gnu: rust-cargo-c: Update to 0.10.22+cargo-0.96.0.

* gnu/packages/rust-apps.scm (0.10.22+cargo-0.96.0): Update to 0.10.22+cargo-0.96.0. * gnu/packages/rust-crates.scm (lookup-cargo-inputs)[rust-cargo-c]: Update entry. Change-Id: I8460cb49440e0cd9d7e6e1666ab123f3e877b79d
gnu: rust: Update to 1.95.
2026-07-08 13:34:09 +02:00 · 2026-05-25 14:05:08 +03:00 · 2026-05-25 13:50:50 +03:00 · 2026-05-25 13:50:50 +03:00 · 2026-05-25 13:50:50 +03:00 · 2026-05-25 13:50:50 +03:00
129 changed files with 11371 additions and 13947 deletions
@@ -120,7 +120,6 @@ running 'guix-daemon $extra_options'" >&2
    "@abs_top_builddir@/pre-inst-env"				\
 	"@abs_top_builddir@/guix-daemon"			\
        $extra_options						\
-        --allow-aslr                                            \
 	--substitute-urls="$GUIX_BINARY_SUBSTITUTE_URL" &

    daemon_pid=$!
@@ -618,33 +618,6 @@ enhance @code{scheme-mode} and Geiser.  @xref{Introduction,,,
 emacs-guix, Emacs-Guix Reference Manual}, to make sure you don't miss
 out!

-@unnumberedsubsubsec Submitting Pull Requests Following the AGit Workflow
-
-@cindex AGit workflow, for pull requests (Emacs).
-@url{https://codeberg.org/halvin/agitjo, Agitjo} is a helper to ease
-AGit workflow based patch submission (@pxref{Submitting Patches}).
-Install it with:
-
-@example
-guix install emacs-agitjo
-@end example
-
-Assuming your local checkout is on the branch containing the changes you
-would like to submit for inclusion in the @code{master} branch, use
-@command{M-x agitjo-push} then:
-
-@itemize
-@item
-Set options like the title @option{-t} and the session identifier
-@option{-s}.
-@item
-Invoke one of the push commands to execute a @command{git push} operation.
-@end itemize
-
-When creating a new pull request, a dedicated buffer will open for
-drafting a description. The force-push option @option{-f} is enabled to
-push changes to the existing pull request.
-
@unnumberedsubsubsec Taming Boilerplate with Templates

@cindex code snippets
@@ -152,7 +152,6 @@ Copyright @copyright{} 2026 David Elsing@*
 Copyright @copyright{} 2026 Nguyễn Gia Phong@*
 Copyright @copyright{} 2026 Yarl Baudig@*
 Copyright @copyright{} 2026 Joan Vilardaga Castro@*
-Copyright @copyright{} 2026 Nemin@*

 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -306,7 +305,6 @@ Package Management
 Substitutes

 * Official Substitute Servers::  One particular source of substitutes.
-* Volunteer Run Mirrors::        Additional, regional sources of substitutes.
 * Substitute Server Authorization::  How to enable or disable substitutes.
 * Getting Substitutes from Other Servers::  Substitute diversity.
 * Substitute Authentication::   How Guix verifies substitutes.
@@ -1781,21 +1779,6 @@ user namespaces is missing (@pxref{Build Environment Setup}).  Use at
 your own risk!
@end quotation

-@cindex ASLR (address space layout randomization), for builds
-@cindex address space layout randomization (ASLR), for builds
-@cindex Docker, running @command{guix-daemon}
-@cindex @command{guix-daemon}, running under Docker
-@item --allow-aslr
-Allow builds to start even if @acronym{ASLR, Address Space Layout
-Randomization} cannot be disabled on Linux systems.  This is normally
-done so as to increase reproducibility, but some environments, such as
-those affected by Docker's default seccomp policy, don't permit
-disabling ASLR.  Passing this option will allow builds to start with
-reduced reproducibility regardless.
-
-Note that passing this option doesn't ensure that ASLR is enabled, it
-only allows builds to start even when disabling it is blocked.
-
@item --isolate-host-loopback
 Prevent fixed-output chroot builds from accessing the host loopback.
 When this is used, fixed-output builds will have their own loopback
@@ -3953,7 +3936,6 @@ also result from derivation builds, can be available as substitutes.

@menu
 * Official Substitute Servers::  One particular source of substitutes.
-* Volunteer Run Mirrors::  Additional, regional sources of substitutes.
 * Substitute Server Authorization::  How to enable or disable substitutes.
 * Getting Substitutes from Other Servers::  Substitute diversity.
 * Substitute Authentication::   How Guix verifies substitutes.
@@ -3984,54 +3966,13 @@ could use the information gathered to determine, for instance, whether
 your system has unpatched security vulnerabilities.

 Substitutes from the official build farms are enabled by default when
-using Guix System (@pxref{GNU Distribution}).  However, they are
-disabled by default when using Guix on a foreign distribution, unless
-you have explicitly enabled them via one of the recommended installation
-steps (@pxref{Installation}).  Please @pxref{Substitute Server
-Authorization} on how to enable or disable substitutes for the official
-build farm; the same procedure can also be used to enable substitutes
-for any other substitute server.
-
-@node Volunteer Run Mirrors
-@subsection Volunteer Run Mirrors
-
-@cindex substitutes
-@cindex mirrors
-Beyond the two official substitute servers, there are additionally
-volunteer run mirrors.  These mirrors do not build their own
-substitutes, but rather copy them from the official build farm and
-distribute them to users.  Enabling a mirror may be beneficial in case
-the official servers are temporarily unavailable or provide inadequate
-bandwidth at the user's location.
-
-@quotation Note
-Mirrored substitutes are signed by the original builder, not the mirror.
-This means that mirror operators @strong{cannot} add or modify binaries,
-as long as you trust only the official substitute servers,
-@pxref{Substitute Server Authorization}.
-@end quotation
-
-List of volunteer run mirrors, grouped by location (with the build farm
-they mirror in parentheses):
-
-@table @asis
-@item Germany
-@itemize
-@item @code{https://hydra-guix-129.guix.gnu.org} (bordeaux.guix.gnu.org)
-@end itemize
-@item People's Republic of China
-@itemize
-@item @code{https://mirrors.sjtug.sjtu.edu.cn/guix} (ci.guix.gnu.org)
-@item @code{https://mirrors.sjtug.sjtu.edu.cn/guix-bordeaux} (bordeaux.guix.gnu.org)
-@end itemize
-@item Russia
-@itemize
-@item @code{https://mirror.yandex.ru/mirrors/guix/} (bordeaux.guix.gnu.org)
-@end itemize
-@end table
-
-To enable receiving substitutions from these mirrors, please @pxref{Getting
-Substitutes from Other Servers}.
+using Guix System (@pxref{GNU Distribution}).  However,
+they are disabled by default when using Guix on a foreign distribution,
+unless you have explicitly enabled them via one of the recommended
+installation steps (@pxref{Installation}).  The following paragraphs
+describe how to enable or disable substitutes for the official build
+farm; the same procedure can also be used to enable substitutes for any
+other substitute server.

@node Substitute Server Authorization
@subsection Substitute Server Authorization
@@ -36293,10 +36234,6 @@ Launch the app as this group (it must be an existing group).
 A list of sockets (as path strings) which gunicorn will be listening
 on.  This list must contain at least one socket.

-@item @code{control-socket} (default: #f) (type: string)
-If set, creates a gunicorn control-socket at the given path.  Note that,
-the control socket should refer to a path listed in @code{mappings}.
-
@item @code{socket-user} (default: @code{user}) (type: string)
 Owner of the directory containing the socket (must be an existing user).

@@ -38132,21 +38069,6 @@ This is the type of the dnsmasq service, whose value should be a
           (servers '("192.168.1.1"))))
@end lisp

-The following example shows a slightly more complex configuration that
-defines an authoritative DNS server on a given subdomain.
-@lisp
-(service dnsmasq-service-type
-         (dnsmasq-configuration
-           (listen-addresses '("10.1.1.1"))
-           (no-resolv? #t)
-           (no-hosts? #t)
-           (authoritative-servers '("vpn.example.com")) ;self
-           (authoritative-zones '("vpn.example.com"))
-           (host-records '("some-service.vpn.example.com,10.1.1.1"))))
-@end lisp
-
-For more examples, refer to @samp{man 8 dnsmasq.}
-
@code{dnsmasq-service-type} provides two actions:

@table @code
@@ -38236,33 +38158,12 @@ ie a subnet for which an interface exists on the server.
@item @code{listen-addresses} (default: @code{'()})
 Listen on the given IP addresses.

-@item @code{ipv4?} (default: @code{#t})
-Whether to include A records in answers.
-
-@item @code{ipv6?} (default: @code{#t})
-Whether to include AAAA records in answers.
-
@item @code{resolv-file} (default: @code{"/etc/resolv.conf"})
 The file to read the IP address of the upstream nameservers from.

@item @code{no-resolv?} (default: @code{#f})
 When true, don't read @var{resolv-file}.

-@item @code{authoritative-servers} (default: @code{'()})
-A list of strings corresponding to valid @option{--auth-server} values,
-such as a domain name.  This is useful to make @command{dnsmasq}
-authoritative for a given domain name or interface.
-
-@item @code{authoritative-zones} (default: @code{'()})
-A list of strings corresponding to valid @option{--auth-zone} values,
-such as a domain name.  This is useful to make @command{dnsmasq}
-authoritative for a given domain name.  Note that this must be used in
-conjunction with the @code{authoritative-servers} option.
-
-@item @code{host-records} (default: @code{'()})
-A list of strings corresponding to valid @option{--host-record} values,
-for example @code{'("some-service.example.com,10.1.1.1")}.
-
@item @code{forward-private-reverse-lookup?} (default: @code{#t})
 When false, all reverse lookups for private IP ranges are answered with
 "no such domain" rather than being forwarded upstream.
@@ -38271,12 +38172,6 @@ When false, all reverse lookups for private IP ranges are answered with
 When true, dnsmasq queries the servers in the same order as they appear
 in @var{servers}.

-@item @code{locals} (default: @code{'()})
-Specify domain name @emph{patterns} which should be treated as local,
-that is, for which there should be no delegation to upstream servers.
-Provided pattern values should be of the form
-@code{'("/vpn.example.com/")}.
-
@item @code{servers} (default: @code{'()})
 Specify IP address of upstream servers directly.

@@ -1577,7 +1577,7 @@ the \"texlive\" importer."
 (define-member (person "Nguyễn Gia Phong"
                       "cnx@loang.net"
                       "cnx")
-  build-tools lua qa-packages sysadmin vcs)
+  build-tools python qa-packages sysadmin vcs)

 (define-member (person "Lilah Tascheter"
                       "lilah@lunabee.space"
@@ -173,16 +173,7 @@ SYSTEM."
 (define (core-packages system)
  "Return the 'core' package set suitable for SYSTEM, which might be a system
 type or a GNU triplet."
-  (cond ((target-linux? system)
-         (append %core-packages
-                 %linux-packages
-                 (cond ((target-arm32? system)
-                        (list linux-libre-arm-generic))
-                       ((target-aarch64? system)
-                        (list linux-libre-arm64-generic))
-                       ((target-riscv64? system)
-                        (list linux-libre-riscv64-generic))
-                       (else '()))))
+  (cond ((target-linux? system) (append %core-packages %linux-packages))
        ((target-hurd? system) (append %core-packages %hurd-packages))
        ((target-mingw? system) %core-packages-for-mingw)
        (else '())))
@@ -1006,7 +1006,6 @@ dist_patch_DATA =						\
  %D%/packages/patches/alure-dumb-2.patch			\
  %D%/packages/patches/amd-smi-newer-libdrm.patch		\
  %D%/packages/patches/amd-smi-python.patch			\
-  %D%/packages/patches/angband-remove-nonfree-tile-options.patch	\
  %D%/packages/patches/ibus-anthy-fix-tests.patch		\
  %D%/packages/patches/ibus-table-paths.patch			\
  %D%/packages/patches/antiword-CVE-2014-8123.patch			\
@@ -1452,7 +1451,6 @@ dist_patch_DATA =						\
  %D%/packages/patches/ghc-aeson-encodeDouble.patch		\
  %D%/packages/patches/ghc-basement-fix-32bit.patch		\
  %D%/packages/patches/ghc-bytestring-handle-ghc9.patch	\
-  %D%/packages/patches/ghc-chell-quickcheck-enable-qc-2.15.patch	\
  %D%/packages/patches/ghc-clock-realfrag.patch	\
  %D%/packages/patches/ghc-language-haskell-extract-ghc-8.10.patch	\
  %D%/packages/patches/ghc-memory-fix-32bit.patch		\
@@ -1882,7 +1880,6 @@ dist_patch_DATA =						\
  %D%/packages/patches/lua-5.4-pkgconfig.patch			\
  %D%/packages/patches/lua-5.4-liblua-so.patch			\
  %D%/packages/patches/lua-5.4-search-paths.patch		\
-  %D%/packages/patches/lua-5.5-search-paths.patch		\
  %D%/packages/patches/lua-5.x-search-path-helpers.patch	\
  %D%/packages/patches/lua-lgi-fix-pango.patch			\
  %D%/packages/patches/lua-lgi-fix-ref.patch			\
@@ -2369,8 +2366,16 @@ dist_patch_DATA =						\
  %D%/packages/patches/renpy-fix-integer-slots.patch			\
  %D%/packages/patches/reposurgeon-add-missing-docbook-files.patch	\
  %D%/packages/patches/rdkit-unbundle-external-dependencies.patch	\
+  %D%/packages/patches/r-biostrings-r4.6.0-compat.patch		\
+  %D%/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch \
  %D%/packages/patches/r-httpuv-1.6.6-unvendor-libuv.patch	\
+  %D%/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch \
+  %D%/packages/patches/r-rsamtools-r-4.6.0-compat.patch		\
+  %D%/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch \
+  %D%/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch \
  %D%/packages/patches/r-sapa-lapack.patch			\
+  %D%/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch \
+  %D%/packages/patches/r-sparsearray-r-4.6.0-compat.patch	\
  %D%/packages/patches/ripperx-missing-file.patch		\
  %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
  %D%/packages/patches/rtosc-0.3.1-fix-invalid-comparison-operator.patch	\
@@ -2455,7 +2460,6 @@ dist_patch_DATA =						\
  %D%/packages/patches/shared-mime-info-xdgmime-path.patch	\
  %D%/packages/patches/sharutils-CVE-2018-1000097.patch		\
  %D%/packages/patches/showtime-python-3.11-compat.patch        \
-  %D%/packages/patches/simpleitk-r-4.6.0.patch			\
  %D%/packages/patches/sipwitch-fix-build-with-exosip5.patch	\
  %D%/packages/patches/slim-config.patch			\
  %D%/packages/patches/slim-gcc-14.patch			\
@@ -2490,7 +2494,6 @@ dist_patch_DATA =						\
  %D%/packages/patches/swift-corelibs-libdispatch-5.7.3-modulemap.patch	\
  %D%/packages/patches/swift-llvm-5.7.3-linux.patch	\
  %D%/packages/patches/swig-support-gcc-12.patch		\
-  %D%/packages/patches/swig-support-r-4.6.0.patch		\
  %D%/packages/patches/swish-e-search.patch			\
  %D%/packages/patches/swish-e-format-security.patch		\
  %D%/packages/patches/t1lib-CVE-2010-2642.patch		\
@@ -1084,7 +1084,7 @@ console.")
 (define-public btop
  (package
    (name "btop")
-    (version "1.4.7")
+    (version "1.4.6")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -1093,7 +1093,7 @@ console.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "0d3cr5l6gpcwhxgnrizny5b5kg6fys2hy9a58bc68w4n2hc040fy"))))
+                "1nj58dbv3c0rj8fngldkyrmdmacmjnbg8ch1c07ik97kqnnzd3l7"))))
    (build-system gnu-build-system)
    (native-inputs (list lowdown))
    (arguments
@@ -137,6 +137,7 @@
  #:use-module (gnu packages music)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages onc-rpc)
  #:use-module (gnu packages oneapi)
  #:use-module (gnu packages perl)
@@ -2135,17 +2136,7 @@ envelope follower, distortion effects, tape effects and more.")
 	        (base32
                 "01hnx4hhbz3ap3bw15s42q4q1mw1mhdjwygq4550wvjfg6k4ga8w"))))
      (build-system waf-build-system)
-      (arguments
-       (list
-        #:tests? #false ;There are no tests.
-        #:phases
-        '(modify-phases %standard-phases
-           (add-after 'unpack 'python3.12-compatibility
-             (lambda _
-               (substitute* "waflib/Context.py"
-                 (("imp.new_module") "types.ModuleType")
-                 (("import os, re, imp, sys")
-                  "import os, re, types, sys")))))))
+      (arguments (list #:tests? #false)) ;There are no tests.
      (inputs (list lv2))
      (native-inputs (list pkg-config))
      (home-page "https://git.drobilla.net/cgit.cgi/omins.lv2.git/")
@@ -1430,86 +1430,33 @@ within this package are the 3000 bone marrow cells used for vignettes.")
      (license license:gpl3))))

 (define-public r-pizzarr
-  (package
-    (name "r-pizzarr")
-    (version "0.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/keller-mark/pizzarr")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1m38c57pfliycxkhb3mwgh01cl2q76r1jhd3vnk07dbfhqdbqai6"))))
-    (properties `((upstream-name . "pizzarr")))
-    (build-system cargo-build-system)
-    (arguments
-     (list
-      #:imported-modules
-      (append %cargo-build-system-modules
-              %r-build-system-modules)
-      #:modules
-      '((guix build cargo-build-system)
-        ((guix build r-build-system) #:prefix r:)
-        (guix build utils))
-      #:cargo-build-flags
-      '(list "--target-dir=./target" "--release")
-      #:phases
-      #~(append (modify-phases %standard-phases
-                  (add-after 'unpack 'patch-Makevars
-                    (lambda _
-                      ;; At this point we've already built the Rust parts.
-                      (substitute* "src/Makevars.in"
-                        (("^all:.*") "all:")
-                        (("^\\$\\(STATLIB\\):") "NOBODYCARES:")
-                        (("@PKG_LIBS_EXTRA@") "@PKG_LIBS_EXTRA@ -lzstd -lz"))))
-                  (add-after 'patch-Makevars 'chdir
-                    (lambda _ (chdir "src/rust")))
-                  (add-after 'chdir 'patch-rust-dependency
-                    (lambda _
-                      (setenv "RUSTFLAGS" "--print=native-static-libs")
-                      (substitute* "Cargo.toml"
-                        (("extendr-api = \\{ git.* \\}") "extendr-api = \"0.8.1\""))))
-                  (add-after 'package 'chdir-back
-                    (lambda _ (chdir "../..")))
-                  (delete 'install)
-                  (delete 'check))
-                (modify-phases (@ (guix build r-build-system) %standard-phases)
-                  (delete 'unpack)
-                  (replace 'patch-tests
-                    (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-                      ((assoc-ref (@ (guix build r-build-system) %standard-phases)
-                                  'patch-tests)
-                       #:skipped-tests
-                       ;; These files contain tests that require Internet access.
-                       '("test-compat.R" "test-get.R"
-                         ;; HttpStore requires the crul package
-                         ("test-zarrs-dispatch.R" "can_use_zarrs_create returns FALSE for HttpStore")
-                         ("test-zarrs-store-cache.R" "HttpStore get_store_identifier returns URL")))))
-                  (replace 'check
-                    (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-                      ((assoc-ref (@ (guix build r-build-system) %standard-phases)
-                                  'check)
-                       #:test-target "tests"
-                       #:test-types #false
-                       #:inputs inputs
-                       #:outputs outputs
-                       #:tests? tests?)))))))
-    (propagated-inputs (list r-jsonlite r-memoise r-qs2 r-r6 r-stringr))
-    (inputs
-     (cons* openssl zlib `(,zstd "lib")
-            (cargo-inputs 'r-pizzarr)))
-    (native-inputs
-     (list pkg-config
-           r-minimal r-pbapply r-testthat r-vcr))
-    (home-page "https://github.com/keller-mark/pizzarr")
-    (synopsis "Slice into Zarr arrays in R")
-    (description
-     "This package provides an implementation of chunked, compressed,
+  (let ((commit "5f4705789ba29344dcb97023f290a26a7f7abd0c")
+        (revision "2"))
+    (package
+      (name "r-pizzarr")
+      (version (git-version "0.1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/keller-mark/pizzarr")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "17pd6bk8kvnrvvyfqvm8q47kzghlfyfjdd9b7cwiazc5xr4vz6f0"))))
+      (properties `((upstream-name . "pizzarr")))
+      (build-system r-build-system)
+      ;; Some tests require Internet access.
+      (arguments (list #:tests? #false))
+      (propagated-inputs (list r-jsonlite r-memoise r-qs r-r6 r-stringr))
+      (native-inputs (list r-pbapply r-testthat r-vcr))
+      (home-page "https://github.com/keller-mark/pizzarr")
+      (synopsis "Slice into Zarr arrays in R")
+      (description
+       "This package provides an implementation of chunked, compressed,
 N-dimensional arrays for R, Zarr specification version 2 (2024)
 <doi:10.5281/zenodo.11320255>.")
-    (license license:expat)))
+      (license license:expat))))

 (define-public r-rhtslib12
  (let ((commit "ee186daf04876969c7f31c16a0e0fda8e7c16a30")
@@ -4625,11 +4572,8 @@ into separate processes; and more.")
     (list
      #:phases
      #~(modify-phases %standard-phases
-          (add-after 'unpack 'python3.12-compatibility
+          (add-after 'unpack 'python3.11-compatibility
            (lambda _
-              ;; This was removed in Python 3.12
-              (substitute* "Bio/Align/_aligners.c"
-                (("case PyUnicode_WCHAR_KIND:") ""))
              ;; Py_TYPE was changed to an inline static function in Python
              ;; 3.11, so it cannot be used on the left-hand side.
              (substitute* "Bio/triemodule.c"
@@ -14046,20 +13990,33 @@ of scRNA-seq data.")
 (define-public r-misha
  (package
    (name "r-misha")
-    (version "5.6.23")
+    (version "4.1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/tanaylab/misha")
-             (commit (string-append "v" version))))
+             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "1k973j04iq02dy4f7qgi3cmp3rcx5yinyx0m7vyag54rqanird8x"))))
+         "0bgivx3lzjh3173jsfrhb5kvhjsn53br0n4hmyx7i3dwy2cnnp2p"))
+       ;; Delete bundled executable.
+       (snippet
+        '(delete-file "exec/bigWigToWig"))))
    (build-system r-build-system)
-    (propagated-inputs (list r-curl r-digest r-magrittr r-ps r-yaml))
-    (native-inputs (list r-knitr r-testthat))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-use-bundled-bigWigToWig
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "R/misha.R"
+               (("get\\(\".GLIBDIR\"\\), \"/exec/bigWigToWig")
+                (string-append "\""
+                               (assoc-ref inputs "kentutils")
+                               "/bin/bigWigToWig"))))))))
+    (inputs
+     (list kentutils))
    (home-page "https://github.com/tanaylab/misha")
    (synopsis "Toolkit for analysis of genomic data")
    (description "This package is intended to help users to efficiently
@@ -18859,28 +18816,26 @@ activity prediction from transcriptomics data, and its R implementation
      (build-system r-build-system)
      (arguments
       (list
-        #:skipped-tests
-        ;; These tests attempt to connect to the Internet.
-        '(("test-liana_utils.R" "Test liana pipe")
-          ("test-liana_tensor.R"
-           ".*Test tensor wrapper.*"
-           ".*Test decompose_tensor.*")
-          ;; XXX: This test returns a data.frame instead of an error.
-          ("test-liana_cytotalk.R" ".*Test Cytotalk Wrap.*"))
        #:phases
        '(modify-phases %standard-phases
           ;; This is needed to find ~/.config/OmnipathR/omnipathr.yml
           (add-after 'unpack 'set-HOME
             (lambda _ (setenv "HOME" "/tmp")))
-           (add-after 'unpack 'seurat-compatibility
+           (add-after 'unpack 'disable-bad-tests
             (lambda _
-               ;; The `slot` argument of `GetAssayData()` was deprecated in
-               ;; SeuratObject 5.0.0.
-               (substitute* '("R/cellchat_pipe.R"
-                              "R/sca_pipe.R"
-                              "R/liana_prep.R"
-                              "R/natmi_pipe.R")
-                 (("slot =") "layer =")))))))
+               ;; These tests attempt to connect to the Internet.
+               (substitute* "tests/testthat/test-liana_utils.R"
+                 ((".*Test liana pipe.*" m)
+                  (string-append m "skip('guix')\n")))
+               (substitute* "tests/testthat/test-liana_tensor.R"
+                 ((".*Test tensor wrapper.*" m)
+                  (string-append m "skip('guix')\n"))
+                 ((".*Test decompose_tensor.*" m)
+                  (string-append m "skip('guix')\n")))
+               ;; XXX: This test returns a data.frame instead of an error.
+               (substitute* "tests/testthat/test-liana_cytotalk.R"
+                 ((".*Test Cytotalk Wrap.*" m)
+                  (string-append m "skip('guix')\n"))))))))
      (propagated-inputs
       (list r-basilisk
             r-basilisk-utils
@@ -21745,6 +21700,70 @@ want to explore e.g.: the function of a set of differentially expressed
 genes.")
      (license license:gpl3))))

+(define-public r-seurat-utils
+  (let ((commit "c0374cc9e25ce391ba8013fda0f8c7babbb9201d")
+        (revision "1"))
+    (package
+      (name "r-seurat-utils")
+      (version (git-version "2.5.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/Seurat.utils")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "15l86b43q245gzz7gsr5rhs4sir74lc14d64yqxfqcb0zrb2bzzd"))))
+      (properties `((upstream-name . "Seurat.utils")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-codeandroll2
+                               r-cowplot
+                               r-databaselinke-r
+                               r-dplyr
+                               r-enhancedvolcano
+                               r-foreach
+                               r-ggcorrplot
+                               r-ggexpress
+                               r-ggplot2
+                               r-ggpubr
+                               r-ggrepel
+                               r-hgnchelper
+                               r-htmlwidgets
+                               r-job
+                               r-magrittr
+                               r-markdownhelpers
+                               r-markdownreports
+                               r-matrix
+                               r-matrixstats
+                               r-pheatmap
+                               r-plotly
+                               r-princurve
+                               r-qs
+                               r-r-utils
+                               r-readr
+                               r-readwriter
+                               r-reshape2
+                               r-rstudioapi
+                               r-scales
+                               r-seurat
+                               r-soupx
+                               r-sparsematrixstats
+                               r-stringendo
+                               r-stringr
+                               r-tibble
+                               r-tictoc
+                               r-tidyverse
+                               r-vroom))
+      (home-page "https://github.com/vertesy/Seurat.utils")
+      (synopsis "Collection of utility functions for Seurat")
+      (description
+       "This is a collection of utility functions for Seurat.  These functions
+allow the automation and multiplexing of plotting, 3D plotting, visualization
+of statistics & QC, interaction with the Seurat object.  Some functionalities
+require functions from CodeAndRoll and MarkdownReports libraries.")
+      (license license:gpl3))))
+
 (define-public r-seuratextend
  (let ((commit "5dacd7c1e1da3bc0e78ab81d60056f6d7da3d386")
        (revision "1"))
@@ -22459,39 +22478,38 @@ frames with arbitrary sets of columns.")
      (license license:expat))))

 (define-public r-imagearray
-  (package
-    (name "r-imagearray")
-    (version "1.0.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ImageArray" version))
-       (sha256
-        (base32 "07zq5fcw2dsvm4qaksaj4gy9gj5lxcgq82l497c5kgvl4wba049c"))))
-    (properties `((upstream-name . "ImageArray")))
-    (build-system r-build-system)
-    (arguments
-     (list
-      #:skipped-tests
-      ;; RBiomFormats is not installed.
-      '(("test-array.R" "check indexing \\(BFArray\\)"))))
-    (propagated-inputs (list r-delayedarray
-                             r-ebimage
-                             r-hdf5array
-                             r-magick
-                             r-rarr
-                             r-rhdf5
-                             r-s4arrays
-                             r-s4vectors
-                             r-zarrarray))
-    (native-inputs (list r-ggplot2 r-knitr r-testthat))
-    (home-page "https://github.com/BIMSBbioinfo/ImageArray")
-    (synopsis "Framework for on-disk and in-memory image arrays")
-    (description
-     "@code{ImageArray} provides a framework for on-disk and in-memory image
-arrays, specifically for pyramidal images stored in HDF5, Zarr and life
-sciences image file formats (OME Bio-Formats).")
-    (license license:expat)))
+  (let ((commit "2f90694fa33ed8320a6a2f7e0ad5c8a1796cbfc6")
+        (revision "1"))
+    (package
+      (name "r-imagearray")
+      (version (git-version "0.99.6" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/BIMSBbioinfo/ImageArray")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1mf68b007dc5wdzdva4vkjgkavgagjk45qv05f7vahbpi24yjj4n"))))
+      (properties `((upstream-name . "ImageArray")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-delayedarray
+                               r-ebimage
+                               r-hdf5array
+                               r-magick
+                               r-rarr
+                               r-rhdf5
+                               r-s4arrays
+                               r-s4vectors))
+      (native-inputs (list r-knitr r-testthat))
+      (home-page "https://github.com/BIMSBbioinfo/ImageArray")
+      (synopsis "Framework for on-disk and in-memory image arrays")
+      (description
+       "@code{ImageArray} provides a framework for on-disk and in-memory image
+arrays, specifically for pyramidal images stored in either HDF5 files or Zarr
+stores.")
+      (license license:expat))))

