h -+++ b/js/src/vm/TraceLogging.h -@@ -110,6 +110,9 @@ class TraceLoggerEvent { - bool hasPayload() const { - return !!payload_; - } -+ -+ TraceLoggerEvent& operator=(const TraceLoggerEvent& other); -+ TraceLoggerEvent(const TraceLoggerEvent& event) = delete; - }; - - /** -@@ -130,6 +133,10 @@ class TraceLoggerEventPayload { - uses_(0) - { } - -+ ~TraceLoggerEventPayload() { -+ MOZ_ASSERT(uses_ == 0); -+ } -+ - uint32_t textId() { - return textId_; - } -@@ -166,7 +173,8 @@ class TraceLoggerThread - mozilla::UniquePtr graph; - - PointerHashMap pointerMap; -- TextIdHashMap extraTextId; -+ TextIdHashMap textIdPayloads; -+ uint32_t nextTextId; - - ContinuousSpace events; - -@@ -181,6 +189,7 @@ class TraceLoggerThread - : enabled(0), - failed(false), - graph(), -+ nextTextId(TraceLogger_Last), - iteration_(0), - top(nullptr) - { } -@@ -195,22 +204,22 @@ class TraceLoggerThread - bool enable(JSContext* cx); - bool disable(); - -- // Given the previous iteration and lastEntryId, return an array of events -+ // Given the previous iteration and size, return an array of events - // (there could be lost events). At the same time update the iteration and -- // lastEntry and gives back how many events there are. -- EventEntry* getEventsStartingAt(uint32_t* lastIteration, uint32_t* lastEntryId, size_t* num) { -+ // size and gives back how many events there are. -+ EventEntry* getEventsStartingAt(uint32_t* lastIteration, uint32_t* lastSize, size_t* num) { - EventEntry* start; - if (iteration_ == *lastIteration) { -- MOZ_ASSERT(events.lastEntryId() >= *lastEntryId); -- *num = events.lastEntryId() - *lastEntryId; -- start = events.data() + *lastEntryId + 1; -+ MOZ_ASSERT(*lastSize <= events.size()); -+ *num = events.size() - *lastSize; -+ start = events.data() + *lastSize; - } else { -- *num = events.lastEntryId() + 1; -+ *num = events.size(); - start = events.data(); - } - - *lastIteration = iteration_; -- *lastEntryId = events.lastEntryId(); -+ *lastSize = events.size(); - return start; - } - -@@ -220,16 +229,16 @@ class TraceLoggerThread - const char** lineno, size_t* lineno_len, const char** colno, - size_t* colno_len); - -- bool lostEvents(uint32_t lastIteration, uint32_t lastEntryId) { -+ bool lostEvents(uint32_t lastIteration, uint32_t lastSize) { - // If still logging in the same iteration, there are no lost events. - if (lastIteration == iteration_) { -- MOZ_ASSERT(lastEntryId <= events.lastEntryId()); -+ MOZ_ASSERT(lastSize <= events.size()); - return false; - } - -- // When proceeded to the next iteration and lastEntryId points to -- // the maximum capacity there are no logs that are lost. -- if (lastIteration + 1 == iteration_ && lastEntryId == events.capacity()) -+ // If we are in a consecutive iteration we are only sure we didn't lose any events, -+ // when the lastSize equals the maximum size 'events' can get. -+ if (lastIteration == iteration_ - 1 && lastSize == events.maxSize()) - return false; - - return true; -@@ -268,6 +277,7 @@ class TraceLoggerThread - void stopEvent(uint32_t id); - private: - void stopEvent(); -+ void log(uint32_t id); - - public: - static unsigned offsetOfEnabled() { -diff --git a/js/src/vm/TraceLoggingGraph.cpp b/js/src/vm/TraceLoggingGraph.cpp -index d1b7f2e..a4eb273 100644 ---- a/js/src/vm/TraceLoggingGraph.cpp -+++ b/js/src/vm/TraceLoggingGraph.cpp -@@ -276,7 +276,7 @@ TraceLoggerGraph::flush() - if (bytesWritten < tree.size()) - return false; - -- treeOffset += tree.lastEntryId(); -+ treeOffset += tree.size(); - tree.clear(); - } - -@@ -359,7 +359,7 @@ TraceLoggerGraph::startEventInternal(uint32_t id, uint64_t timestamp) - - if (parent.lastChildId() == 0) { - MOZ_ASSERT(!entry.hasChildren()); -- MOZ_ASSERT(parent.treeId() == tree.lastEntryId() + treeOffset); -+ MOZ_ASSERT(parent.treeId() == treeOffset + tree.size() - 1); - - if (!updateHasChildren(parent.treeId())) - return false; -diff --git a/js/src/vm/TraceLoggingTypes.h b/js/src/vm/TraceLoggingTypes.h -index f1c9d0c..10b76d6 100644 ---- a/js/src/vm/TraceLoggingTypes.h -+++ b/js/src/vm/TraceLoggingTypes.h -@@ -21,7 +21,6 @@ - _(Internal) \ - _(Interpreter) \ - _(InlinedScripts) \ -- _(Invalidation) \ - _(IonCompilation) \ - _(IonCompilationPaused) \ - _(IonLinking) \ -@@ -60,6 +59,7 @@ - - #define TRACELOGGER_LOG_ITEMS(_) \ - _(Bailout) \ -+ _(Invalidation) \ - _(Disable) \ - _(Enable) \ - _(Stop) -@@ -130,6 +130,9 @@ class ContinuousSpace { - uint32_t size_; - uint32_t capacity_; - -+ // The maximum amount of ram memory a continuous space structure can take (in bytes). -+ static const uint32_t LIMIT = 200 * 1024 * 1024; -+ - public: - ContinuousSpace () - : data_(nullptr) -@@ -151,6 +154,10 @@ class ContinuousSpace { - data_ = nullptr; - } - -+ static uint32_t maxSize() { -+ return LIMIT / sizeof(T); -+ } -+ - T* data() { - return data_; - } -@@ -187,11 +194,14 @@ class ContinuousSpace { - if (hasSpaceForAdd(count)) - return true; - -+ // Limit the size of a continuous buffer. -+ if (size_ + count > maxSize()) -+ return false; -+ - uint32_t nCapacity = capacity_ * 2; -- if (size_ + count > nCapacity) -- nCapacity = size_ + count; -- T* entries = (T*) js_realloc(data_, nCapacity * sizeof(T)); -+ nCapacity = (nCapacity < maxSize()) ? nCapacity : maxSize(); - -+ T* entries = (T*) js_realloc(data_, nCapacity * sizeof(T)); - if (!entries) - return false; - diff --git a/gnu/packages/patches/mozjs38-version-detection.patch b/gnu/packages/patches/mozjs38-version-detection.patch deleted file mode 100644 index ec2d264cccf..00000000000 --- a/gnu/packages/patches/mozjs38-version-detection.patch +++ /dev/null @@ -1,180 +0,0 @@ -Taken from -https://trac.wildfiregames.com/export/18656/ps/trunk/libraries/source/spidermonkey/FixVersionDetectionConfigure.diff. - -Fixes a version detection issue in 0ad. See -https://lists.gnu.org/archive/html/guix-devel/2017-01/msg00625.html. - -diff --git a/js/src/configure b/js/src/configure ---- a/js/src/configure -+++ b/js/src/configure -@@ -1662,70 +1662,6 @@ esac - - fi - --MOZILLA_VERSION=`$PYTHON $srcdir/python/mozbuild/mozbuild/milestone.py --topsrcdir $srcdir` --MOZILLA_UAVERSION=`$PYTHON $srcdir/python/mozbuild/mozbuild/milestone.py --topsrcdir $srcdir --uaversion` --MOZILLA_SYMBOLVERSION=`$PYTHON $srcdir/python/mozbuild/mozbuild/milestone.py --topsrcdir $srcdir --symbolversion` -- --cat >> confdefs.pytmp <> confdefs.h <> confdefs.pytmp <> confdefs.h <> confdefs.pytmp <> confdefs.h <> confdefs.pytmp <> confdefs.h <> confdefs.pytmp <> confdefs.h <> confdefs.pytmp <> confdefs.h <> confdefs.pytmp <> confdefs.h <> confdefs.pytmp <> confdefs.h <> confdefs.pytmp <> confdefs.h <> confdefs.pytmp <> confdefs.h <> $CONFIG_STATUS <> $CONFIG_STATUS < Date: Fri, 13 May 2022 14:12:02 -0400 Subject: [PATCH 1334/1394] gnu: icedove: Delete obsolete Python 2 input. * gnu/packages/gnuzilla.scm (icedove)[native-inputs]: Replace python-2 with python-wrapper. Delete python. [phases]: Delete trailing #t. --- gnu/packages/gnuzilla.scm | 24 ++++++++---------------- 1 file changed, 8 insertions(+), 16 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 0c64c44adf1..7f8cbe1120f 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -1000,8 +1000,7 @@ standards of the IceCat project.") (mkdir "comm") (copy-recursively (assoc-ref inputs "thunderbird-sources") "comm") - (delete-file "sourcestamp.txt") - #t)) + (delete-file "sourcestamp.txt"))) (add-after 'patch-source-shebangs 'patch-cargo-checksums (lambda _ (use-modules (guix build cargo-utils)) @@ -1014,16 +1013,14 @@ standards of the IceCat project.") (find-files "." "Cargo.lock$")) (for-each generate-all-checksums '("third_party/rust" - "toolkit/library/rust"))) - #t)) + "toolkit/library/rust"))))) ;; Fixes issue where each installation directory generates its own profile. ;; See e.g. https://trac.torproject.org/projects/tor/ticket/31457 (add-after 'patch-source-shebangs 'fix-profile-setting (lambda _ (substitute* "comm/mail/moz.configure" (("MOZ_DEDICATED_PROFILES, True") - "MOZ_DEDICATED_PROFILES, False")) - #t)) + "MOZ_DEDICATED_PROFILES, False")))) (add-after 'prepare-thunderbird-sources 'rename-to-icedove (lambda _ (substitute* "comm/mail/confvars.sh" @@ -1086,8 +1083,7 @@ standards of the IceCat project.") (("(pref\\(\"extensions.systemAddon.update.enabled\").*" _ m) (string-append m ", false);")) (("(pref\\(\"lightweightThemes.update.enabled\").*" _ m) - (string-append m ", false);"))) - #t)) + (string-append m ", false);"))))) (add-after 'build 'neutralize-store-references (lambda _ ;; Mangle the store references to compilers & other build tools in @@ -1103,8 +1099,7 @@ standards of the IceCat project.") (string-append store (string-take hash 8) "" - (string-drop hash 8)))) - #t)) + (string-drop hash 8)))))) (delete 'bootstrap) (replace 'configure (lambda* (#:key inputs outputs configure-flags #:allow-other-keys) @@ -1206,8 +1201,7 @@ standards of the IceCat project.") [Desktop Action ComposeMessage]~@ Name=Write new message~@ Exec=~@*~a/bin/icedove -compose~%" - out)))) - #t)) + out)))))) (add-after 'install 'wrap-program (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -1220,8 +1214,7 @@ standards of the IceCat project.") (eudev-lib (string-append eudev "/lib"))) (wrap-program (car (find-files lib "^icedove$")) `("XDG_DATA_DIRS" prefix (,gtk-share)) - `("LD_LIBRARY_PATH" prefix (,pulseaudio-lib ,eudev-lib))) - #t)))))) + `("LD_LIBRARY_PATH" prefix (,pulseaudio-lib ,eudev-lib))))))))) (inputs `(("bzip2" ,bzip2) ("cairo" ,cairo) @@ -1285,8 +1278,7 @@ standards of the IceCat project.") ("node" ,node) ("perl" ,perl) ("pkg-config" ,pkg-config) - ("python" ,python) - ("python2" ,python-2.7) + ("python" ,python-wrapper) ("rust" ,rust) ("rust-cbindgen" ,rust-cbindgen-0.19) ("which" ,which) From 2cd3e8ac346f2d876ffa1498ddc867a3d89654e1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 14:14:11 -0400 Subject: [PATCH 1335/1394] gnu: icedove: Use new style for inputs. * gnu/packages/gnuzilla.scm (icecat)[inputs]: Use new style. --- gnu/packages/gnuzilla.scm | 78 +++++++++++++++++++-------------------- 1 file changed, 39 insertions(+), 39 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 7f8cbe1120f..41dd32955d1 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -989,7 +989,7 @@ standards of the IceCat project.") (arguments `(#:tests? #f ; no check target #:imported-modules ,%cargo-utils-modules ;for `generate-all-checksums' - #:modules ((guix build utils) ;find-files + #:modules ((guix build utils) ;find-files (sxml simple) (ice-9 regex) ,@%gnu-build-system-modules) @@ -1216,44 +1216,44 @@ standards of the IceCat project.") `("XDG_DATA_DIRS" prefix (,gtk-share)) `("LD_LIBRARY_PATH" prefix (,pulseaudio-lib ,eudev-lib))))))))) (inputs - `(("bzip2" ,bzip2) - ("cairo" ,cairo) - ("cups" ,cups) - ("dbus-glib" ,dbus-glib) - ("ffmpeg" ,ffmpeg) - ("freetype" ,freetype) - ("gdk-pixbuf" ,gdk-pixbuf) - ("glib" ,glib) - ("gtk+" ,gtk+) - ("gtk+-2" ,gtk+-2) - ("hunspell" ,hunspell) - ("icu4c" ,icu4c) - ("libcanberra" ,libcanberra) - ("libevent" ,libevent) - ("libffi" ,libffi) - ("libgnome" ,libgnome) - ("libjpeg-turbo" ,libjpeg-turbo) - ("libpng-apng" ,libpng-apng) - ("libvpx" ,libvpx) - ("libxcomposite" ,libxcomposite) - ("libxft" ,libxft) - ("libxinerama" ,libxinerama) - ("libxscrnsaver" ,libxscrnsaver) - ("libxt" ,libxt) - ("mesa" ,mesa) - ("mit-krb5" ,mit-krb5) - ("nspr" ,nspr-4.32) - ; FIXME: create nss >= 3.68 after core-updates merge - ;("nss" ,nss) - ("pango" ,pango) - ("pixman" ,pixman) - ("pulseaudio" ,pulseaudio) - ("sqlite" ,sqlite) - ("startup-notification" ,startup-notification) - ("eudev" ,eudev) - ("unzip" ,unzip) - ("zip" ,zip) - ("zlib" ,zlib))) + (list bzip2 + cairo + cups + dbus-glib + ffmpeg + freetype + gdk-pixbuf + glib + gtk+ + gtk+-2 + hunspell + icu4c + libcanberra + libevent + libffi + libgnome + libjpeg-turbo + libpng-apng + libvpx + libxcomposite + libxft + libxinerama + libxscrnsaver + libxt + mesa + mit-krb5 + nspr-4.32 + ;; FIXME: create nss >= 3.68 after core-updates merge + ;;nss + pango + pixman + pulseaudio + sqlite + startup-notification + eudev + unzip + zip + zlib)) (native-inputs `(("thunderbird-sources" ;; The changeset identifier is taken from the file "sourcestamp.txt" From abadac23666c8e0e29f1cb6bdfbc99be452b3c87 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 14:27:41 -0400 Subject: [PATCH 1336/1394] gnu: jack-2: Update to 1.9.21. * gnu/packages/audio.scm (jack-2): Update to 1.9.21. [source]: Use git. [phases]: Delete trailing #t. {wrap-python-scripts}: Use search-input-file. --- gnu/packages/audio.scm | 39 ++++++++++++++++++--------------------- 1 file changed, 18 insertions(+), 21 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 01f809d5e98..8ec78f665cd 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2239,23 +2239,23 @@ synchronous execution of all clients, and low latency operation.") ;; jack-2 implement the same API. JACK2 is provided primarily as a client ;; program for users who might benefit from the D-BUS features. (define-public jack-2 - (package (inherit jack-1) + (package + (inherit jack-1) (name "jack2") - (version "1.9.14") + (version "1.9.21") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/jackaudio/jack2/releases/" - "download/v" version "/jack2-" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0z11hf55a6mi8h50hfz5wry9pshlwl4mzfwgslghdh40cwv342m2")))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/jackaudio/jack2") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0sbrffmdbajvrk7iqvsvrnwnpvmicvbjyq3f52r6ashdsznsz03b")))) (build-system waf-build-system) (arguments - `(#:tests? #f ; no check target - #:configure-flags '("--dbus" - "--alsa") + `(#:tests? #f ; no check target + #:configure-flags '("--dbus" "--alsa") #:phases (modify-phases %standard-phases (add-before 'configure 'set-linkflags @@ -2269,16 +2269,13 @@ synchronous execution of all clients, and low latency operation.") ((".