 (define-public r-velocyto
  (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350")
@@ -22575,7 +22593,7 @@ dependencies of @code{VoltRon} package.")
 (define-public r-voltron
  (package
    (name "r-voltron")
-    (version "0.2.6")
+    (version "0.2.5")
    (source
     (origin
       (method git-fetch)
@@ -22584,7 +22602,7 @@ dependencies of @code{VoltRon} package.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "00fl5dmyd9ad4hd0cblgi0415sf6q4q67wh04r7fws828vs5vaj1"))))
+        (base32 "057n4yipkq3gnlyrb63l2ryi78nlmaas02avargm352g5ra1xl9s"))))
    (properties `((upstream-name . "VoltRon")))
    (build-system r-build-system)
    (arguments
@@ -22648,15 +22666,18 @@ guix_python <- \"~a\";"
                             r-irlba
                             r-magick
                             r-matrix
+                             r-pizzarr
                             r-rann
                             r-rcdt
                             r-rcpp
                             r-rcppannoy
                             r-rcpparmadillo
+                             r-reshape2
+                             r-reticulate
+                             r-rhdf5
                             r-rjson
                             r-rlang
                             r-s4arrays
-                             r-s4vectors
                             r-shiny
                             r-shinyjs
                             r-sp
@@ -22709,8 +22730,8 @@ spots, cells and even molecules.")
    (license license:expat)))

 (define-public r-zarrdataframe
-  (let ((commit "f5f671521934b2afc3c511f8c09181bc7bb789a4")
-        (revision "3"))
+  (let ((commit "84c7db2f6f5f84b4a4308f8eb72bedc131fb68bc")
+        (revision "2"))
    (package
      (name "r-zarrdataframe")
      (version (git-version "0.0.0" revision commit))
@@ -22722,13 +22743,13 @@ spots, cells and even molecules.")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
-          (base32 "0klp2njn6qsa8n6c01v1z2dfaa93lhbzhwhbyhl23h8gg7d28yc1"))))
+          (base32 "1idrvdlzbwyixlg830sn19vfdn3n3irmlyr4ncf7dpk72r08g3hw"))))
      (properties
       '((upstream-name . "ZarrDataFrame")
         (updater-extra-native-inputs . ("r-testthat"))))
      (build-system r-build-system)
      (propagated-inputs (list r-biocgenerics r-delayedarray r-rarr
-                               r-s4vectors r-zarrarray))
+                               r-s4vectors))
      (native-inputs (list r-knitr r-testthat))
      (home-page "https://github.com/BIMSBbioinfo/ZarrDataFrame")
      (synopsis "Bioconductor-friendly Bindings for Zarr")
@@ -22740,35 +22761,39 @@ frames with arbitrary sets of columns.")
      (license license:expat))))

 (define-public r-zarrarray
-  (package
-    (name "r-zarrarray")
-    (version "1.0.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ZarrArray" version))
-       (sha256
-        (base32 "1ny91qg257kgb1hz2h4jvb0rna9cwyw7fqyj5axv52r3b98xn040"))))
-    (properties `((upstream-name . "ZarrArray")))
-    (build-system r-build-system)
-    (propagated-inputs (list r-biocgenerics
-                             r-delayedarray
-                             r-iranges
-                             r-rarr
-                             r-s4arrays
-                             r-s4vectors
-                             r-sparsearray))
-    (native-inputs (list r-knitr r-testthat))
-    (home-page "https://bioconductor.org/packages/ZarrArray")
-    (synopsis "Bring Zarr datasets in R as DelayedArray objects")
-    (description
-     "The @code{ZarrArray} package leverages the Rarr package to bring Zarr
-datasets in R as @code{DelayedArray} objects.  The main class in the package
-is the @code{ZarrArray} class.  A @code{ZarrArray} object is an array-like
-object that represents a Zarr dataset in R. @code{ZarrArray} objects are
-@code{DelayedArray} derivatives and therefore support all operations (delayed
-or block-processed) supported by @code{DelayedArray} objects.")
-    (license license:artistic2.0)))
+  (let ((commit "3cc3e6acf986074dfaece2ad23f9b56962054625")
+        (revision "2"))
+    (package
+      (name "r-zarrarray")
+      (version (git-version "1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/BIMSBbioinfo/ZarrArray")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1qjj92cpxpm3zh05vf60h5gmcn1qady0s38hibb0l57iwdhlhrb3"))))
+      (properties
+       '((upstream-name . "ZarrArray")
+         (updater-extra-native-inputs . ("r-testthat"))))
+      (build-system r-build-system)
+      ;; The tests seem to be outdated.
+      (arguments (list #:tests? #false))
+      (propagated-inputs (list r-biocgenerics
+                               r-delayedarray
+                               r-iranges
+                               r-matrix
+                               r-rarr
+                               r-s4arrays
+                               r-s4vectors
+                               r-sparsearray))
+      (native-inputs (list r-testthat))
+      (home-page "https://github.com/BIMSBbioinfo/ZarrArray")
+      (synopsis "Zarr backend for DelayedArray objects")
+      (description "Zarr backend for @code{DelayedArray} objects.")
+      (license license:expat))))

 (define-public methyldackel
  (package
@@ -24406,77 +24431,79 @@ It also handles cell type-specific differential expression.")
      (license license:gpl3))))

 (define-public r-spectre
-  (package
-    (name "r-spectre")
-    (version "1.3.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/ImmuneDynamics/Spectre")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "15g9w08x0pz2ia9qfalhcg3z5z2zx2085mfbr8gx9w5yxnw475ld"))))
-    (properties `((upstream-name . "Spectre")))
-    (build-system r-build-system)
-    (propagated-inputs
-     (list r-biobase
-           r-biocmanager
-           r-caret
-           r-class
-           r-colorramps
-           r-data-table
-           r-dendsort
-           r-devtools
-           r-dplyr
-           r-exactextractr
-           r-factoextra
-           r-flowcore
-           r-flowsom
-           r-flowviz
-           r-fnn
-           r-ggplot2
-           r-ggpointdensity
-           r-ggpubr
-           r-ggraph
-           r-ggthemes
-           r-gridextra
-           r-gridextra
-           r-gtools
-           r-hdf5array
-           r-irlba
-           r-patchwork
-           r-pheatmap
-           r-plyr
-           r-qs2
-           r-raster
-           r-rcolorbrewer
-           r-rhdf5
-           r-rstudioapi
-           r-rsvd
-           r-rtsne
-           r-s2
-           r-scales
-           r-scattermore
-           r-sf
-           r-sp
-           r-stars
-           r-stringr
-           r-tidygraph
-           r-tidyr
-           r-tidyr
-           r-tiff
-           r-umap
-           r-uwot))
-    (home-page "https://github.com/ImmuneDynamics/Spectre")
-    (synopsis "High-dimensional cytometry and imaging analysis")
-    (description
-     "This package provides a computational toolkit in R for the
+  (let ((commit "ff5314fd5b3f29121e52f948d91e222a19dd4d25")
+        (revision "1"))
+    (package
+      (name "r-spectre")
+      (version "1.2.0")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/ImmuneDynamics/Spectre")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0hziqlaq6mnkxi4bwp5xilxy90yh1vz1j1n117d38vmchvclx9yq"))))
+      (properties `((upstream-name . "Spectre")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-biobase
+             r-biocmanager
+             r-caret
+             r-class
+             r-colorramps
+             r-data-table
+             r-dendsort
+             r-devtools
+             r-dplyr
+             r-exactextractr
+             r-factoextra
+             r-flowcore
+             r-flowsom
+             r-flowviz
+             r-fnn
+             r-ggplot2
+             r-ggpointdensity
+             r-ggpubr
+             r-ggraph
+             r-ggthemes
+             r-gridextra
+             r-gridextra
+             r-gtools
+             r-hdf5array
+             r-irlba
+             r-patchwork
+             r-pheatmap
+             r-plyr
+             r-qs
+             r-raster
+             r-rcolorbrewer
+             r-rhdf5
+             r-rstudioapi
+             r-rsvd
+             r-rtsne
+             r-s2
+             r-scales
+             r-scattermore
+             r-sf
+             r-sp
+             r-stars
+             r-stringr
+             r-tidygraph
+             r-tidyr
+             r-tidyr
+             r-tiff
+             r-umap
+             r-uwot))
+      (home-page "https://github.com/ImmuneDynamics/Spectre")
+      (synopsis "High-dimensional cytometry and imaging analysis")
+      (description
+       "This package provides a computational toolkit in R for the
 integration, exploration, and analysis of high-dimensional single-cell
 cytometry and imaging data.")
-    (license license:expat)))
+      (license license:expat))))

 (define-public r-compgenomrdata
  (let ((commit "24484cb77631e1123ead6c329b9d62c160e600c6")
@@ -48,7 +48,6 @@
  #:use-module (gnu packages base)
  #:use-module (gnu packages disk)
  #:use-module (gnu packages bison)
-  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cdrom)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
@@ -66,6 +65,7 @@
  #:use-module (gnu packages man)
  #:use-module (gnu packages mtools)
  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages package-management)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
@@ -1815,68 +1815,63 @@ For more information, refer to
 (define-public os-prober
  (package
    (name "os-prober")
-    (version "1.84")
+    (version "1.81")
    (source
     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://salsa.debian.org/installer-team/os-prober.git")
-              (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (string-append "mirror://debian/pool/main/o/os-prober/os-prober_"
+                           version ".tar.xz"))
       (sha256
-        (base32 "1bji3w6nbqaz8zqrbmy8b1j5dph9xn7bdh1cd2z8ia1q125i6mgp"))))
+        (base32 "10w8jz6mqhp0skdcam9mpgv79vx1sv7lkpra3rqjg0jkhvn2in9g"))))
    (build-system gnu-build-system)
    (arguments
-     (list
-      #:tests? #f                       ; No tests.
-      #:modules '((guix build gnu-build-system)
+     `(#:modules ((guix build gnu-build-system)
                  (guix build utils)
-                  (ice-9 regex)         ; string-match
-                  (srfi srfi-26))       ; cut
-      #:make-flags
-      #~(list (string-append "CC=" #$(cc-for-target)))
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'configure
-            (lambda _
-              (substitute* (find-files ".")
-                (("/usr") #$output))
-              (substitute* (find-files "." "50mounted-tests$")
-                (("mkdir") "mkdir -p -v"))))
-          (replace 'install
-            (lambda _
-              (define (find-files-non-recursive directory)
-                (find-files directory
-                            (lambda (file stat)
-                              (string-match (string-append "^" directory "/[^/]*$")
-                                            file))
-                            #:directories? #t))
+                  (ice-9 regex)         ; for string-match
+                  (srfi srfi-26))       ; for cut
+       #:make-flags
+       (list ,(string-append "CC=" (cc-for-target)))
+       #:tests? #f                      ; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* (find-files ".")
+               (("/usr") (assoc-ref outputs "out")))
+             (substitute* (find-files "." "50mounted-tests$")
+               (("mkdir") "mkdir -p"))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (define (find-files-non-recursive directory)
+               (find-files directory
+                           (lambda (file stat)
+                             (string-match (string-append "^" directory "/[^/]*$")
+                                           file))
+                           #:directories? #t))

-              (let ((bin (string-append #$output "/bin"))
-                     (lib (string-append #$output "/lib"))
-                     (share (string-append #$output "/share")))
-                (for-each (cut install-file <> bin)
-                          (list "linux-boot-prober" "os-prober"))
-                (install-file "newns" (string-append lib "/os-prober"))
-                (install-file "common.sh" (string-append share "/os-prober"))
-                (install-file "os-probes/mounted/powerpc/20macosx"
-                              (string-append lib "/os-probes/mounted"))
-                (for-each
-                 (lambda (directory)
-                   (for-each
-                    (lambda (file)
-                      (let ((destination (string-append lib "/" directory
-                                                        "/" (basename file))))
-                        (mkdir-p (dirname destination))
-                        (copy-recursively file destination)))
-                    (append (find-files-non-recursive (string-append directory "/common"))
-                            (find-files-non-recursive (string-append directory "/x86")))))
-                 (list "linux-boot-probes"
-                       "linux-boot-probes/mounted"
-                       "os-probes"
-                       "os-probes/init"
-                       "os-probes/mounted"))))))))
-    (home-page "https://joeyh.name/code/os-prober/")
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (lib (string-append out "/lib"))
+                    (share (string-append out "/share")))
+               (for-each (cut install-file <> bin)
+                         (list "linux-boot-prober" "os-prober"))
+               (install-file "newns" (string-append lib "/os-prober"))
+               (install-file "common.sh" (string-append share "/os-prober"))
+               (install-file "os-probes/mounted/powerpc/20macosx"
+                             (string-append lib "/os-probes/mounted"))
+               (for-each
+                (lambda (directory)
+                  (for-each
+                   (lambda (file)
+                     (let ((destination (string-append lib "/" directory
+                                                       "/" (basename file))))
+                       (mkdir-p (dirname destination))
+                       (copy-recursively file destination)))
+                   (append (find-files-non-recursive (string-append directory "/common"))
+                           (find-files-non-recursive (string-append directory "/x86")))))
+                (list "os-probes" "os-probes/mounted" "os-probes/init"
+                      "linux-boot-probes" "linux-boot-probes/mounted"))))))))
+    (home-page "https://joeyh.name/code/os-prober")
    (synopsis "Detect other operating systems")
    (description "os-prober probes disks on the system for other operating
 systems so that they can be added to the bootloader.  It also works out how to
@@ -64,6 +64,7 @@
  #:use-module (gnu packages logging)
  #:use-module (gnu packages lua)
  #:use-module (gnu packages man)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages package-management)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages perl)
@@ -76,7 +77,6 @@
  #:use-module (gnu packages python-crypto)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages python-xyz)
-  #:use-module (gnu packages re2c)
  #:use-module (gnu packages regex)
  #:use-module (gnu packages rpc)
  #:use-module (gnu packages serialization)
@@ -104,8 +104,7 @@
  #:use-module (guix packages)
  #:use-module (guix search-paths)
  #:use-module (guix utils)
-  #:use-module (ice-9 optargs)
-  #:use-module (srfi srfi-1))
+  #:use-module (ice-9 optargs))

 (define-public acr
  (package
@@ -1484,114 +1483,3 @@ Features:
@item Support for languages outside C/C++ (e.g. Go, Rust, Zig).
@end itemize")
   (license license:asl2.0)))
-
-(define-public ninja/pinned
-  (hidden-package
-   (package
-     (name "ninja")
-     (version "1.13.2")
-     (source (origin
-               (method git-fetch)
-               (uri (git-reference
-                     (url "https://github.com/ninja-build/ninja")
-                     (commit (string-append "v" version))))
-               (file-name (git-file-name name version))
-               (sha256
-                (base32
-                 "0lp9dmxbjyjwv089i8mgq3nvnhpbnsn01ifm05m9s47w7cifrl8g"))))
-     (build-system gnu-build-system)
-     (inputs (list python-wrapper re2c))
-     (arguments
-      '(; Tests now require googletest, which is a circular dependency.
-        #:tests? #f
-        #:phases
-        (modify-phases %standard-phases
-          (replace 'configure
-            (lambda _
-              (substitute* "src/subprocess-posix.cc"
-                (("/bin/sh") (which "sh")))
-              (substitute* "src/subprocess_test.cc"
-                (("/bin/echo") (which "echo")))))
-          (replace 'build
-            (lambda _
-              (invoke "./configure.py" "--bootstrap")))
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                (invoke "./configure.py")
-                (invoke "./ninja" "ninja_test")
-                (invoke "./ninja_test"))))
-          (replace 'install
-            (lambda* (#:key outputs #:allow-other-keys)
-              (let* ((out (assoc-ref outputs "out"))
-                     (bin (string-append out "/bin"))
-                     (doc (string-append out "/share/doc/ninja")))
-                (install-file "ninja" bin)
-                (install-file "doc/manual.asciidoc" doc)))))))
-     (home-page "https://ninja-build.org/")
-     (synopsis "Small build system")
-     (description
-      "Ninja is a small build system with a focus on speed.  It differs from
-other build systems in two major respects: it is designed to have its input
-files generated by a higher-level build system, and it is designed to run
-builds as fast as possible.")
-    (license license:asl2.0))))
-
-(define-public ninja
-  (package/inherit ninja/pinned
-    (properties (alist-delete 'hidden? (package-properties ninja/pinned)))))
-
-(define-public samurai
-  (package
-    (name "samurai")
-    (version "1.2")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/michaelforney/samurai")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "04iw18hgkm72yrl83a2xh1jc47w9rilpb95kwick0j37b4q3gxj4"))))
-    (build-system gnu-build-system)
-    (arguments
-     (list #:tests? #f                  ;no test suite
-           #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
-                                (string-append "PREFIX=" #$output))
-           #:phases #~(modify-phases %standard-phases
-                        (add-after 'unpack 'patch-/bin/sh
-                          (lambda* (#:key inputs #:allow-other-keys)
-                            (substitute* "build.c"
-                              (("/bin/sh")
-                               (search-input-file inputs "bin/sh")))))
-                        (delete 'configure))))
-    (inputs (list bash-minimal))
-    (home-page "https://github.com/michaelforney/samurai")
-    (synopsis "Ninja-compatible build tool written in C")
-    (description "@code{samurai} is a ninja-compatible build tool written in
-C99 with a focus on simplicity, speed, and portability.  It is
-feature-complete and supports most of the same options as ninja.  This package
-provides the command @command{samu}.  For a @command{ninja} command
-replacement, use the @code{samu-as-ninja-wrapper} package.")
-    (license (list license:asl2.0               ;for the most part
-                   license:expat))))            ;htab.h, htab.c and tree.c
-
-(define-public samu-as-ninja-wrapper
-  (package/inherit samurai
-    (name "samu-as-ninja-wrapper")
-    (build-system trivial-build-system)
-    (arguments
-     (list #:builder
-           (with-imported-modules '((guix build utils))
-             #~(begin
-                 (use-modules (guix build utils))
-                 (let ((bindir (string-append #$output "/bin"))
-                       (samu (string-append #$(this-package-input "samurai")
-                                            "/bin/samu")))
-                   (mkdir-p bindir)
-                   (symlink samu (string-append bindir "/ninja")))))))
-    (inputs (list samurai))
-    (description "This package provides the @command{ninja} command,
-implemented as a symbolic link to the @command{samu} command of @code{samurai}
-package.")))
@@ -302,7 +302,7 @@ will name the threaded machine type unless THREADS? is provided as #f."
    (name "chez-scheme-for-racket")
    ;; The version should match `(scheme-version #t)`.
    ;; See s/cmacros.ss c. line 360.
-    (version "10.4.0-pre-release.1-1") ; expect a chez-nanopass-bootstrap update
+    (version "10.3.0-pre-release.2") ; expect a chez-nanopass-bootstrap update
    (source #f)
    (build-system gnu-build-system)
    (inputs `(,@(if (nix-system->native-chez-machine-type)
@@ -507,7 +507,7 @@ version of Chez Scheme.")
    (name "chez-scheme")
    ;; The version should match `(scheme-version-number #t)`.
    ;; See s/cmacros.ss c. line 360.
-    (version "10.4.0") ; expect a chez-nanopass-bootstrap update
+    (version "10.2.0") ; expect a chez-nanopass-bootstrap update
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -515,7 +515,7 @@ version of Chez Scheme.")
                    (commit (string-append "v" version))))
              (sha256
               (base32
-                "079vlkl27qdvsg1rsynmd828m42n98c2dnldkhsxf2slfsqd9kv5"))
+                "14iv4kfkyvrkigr1n2prf71n2l3vs0sf0549rvh6y4x2faa2l329"))
              (file-name (git-file-name name version))
              (patches (search-patches "chez-scheme-bin-sh.patch"))
              (snippet #~(begin
@@ -840,9 +840,9 @@ User's Guix}, among other documents.")
 (define-public chez-nanopass-bootstrap
  (hidden-package
   (package
-     (name "chez-nanopass-bootstrap")
-     (version "1.9.4")
-     (properties '((chez-nanopass-release-date . "December 29, 2025")))
+     (name "chez-nanopass")
+     (version "1.9.2")
+     (properties `((chez-nanopass-release-date . "October 18, 2020")))
     (source
      (origin
        (method git-fetch)
@@ -850,7 +850,7 @@ User's Guix}, among other documents.")
              (url "https://github.com/nanopass/nanopass-framework-scheme")
              (commit (string-append "v" version))))
        (sha256
-         (base32 "1qq0vnbrvcialgjgnblfq3qp1ilqg94h0kg896ksd9v4g7ipj9v0"))
+         (base32 "16vjsik9rrzbabbhbxbaha51ppi3f9n8rk59pc6zdyffs0vziy4i"))
        (file-name (git-file-name "nanopass-framework-scheme" version))
        (snippet
         #~(begin
@@ -929,9 +929,10 @@ create compilers, making them easier to understand and maintain.")
 (define-public chez-nanopass
  (package
    (inherit chez-nanopass-bootstrap)
-    (name "chez-nanopass")
-    (version "1.9.4")
-    (properties '((chez-nanopass-release-date . "December 29, 2025")))
+    ;; This release has a significant bug fix.  Expect the next releases of
+    ;; chez-scheme{,-for-racket} to want this for chez-nanopass-bootstrap.
+    (version "1.9.3")
+    (properties '((chez-nanopass-release-date . "August 24, 2025")))
    (source
     (let ((bootstrap-origin (package-source chez-nanopass-bootstrap)))
       (origin
@@ -940,7 +941,7 @@ create compilers, making them easier to understand and maintain.")
                (url (git-reference-url (origin-uri bootstrap-origin)))
                (commit (string-append "v" version))))
         (sha256
-          (base32 "1qq0vnbrvcialgjgnblfq3qp1ilqg94h0kg896ksd9v4g7ipj9v0"))
+          (base32 "0757x3a3b4kcd3jk52h4ikqzv7cc1mvphlw592f0r5pz99bkxiin"))
         (file-name (git-file-name "nanopass-framework-scheme" version)))))
    (native-inputs (list chez-scheme stex))))

@@ -53,6 +53,7 @@
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages kerberos)
  #:use-module (gnu packages maths)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages node)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages pciutils)
@@ -1475,7 +1475,7 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
 (define-public 7zip
  (package
    (name "7zip")
-    (version "26.01")
+    (version "26.00")
    (source
     (origin
       (method git-fetch)
@@ -1483,7 +1483,7 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
              (url "https://github.com/ip7z/7zip")
              (commit version)))
       (sha256
-        (base32 "0qwzn9pz1m6f8q20cqgmfqp1qx6s7959xnyikpr60n1v8c1mj98q"))
+        (base32 "1fvgl9qp2pl5c0jmvgbdx6qig3qd80mhxvml42yby8y412x65sh7"))
       (file-name (git-file-name name version))
       (modules '((guix build utils)
                  (ice-9 regex)))
@@ -127,76 +127,6 @@ formats:
 It also comes with example files generated by bincfg.")
    (license license:gpl3+)))

-(define-public bucts
-  (package
-    (name "bucts")
-    (version %coreboot-version)
-    (source %coreboot-origin)
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:tests? #f ;no tests
-      #:make-flags #~(list (string-append "CC=" #$(cc-for-target)))
-      #:phases #~(modify-phases %standard-phases
-                   (delete 'configure) ;no configure script
-                   (add-after 'unpack 'enter-source
-                     (lambda _
-                       (chdir "util/bucts")))
-                   (add-after 'enter-source 'set-version
-                     (lambda _
-                       (substitute* "Makefile"
-                         (("^VERSION:=*")
-                          #$(string-append "VERSION:=" version)))))
-                   ;; no install target
-                   (replace 'install
-                     (lambda _
-                       (let ((bin (string-append #$output "/bin"))
-                             (doc (string-append #$output "/share/doc/bucts/"))
-                             (licenses (string-append #$output
-                                        "/share/licenses/bucts/")))
-                         (install-file "bucts" bin)
-                         (install-file "readme.md" doc)
-                         (install-file "../../COPYING" licenses)))))))
-    (inputs (list pciutils))
-    (home-page "https://coreboot.org")
-    (synopsis "Tool to swap the BIOS bootblock and backup bootblock on the
-Intel I945 chipsets")
-    (description
-     "The @command{bucts} command can flip a bit in the BUC.TS register of the
-Intel I945 chipsets and show the register status.  When the bit is set, it
-swaps the bootblock location.  Because the bootblock region is often set
-read-only by the default BIOS, this enables to bypass that restriction and is
-used as part of a procedure to replace the nonfree BIOS with free software on
-various computers (Lenovo X60, X60s, X60T, T60, probably more).")
-    (license license:gpl2)))
-
-(define-public ectool
-  (package
-    (name "ectool")
-    (version %coreboot-version)
-    (source %coreboot-origin)
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:tests? #f ; no test suite
-      #:make-flags
-      #~(list (string-append "CC=" #$(cc-for-target))
-              "INSTALL=install"
-              (string-append "PREFIX=" #$output))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'chdir
-            (lambda _
-              (chdir "util/ectool")))
-          (delete 'configure)))) ; no configure script
-    (home-page "https://doc.coreboot.org/util.html")
-    (synopsis "Tool to dump and modify @acronym{EC, Embedded Controller} RAM
-on computers such as laptops")
-    (description "This package provides @command{ectool}, a program to dump
-and modify the contents of @acronym{EC, Embedded Controller} RAM
-on mobile computers.")
-    (license license:gpl2)))
-
 (define-public ifdtool
  (package
    (name "ifdtool")
@@ -5645,7 +5645,7 @@ with integrated support for finding required rows quickly.")
 (define-public apache-arrow
  (package
    (name "apache-arrow")
-    (version "24.0.0")
+    (version "23.0.1")
    (source
     (origin
       (method git-fetch)
@@ -5655,7 +5655,7 @@ with integrated support for finding required rows quickly.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "1j3gs5ffa9gx2y2nggmi2zn5rj0bsnjnxrzfnipx6050jz6n8dx9"))))
+         "1qn7wgavi3kiz4d6w1naqj5631bg87fnj6gbhaxmpmynm5hi9wm7"))))
    (build-system cmake-build-system)
    (arguments
     (list
@@ -5823,8 +5823,6 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
           pkg-config
           python-cython
           python-pytest
-           python-pytest-runner
-           python-scikit-build-core
           python-setuptools-scm
           python-setuptools))
    (outputs '("out"))
@@ -77,6 +77,7 @@
  #:use-module (gnu packages mail)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages pretty-print)
@@ -31,13 +31,13 @@
 (define-public dhall
  (package
    (name "dhall")
-    (version "1.42.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "dhall" version))
-       (sha256
-        (base32 "0fvvqvh6diqi55dmncfs06rvcw8k0a1hs2gq228yxvsfbzcpv44s"))))
+    (version "1.41.2")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "dhall" version))
+              (sha256
+               (base32
+                "14m5rrvkid76qnvg0l14xw1mnqclhip3gjrz20g1lp4fd5p056ka"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "dhall")))
    (inputs (list ghc-aeson
@@ -73,8 +73,8 @@
                  ghc-text-manipulate
                  ghc-text-short
                  ghc-th-lift-instances
-                  ghc-unix-compat
                  ghc-unordered-containers
+                  ghc-uri-encode
                  ghc-vector
                  ghc-cryptohash-sha256
                  ghc-http-types
@@ -86,6 +86,7 @@
                         ghc-quickcheck-instances
                         ghc-special-values
                         ghc-spoon
+                         ghc-system-filepath
                         ghc-tasty
                         ghc-tasty-expected-failure
                         ghc-tasty-hunit
@@ -96,8 +97,9 @@
                         ghc-mockery
                         ghc-doctest))
    (arguments
-     `(#:cabal-revision ("2"
-                         "1h9kxpn3kzwmxj07mqc0cxjj2ak3dyxnifb78z5vn34xn747j5bk")))
+     `(#:tests? #f ; Tries to access httpbin.org
+       #:cabal-revision ("4"
+                         "0innb3cn98ynb8bd83jdyrm64ij7wcvajg5qcwzdwbyzpr62anfx")))
    (home-page "http://hackage.haskell.org/package/dhall")
    (synopsis "Configuration language guaranteed to terminate")
    (description
@@ -105,6 +105,7 @@
  #:use-module (gnu packages libbsd)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages perl-web)
@@ -41,7 +41,6 @@
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
-  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages curl)
@@ -49,6 +48,7 @@
  #:use-module (gnu packages gdb)
  #:use-module (gnu packages libedit)
  #:use-module (gnu packages llvm)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
@@ -1425,7 +1425,7 @@ and TCP-capable recursive DNS server for finding domains on the internet.")
 (define-public openresolv
  (package
    (name "openresolv")
-    (version "3.13.2")
+    (version "3.17.4")
    (source
     (origin
       (method git-fetch)
@@ -1435,7 +1435,7 @@ and TCP-capable recursive DNS server for finding domains on the internet.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "03m8n0j0kxxm5kpl66gz4lxr1qqgrp8zlkaq9j8fz27fih0g75xf"))
+         "1lawj50qhr2yj7fy3p8x4m3kqz4lbvghnjc4jlqnxp484hg83ki3"))
       (patches
        (search-patches "openresolv-restartcmd-guix.patch"))))
    (build-system gnu-build-system)
@@ -1314,7 +1314,7 @@ package.")
       #:tests? #f)) ;no test suite
    (native-inputs (list asciidoc
                         gettext-minimal
-                         git-minimal/pinned
+                         git-minimal
                         perl
                         perl-unicode-linebreak
                         perl-yaml-tiny
@@ -2521,7 +2521,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
 (define-public nvc
  (package
    (name "nvc")
-    (version "1.21.0")
+    (version "1.20.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -2530,7 +2530,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "00hnrzk9dw88srfmjxxb9xkgnd5n26pmqlcw1bff1y0bckblsr38"))))
+                "1b38x2ch468s4p6mrq6c8s0d95vb84p6w4v8in79l4w7sfy8jnr0"))))
    (build-system gnu-build-system)
    (arguments
     (list #:out-of-source? #t
@@ -15526,6 +15526,34 @@ underlying library functionality for performing various activities related to
 the game of chess.")
    (license license:gpl3+)))

+(define-public emacs-4clojure
+  ;; There is no release.  Base version is extracted from Version keyword in
+  ;; the main file.
+  (let ((commit "4eccf8c7d4341a36c269451838114b27836699f9")
+        (revision "1"))
+    (package
+      (name "emacs-4clojure")
+      (version (git-version "0.2.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/emacsorphanage/4clojure")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "19x653lzc1dxil4ix257hciidbdmbhaxhs6qhlkwi9ygjrlrgvnk"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       (list emacs-request))
+      (home-page "https://github.com/emacsorphanage/4clojure/")
+      (synopsis "Open and evaluate 4clojure questions in Emacs")
+      (description "Emacs 4clojure interacts with
+@url{http://www.4clojure.com, 4clojure} problems.  You can open a specific
+question and move to the next or previous one.  You can also verify your
+answers.")
+      (license license:gpl3+))))
+
 (define-public emacs-base16-theme
  (package
    (name "emacs-base16-theme")
@@ -23831,8 +23859,8 @@ actually changing the buffer's text.")