*CFLAGS.*-Wall.*" m) (string-append m " conf.env.append_unique('LINKFLAGS'," - "'-Wl,-rpath=" %output "/lib')\n"))) - #t)) + "'-Wl,-rpath=" %output "/lib')\n"))))) (add-after 'install 'wrap-python-scripts - (lambda* (#:key inputs outputs #:allow-other-keys) + (lambda* (#:key outputs #:allow-other-keys) ;; Make sure 'jack_control' runs with the correct PYTHONPATH. - (let* ((out (assoc-ref outputs "out")) - (path (getenv "GUIX_PYTHONPATH"))) - (wrap-program (string-append out "/bin/jack_control") - `("GUIX_PYTHONPATH" ":" prefix (,path)))) - #t))))) + (wrap-program (search-input-file outputs "bin/jack_control") + `("GUIX_PYTHONPATH" ":" + prefix (,(getenv "GUIX_PYTHONPATH"))))))))) (inputs (list alsa-lib dbus From d986c345601654d7f04a5c82611b76c8da1d44aa Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 14:29:15 -0400 Subject: [PATCH 1337/1394] gnu: mod-host: Update to 0.10.6-4.cdd30dd. * gnu/packages/music.scm (mod-host): Update to 0.10.6-4.cdd30dd. [source]: Use git-version and git-file-name. [arguments]: Use gexps. [phases]: Delete trailing #t. [inputs]: Replace jack-1 with jack-2. [native-inputs]: replace python-2 with python-wrapper. --- gnu/packages/music.scm | 43 +++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 22 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index b3989e11f9b..554d70f2661 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3401,11 +3401,11 @@ analogue-like user interface.") (define-public mod-host ;; The last release was in 2014 but since then hundreds of commits have ;; been made. - (let ((commit "1726ad06b11323da7e1aaed690ff8aef91f702b5") - (revision "3")) + (let ((commit "cdd30ddbd2cc916be8a0364275071c3d8335b3a7") + (revision "4")) (package (name "mod-host") - (version (string-append "0.10.6-" revision "." (string-take commit 9))) + (version (git-version "0.10.6" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -3413,34 +3413,33 @@ analogue-like user interface.") (commit commit))) (sha256 (base32 - "1nrd37c35w6z6ldczgrwmmd9hx1n3zyvcjcgb3mi4cygqdanvspv")) - (file-name (string-append name "-" version "-checkout")))) + "1xnflvcyj071gn9nhv5dynd0v85nq99sz1wn3adlj43l5m4fbx3a")) + (file-name (git-file-name name version)))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; no tests included - #:make-flags - (list (string-append "PREFIX=" (assoc-ref %outputs "out")) - "CC=gcc") - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'fix-jack-installation-directory - (lambda _ - ;; Do not attempt to install files to output of "jack" package. - (substitute* "Makefile" - (("\\$\\(shell pkg-config --variable=libdir jack\\)") - "lib")) - #t))))) + (list + #:tests? #f ; no tests included + #:make-flags + #~(list (string-append "PREFIX=" #$output) "CC=gcc") + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'fix-jack-installation-directory + (lambda _ + ;; Do not attempt to install files to output of "jack" package. + (substitute* "Makefile" + (("\\$\\(shell pkg-config --variable=libdir jack\\)") + "lib"))))))) (inputs (list lilv fftw fftwf lv2 - jack-1 + jack-2 readline)) (native-inputs - `(("pkg-config" ,pkg-config) - ("python" ,python-2))) + (list pkg-config + python-wrapper)) (home-page "https://github.com/moddevices/mod-host") (synopsis "LV2 host for Jack controllable via socket or command line") (description "mod-host is an LV2 plugin host for JACK, controllable via From 38cb3572134c673460099a091a93abcb320e497f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 14:31:23 -0400 Subject: [PATCH 1338/1394] gnu: Remove python2-pyfakefs-bootstrap. * gnu/packages/check.scm (python2-pyfakefs-bootstrap): Delete variable. --- gnu/packages/check.scm | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 471150c4df1..fdf14f7cf2d 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -3056,19 +3056,6 @@ under test to interact with a fake file system instead of the real file system. The code under test requires no modification to work with pyfakefs.") (license license:asl2.0))) -;; This minimal variant is used to avoid a circular dependency between -;; python2-importlib-metadata, which requires pyfakefs for its tests, and -;; python2-pytest, which requires python2-importlib-metadata. -(define-public python2-pyfakefs-bootstrap - (hidden-package - (package - (inherit (package-with-python2 python-pyfakefs)) - (name "python2-pyfakefs-bootstrap") - (native-inputs '()) - (arguments - `(#:python ,python-2 - #:tests? #f))))) - (define-public python-aiounittest (package (name "python-aiounittest") From e7ccfbed19ed385c7687414beb3279d8649d9a97 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 14:41:54 -0400 Subject: [PATCH 1339/1394] gnu: libpqxx: Update to 7.7.3. * gnu/packages/databases.scm (libpqxx): Update to 7.7.3. [source]: Use git. [native-inputs]: Replace python-2 with python-wrapper. Add gcc-11. [tests?]: Expound comment. [phases]: Delete argument. --- gnu/packages/databases.scm | 27 +++++++++------------------ 1 file changed, 9 insertions(+), 18 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index cd5045ed125..56f6b92b4ca 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2788,29 +2788,20 @@ semantics.") (define-public libpqxx (package (name "libpqxx") - (version "4.0.1") + (version "7.7.3") (source (origin - (method url-fetch) - (uri (string-append - "http://pqxx.org/download/software/libpqxx/" - name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/jtv/libpqxx") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0f6wxspp6rx12fkasanb0z2g2gc8dhcfwnxagx8wwqbpg6ifsz09")))) + "1mrhsih5bhiin0l3c4vp22l9p7c5035m0vvqpx18c0407fkzc7hp")))) (build-system gnu-build-system) - (native-inputs - `(("python" ,python-2))) + (native-inputs (list gcc-11 python-wrapper)) (inputs (list postgresql)) - (arguments - `(#:tests? #f ; # FAIL: 1 - #:phases - (modify-phases %standard-phases - (add-before 'configure 'fix-sed-command - (lambda _ - ;; Newer sed versions error out if double brackets are not used. - (substitute* "configure" - (("\\[:space:\\]") "[[:space:]]")) - #t))))) + (arguments '(#:tests? #f)) ;tests require a running PostgreSQL server (synopsis "C++ connector for PostgreSQL") (description "Libpqxx is a C++ library to enable user programs to communicate with the From b0193c649fa70b31c2c63f82abb7cf9309066b6c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 14:56:29 -0400 Subject: [PATCH 1340/1394] gnu: Remove 4store. * gnu/packages/databases.scm (4store): Delete variable. * gnu/packages/patches/4store-fix-buildsystem.patch: Delete file. * gnu/packages/patches/4store-unset-preprocessor-directive.patch: Likewise. * gnu/local.mk (dist_patch_DATA): De-register them. --- gnu/local.mk | 2 - gnu/packages/databases.scm | 41 -------------- .../patches/4store-fix-buildsystem.patch | 56 ------------------- .../4store-unset-preprocessor-directive.patch | 16 ------ 4 files changed, 115 deletions(-) delete mode 100644 gnu/packages/patches/4store-fix-buildsystem.patch delete mode 100644 gnu/packages/patches/4store-unset-preprocessor-directive.patch diff --git a/gnu/local.mk b/gnu/local.mk index 947669459e4..06cf32b9169 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -825,8 +825,6 @@ MODULES_NOT_COMPILED += \ patchdir = $(guilemoduledir)/%D%/packages/patches dist_patch_DATA = \ - %D%/packages/patches/4store-fix-buildsystem.patch \ - %D%/packages/patches/4store-unset-preprocessor-directive.patch \ %D%/packages/patches/a2ps-CVE-2001-1593.patch \ %D%/packages/patches/a2ps-CVE-2014-0466.patch \ %D%/packages/patches/a2ps-CVE-2015-8107.patch \ diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 56f6b92b4ca..09d825af3e2 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -177,47 +177,6 @@ #:use-module (srfi srfi-26) #:use-module (ice-9 match)) -(define-public 4store - (package - (name "4store") - (version "1.1.6") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/4store/4store") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1kzdfmwpzy64cgqlkcz5v4klwx99w0jk7afckyf7yqbqb4rydmpk")) - (patches (search-patches "4store-unset-preprocessor-directive.patch" - "4store-fix-buildsystem.patch")))) - (build-system gnu-build-system) - (native-inputs - (list perl - python-2 - autoconf - automake - gettext-minimal - libtool - `(,pcre "bin") ;for 'pcre-config' - pkg-config)) - (inputs - (list glib - rasqal - libxml2 - raptor2 - readline - avahi - cyrus-sasl - openssl - `(,util-linux "lib"))) - ;; http://www.4store.org has been down for a while now. - (home-page "https://github.com/4store/4store") - (synopsis "Clustered RDF storage and query engine") - (description "4store is a RDF/SPARQL store written in C, supporting -either single machines or networked clusters.") - (license license:gpl3+))) - (define-public ephemeralpg (package (name "ephemeralpg") diff --git a/gnu/packages/patches/4store-fix-buildsystem.patch b/gnu/packages/patches/4store-fix-buildsystem.patch deleted file mode 100644 index 383baa94613..00000000000 --- a/gnu/packages/patches/4store-fix-buildsystem.patch +++ /dev/null @@ -1,56 +0,0 @@ -This patch sets a fixed version to avoid needing Git and the .git/ folder. -It also removes the creation of "/var/lib/4store", which is not available -during the install phase in GNU Guix. - -Patch by Roel Janssen -*** a/configure.ac Wed Feb 4 19:05:24 2015 ---- b/configure.ac Wed Mar 23 11:20:38 2016 -*************** -*** 2,13 **** - # Process this file with autoconf to produce a configure script. - - AC_PREREQ([2.50]) -! AC_INIT([4store], m4_esyscmd([./version.sh .version]), [http://4store.org/support/], [4store]) - AC_CONFIG_SRCDIR([src/backend/backend-intl.h]) -! AM_INIT_AUTOMAKE([1.7 std-options -Wall]) - AC_CONFIG_HEADERS(4store-config.h) - - # Checks for programs. - AC_PROG_LIBTOOL - AC_PROG_AWK - AC_PROG_CC ---- 2,14 ---- - # Process this file with autoconf to produce a configure script. - - AC_PREREQ([2.50]) -! AC_INIT([4store], [1.1.6], [http://4store.org/support/], [4store]) - AC_CONFIG_SRCDIR([src/backend/backend-intl.h]) -! AM_INIT_AUTOMAKE([1.7 std-options foreign -Wall]) - AC_CONFIG_HEADERS(4store-config.h) - - # Checks for programs. -+ AM_PROG_AR - AC_PROG_LIBTOOL - AC_PROG_AWK - AC_PROG_CC - -*** a/src/utilities/Makefile.am Wed Feb 4 19:05:24 2015 ---- b/src/utilities/Makefile.am Wed Mar 23 14:05:56 2016 -*************** -*** 13,20 **** - noinst_PROGRAMS = lex-file-verify 4s-rid - - install-data-local: -! mkdir -p $(DESTDIR)@FS_STORE_ROOT@ -! chmod 1777 $(DESTDIR)@FS_STORE_ROOT@ - - 4s_backend_destroy_SOURCES = backend-destroy.c - 4s_backend_destroy_LDADD = ../common/lib4sintl.a ---- 13,19 ---- - noinst_PROGRAMS = lex-file-verify 4s-rid - - install-data-local: -! echo "Please create the following directory: " $(DESTDIR)@FS_STORE_ROOT@ - - 4s_backend_destroy_SOURCES = backend-destroy.c - 4s_backend_destroy_LDADD = ../common/lib4sintl.a diff --git a/gnu/packages/patches/4store-unset-preprocessor-directive.patch b/gnu/packages/patches/4store-unset-preprocessor-directive.patch deleted file mode 100644 index c4b1d6eda4f..00000000000 --- a/gnu/packages/patches/4store-unset-preprocessor-directive.patch +++ /dev/null @@ -1,16 +0,0 @@ -This patch removes the _XOPEN_SOURCE preprocessor directive as it does not seem to be needed. -Setting it removes the definition of strdup, which is used in filter-datatypes.c. - -Patch by Roel Janssen -*** a/src/frontend/filter-datatypes.c 1970-01-01 01:00:00.000000000 +0100 ---- b/src/frontend/filter-datatypes.c 2018-04-03 17:39:23.177905592 +0200 -*************** -*** 18,24 **** - * Copyright (C) 2006 Steve Harris for Garlik - */ - -- #define _XOPEN_SOURCE - #include - #include - #include ---- 18,23 ---- From afde361377478ad9d2b12467e9e8890f227629bd Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:00:02 -0400 Subject: [PATCH 1341/1394] gnu: Remove python2-libxml2. * gnu/packages/xml.scm (python2-libxml2): Delete variable. --- gnu/packages/xml.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 99cb02a09af..c26ca686729 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -345,9 +345,6 @@ formulas and hyperlinks to multiple worksheets in an Excel 2007+ XLSX file.") (inputs `(("libxml2" ,libxml2))) (synopsis "Python bindings for the libxml2 library"))) -(define-public python2-libxml2 - (package-with-python2 python-libxml2)) - (define-public libxslt (package (name "libxslt") From 61d0c52b9d0bba9425df76781d58618cb655c4f3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:00:50 -0400 Subject: [PATCH 1342/1394] gnu: Remove python2-attrs-bootstrap. * gnu/packages/python-xyz.scm (python2-attrs-bootstrap): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e1627a960a2..9b78bee8e25 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18413,9 +18413,6 @@ JSON) codec.") (native-inputs `()) (arguments `(#:tests? #f)))) -(define-public python2-attrs-bootstrap - (package-with-python2 python-attrs-bootstrap)) - (define-public python-cliapp (package (name "python-cliapp") From 4a0e996ada9cd76e302d7f97446513cea1391c09 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:03:26 -0400 Subject: [PATCH 1343/1394] gnu: pdf2djvu: Disable tests to avoid Python 2 dependencies. * gnu/packages/djvu.scm (pdf2djvu)[tests]: Set to #f. [test-target]: Delete argument. [native-inputs]: Use new style. Delete python-2 and python2-nose. [inputs]: Use new style. --- gnu/packages/djvu.scm | 32 ++++++++------------------------ 1 file changed, 8 insertions(+), 24 deletions(-) diff --git a/gnu/packages/djvu.scm b/gnu/packages/djvu.scm index f27dc70b70e..b85193ccdb8 100644 --- a/gnu/packages/djvu.scm +++ b/gnu/packages/djvu.scm @@ -151,31 +151,15 @@ a continuous layout.") (sha256 (base32 "0c595yziz81c9izf9s5sskd00qmgz2n1hp2vdcgg0dx81g3xfidb")))) (build-system gnu-build-system) - (native-inputs - `(("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config) - ("python2" ,python-2) - ("python2-nose" ,python2-nose))) + (arguments (list #:tests? #f)) ;requires Python 2 + (native-inputs (list gettext-minimal pkg-config)) (inputs - `(("djvulibre" ,djvulibre) - ("exiv2" ,exiv2) - ("graphicsmagick" ,graphicsmagick) - ("poppler" ,poppler) - ("poppler-data" ,poppler-data) - ("util-linux-lib" ,util-linux "lib"))) ; for libuuid - (arguments - `(#:test-target "test" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-tests - (lambda _ - (substitute* "tests/test-xmp-broken.py" - ;; Error message changed in recent versions of XML parser - (("XML parsing failure") - "Error in XMLValidator")))) - (add-before 'check 'set-home-for-tests - (lambda _ - (setenv "HOME" "/tmp")))))) + (list djvulibre + exiv2 + graphicsmagick + poppler + poppler-data + `(,util-linux "lib"))) ;for libuuid (synopsis "PDF to DjVu converter") (description "@code{pdf2djvu} creates DjVu files from PDF files. From 9c19bdbf5cb0da0579db19d2759b91f28fc00220 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:06:14 -0400 Subject: [PATCH 1344/1394] gnu: python-setproctitle: Delete obsolete phase. * gnu/packages/python-xyz.scm (python-setproctitle) [phases]{patch-Makefile}: Delete phase. --- gnu/packages/python-xyz.scm | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9b78bee8e25..d3e3da4e05b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17608,17 +17608,6 @@ JSON) codec.") (arguments '(#:phases (modify-phases %standard-phases - (add-before 'check 'patch-Makefile - ;; Stricly this is only required for the python2 variant. - ;; But adding a phase in an inherited package seems to be - ;; cumbersum. So we patch even for python3. - (lambda _ - (let ((nose (assoc-ref %build-inputs "python2-nose"))) - (when nose - (substitute* "Makefile" - (("\\$\\(PYTHON\\) [^ ]which nosetests[^ ] ") - (string-append nose "/bin/nosetests ")))) - #t))) (replace 'check (lambda _ (setenv "PYTHON" (or (which "python3") (which "python"))) From 0fa989172df685170590e42b6eadc151cbd2acba Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:07:07 -0400 Subject: [PATCH 1345/1394] gnu: Remove python2-nose. * gnu/packages/check.scm (python2-nose): Delete variable. (python-nose)[properties]: Delete field. --- gnu/packages/check.scm | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index fdf14f7cf2d..66e7993996c 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -887,17 +887,7 @@ available via the @code{unittest.mock} module.") (synopsis "Python testing library") (description "Nose extends the unittest library to make testing easier.") - (license license:lgpl2.0+) - (properties `((python2-variant . ,(delay python2-nose)))))) - -(define-public python2-nose - (let ((base (package-with-python2 - (strip-python2-variant python-nose)))) - (package/inherit base - (arguments (substitute-keyword-arguments (package-arguments base) - ((#:phases phases) - `(modify-phases ,phases - (delete 'invoke-2to3)))))))) + (license license:lgpl2.0+))) (define-public python-nose2 (package From cfa04b1c6c640e9450eaf574fb60ce493825a3ee Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:09:25 -0400 Subject: [PATCH 1346/1394] gnu: ocaml-dose3: Disable tests to avoid Python 2 dependencies. * gnu/packages/ocaml.scm (ocaml-dose3)[tests?]: Set to #f. [native-inputs]: Use new style. Remove python-2 and python2-pyyaml. --- gnu/packages/ocaml.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index e6d6bc7a89e..5591e08d785 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -24,6 +24,7 @@ ;;; Copyright © 2021 Ivan Gankevich ;;; Copyright © 2021 Maxime Devos ;;; Copyright © 2021 Sarah Morgensen +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -663,21 +664,20 @@ underlying solvers like Cplex, Gurobi, Lpsolver, Glpk, CbC, SCIP or WBO.") "ocaml-dose3-Install-mli-cmx-etc.patch")))) (build-system ocaml-build-system) (arguments - `(#:configure-flags + `(#:tests? #f ;the test suite requires python 2 + #:configure-flags ,#~(list (string-append "SHELL=" #+(file-append (canonical-package bash-minimal) "/bin/sh"))) #:make-flags ,#~(list (string-append "LIBDIR=" #$output "/lib/ocaml/site-lib")))) (propagated-inputs - (list ocaml-graph ocaml-cudf ocaml-extlib ocaml-re)) + (list ocaml-graph ocaml-cudf ocaml-extlib ocaml-re)) (native-inputs - `(("perl" ,perl) - ("python" ,python-2) ; for a test script - ("python2-pyyaml" ,python2-pyyaml) ; for a test script - ("ocaml-extlib" ,ocaml-extlib) - ("ocamlbuild" ,ocamlbuild) - ("ocaml-cppo" ,ocaml-cppo))) + (list perl + ocaml-extlib + ocamlbuild + ocaml-cppo)) (home-page "https://www.mancoosi.org/software/") (synopsis "Package distribution management framework") (description "Dose3 is a framework made of several OCaml libraries for From 88739a96be164e19dbe79c690e94f90cb025d69e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:10:52 -0400 Subject: [PATCH 1347/1394] gnu: Remove python2-pyyaml. * gnu/packages/python-xyz.scm (python2-pyyaml): Delete variable. (python-jsonschema)[properties]: Delete field. --- gnu/packages/python-xyz.scm | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d3e3da4e05b..2aea3d6c258 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3746,8 +3746,7 @@ environments and back.") complete YAML 1.1 parser, Unicode support, pickle support, capable extension API, and sensible error messages. PyYAML supports standard YAML tags and provides Python-specific tags that represent an arbitrary Python object.") - (license license:expat) - (properties `((python2-variant . ,(delay python2-pyyaml)))))) + (license license:expat))) (define-public python-pyyaml-5 (package @@ -3761,19 +3760,6 @@ provides Python-specific tags that represent an arbitrary Python object.") (base32 "0pm440pmpvgv5rbbnm8hk4qga5a292kvlm1bh3x2nwr8pb5p8xv0")))))) -(define-public python2-pyyaml - (let ((base (package-with-python2 (strip-python2-variant python-pyyaml)))) - (package - (inherit base) - (version "5.4.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "PyYAML" version)) - (sha256 - (base32 - "0pm440pmpvgv5rbbnm8hk4qga5a292kvlm1bh3x2nwr8pb5p8xv0"))))))) - (define-public python-vine (package (name "python-vine") From f451a8e80cf8d2da08bb65c4c07e3d41d7a17e58 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:19:31 -0400 Subject: [PATCH 1348/1394] gnu: openbox: Patch for Python 3. * gnu/packages/patches/openbox-python3.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/openbox.scm (openbox)[source]: Apply it. [arguments]: New field. [propagated-inputs]: Replace python2-pyxdg with python-pyxdg. [native-inputs]: Replace python-2 with python-wrapper. Add autoconf, automake, gettext-minimal and libtool. --- gnu/local.mk | 1 + gnu/packages/openbox.scm | 20 ++- gnu/packages/patches/openbox-python3.patch | 165 +++++++++++++++++++++ 3 files changed, 182 insertions(+), 4 deletions(-) create mode 100644 gnu/packages/patches/openbox-python3.patch diff --git a/gnu/local.mk b/gnu/local.mk index 06cf32b9169..af92253dddc 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1561,6 +1561,7 @@ dist_patch_DATA = \ %D%/packages/patches/onnx-skip-model-downloads.patch \ %D%/packages/patches/openboardview-use-system-imgui.patch \ %D%/packages/patches/openboardview-use-system-utf8.patch \ + %D%/packages/patches/openbox-python3.patch \ %D%/packages/patches/opencascade-oce-glibc-2.26.patch \ %D%/packages/patches/openfoam-4.1-cleanup.patch \ %D%/packages/patches/openjdk-10-idlj-reproducibility.patch \ diff --git a/gnu/packages/openbox.scm b/gnu/packages/openbox.scm index 873592c19eb..2dac9ec6449 100644 --- a/gnu/packages/openbox.scm +++ b/gnu/packages/openbox.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2014 Julien Lepiller ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2017 Nikita +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -24,6 +25,9 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system gnu) + #:use-module (guix gexp) + #:use-module (gnu packages) + #:use-module (gnu packages autotools) #:use-module (gnu packages freedesktop) #:use-module (gnu packages gettext) #:use-module (gnu packages gnome) @@ -46,10 +50,18 @@ version ".tar.xz")) (sha256 (base32 - "0vg2y1qddsdxkjv806mzpvmkgzliab8ll4s7zm7ma5jnriamirxb")))) + "0vg2y1qddsdxkjv806mzpvmkgzliab8ll4s7zm7ma5jnriamirxb")) + (patches (search-patches "openbox-python3.patch")))) (build-system gnu-build-system) - (native-inputs (list pkg-config)) - (propagated-inputs (list python2-pyxdg)) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'force-reconfigure + ;; This is made necessary by the openbox-python3 patch. + (lambda _ + (delete-file "configure")))))) + (native-inputs (list autoconf automake gettext-minimal libtool pkg-config)) + (propagated-inputs (list python-pyxdg)) (inputs (list imlib2 libxml2 (librsvg-for-system) @@ -60,7 +72,7 @@ libxrandr libxft pango - python-2)) + python-wrapper)) (synopsis "Box style window manager") (description "Openbox is a highly configurable, next generation window manager with diff --git a/gnu/packages/patches/openbox-python3.patch b/gnu/packages/patches/openbox-python3.patch new file mode 100644 index 00000000000..782524d8a74 --- /dev/null +++ b/gnu/packages/patches/openbox-python3.patch @@ -0,0 +1,165 @@ +Retrieved from the openbox Debian package. + +From acfbbc4ea40932f183617bb7006700140fe5f61e Mon Sep 17 00:00:00 2001 +From: Troy Curtis Jr +Date: Wed, 13 Sep 2017 21:59:48 -0500 +Subject: [PATCH] Add python3 support to openbox-xdg-autostart. + +Updated syntax in openbox-xdg-autostart to support both python2 and +python3. + +Added a configure substitution to set the chosen python at build time. + +https://bugzilla.icculus.org/show_bug.cgi?id=6444 +--- + .gitignore | 1 + + configure.ac | 3 + + ...xdg-autostart => openbox-xdg-autostart.in} | 70 +++++++++---------- + 3 files changed, 38 insertions(+), 36 deletions(-) + rename data/autostart/{openbox-xdg-autostart => openbox-xdg-autostart.in} (77%) + +diff --git a/configure.ac b/configure.ac +index ca1602670..9a31e9845 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -103,6 +103,8 @@ AC_CHECK_HEADERS(ctype.h dirent.h errno.h fcntl.h grp.h locale.h pwd.h) + AC_CHECK_HEADERS(signal.h string.h stdio.h stdlib.h unistd.h sys/stat.h) + AC_CHECK_HEADERS(sys/select.h sys/socket.h sys/time.h sys/types.h sys/wait.h) + ++AM_PATH_PYTHON([2],,) ++ + AC_PATH_PROG([SED], [sed], [no]) + if test "$SED" = "no"; then + AC_MSG_ERROR([The program "sed" is not available. This program is required to build Openbox.]) +@@ -259,6 +261,7 @@ AC_CONFIG_FILES([ + obrender/version.h + obt/version.h + version.h ++ data/autostart/openbox-xdg-autostart + ]) + AC_CONFIG_COMMANDS([doc], + [test -d doc || mkdir doc]) +diff --git a/data/autostart/openbox-xdg-autostart b/data/autostart/openbox-xdg-autostart.in +similarity index 77% +rename from data/autostart/openbox-xdg-autostart +rename to data/autostart/openbox-xdg-autostart.in +index 04a17a199..3c365b112 100755 +--- a/data/autostart/openbox-xdg-autostart ++++ b/data/autostart/openbox-xdg-autostart.in +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!