 (define-public emacs-diff-hl
  ;; No new tags or releases since 2024.
-  (let ((commit "7d873b2f58908de1ea2f499da9bf993e088953d7")
-        (revision "1"))
+  (let ((commit "e79aa49ad3cbbe85379cf6646db3aaacd3b04708")
+        (revision "0"))
    (package
      (name "emacs-diff-hl")
      (version (git-version "1.10.0" revision commit))
@@ -23844,7 +23872,7 @@ actually changing the buffer's text.")
                (commit commit)))
         (file-name (git-file-name name version))
         (sha256
-          (base32 "15a9cjlpjsfcb2hxqbb123389qhiqs06mn01pas2l0jqhc2p86v9"))))
+          (base32 "0fvxngcbx36vqj72fllfp5iqwihcqd1dfhmqr3m1284191q83na3"))))
      (build-system emacs-build-system)
      (arguments
       (list
@@ -23867,7 +23895,7 @@ actually changing the buffer's text.")
                (invoke "git" "init")
                (invoke "git" "add" ".")
                (invoke "git" "commit" "-m" "Commit all."))))))
-      (native-inputs (list git-minimal/pinned))
+      (native-inputs (list git-minimal))
      (home-page "https://github.com/dgutov/diff-hl")
      (synopsis "Highlight uncommitted changes using VC")
      (description
@@ -68,7 +68,6 @@
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages boost)
-  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cdrom)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cmake)
@@ -108,6 +107,7 @@
  #:use-module (gnu packages music)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages parallel)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages pretty-print)
@@ -129,6 +129,7 @@
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pdf)
@@ -321,41 +322,37 @@ based on Qt.")
 (define-public ghc-hledger
  (package
    (name "ghc-hledger")
-    (version "1.43.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hledger" version))
-       (sha256
-        (base32 "043gw3amc29fbjxlzyc4m97bw5i5462352lmk61adlxcd12l47i1"))))
+    (version "1.27.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hledger" version))
+              (sha256
+               (base32
+                "0qdg87m7ys2ykqqq32p7h7aw827w4f5bcqx4dspxxq6zqlvzddqb"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hledger")))
    (inputs (list ghc-decimal
                  ghc-diff
                  ghc-aeson
                  ghc-ansi-terminal
+                  ghc-breakpoint
                  ghc-cmdargs
                  ghc-data-default
                  ghc-extra
                  ghc-githash
                  ghc-hashable
                  ghc-hledger-lib
-                  ghc-http-client
-                  ghc-http-types
                  ghc-lucid
                  ghc-math-functions
                  ghc-megaparsec
                  ghc-microlens
-                  ghc-modern-uri
                  ghc-regex-tdfa
-                  ghc-req
                  ghc-safe
                  ghc-shakespeare
                  ghc-split
                  ghc-tabular
                  ghc-tasty
                  ghc-temporary
-                  ghc-text-ansi
                  ghc-timeit
                  ghc-unordered-containers
                  ghc-utf8-string
@@ -386,8 +383,8 @@ Accounting.")
      #~(modify-phases %standard-phases
          (add-after 'install 'install-doc
            (lambda _
-              (install-file "embeddedfiles/hledger.info" (string-append #$output "/share/info"))
-              (install-file "embeddedfiles/hledger.1" (string-append #$output "/man/man1"))))
+              (install-file "hledger.info" (string-append #$output "/share/info"))
+              (install-file "hledger.1" (string-append #$output "/man/man1"))))
           (add-after 'register 'remove-libraries
             (lambda* (#:key outputs #:allow-other-keys)
               (delete-file-recursively (string-append (assoc-ref outputs "out") "/lib")))))))))
@@ -2284,13 +2281,13 @@ textual ledgers to Beancount files.")
 (define-public hledger-web
  (package
    (name "hledger-web")
-    (version "1.43.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hledger-web" version))
-       (sha256
-        (base32 "0d4sv9k3m7s0764lbq2l8w9p2p47cby177l0avl5w3fa9y8d0gyd"))))
+    (version "1.27.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hledger-web" version))
+              (sha256
+               (base32
+                "151dxci7dld8626dzw823sr3d9iaac92wfzbfcbdz4jh9f7n07wa"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hledger-web")))
    (inputs (list ghc-decimal
@@ -2298,6 +2295,7 @@ textual ledgers to Beancount files.")
                  ghc-base64
                  ghc-blaze-html
                  ghc-blaze-markup
+                  ghc-breakpoint
                  ghc-case-insensitive
                  ghc-clientsession
                  ghc-cmdargs
@@ -2305,8 +2303,6 @@ textual ledgers to Beancount files.")
                  ghc-conduit-extra
                  ghc-data-default
                  ghc-extra
-                  ghc-file-embed
-                  ghc-githash
                  ghc-hjsmin
                  ghc-hledger
                  ghc-hledger-lib
@@ -2316,7 +2312,6 @@ textual ledgers to Beancount files.")
                  ghc-http-types
                  ghc-megaparsec
                  ghc-network
-                  ghc-safe
                  ghc-shakespeare
                  ghc-unix-compat
                  ghc-unordered-containers
@@ -74,7 +74,6 @@
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2026 Joan Vilardaga Castro <codeberg-hn80@joanvc.cat>
 ;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
-;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2818,32 +2817,6 @@ family.")
 (define-deprecated-package font-adobe-source-serif-pro
  font-adobe-source-serif)

-(define-public font-medieval-sharp
-  ;; No releases, use newest commit.
-  (let ((commit "ee7510b6b13854fd340e7d2e44c218780f672cd1")
-        (revision "1"))
-    (package
-      (name "font-medieval-sharp")
-      ;; From FONTLOG.txt.
-      (version (git-version "3.1.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-                (url "https://github.com/wmk69/Medieval-Sharp")
-                (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "1r300591pra4nxpm5kppl5q3ihsp01wk2zh24f9pvv0jgf1ik87x"))))
-      (build-system font-build-system)
-      (home-page "https://github.com/wmk69/Medieval-Sharp")
-      (synopsis "Font based on gothic letters")
-      (description
-       "Medieval Sharp is a font created for inscriptions on stone, based on
-gothic letters.")
-      (license license:silofl1.1))))
-
 (define-public font-microsoft-cascadia
  (package
    (name "font-microsoft-cascadia")
@@ -47,7 +47,6 @@
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bison)
-  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages datastructures)
@@ -70,6 +69,7 @@
  #:use-module (gnu packages linux)
  #:use-module (gnu packages man)
  #:use-module (gnu packages mc)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
@@ -98,7 +98,6 @@
 ;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2026 Nikita Alkhovik <forgoty13@gmail.com>
-;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -201,6 +200,7 @@
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages netpbm)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages oneapi)
  #:use-module (gnu packages opencl)
@@ -3988,26 +3988,27 @@ that beneath its ruins lay buried an ancient evil.")
        (base32 "0hgzdvlh0j42w4q9kch9xvhnbvcrypac01xhpksw35gj9my887cp"))
       (modules '((guix build utils)))
       (snippet
+        ;; So, some of the sounds/graphics/tilesets are under different
+        ;; licenses... some of them even nonfree!  This is a console-only
+        ;; version of this package so we just remove them.
+        ;; In the future, if someone tries to make a graphical variant of
+        ;; this package, they can deal with that mess themselves. :)
        '(begin
-           (for-each delete-file-recursively
-                     '("lib/tiles/shockbolt" ;nonfree
-                       "src/win"))      ;contains .dlls!
-           ;; Don't build the shockbolt directory either.
-           (substitute* "lib/tiles/Makefile"
-             (("shockbolt") ""))))
-       (patches (search-patches "angband-remove-nonfree-tile-options.patch"))))
+           (for-each (lambda (subdir)
+                       (let ((lib-subdir (string-append "lib/" subdir)))
+                         (delete-file-recursively lib-subdir)))
+                     '("fonts" "icons" "sounds" "tiles"))
+           (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"))
+           ;; Remove nonfree .dll files too.
+           (delete-file-recursively "src/win")))))
    (build-system gnu-build-system)
    (arguments
-     `(#:configure-flags (list (string-append "--bindir=" %output "/bin")
-                               "--disable-x11")
+     `(#:configure-flags (list (string-append "--bindir=" %output "/bin"))
       #:phases
       (modify-phases %standard-phases
-         (add-after 'unpack 'disable-graphics-and-sounds
-           (lambda _
-             (substitute* "lib/Makefile"
-               ;; Do not build any graphics for this version.
-               (("gamedata customize help screens fonts tiles sounds icons user")
-                "gamedata customize help screens user"))))
         (add-before 'build 'fix-infinite-loop-on-sighup
           ;; XXX Release 4.2.6 has a major bug where sending the process a
           ;; SIGHUP when closing the terminal causes it to infinite loop
@@ -4057,59 +4058,6 @@ the depths below Angband, seeking riches, fighting monsters, and preparing to
 fight Morgoth, the Lord of Darkness.")
    (license license:gpl2)))

-(define-public angband-sdl2
-  (package
-    (inherit angband)
-    (name "angband-sdl2")
-    (arguments
-     (substitute-keyword-arguments
-         (package-arguments angband)
-       ((#:configure-flags flags)
-        #~(cons* "--enable-sdl2" #$flags))
-       ((#:phases phases)
-        #~(modify-phases #$phases
-            (delete 'disable-graphics-and-sounds)
-            (add-after 'unpack 'patch-sdl-wrapper-headers
-              (lambda _
-                (with-directory-excursion "src"
-                  (substitute* '("snd-sdl.c"
-                                 "main-sdl2.c"
-                                 "sdl2/pui-win.h")
-                    (("\"SDL_image.h\"") "\"SDL2/SDL_image.h\"")
-                    (("\"SDL_mixer.h\"") "\"SDL2/SDL_mixer.h\"")
-                    (("\"SDL_ttf.h\"") "\"SDL2/SDL_ttf.h\"")))))
-            (add-after 'unpack 'patch-desktop-file
-              (lambda* (#:key outputs #:allow-other-keys)
-                 (let ((out (assoc-ref outputs "out")))
-                   (substitute* "lib/icons/angband-sdl2.desktop"
-                     (("Exec=angband" _)
-                      (string-append "Exec=" #$output "/bin/angband-sdl2"))))))
-            (add-after 'install 'rename-binary
-              (lambda _
-                (with-directory-excursion #$output
-                  ;; allows parallel installation with angband
-                  (rename-file "bin/angband"
-                               "bin/angband-sdl2"))))))))
-    (inputs
-     (modify-inputs inputs
-       (prepend sdl2
-                sdl2-image
-                sdl2-mixer
-                sdl2-ttf)))
-    (description "Angband is a Classic dungeon exploration roguelike.  Explore
-the depths below Angband, seeking riches, fighting monsters, and preparing to
-fight Morgoth, the Lord of Darkness.
-
-This version includes the SDL2 frontend, providing tilesets and sounds which
-can be enabled through in-game options.")
-    ;; XXX: fonts and adam bolt tileset are free but being clarified:
-    ;; https://github.com/angband/angband/issues/6608
-    ;; For the rest, see:
-    ;; https://github.com/angband/angband/blob/master/docs/copying.rst
-    (license (list license:gpl2            ;code, nomad+old tilesets
-                   license:cc-by-sa3.0     ;david gervais tileset
-                   license:cc-by-sa4.0)))) ;sounds
-
 (define-public pingus
  ;; Latest release is from 2021-12-24.
  (let ((commit "7d65221e1cd1026053c8a5a08ad911fbdd13d3ed")
@@ -80,14 +80,14 @@
 (define-public gdb-17
  (package
    (name "gdb")
-    (version "17.2")
+    (version "17.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/gdb/gdb-"
                                  version ".tar.xz"))
              (sha256
               (base32
-                "1312lccryan1jfkjwkbw9mpxgyfnmlr8dj4lbkxx3cz4f86nq0qw"))))
+                "0xnqqv3j463r5rnfmblj3zwhf0l0lyy4bp1zaid8zxn9fignz68l"))))
    (build-system gnu-build-system)
    (outputs '("out" "debug"))
    (arguments
@@ -128,6 +128,7 @@
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages pdf)
  #:use-module (gnu packages perl)
@@ -2529,7 +2529,7 @@ forgotten when the session ends.")
 (define-public evince
  (package
    (name "evince")
-    (version "48.4")
+    (version "48.1")
    (source
     (origin
       (method url-fetch)
@@ -2537,7 +2537,7 @@ forgotten when the session ends.")
                           (version-major version) "/"
                           "evince-" version ".tar.xz"))
       (sha256
-        (base32 "0s46prlb55ghnz136ra8whmrirydmz08lzjrrpa3arl8cb3cb5pj"))))
+        (base32 "047s8d4qh9jijk1kp4kfzy4afwwcd0kr11a8j1dkypd0ldprm2vx"))))
    (build-system meson-build-system)
    (arguments
     `(#:glib-or-gtk? #t
@@ -2,9 +2,8 @@
 ;;; Copyright © 2023 JOULAUD François <Francois.JOULAUD@radiofrance.com>
 ;;; Copyright © 2025 Maxim Cournoyer <maxim@guixotic.coop>
 ;;; Copyright © 2025 Tomas Volf <~@wolfsden.cz>
-;;; Copyright © 2025-2026 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2025 jgart <jgart@dismail.de>
-;;; Copyright © 2026 Ankit Gadiya <git@argp.in>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -49,7 +48,7 @@
 (define-public go-chroma
  (package
    (name "go-chroma")
-    (version "2.24.1")
+    (version "2.20.0")
    (source
     (origin
       (method git-fetch)
@@ -58,7 +57,7 @@
              (commit (string-append "v" version ))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0kww0yhwqzzgl8n3alislf0136rk7kh507bbvr32a30wmk5dzi81"))))
+        (base32 "05w4hnfcxqdlsz7mkc0m3jbp1aj67wzyhq5jh8ldfgnyjnlafia3"))))
    (build-system go-build-system)
    (arguments
     (list
@@ -84,16 +83,17 @@ translators for Pygments lexers and styles.")
 (define-public go-fxlint
  (package
    (name "go-fxlint")
-    (version "1.24.0")
+    (version "0.0.0-20251227140935-d5da5b04ac90")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/uber-go/fx")
-              (commit (string-append "v" version ))))
+              (commit (go-version->git-ref version
+                                           #:subdir "tools"))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0iifq4gjd873l444qh32x2zzsz2yinrvpjsdfphxsfk1h0cyk4q9"))))
+        (base32 "0yw9x95v82dcxh0zf13inz8c3q7p2hmzqzgja360b1yifi01rvrc"))))
    (build-system go-build-system)
    (arguments
     (list
@@ -115,7 +115,7 @@ that handle none of the event types.")
 (define-public go-jsonnet
  (package
    (name "go-jsonnet")
-    (version "0.22.0")
+    (version "0.21.0")
    (source
     (origin
       (method git-fetch)
@@ -124,7 +124,7 @@ that handle none of the event types.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1c7h14rvavgadvbsyfa9j4rchsgxb5j363f53rhcvghvmblzddiv"))))
+        (base32 "0d05f16qxabfhaj0l3da3x7zl5g8jbvkcyn39bidd2a278sb3p97"))))
    (build-system go-build-system)
    (arguments
     (list
@@ -276,20 +276,19 @@ import of a 3rd party package at runtime).")
    (name "gopls")
    ;; XXX: Starting from 0.14.0 gppls needs golang.org/x/telemetry, which
    ;; needs to be discussed if it may be included in Guix.
-    (version "0.22.0")
+    (version "0.19.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
-              (url "https://go.googlesource.com/tools")
-              (commit (go-version->git-ref version #:subdir "gopls"))))
+             (url "https://go.googlesource.com/tools")
+             (commit (go-version->git-ref version #:subdir "gopls"))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0n5ixvk6c8hww5z9lvf74dx6p4j573bq3ssvp77n6033l0fcbv94"))))
+        (base32 "1dihdw4nzp21hlbwxf6qyhyfgavi1a55lmlyk36czd85v0jcp6a0"))))
    (build-system go-build-system)
    (arguments
     (list
-      #:go go-1.26
      #:install-source? #f
      #:import-path "golang.org/x/tools/gopls"
      #:unpack-path "golang.org/x/tools"
@@ -312,13 +311,11 @@ import of a 3rd party package at runtime).")
              (setenv "GODEBUG" "gotypesalias=1"))))))
    (native-inputs
     (list go-github-com-fatih-gomodifytags
-           go-github-com-fsnotify-fsnotify
           go-github-com-google-go-cmp
-           go-github-com-google-jsonschema-go
           go-github-com-jba-templatecheck
-           go-github-com-modelcontextprotocol-go-sdk
           go-golang-org-x-mod
           go-golang-org-x-sync
+           go-golang-org-x-sys
           go-golang-org-x-telemetry
           go-golang-org-x-text
           go-golang-org-x-tools
@@ -150,31 +150,6 @@ the @code{c2go} tool at
@url{https://github.com/andybalholm/c2go,https://github.com/andybalholm/c2go}.")
    (license license:expat)))

-(define-public go-github-com-blakesmith-ar
-  (package
-    (name "go-github-com-blakesmith-ar")
-    (version "0.0.0-20190502131153-809d4375e1fb")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/blakesmith/ar")
-              (commit (go-version->git-ref version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "00fxkc04b9cb53xxzw5gdqqpwlqv9n5kk0yn2lb5w4rgj5gm8ph1"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/blakesmith/ar"
-      #:test-flags #~(list "-vet=off")))
-    (home-page "https://github.com/blakesmith/ar")
-    (synopsis "Golang archive file reader")
-    (description
-     "This package provides a Golang file reader for archive files generated
-with @code{ar}.")
-    (license license:expat)))
-
 (define-public go-github-com-bodgit-sevenzip
  (package
    (name "go-github-com-bodgit-sevenzip")
@@ -246,31 +221,6 @@ blocks allowing it to only read the compressed blocks required.")
    (license (list license:bsd-3
                   license:expat))))

-(define-public go-github-com-cavaliergopher-cpio
-  (package
-    (name "go-github-com-cavaliergopher-cpio")
-    (version "1.0.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/cavaliergopher/cpio")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0b1ix8z9kwfpwqi0q08ivcfcimlqk781jbzbfw7qbqavh702w3m2"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/cavaliergopher/cpio"))
-    (home-page "https://github.com/cavaliergopher/cpio")
-    (synopsis "Readers and writers for CPIO archives")
-    (description
-     "This package provides readers and writers for CPIO archives.  Currently,
-only the SVR4 (New ASCII) format is supported, both with and without
-checksums.")
-    (license license:bsd-3)))
-
 (define-public go-github-com-containerd-stargz-snapshotter-estargz
  (package
    (name "go-github-com-containerd-stargz-snapshotter-estargz")
@@ -435,37 +385,6 @@ Implements the XFLATE format, an random-access extension to DEFLATE.
 compression format.")
    (license license:bsd-3)))

-(define-public go-github-com-google-rpmpack
-  (package
-    (name "go-github-com-google-rpmpack")
-    (version "0.7.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/google/rpmpack")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "17h2s1g191cvbs16fnclkpb42d9mx6mdmhd04kxzv8bss7m59pr4"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/google/rpmpack"))
-    (native-inputs
-     (list go-github-com-google-go-cmp))
-    (propagated-inputs
-     (list go-github-com-cavaliergopher-cpio
-           go-github-com-klauspost-compress
-           go-github-com-klauspost-pgzip
-           go-github-com-ulikunitz-xz))
-    (home-page "https://github.com/google/rpmpack")
-    (synopsis "Pack files to rpm files")
-    (description
-     "Package rpmpack packs files to rpm files.  It is designed to be simple
-to use and deploy, not requiring any filesystem access to create rpm files.")
-    (license license:asl2.0)))
-
 (define-public go-github-com-hhrutter-lzw
  (package
    (name "go-github-com-hhrutter-lzw")
@@ -965,40 +884,6 @@ format's \"Extra Fields\".  The intention is to eventually support and provide
 a low-level API for the majority of PKWARE's and Info-ZIP's extra fields.")
    (license license:expat)))

-(define-public go-github-com-sassoftware-go-rpmutils
-  (package
-    (name "go-github-com-sassoftware-go-rpmutils")
-    (version "0.4.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/sassoftware/go-rpmutils")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "06ymwjn6xvc4cpxcsh5achwgma4i075ikbzq8jm143m0pck4pmfi"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/sassoftware/go-rpmutils"))
-    (native-inputs
-     (list go-github-com-stretchr-testify
-           go-go-uber-org-goleak))
-    (propagated-inputs
-     (list go-github-com-datadog-zstd
-           go-github-com-klauspost-compress
-           go-github-com-protonmail-go-crypto
-           go-github-com-ulikunitz-xz
-           go-github-com-xi2-xz
-           go-golang-org-x-sys))
-    (home-page "https://github.com/sassoftware/go-rpmutils")
-    (synopsis "Parse RPM packages in Golang")
-    (description
-     "This package provides some Golang interfaces for handling RPM packages,
-such extracting RPM header and CPIO content.")
-    (license license:asl2.0)))
-
 (define-public go-github-com-sorairolake-lzip-go
  (package
    (name "go-github-com-sorairolake-lzip-go")
@@ -607,30 +607,6 @@ Actions} locally.")
 It's a static checker for GitHub Actions workflow files.")
    (license license:expat)))

-(define-public go-gitlab-com-digitalxero-go-conventional-commit
-  (package
-    (name "go-gitlab-com-digitalxero-go-conventional-commit")
-    (version "1.0.7")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://gitlab.com/digitalxero/go-conventional-commit.git")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1191j3k9ma5sv8w2zsw8gb1407561zll0ca8hwy0dja6s0b3z0xy"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "gitlab.com/digitalxero/go-conventional-commit"))
-    (home-page "https://gitlab.com/digitalxero/go-conventional-commit")
-    (synopsis "Go parser for conventional commits")
-    (description
-     "This package provides a Go parser for conventional-commit messages
-@url{https://www.conventionalcommits.org/}.")
-    (license license:expat)))
-
 (define-public go-github-com-xanzy-go-gitlab
  (package
    (name "go-github-com-xanzy-go-gitlab")
@@ -10796,33 +10796,6 @@ dhcpv6 and dhcpv4
@end itemize")
    (license license:bsd-3)))

-(define-public go-github-com-invopop-jsonschema
-  (package
-    (name "go-github-com-invopop-jsonschema")
-    (version "0.14.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/invopop/jsonschema")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0y881agfaycn5l5qn2y2jmiskchi0cvn5v602hna4ljy9rv5jxw2"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/invopop/jsonschema"))
-    (native-inputs
-     (list go-github-com-stretchr-testify))
-    (propagated-inputs
-     (list go-github-com-pb33f-ordered-map-v2))
-    (home-page "https://github.com/invopop/jsonschema")
-    (synopsis "Go JSON Schema Reflection")
-    (description
-     "Package jsonschema uses reflection to generate JSON Schemas from Go types.")
-    (license license:expat)))
-
 (define-public go-github-com-ipfs-go-cid
  (package
    (name "go-github-com-ipfs-go-cid")
@@ -17012,11 +16985,9 @@ kinds of referrer URLs (search, social, ...).")
     (list
      #:skip-build? #t
      #:import-path "github.com/sigstore/rekor"
-      #:embed-files #~(list ".*\\.json")
-      ;; ;; XXX: Remove when all inputs are packaged.
+      ;; XXX: Remove when all inputs are packaged.
      #:test-subdirs
-      #~(list "pkg/client"
-              "pkg/events/newentry"
+      #~(list "pkg/events/newentry"
              "pkg/indexstorage/mysql"
              "pkg/pki/minisign"
              "pkg/pki/pgp"
@@ -17024,10 +16995,7 @@ kinds of referrer URLs (search, social, ...).")
              "pkg/pki/tuf"
              "pkg/pki/x509"
              "pkg/pubsub/gcp"
-              "pkg/tle"
-              "pkg/types"
-              "pkg/util"
-              "pkg/verify")))
+              "pkg/util")))
    (native-inputs
     (list go-github-com-asaskevich-govalidator
           go-github-com-data-dog-go-sqlmock
@@ -17055,7 +17023,6 @@ kinds of referrer URLs (search, social, ...).")
           go-github-com-go-openapi-validate
           go-github-com-go-sql-driver-mysql
           go-github-com-go-viper-mapstructure-v2
-           go-github-com-google-rpmpack
           go-github-com-google-trillian
           go-github-com-grpc-ecosystem-go-grpc-middleware
           go-github-com-hashicorp-go-cleanhttp
@@ -17099,6 +17066,7 @@ kinds of referrer URLs (search, social, ...).")
           ;; go-github-com-adamkorcz-go-fuzz-headers-1
           ;; go-github-com-cavaliercoder-go-rpm
           ;; go-github-com-go-redis-redismock-v9
+           ;; go-github-com-google-rpmpack
           ;; go-github-com-sassoftware-relic
           ;; go-github-com-sassoftware-relic-v7
           ;; go-go-step-sm-crypto
@@ -18581,31 +18549,6 @@ Tailscale for access control.")
 Tailscale.")
    (license license:bsd-3)))

-(define-public go-github-com-tcnksm-go-httpstat
-  (package
-    (name "go-github-com-tcnksm-go-httpstat")
-    (version "0.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/tcnksm/go-httpstat")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "18jn40ra97waxx1mf23pkh6rq46y0nqd7vi3zcx9cwc39zqaf9bc"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:tests? #f ;Tests require network connection
-      #:import-path "github.com/tcnksm/go-httpstat"))
-    (home-page "https://github.com/tcnksm/go-httpstat")
-    (synopsis "Trace HTTP latency information in Go")
-    (description
-     "Package httpstat traces HTTP latency infomation, such as DNSLookup and
-TCP Connection, on any Golang HTTP request with no big code modification.")
-    (license license:expat)))
-
 (define-public go-github-com-tdewolff-minify-v2
  (package
    (name "go-github-com-tdewolff-minify-v2")
@@ -19137,30 +19080,6 @@ caching protocol.  It provides support to programmatically store and retrieve
 build caches, instead of relying on the standard actions/cache YAML step.")
    (license license:expat)))

-(define-public go-github-com-toqueteos-webbrowser
-  (package
-    (name "go-github-com-toqueteos-webbrowser")
-    (version "1.2.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/toqueteos/webbrowser")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0bnn02zcfc9xkxc2qvv4q6wy5sipcwc0hwmx7hdhvv3lsw177flw"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/toqueteos/webbrowser"))
-    (home-page "https://github.com/toqueteos/webbrowser")
-    (synopsis "Simple API for opening web pages")
-    (description
-     "This package provides a simple API for opening web pages on your default
-browser.")
-    (license license:expat)))
-
 (define-public go-github-com-transparency-dev-tessera
  (package
    (name "go-github-com-transparency-dev-tessera")
@@ -114,7 +114,6 @@
  #:use-module (gnu packages golang-compression)
  #:use-module (gnu packages golang-crypto)
  #:use-module (gnu packages golang-maths)
-  #:use-module (gnu packages golang-vcs)
  #:use-module (gnu packages golang-web)
  #:use-module (gnu packages graph)
  #:use-module (gnu packages imagemagick)
@@ -1762,30 +1761,6 @@ strings for a safe use as command line arguments in the most common POSIX
 shells.")
    (license license:expat)))

-(define-public go-github-com-aleksi-pointer
-  (package
-    (name "go-github-com-aleksi-pointer")
-    (version "1.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/AlekSi/pointer")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0rncmanv62wwy7ihvjhvb695mkvy4kdzhgnn90zygs9yrfzzk0wk"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/AlekSi/pointer"))
-    (home-page "https://github.com/AlekSi/pointer")
-    (synopsis "Helper Go library to convert between pointers and values")
-    (description
-     "This package provides helpers to convert between pointers and values of
-built-in and, with generics, of any types.")
-    (license license:expat)))
-
 (define-public go-github-com-alexflint-go-filemutex
  (package
    (name "go-github-com-alexflint-go-filemutex")
@@ -4434,29 +4409,6 @@ information for Golang.")
 variables into structs.")
    (license license:expat)))