@PYTHON@ + + # openbox-xdg-autostart runs things based on the XDG autostart specification + # Copyright (C) 2008 Dana Jansens +@@ -28,9 +28,7 @@ try: + from xdg.DesktopEntry import DesktopEntry + from xdg.Exceptions import ParsingError + except ImportError: +- print +- print >>sys.stderr, "ERROR:", ME, "requires PyXDG to be installed" +- print ++ sys.stderr.write("\nERROR: %s requires PyXDG to be installed\n" % ME) + sys.exit(1) + + def main(argv=sys.argv): +@@ -51,7 +49,7 @@ def main(argv=sys.argv): + try: + autofile = AutostartFile(path) + except ParsingError: +- print "Invalid .desktop file: " + path ++ print("Invalid .desktop file: " + path) + else: + if not autofile in files: + files.append(autofile) +@@ -99,9 +97,9 @@ class AutostartFile: + + def _alert(self, str, info=False): + if info: +- print "\t ", str ++ print("\t ", str) + else: +- print "\t*", str ++ print("\t*", str) + + def _showInEnvironment(self, envs, verbose=False): + default = not self.de.getOnlyShowIn() +@@ -146,14 +144,14 @@ class AutostartFile: + + def display(self, envs): + if self._shouldRun(envs): +- print "[*] " + self.de.getName() ++ print("[*] " + self.de.getName()) + else: +- print "[ ] " + self.de.getName() ++ print("[ ] " + self.de.getName()) + self._alert("File: " + self.path, info=True) + if self.de.getExec(): + self._alert("Executes: " + self.de.getExec(), info=True) + self._shouldRun(envs, True) +- print ++ print() + + def run(self, envs): + here = os.getcwd() +@@ -165,34 +163,34 @@ class AutostartFile: + os.chdir(here) + + def show_help(): +- print "Usage:", ME, "[OPTION]... [ENVIRONMENT]..." +- print +- print "This tool will run xdg autostart .desktop files" +- print +- print "OPTIONS" +- print " --list Show a list of the files which would be run" +- print " Files which would be run are marked with an asterix" +- print " symbol [*]. For files which would not be run," +- print " information is given for why they are excluded" +- print " --help Show this help and exit" +- print " --version Show version and copyright information" +- print +- print "ENVIRONMENT specifies a list of environments for which to run autostart" +- print "applications. If none are specified, only applications which do not " +- print "limit themselves to certain environments will be run." +- print +- print "ENVIRONMENT can be one or more of:" +- print " GNOME Gnome Desktop" +- print " KDE KDE Desktop" +- print " ROX ROX Desktop" +- print " XFCE XFCE Desktop" +- print " Old Legacy systems" +- print ++ print("Usage:", ME, "[OPTION]... [ENVIRONMENT]...") ++ print() ++ print("This tool will run xdg autostart .desktop files") ++ print() ++ print("OPTIONS") ++ print(" --list Show a list of the files which would be run") ++ print(" Files which would be run are marked with an asterix") ++ print(" symbol [*]. For files which would not be run,") ++ print(" information is given for why they are excluded") ++ print(" --help Show this help and exit") ++ print(" --version Show version and copyright information") ++ print() ++ print("ENVIRONMENT specifies a list of environments for which to run autostart") ++ print("applications. If none are specified, only applications which do not ") ++ print("limit themselves to certain environments will be run.") ++ print() ++ print("ENVIRONMENT can be one or more of:") ++ print(" GNOME Gnome Desktop") ++ print(" KDE KDE Desktop") ++ print(" ROX ROX Desktop") ++ print(" XFCE XFCE Desktop") ++ print(" Old Legacy systems") ++ print() + + def show_version(): +- print ME, VERSION +- print "Copyright (c) 2008 Dana Jansens" +- print ++ print(ME, VERSION) ++ print("Copyright (c) 2008 Dana Jansens") ++ print() + + if __name__ == "__main__": + sys.exit(main()) From e5c6816ddffd597f6f203a5ba686c0113ecd9f33 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:35:25 -0400 Subject: [PATCH 1349/1394] gnu: Remove python2-wcwidth. * gnu/packages/python-xyz.scm (python2-wcwidth): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2aea3d6c258..83200aa8137 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16024,9 +16024,6 @@ Python implementation of the @code{wcwidth} and @code{wcswidth} C functions specified in POSIX.1-2001 and POSIX.1-2008.") (license license:expat))) -(define-public python2-wcwidth - (package-with-python2 python-wcwidth)) - (define-public python-chai (package (name "python-chai") From 9fe706c92e0fea3d490adf615727ea1af3661336 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:35:42 -0400 Subject: [PATCH 1350/1394] gnu: Remove python2-pyxdg. * gnu/packages/freedesktop.scm (python2-pyxdg): Delete variable. --- gnu/packages/freedesktop.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index c94cacbbfff..b9f3c91558f 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -960,9 +960,6 @@ manager for the current system.") Python.") (license license:lgpl2.0))) -(define-public python2-pyxdg - (package-with-python2 python-pyxdg)) - (define-public wayland (package (name "wayland") From a683c74e9a1d7eb41714625f21da5afcf36f549d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:36:06 -0400 Subject: [PATCH 1351/1394] gnu: Remove python2-six-bootstrap. * gnu/packages/python-build.scm (python2-six-bootstrap): Delete variable. --- gnu/packages/python-build.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-build.scm b/gnu/packages/python-build.scm index 3fb01199a88..c64a7732be5 100644 --- a/gnu/packages/python-build.scm +++ b/gnu/packages/python-build.scm @@ -162,9 +162,6 @@ Six supports every Python version since 2.5. It is contained in only one Python file, so it can be easily copied into your project.") (license license:x11))) -(define-public python2-six-bootstrap - (package-with-python2 python-six-bootstrap)) - (define-public python-tomli (package (name "python-tomli") From 9165283a1cdd087d76b70563315eb59e8a608704 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:36:29 -0400 Subject: [PATCH 1352/1394] gnu: Remove python2-setuptools-scm. * gnu/packages/python-xyz.scm (python2-setuptools-scm): Delete variable. (python-lfdfiles)[properties]: Delete field. --- gnu/packages/python-xyz.scm | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 83200aa8137..cd5bf33981d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7713,21 +7713,7 @@ child application and control it as if a human were typing commands.") "Setuptools_scm handles managing your Python package versions in @dfn{software configuration management} (SCM) metadata instead of declaring them as the version argument or in a SCM managed file.") - (license license:expat) - (properties `((python2-variant . ,(delay python2-setuptools-scm)))))) - -(define-public python2-setuptools-scm - (let ((base (package-with-python2 - (strip-python2-variant python-setuptools-scm)))) - (package/inherit base - (version "5.0.2") ;no python 2 support in version 6 - (source (origin - (method url-fetch) - (uri (pypi-uri "setuptools_scm" version)) - (sha256 - (base32 - "1j75i8avp9fhrkpbabsa8vyvbi49kmxlq6l10xir9qs96kfwx843")))) - (propagated-inputs '())))) + (license license:expat))) (define-public python-sexpdata (package From 28bddb7d4f0acb1ad8a61fd9dec7923487c0803c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:37:06 -0400 Subject: [PATCH 1353/1394] gnu: Remove python2-pyparsing. * gnu/packages/python-build.scm (python2-pyparsing): Delete variable. (python-pyparsing)[properties]: Delete field. --- gnu/packages/python-build.scm | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/gnu/packages/python-build.scm b/gnu/packages/python-build.scm index c64a7732be5..d85463ebabd 100644 --- a/gnu/packages/python-build.scm +++ b/gnu/packages/python-build.scm @@ -261,8 +261,7 @@ Python file, so it can be easily copied into your project.") executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions. The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code.") - (license license:expat) - (properties `((python2-variant . ,(delay python2-pyparsing)))))) + (license license:expat))) ;;; This is the last release compatible with Python 2. (define-public python-pyparsing-2.4.7 @@ -276,9 +275,6 @@ that client code uses to construct the grammar directly in Python code.") (sha256 (base32 "1hgc8qrbq1ymxbwfbjghv01fm3fbpjwpjwi0bcailxxzhf3yq0y2")))))) -(define-public python2-pyparsing - (package-with-python2 (strip-python2-variant python-pyparsing-2.4.7))) - (define-public python-packaging-bootstrap (package (name "python-packaging-bootstrap") From 25a1d0f63d52c244e813aa49234e602ae54eb54f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 15:37:45 -0400 Subject: [PATCH 1354/1394] gnu: Remove python2-py. * gnu/packages/python-xyz.scm (python2-py): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cd5bf33981d..daf721e89db 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3144,9 +3144,6 @@ port forwards using @acronym{UPnP, Universal Plug and Play}.") code introspection, and logging.") (license license:expat))) -(define-public python2-py - (package-with-python2 python-py)) - ;; Recent versions of python-fixtures and python-testrepository need ;; python-pbr for packaging, which itself needs these two packages for ;; testing. From b89669f0346888a556061cb35b4a74b13ee3daa4 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 16:27:37 -0400 Subject: [PATCH 1355/1394] gnu: Remove python2-fonttools. * gnu/packages/python-xyz.scm (python2-fonttools): Delete variable. (python-fonttools)[properties]: Delete field. --- gnu/packages/python-xyz.scm | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index daf721e89db..fbb0fc399bc 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10921,8 +10921,7 @@ supports reading and writing of TrueType/OpenType fonts, reading and writing of AFM files, reading (and partially writing) of PS Type 1 fonts. The package also contains a tool called “TTX” which converts TrueType/OpenType fonts to and from an XML-based format.") - (license license:expat) - (properties `((python2-variant . ,(delay python2-fonttools))))))) + (license license:expat)))) ;;; Rename 'python-fonttools' in next cycle, renaming the current ;;; 'python-fonttools' to 'python-fonttools-minimal'. @@ -10962,19 +10961,6 @@ from an XML-based format.") python-zopfli)) (properties (alist-delete 'hidden? (package-properties python-fonttools))))) -;; Fonttools 4.x dropped support for Python 2, so stick with 3.x here. -(define-public python2-fonttools - (let ((base (package-with-python2 (strip-python2-variant python-fonttools)))) - (package - (inherit base) - (version "3.44.0") - (source (origin - (method url-fetch) - (uri (pypi-uri "fonttools" version ".zip")) - (sha256 - (base32 - "0v6399g755f2hn1ry62i5b6gdinf2fpx2966v3bxh6bjw1accb5p"))))))) - (define-public python-fonttools-next (package (inherit python-fonttools-full) From a55151703f060239ef1bcd080e29bdcddc4e21d7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 16:34:56 -0400 Subject: [PATCH 1356/1394] gnu: python2-six: Disable tests. * gnu/packages/python-xyz.scm (python2-six)[native-inputs]: Clear. [phases]: Delete check phase. --- gnu/packages/python-xyz.scm | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index fbb0fc399bc..74becc79973 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2573,7 +2573,16 @@ in the current session, Python, and the OS.") `(("python-pytest" ,python-pytest-bootstrap))))) (define-public python2-six - (package-with-python2 python-six)) + (let ((base (package-with-python2 python-six))) + (package + (inherit base) + ;; Reduce Python 2 closure by disabling tests and removing the native + ;; inputs. + (arguments (substitute-keyword-arguments (package-arguments base) + ((#:phases phases) + `(modify-phases ,phases + (delete 'check))))) + (native-inputs '())))) (define-public python-schedule (package From 0740b12df3ca5c173f6ec4ae0aa41e0109337f6d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 16:36:49 -0400 Subject: [PATCH 1357/1394] gnu: Remove python2-backports-csv. * gnu/packages/python-xyz.scm (python2-backports-csv): Delete variable. --- gnu/packages/python-xyz.scm | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 74becc79973..0435b2c7f4c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9824,16 +9824,6 @@ This is due, for the most part, to the difference between str in Python 2 and Python 3.") (license license:psfl))) -(define-public python2-backports-csv - (package - (inherit (package-with-python2 python-backports-csv)) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; The sanity-check attempts attempts to import the non-existent - ;; module "backports". - (delete 'sanity-check)))))) - (define-public python-waf (package (name "python-waf") From 12a16c3166f3d3fcee9dd579a3c26ea3d92718b7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 14 May 2022 02:18:11 -0400 Subject: [PATCH 1358/1394] gnu: qtwebengine: Re-style inputs. * gnu/packages/qt.scm (qtwebengine)[phases]: Delete trailing #t. {substitute-source}: Use search-input-file. [inputs, native-inputs]: Use new style. --- gnu/packages/qt.scm | 140 +++++++++++++++++++++----------------------- 1 file changed, 68 insertions(+), 72 deletions(-) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index ea82ab07d0e..9920af74fb8 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -1771,69 +1771,68 @@ using the Enchant spell-checking library.") ;; Do not enable support for loading the Widevine DRM plugin. (substitute* "src/buildtools/config/common.pri" (("enable_widevine=true") - "enable_widevine=false")) - #t))))) + "enable_widevine=false"))))))) (build-system gnu-build-system) (native-inputs - `(("bison" ,bison) - ("flex" ,flex) - ("gperf" ,gperf) - ("ninja" ,ninja) - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("python-2" ,python-2) - ("python-six" ,python2-six) - ("ruby" ,ruby))) + (list bison + flex + gperf + ninja + perl + pkg-config + python2-six + python-2 + ruby)) (inputs - `(("alsa-lib" ,alsa-lib) - ("atk" ,atk) - ("cups-minimal" ,cups-minimal) - ("curl" ,curl) - ("dbus" ,dbus) - ("ffmpeg" ,ffmpeg) - ("fontconfig" ,fontconfig) - ("harbuzz" ,harfbuzz) - ("icu4c" ,icu4c) - ("jsoncpp" ,jsoncpp) - ("lcms" ,lcms) - ("libcap" ,libcap) - ("libevent" ,libevent) - ("libgcrypt" ,libgcrypt) - ("libjpeg" ,libjpeg-turbo) - ("libvpx" ,libvpx) - ("libwebp" ,libwebp) - ("libx11" ,libx11) - ("libxcb" ,libxcb) - ("libxcomposite" ,libxcomposite) - ("libxcursor" ,libxcursor) - ("libxi" ,libxi) - ("libxkbcommon" ,libxkbcommon) - ;; FIXME: libxml2 needs to built with icu support though it links to - ;; libxml2 configure summary still states "Checking for compatible - ;; system libxml2... no" - ("libxml2" ,libxml2) - ("openh264" ,openh264) - ("libxrandr" ,libxrandr) - ("libxrender" ,libxrender) - ("libxslt" ,libxslt) - ("libxtst" ,libxtst) - ("mesa" ,mesa) - ("minizip" ,minizip) - ("nss" ,nss) - ("opus" ,opus) - ("pciutils" ,pciutils) - ("protobuf" ,protobuf) - ("pulseaudio" ,pulseaudio) - ("qtbase" ,qtbase-5) - ("qtdeclarative" ,qtdeclarative) - ("qtmultimedia" ,qtmultimedia) - ("qtwebchannel" ,qtwebchannel) - ("re2" ,re2) - ("snappy" ,snappy) - ("udev" ,eudev) - ("valgrind" ,valgrind) - ("vulkan-headers" ,vulkan-headers) - ("xcb-util" ,xcb-util))) + (list alsa-lib + atk + cups-minimal + curl + dbus + ffmpeg + fontconfig + harfbuzz + icu4c + jsoncpp + lcms + libcap + libevent + libgcrypt + libjpeg-turbo + libvpx + libwebp + libx11 + libxcb + libxcomposite + libxcursor + libxi + libxkbcommon + ;; FIXME: libxml2 needs to built with icu support though it links to + ;; libxml2 configure summary still states "Checking for compatible + ;; system libxml2... no" + libxml2 + openh264 + libxrandr + libxrender + libxslt + libxtst + mesa + minizip + nss + opus + pciutils + protobuf + pulseaudio + qtbase-5 + qtdeclarative + qtmultimedia + qtwebchannel + re2 + snappy + eudev + valgrind + vulkan-headers + xcb-util)) (arguments (substitute-keyword-arguments (package-arguments qtsvg) ((#:modules modules '()) @@ -1844,13 +1843,12 @@ using the Enchant spell-checking library.") `(modify-phases ,phases (add-before 'configure 'substitute-source (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (nss (assoc-ref inputs "nss")) - (udev (assoc-ref inputs "udev"))) - (with-atomic-file-replacement "src/buildtools/config/linux.pri" - (lambda (in out) - (display (get-string-all in) out) - (display "\ngn_args += use_system_openh264=true\n" out))) + (let ((out (assoc-ref outputs "out"))) + (with-atomic-file-replacement + "src/buildtools/config/linux.pri" + (lambda (in out) + (display (get-string-all in) out) + (display "\ngn_args += use_system_openh264=true\n" out))) ;; Qtwebengine is not installed into the same prefix as ;; qtbase. Some qtbase QTLibraryInfo constants will not ;; work. Replace with the full path to the qtwebengine @@ -1863,12 +1861,11 @@ using the Enchant spell-checking library.") ;; Substitute full dynamic library path for nss. (substitute* "src/3rdparty/chromium/crypto/nss_util.cc" (("libnssckbi.so") - (string-append nss "/lib/nss/libnssckbi.so"))) + (search-input-file inputs "lib/nss/libnssckbi.so"))) ;; Substitute full dynamic library path for udev. (substitute* "src/3rdparty/chromium/device/udev_linux/udev1_loader.cc" (("libudev.so.1") - (string-append udev "/lib/libudev.so.1"))) - #t))) + (search-input-file inputs "lib/libudev.so.1")))))) (add-before 'configure 'set-env (lambda _ ;; Avoids potential race conditions. @@ -1876,8 +1873,7 @@ using the Enchant spell-checking library.") (setenv "NINJAFLAGS" (string-append "-k1" ;less verbose build output ;; Respect the '--cores' option of 'guix build'. - " -j" (number->string (parallel-job-count)))) - #t)) + " -j" (number->string (parallel-job-count)))))) (replace 'configure (lambda _ ;; Valid QT_BUILD_PARTS variables are: From 026fca8b5b30aaa584e3c2b8144bf21a882a5edd Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 14 May 2022 11:22:07 -0400 Subject: [PATCH 1359/1394] gnu: Remove python2-checkm-genome. * gnu/packages/bioinformatics.scm (python2-checkm-genome): Delete variable. --- gnu/packages/bioinformatics.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3223d6eea8a..b92a0b5829d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13438,9 +13438,6 @@ on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome.") (license license:gpl3+))) -(define-public python2-checkm-genome - (deprecated-package "python2-checkm-genome" checkm)) - (define-public umi-tools (package (name "umi-tools") From 5d8fb87127beee50671a9506013be541a8b45ea8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 14 May 2022 11:24:10 -0400 Subject: [PATCH 1360/1394] gnu: Remove python2-setuptools. * gnu/packages/python-xyz.scm (python2-setuptools): Delete variable. (python-setuptools)[properties]: Delete field. * gnu/packages/syncthing.scm (syncthing-gtk): Delete commented native input. * guix/lint.scm (check-inputs-should-not-be-an-input-at-all): Remove obsolete entries. --- gnu/packages/python-xyz.scm | 57 ------------------------------------- gnu/packages/syncthing.scm | 2 -- guix/lint.scm | 4 +-- 3 files changed, 1 insertion(+), 62 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0435b2c7f4c..d59d353009e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1843,63 +1843,6 @@ facilitate packaging Python projects, where packaging includes: (license (list license:psfl ;setuptools itself license:expat ;six, appdirs, pyparsing license:asl2.0 ;packaging is dual ASL2/BSD-2 - license:bsd-2)) - (properties `((python2-variant . ,(delay python2-setuptools)))))) - -;; Newer versions of setuptools no longer support Python 2. -(define-public python2-setuptools - (package - (name "python2-setuptools") - (version "41.0.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "setuptools" version ".zip")) - (sha256 - (base32 - "04sns22y2hhsrwfy1mha2lgslvpjsjsz8xws7h2rh5a7ylkd28m2")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Remove included binaries which are used to build self-extracting - ;; installers for Windows. - ;; TODO: Find some way to build them ourself so we can include them. - (for-each delete-file (find-files "setuptools" "^(cli|gui).*\\.exe$")) - #t)))) - (build-system python-build-system) - ;; FIXME: Tests require pytest, which itself relies on setuptools. - ;; One could bootstrap with an internal untested setuptools. - (arguments - `(#:tests? #f - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'compatibility-fixes - (lambda _ - ;; HTMLParser no longer exists. - (substitute* "setuptools/py33compat.py" - (("html_parser.HTMLParser\\(\\).unescape") - "html.unescape")) - ;; This needs distutils.msvc9compiler - (delete-file "setuptools/tests/test_msvc.py")))))) - (native-inputs - (list unzip)) - (home-page "https://pypi.org/project/setuptools/") - (synopsis - "Library designed to facilitate packaging Python projects") - (description - "Setuptools is a fully-featured, stable library designed to facilitate -packaging Python projects, where packaging includes: -Python package and module definitions, -distribution package metadata, -test hooks, -project installation, -platform-specific details, -Python 3 support.") - ;; TODO: setuptools now bundles the following libraries: - ;; packaging, pyparsing, six and appdirs. How to unbundle? - (license (list license:psfl ; setuptools itself - license:expat ; six, appdirs, pyparsing - license:asl2.0 ; packaging is dual ASL2/BSD-2 license:bsd-2)))) (define-public python-setuptools-declarative-requirements diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index 6002c10560e..4dfa62c017c 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -202,8 +202,6 @@ Protocol.") python-pygobject psmisc syncthing)) - ;; (native-inputs - ;; `(("python2-setuptools" ,python2-setuptools))) (home-page "https://github.com/syncthing/syncthing-gtk") (synopsis "GTK3 based GUI and notification area icon for Syncthing") (description "@code{syncthing-gtk} is a GTK3 Python based GUI and diff --git a/guix/lint.scm b/guix/lint.scm index aa16efe6dbb..73581b518f9 100644 --- a/guix/lint.scm +++ b/guix/lint.scm @@ -523,9 +523,7 @@ of a package, and INPUT-NAMES, a list of package specifications such as ;; Emit a warning if some inputs of PACKAGE are likely to should not be ;; an input at all. (let ((input-names '("python-setuptools" - "python2-setuptools" - "python-pip" - "python2-pip"))) + "python-pip"))) (map (lambda (input) (make-warning package From 96c0c18c3e65b59f365b06e478fbcb71f272ed25 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 14 May 2022 11:26:05 -0400 Subject: [PATCH 1361/1394] gnu: Remove python-prompt-toolkit-2. * gnu/packages/python-xyz.scm (python-prompt-toolkit-2): Delete variable. (python-prompt-toolkit)[properties]: Delete field. (python-jupyter-console): Replace python-prompt-toolkit-2 with python-prompt-toolkit. --- gnu/packages/python-xyz.scm | 18 +----------------- 1 file changed, 1 insertion(+), 17 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d59d353009e..8088761f0fa 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16623,8 +16623,7 @@ interfaces in Python. It's like GNU Readline but it also features syntax highlighting while typing, out-of-the-box multi-line input editing, advanced code completion, incremental search, support for Chinese double-width characters, mouse support, and auto suggestions.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python-prompt-toolkit-2)))))) + (license license:bsd-3))) (define-public python-proselint (package @@ -16653,21 +16652,6 @@ characters, mouse support, and auto suggestions.") scans through a file and detects issues.") (license license:bsd-3))) -(define-public python-prompt-toolkit-2 - (package (inherit python-prompt-toolkit) - (name "python-prompt-toolkit") - (version "2.0.7") - (source - (origin - (method url-fetch) - (uri (pypi-uri "prompt_toolkit" version)) - (sha256 - (base32 - "0fgacqk73w7s932vy46pan2yp8rvjmlkag20xvaydh9mhf6h85zx")))) - (propagated-inputs - (list python-wcwidth python-six python-pygments)) - (properties '()))) - (define-public python-jedi (package (name "python-jedi") From f7cfb57bb5afd9f76e298586005aeedc3609e537 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 14 May 2022 14:02:49 -0400 Subject: [PATCH 1362/1394] gnu: Remove python2-called-python. * gnu/packages/python.scm (python2-called-python): Delete variable. --- gnu/packages/python.scm | 8 -------- 1 file changed, 8 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index bcaf06977c4..db8bf5d5760 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -419,14 +419,6 @@ data types.") ;; Current 2.x version. (define-public python-2 python-2.7) -(define-public python2-called-python - ;; Both 2.x and 3.x used to be called "python". In commit - ;; a7714d42de2c3082f3609d1e63c83d703fb39cf9 (March 2018), we renamed the - ;; Python 2.x package to "python2". - (package/inherit python-2 - (name "python") - (properties `((superseded . ,python-2))))) - (define-public python-3.9 (package (inherit python-2) From 962d02904fe907d3cb3d96bc220ce7c759ad4425 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 16 May 2022 10:01:57 -0400 Subject: [PATCH 1363/1394] gnu: Remove python2-pytest-cov. * gnu/packages/check.scm (python2-pytest-cov): Delete variable. --- gnu/packages/check.scm | 32 -------------------------------- 1 file changed, 32 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 66e7993996c..2340ef72d97 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -1078,38 +1078,6 @@ distributed testing in both @code{load} and @code{each} modes. It also supports coverage of subprocesses.") (license license:expat))) -(define-public python2-pytest-cov - (package - (name "python2-pytest-cov") - (version "2.8.