-(define-public go-github-com-caarlos0-go-version
-  (package
-    (name "go-github-com-caarlos0-go-version")
-    (version "0.2.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/caarlos0/go-version")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0kp78am3yzffz8r70f1skq0m2vms0wk37f76hqbfg1r29hay1ban"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/caarlos0/go-version"))
-    (home-page "https://github.com/caarlos0/go-version")
-    (synopsis "Fetch Go module version")
-    (description
-     "Package goversion provides utilities to get the Go module version information.")
-    (license license:expat)))
-
 (define-public go-github-com-calebcase-tmpfile
  (package
    (name "go-github-com-calebcase-tmpfile")
@@ -4509,36 +4461,6 @@ color palette} for Go applications.  Catppuccin is a community-driven pastel
 theme with four flavors: Latte, Frappe, Macchiato, and Mocha.")
    (license license:expat)))

-(define-public go-github-com-ccojocar-zxcvbn-go
-  (package
-    (name "go-github-com-ccojocar-zxcvbn-go")
-    (version "1.0.4")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/ccojocar/zxcvbn-go")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0dlrd6afpfwnpj6cbbvjhwbf33ldr0nzffl8p43jrmn62mwf7cn7"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/ccojocar/zxcvbn-go"))
-    (native-inputs
-     (list go-github-com-stretchr-testify))
-    (home-page "https://github.com/ccojocar/zxcvbn-go")
-    (synopsis "Password-strength generator in Go")
-    (description
-     "This package provides a password strength generators written in Golang.
-It attempts to give sound password advice through pattern matching and
-conservative entropy calculations.  It finds 10k common passwords, common
-American names and surnames, common English words, and common patterns like
-dates, repeats (aaa), sequences (abcd), and QWERTY patterns. It's an active
-fork of @url{https://github.com/nbutton23/zxcvbn-go}.")
-    (license license:expat)))
-
 (define-public go-github-com-cention-sany-utf7
  (package
    (name "go-github-com-cention-sany-utf7")
@@ -11804,33 +11726,6 @@ native Go structure.")
    (description "Package yaml implements YAML support for the Go language.")
    (license license:asl2.0)))

-(define-public go-github-com-gobuffalo-flect
-  (package
-    (name "go-github-com-gobuffalo-flect")
-    (version "1.0.3")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/gobuffalo/flect")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0lyb1876byv9q52y6dlq17aahwl108mhp67cmxykckjpxxykb442"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/gobuffalo/flect"))
-    (native-inputs
-     (list go-github-com-stretchr-testify))
-    (home-page "https://github.com/gobuffalo/flect")
-    (synopsis "Inflection engine for Golang")
-    (description
-     "This package provides a new inflection engine to replace
-@url{https://github.com/markbates/inflect,} designed to be more modular,
-readable, and easier to fix issues on than the original.")
-    (license license:expat)))
-
 (define-public go-github-com-gobwas-glob
  (package
    (name "go-github-com-gobwas-glob")
@@ -12674,41 +12569,6 @@ color (24-bit, RGB)
@end itemize")
    (license license:expat)))

-(define-public go-github-com-goreleaser-chglog
-  (package
-    (name "go-github-com-goreleaser-chglog")
-    (version "0.7.4")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/goreleaser/chglog")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "09ni4y644zhp3bf9nwy9qc9wkxrn2hla6nczg3zpn0ls8qaxjd40"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/goreleaser/chglog"))
-    (native-inputs
-     (list go-github-com-go-git-go-billy-v5
-	   go-github-com-google-go-cmp
-           go-github-com-smartystreets-goconvey
-	   go-github-com-spf13-cobra
-           go-github-com-spf13-viper))
-    (propagated-inputs
-     (list go-github-com-go-git-go-git-v5
-           go-github-com-masterminds-semver-v3
-           go-github-com-masterminds-sprig-v3
-           go-gitlab-com-digitalxero-go-conventional-commit
-           go-go-yaml-in-yaml-v3))
-    (home-page "https://github.com/goreleaser/chglog")
-    (synopsis "Changelog management Go library")
-    (description
-     "This package provides Go functions to manage changelogs.")
-    (license license:expat)))
-
 (define-public go-github-com-goreleaser-fileglob
  (package
    (name "go-github-com-goreleaser-fileglob")
@@ -12739,66 +12599,6 @@ underneath and returns only matching files or directories, depending on the
 configuration.")
    (license license:expat)))

-(define-public go-github-com-goreleaser-nfpm-v2
-  (package
-    (name "go-github-com-goreleaser-nfpm-v2")
-    (version "2.44.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/goreleaser/nfpm")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "17dmzkvy3ihjjaxi10l9xc1mcg9vmlr2v1xc4a361fa22aqigz0v"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:go go-1.25
-      #:import-path "github.com/goreleaser/nfpm/v2"
-      #:unpack-path "github.com/goreleaser/nfpm/v2"
-      ;; Tests fail due to read-only filesystem when trying to manipulate mode
-      ;; of the files.
-      #:test-flags
-      #~(list "-skip" "TestPrepareForPackager|TestDeepPathsWithGlobAndUmask")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'fix-tests
-            (lambda* (#:key unpack-path #:allow-other-keys)
-              (with-directory-excursion (string-append "src/" unpack-path)
-                (substitute*  "rpm/rpm_test.go"
-                  (("/bin/bash") (which "bash")))))))))
-    (native-inputs
-     (list go-github-com-caarlos0-go-version
-           go-github-com-invopop-jsonschema
-           go-github-com-muesli-mango-cobra
-           go-github-com-muesli-roff
-           go-github-com-sassoftware-go-rpmutils
-           go-github-com-stretchr-testify))
-    (propagated-inputs
-     (list go-dario-cat-mergo
-           go-github-com-aleksi-pointer
-           go-github-com-blakesmith-ar
-           go-github-com-google-rpmpack
-           go-github-com-goreleaser-chglog
-           go-github-com-goreleaser-fileglob
-           go-github-com-klauspost-compress
-           go-github-com-klauspost-pgzip
-           go-github-com-masterminds-semver-v3
-           go-github-com-protonmail-go-crypto
-           go-github-com-protonmail-gopenpgp-v2
-           go-github-com-spf13-cobra
-           go-github-com-ulikunitz-xz
-           go-gopkg-in-yaml-v3))
-    (home-page "https://github.com/goreleaser/nfpm")
-    (synopsis "Go library to package programs in various Linux formats")
-    (description
-     "nFPM is Not FPM -- provides ways to package programs in popular Linux
-packaging formats, such as @code{deb}, @code{rpm}, @code{apk}, @code{ipk} and
-Arch.")
-    (license license:expat)))
-
 (define-public go-github-com-gorhill-cronexpr
  (package
    (name "go-github-com-gorhill-cronexpr")
@@ -20720,90 +20520,6 @@ for any given struct and a set of its potential member values.  This can be
 used to generate extensive test matrixes among other things.")
    (license license:expat)))

-(define-public go-github-com-muesli-mango
-  (package
-    (name "go-github-com-muesli-mango")
-    (version "0.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/muesli/mango")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "16d0sga6cbdxzlqkibcgw0civkw11fpkcjpgv21i0q5j9mjbsjw4"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/muesli/mango"))
-    (propagated-inputs
-     (list go-github-com-muesli-roff))
-    (home-page "https://github.com/muesli/mango")
-    (synopsis "Golang man-page generator")
-    (description
-     "This package provides a man-page generator for the Go flag, pflag, cobra, coral,
-and kong packages.  It extracts commands, flags, and arguments from the target
-program and enables it to self-document.")
-    (license license:expat)))
-
-(define-public go-github-com-muesli-mango-cobra
-  (package
-    (name "go-github-com-muesli-mango-cobra")
-    (version "1.3.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/muesli/mango-cobra")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "11vvm3f2mq8yaqbfrjbzdcyvkn9f75rp4kygxyvqwc5jsw1kdwal"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/muesli/mango-cobra"))
-    (propagated-inputs
-     (list go-github-com-muesli-mango
-           go-github-com-muesli-mango-pflag
-           go-github-com-muesli-roff
-           go-github-com-spf13-cobra))
-    (home-page "https://github.com/muesli/mango-cobra")
-    (synopsis "Cobra adapter for mango")
-    (description
-     "This package provides a cobra adapter for the
-@url{https://github.com/muesli/mango,mango} man-page generator.")
-    (license license:expat)))
-
-(define-public go-github-com-muesli-mango-pflag
-  (package
-    (name "go-github-com-muesli-mango-pflag")
-    (version "0.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/muesli/mango-pflag")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1k4m88i9shs36a8n86k3a1vlxmdf5vwavkih2f2j3xj718hnhpw0"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/muesli/mango-pflag"))
-    (propagated-inputs
-     (list go-github-com-muesli-mango
-           go-github-com-muesli-roff
-           go-github-com-spf13-pflag))
-    (home-page "https://github.com/muesli/mango-pflag")
-    (synopsis "Pflag adapter for mango")
-    (description
-     "This package provides a pflag adapter for the
-@url{https://github.com/muesli/mango, mango} man-page generator.")
-    (license license:expat)))
-
 (define-public go-github-com-muesli-reflow
  (package
    (name "go-github-com-muesli-reflow")
@@ -20831,32 +20547,6 @@ program and enables it to self-document.")
 helping you to transform blocks of text.")
    (license license:expat)))

-(define-public go-github-com-muesli-roff
-  (package
-    (name "go-github-com-muesli-roff")
-    (version "0.1.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/muesli/roff")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0l263rqwq2ccr1lpamsvs48dddsr70xim8mv6rsj2x9y3prcq3yh"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/muesli/roff"
-      ;; Expected title heading, got:
-      ;; .TH TITLE 1 "2026-05-22" "Title" "A short description"
-      #:test-flags #~(list "-skip" "TestTitleHeading")))
-    (home-page "https://github.com/muesli/roff")
-    (synopsis "Write roff documents in Go")
-    (description "This package provides tools to write @code{roff}
-documents in Golang.")
-    (license license:expat)))
-
 (define-public go-github-com-muesli-termenv
  (package
    (name "go-github-com-muesli-termenv")
@@ -22816,36 +22506,6 @@ expiration times, it doesn't need to serialize or transmit its contents over
 the network.")
    (license license:expat)))

-(define-public go-github-com-pb33f-ordered-map-v2
-  (package
-    (name "go-github-com-pb33f-ordered-map-v2")
-    (version "2.3.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/pb33f/ordered-map")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1k4r1rvlziddaszm1jvgz27nkrk1jfka0zik16f4b3gmhdnmd9vc"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/pb33f/ordered-map/v2"))
-    (native-inputs
-     (list go-github-com-stretchr-testify))
-    (propagated-inputs
-     (list go-github-com-bahlo-generic-list-go
-           go-github-com-buger-jsonparser
-           go-go-yaml-in-yaml-v4))
-    (home-page "https://github.com/pb33f/ordered-map")
-    (synopsis "Ordered maps in Golang")
-    (description
-     "This package provides a Golang implementation of an ordered map, which
-is a map that also keeps track of the order in which keys were inserted.")
-    (license license:asl2.0)))
-
 (define-public go-github-com-pbnjay-memory
  (let ((commit "7b4eea64cf580186c0eceb10dc94ba3a098af46c")
        (revision "2"))
@@ -33977,22 +33637,6 @@ library.")
 ;;; Executables:
 ;;;

-(define-public chglog
-  (package/inherit go-github-com-goreleaser-chglog
-    (name "chglog")
-    (arguments
-     (substitute-keyword-arguments arguments
-       ((#:tests? _ #t) #f)
-       ((#:install-source? _ #t) #f)
-       ((#:import-path _) "github.com/goreleaser/chglog/cmd/chglog")
-       ((#:unpack-path _ "") "github.com/goreleaser/chglog")))
-    (native-inputs
-     (append
-      (package-native-inputs go-github-com-goreleaser-chglog)
-      (package-propagated-inputs go-github-com-goreleaser-chglog)))
-    (inputs '())
-    (propagated-inputs '())))
-
 (define-public containers-storage
  (package/inherit go-github-com-containers-storage
    (name "containers-storage")
@@ -34533,22 +34177,6 @@ various modes for analyzing and transforming YAML data.")))
    (propagated-inputs '())
    (inputs '())))

-(define-public nfpm
-  (package/inherit go-github-com-goreleaser-nfpm-v2
-    (name "nfpm")
-    (arguments
-     (substitute-keyword-arguments arguments
-       ((#:import-path _) "github.com/goreleaser/nfpm/v2/cmd/nfpm")
-       ((#:install-source? _ #t) #f)
-       ((#:tests? _ #t) #f)
-       ((#:unpack-path _ "") "github.com/goreleaser/nfpm/v2")))
-    (native-inputs
-     (append
-      (package-native-inputs go-github-com-goreleaser-nfpm-v2)
-      (package-propagated-inputs go-github-com-goreleaser-nfpm-v2)))
-    (inputs '())
-    (propagated-inputs '())))
-
 (define-public oci-runtime-tool
  (package/inherit go-github-com-opencontainers-runtime-tools
    (name "oci-runtime-tool")
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017-2026 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017-2025 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018, 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2021, 2022, 2024 Efraim Flashner <efraim@flashner.co.il>
@@ -227,7 +227,7 @@ more.")
   (package
     (inherit igraph)
     (name "igraph")
-     (version "1.0.1")
+     (version "0.10.15")
     (source
      (origin
        (inherit (package-source igraph))
@@ -239,39 +239,7 @@ more.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-          "01mynhbl2ph0gkc0zr5klwqvczwcimfs2kdn6didwg4k8gsrcxlr"))
-        (modules '((guix build utils)
-                   (ice-9 ftw)
-                   (srfi srfi-26)))
-        ;; We need the vendored versions of qhull and cxsparse.
-        (snippet '(begin
-                    (delete-file-recursively "src/isomorphism/bliss")
-                    (substitute* '("src/CMakeLists.txt"
-                                   "etc/cmake/benchmark_helpers.cmake")
-                      ;; Remove extraneous bundling related variables.
-                      ((".*_IS_VENDORED.*") "")
-                      ((".*add_sub.*isomorphism/bliss.*") "")
-                      (("(.*TARGETS.*)bliss(.*)pcg(.*)"
-                        _ part1 part2 part3)
-                       (string-append part1 part2 part3))
-                      ((" pcg ") " pcg_random "))))))
-     (arguments
-      (substitute-keyword-arguments (package-arguments igraph)
-        ((#:phases phases '%standard-phases)
-         #~(modify-phases #$phases
-             ;; We have to use the bundled version because it has been
-             ;; modified from upstream.
-             (delete 'patch-suitesparse)))
-        ((#:configure-flags flags)
-         #~(list "-DBUILD_SHARED_LIBS=ON"
-                 "-DIGRAPH_INFOMAP_SUPPORT=OFF"
-                 "-DCMAKE_C_FLAGS=-Wno-error=incompatible-pointer-types"
-                 ;; Use the same integer width as suitesparse-cxsparse, which
-                 ;; uses int64_t in SuiteSparse v6.0.0 and later.
-                 "-DIGRAPH_INTEGER_SIZE=64"))))
-     (inputs
-      (modify-inputs (package-inputs igraph)
-        (delete "suitesparse-cxsparse"))))))
+          "0z9jqvl65j4z6brrjlfyykba2bs10az6dx6m8g41snlfnx21a82d")))))))

 (define-public python-igraph
  (package
@@ -111,6 +111,7 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mp3)
  #:use-module (gnu packages multiprecision)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages opencl)
  #:use-module (gnu packages oneapi)
  #:use-module (gnu packages pciutils)
@@ -997,17 +998,24 @@ baking tools to produce normal maps.")
                   (string-append "-DLLVM_BC_GENERATOR="
                                  #$(this-package-native-input "clang")
                                  "/bin/clang++"))
-           #:test-exclude (string-join
-                           (list
-                            "osl-imageio" ; file does not exist
-                            "osl-imageio.opt" ; file does not exist
-                            "osl-imageio.opt.rs_bitcode" ; file does not exist
-                            "texture-udim"    ; file does not exist
-                            "texture-udim.opt" ; file does not exist
-                            "texture-udim.opt.rs_bitcode" ; file does not exist
-                            "example-deformer" ; could not find OSLConfig
-                            "python-oslquery") ; no module oslquery
-                           "|")))
+           #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke
+                      "ctest" "--exclude-regex"
+                      (string-join
+                       (list
+                        "osl-imageio" ; file does not exist
+                        "osl-imageio.opt" ; file does not exist
+                        "osl-imageio.opt.rs_bitcode" ; file does not exist
+                        "texture-udim"    ; file does not exist
+                        "texture-udim.opt" ; file does not exist
+                        "texture-udim.opt.rs_bitcode" ; file does not exist
+                        "example-deformer" ; could not find OSLConfig
+                        "python-oslquery") ; no module oslquery
+                       "|"))))))))
    (native-inputs
     (list bison
           clang
@@ -1339,19 +1347,6 @@ basic geometries.")
       (file-name (git-file-name name version))
       (sha256
        (base32 "0gfgzwm5s50caj5s6l7irgmlifpmypd0fnm6ckzli1fdziwjgdwi"))))
-    (arguments
-     ;; https://gitlab.com/inkscape/lib2geom/-/work_items/82
-     (if (or (target-aarch64?)
-             (target-riscv64?)
-             (target-ppc64le?))
-         (substitute-keyword-arguments arguments
-           ((#:phases phases #~%standard-phases)
-            #~(modify-phases #$phases
-                (add-after 'unpack 'disable-polynomial-test
-                  (lambda _
-                    (substitute* "tests/CMakeLists.txt"
-                      (("polynomial-test") "")))))))
-         arguments))
    (properties '((hidden? . #f)))))

 (define-public pstoedit
@@ -2397,71 +2392,6 @@ and engineering community.")
 (define-deprecated coin3D-4 coin3d)
 (export coin3D-4)

-(define-public skcms
-  ;; No tags are available.
-  (let ((commit "a7a3b15f06355692d86a3b8373c579a521598f4c")
-        (revision "0"))
-    (package
-      (name "skcms")
-      (version (git-version "0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://skia.googlesource.com/skcms")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "0ylrsm7cinw59ilgbffazbgifax81kkya5cxq8q8wybnxx6z6ps6"))))
-      (build-system gnu-build-system)
-      (arguments
-       (list
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-after 'unpack 'patch-includes
-              (lambda _
-                (substitute* "skcms.h"
-                  (("src\\/skcms_public\\.h") "skcms/skcms_public.h"))))
-            (delete 'configure)
-            (replace 'build
-              (lambda _
-                ;; Some CPUs may not support these features.
-                (let ((cflags (append '("-DSKCMS_DISABLE_HSW=1"
-                                        "-DSKCMS_DISABLE_SKX=1")
-                                      (if #$(target-mingw?)
-                                          '("-DSKCMS_HAS_MUSTTAIL=0")
-                                          '())))
-                      (ldflags '("-lstdc++")))
-                  (apply invoke #$(cc-for-target)
-                         `("-O2" "-g" "-fPIC" ,@cflags
-                           "skcms.cc"
-                           "src/skcms_TransformBaseline.cc"
-                           "src/skcms_TransformHsw.cc"
-                           "src/skcms_TransformSkx.cc"
-                           "-shared" ,@ldflags
-                           "-o" "libskcms.so"))
-                  (apply invoke #$(cc-for-target)
-                         `(,@cflags
-                           "tests.c" "test_only.c"
-                           "-Wl,-rpath=." "-L." "-lskcms" ,@ldflags
-                           "-o" "tests")))))
-            (replace 'check
-              (lambda* (#:key tests? #:allow-other-keys)
-                (when tests?
-                  (invoke "./tests"))))
-            (replace 'install
-              (lambda _
-                (install-file "libskcms.so" (string-append #$output "/lib"))
-                (install-file "skcms.h" (string-append #$output "/include"))
-                (install-file "src/skcms_public.h"
-                              (string-append #$output "/include/skcms")))))))
-      (native-inputs (list ninja))
-      (home-page "https://skia.org/")
-      (synopsis "Color management engine")
-      (description
-       "skcms is the color management engine.  It is a part of @code{skia}.")
-      (license license:bsd-3))))
-
 (define-public skia
  ;; Releases follow those of Chromium, about every 6 weeks.  The release
  ;; version can be found on this page:
@@ -341,7 +341,7 @@ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) $(srcdir)/predicates_init.c \
 (define-public xdot
  (package
    (name "xdot")
-    (version "1.6")
+    (version "1.4")
    (source
     (origin
       ;; PyPI tarball is missing some test files.
@@ -351,7 +351,7 @@ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) $(srcdir)/predicates_init.c \
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0gg54k6zhdviz17aa3harc82f7bx4mpwnj292q066dzamvr87svq"))))
+        (base32 "1l34ahvcz90j3j7aspp9wqvxpq10mzgq7l0sanrj142ihdnbahvy"))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -1173,8 +1173,7 @@ application suites.")
                     '("--no-suite=gsk-compare-gl"
                       "--no-suite=gsk-compare-cairo"
                       "--no-suite=gsk-compare-ngl"
-                       "--no-suite=gsk-compare-vulkan"
-                       "--no-suite=svg")
+                       "--no-suite=gsk-compare-vulkan")
                     '()))
      #:phases
      #~(modify-phases %standard-phases
@@ -529,17 +529,6 @@ without requiring the source code to be rewritten.")
 ;;; (security or else) and this deprecation could be removed.
 (define-deprecated/public-alias guile-3.0/fixed guile-3.0/pinned)