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pytest-cov" version)) - (sha256 - (base32 "0avzlk9p4nc44k7lpx9109dybq71xqnggxb9f4hp0l64pbc44ryc")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - ;; Options taken from tox.ini. - ;; TODO: make "--restructuredtext" tests pass. They currently fail - ;; with "Duplicate implicit target name". - (invoke "python" "./setup.py" "check" - "--strict" "--metadata")))))) - (propagated-inputs - (list python2-coverage python2-pytest)) - (home-page "https://github.com/pytest-dev/pytest-cov") - (synopsis "Pytest plugin for measuring coverage") - (description - "Pytest-cov produces coverage reports. It supports centralised testing and -distributed testing in both @code{load} and @code{each} modes. It also -supports coverage of subprocesses.") - (license license:expat))) - (define-public python-pytest-httpserver (package (name "python-pytest-httpserver") From d397cb6207ab96d476d4ea8880a675b67f429bf5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 31 May 2022 14:19:46 -0400 Subject: [PATCH 1364/1394] gnu: Remove pplacer. * gnu/packages/bioinformatics.scm (pplacer): Delete variable. --- gnu/packages/bioinformatics.scm | 117 -------------------------------- 1 file changed, 117 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b92a0b5829d..64e4171f8f7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13245,123 +13245,6 @@ Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is not available.") (license license:gpl3+))) -(define-public pplacer - (let ((commit "807f6f3")) - (package - (name "pplacer") - ;; The commit should be updated with each version change. - (version "1.1.alpha19") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/matsen/pplacer") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn")))) - (build-system ocaml-build-system) - (arguments - `(#:modules ((guix build ocaml-build-system) - (guix build utils) - (ice-9 ftw)) - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'fix-build-with-latest-ocaml - (lambda _ - (substitute* "myocamlbuild.ml" - (("dep \\[\"c_pam\"\\]" m) - (string-append "flag [\"ocaml\"; \"compile\"] (A \"-unsafe-string\");\n" - m)) - (("let run_and_read" m) - (string-append " -let split s ch = - let x = ref [] in - let rec go s = - let pos = String.index s ch in - x := (String.before s pos)::!x; - go (String.after s (pos + 1)) - in - try go s - with Not_found -> !x -let split_nl s = split s '\\n' -let before_space s = - try String.before s (String.index s ' ') - with Not_found -> s - -" m)) - (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m) - (string-append "List.map before_space (split_nl & " m ")")) - ((" blank_sep_strings &") "") - ((" Lexing.from_string &") "")) - #t)) - (add-after 'unpack 'replace-bundled-cddlib - (lambda* (#:key inputs #:allow-other-keys) - (let* ((cddlib-src (assoc-ref inputs "cddlib-src")) - (local-dir "cddlib_guix")) - (mkdir local-dir) - (with-directory-excursion local-dir - (invoke "tar" "xvf" cddlib-src)) - (let ((cddlib-src-folder - (string-append local-dir "/" - (list-ref (scandir local-dir) 2) - "/lib-src"))) - (for-each make-file-writable (find-files "cdd_src" ".*")) - (for-each - (lambda (file) - (copy-file file - (string-append "cdd_src/" (basename file)))) - (find-files cddlib-src-folder ".*[ch]$"))) - #t))) - (add-after 'unpack 'fix-makefile - (lambda _ - ;; Remove system calls to 'git'. - (substitute* "Makefile" - (("^DESCRIPT:=pplacer-.*") - (string-append - "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n"))) - (substitute* "myocamlbuild.ml" - (("git describe --tags --long .*\\\" with") - (string-append - "echo -n v" ,version "-" ,commit "\" with"))) - #t)) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (copy-recursively "bin" bin)) - #t))) - #:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib)) - (inputs - `(("zlib" ,zlib "static") - ("gsl" ,gsl-static) - ("ocaml-ounit" ,(package-with-ocaml4.07 ocaml-ounit)) - ("ocaml-batteries" ,(package-with-ocaml4.07 ocaml-batteries)) - ("ocaml-camlzip" ,(package-with-ocaml4.07 camlzip)) - ("ocaml-csv" ,(package-with-ocaml4.07 ocaml-csv)) - ("ocaml-sqlite3" ,(package-with-ocaml4.07 ocaml-sqlite3)) - ("ocaml-xmlm" ,(package-with-ocaml4.07 ocaml-xmlm)) - ("ocaml-mcl" ,(package-with-ocaml4.07 ocaml-mcl)) - ("ocaml-gsl" ,ocaml4.07-gsl-1) - ("sqlite:static" ,sqlite "static"))) - (native-inputs - `(("cddlib-src" ,(package-source cddlib)) - ("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild)) - ("pkg-config" ,pkg-config))) - (propagated-inputs - (list pplacer-scripts)) - (synopsis "Phylogenetic placement of biological sequences") - (description - "Pplacer places query sequences on a fixed reference phylogenetic tree -to maximize phylogenetic likelihood or posterior probability according to a -reference alignment. Pplacer is designed to be fast, to give useful -information about uncertainty, and to offer advanced visualization and -downstream analysis.") - (home-page "https://matsen.fhcrc.org/pplacer/") - (license license:gpl3)))) - ;; This package is installed alongside 'pplacer'. It is a separate package so ;; that it can use the python-build-system for the scripts that are ;; distributed alongside the main OCaml binaries. From ad030a0b7dc0225dae03686a51a9b7b0236cad34 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 31 May 2022 14:19:59 -0400 Subject: [PATCH 1365/1394] gnu: Remove pplacer-scripts. * gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable. --- gnu/packages/bioinformatics.scm | 39 --------------------------------- 1 file changed, 39 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 64e4171f8f7..d004124ddb6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13245,45 +13245,6 @@ Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is not available.") (license license:gpl3+))) -;; This package is installed alongside 'pplacer'. It is a separate package so -;; that it can use the python-build-system for the scripts that are -;; distributed alongside the main OCaml binaries. -(define pplacer-scripts - (package - (inherit pplacer) - (name "pplacer-scripts") - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'enter-scripts-dir - (lambda _ (chdir "scripts") #t)) - (replace 'check - (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)) - (add-after 'install 'wrap-executables - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (let ((path (string-append - (assoc-ref inputs "hmmer") "/bin:" - (assoc-ref inputs "infernal") "/bin"))) - (display path) - (wrap-program (string-append bin "/refpkg_align.py") - `("PATH" ":" prefix (,path)))) - (let ((path (string-append - (assoc-ref inputs "hmmer") "/bin"))) - (wrap-program (string-append bin "/hrefpkg_query.py") - `("PATH" ":" prefix (,path))))) - #t))))) - (inputs - `(("infernal" ,infernal) - ("hmmer" ,hmmer))) - (propagated-inputs - `(("python-biopython" ,python2-biopython) - ("taxtastic" ,taxtastic))) - (synopsis "Pplacer Python scripts"))) - (define-public checkm (package (name "checkm") From c35e508b4a317e3c06e1553833b0979e1620f582 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 31 May 2022 14:20:36 -0400 Subject: [PATCH 1366/1394] gnu: Remove python2-biopython. * gnu/packages/bioinformatics.scm (python2-biopython): Delete variable. --- gnu/packages/bioinformatics.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d004124ddb6..679b5af4a2e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1150,9 +1150,6 @@ into separate processes; and more.") (base32 "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))))) -(define-public python2-biopython - (package-with-python2 python-biopython)) - (define-public python-fastalite (package (name "python-fastalite") From a484e019d3f8c336b93edad2404f67c9ec83eaa1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 31 May 2022 20:08:11 +0200 Subject: [PATCH 1367/1394] gnu: Add glibc-2.32. * gnu/packages/base.scm (glibc-2.32): New variable. --- gnu/packages/base.scm | 54 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index b8534655780..bef45199e70 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -930,6 +930,60 @@ with the Linux kernel.") ;; Below are old libc versions, which we use mostly to build locale data in ;; the old format (which the new libc cannot cope with.) +(define-public glibc-2.32 + (package + (inherit glibc) + (version "2.32") + (source (origin + (inherit (package-source glibc)) + (uri (string-append "mirror://gnu/glibc/glibc-" version ".tar.xz")) + (sha256 + (base32 + "0di848ibffrnwq7g2dvgqrnn4xqhj3h96csn69q4da51ymafl9qn")) + (patches (search-patches + "glibc-skip-c++.patch" + "glibc-ldd-powerpc.patch" + "glibc-ldd-x86_64.patch" + "glibc-dl-cache.patch" + "glibc-hidden-visibility-ldconfig.patch" + "glibc-versioned-locpath.patch" + "glibc-allow-kernel-2.6.32.patch" + "glibc-reinstate-prlimit64-fallback.patch" + "glibc-supported-locales.patch" + "glibc-hurd-clock_t_centiseconds.patch" + "glibc-2.31-hurd-clock_gettime_monotonic.patch" + "glibc-hurd-signal-sa-siginfo.patch" + "glibc-hurd-mach-print.patch" + "glibc-hurd-gettyent.patch")) + #; + (patches (search-patches "glibc-ldd-x86_64.patch" + "glibc-hidden-visibility-ldconfig.patch" + "glibc-versioned-locpath.patch" + "glibc-allow-kernel-2.6.32.patch" + "glibc-reinstate-prlimit64-fallback.patch" + "glibc-supported-locales.patch" + "glibc-hurd-clock_t_centiseconds.patch" + "glibc-hurd-clock_gettime_monotonic.patch" + "glibc-hurd-signal-sa-siginfo.patch")))) + + (arguments + (substitute-keyword-arguments (package-arguments glibc) + ((#:make-flags flags '()) + ;; Arrange so that /etc/rpc & co. go to $out/etc. + `(list (string-append "sysconfdir=" + (assoc-ref %outputs "out") + "/etc"))) + ((#:phases phases) + `(modify-phases ,phases + (add-before 'configure 'set-etc-rpc-installation-directory + (lambda* (#:key outputs #:allow-other-keys) + ;; Install the rpc data base file under `$out/etc/rpc'. + (let ((out (assoc-ref outputs "out"))) + (substitute* "sunrpc/Makefile" + (("^\\$\\(inst_sysconfdir\\)/rpc(.*)$" _ suffix) + (string-append out "/etc/rpc" suffix "\n")) + (("^install-others =.*$") + (string-append "install-others = " out "/etc/rpc\n")))))))))))) (define-public glibc-2.31 (package From 70f88d53b6b425d45a178ca6506df24ff720f8c5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 31 May 2022 20:08:34 +0200 Subject: [PATCH 1368/1394] gnu: Add glibc-locales-2.30. * gnu/packages/base.scm (glibc-locales-2.30): New variable. --- gnu/packages/base.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index bef45199e70..8bab17723b0 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -1229,6 +1229,9 @@ test environments.") (make-glibc-utf8-locales glibc))) ;; Packages provided to ease use of binaries linked against the previous libc. +(define-public glibc-locales-2.30 + (package (inherit (make-glibc-locales glibc-2.30)) + (name "glibc-locales-2.30"))) (define-public glibc-locales-2.29 (package (inherit (make-glibc-locales glibc-2.29)) (name "glibc-locales-2.29"))) From 16ff4bc024f69dd45a95baa8048b662de9983e08 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 31 May 2022 20:08:42 +0200 Subject: [PATCH 1369/1394] gnu: Add glibc-locales-2.31. * gnu/packages/base.scm (glibc-locales-2.31): New variable. --- gnu/packages/base.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 8bab17723b0..e566ecfb764 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -1229,6 +1229,9 @@ test environments.") (make-glibc-utf8-locales glibc))) ;; Packages provided to ease use of binaries linked against the previous libc. +(define-public glibc-locales-2.31 + (package (inherit (make-glibc-locales glibc-2.31)) + (name "glibc-locales-2.31"))) (define-public glibc-locales-2.30 (package (inherit (make-glibc-locales glibc-2.30)) (name "glibc-locales-2.30"))) From 6d8a3aa9c9594c2601306cb495ddc6cba9a65948 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 31 May 2022 20:08:51 +0200 Subject: [PATCH 1370/1394] gnu: Add glibc-locales-2.32. * gnu/packages/base.scm (glibc-locales-2.32): New variable. --- gnu/packages/base.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index e566ecfb764..33b9a672fc0 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -1229,6 +1229,9 @@ test environments.") (make-glibc-utf8-locales glibc))) ;; Packages provided to ease use of binaries linked against the previous libc. +(define-public glibc-locales-2.32 + (package (inherit (make-glibc-locales glibc-2.32)) + (name "glibc-locales-2.32"))) (define-public glibc-locales-2.31 (package (inherit (make-glibc-locales glibc-2.31)) (name "glibc-locales-2.31"))) From c4e03f82047a6a2a07cb34c94d2280183a901e8e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 31 May 2022 23:43:37 +0200 Subject: [PATCH 1371/1394] gnu: Add r-gsalib. * gnu/packages/cran.scm (r-gsalib): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 26e3e0e87af..0299e0041e0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31347,6 +31347,25 @@ indicator, a quantitative variable or a survival time.