-(define-public guile-with-gmp
-  (package/inherit guile-3.0-latest
-    (name "guile-with-gmp")
-    (propagated-inputs
-      (modify-inputs propagated-inputs
-        (append gmp)))
-    (arguments
-     (substitute-keyword-arguments arguments
-       ((#:configure-flags flags #~'())
-        #~(delete "--enable-mini-gmp" #$flags))))))
-
 (define-public guile-3.0/pinned
  ;; A package of Guile that's rarely changed.  It is the one used in the
  ;; `base' module, and thus changing it entails a full rebuild.
@@ -64,17 +64,16 @@
 (define-public apply-refact
  (package
    (name "apply-refact")
-    (version "0.15.0.0")
+    (version "0.10.0.0")
    (source (origin
              (method url-fetch)
              (uri (hackage-uri "apply-refact" version))
              (sha256
               (base32
-                "0iny8ynxx46afbzjp14rvpd4sqk8c1p5883mbln53gmlxcm8zq53"))))
+                "129bf8n66kpwh5420rxprngg43bqr2agyd8q8d7l49k2rxsjl1fb"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "apply-refact")))
    (inputs (list ghc-refact
-                  ghc-data-default
                  ghc-exactprint
                  ghc-paths
                  ghc-extra
@@ -97,13 +96,13 @@ library.  It is primarily used with HLint's @code{--refactor} flag.")
 (define-public cabal-install
 (package
   (name "cabal-install")
-   (version "3.12.1.0")
-   (source
-    (origin
-      (method url-fetch)
-      (uri (hackage-uri "cabal-install" version))
-      (sha256
-       (base32 "1cmifq189i4x0r0yha3dl8nrzzfh92bnd2saak7dqvvjkkysqj38"))))
+   (version "3.6.2.0")
+   (source (origin
+             (method url-fetch)
+             (uri (hackage-uri "cabal-install" version))
+             (sha256
+              (base32
+               "0dihpm4h3xh13vnpvwflnb7v614qdvljycc6ffg5cvhwbwfrxyfw"))))
   (build-system haskell-build-system)
   (properties '((upstream-name . "cabal-install")))
   (inputs (list ghc-async
@@ -118,35 +117,13 @@ library.  It is primarily used with HLint's @code{--refactor} flag.")
                 ghc-tar
                 ghc-zlib
                 ghc-hackage-security
-                 ghc-open-browser
                 ghc-regex-base
                 ghc-regex-posix
-                 ghc-safe-exceptions
-                 ghc-semaphore-compat
                 ghc-resolv
                 ghc-lukko))
-   (native-inputs (list ghc-tasty
-                        ghc-tasty-golden
-                        ghc-tasty-quickcheck
-                        ghc-tasty-expected-failure
-                        ghc-tasty-hunit
-                        ghc-tree-diff
-                        ghc-quickcheck
-                        ghc-tasty
-                        ghc-tasty-hunit
-                        ghc-tasty
-                        ghc-tasty-hunit
-                        ghc-tagged
-                        ghc-tagged
-                        ghc-tasty
-                        ghc-tasty-expected-failure
-                        ghc-tasty-hunit
-                        ghc-tasty-quickcheck
-                        ghc-quickcheck
-                        ghc-pretty-show))
   (arguments
    `(#:cabal-revision ("2"
-                        "0fdzqdkg2vbyg0lnbk9bdskr2d23hwjpmnc7jnvpzkcmxmcvl99n")))
+                        "1kpgyfl5njxp4c8ax5ziag1bhqvph3h0pn660v3vpxalz8d1j6xv")))
   (home-page "https://www.haskell.org/cabal/")
   (synopsis "Command-line interface for Cabal and Hackage")
   (description
@@ -168,10 +145,11 @@ installation of Haskell libraries and programs.")
         "17wi7fma2qaqdm1hwgaam3fd140v9bpa8ky0wg708h1pqc5v2nbz"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "cpphs")))
-    (inputs (list ghc-polyparse))
+    (inputs
+     (list ghc-polyparse ghc-old-locale ghc-old-time))
    (arguments
-     `(#:cabal-revision ("2"
-                         "0vxav36p0kplp4dpd17i4cfzrsl3r437d840xwv83lf1bqp7mrxc")))
+     `(#:cabal-revision ("1"
+                         "1f8jzs8zdh4wwbcq8fy6qqxkv75ypnvsm4yzw49wpr3b9vpnzlha")))
    (home-page "https://projects.haskell.org/cpphs/")
    (synopsis "Liberalised re-implementation of cpp, the C pre-processor")
    (description "Cpphs is a re-implementation of the C pre-processor that is
@@ -291,18 +269,20 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
 (define-public ghcid
  (package
    (name "ghcid")
-    (version "0.8.9")
+    (version "0.8.7")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "ghcid" version))
       (sha256
-        (base32 "1dq8lc0dwzib8y21279q4j54cmm7lvx64b3hw2yiym1kzi9rrhj4"))))
+        (base32 "0yqc1pkfajnr56gnh43sbj50r7c3r41b2jfz07ivgl6phi4frjbq"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "ghcid")))
-    (inputs (list ghc-extra ghc-ansi-terminal ghc-cmdargs ghc-fsnotify
-                  ghc-terminal-size))
-    (native-inputs (list ghc-tasty ghc-tasty-hunit))
+    (inputs
+     (list ghc-extra ghc-ansi-terminal ghc-cmdargs ghc-fsnotify
+           ghc-terminal-size))
+    (native-inputs
+     (list ghc-tasty ghc-tasty-hunit))
    (home-page "https://github.com/ndmitchell/ghcid#readme")
    (synopsis "GHCi based bare bones IDE")
    (description
@@ -424,97 +404,95 @@ to @code{cabal repl}).")
                        (string-append bin "/git-remote-annex"))
               (symlink (string-append bin "/git-annex")
                        (string-append bin "/git-remote-tor-annex"))))))))
-    (inputs (list ghc-network-uri
-                  ghc-optparse-applicative
-                  ghc-uuid
-                  ghc-data-default
-                  ghc-case-insensitive
-                  ghc-random
-                  ghc-dlist
-                  ghc-unix-compat
-                  ghc-safesemaphore
-                  ghc-async
-                  ghc-disk-free-space
-                  ghc-ifelse
-                  ghc-monad-logger
-                  ghc-free
-                  ghc-utf8-string
-                  ghc-sandi
-                  ghc-monad-control
-                  ghc-bloomfilter
-                  ghc-edit-distance
-                  ghc-resourcet
-                  ghc-http-client
-                  ghc-http-client-tls
-                  ghc-http-types
-                  ghc-http-conduit
-                  ghc-http-client-restricted
-                  ghc-conduit
-                  ghc-old-locale
-                  ghc-persistent-sqlite
-                  ghc-persistent
-                  ghc-persistent-template
-                  ghc-unliftio-core
-                  ghc-microlens
-                  ghc-aeson
-                  ghc-vector
-                  ghc-tagsoup
-                  ghc-unordered-containers
-                  ghc-feed
-                  ghc-regex-tdfa
-                  ghc-socks
-                  ghc-byteable
-                  ghc-stm-chans
-                  ghc-securemem
-                  ghc-crypto-api
-                  ghc-memory
-                  ghc-split
-                  ghc-attoparsec
-                  ghc-concurrent-output
-                  ghc-unbounded-delays
-                  ghc-quickcheck
-                  ghc-tasty
-                  ghc-tasty-hunit
-                  ghc-tasty-quickcheck
-                  ghc-tasty-rerun
-                  ghc-ansi-terminal
-                  ghc-aws
-                  ghc-dav
-                  ghc-network
-                  ghc-network-bsd
-                  ghc-git-lfs
-                  ghc-clock
-                  ghc-crypton
-                  ghc-servant
-                  ghc-servant-server
-                  ghc-servant-client
-                  ghc-servant-client-core
-                  ghc-warp
-                  ghc-warp-tls
-                  ghc-os-string
-                  ghc-file-io
-                  ghc-mountpoints
-                  ghc-yesod
-                  ghc-yesod-static
-                  ghc-yesod-form
-                  ghc-yesod-core
-                  ghc-path-pieces
-                  ghc-wai
-                  ghc-wai-extra
-                  ghc-blaze-builder
-                  ghc-clientsession
-                  ghc-shakespeare
-                  ghc-hinotify
-                  ghc-dbus
-                  ghc-fdo-notify
-                  ghc-network-multicast
-                  ghc-network-info
-                  ghc-torrent
-                  ghc-magic
-                  ghc-criterion))
+    (inputs
+     (list curl
+           ghc-aeson
+           ghc-ansi-terminal
+           ghc-async
+           ghc-attoparsec
+           ghc-aws
+           ghc-bloomfilter
+           ghc-byteable
+           ghc-case-insensitive
+           ghc-clientsession
+           ghc-concurrent-output
+           ghc-conduit
+           ghc-connection
+           ghc-crypto-api
+           ghc-cryptonite
+           ghc-data-default
+           ghc-dav
+           ghc-dbus
+           ghc-disk-free-space
+           ghc-dlist
+           ghc-edit-distance
+           ghc-exceptions
+           ghc-fdo-notify
+           ghc-feed
+           ghc-filepath-bytestring
+           ghc-free
+           ghc-git-lfs
+           ghc-hinotify
+           ghc-http-client
+           ghc-http-client-tls
+           ghc-http-client-restricted
+           ghc-http-conduit
+           ghc-http-types
+           ghc-ifelse
+           ghc-magic
+           ghc-memory
+           ghc-microlens
+           ghc-monad-control
+           ghc-monad-logger
+           ghc-mountpoints
+           ghc-network
+           ghc-network-bsd
+           ghc-network-info
+           ghc-network-multicast
+           ghc-network-uri
+           ghc-old-locale
+           ghc-optparse-applicative
+           ghc-persistent
+           ghc-persistent-sqlite
+           ghc-persistent-template
+           ghc-quickcheck
+           ghc-random
+           ghc-regex-tdfa
+           ghc-resourcet
+           ghc-safesemaphore
+           ghc-sandi
+           ghc-securemem
+           ghc-servant-client
+           ghc-servant-server
+           ghc-socks
+           ghc-split
+           ghc-stm-chans
+           ghc-tagsoup
+           ghc-torrent
+           ghc-transformers
+           ghc-unbounded-delays
+           ghc-unix-compat
+           ghc-unliftio-core
+           ghc-unordered-containers
+           ghc-utf8-string
+           ghc-uuid
+           ghc-vector
+           ghc-wai
+           ghc-wai-extra
+           ghc-warp
+           ghc-warp-tls
+           ghc-yesod
+           ghc-yesod-core
+           ghc-yesod-form
+           ghc-yesod-static
+           lsof
+           rsync
+           xdg-utils))
    (propagated-inputs
     (list git))
-    (native-inputs (list ghc-filepath-bytestring))
+    (native-inputs
+     (list ghc-tasty ghc-tasty-hunit ghc-tasty-quickcheck ghc-tasty-rerun
+           perl))
    (home-page "https://git-annex.branchable.com/")
    (synopsis "Manage files with Git, without checking in their contents")
    (description "This package allows managing files with Git, without
@@ -535,13 +513,13 @@ used to keep a folder in sync between computers.")
 (define-public hlint
  (package
    (name "hlint")
-    (version "3.10")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hlint" version))
-       (sha256
-        (base32 "0dzy7spc45v88yplczhd3la464bhcbaihi619a45bd06ghrp55nr"))))
+    (version "3.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hlint" version))
+              (sha256
+               (base32
+                "0bkk03c9hacvfd73dk89g4r81b50g7pjgw5pavldali4qwss34cz"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hlint")))
    (inputs (list ghc-unordered-containers
@@ -558,10 +536,12 @@ used to keep a folder in sync between computers.")
                  ghc-aeson
                  ghc-deriving-aeson
                  ghc-filepattern
-                  ghc-lib-parser
                  ghc-lib-parser-ex
                  hscolour
                  ghc-yaml))
+    (arguments
+     `(#:cabal-revision ("1"
+                         "1rdaffg5n179yfcn5zjwjb0bki09qy13gz2ijky455y9pbaz8yz9")))
    (home-page "https://github.com/ndmitchell/hlint#readme")
    (synopsis "Suggest improvements for Haskell source code")
    (description
@@ -573,13 +553,13 @@ unwanted suggestions, and to add your own custom suggestions.")
 (define-public hoogle
  (package
    (name "hoogle")
-    (version "5.0.18.4")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hoogle" version))
-       (sha256
-        (base32 "08z32d87vqzhapb2vw21h25jb2g74csxlpvd8f54xl91k3ijs3wx"))))
+    (version "5.0.18.3")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hoogle" version))
+              (sha256
+               (base32
+                "0v6k75w0an9pqgb7a6cicnpf9rz77xd2lmxfbafc5l4f99jg83bn"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hoogle")))
    (inputs (list ghc-quickcheck
@@ -589,7 +569,7 @@ unwanted suggestions, and to add your own custom suggestions.")
                  ghc-cmdargs
                  ghc-conduit
                  ghc-conduit-extra
-                  ghc-crypton-connection
+                  ghc-connection
                  ghc-extra
                  ghc-foundation
                  ghc-old-locale
@@ -602,7 +582,6 @@ unwanted suggestions, and to add your own custom suggestions.")
                  ghc-mmap
                  ghc-process-extras
                  ghc-resourcet
-                  ghc-safe
                  ghc-storable-tuple
                  ghc-tar
                  ghc-uniplate
@@ -614,9 +593,6 @@ unwanted suggestions, and to add your own custom suggestions.")
                  ghc-warp-tls
                  ghc-zlib
                  ghc-semigroups))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "1129flhhb1992rijw46dclvmpqlylmbrzl4swsnk2knylx6jgw5a")))
    (home-page "https://hoogle.haskell.org/")
    (synopsis "Haskell API Search")
    (description
@@ -628,13 +604,14 @@ or by approximate type signature.")
 (define-public hscolour
  (package
    (name "hscolour")
-    (version "1.25")
+    (version "1.24.4")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "hscolour" version))
       (sha256
-        (base32 "0z679khnmb6as1zcdb44n9qjk7in32jpm4ldscpqg7jrapd31kjl"))))
+        (base32
+         "079jwph4bwllfp03yfr26s5zc6m6kw3nhb1cggrifh99haq34cr4"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hscolour")))
    (home-page "https://hackage.haskell.org/package/hscolour")
@@ -783,12 +760,12 @@ Wayland, and Linux console environments alike.")
                  ghc-text-zipper
                  ghc-timezone-olson
                  ghc-timezone-series
-                  ghc-unix-compat
+                  ghc-unix-compat-7
                  ghc-unordered-containers
                  ghc-utf8-string
                  ghc-uuid
                  ghc-vector
-                  ghc-vty
+                  ghc-vty-6
                  ghc-vty-crossplatform
                  ghc-word-wrap
                  ghc-xdg-basedir))
@@ -834,31 +811,20 @@ Wayland, and Linux console environments alike.")
 (define-public nixfmt
  (package
    (name "nixfmt")
-    (version "1.1.0")
+    (version "0.5.0")
    (source
     (origin
-       (method git-fetch)
-       (uri
-        (git-reference
-          (url "https://github.com/NixOS/nixfmt")
-          (commit (string-append "v" version))))
+       (method url-fetch)
+       (uri (hackage-uri "nixfmt" version))
       (sha256
-        (base32 "19sydkdw1579qmvzx0zq06s23bm6m6l9wp1kvsfhxawk8pkz2pc2"))
-       (snippet
-        #~(substitute* "nixfmt.cabal"
-            (("(megaparsec|filepath)  *[0-9<>=^&|. ]*" _ package)
-             package)))
-       (modules '((guix build utils)))))
+        (base32 "0rxi8zrd2xr72w673nvgnhb0g3r7rssc1ahlhz8rmdpc6c1a82wl"))))
    (build-system haskell-build-system)
-    (inputs (list ghc-megaparsec
-                  ghc-parser-combinators
-                  ghc-scientific
-                  ghc-pretty-simple
-                  ghc-cmdargs
-                  ghc-file-embed
-                  ghc-safe-exceptions))
-    (home-page "https://github.com/NixOS/nixfmt")
-    (synopsis "Official formatter for Nix code")
+    (properties '((upstream-name . "nixfmt")))
+    (inputs
+     (list ghc-megaparsec ghc-parser-combinators ghc-cmdargs
+           ghc-safe-exceptions))
+    (home-page "https://github.com/serokell/nixfmt")
+    (synopsis "Opinionated formatter for Nix")
    (description
     "Nixfmt is a formatter for Nix that ensures consistent and clear
 formatting by forgetting all existing formatting during parsing.")
@@ -988,7 +954,6 @@ too slow and you'll get wound up in the scroll and crushed.")
    (build-system haskell-build-system)
    (arguments
     (list #:haddock? #f ; TODO: Fails to build.
-           #:cabal-revision '("1" "1935jrzy1r3g9cc74b330fmxnz2i1j8hsdk9jnl557qgk6xjqzs7")
           #:phases
           #~(modify-phases %standard-phases
               (add-after 'build 'build-man-page
@@ -1028,13 +993,13 @@ advanced user's otherwise working script to fail under future circumstances.
 (define-public shelltestrunner
  (package
    (name "shelltestrunner")
-    (version "1.10")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "shelltestrunner" version))
-       (sha256
-        (base32 "1c6bjyxqa4mgnh3w4pqp6sbr5cf160n7jf9i1b4b9sdxzdjk7g87"))))
+    (version "1.9")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "shelltestrunner" version))
+              (sha256
+               (base32
+                "1a5kzqbwg6990249ypw0cx6cqj6663as1kbj8nzblcky8j6kbi6b"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "shelltestrunner")))
    (arguments
@@ -1057,19 +1022,17 @@ advanced user's otherwise working script to fail under future circumstances.
                           "tests/examples")
                   (format #t "test suite not run~%"))
               #t))))))
-    (inputs (list ghc-diff
-                  ghc-filemanip
-                  ghc-hunit
-                  ghc-cmdargs
-                  ghc-pretty-show
-                  ghc-regex-tdfa
-                  ghc-safe
-                  ghc-test-framework
-                  ghc-test-framework-hunit
-                  ghc-utf8-string
-                  ghc-hspec
-                  ghc-hspec-core
-                  ghc-hspec-contrib))
+    (inputs
+     (list ghc-diff
+           ghc-cmdargs
+           ghc-filemanip
+           ghc-hunit
+           ghc-pretty-show
+           ghc-regex-tdfa
+           ghc-safe
+           ghc-utf8-string
+           ghc-test-framework
+           ghc-test-framework-hunit))
    (home-page "https://github.com/simonmichael/shelltestrunner")
    (synopsis "Test CLI programs")
    (description
@@ -1082,13 +1045,13 @@ output, stderr, and exit status.")
 (define-public stylish-haskell
  (package
    (name "stylish-haskell")
-    (version "0.15.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "stylish-haskell" version))
-       (sha256
-        (base32 "06y6f7bv5j5k7q81194v9jqcbmmqcv7h8ii3lq1783bpfnyd6h19"))))
+    (version "0.14.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "stylish-haskell" version))
+              (sha256
+               (base32
+                "17w92v0qnwj7m6yqdq5cxbr04xiz0yfnnyx5q54218wdl7n5lf6d"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "stylish-haskell")))
    (inputs (list ghc-aeson
@@ -1098,7 +1061,6 @@ output, stderr, and exit status.")
                  ghc-hsyaml-aeson
                  ghc-hsyaml
                  ghc-semigroups
-                  ghc-lib-parser
                  ghc-lib-parser-ex
                  ghc-strict
                  ghc-optparse-applicative))
@@ -45,18 +45,22 @@
 (define-public ghc-tasty-ant-xml
  (package
    (name "ghc-tasty-ant-xml")
-    (version "1.1.9")
+    (version "1.1.8")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "tasty-ant-xml" version))
       (sha256
-        (base32 "00zgsd6jjfwasr69d0y781vhjr7d8p1jbaaz4pn75ljf33akd92l"))))
+        (base32
+         "0h9mllhw9cd0rn34xhj8grwmbny7z7hpd8qmp9lfcdj0s4qx9vx8"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty-ant-xml")))
-    (inputs (list ghc-generic-deriving ghc-tagged ghc-tasty ghc-xml))
-    (home-page "http://github.com/ocharles/tasty-ant-xml")
-    (synopsis "Render tasty output to XML for Jenkins")
+    (inputs
+     (list ghc-generic-deriving ghc-xml ghc-tagged ghc-tasty))
+    (home-page
+     "https://github.com/ocharles/tasty-ant-xml")
+    (synopsis
+     "Render tasty output to XML for Jenkins")
    (description
     "A tasty ingredient to output test results in XML, using the Ant
 schema.  This XML can be consumed by the Jenkins continuous integration
@@ -72,37 +76,33 @@ framework.")
       (method url-fetch)
       (uri (hackage-uri "tasty-smallcheck" version))
       (sha256
-        (base32 "0csgwn3vch0jnpqyyfnrfjq4z0dpl67imh5a7byll3hhlyidgjym"))))
+        (base32
+         "0csgwn3vch0jnpqyyfnrfjq4z0dpl67imh5a7byll3hhlyidgjym"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty-smallcheck")))
-    (inputs (list ghc-tasty ghc-smallcheck ghc-tagged ghc-optparse-applicative))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "0033ha2w9rzc1rxpzh1dkfdrn256i5lvb41pqbdh2i6kli0v5vmh")))
-    (home-page "https://github.com/feuerbach/tasty")
+    (inputs
+     (list ghc-tasty ghc-smallcheck ghc-async ghc-tagged))
+    (home-page "https://documentup.com/feuerbach/tasty")
    (synopsis "SmallCheck support for the Tasty test framework")
    (description "This package provides SmallCheck support for the Tasty
 Haskell test framework.")
-    (license license:expat)))
+    (license license:bsd-3)))

 (define-public ghc-tasty-quickcheck
  (package
    (name "ghc-tasty-quickcheck")
-    (version "0.11.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-quickcheck" version))
-       (sha256
-        (base32 "0si4ccgqlv8h33d6310rrqba7f4pz3g8cinqfj42yd7damsdxm73"))))
+    (version "0.10.2")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-quickcheck" version))
+              (sha256
+               (base32
+                "1qnc6rdvjvlw08q6sln2n98rvj0s0pp689h6w4z58smjbn0lr25l"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty-quickcheck")))
    (inputs (list ghc-tagged ghc-tasty ghc-random ghc-quickcheck
                  ghc-optparse-applicative))
-    (native-inputs (list ghc-regex-tdfa ghc-tasty-hunit))
-    (arguments
-     `(#:cabal-revision ("3"
-                         "1wzvha4xam8npx5mk33c056grmrqnjd6m38nnm6d7y99w2mn1a7w")))
+    (native-inputs (list ghc-tasty-hunit ghc-pcre-light))
    (home-page "https://github.com/UnkindPartition/tasty")
    (synopsis "QuickCheck support for the Tasty test framework")
    (description "This package provides QuickCheck support for the Tasty
@@ -140,23 +140,22 @@ contains the correct result for the test.")
 (define-public ghc-tasty
  (package
    (name "ghc-tasty")
-    (version "1.5.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty" version))
-       (sha256
-        (base32 "10076vlklbcyiz7plakrihava5sy3dvwhskjldqzhfl18jvcg82l"))))
+    (version "1.4.3")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty" version))
+              (sha256
+               (base32
+                "006bf4gyc30i2gvb17hj1mzrh1kwnwf7l050x3f72wi6c2axl87l"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty")))
    (inputs
-      (list ghc-tagged
-            ghc-optparse-applicative
-            ghc-ansi-terminal
-            ghc-unbounded-delays)) ; needed on 32-bit architectures
-    (arguments
-     `(#:cabal-revision ("2"
-                         "04llcf1i3gawdik0bjhxdgls2wkiqlx0gi76nfh784nv2qzxlpbb")))
+      (append
+        (list ghc-tagged ghc-optparse-applicative ghc-ansi-terminal)
+        ;; TODO: Add ghc-unbounded-delays unconditionally on next rebuild cycle.
+        (if (member (%current-system) '("i686-linux"))
+            (list ghc-unbounded-delays)
+            '())))
    (home-page "https://github.com/UnkindPartition/tasty")
    (synopsis "Modern and extensible testing framework")
    (description
@@ -168,20 +167,17 @@ and any other types of tests into a single test suite.")
 (define-public ghc-tasty-hedgehog
  (package
    (name "ghc-tasty-hedgehog")
-    (version "1.4.0.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-hedgehog" version))
-       (sha256
-        (base32 "0lki03z0p38x0dkqx5cqga30zy5m31gxn1saqylja9bi6bbq8d25"))))
+    (version "1.3.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-hedgehog" version))
+              (sha256
+               (base32
+                "1iq452mvd9wc9pfmjsmm848jwp3cvsk1faf2mlr21vcs0yaxvq3m"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty-hedgehog")))
    (inputs (list ghc-tagged ghc-tasty ghc-hedgehog))
    (native-inputs (list ghc-tasty-expected-failure))
-    (arguments
-     `(#:cabal-revision ("6"
-                         "1rb8ncp6xyy7jr6v0hyls9m529ba0djndsxgxmkgr52rk3qq8lrc")))
    (home-page "https://github.com/qfpl/tasty-hedgehog")
    (synopsis "Integration for tasty and hedgehog")
    (description
@@ -194,25 +190,22 @@ framework}.")
 (define-public ghc-tasty-hspec
  (package
    (name "ghc-tasty-hspec")
-    (version "1.2.0.4")
+    (version "1.2.0.2")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "tasty-hspec" version))
       (sha256
-        (base32 "1hk1nkjvhp89xxgzj6dhbgw0fknnghpng6afq4i39hjkwv5p78ni"))))
+        (base32 "0cfcpi25jmnmzfzsx364qsj68q6gyph5z112kl8ja222hnhhr2n2"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty-hspec")))
    (inputs (list ghc-hspec
-                  ghc-hspec-api
                  ghc-hspec-core
                  ghc-quickcheck
                  ghc-tasty
                  ghc-tasty-smallcheck
-                  ghc-tasty-quickcheck))
-    (arguments
-     `(#:cabal-revision ("7"
-                         "0s1y34i8g7fva0z10ws3ipcy2jmlvqk0v4hdbx8rqnby5n0l5kay")))
+                  ghc-tasty-quickcheck
+                  ghc-tagged))
    (home-page "https://github.com/mitchellwrosen/tasty-hspec")
    (synopsis "Hspec support for the Tasty test framework")
    (description
@@ -222,17 +215,19 @@ framework}.")
 (define-public ghc-tasty-hunit
  (package
    (name "ghc-tasty-hunit")
-    (version "0.10.2")
+    (version "0.10.0.3")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "tasty-hunit" version))
       (sha256
-        (base32 "1xh33ss7dncm7zanzkzh7ywb3a46k7vkcbh6v8jb767gq6kizw2s"))))
+        (base32
+         "0gz6zz3w7s44pymw33xcxnawryl27zk33766sab96nz2xh91kvxp"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty-hunit")))
-    (inputs (list ghc-tasty ghc-call-stack-boot))
-    (home-page "https://github.com/UnkindPartition/tasty")
+    (inputs
+     (list ghc-call-stack-boot ghc-tasty))
+    (home-page "http://documentup.com/feuerbach/tasty")
    (synopsis "HUnit support for the Tasty test framework")
    (description "This package provides HUnit support for the Tasty Haskell
 test framework.")
@@ -262,13 +257,13 @@ tasty.")
 (define-public ghc-tasty-lua
  (package
    (name "ghc-tasty-lua")
-    (version "1.1.1.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-lua" version))
-       (sha256
-        (base32 "03b2n3gw2w70cnl57w3sh3cv5ka270sf07jlxpb4zs0z5gh83p1r"))))
+    (version "1.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-lua" version))
+              (sha256
+               (base32
+                "1vnyvgcjsvqhwwyqkbgqksr9ppj5whiihpwcqkg33sl7jj3ysdwv"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty-lua")))
    (inputs (list ghc-hslua-core
@@ -293,15 +288,16 @@ from Lua.")
       (method url-fetch)
       (uri (hackage-uri "tasty-th" version))
       (sha256
-        (base32 "0b2ivrw2257m4cy4rjnkwqlarh83j1y3zywnmaqqqbvy667sqnj3"))))
+        (base32
+         "0b2ivrw2257m4cy4rjnkwqlarh83j1y3zywnmaqqqbvy667sqnj3"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty-th")))
-    (inputs (list ghc-haskell-src-exts ghc-tasty))
-    (native-inputs (list ghc-tasty-hunit))
+    (inputs
+     (list ghc-haskell-src-exts ghc-tasty ghc-tasty-hunit))
    (home-page "https://github.com/bennofs/tasty-th")
    (synopsis "Automatically generate tasty TestTrees")
    (description
-     "Tasty-th automatically generates tasty TestTrees from functions of the
+      "Tasty-th automatically generates tasty TestTrees from functions of the
 current module, using TemplateHaskell.  This is a fork the original
 test-framework-th package, modified to work with tasty instead of
 test-framework.")
@@ -310,27 +306,28 @@ test-framework.")
 (define-public ghc-tasty-rerun
  (package
    (name "ghc-tasty-rerun")
-    (version "1.1.20")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-rerun" version))
-       (sha256
-        (base32 "0px58jm1yqbg32qf2s0yk09d2qdjxkkz9df89f31q3nzw85jv2ky"))))
+    (version "1.1.18")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-rerun" version))
+              (sha256
+               (base32
+                "0sccp5zx9v2rx741nbmgd8mzjhy5m4v74hk26d23xz93ph8aqx7s"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty-rerun")))
-    (inputs (list ghc-optparse-applicative ghc-split ghc-tagged ghc-tasty))
+    (inputs
+     (list ghc-optparse-applicative ghc-reducers ghc-split ghc-tagged
+           ghc-tasty))
    (arguments
-     `(#:cabal-revision ("1"
-                         "13xmx91hp7i0qzrhada9ckliqkynwlwa8x6pjbvxjcy1y0qsd7hk")))
+     `(#:cabal-revision ("3"
+                         "0091arn90cx5rzn5n2bpb9alzybwraf9yj7hb0bwdfyamzpf3pkb")))
    (home-page "https://github.com/ocharles/tasty-rerun")
    (synopsis "Run tests by filtering the test tree")
-    (description
-     "This package adds the ability to run tests by filtering the
+    (description "This package adds the ability to run tests by filtering the
 test tree based on the result of a previous test run.  You can use this to run
 only those tests that failed in the last run, or to only run the tests that have
 been added since previous test run.")
-    (license license:bsd-3)))
+  (license license:bsd-3)))

 (define-public ghc-tasty-expected-failure
  (package
@@ -365,17 +362,17 @@ development.")
 (define-public ghc-quickcheck-instances
  (package
    (name "ghc-quickcheck-instances")
-    (version "0.3.33")
+    (version "0.3.29.1")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "quickcheck-instances" version))
       (sha256
-        (base32 "0rl8y3rb4fm4nqz122bp5f2aya4f8bc9m9i9n2vwlyq2gdacs0v8"))))
+        (base32 "0jx2wfy7y5dr14s9i457g2aah4isjxry4mlbqhj7vlav6ib84gdj"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "quickcheck-instances")))
    (inputs (list ghc-quickcheck
-                  ghc-splitmix-bootstrap
+                  ghc-splitmix
                  ghc-case-insensitive
                  ghc-data-fix
                  ghc-hashable
@@ -386,15 +383,17 @@ development.")
                  ghc-scientific
                  ghc-strict
                  ghc-tagged
-                  ghc-text-short
                  ghc-these
                  ghc-time-compat
+                  ghc-transformers-compat
                  ghc-unordered-containers
                  ghc-uuid-types
-                  ghc-vector))
+                  ghc-vector
+                  ghc-data-array-byte
+                  ghc-text-short))
    (arguments
-     `(#:cabal-revision ("1"
-                         "1xkc7rsfgya4rwiizh0yfincws3knpdnh08m280v1dgik4kv37vh")))
+     `(#:cabal-revision ("2"
+                         "118xy4z4dy4bpkzsp98daiv3l4n5j7ph9my0saca7cqjybqwkcip")))
    (home-page "https://github.com/haskellari/qc-instances")
    (synopsis "Common quickcheck instances")
    (description "This package provides QuickCheck instances for types
@@ -410,38 +409,17 @@ provided by the Haskell Platform.")
       (method url-fetch)
       (uri (hackage-uri "quickcheck-unicode" version))
       (sha256
-        (base32 "0s43s1bzbg3gwsjgm7fpyksd1339f0m26dlw2famxwyzgvm0a80k"))))
+        (base32
+         "0s43s1bzbg3gwsjgm7fpyksd1339f0m26dlw2famxwyzgvm0a80k"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "quickcheck-unicode")))
    (inputs (list ghc-quickcheck))
-    (home-page "https://github.com/bos/quickcheck-unicode")
+    (home-page
+     "https://github.com/bos/quickcheck-unicode")
    (synopsis "Generator functions Unicode-related tests")
    (description "This package provides generator and shrink functions for
 testing Unicode-related software.")
-    (license license:bsd-2)))
-
-(define-public ghc-quickcheck-text
-  (package
-    (name "ghc-quickcheck-text")
-    (version "0.1.2.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "quickcheck-text" version))
-       (sha256
-        (base32 "02dbs0k6igmsa1hcw8yfvp09v7038vp4zlsp9706km3cmswgshj4"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "quickcheck-text")))
-    (inputs (list ghc-quickcheck))
-    (home-page "https://github.com/olorin/quickcheck-text")
-    (synopsis "Alternative arbitrary instance for Text")
-    (description
-     "The usual Arbitrary instance for Text (in
-<https://hackage.haskell.org/package/quickcheck-instances quickcheck-instances>)
-only has single-byte instances and so isn't an ideal representation of a valid
-UTF-8 character.  This package has generators for one-, two- and three-byte
-UTF-8 characters (all that are currently in use).")
-    (license license:expat)))
+    (license license:bsd-3)))