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-gsalib + (package + (name "r-gsalib") + (version "2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gsalib" version)) + (sha256 + (base32 + "1k3zjdydzb0dfh1ihih08d4cw6rdamgb97cdqna9mf0qdjc3pcp1")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/gsalib") + (synopsis "Utility functions for GATK") + (description "This package contains utility functions used by the Genome +Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit +for variant discovery in high-throughput sequencing data.") + (license license:expat))) + (define-public r-randomforestsrc (package (name "r-randomforestsrc") From cae7ed2aed89b8c1d553079f98a4d8f25f5d3d5e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 31 May 2022 00:29:51 -0400 Subject: [PATCH 1372/1394] gnu: linux-libre: Update to 5.17.12. * gnu/packages/linux.scm (linux-libre-5.17-version): Update to 5.17.12. (linux-libre-5.17-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 2af32fc88f4..8d450614ef5 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -348,7 +348,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-5.17-version "5.17.11") +(define-public linux-libre-5.17-version "5.17.12") (define-public linux-libre-5.17-gnu-revision "gnu") (define deblob-scripts-5.17 (linux-libre-deblob-scripts @@ -358,7 +358,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1zd4ds6ha4a2acqnalp234r2m9rz9p30qmy1aqri78i06aw7flwn"))) (define-public linux-libre-5.17-pristine-source (let ((version linux-libre-5.17-version) - (hash (base32 "0c8vz02lbfm0zkgsr1gvdp8bzxz255dk863pnakw6d77z9bfc22p"))) + (hash (base32 "0yr8xfds5l1s3lk8qk67mgy0l4yh2jfvjc7xwrfws3ci020ss9a2"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.17))) From da30df085ecd393775596ea77e07546d2cdc67e6 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 31 May 2022 00:30:08 -0400 Subject: [PATCH 1373/1394] gnu: linux-libre 5.15: Update to 5.15.44. * gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.44. (linux-libre-5.15-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 8d450614ef5..a85e7bc2d60 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -366,7 +366,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.15-version "5.15.43") +(define-public linux-libre-5.15-version "5.15.44") (define-public linux-libre-5.15-gnu-revision "gnu") (define deblob-scripts-5.15 (linux-libre-deblob-scripts @@ -376,7 +376,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0gs92qbpvirwd02rpwwnja7771z2azbiy9ppy9ynpr14lxmzxnnh"))) (define-public linux-libre-5.15-pristine-source (let ((version linux-libre-5.15-version) - (hash (base32 "04hwaykdjdqhcdk1pr6p4kkyw6h3z6ig4qpsra2klxsqklx92jq6"))) + (hash (base32 "1p1jz0lxmzyj0c51afqghylg9kblk8zmlw92zq6bsn37wlwbrylv"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.15))) From 95792a26c3a0b8f3cd54bc5f490ec28085ad01f1 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 31 May 2022 00:30:25 -0400 Subject: [PATCH 1374/1394] gnu: linux-libre 5.10: Update to 5.10.119. * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.119. (linux-libre-5.10-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a85e7bc2d60..e7724b0e4e1 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -381,7 +381,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.15))) -(define-public linux-libre-5.10-version "5.10.118") +(define-public linux-libre-5.10-version "5.10.119") (define-public linux-libre-5.10-gnu-revision "gnu1") (define deblob-scripts-5.10 (linux-libre-deblob-scripts @@ -391,7 +391,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1xyhz0dyrkg2avz382ly3dzpa5v89x49gfzx80c1drpwsk7jg6gp"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "0jqbzvgbvaldwwarvg27mcv2kfcgmfw72zpy4h4sp5d1hzqj1q65"))) + (hash (base32 "04952zaz2kfwf7agy4laz50f9sl3mrnpqlbwbj84q1xpl9akwd9y"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) From b279e778ab510e7a789205fe11107daac85147f4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 1 Jun 2022 00:14:30 +0200 Subject: [PATCH 1375/1394] gnu: Add sylamer. * gnu/packages/bioinformatics.scm (sylamer): New variable. --- gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 679b5af4a2e..7059be7d242 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13674,6 +13674,47 @@ some of the details of opening and jumping in tabix-indexed files.") ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. (license (list license:gpl2 license:expat))))) +(define-public sylamer + (package + (name "sylamer") + (version "18-131") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/micans/sylamer/") + (commit "aa75c3584797c0c15f860addb645f7bc1dd7627d"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ddiwlrdghhb4574rvfw0brjp9gs5l6nfsy82h0m4mvz1dr3gkj5")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; no test target + #:make-flags + #~(list (string-append "GSLPREFIX=" #$(this-package-input "gsl"))) + #:phases + '(modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile" + (("cp sylamer \\$\\(HOME\\)/local/bin") + (string-append "install -D -t " (assoc-ref outputs "out") + "/bin sylamer"))) + (install-file "Makefile" "src") + (chdir "src")))))) + (inputs (list gsl zlib)) + (home-page "https://www.ebi.ac.uk/research/enright/software/sylamer") + (synopsis "Asses microRNA binding and siRNA off-target effects") + (description "Sylamer is a system for finding significantly over or +under-represented words in sequences according to a sorted gene list. +Typically it is used to find significant enrichment or depletion of microRNA +or siRNA seed sequences from microarray expression data. Sylamer is extremely +fast and can be applied to genome-wide datasets with ease. Results are +plotted in terms of a significance landscape plot. These plots show +significance profiles for each word studied across the sorted genelist.") + (license license:gpl3+))) + (define-public multichoose (package (name "multichoose") From bc95e0c8d6aa0e993862a22bfd128e2327630711 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:00 +0200 Subject: [PATCH 1376/1394] gnu: foomatic-filters: Use project home page. * gnu/packages/cups.scm (foomatic-filters)[home-page]: Point upstream. --- gnu/packages/cups.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm index 617a89d9545..005ec15f116 100644 --- a/gnu/packages/cups.scm +++ b/gnu/packages/cups.scm @@ -716,8 +716,7 @@ should only be used as part of the Guix cups-pk-helper service.") (search-patches "foomatic-filters-CVE-2015-8327.patch" "foomatic-filters-CVE-2015-8560.patch")))) (build-system gnu-build-system) - (home-page - "https://wiki.linuxfoundation.org/openprinting/database/foomatic") + (home-page "https://openprinting.github.io/projects/02-foomatic/") (native-inputs (list perl pkg-config)) (inputs From 3f4850f0ae55164751094f0733a81a90ed0e8fe6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:01 +0200 Subject: [PATCH 1377/1394] gnu: quazip: Update to 1.3. * gnu/packages/compression.scm (quazip): Update to 1.3. --- gnu/packages/compression.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index a70c6c42161..382fe348a07 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -2321,7 +2321,7 @@ reading from and writing to ZIP archives.") (package (inherit quazip-0) (name "quazip") - (version "1.2") + (version "1.3") (source (origin (method git-fetch) @@ -2330,7 +2330,7 @@ reading from and writing to ZIP archives.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1dwld7jxhjz9l33lrqwvklazdy7ygi6n1m4ry1n1sk5dnschrhby")))))) + (base32 "0njgbdm3dm5p7xic5mhppbqsl36zn83zz0xfsfh624hlk0ff7n0a")))))) (define-public zchunk (package From c6c32ab96666b0b23e080213d3c3371f499f8f1f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:00 +0200 Subject: [PATCH 1378/1394] gnu: caf: Update to 0.18.6. * gnu/packages/cpp.scm (caf): Update to 0.18.6. --- gnu/packages/cpp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index fafa55c3cd2..87bd43356ab 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -1391,7 +1391,7 @@ feature set with a simple and intuitive interface.") (define-public caf (package (name "caf") - (version "0.18.5") + (version "0.18.6") (source (origin (method git-fetch) (uri (git-reference @@ -1400,7 +1400,7 @@ feature set with a simple and intuitive interface.") (file-name (git-file-name name version)) (sha256 (base32 - "04b4kjisb5wzq6pilh8xzbxn7qcjgppl8k65hfv0zi0ja8fyp1xk")))) + "055y82044djphpwbazaxsvmb66c2xfdi8vyny8pzdxkdgxfh0vq1")))) (build-system cmake-build-system) (arguments '(#:configure-flags From 56107782660039fd5a7ea99f6a76e99e721ade4c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:00 +0200 Subject: [PATCH 1379/1394] gnu: beancount: Update to 2.3.5. * gnu/packages/finance.scm (beancount): Update to 2.3.5. --- gnu/packages/finance.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 0f9a50045b9..f2904d21068 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -1677,14 +1677,13 @@ that allows you to run services and through them access the Bitcoin Cash network (define-public beancount (package (name "beancount") - (version "2.3.4") + (version "2.3.5") (source (origin (method url-fetch) (uri (pypi-uri "beancount" version)) (sha256 - (base32 - "1h465zc7gb0bc5pagm9fsp083sqxrn2mjfbk9l7h162xm7k8rw1b")) + (base32 "0sn3x6c5vwvdfak1qm0y4vv284izrc4dly31mqyd9jz9l8jmdqql")) (patches (search-patches "beancount-disable-googleapis-fonts.patch")))) (build-system python-build-system) (arguments From eded213cbc5af2ca153b344992e34cdedc568e40 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:12 +0200 Subject: [PATCH 1380/1394] gnu: fprintd: Fix build. * gnu/packages/freedesktop.scm (fprintd)[native-inputs]: Add python. --- gnu/packages/freedesktop.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index b9f3c91558f..7627238a192 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -12,7 +12,7 @@ ;;; Copyright © 2017, 2018, 2019, 2020 Marius Bakke ;;; Copyright © 2017, 2018, 2019 Rutger Helling ;;; Copyright © 2017, 2020, 2021 Brendan Tildesley -;;; Copyright © 2018, 2020, 2021 Tobias Geerinckx-Rice +;;; Copyright © 2018, 2020–2022 Tobias Geerinckx-Rice ;;; Copyright © 2018 Pierre Neidhardt ;;; Copyright © 2018 Stefan Stefanović ;;; Copyright © 2019 Reza Alizadeh Majd @@ -1763,8 +1763,9 @@ software.") `(("gettext" ,gettext-minimal) ("glib:bin" ,glib "bin") ; for glib-genmarshal ("perl" ,perl) ; for pod2man - ("pkg-config" ,pkg-config))) + ("pkg-config" ,pkg-config) ;; For tests. + ("python" ,python))) ; needed unconditionally ;;("pam_wrapper" ,pam_wrapper) ;;("python-pycairo" ,python-pycairo) ;;("python-dbus" ,python-dbus) From 78879b10c237157f4df7fef3fb6756f94c63fa99 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:04 +0200 Subject: [PATCH 1381/1394] gnu: fprintd: Remove input labels. * gnu/packages/freedesktop.scm (fprintd)[native-inputs]: Remove input labels. --- gnu/packages/freedesktop.scm | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 7627238a192..fc1ec0265a5 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -1760,18 +1760,18 @@ software.") ((".*pam_wrapper.*") ""))))) #:tests? #f)) ; XXX depend on unpackaged packages (native-inputs - `(("gettext" ,gettext-minimal) - ("glib:bin" ,glib "bin") ; for glib-genmarshal - ("perl" ,perl) ; for pod2man - ("pkg-config" ,pkg-config) - ;; For tests. - ("python" ,python))) ; needed unconditionally - ;;("pam_wrapper" ,pam_wrapper) - ;;("python-pycairo" ,python-pycairo) - ;;("python-dbus" ,python-dbus) - ;;("python-dbusmock" ,python-dbusmock) - ;;("python-pygobject" ,python-pygobject) - ;;("python-pypamtest" ,python-pypamtest) + (list gettext-minimal + `(,glib "bin") ; for glib-genmarshal + perl ; for pod2man + pkg-config + ;; For tests. + python)) ; needed unconditionally + ;; pam_wrapper + ;; python-pycairo + ;; python-dbus + ;; python-dbusmock + ;; python-pygobject + ;; python-pypamtest (inputs (list dbus-glib elogind From 72b2412add0499cc005780a3c41b687bff826574 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:01 +0200 Subject: [PATCH 1382/1394] gnu: fprintd: Update to 1.94.2. * gnu/packages/freedesktop.scm (fprintd): Update to 1.94.2. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index fc1ec0265a5..8d4d3535fe8 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -1712,7 +1712,7 @@ software.") (define-public fprintd (package (name "fprintd") - (version "1.94.1") + (version "1.94.2") (source (origin (method git-fetch) @@ -1721,7 +1721,7 @@ software.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "015j8ikyv48qz8vn6kfvkwwg5ydzppl1lzf7vkali9ymywywfxsw")))) + (base32 "015k3kc4fmas0vc2b21qzq7kvdc9x6lcqvjhbvy6m84pkhhmry3q")))) (build-system meson-build-system) (arguments (list #:configure-flags From 4ac15e44e54c09693adfcb95fb16938aed1b3160 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:01 +0200 Subject: [PATCH 1383/1394] gnu: libfprint: Update to 1.94.4. * gnu/packages/freedesktop.scm (libfprint): Update to 1.94.4. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 8d4d3535fe8..fc2c45c1f13 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -1670,7 +1670,7 @@ wish to perform colour calibration.") (define-public libfprint (package (name "libfprint") - (version "1.94.2") + (version "1.94.4") (source (origin (method git-fetch) @@ -1679,7 +1679,7 @@ wish to perform colour calibration.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0y3wz5hlxpnvqj67bihvzfi4dwx2m2nx9byppf4jjd80x0j2630m")))) + (base32 "1wfd2svsq26wizhsaifnr74havswbc1rlfm79b36yrhw9n7c3jqb")))) (build-system meson-build-system) (arguments (list #:configure-flags From 4cb6994790d1b499bc07f183ac9d7b4fbfc3c9bc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:10 +0200 Subject: [PATCH 1384/1394] gnu: services: Update setuid service description. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services.scm (setuid-program-service-type)[description]: Remove ‘root’, add ‘setgid’. --- gnu/services.