 (define-public ghc-quickcheck-io
  (package
@@ -468,19 +446,17 @@ use HUnit assertions as QuickCheck properties.")
 (define-public ghc-quickcheck
  (package
    (name "ghc-quickcheck")
-    (version "2.15.0.1")
+    (version "2.14.3")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "QuickCheck" version))
       (sha256
-        (base32 "0zvfydg44ibs1br522rzvdlxj9mpz0h62js1hay1sj5gvdnj3cm3"))))
+        (base32 "0085lwy14r7hk7ibmv8d7d54ja9zin0ijf0b27xai898dfrj43sw"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "QuickCheck")))
-    (inputs (list ghc-random-bootstrap ghc-splitmix-bootstrap))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "0cgfp4s51cjphsn9cls6rndisvqmi94vn95xan9g1yz6p5xk7z8c")))
+    (inputs
+     (list ghc-random ghc-splitmix-bootstrap))
    (home-page "https://github.com/nick8325/quickcheck")
    (synopsis "Automatic testing of Haskell programs")
    (description
@@ -503,8 +479,10 @@ expressed in Haskell, using combinators defined in the QuickCheck library.")
        (base32 "1kyam4cy7qmnizjwjm8jamq43w7f0fs6ljfplwj0ib6wi2kjh0wv"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "quickcheck-assertions")))
-    (inputs (list ghc-quickcheck ghc-ieee754 ghc-pretty-show))
-    (native-inputs (list ghc-hspec))
+    (native-inputs
+     (list ghc-hspec))
+    (inputs
+     (list ghc-ieee754 ghc-pretty-show ghc-quickcheck))
    (home-page "https://github.com/s9gf4ult/quickcheck-assertions")
    (synopsis "HUnit-like assertions for QuickCheck")
    (description
@@ -516,27 +494,33 @@ HUnit.")
 (define-public ghc-test-framework
  (package
    (name "ghc-test-framework")
-    (version "0.8.2.2")
+    (version "0.8.2.0")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "test-framework" version))
       (sha256
-        (base32 "04ijf5x6xx8i5lqv9ir33zs1rfzc4qkwwz8c1fdycnzvydcv4dnp"))))
+        (base32
+         "1hhacrzam6b8f10hyldmjw8pb7frdxh04rfg3farxcxwbnhwgbpm"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "test-framework")))
-    (inputs (list ghc-ansi-terminal
-                  ghc-ansi-wl-pprint
-                  ghc-random
-                  ghc-regex-posix
-                  ghc-old-locale
-                  ghc-xml
-                  ghc-hostname))
-    (native-inputs (list ghc-hunit ghc-quickcheck ghc-semigroups-bootstrap))
    (arguments
-     `(#:cabal-revision ("1"
-                         "1yv1qsr6bxphxk9430id9bqhfmkffdqmfg0k017dp9pnn4pqj0zh")))
-    (home-page "https://github.com/haskell/test-framework#readme")
+     `(#:tests? #f  ; FIXME: Tests do not build.
+       #:cabal-revision
+       ("6" "0wbq9wiaag69nsqxwijzhs5y1hb9kbpkp1x65dvx158cxp8i9w9r")))
+    ;(native-inputs
+    ; (list ghc-hunit ghc-quickcheck))
+    (inputs
+     `(("ghc-ansi-terminal" ,ghc-ansi-terminal)
+       ("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint)
+       ("ghc-hostname" ,ghc-hostname)
+       ("ghc-old-locale" ,ghc-old-locale)
+       ("ghc-random" ,ghc-random)
+       ("ghc-regex-posix" ,ghc-regex-posix)
+       ("ghc-xml" ,ghc-xml)
+       ("ghc-libxml" ,ghc-libxml)
+       ("ghc-semigroups" ,ghc-semigroups-bootstrap)))
+    (home-page "https://batterseapower.github.io/test-framework/")
    (synopsis "Framework for running and organising tests")
    (description
     "This package allows tests such as QuickCheck properties and HUnit test
@@ -573,21 +557,23 @@ reporting and test statistics output.")
 (define-public ghc-test-framework-quickcheck2
  (package
    (name "ghc-test-framework-quickcheck2")
-    (version "0.3.0.6")
+    (version "0.3.0.5")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "test-framework-quickcheck2" version))
       (sha256
-        (base32 "1d0w2q9sm8aayk0aj1zr2irpnqwpzixn6pdfq1i904vs1kkb2xin"))))
+        (base32
+         "0ngf9vvby4nrdf1i7dxf5m9jn0g2pkq32w48xdr92n9hxka7ixn9"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "test-framework-quickcheck2")))
-    (inputs (list ghc-test-framework ghc-quickcheck ghc-extensible-exceptions
-                  ghc-random))
    (arguments
-     `(#:cabal-revision ("1"
-                         "1af2gw9gvq143jdqmsnxj23cgss9ffdyr67951a5x151aps04y7z")))
-    (home-page "https://github.com/haskell/test-framework")
+     `(#:cabal-revision
+       ("3" "0mglqfimla4vvv80mg08aj76zf4993wmngqlirh05h8i9nmgv6lh")))
+    (inputs
+     (list ghc-extensible-exceptions ghc-quickcheck ghc-random
+           ghc-test-framework))
+    (home-page "https://batterseapower.github.io/test-framework/")
    (synopsis "QuickCheck2 support for test-framework")
    (description
     "This package provides QuickCheck2 support for the test-framework
@@ -606,8 +592,9 @@ package.")
        (base32 "1xpgpk1gp4w7w46b4rhj80fa0bcyz8asj2dcjb5x1c37b7rw90b0"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "test-framework-smallcheck")))
-    (inputs (list ghc-test-framework ghc-smallcheck))
-    (home-page "https://github.com/feuerbach/smallcheck")
+    (inputs
+     (list ghc-smallcheck ghc-test-framework))
+    (home-page "https://github.com/Bodigrim/smallcheck")
    (synopsis "SmallCheck support for test-framework")
    (description
     "This package lets programmers use SmallCheck properties in Haskell's
@@ -673,17 +660,17 @@ JUnit tool for Java.")
 (define-public hspec-discover
  (package
    (name "hspec-discover")
-    (version "2.11.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hspec-discover" version))
-       (sha256
-        (base32 "044vgsy45ff00h9z2k3jgn2m37npcjiacc4cifahrjlmwa7a7ylp"))))
+    (version "2.9.7")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hspec-discover" version))
+              (sha256
+               (base32
+                "0536kdxjw6p8b6gcwvmr22jbmb6cgzbddi0fkd01b2m847z37sb5"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hspec-discover")))
    (native-inputs (list ghc-quickcheck ghc-hspec-meta ghc-mockery-bootstrap))
-    (home-page "https://hspec.github.io/")
+    (home-page "http://hspec.github.io/")
    (synopsis "Automatically discover and run Hspec tests")
    (description "hspec-discover is a tool which automatically discovers and
 runs Hspec tests.")
@@ -692,30 +679,28 @@ runs Hspec tests.")
 (define-public ghc-hspec-core
  (package
    (name "ghc-hspec-core")
-    (version "2.11.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hspec-core" version))
-       (sha256
-        (base32 "030400w95775jrivbi7n1nnx6j5z717rqd3986ggklb8h9hjalfc"))))
+    (version "2.9.7")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hspec-core" version))
+              (sha256
+               (base32
+                "040rzqiqwkp373jjpij8lkmv08pp2ya92zzcf95bw8px215rp08n"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hspec-core")))
    (inputs (list ghc-hunit
                  ghc-quickcheck
                  ghc-ansi-terminal
                  ghc-call-stack
-                  ghc-haskell-lexer
+                  ghc-clock
                  ghc-hspec-expectations
                  ghc-quickcheck-io
                  ghc-random
+                  ghc-setenv
                  ghc-tf-random))
    (native-inputs (list ghc-base-orphans-bootstrap ghc-hspec-meta
-                         ghc-silently-bootstrap ghc-temporary-bootstrap))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "0yq9nnawcgbgxiz4ymfa8k66jrvgrhmv8j7g880x8k6q8q4ncqlq")))
-    (home-page "https://hspec.github.io/")
+                         ghc-silently-bootstrap ghc-temporary))
+    (home-page "http://hspec.github.io/")
    (synopsis "Testing framework for Haskell")
    (description "This library exposes internal types and functions that can
 be used to extend Hspec's functionality.")
@@ -724,28 +709,23 @@ be used to extend Hspec's functionality.")
 (define-public ghc-hspec-meta
  (package
    (name "ghc-hspec-meta")
-    (version "2.11.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hspec-meta" version))
-       (sha256
-        (base32 "1612pg5gihqjxrzqqvbbgckaqiwq3rmz3rg07lrjhzklg975nj69"))))
+    (version "2.9.3")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hspec-meta" version))
+              (sha256
+               (base32
+                "1raxwpsmcijl3x2h5naw6aydhbiknxvhj3x7v384bi1rqi51ainm"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hspec-meta")))
-    (inputs (list ghc-hunit
-                  ghc-quickcheck
+    (inputs (list ghc-quickcheck
                  ghc-ansi-terminal
                  ghc-call-stack-boot
-                  ghc-haskell-lexer
-                  ghc-hspec-expectations
+                  ghc-clock
                  ghc-quickcheck-io
                  ghc-random
-                  ghc-tf-random))
-    (arguments
-     `(#:cabal-revision ("2"
-                         "1jrk14s51psb0zjici56220iyb98i3q06sd3rsyx594s3cddgn5d")))
-    (home-page "https://hspec.github.io/")
+                  ghc-setenv))
+    (home-page "http://hspec.github.io/")
    (synopsis "Version of Hspec to test Hspec itself")
    (description "This library provides a stable version of Hspec which is
 used to test the in-development version of Hspec.")
@@ -754,58 +734,38 @@ used to test the in-development version of Hspec.")
 (define-public ghc-hspec
  (package
    (name "ghc-hspec")
-    (version "2.11.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hspec" version))
-       (sha256
-        (base32 "1zdgkn0gkcphcsfqcqwcfqiqvkz12ljks46v3czpaysndz8icfip"))))
+    (version "2.9.7")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hspec" version))
+              (sha256
+               (base32
+                "092sfqjkargxxszp9jjqa8ldjz0xv34jwn6k21q59ys5ckvsrpc1"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hspec")))
    (inputs (list ghc-quickcheck ghc-hspec-core hspec-discover
                  ghc-hspec-expectations))
-    (home-page "https://hspec.github.io/")
+    (home-page "http://hspec.github.io/")
    (synopsis "Testing Framework for Haskell")
    (description "This library provides the Hspec testing framework for
 Haskell, inspired by the Ruby library RSpec.")
    (license license:expat)))

-(define-public ghc-hspec-api
-  (package
-    (name "ghc-hspec-api")
-    (version "2.11.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hspec-api" version))
-       (sha256
-        (base32 "1xn2b2hafyq6qm3zaia9nw27ir4cg8v2qn499bz2zwnp2vkjra07"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "hspec-api")))
-    (inputs (list ghc-hspec-core))
-    (native-inputs (list ghc-hspec))
-    (home-page "https://hspec.github.io/")
-    (synopsis "A Testing Framework for Haskell")
-    (description
-     "This package provides a stable API that can be used to extend Hspec's
-functionality.")
-    (license license:expat)))
-
 (define-public ghc-hspec-contrib
  (package
    (name "ghc-hspec-contrib")
-    (version "0.5.2")
+    (version "0.5.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "hspec-contrib" version))
       (sha256
-        (base32 "0002xzvyh790iwf1y33d4nflrbp5sxvpsp010srcfryf1n3qx2b0"))))
+        (base32 "1nyb5n2jiq920yyf3flzyxrs5xpfyppl3jn18zhviyysjjk5drpx"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hspec-contrib")))
    (inputs (list ghc-hunit ghc-call-stack ghc-hspec-core))
    (native-inputs (list ghc-quickcheck ghc-hspec hspec-discover))
+    (arguments (list #:tests? #f)) ; Fail to build.
    (home-page "https://hspec.github.io/")
    (synopsis "Contributed functionality for Hspec")
    (description "This package provides contributed Hspec extensions.")
@@ -814,25 +774,22 @@ functionality.")
 (define-public ghc-hspec-expectations
  (package
    (name "ghc-hspec-expectations")
-    (version "0.8.4")
+    (version "0.8.2")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "hspec-expectations" version))
       (sha256
-        (base32 "1zr1pqchcwglfr5dvcrgc1l5x924n9w09n2zr68dmkqf4dzdx3bv"))))
+        (base32
+         "1vxl9zazbaapijr6zmcj72j9wf7ka1pirrjbwddwwddg3zm0g5l1"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hspec-expectations")))
-    (inputs (list ghc-hunit ghc-call-stack))
-    (arguments
    ;; Tests depend on ghc-nanospec.
-     `(#:tests? #f
-       #:cabal-revision ("2"
-                         "14zzsjqcz1zbnvi50i82lx84nc8b5da7ar5cazzh44lklyag0ds2")))
-    (home-page "https://github.com/hspec/hspec-expectations#readme")
+    (arguments '(#:tests? #f))
+    (inputs (list ghc-hunit))
+    (home-page "https://github.com/sol/hspec-expectations")
    (synopsis "Catchy combinators for HUnit")
-    (description
-     "This library provides catchy combinators for HUnit, see
+    (description "This library provides catchy combinators for HUnit, see
@uref{https://github.com/sol/hspec-expectations#readme, the README}.")
    (license license:expat)))

@@ -897,13 +854,13 @@ implementations of cryptographic ciphers.")
 (define-public ghc-hedgehog
  (package
    (name "ghc-hedgehog")
-    (version "1.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hedgehog" version))
-       (sha256
-        (base32 "0sl6x9q9kyrpv73565w9na9dm10wzxdl0qgiraqarffynfgn0hg9"))))
+    (version "1.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hedgehog" version))
+              (sha256
+               (base32
+                "0dbk75hk6hqpzkjdlpw3s63qhm42kqigij33p321by6xndb59jg1"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "hedgehog")))
    (inputs (list ghc-ansi-terminal
@@ -918,12 +875,8 @@ implementations of cryptographic ciphers.")
                  ghc-primitive
                  ghc-random
                  ghc-resourcet
-                  ghc-safe-exceptions
                  ghc-transformers-base
                  ghc-wl-pprint-annotated))
-    (arguments
-     `(#:cabal-revision ("2"
-                         "1m0b9m8dw5nw4b3w1jbp5fd0b0kqlyvvy3qsfxc7md77iafxq169")))
    (home-page "https://hedgehog.qa")
    (synopsis "Property-based testing in the spirt of QuickCheck")
    (description
@@ -939,16 +892,26 @@ To get started quickly, see the examples:
 (define-public cabal-doctest
  (package
    (name "cabal-doctest")
-    (version "1.0.11")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "cabal-doctest" version))
-       (sha256
-        (base32 "0gwjpwv2v7c7gs2dvf7ixsxx6likmgw5yi0fy4bqc0i7nkqg4bfw"))))
+    (version "1.0.9")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "cabal-doctest" version))
+              (sha256
+               (base32
+                "0wxs0xkspc80h0g8ks792lrzldxvcnhc9rja1j0k678ijs20hmjm"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "cabal-doctest")))
-    (home-page "https://github.com/ulidtko/cabal-doctest")
+    (arguments
+     `(#:cabal-revision ("2"
+                         "0868js0qgfhvmyw4hjzrvmlzyqsm8dfsbmqhybxb90x44xi3r0i1")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "cabal-doctest.cabal"
+               (("\\b(Cabal|base)\\s+[^,]+" all dep)
+                dep)))))))
+    (home-page "https://github.com/haskellari/cabal-doctest")
    (synopsis "Setup.hs helper for running doctests")
    (description
     "To properly work, the @code{doctest} package needs plenty of
@@ -1008,13 +971,13 @@ random testing, and hybrids of the two.")
 (define-public ghc-inspection-testing
  (package
    (name "ghc-inspection-testing")
-    (version "0.6.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "inspection-testing" version))
-       (sha256
-        (base32 "0zi1q86sd9jy5dpqfs2j71acdl7kvik0ps78xirpdhyldhwwyqws"))))
+    (version "0.4.6.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "inspection-testing" version))
+              (sha256
+               (base32
+                "0mxff0v3ciccbk4b8kxnh4752fzbwn7213qd8xji0csv6gi2w83y"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "inspection-testing")))
    (home-page "https://github.com/nomeata/inspection-testing")
@@ -1047,33 +1010,33 @@ examples and more information.")
    (name "ghc-quickcheck-classes")
    (version "0.6.5.0")
    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "quickcheck-classes" version))
-       (sha256
-        (base32 "19iw15mvb7gws3ljdxqwsbb4pmfc0sfflf8szgmrhiqr3k82mqv2"))))
+      (origin
+        (method url-fetch)
+        (uri (hackage-uri "quickcheck-classes" version))
+        (sha256
+          (base32 "19iw15mvb7gws3ljdxqwsbb4pmfc0sfflf8szgmrhiqr3k82mqv2"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "quickcheck-classes")))
-    (inputs (list ghc-quickcheck
-                  ghc-primitive
-                  ghc-primitive-addr
-                  ghc-quickcheck-classes-base
-                  ghc-semigroups-bootstrap
-                  ghc-fail
-                  ghc-tagged
-                  ghc-aeson
-                  ghc-semigroupoids
-                  ghc-semirings
-                  ghc-vector))
-    (native-inputs (list ghc-base-orphans ghc-base-orphans ghc-tasty
-                         ghc-tasty-quickcheck))
-    (arguments
-     `(#:cabal-revision ("3"
-                         "1pawam5rsdcdv21fqc87khzqjm0ixwzklfxd6gk3b2qrr5q66bn5")))
+    (inputs
+      (list ghc-quickcheck
+            ghc-primitive
+            ghc-primitive-addr
+            ghc-quickcheck-classes-base
+            ghc-aeson
+            ghc-semigroupoids
+            ghc-semirings
+            ghc-vector))
+    (native-inputs
+      (list ghc-base-orphans
+            ghc-tagged
+            ghc-base-orphans
+            ghc-tagged
+            ghc-tasty
+            ghc-tasty-quickcheck))
    (home-page "https://github.com/andrewthad/quickcheck-classes#readme")
    (synopsis "QuickCheck common typeclasses")
    (description
-     "This library provides QuickCheck properties to ensure that typeclass
+      "This library provides QuickCheck properties to ensure that typeclass
 instances adhere to the set of laws that they are supposed to.  There are
 other libraries that do similar things, such as @code{genvalidity-hspec} and
@code{checkers}.  This library differs from other solutions by not introducing
@@ -1089,26 +1052,24 @@ constraints more cleanly.")
    (name "ghc-quickcheck-classes-base")
    (version "0.6.2.0")
    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "quickcheck-classes-base" version))
-       (sha256
-        (base32 "16c6gq4cqpkwnq1pzkhm6r7mrwk4an50ha5w77bmiia2qkhla6ch"))))
+      (origin
+        (method url-fetch)
+        (uri (hackage-uri "quickcheck-classes-base" version))
+        (sha256
+          (base32 "16c6gq4cqpkwnq1pzkhm6r7mrwk4an50ha5w77bmiia2qkhla6ch"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "quickcheck-classes-base")))
-    (inputs (list ghc-quickcheck
-                  ghc-contravariant
-                  ghc-bifunctors
-                  ghc-semigroups-bootstrap
-                  ghc-fail
-                  ghc-tagged))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "1p3v38jhpx0r6rnvaspkkivl8xyq2mq4xnmycgmkj1gr77vplkdr")))
+    (inputs
+      (list ghc-quickcheck
+            ghc-contravariant
+            ghc-bifunctors
+            ghc-semigroups
+            ghc-fail
+            ghc-tagged))
    (home-page "https://github.com/andrewthad/quickcheck-classes#readme")
    (synopsis "QuickCheck common typeclasses from `base`")
    (description
-     "This library is a minimal variant of `quickcheck-classes` that only
+      "This library is a minimal variant of `quickcheck-classes` that only
 provides laws for typeclasses from `base`.  The main purpose of splitting this
 out is so that `primitive` can depend on `quickcheck-classes-base` in its test
 suite, avoiding the circular dependency that arises if `quickcheck-classes` is
@@ -1126,61 +1087,67 @@ this library uses the higher-kinded typeclasses
 (define-public ghc-doctest-lib
  (package
    (name "ghc-doctest-lib")
-    (version "0.1.1.1")
+    (version "0.1")
    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "doctest-lib" version))
-       (sha256
-        (base32 "1hb3zx1xzib3v41blnwcbhc2v0rzwdzq7gm4sajqndimwjkkxc67"))))
+      (origin
+        (method url-fetch)
+        (uri (hackage-uri "doctest-lib" version))
+        (sha256
+          (base32 "1vswam0dhw52dihgnzirh18gqs8rj8h6jd7pl6y1mg2f9f9zmih2"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "doctest-lib")))
    (home-page "https://hub.darcs.net/thielema/doctest-lib/")
    (synopsis "Parts of doctest exposed as library")
    (description
-     "Parts of doctest exposed as library.  For use with the doctest-extract utility.")
+      "Parts of doctest exposed as library.  For use with the doctest-extract utility.")
    (license license:expat)))

 (define-public ghc-doctest-exitcode-stdio
  (package
    (name "ghc-doctest-exitcode-stdio")
-    (version "0.0.0.1")
+    (version "0.0")
    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "doctest-exitcode-stdio" version))
-       (sha256
-        (base32 "0kg5xiw4giyvqpcj6cxqqnysvixhxlwm0pbg3qks8dzwb5w79dvk"))))
+      (origin
+        (method url-fetch)
+        (uri (hackage-uri "doctest-exitcode-stdio" version))
+        (sha256
+          (base32 "1g3c7yrqq2mwqbmvs8vkx1a3cf0p0x74b7fnn344dsk7bsfpgv0x"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "doctest-exitcode-stdio")))
-    (inputs (list ghc-doctest-lib ghc-quickcheck ghc-semigroups))
+    (inputs
+      (list ghc-doctest-lib ghc-quickcheck ghc-semigroups))
+    (arguments
+     `(#:cabal-revision ("1"
+                         "1065s8bch6zhl6mc8nhvfpwd1irmjd04z7xgycbpihc14x4ijim3")))
    (home-page "https://hub.darcs.net/thielema/doctest-exitcode-stdio/")
    (synopsis "Run Doctests in a @code{Cabal.Test.exitcode-stdio} environment")
    (description
-     "This package allows on to run Doctests in a Cabal.Test.exitcode-stdio
+      "This package allows on to run Doctests in a Cabal.Test.exitcode-stdio
 environment.")
    (license license:bsd-3)))

 (define-public ghc-tasty-silver
  (package
    (name "ghc-tasty-silver")
-    (version "3.3.2.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-silver" version))
-       (sha256
-        (base32 "01w3576kymglcddinh10m1wgy71dia49k2pnw5y1c97jjrhanf17"))))
+    (version "3.3.1.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-silver" version))
+              (sha256
+               (base32
+                "13j0zs0ciijv9q2nncna1gbgsgw2g7xc228hzmqic1750n3ybz9m"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty-silver")))
    (inputs (list ghc-ansi-terminal
+                  ghc-async
                  ghc-optparse-applicative
                  ghc-process-extras
                  ghc-regex-tdfa
                  ghc-silently
                  ghc-tagged
                  ghc-tasty
-                  ghc-temporary))
+                  ghc-temporary
+                  ghc-semigroups))
    (native-inputs (list ghc-tasty-hunit))
    (home-page "https://github.com/phile314/tasty-silver")
    (synopsis "Fancy test runner, including support for golden tests")
@@ -1196,19 +1163,16 @@ result of golden tests.")
 (define-public ghc-tasty-inspection-testing
  (package
    (name "ghc-tasty-inspection-testing")
-    (version "0.2.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-inspection-testing" version))
-       (sha256
-        (base32 "0wl2xlnbmqdkwhi4ic6a4q4lxf9qg433lidi8d0hlp3ykrjpbcay"))))
+    (version "0.1.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-inspection-testing" version))
+              (sha256
+               (base32
+                "0p46w44f19w7lvdzyg3vq6qzix0rjp8p23ilxz82dviq38lgmifp"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tasty-inspection-testing")))
    (inputs (list ghc-inspection-testing ghc-tasty))
-    (arguments
-     `(#:cabal-revision ("2"
-                         "0z9al0hyq381fw146agbpz7rf24rwms1w91m7s0k1w3xbfw16l9n")))
    (home-page "https://github.com/Bodigrim/tasty-inspection-testing")
    (synopsis "Inspection testing support for tasty")
    (description
@@ -1218,13 +1182,13 @@ result of golden tests.")
 (define-public ghc-proctest
  (package
    (name "ghc-proctest")
-    (version "0.1.3.1")
+    (version "0.1.3.0")
    (source (origin
              (method url-fetch)
              (uri (hackage-uri "proctest" version))
              (sha256
               (base32
-                "0yvhc0l5aj170ymhjx4ig0im0yd7wfa150m5lqhabr8j7cf16l7y"))))
+                "02iz323arx9zwclvspgaaqz81bp6jdnj89pjm08n2gamg39zsbdn"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "proctest")))
    (inputs (list ghc-hunit ghc-hspec ghc-quickcheck))
@@ -62,19 +62,18 @@ format.")
  (package
    (name "ghc-asn1-encoding")
    (version "0.9.6")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "asn1-encoding" version))
-       (sha256
-        (base32 "02nsr30h5yic1mk7znf0q4z3n560ip017n60hg7ya25rsfmxxy6r"))))
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "asn1-encoding" version))
+              (sha256
+               (base32
+                "02nsr30h5yic1mk7znf0q4z3n560ip017n60hg7ya25rsfmxxy6r"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "asn1-encoding")))
-    (inputs (list ghc-hourglass ghc-asn1-types))
-    (native-inputs (list ghc-tasty ghc-tasty-quickcheck))
-    (arguments
-     `(#:cabal-revision ("2"
-                         "16503ryhq15f2rfdav2qnkq11dg2r3vk3f9v64q9dmxf8dh8zv97")))
+    (inputs
+     (list ghc-hourglass ghc-asn1-types))
+    (native-inputs
+     (list ghc-tasty ghc-tasty-quickcheck))
    (home-page "https://github.com/vincenthz/hs-asn1")
    (synopsis "ASN1 data reader and writer in RAW, BER and DER forms")
    (description
@@ -112,18 +111,15 @@ when ASN1 pattern matching is not convenient.")
       (method url-fetch)
       (uri (hackage-uri "crypto-api" version))
       (sha256
-        (base32 "19bsmkqkpnvh01b77pmyarx00fic15j4hvg4pzscrj4prskrx2i9"))))
+        (base32
+         "19bsmkqkpnvh01b77pmyarx00fic15j4hvg4pzscrj4prskrx2i9"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "crypto-api")))
    (inputs (list ghc-cereal ghc-tagged ghc-entropy))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "1z6n1sa5pn3iqvqjrd8hv4bc2pxzsrhm5sh0l8z7g9lbqp6w0wp5")))
    (home-page "https://github.com/TomMD/crypto-api")
    (synopsis "Provides generic interface for cryptographic operations
 for Haskell")
-    (description
-     "This Haskell package provides a generic interface for
+    (description "This Haskell package provides a generic interface for
 cryptographic operations (hashes, ciphers, randomness).

 Maintainers of hash and cipher implementations are encouraged to add instances
@@ -201,15 +197,13 @@ that hides the C implementation.")
       (method url-fetch)
       (uri (hackage-uri "cryptohash-md5" version))
       (sha256
-        (base32 "018g13hkmq5782i24b4518hcd926fl6x6fh5hd7b9wlxwc5dn21v"))))
+        (base32
+         "018g13hkmq5782i24b4518hcd926fl6x6fh5hd7b9wlxwc5dn21v"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "cryptohash-md5")))
    (native-inputs (list ghc-base16-bytestring ghc-puremd5 ghc-tasty
-                         ghc-tasty-quickcheck ghc-tasty-hunit))
-    (arguments
-     `(#:cabal-revision ("6"
-                         "0m7f9mgw4w9vcch37ja9zgbn0knq8rjppqr9x2ylkcdxfdnmhhif")))
-    (home-page "https://github.com/haskell-hvr/cryptohash-md5")
+                         ghc-tasty-hunit ghc-tasty-quickcheck))
+    (home-page "https://github.com/hvr/cryptohash-md5")
    (synopsis "MD5 implementation for Haskell")
    (description "This Haskell package provides implementation of MD5.")
    (license license:bsd-3)))
@@ -218,20 +212,20 @@ that hides the C implementation.")
  (package
    (name "ghc-cryptohash-sha1")
    (version "0.11.101.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "cryptohash-sha1" version))
-       (sha256
-        (base32 "0h9jl9v38gj0vnscqx7xdklk634p05fa6z2pcvknisq2mnbjq154"))))
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "cryptohash-sha1" version))
+              (sha256
+               (base32
+                "0h9jl9v38gj0vnscqx7xdklk634p05fa6z2pcvknisq2mnbjq154"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "cryptohash-sha1")))
    (native-inputs (list ghc-base16-bytestring ghc-sha ghc-tasty
                         ghc-tasty-quickcheck ghc-tasty-hunit))
    (arguments
-     `(#:cabal-revision ("6"
-                         "1cxdw2y10z4v0mz91wki7f233jziipx85j4qy5msig4nv3djkprb")))
-    (home-page "https://github.com/haskell-hvr/cryptohash-sha1")
+     `(#:cabal-revision ("1"
+                         "0bz9rfl7b2iwn45m0lxcmsyi5rrv3xdgzx2lzr79bds91dw6i25b")))
+    (home-page "https://github.com/hvr/cryptohash-sha1")
    (synopsis "SHA-1 implementation for Haskell")
    (description
     "This Haskell package provides an incremental and one-pass,
@@ -252,18 +246,20 @@ the C implementation.")
       (method url-fetch)
       (uri (hackage-uri "cryptohash-sha256" version))
       (sha256
-        (base32 "1xkb7iqplbw4fy1122p79xf1zcb7k44rl0wmfj1q06l7cdqxr9vk"))))
+        (base32
+         "1xkb7iqplbw4fy1122p79xf1zcb7k44rl0wmfj1q06l7cdqxr9vk"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "cryptohash-sha256")))
-    (native-inputs (list ghc-base16-bytestring ghc-sha ghc-tasty
-                         ghc-tasty-quickcheck ghc-tasty-hunit))
    (arguments
-     `(#:cabal-revision ("6"
-                         "01s12sl5mxvraj5fj3cs0pkb03pm8xpjz13y09dpl7i6rv6f578f")))
-    (home-page "https://github.com/haskell-hvr/cryptohash-sha256")
+     `(#:cabal-revision
+       ("1" "1hyzqv30rpj920ddnr0zypyjjlh52vyp2d140pn2byayj820rkgs")
+       #:tests? #f)) ; TODO: tasty ==1.1.*
+    (native-inputs
+     (list ghc-base16-bytestring ghc-sha ghc-tasty ghc-tasty-hunit
+           ghc-tasty-quickcheck))
+    (home-page "https://github.com/hvr/cryptohash-sha1")
    (synopsis "SHA-256 implementation for Haskell")
-    (description
-     "This Haskell package provides an incremental and
+    (description "This Haskell package provides an incremental and
 one-pass, pure API to the @uref{https://en.wikipedia.org/wiki/SHA-2,
 SHA-256 cryptographic hash algorithm}, with performance close to the
 fastest implementations available in other languages.
@@ -276,12 +272,12 @@ the C implementation.")
  (package
    (name "ghc-cryptonite")
    (version "0.30")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "cryptonite" version))
-       (sha256
-        (base32 "07bb97iszhnrfddh5ql6p3dqd0c13xycjw5n2kljw7d0ia59q2an"))))
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "cryptonite" version))
+              (sha256
+               (base32
+                "07bb97iszhnrfddh5ql6p3dqd0c13xycjw5n2kljw7d0ia59q2an"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "cryptonite")))
    (inputs (list ghc-memory ghc-basement))
@@ -299,13 +295,13 @@ generators, and more.")
 (define-public ghc-curve25519
  (package
  (name "ghc-curve25519")
-  (version "0.2.8.1")
+  (version "0.2.7")
  (source
   (origin
     (method url-fetch)
     (uri (hackage-uri "curve25519" version))
     (sha256
-      (base32 "0p2rxad477cxbpxryvp78v8nrrf5gm35106jbqrj5cjgksappkdj"))))
+      (base32 "1p8b1lppkvc19974hr43lcqdi4nj55j2nf7gsnp8dn7gyf23aayq"))))
  (build-system haskell-build-system)
  (native-inputs
   (list ghc-hunit
@@ -330,17 +326,19 @@ elsewhere.")
 (define-public ghc-digest
  (package
    (name "ghc-digest")
-    (version "0.0.2.1")
+    (version "0.0.1.7")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "digest" version))
       (sha256
-        (base32 "163418p50bqdxn8ajzj6x3455xbch9jq1w6psbkdz5qzw017py6b"))))
+        (base32 "02jzw0bsng87y1n2kgpy7vb30lvqsnpbfd8dpg4hmvbg9s06qgdj"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "digest")))
    (arguments
-     `(#:extra-directories ("zlib")))
+     `(#:extra-directories ("zlib")
+       #:cabal-revision ("1"
+                         "0wh34kyag2vhwvsdwv8qmvm13gy32nc94yfyqfdnl67nyc2sx8wl")))
    (inputs (list zlib))
    (native-inputs (list pkg-config))
    (home-page "http://hackage.haskell.org/package/digest")
@@ -354,13 +352,13 @@ are implemented as FFI bindings to efficient code from zlib.")
 (define-public ghc-entropy
  (package
    (name "ghc-entropy")
-    (version "0.4.1.11")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "entropy" version))
-       (sha256
-        (base32 "1slj5n783k2amsx2hqs5qwvcw4rgfhdhgmiyg7cii0wg4w0mmpgm"))))
+    (version "0.4.1.10")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "entropy" version))
+              (sha256
+               (base32
+                "1rbx4ydabrjs8kkdg9laznkh9nisiq6b5z93vnp9bh6iy59ivb45"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "entropy")))
    (home-page "https://github.com/TomMD/entropy")
@@ -417,35 +415,6 @@ the MD5 digest (hash) algorithm.  This now supports the @code{crypto-api} class
 interface.")
    (license license:bsd-3)))

-(define-public ghc-rsa
-  (package
-    (name "ghc-rsa")
-    (version "2.4.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "RSA" version))
-       (sha256
-        (base32 "0hchsqrxpfw7mqrqwscfy8ig1w2di6w3nxpzi873w0gibv2diibj"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "RSA")))
-    (inputs (list ghc-crypto-api ghc-crypto-pubkey-types ghc-sha))
-    (native-inputs (list ghc-quickcheck ghc-tagged ghc-test-framework
-                         ghc-test-framework-quickcheck2))
-    (arguments
-     `(#:cabal-revision ("2"
-                         "090yzm99fmh7c6z4m9hbkasqhc3xlw104g2b6wnk77n1abd13ryj")))
-    (home-page "http://hackage.haskell.org/package/RSA")
-    (synopsis
-     "Implementation of RSA, using the padding schemes of PKCS#1 v2.1.")
-    (description
-     "This library implements the RSA encryption and signature algorithms for
-arbitrarily-sized @code{ByteStrings}.  While the implementations work, they are
-not necessarily the fastest ones on the planet.  Particularly key generation.
-The algorithms included are based of RFC 3447, or the Public-Key Cryptography
-Standard for RSA, version 2.1 (a.k.a, PKCS#1 v2.1).")
-    (license license:bsd-3)))
-
 (define-public ghc-sha
  (package
    (name "ghc-sha")
@@ -625,24 +594,6 @@ implementation.  If it matters for your case, you should make sure you have
 AES-NI available, or you'll need to use a different implementation.")
    (license license:bsd-3)))

-(define-public ghc-crypto-pubkey-types
-  (package
-    (name "ghc-crypto-pubkey-types")
-    (version "0.4.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "crypto-pubkey-types" version))
-       (sha256
-        (base32 "0q0wlzjmpx536h1zcdzrpxjkvqw8abj8z0ci38138kpch4igbnby"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "crypto-pubkey-types")))
-    (inputs (list ghc-asn1-types ghc-asn1-encoding))
-    (home-page "http://github.com/vincenthz/hs-crypto-pubkey-types")
-    (synopsis "Generic cryptography Public keys algorithm types")
-    (description "Generic cryptography public keys algorithm types.")
-    (license license:bsd-3)))
-
 (define-public ghc-crypto-random
  (package
    (name "ghc-crypto-random")
@@ -666,13 +617,13 @@ abstraction for CPRNGs.")
 (define-public ghc-crypton
  (package
    (name "ghc-crypton")
-    (version "1.0.4")
+    (version "0.34")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "crypton" version))
       (sha256
-        (base32 "06h1qjvqd8gmiyzvh31sc061vcgns101l0774c44a8k44015925l"))))
+        (base32 "1mhypjhzn95in853bp7ary0a2xc6lsji6j8hrrgn2mfa4ilq8i24"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "crypton")))
    (inputs (list ghc-memory ghc-basement))
@@ -702,13 +653,13 @@ abstraction for CPRNGs.")
 (define-public ghc-crypton-x509
  (package
    (name "ghc-crypton-x509")
-    (version "1.7.7")
+    (version "1.7.6")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "crypton-x509" version))
       (sha256
-        (base32 "10pkva9wvm6ih48bprxlnyhnn3nr6xq9dhkrk4hfxpsaij6f9v7g"))))
+        (base32 "1zyaz0krf08g36g30zr5wn8f2x51l4dj2zcjnhpiw9h05p54mdzb"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "crypton-x509")))
    (inputs (list ghc-memory
@@ -718,7 +669,13 @@ abstraction for CPRNGs.")
                  ghc-asn1-encoding
                  ghc-asn1-parse
                  ghc-crypton))
-    (native-inputs (list ghc-tasty ghc-tasty-quickcheck))
+    (native-inputs (list ghc-tasty ghc-tasty-quickcheck ghc-x509))
+    (arguments
+     `(#:cabal-revision ("1"
+                         "10a2x47znhbayyfr6fqgq27623akpycyjbfxz4hnavavf1x6ary5")
+       ;; build phase fails when tests are activated.
+       ;; See https://github.com/kazu-yamamoto/crypton-certificate/pull/7
+       #:tests? #f))
    (home-page "https://github.com/kazu-yamamoto/crypton-certificate")
    (synopsis "X509 reader and writer")
    (description "This package provides generic X509 support for Haskell.")
@@ -727,13 +684,13 @@ abstraction for CPRNGs.")
 (define-public ghc-crypton-x509-store
  (package
    (name "ghc-crypton-x509-store")
-    (version "1.6.11")
+    (version "1.6.9")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "crypton-x509-store" version))
       (sha256
-        (base32 "07vq7f883cm5krqz2kc0qkh9ks54jknrwdqvfqsk91s12b693a83"))))
+        (base32 "0vr5b9cyf9x016wn1g0bryslf5nz8jq2sy8r3llwqfg02apihqiy"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "crypton-x509-store")))
    (inputs (list ghc-pem ghc-asn1-types ghc-asn1-encoding ghc-crypton
@@ -770,25 +727,24 @@ storage methods, and accessors.")
 (define-public ghc-crypton-x509-validation
  (package
    (name "ghc-crypton-x509-validation")
-    (version "1.6.14")
+    (version "1.6.12")
    (source
     (origin
       (method url-fetch)
       (uri (hackage-uri "crypton-x509-validation" version))
       (sha256
-        (base32 "07b09kgrd3m5ahxpj458r5ycd30bz8ldwjwf19mdcnfv4x0kj3pd"))))
+        (base32 "1xjhwvmkcy47a6xiqxb3xy944ca7g660203jdrz5xzd46zibfq0f"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "crypton-x509-validation")))
    (inputs (list ghc-memory
                  ghc-hourglass
-                  ghc-data-default
+                  ghc-data-default-class
                  ghc-pem
                  ghc-asn1-types
                  ghc-asn1-encoding
                  ghc-crypton-x509
                  ghc-crypton-x509-store
-                  ghc-crypton
-                  ghc-iproute))
+                  ghc-crypton))
    (native-inputs (list ghc-tasty ghc-tasty-hunit))
    (home-page "https://github.com/kazu-yamamoto/crypton-certificate")
    (synopsis "X.509 Certificate and CRL validation")
@@ -796,44 +752,6 @@ storage methods, and accessors.")
 and @dfn{Certificates revocation list} (CRL) validation.")
    (license license:bsd-3)))

-(define-public ghc-crypton-socks
-  (package
-    (name "ghc-crypton-socks")
-    (version "0.6.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "crypton-socks" version))
-       (sha256
-        (base32 "0fwzlvndyxjwhxambxdjzzm63yvb6jzsg53dkv3i6x17biz0hdm8"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "crypton-socks")))
-    (inputs (list ghc-cereal ghc-network ghc-network-bsd))
-    (home-page "http://github.com/mpilgrem/crypton-socks")
-    (synopsis "SOCKS Protocol Version 5")
-    (description
-     "This package provides a library implementing SOCKS Protocol Version 5.")
-    (license license:bsd-3)))
-
-(define-public ghc-crypto-token
-  (package
-    (name "ghc-crypto-token")
-    (version "0.1.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "crypto-token" version))
-       (sha256
-        (base32 "18xphlvn6wzyi6lqrvm5vic97pkcbiph1938p5l1mb22rj5215zm"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "crypto-token")))
-    (inputs (list ghc-crypton ghc-memory ghc-network-byte-order))
-    (native-inputs (list ghc-hspec hspec-discover))
-    (home-page "http://hackage.haskell.org/package/crypto-token")
-    (synopsis "crypto tokens")
-    (description "Encrypted tokens/tickets to keep state in the client side.")
-    (license license:bsd-3)))
-
 (define-public ghc-cprng-aes
  (package
    (name "ghc-cprng-aes")
@@ -886,19 +804,20 @@ percent.
       (method url-fetch)
       (uri (hackage-uri "ed25519" version))
       (sha256
-        (base32 "0v8msqvgzimhs7p5ri25hrb1ni2wvisl5rmdxy89fc59py79b9fq"))))
+        (base32
+         "0v8msqvgzimhs7p5ri25hrb1ni2wvisl5rmdxy89fc59py79b9fq"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "ed25519")))
-    (native-inputs (list ghc-quickcheck ghc-doctest))
    (arguments
-     `(#:cabal-revision ("9"
-                         "0y5vfdcys18waa5k5zxiq9n8jq0l05j76riml23i0gxmwgdhsmgi")
-       ;; the tests don't work with current versions of the test frameworks
-       #:tests? #f))
-    (home-page "https://github.com/thoughtpolice/hs-ed25519/")
+     `(#:cabal-revision
+       ("6" "0qyx6cl52fnll8lp6v9133wfvv3zhvq7v2crn441mng520j9wp48")
+       ;; We omit these test suites because they require old versions of
+       ;; packages and packages we do not have.
+       #:configure-flags
+       '("--flags=-test-hlint -test-doctests -test-properties")))
+    (home-page "http://thoughtpolice.github.com/hs-ed25519")
    (synopsis "Ed25519 cryptographic signatures")
-    (description
-     "This package provides a simple, fast, self-contained
+    (description "This package provides a simple, fast, self-contained
 copy of the Ed25519 public-key signature system with a clean interface.
 It also includes support for detached signatures, and thorough
 documentation on the design and implementation, including usage
@@ -908,41 +827,29 @@ guidelines.")
 (define-public ghc-tls
  (package
    (name "ghc-tls")
-    (version "2.1.8")
+    (version "1.5.8")
    (source (origin
              (method url-fetch)
              (uri (hackage-uri "tls" version))
              (sha256
               (base32
-                "1csdy3426lva1a5f7gh9qm96vzfraqj91jbxlm79wbf1jsdzfhsq"))))
+                "0rxdv8ab98kd4nqql7djmmi51k4vayq21s38s43sx3rzn0iyla3b"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "tls")))
-    (inputs (list ghc-asn1-types
-                  ghc-asn1-encoding
-                  ghc-base16-bytestring
-                  ghc-cereal
-                  ghc-crypton
-                  ghc-crypton-x509
-                  ghc-crypton-x509-store
-                  ghc-crypton-x509-validation
-                  ghc-data-default
+    (inputs (list ghc-cereal
+                  ghc-data-default-class
                  ghc-memory
-                  ghc-network
-                  ghc-serialise
-                  ghc-transformers
-                  ghc-unix-time
-                  ghc-zlib))
-    (native-inputs (list ghc-quickcheck
-                         ghc-asn1-types
-                         ghc-async
-                         ghc-crypton
-                         ghc-crypton-x509
-                         ghc-crypton-x509-validation
-                         ghc-hourglass
-                         ghc-hspec
-                         ghc-serialise
-                         hspec-discover))
-    (home-page "http://github.com/haskell-tls/hs-tls")
+                  ghc-cryptonite
+                  ghc-asn1-types
+                  ghc-asn1-encoding
+                  ghc-x509
+                  ghc-x509-store
+                  ghc-x509-validation
+                  ghc-async
+                  ghc-hourglass
+                  ghc-network))
+    (native-inputs (list ghc-tasty ghc-tasty-quickcheck ghc-quickcheck))
+    (home-page "http://github.com/vincenthz/hs-tls")
    (synopsis "TLS/SSL protocol native implementation (Server and Client)")
    (description
     "Native Haskell TLS and SSL protocol implementation for server and client.
@@ -954,6 +861,43 @@ Ephemeral (Elliptic curve and regular) Diffie Hellman key exchanges, and many
 extensions.")
    (license license:bsd-3)))

+(define-public ghc-tls-1.9
+  (package
+    (name "ghc-tls")
+    (version "1.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (hackage-uri "tls" version))
+       (sha256
+        (base32 "0gj3af9sqd0bw7dpcqfyvbslpxsk2ij00a77kl710fwhw35vj1an"))))
+    (build-system haskell-build-system)
+    (properties '((upstream-name . "tls")))
+    (inputs (list ghc-cereal
+                  ghc-data-default-class
+                  ghc-memory
+                  ghc-crypton
+                  ghc-asn1-types
+                  ghc-asn1-encoding
+                  ghc-crypton-x509
+                  ghc-crypton-x509-store
+                  ghc-crypton-x509-validation
+                  ghc-async
+                  ghc-unix-time
+                  ghc-network))
+    (native-inputs (list ghc-tasty ghc-tasty-quickcheck ghc-quickcheck))
+    (home-page "https://github.com/haskell-tls/hs-tls")
+    (synopsis "TLS/SSL protocol native implementation (server and client)")
+    (description
+     "This package provides a native Haskell TLS and SSL protocol
+implementation for server and client.  It provides a high-level implementation
+of a sensitive security protocol, eliminating a common set of security issues
+through the use of the advanced type system, high level constructions and
+common Haskell features.  It currently implements the SSL3.0, TLS1.0, TLS1.1
+and TLS1.2 protocol, and supports RSA and Ephemeral (Elliptic curve and
+regular) Diffie Hellman key exchanges, and many extensions.")
+    (license license:bsd-3)))
+
 (define-public ghc-hsopenssl
  (package
    (name "ghc-hsopenssl")
@@ -1016,14 +960,17 @@ the tls package, and borrows some ideas from x509-system.")
       (method url-fetch)
       (uri (hackage-uri "openssl-streams" version))
       (sha256
-        (base32 "10pnnpzgb5xr811kc9qdk7h2cgn6hk2yiyhnzz8f8p0fjzc0pwjm"))))
+        (base32
+         "10pnnpzgb5xr811kc9qdk7h2cgn6hk2yiyhnzz8f8p0fjzc0pwjm"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "openssl-streams")))
-    (inputs (list ghc-hsopenssl ghc-io-streams ghc-network))
-    (native-inputs (list ghc-hunit ghc-test-framework ghc-test-framework-hunit))
+    (inputs
+     (list ghc-hsopenssl ghc-io-streams ghc-network))
+    (native-inputs
+     (list ghc-hunit ghc-test-framework ghc-test-framework-hunit))
    (arguments
-     `(#:cabal-revision ("3"
-                         "1vizl9yajkbd59rrnfb38xwq7hfj36avbv6vwqnkhbvz3qaj3dwg")))
+     `(#:cabal-revision ("1"
+                         "0vfawnfcjrw29qg1n7k6z6bk4bmnk869gjlr9mxw4mzxgl80b2vp")))
    (home-page "https://hackage.haskell.org/package/openssl-streams")
    (synopsis "OpenSSL network support for io-streams")
    (description "This library contains io-streams routines for secure
@@ -1686,6 +1686,12 @@ SRC_HC_OPTS += -optc-mno-outline-atomics
              (file-pattern ".*\\.conf\\.d$")
              (file-type 'directory)))))))

+;; Versions newer than ghc defined below (i.e. the compiler
+;; haskell-build-system uses) should use ghc-next as their name to
+;; ensure ghc (without version specification) and ghc-* packages are
+;; always compatible. See https://issues.guix.gnu.org/issue/47335.
+(define-public ghc ghc-9.2)
+
 ;; 9.4 is the last version to support the make-based build system,
 ;; but it boot with 9.2, only 9.0 is supported.
 (define ghc-bootstrap-for-9.4 ghc-9.0)
@@ -1749,24 +1755,22 @@ SRC_HC_OPTS += -optc-mno-outline-atomics
  (let ((base ghc-9.2))
    (package
      (inherit base)
-      (name "ghc")
-      (version "9.4.3")
+      (name "ghc-next")
+      (version "9.4.4")
      (source (origin
                (method url-fetch)
                (uri (string-append "https://www.haskell.org/ghc/dist/" version
                                    "/ghc-" version "-src.tar.xz"))
                (sha256
                 (base32
-                  "0nlhx2cbq1jh2yr6zk475lavjkh9sncj57qp77p51pkfad4kkxpa"))
+                  "1qk7rlqf02s3b6m6sqqngmjq1mxnrz88h159lz6k25gddmdg5kp8"))
                (patches (search-patches "ghc-9-StgCRunAsm-only-when-needed.patch"))))
      (arguments
       (substitute-keyword-arguments arguments
         ((#:phases phases '%standard-phases)
          #~(modify-phases #$phases
             ;; Files don’t exist any more.
-             (delete 'skip-tests)))
-         ((#:tests? _ #f)
-          #f)))
+             (delete 'skip-tests)))))
      (native-inputs
       `(;; GHC 9.4 must be built with GHC >= 9.0.
         ("ghc-bootstrap" ,ghc-bootstrap-for-9.4)
@@ -1778,7 +1782,8 @@ SRC_HC_OPTS += -optc-mno-outline-atomics
                    version "/ghc-" version "-testsuite.tar.xz"))
             (sha256
              (base32
-               "1xbps33pq6mg2bwp5gvmc4qhgdq52yng5993if99b9s3fylqk86l"))))
+               "04p2lawxxg3nyv6frzhyjyh3arhqqyh5ka3alxa2pxhcd2hdcja3"))
+             (patches (search-patches "ghc-testsuite-recomp015-execstack.patch"))))
         ("ghc-alex" ,ghc-alex-bootstrap-for-9.4)
         ("ghc-happy" ,ghc-happy-bootstrap-for-9.4)
         ,@(filter (match-lambda
@@ -1793,326 +1798,4 @@ SRC_HC_OPTS += -optc-mno-outline-atomics
              (file-pattern ".*\\.conf\\.d$")
              (file-type 'directory)))))))

-;;; GHC >= 9.6 must be built using it's new haskell-written Hadrian build
-;;; system. Use this opportunity to cut the inheritance chain to simplify
-;;; understanding what building ghc requires with the new build system.
-
-(define-public ghc-9.8
-  (let ((ghc-bootstrap ghc-9.4))
-    (package
-      (name "ghc")
-      (version "9.8.1")
-      (source (origin
-                (method url-fetch)
-                (uri (string-append "https://downloads.haskell.org/~ghc/" version
-                                    "/ghc-" version "-src.tar.xz"))
-                (sha256
-                 (base32
-                  "0l87yb8hmd350klrp6lw2h9hjlla11pgzx1n4jlrfdvkgxmyvy5j"))))
-      (outputs (list "out" "doc"))
-      (arguments
-       (list
-        #:make-flags #~(list "-V" "--docs=no-sphinx")
-       #:configure-flags
-       #~(list
-           (string-append "--with-gmp-libraries="
-                          (assoc-ref %build-inputs "gmp") "/lib")
-           (string-append "--with-gmp-includes="
-                          (assoc-ref %build-inputs "gmp") "/include")
-           "--with-system-libffi"
-           (string-append "--with-ffi-libraries="
-                          (assoc-ref %build-inputs "libffi") "/lib")
-           (string-append "--with-ffi-includes="
-                          (assoc-ref %build-inputs "libffi") "/include")
-           (string-append "--with-curses-libraries="
-                          (assoc-ref %build-inputs "ncurses") "/lib")
-           (string-append "--with-curses-includes="
-                          (assoc-ref %build-inputs "ncurses") "/include"))
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-before 'build 'fix-iserv-rpath
-              (lambda _
-                (mkdir-p "_build")
-                (call-with-output-file
-                 "_build/hadrian.settings"
-                 (lambda (port)
-                   (display
-                    (string-append
-                     "*.iserv.ghc.link.opts += -optl-Wl,-rpath,"
-                     #$output "/lib/ghc-" #$(package-version this-package)
-                     "/lib/" #$(or (%current-target-system)
-                                   (%current-system))
-                     "-ghc-" #$(package-version this-package) "/")
-                    port)))))
-            ;; This phase patches the 'ghc-pkg' command so that it sorts the list
-            ;; of packages in the binary cache it generates.
-            (add-before 'build 'fix-ghc-pkg-nondeterminism
-              (lambda _
-                (substitute* "utils/ghc-pkg/Main.hs"
-                  (("confs = map \\(path </>\\) \\$ filter \\(\".conf\" `isSuffixOf`\\) fs")
-                   "confs = map (path </>) $ filter (\".conf\" `isSuffixOf`) (sort fs)"))))
-            (add-after 'unpack 'unpack-testsuite
-              (lambda* (#:key inputs #:allow-other-keys)
-                (with-directory-excursion ".."
-                  (invoke "tar" "xvf" (assoc-ref inputs "ghc-testsuite")))))
-            (add-after 'unpack-testsuite 'fix-/bin/sh-references
-              (lambda* (#:key inputs #:allow-other-keys)
-                (substitute*
-                 (list "hadrian/src/Rules/BinaryDist.hs"
-                       "hadrian/src/Rules/Test.hs"
-                       "libraries/process/System/Process/Posix.hs"
-                       "libraries/process/jsbits/process.js"
-                       "libraries/unix/cbits/execvpe.c"
-                       "testsuite/tests/driver/T8602/T8602.script"
-                       "testsuite/timeout/timeout.py")
-                 (("/bin/sh") (search-input-file inputs "/bin/sh")))))
-            (add-after 'unpack-testsuite 'fix-cc-reference
-              (lambda* (#:key inputs #:allow-other-keys)
-                (substitute*
-                 (list "utils/hsc2hs/src/Common.hs")
-                 (("\"cc\"") "\"gcc\""))))
-            ;; XXX: something causes ld-wrapper to see test\ \ \ spaces/... and
-            ;; look for the files "test\", "\", "\" and "spaces/...", which obviously
-            ;; don't exist
-            (add-after 'unpack-testsuite 'fix-testsuite
-              (lambda _
-                (substitute*
-                  (list "testsuite/driver/runtests.py")
-                  (("'test   spaces'") "'dont-test-spaces'"))))
-            (add-before 'configure 'set-target-programs
-              (lambda* (#:key inputs #:allow-other-keys)
-                (let ((binutils (assoc-ref inputs "binutils"))
-                      (gcc (assoc-ref inputs "gcc"))
-                      (ld-wrapper (assoc-ref inputs "ld-wrapper")))
-                  (setenv "CC" (string-append gcc "/bin/gcc"))
-                  (setenv "CXX" (string-append gcc "/bin/g++"))
-                  (setenv "LD" (string-append ld-wrapper "/bin/ld"))
-                  (setenv "NM" (string-append binutils "/bin/nm"))
-                  (setenv "RANLIB" (string-append binutils "/bin/ranlib"))
-                  (setenv "STRIP" (string-append binutils "/bin/strip"))
-                  ;; The 'ar' command does not follow the same pattern.
-                  (setenv "fp_prog_ar" (string-append binutils "/bin/ar")))))
-            (add-before 'build 'build-hadrian
-              (lambda* (#:key (inputs '()) #:allow-other-keys)
-                (invoke "./hadrian/bootstrap/bootstrap.py"
-                        "-s" (assoc-ref inputs "hadrian-bootstrap")
-                        "-w" (which "ghc"))))
-            (add-before 'build-hadrian 'fix-environment
-              (lambda _
-                (unsetenv "GHC_PACKAGE_PATH")
-                (setenv "CONFIG_SHELL" (which "bash"))))
-            (replace 'build
-              (lambda* (#:key (parallel-build? #f) (make-flags '())
-                       #:allow-other-keys)
-                (apply invoke "_build/bin/hadrian"
-                       `("binary-dist-dir"
-                         ,@(if parallel-build?
-                             (list (string-append
-                                    "-j" (number->string
-                                          (parallel-job-count)))))
-                         ,@make-flags))))
-            (replace 'check
-              (lambda* (#:key (tests? #t) (parallel-tests? #f) (make-flags '())
-                        #:allow-other-keys)
-                (if tests?
-                  (apply invoke "_build/bin/hadrian"
-                         `(,@(if parallel-tests?
-                               (list (string-append
-                                      "-j"
-                                      (number->string (parallel-job-count))))
-                               '())
-                           ,@make-flags
-                           "test"
-                           ,(string-append
-                             "--broken-test="
-                             (string-join
-                              (list  "T15904" ; ld-wrapper, apparently
-                                     "T16521" ; no idea
-                                     ;; These fail due to gcc
-                                     ;; -Wincompatible-pointer-types, which
-                                     ;; apparently is not used in GHC's CI
-                                     ;; https://gitlab.haskell.org/ghc/ghc/-/issues/22263
-                                     "hs_try_putmvar001"
-                                     "list_threads_and_misc_roots"
-                                     "testwsdeque")))
-                           "--skip-perf"))
-                  (format #t "test suite not run~%"))))
-            (replace 'install
-              (lambda* (#:key (make-flags '()) #:allow-other-keys)
-                (apply invoke "_build/bin/hadrian"
-                       `("install"
-                         ,@make-flags
-                         ,(string-append "--prefix=" #$output)))))
-           (add-after 'install 'remove-unnecessary-references
-             (lambda* (#:key outputs #:allow-other-keys)
-               (substitute* (find-files (string-append (assoc-ref outputs "out") "/lib/")
-                                        "settings")
-                 (("/gnu/store/.*/bin/(.*)" m program) program))
-
-               ;; Remove references to "doc" output from "out" by rewriting
-               ;; the "haddock-interfaces" fields and removing the optional
-               ;; "haddock-html" field in the generated .conf files.
-               (let ((doc (assoc-ref outputs "doc"))
-                     (out (assoc-ref outputs "out")))
-                 (with-fluids ((%default-port-encoding #f))
-                   (for-each (lambda (config-file)
-                               (substitute* config-file
-                                 (("^haddock-html: .*") "\n")
-                                 (((format #f "^haddock-interfaces: ~a" doc))
-                                  (string-append "haddock-interfaces: " out))))
-                             (find-files (string-append out "/lib") ".conf")))
-                 ;; Move the referenced files to the "out" output.
-                 (for-each (lambda (haddock-file)
-                             (let* ((subdir (string-drop haddock-file (string-length doc)))
-                                    (new    (string-append out subdir)))
-                               (mkdir-p (dirname new))
-                               (rename-file haddock-file new)))
-                           (find-files doc "\\.haddock$")))))
-            (add-after 'install 'replace-$pkgroot
-              (lambda* (#:key outputs #:allow-other-keys)
-                ((@ (srfi srfi-11) let*-values)
-                  (((out) (assoc-ref outputs "out"))
-                   ((_ version) (package-name->name+version
-                                    (strip-store-file-name out))))
-                 ;; We split out the version because we want this to also work
-                 ;; with packages named "ghc-next" instead of "ghc"
-                 (substitute*
-                   (find-files
-                    (string-append (assoc-ref outputs "out") "/lib/ghc-"
-                                   version "/lib/package.conf.d/")
-                    "^.*\\.conf$")
-                   (("\\$\\{pkgroot\\}/")
-                    (string-append (assoc-ref outputs "out") "/lib/ghc-"
-                                   version "/lib/")))))))))
-      (build-system gnu-build-system)
-      (inputs (list bash-minimal gmp ncurses libffi))
-      (native-inputs
-       `(("perl" ,perl)
-         ("python" ,python)
-         ("git" ,git-minimal/pinned)
-         ("which" ,which)
-         ("ghostscript" ,ghostscript)
-         ("autoconf" ,autoconf)
-         ("automake" ,automake)
-
-         ("ghc-bootstrap" ,ghc-bootstrap)
-         ("ghc-alex" ,ghc-alex-bootstrap-for-9.4)
-         ("ghc-happy" ,ghc-happy-bootstrap-for-9.4)
-         ("ghc-testsuite"
-          ,(origin
-             (method url-fetch)
-             (uri (string-append
-                   "https://www.haskell.org/ghc/dist/"
-                   version "/ghc-" version "-testsuite.tar.xz"))
-             (sha256
-              (base32
-               "1hxylm3nhxzl7yidarlavvcg1240w4bk0hy5jnvwna24jyxz69i6"))
-             (patches (search-patches "ghc-testsuite-recomp015-execstack.patch"))))
-         ("hadrian-bootstrap"
-          ,(origin
-             (method url-fetch)
-             (uri (string-append "https://downloads.haskell.org/~ghc/"
-                                 version "/hadrian-bootstrap-sources/"
-                                 "hadrian-bootstrap-sources-"
-                                 (package-version ghc-bootstrap) ".tar.gz"))
-             (sha256
-               (base32
-                 "14dkxif9x4hy85phcj3j0glf95k04g4ab6hfchpw9vxgvk97syi1"))))))
-      (native-search-paths
-       (list (search-path-specification
-              (variable "GHC_PACKAGE_PATH")
-              (files (list (string-append "lib/ghc-" version)))
-              (file-pattern ".*\\.conf\\.d$")
-              (file-type 'directory))))
-      (home-page "https://www.haskell.org/ghc")
-      (synopsis "The Glasgow Haskell Compiler")
-      (description
-        "The Glasgow Haskell Compiler (GHC) is a state-of-the-art compiler and
-interactive environment for the functional language Haskell.")
-      (license license:bsd-3))))
-
-(define-public ghc-9.10
-  (let ((base ghc-9.8))
-    (package
-      (inherit base)
-      (name "ghc")
-      (version "9.10.2")
-      (source
-        (origin
-          (method url-fetch)
-          (uri (string-append "https://downloads.haskell.org/~ghc/" version
-                              "/ghc-" version "-src.tar.xz"))
-          (sha256
-            (base32
-             "1pm84cgr3yg99r3srdjllgz6zig8h7dbwa597srwcnjp0nh41zam"))))
-      (arguments
-        (substitute-keyword-arguments (package-arguments base)
-          ((#:phases phases #~%standard-phases)
-           #~(modify-phases #$phases
-               (replace 'check
-                 (lambda* (#:key (tests? #t) (parallel-tests? #f) (make-flags '())
-                           #:allow-other-keys)
-                   (if tests?
-                     (apply invoke "_build/bin/hadrian"
-                            `(,@(if parallel-tests?
-                                  (list (string-append
-                                         "-j"
-                                         (number->string (parallel-job-count))))
-                                  '())
-                              ,@make-flags
-                              "test"
-                              ,(string-append
-                                "--broken-test="
-                                (string-join
-                                 (list  "T15904" ; ld-wrapper, apparently
-                                        "T16521" ; no idea
-                                        ;; These fail due to gcc
-                                        ;; -Wincompatible-pointer-types, which
-                                        ;; apparently is not used in GHC's CI
-                                        ;; https://gitlab.haskell.org/ghc/ghc/-/issues/22263
-                                        "list_threads_and_misc_roots"
-                                        "stack_misc_closures")))
-                              "--skip-perf"))
-                     (format #t "test suite not run~%"))))))))
-      (native-inputs
-       `(("ghc-bootstrap" ,base)
-         ("ghc-testsuite"
-          ,(origin
-             (method url-fetch)
-             (uri (string-append
-                    "https://downloads.haskell.org/~ghc/"
-                    version "/ghc-" version "-testsuite.tar.xz"))
-             (sha256
-              (base32
-               "143ifc4g3jc6s9hcry5qha913rzwg4hpsvk6pqvxk5r0qigfxjwx"))
-             (patches (search-patches "ghc-testsuite-recomp015-execstack.patch"))))
-         ("hadrian-bootstrap"
-          ,(origin
-             (method url-fetch)
-             (uri (string-append "https://downloads.haskell.org/~ghc/" version
-                                 "/hadrian-bootstrap-sources/"
-                                 "hadrian-bootstrap-sources-"
-                                 (package-version base) ".tar.gz"))
-             (sha256
-               (base32
-                 "162lbafvdamfhx1jldax3shgk8jbbqn4an97ny363lxbdjgdn708"))))
-         ,@(filter (match-lambda
-                     (("ghc-bootstrap" . _) #f)
-                     (("ghc-testsuite" . _) #f)
-                     (("hadrian-bootstrap" . _) #f)
-                     (_ #t))
-                   (package-native-inputs base))))
-      (native-search-paths
-       (list (search-path-specification
-              (variable "GHC_PACKAGE_PATH")
-              (files (list (string-append "lib/ghc-" version)))
-              (file-pattern ".*\\.conf\\.d$")
-              (file-type 'directory)))))))
-
-;; Versions newer than ghc defined below (i.e. the compiler
-;; haskell-build-system uses) should use ghc-next as their name to
-;; ensure ghc (without version specification) and ghc-* packages are
-;; always compatible. See https://issues.guix.gnu.org/issue/47335.
-(define-public ghc ghc-9.10)
-
 ;;; haskell.scm ends here
@@ -1923,7 +1923,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
 (define-public simpleitk
  (package
    (name "simpleitk")
-    (version "2.5.4")
+    (version "2.5.3")
    (source
     (origin
       (method git-fetch)
@@ -1932,9 +1932,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1bzj5naqbgv2b31iqgz7qqk9rixsvjqycjz6l7w3gm7v1aj14jpb"))
-       (patches
-        (search-patches "simpleitk-r-4.6.0.patch"))))
+        (base32 "0fvacjfq0p8v7r2cmzwwh7bxb6ayavznhj0m81dah463x472qkd2"))))
    (build-system cmake-build-system)
    (outputs '("out" "python" "r"))
    (arguments
@@ -2034,7 +2032,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
                   version "/SimpleITKData-" version ".tar.gz"))
             (sha256
              (base32
-               "0hryvi9fgqac00ng1bfhw3lm0al1dh0ka6jglba2q368nls428nx")))))
+               "0i4f87g1rh6xxisw06gwwyi8f216qqs6ih3gghi3k49vsl0h4g5d")))))
    (synopsis "Simplified interface to @acronym{ITK, Insight Toolkit}")
    (description
     "SimpleITK is an image analysis toolkit built on top of @acronym{ITK,
@@ -45,7 +45,6 @@
 ;;; Copyright © 2025 Junker <dk@junkeria.club>
 ;;; Copyright © 2025 Hugo Buddelmeijer <hugo@buddelmeijer.nl>
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
-;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1105,53 +1104,6 @@ images of initially unknown height.")
    (license (list license:isc          ; pbmtools/p?m.5
                   license:gpl2+))))    ; the rest