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/services.scm b/gnu/services.scm index 6f0f4d5bdc2..cc2540ee50d 100644 --- a/gnu/services.scm +++ b/gnu/services.scm @@ -846,7 +846,7 @@ FILES must be a list of name/file-like object pairs." (append config extensions))) (description "Populate @file{/run/setuid-programs} with the specified -executables, making them setuid-root."))) +executables, making them setuid and/or setgid."))) (define (packages->profile-entry packages) "Return a system entry for the profile containing PACKAGES." From dc6d92ac93cedd65f6c99daa530b69f43f6039ec Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:00 +0200 Subject: [PATCH 1385/1394] bash completion: Fix & unify option parsing. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit We now correctly recognise ‘guix -Abcdef’ as equivalent to ‘guix -f’. * etc/completion/bash/guix (_guix_is_short_option, guix_is_long_option): New functions. (_guix_is_dash_f, _guix_is_dash_l, _guix_is_dash_L, _guix_is_dash_m) (_guix_is_dash_C, _guix_is_dash_p): Use them. --- etc/completion/bash/guix | 61 ++++++++++++++++++++-------------------- 1 file changed, 31 insertions(+), 30 deletions(-) diff --git a/etc/completion/bash/guix b/etc/completion/bash/guix index 6b1b70aac1d..7b1f639371f 100644 --- a/etc/completion/bash/guix +++ b/etc/completion/bash/guix @@ -117,58 +117,59 @@ _guix_is_removing () $result } +_guix_is_short_option () +{ + case "${COMP_WORDS[$COMP_CWORD - 1]}" in + --*) false;; + -*$1) true ;; + *) false ;; + esac +} + +_guix_is_long_option () +{ + # Don't handle (non-GNU?) ‘--long-option VALUE’, as Guix doesn't either. + case "${COMP_WORDS[$COMP_CWORD]}" in + --$1=*) true ;; + *) false ;; + esac +} + _guix_is_dash_f () { - [ "${COMP_WORDS[$COMP_CWORD - 1]}" = "-f" ] \ - || { case "${COMP_WORDS[$COMP_CWORD]}" in - --file=*|--install-from-file=*) true;; - *) false;; - esac } + _guix_is_short_option f || + _guix_is_long_option file || + _guix_is_long_option install-from-file } _guix_is_dash_l () { - [ "${COMP_WORDS[$COMP_CWORD - 1]}" = "-l" ] \ - || { case "${COMP_WORDS[$COMP_CWORD]}" in - --load=*) true;; - *) false;; - esac } + _guix_is_short_option l || + _guix_is_long_option load } _guix_is_dash_L () { - [ "${COMP_WORDS[$COMP_CWORD - 1]}" = "-L" ] \ - || { case "${COMP_WORDS[$COMP_CWORD]}" in - --load-path=*) true;; - *) false;; - esac } + _guix_is_short_option L || + _guix_is_long_option load-path } _guix_is_dash_m () { - [ "${COMP_WORDS[$COMP_CWORD - 1]}" = "-m" ] \ - || { case "${COMP_WORDS[$COMP_CWORD]}" in - --manifest=*) true;; - *) false;; - esac } + _guix_is_short_option m || + _guix_is_long_option manifest } _guix_is_dash_C () { - [ "${COMP_WORDS[$COMP_CWORD - 1]}" = "-C" ] \ - || { case "${COMP_WORDS[$COMP_CWORD]}" in - --channels=*) true;; - *) false;; - esac } + _guix_is_short_option C || + _guix_is_long_option channels } _guix_is_dash_p () { - [ "${COMP_WORDS[$COMP_CWORD - 1]}" = "-p" ] \ - || { case "${COMP_WORDS[$COMP_CWORD]}" in - --profile=*) true;; - *) false;; - esac } + _guix_is_short_option p || + _guix_is_long_option profile } _guix_complete_file () From a3ea97976b15b77a499d6f8a6c1933cc4794393e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 22 May 2022 02:00:01 +0200 Subject: [PATCH 1386/1394] gnu: corefreq: Update to 1.90.1. * gnu/packages/linux.scm (corefreq): Update to 1.90.1. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index e7724b0e4e1..4fc0ac16af4 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1226,7 +1226,7 @@ and should be used with caution, especially on untested models.") (define-public corefreq (package (name "corefreq") - (version "1.87.4") + (version "1.90.1") (source (origin (method git-fetch) @@ -1235,7 +1235,7 @@ and should be used with caution, especially on untested models.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "01g1smhfzb02gmfjm8c7rchc79dan9jc9pv9c0f8f7fly2hy5zvs")))) + (base32 "1fpmrqjwxvjbs23r73agjs322fbi4v1013cncbfyk6lcjghxab76")))) (build-system linux-module-build-system) (outputs (list "out" "linux-module")) (arguments From 22f56dda8e469cabbe5712f795bbc1a0a1143d2a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:00 +0200 Subject: [PATCH 1387/1394] import: minetest: Fix typo. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * guix/import/minetest.scm (important-dependencies): Fix ‘choosen’ typo. --- guix/import/minetest.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/guix/import/minetest.scm b/guix/import/minetest.scm index 3b2cdcdcacd..43cfb533e2f 100644 --- a/guix/import/minetest.scm +++ b/guix/import/minetest.scm @@ -427,10 +427,10 @@ DEPENDENCIES as a list of AUTHOR/NAME strings." (match sort ("score" (warning - (G_ "The implementation with the highest score will be choosen!~%"))) + (G_ "The implementation with the highest score will be chosen!~%"))) ("downloads" (warning - (G_ "The implementation that has been downloaded the most will be choosen!~%")))) + (G_ "The implementation that has been downloaded the most will be chosen!~%")))) (package-full-name too)) (() (warning From a01cc9f97fdd2d1540ea349857f50b3f0f6033c5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:01 +0200 Subject: [PATCH 1388/1394] gnu: freeipmi: Update to 1.6.9. * gnu/packages/freeipmi.scm (freeipmi): Update to 1.6.9. --- gnu/packages/freeipmi.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/freeipmi.scm b/gnu/packages/freeipmi.scm index 762cfcee783..87b7ac139fa 100644 --- a/gnu/packages/freeipmi.scm +++ b/gnu/packages/freeipmi.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Ludovic Courtès ;;; Copyright © 2015, 2016, 2017, 2020, 2021, 2022 Efraim Flashner -;;; Copyright © 2019–2021 Tobias Geerinckx-Rice +;;; Copyright © 2019–2022 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -28,14 +28,14 @@ (define-public freeipmi (package (name "freeipmi") - (version "1.6.8") + (version "1.6.9") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/freeipmi/freeipmi-" version ".tar.gz")) (sha256 (base32 - "0w8af1i57szmxl9vfifwwyal7xh8aixz2l9487wvy6yckqk6m92a")))) + "01l2kkf2f0c7p8pq8qsil53fv0yaaciwq7n3kjlvbwfhycsiqppj")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--disable-static" From 6c345a24657762e460495a9a1d2540a1b514be9b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:01 +0200 Subject: [PATCH 1389/1394] gnu: angband: Update to 4.2.4. * gnu/packages/games.scm (angband): Update to 4.2.4. [arguments]: Don't explicitly return #t from phases. --- gnu/packages/games.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 05bcdc9b989..58ccf080a7d 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -3080,7 +3080,7 @@ that beneath its ruins lay buried an ancient evil.") (define-public angband (package (name "angband") - (version "4.2.3") + (version "4.2.4") (source (origin (method git-fetch) @@ -3089,7 +3089,7 @@ that beneath its ruins lay buried an ancient evil.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1psrdbf90mb6dhq0b9z18pz1csnshz1kvwg82dvwa99apqdw0la8")) + (base32 "1x0qqsv7xa3figcl4v35sin64ffgz32652vk541d8qaq4qcc378n")) (modules '((guix build utils))) (snippet ;; So, some of the sounds/graphics/tilesets are under different @@ -3105,14 +3105,12 @@ that beneath its ruins lay buried an ancient evil.") (substitute* "lib/Makefile" ;; And don't try to invoke makefiles in the directories we removed. (("gamedata customize help screens fonts tiles sounds icons user") - "gamedata customize help screens user")) - #t)))) + "gamedata customize help screens user")))))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no check target #:configure-flags (list (string-append "--bindir=" %output "/bin")))) - (native-inputs - (list autoconf automake)) + (native-inputs (list autoconf automake)) (inputs (list ncurses)) (home-page "https://rephial.org/") (synopsis "Dungeon exploration roguelike") From 1600d5cd3a829f9472a64bbacad58887265f9e34 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 29 May 2022 02:00:01 +0200 Subject: [PATCH 1390/1394] gnu: gnome-commander: Update to 1.14.2. * gnu/packages/gnome.scm (gnome-commander): Update to 1.14.2. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 15d0d5f6a04..fbd31450f77 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1849,7 +1849,7 @@ either on a local, or remote machine via a number of methods.") (define-public gnome-commander (package (name "gnome-commander") - (version "1.14.0") + (version "1.14.2") (source (origin (method url-fetch) @@ -1857,7 +1857,7 @@ either on a local, or remote machine via a number of methods.") (version-major+minor version) "/" "gnome-commander-" version ".tar.xz")) (sha256 - (base32 "1zdz82j7vpxiqa188zmsxliqk60g331ycaxfbhx5bzyqfjgrh7gd")))) + (base32 "1s8fdwp0z1smzkwrsvssp9g3yak6z4cdk0qx0c4qmwca9z9fyy0k")))) (build-system glib-or-gtk-build-system) (native-inputs (list desktop-file-utils From 0c26c8da9d9bb86bfbe8fe9a52ba7b2ba9c6e3ec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 1 Jun 2022 10:45:23 +0200 Subject: [PATCH 1391/1394] gnu: pigx-rnaseq: Fix build. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7059be7d242..6ce011af0f6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10455,6 +10455,13 @@ once. This package provides tools to perform Drop-seq analyses.") `(#:parallel-tests? #f ; not supported #:phases (modify-phases %standard-phases + ;; knitr 0.39 changes the default behavior of how graphics are + ;; included. + (add-after 'unpack 'patch-knitr + (lambda _ + (substitute* "scripts/runDeseqReport.R" + (("outFile <- paste0" m) + (string-append "options(knitr.graphics.rel_path = FALSE)\n" m))))) ;; "test.sh" runs the whole pipeline, which takes a long time and ;; might fail due to OOM. The MultiQC is also resource intensive. (add-after 'unpack 'disable-resource-intensive-test From 0aae2f7f013e3f12eb573bdda4d0b64bb536d25f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 1 Jun 2022 10:45:44 +0200 Subject: [PATCH 1392/1394] gnu: pigx-rnaseq: Update to 0.0.21. * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6ce011af0f6..9811a0b9e2e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10441,7 +10441,7 @@ once. This package provides tools to perform Drop-seq analyses.") (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.20") + (version "0.0.21") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" @@ -10449,7 +10449,7 @@ once. This package provides tools to perform Drop-seq analyses.") "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "0bf65qqvlkc77vl7cmmzacq70f0qav4p6nf8pp3x1vdd0nvhr24f")))) + "0367jn73vja94ch9fwgaiwy62rbxfzc85xz6blzbkjyzhph1r173")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported From cd95d7ddd180f244059e1b3585b2f8ba4c9d5024 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 1 Jun 2022 11:07:27 +0200 Subject: [PATCH 1393/1394] gnu: pigx-rnaseq: Update to 0.1.0. * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0. [arguments]: Remove phase 'patch-knitr. --- gnu/packages/bioinformatics.scm | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9811a0b9e2e..1ffac1a0ca4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10441,7 +10441,7 @@ once. This package provides tools to perform Drop-seq analyses.") (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.21") + (version "0.1.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" @@ -10449,19 +10449,12 @@ once. This package provides tools to perform Drop-seq analyses.") "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "0367jn73vja94ch9fwgaiwy62rbxfzc85xz6blzbkjyzhph1r173")))) + "0acdjimfb9ywba8zsv7lavv436pmcmp8ra683h11wr4s3681pqk8")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported #:phases (modify-phases %standard-phases - ;; knitr 0.39 changes the default behavior of how graphics are - ;; included. - (add-after 'unpack 'patch-knitr - (lambda _ - (substitute* "scripts/runDeseqReport.R" - (("outFile <- paste0" m) - (string-append "options(knitr.graphics.rel_path = FALSE)\n" m))))) ;; "test.sh" runs the whole pipeline, which takes a long time and ;; might fail due to OOM. The MultiQC is also resource intensive. (add-after 'unpack 'disable-resource-intensive-test From 75af73e1b7ac58770122d8831faa3a8158638bb0 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 1 Jun 2022 11:46:17 +0300 Subject: [PATCH 1394/1394] gnu: vim: Update to 8.2.5048. * gnu/packages/vim.scm (vim): Update to 8.2.5048. [arguments]: Patch another instance of '/bin/sh'. --- gnu/packages/vim.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index caf9ea85b3a..f82f8498e1e 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -77,7 +77,7 @@ (define-public vim (package (name "vim") - (version "8.2.4912") + (version "8.2.5048") (source (origin (method git-fetch) (uri (git-reference @@ -86,7 +86,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0wcvwmybkw76ha58idrq6pf4gxk14wbw1f8cwqs0slvkfdc8jyya")))) + "0bwps6r7g2c3nkn97s5kccqh6pb3a0bc11cmyacydsgxiwzq8xz4")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -95,7 +95,8 @@ (modify-phases %standard-phases (add-after 'configure 'patch-absolute-paths (lambda _ - (substitute* '("src/testdir/Makefile" + (substitute* '("runtime/autoload/context.vim" + "src/testdir/Makefile" "src/testdir/test_filetype.vim" "src/testdir/test_normal.vim" "src/testdir/test_popupwin.vim"