-(define-public sjpeg
-  ;; No tags available.
-  (let ((commit "46da5aec5fce05faabf1facf0066e36e6b1c4dff")
-        (revision "0"))
-    (package
-      (name "sjpeg")
-      (version (git-version "0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/webmproject/sjpeg")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "0r496mp2ylisspwxl4883pzbl0l8qpscd1x9l7sb5nnmknawr868"))))
-      (build-system cmake-build-system)
-      (arguments
-       (list
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-after 'unpack 'patch-cmake
-              (lambda _
-                ;; Enable building shared libraries.
-                (substitute* "CMakeLists.txt"
-                  (("add_library\\(sjpeg " all)
-                   (string-append all "SHARED ")))))
-            (add-before 'check 'patch-tests
-              (lambda _
-                (with-directory-excursion "../source/tests"
-                  (substitute* '("test_cmd.sh" "test_png_jpg.sh")
-                    (("\\.\\./examples") "../../build")))))
-            (replace 'check
-              (lambda* (#:key tests? #:allow-other-keys)
-                (when tests?
-                  (with-directory-excursion "../source/tests"
-                    (invoke "./test_cmd.sh")
-                    (invoke "./test_png_jpg.sh"))))))))
-      (inputs (list freeglut libjpeg-turbo libpng zlib))
-      (home-page "https://github.com/webmproject/sjpeg")
-      (synopsis "Simple JPEG encoder")
-      (description
-       "sjpeg is a simple encoding library for encoding baseline JPEG files.
-It is also a command-line tool that takes PNG or JPEG images as input to
-produce JPEG files.")
-    (license license:asl2.0))))
-
 (define-public openjpeg-data
  (package
    (name "openjpeg-data")
@@ -1228,63 +1180,6 @@ JPEG 2000 Reference Software.")
    (home-page "https://github.com/uclouvain/openjpeg")
    (license license:bsd-2)))

-(define jp2k-test-codestreams
- (origin
-   (method git-fetch)
-   (uri (git-reference
-         (url "https://github.com/aous72/jp2k_test_codestreams")
-         (commit "eda0844b9f3be47d9b64194bcea5eb1ac2285e39")))
-   (sha256
-    (base32 "1sci4a4dvgrgmrf942zdf0hqhcx30a5lffwfy6r3hya35l3q8q8f"))))
-
-(define-public openjph
-  (package
-    (name "openjph")
-    (version "0.27.3")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/aous72/OpenJPH")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1knygwn4bf6n53qr12w05yava7464x3c70rf5r20sz8adjcfccvx"))))
-    (build-system cmake-build-system)
-    (arguments
-     (list
-      #:configure-flags
-      #~(if #$(%current-target-system)
-            '()
-            '("-DOJPH_BUILD_TESTS=ON"))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'patch-cmake
-            (lambda _
-              (substitute* "tests/CMakeLists.txt"
-                (("^FetchContent_MakeAvailable\\(googletest\\)")
-                 #$(if (%current-target-system)
-                       ""
-                       "find_package(GTest REQUIRED)"))
-                (("^FetchContent_MakeAvailable\\(jp2k_test_codestreams\\).*")
-                 ""))))
-          #$@(if (%current-target-system)
-                 #~()
-                 #~((add-before 'check 'unpack-jp2k-test-codestreams
-                      (lambda _
-                        (copy-recursively #$jp2k-test-codestreams
-                                          "tests/jp2k_test_codestreams"))))))))
-    (native-inputs (if (%current-target-system)
-                       '()
-                       (list googletest)))
-    (inputs (list libtiff))
-    (home-page "https://github.com/aous72/OpenJPH")
-    (synopsis "JPEG2000 Part-15 (or JPH or HTJ2K) implementation")
-    (description
-     "OpenJPH is an implementation of @acronym{HTJ2K, High-throughput JPEG2000},
-also known as JPH, JPEG2000 Part 15, ISO/IEC 15444-15, and ITU-T T.814.")
-    (license license:bsd-2)))
-
 (define-public openslide
  (package
    (name "openslide")
@@ -379,15 +379,6 @@ as the native format.")
                   ;; Re-instate the tests disabled in inkscape/pinned, now that
                   ;; their ImageMagick requirement is satisfied.
                   #~((replace 'check (assoc-ref gnu:%standard-phases 'check))))
-            #$@(if (or (target-aarch64?)
-                       (target-ppc64le?)
-                       (target-riscv64?))
-                   '((add-after 'unpack 'disable-geom-pathstroke-test
-                       (lambda _
-                         ;; https://gitlab.com/inkscape/lib2geom/-/work_items/80
-                         (substitute* "testfiles/CMakeLists.txt"
-                           (("    geom-pathstroke-test") "")))))
-                   '())
            (replace 'wrap-program
              ;; Ensure Python is available at runtime.
              (lambda _
@@ -326,6 +326,13 @@ surveys")
 accessibility clients such as screen readers.")
    (license license:lgpl2.1+)))

+(define-public libqaccessibilityclient-qt5
+  (package
+    (inherit libqaccessibilityclient)
+    (name "libqaccessibilityclient-qt5")
+    (inputs (modify-inputs inputs
+              (replace "qtbase" qtbase-5)))))
+
 (define-public qca
  (package
    (name "qca")
@@ -189,14 +189,14 @@ structure.  It features:
 (define-public kcachegrind
  (package
    (name "kcachegrind")
-    (version "26.04.1")
+    (version "25.12.3")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://kde/stable/release-service/" version
                                  "/src/kcachegrind-" version ".tar.xz"))
              (sha256
               (base32
-                "1krd0zbssj5q9shwdpmsnzpah2p6insl0sdh3x6dbrwnlyqaydbv"))))
+                "1lpgx3i2h3iq99nsssgwjpsvsn6izy4sp5l8rh7984lbd06wqsp9"))))
    (build-system cmake-build-system)
    (native-inputs
     (list extra-cmake-modules perl python qttools kdoctools))
@@ -35,50 +35,6 @@
 ;;; Libraries:
 ;;;

-(define-public go-github-com-elastic-crd-ref-docs
-  (package
-    (name "go-github-com-elastic-crd-ref-docs")
-    (version "0.3.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/elastic/crd-ref-docs")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0vg3zjcgcq04cbqc8sk638q9v5r62w8r8x22yl7g9blbbr13sj7s"))
-       (modules '((guix build utils)))
-       (snippet
-        #~(begin
-            ;; Submodules with their own go.mod files and packaged separately:
-            ;;
-            ;; - github.com/elastic/crd-ref-docs/test
-            (delete-file-recursively "test")))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:skip-build? #t
-      #:import-path "github.com/elastic/crd-ref-docs"))
-    (native-inputs
-     (list go-github-com-stretchr-testify))
-    (propagated-inputs
-     (list go-github-com-goccy-go-yaml
-           go-github-com-masterminds-sprig-v3
-           go-github-com-spf13-cobra
-           go-golang-org-x-tools
-           go-go-uber-org-zap
-           go-k8s-io-apimachinery
-           go-sigs-k8s-io-controller-runtime
-           ;; go-sigs-k8s-io-gateway-api
-           go-sigs-k8s-io-controller-tools))
-    (home-page "https://github.com/elastic/crd-ref-docs")
-    (synopsis "Kubernetes CRD reference documentation generator")
-    (description
-     "This package generates API reference documentation by scanning a source
-tree for exported @acronym{CustomResourceDefinition, CRD} types.")
-    (license license:asl2.0)))
-
 (define-public go-go-etcd-io-etcd-client-v3
  (package
    (name "go-go-etcd-io-etcd-client-v3")
@@ -659,95 +615,6 @@ controllers that manipulate both Kubernetes CRDs and aggregated/built-in
 Kubernetes APIs.")
    (license license:asl2.0)))

-(define-public go-sigs-k8s-io-controller-tools
-  (package
-    (name "go-sigs-k8s-io-controller-tools")
-    (version "0.19.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/kubernetes-sigs/controller-tools")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1n6vc681bhhk972l1ijg7m01xy3zvi5i17y6fhac1m7bs7rrgz1l"))
-       (modules '((guix build utils)))
-       (snippet
-        #~(begin
-            ;; Submodules with their own go.mod files and packaged separately:
-            ;;
-            ;; - github.com/google/cel-go/codelab
-            (for-each delete-file-recursively
-                      (list "pkg/crd/testdata"
-                            "pkg/loader/testmod"
-                            "pkg/webhook/testdata"
-                            "pkg/deepcopy/testdata"
-                            "pkg/schemapatcher/testdata"
-                            "pkg/applyconfiguration/testdata/cronjob"))))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:skip-build? #t
-      #:test-flags
-      #~(list "-skip" (string-join
-                       ;;  Expected success, but got an error:
-                       ;;   <*fs.PathError | 0xc000314a20>:
-                       ;;   chdir ./testdata: no such file or directory
-                       ;;   {
-                       ;;       Op: "chdir",
-                       ;;       Path: "./testdata",
-                       ;;       Err: <syscall.Errno>0x2,
-                       ;;   }
-                       ;; 0 Passed | 1 Failed
-                       (list "TestObjectGeneration"
-                             ;; 23 Passed | 19 Failed
-                             "TestCRDGeneration"
-                             ;; validation_test.go:118:
-                             ;; failed to create validator:
-                             ;; open ./testdata/testdata.kubebuilder.io_oneofs.yaml:
-                             ;; no such file or directory
-                             "TestOneOfConstraints"
-                             ;; 3 Passed | 8 Failed
-                             "TestLoader"
-                             ;; 0 Passed | 2 Failed
-                             "TestInPlaceCRDSchemaGeneration"
-                             ;; 0 Passed | 11 Failed
-                             "TestWebhookGeneration"
-                             ;; 1 Passed | 1 Failed
-                             "TestVersioning")
-                       "|"))
-      #:import-path "sigs.k8s.io/controller-tools"
-      #:embed-files
-      #~(list "authoring.tmpl")))
-    (native-inputs
-     (list go-github-com-google-go-cmp
-           go-github-com-onsi-ginkgo
-           go-github-com-onsi-gomega))
-    (propagated-inputs
-     (list go-github-com-fatih-color
-           go-github-com-gobuffalo-flect
-           go-github-com-spf13-cobra
-           go-github-com-spf13-pflag
-           go-golang-org-x-tools
-           go-golang-org-x-tools-go-packages-packagestest
-           go-gopkg-in-yaml-v2
-           go-gopkg-in-yaml-v3
-           go-k8s-io-api
-           go-k8s-io-apiextensions-apiserver
-           go-k8s-io-apimachinery
-           go-k8s-io-apiserver
-           go-k8s-io-code-generator
-           go-k8s-io-gengo-v2
-           go-k8s-io-utils
-           go-sigs-k8s-io-yaml))
-    (home-page "https://sigs.k8s.io/controller-tools")
-    (synopsis "Kubernetes controller-tools Project")
-    (description
-     "The Kubernetes controller-tools Project is a set of go libraries for building
-Controllers.")
-    (license license:asl2.0)))
-

 ;;;
 ;;; Executables:
@@ -820,45 +687,6 @@ api-status.csv files
 functions
@end itemize")))

-(define-public kubernetes-controller-tools
-  (package/inherit go-sigs-k8s-io-controller-tools
-    (name "kubernetes-controller-tools")
-    (arguments
-     (substitute-keyword-arguments arguments
-       ((#:import-path _) "sigs.k8s.io/controller-tools/cmd/...")
-       ((#:install-source? #t #t) #f)
-       ((#:skip-build? #t #t) #f)
-       ((#:tests? #t #t) #f)
-       ((#:unpack-path _ "") "sigs.k8s.io/controller-tools")))
-    (native-inputs
-     (package-propagated-inputs go-sigs-k8s-io-controller-tools))
-    (propagated-inputs '())
-    (inputs '())
-    (description
-     "This package provides helper commands to work with Kubernetes (k8s):
-@itemize:
-@item @command{controller-gen} - generates Kubernetes API extension resources
-and code
-@item @command{helpgen} - generates marker help using @command{godoc}, based
-on the presence of a particular marker
-@item @command{type-scaffold} - scaffolds out basic bits of a Kubernetes type
-@end itemize
-
-For the Go library, refer to go-sigs-k8s-io-controller-tools package.")))
-
-(define-public kubernetes-crd-ref-docs
-  (package/inherit go-github-com-elastic-crd-ref-docs
-    (name "kubernetes-crd-ref-docs")
-    (arguments
-     (substitute-keyword-arguments arguments
-       ((#:install-source? #t #t) #f)
-       ((#:skip-build? #t #t) #f)
-       ((#:tests? #t #t) #f)))
-    (native-inputs
-     (package-propagated-inputs go-github-com-elastic-crd-ref-docs))
-    (propagated-inputs '())
-    (inputs '())))
-
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above in alphabetic order:
@@ -15,7 +15,6 @@
 ;;; Copyright © 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2026 Nguyễn Gia Phong <cnx@loang.net>
 ;;; Copyright © 2026 Artyom V. Poptsov <poptsov.artyom@gmail.com>
-;;; Copyright © 2026 Spencer King <spencer.king@wustl.edu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -38,7 +37,6 @@
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages audio)
  #:use-module (gnu packages base)
-  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages dbm)
@@ -52,7 +50,6 @@
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages ibus)
  #:use-module (gnu packages java)
-  #:use-module (gnu packages libffi)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages man)
@@ -91,8 +88,7 @@
  #:use-module (guix gexp)
  #:use-module (guix git-download)
  #:use-module (guix modules)
-  #:use-module (guix utils)
-  #:use-module (srfi srfi-1))
+  #:use-module (guix utils))

 (define-public nimf
  (package
@@ -1113,106 +1109,6 @@ for longer text sequences.  As it relies on dictionaries,
 if a word is missing or mispelled, the detection will fail.")
    (license license:agpl3)))

-;; This package provides the database files created by
-;; The Árni Magnússon Institute for Icelandic Studies which
-;; are needed for building certain packages.
-;; This package is not intended to be installed directly.
-(define arnastofnun-dim
-  (let ((version "May2026"))
-    (origin
-      (method git-fetch)
-      (uri (git-reference
-             (url "https://codeberg.org/spencerking/DIM-mirror")
-             (commit version)))
-      (file-name (git-file-name "arnastofnun-dim" version))
-      (sha256
-       (base32 "1ribxkdj9clafdqa572bp0qh73spv4wagyx49jqdivq8r3b631n6")))))
-
-(define-public python-islenska-bootstrap
-  (hidden-package
-   (package
-     (name "python-islenska-bootstrap")
-     (version "1.1.1")
-     ;; Use the git source since this should not include database files.
-     (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/mideind/BinPackage")
-               (commit version)))
-        (file-name (git-file-name "python-islenska" version))
-        (sha256
-         (base32 "1wgv2k41m1jmsqr1sdlj92kw5v3d5r9cg2268vfh8308pncn1fya"))))
-     (build-system pyproject-build-system)
-     (arguments
-      (list
-       #:phases
-       ;; Add two new phases to ensure that the database resource files
-       ;; are included in the installed package. This is necessary for
-       ;; running the bundled build scripts (tools/binpack.py and
-       ;; tools/dawgbuilder.py) when bootstrapping.
-       #~(modify-phases %standard-phases
-           (add-after 'unpack 'create-manifest-in
-             (lambda* (#:key inputs #:allow-other-keys)
-               (with-output-to-file "MANIFEST.in"
-                 (lambda ()
-                   (display "graft src/islenska/resources")))))
-           (add-after 'unpack 'patch-setup-py
-             (lambda* (#:key inputs #:allow-other-keys)
-               (substitute* "setup.py"
-                 (("(.*)cffi_modules=.*" cffi indent)
-                  (string-append
-                   cffi
-                   indent "package_data={'islenska':['src/resources/*']},\n"
-                   indent "include_package_data=True,\n"))))))
-       ;; Tests will fail since database files have not been bootstrapped yet.
-       #:tests? #f))
-     (propagated-inputs (list python-cffi python-typing-extensions))
-     (native-inputs (list python-cffi python-pytest python-setuptools))
-     (home-page "https://github.com/mideind/BinPackage")
-     (synopsis
-      "The vocabulary of modern Icelandic, encapsulated in a Python package")
-     (description
-      "Islenska is a Python package that embeds the vocabulary of the Database
-of Icelandic Morphology and offers various lookups and queries of the data.
-The database contains over 6.5 million entries, over 3.1 million unique word
-forms, and about 300,000 distinct lemmas.")
-     (license license:expat))))
-
-(define-public python-islenska
-  (package/inherit python-islenska-bootstrap
-    (name "python-islenska")
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          ;; Delete the phases added for python-islenska-bootstrap.
-          (delete 'create-manifest-in)
-          (delete 'patch-setup-py)
-          ;; Copy KRISTINsnid.csv to the expected directory
-          ;; for the build scripts.
-          (add-after 'unpack 'unpack-resources
-            (lambda* (#:key inputs #:allow-other-keys)
-              (install-file
-               (search-input-file inputs "KRISTINsnid.csv/KRISTINsnid.csv")
-               "src/islenska/resources")))
-          ;; Run the build scripts
-          (add-before 'build 'build-databases
-            (lambda _
-              (invoke "python" "tools/binpack.py")
-              (invoke "python" "tools/dawgbuilder.py"))))
-      #:tests? #t))
-    (native-inputs (list arnastofnun-dim
-                         python-cffi
-                         python-islenska-bootstrap
-                         python-pytest
-                         python-setuptools
-                         unzip))
-    (license (list license:cc-by4.0     ;resource files
-                   license:expat))
-    (properties
-     (alist-delete 'hidden? (package-properties python-islenska-bootstrap)))))
-
 (define-public python-sacremoses
  (package
    (name "python-sacremoses")
@@ -530,7 +530,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."

 ;; The current "mainline" kernel.

-(define-public linux-libre-7.0-version "7.0.10")
+(define-public linux-libre-7.0-version "7.0.8")
 (define-public linux-libre-7.0-gnu-revision "gnu")
 (define deblob-scripts-7.0
  (linux-libre-deblob-scripts
@@ -540,7 +540,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "0a7572zw5y3k4gs4p3h5w0s9bhd63pdjxz6vxbr96sq6r8b6k02n")))
 (define-public linux-libre-7.0-pristine-source
  (let ((version linux-libre-7.0-version)
-        (hash (base32 "1p1j9s0b4qv9m0pm6vj477rqgyd1b0lsk0gy74cks3n2cbmpfj89")))
+        (hash (base32 "08nbdmgy4bbpmjzkh6n4v3shksvxpcxhy8biv5w7qkwz5jrayi8r")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-7.0)))
@@ -563,7 +563,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                            (%upstream-linux-source version hash)
                            deblob-scripts-6.19)))

-(define-public linux-libre-6.18-version "6.18.33")
+(define-public linux-libre-6.18-version "6.18.31")
 (define-public linux-libre-6.18-gnu-revision "gnu")
 (define deblob-scripts-6.18
  (linux-libre-deblob-scripts
@@ -573,7 +573,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "0qlih8w8wg4v5cwbmd34rbhb6mjgbx69i9rx3s2vxw7h42q9l0ai")))
 (define-public linux-libre-6.18-pristine-source
  (let ((version linux-libre-6.18-version)
-        (hash (base32 "10mp1ypsdz42jr26g1xxbw806mvpy0n35418fhsgxxlr4lqgy5kg")))
+        (hash (base32 "1djqya5jlgg0q0ra5mvqdfcsbf13vxffhgxyqvy9qh2x91nvi850")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-6.18)))
@@ -582,7 +582,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; Here are the support timelines:
 ;; <https://www.kernel.org/category/releases.html>

-(define-public linux-libre-6.12-version "6.12.91")
+(define-public linux-libre-6.12-version "6.12.89")
 (define-public linux-libre-6.12-gnu-revision "gnu")
 (define deblob-scripts-6.12
  (linux-libre-deblob-scripts
@@ -592,12 +592,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "1x48hpmvajz7v5wn1vdd7l5r14mq4ngzh5npz3pj81z4f1g61i0a")))
 (define-public linux-libre-6.12-pristine-source
  (let ((version linux-libre-6.12-version)
-        (hash (base32 "0sbrb612b653w64g5jkpbf68y0fka2sgnwblam41k7wz2sgapwhg")))
+        (hash (base32 "184r0wji02qw2n7ncx0jrf382yk20nnf79fvafim6a4x9a0gsnjq")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-6.12)))

-(define-public linux-libre-6.6-version "6.6.141")
+(define-public linux-libre-6.6-version "6.6.138")
 (define-public linux-libre-6.6-gnu-revision "gnu")
 (define deblob-scripts-6.6
  (linux-libre-deblob-scripts
@@ -607,12 +607,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "0xp9b2vkrb0g0rn4i33b59rhp4sgh1dbwzk28vwz7kwac6l5rcpi")))
 (define-public linux-libre-6.6-pristine-source
  (let ((version linux-libre-6.6-version)
-        (hash (base32 "1qbzxgqs7q9gyqfrf0j7p0pgjxnjj5mibamhm280mf9anqp6bhiv")))
+        (hash (base32 "03x8ald0sjzdb6kpzrw8adnc78r3mdxrx8mzbxbpwp35vdgnpl5d")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-6.6)))

-(define-public linux-libre-6.1-version "6.1.174")
+(define-public linux-libre-6.1-version "6.1.172")
 (define-public linux-libre-6.1-gnu-revision "gnu")
 (define deblob-scripts-6.1
  (linux-libre-deblob-scripts
@@ -622,12 +622,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "1w5pfws6l39dpc3lzazs1n6r4m96f6rdf6vb2scy5fhmrd933ldc")))
 (define-public linux-libre-6.1-pristine-source
  (let ((version linux-libre-6.1-version)
-        (hash (base32 "0vp07x4v82qnmc1pifv3ynp2ab5mvlbfnpqvs5893bi3yrnk927d")))
+        (hash (base32 "16dlfdzjcsc21m5sfbhamg8y3ay54rz8a0qqvqrmxq691mhjwrzi")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-6.1)))

-(define-public linux-libre-5.15-version "5.15.208")
+(define-public linux-libre-5.15-version "5.15.206")
 (define-public linux-libre-5.15-gnu-revision "gnu")
 (define deblob-scripts-5.15
  (linux-libre-deblob-scripts
@@ -637,12 +637,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "1s6km2r2mad0wpf7nqn4rqsykw1lm386l1yskmil24239fbva1f1")))
 (define-public linux-libre-5.15-pristine-source
  (let ((version linux-libre-5.15-version)
-        (hash (base32 "0wmi50q8vgblhbh77d1a4sw4snymr6srqd22bxcjg9i7wcv70gdm")))
+        (hash (base32 "07z6lla7xpnn4sn3l4zw3x7m8ih8w6h54k71qrxrf5zv9i7wxijz")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-5.15)))

-(define-public linux-libre-5.10-version "5.10.257")
+(define-public linux-libre-5.10-version "5.10.255")
 (define-public linux-libre-5.10-gnu-revision "gnu1")
 (define deblob-scripts-5.10
  (linux-libre-deblob-scripts
@@ -652,7 +652,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "1hgza8fsps7bkjf4i0f2xgvrh1r183z3i6lxrr2nr8qbi5d13qs7")))
 (define-public linux-libre-5.10-pristine-source
  (let ((version linux-libre-5.10-version)
-        (hash (base32 "1lghcrxc1fqarvym03jrcda2a3labc887ci9yjqgbmv3nphzvc88")))
+        (hash (base32 "19v6g2fq4nqv38irlcd9x14s6d398c56mxzpyc03q4xmpy3v6mir")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-5.10)))
@@ -76,7 +76,6 @@
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bdw-gc)
  #:use-module (gnu packages boost)
-  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages crypto)
@@ -103,6 +102,7 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages notcurses)
  #:use-module (gnu packages onc-rpc)
  #:use-module (gnu packages perl)
@@ -27,7 +27,7 @@
 (define-public lout
  (package
    (name "lout")
-    (version "3.43.4")
+    (version "3.43.2")

    ;; The original version at <https://savannah.nongnu.org/projects/lout/> is
    ;; effectively abandoned, not receiving build fixes and the likes, and
@@ -41,7 +41,7 @@
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "09s6mcimvhw96i3vncqa8cz04xcq9x3qir8m1nzqfny8vdwyz35n"))))
+                "0lvk1ffzgydgj4csaclrh3a9nwla061clgf8lda6n47masg12qzi"))))
    (build-system gnu-build-system)     ; actually, just a makefile
    (outputs '("out" "doc"))
    (native-inputs
@@ -74,6 +74,7 @@
  #:use-module (gnu packages linux)
  #:use-module (gnu packages m4)
  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages pretty-print)
  #:use-module (gnu packages rdf)
@@ -150,22 +151,6 @@ automatic memory management with incremental garbage collection, making it ideal
 for configuration, scripting, and rapid prototyping.")
    (license license:x11)))

-(define-public lua-5.5
-  (package (inherit lua)
-           (version "5.5.0")
-           (source (origin
-                     (method url-fetch)
-                     (uri (string-append "https://www.lua.org/ftp/lua-"
-                                         version ".tar.gz"))
-                     (sha256
-                      (base32 "0gcbsr00difm2s82pflxg28zcnjka9048lncbfvwl1fhpcmw7k2p"))
-                     ;; Note: Some lua-5.4 patches seem to apply without issues
-                     (patches (search-patches "lua-5.4-pkgconfig.patch"
-                                              "lua-5.4-liblua-so.patch"
-                                              "lua-5.x-search-path-helpers.patch"
-                                              "lua-5.5-search-paths.patch"))))
-           (native-search-paths (lua-search-paths "5.5"))))
-
 (define-public lua-5.4
  (package (inherit lua)
           (version "5.4.8")
@@ -96,6 +96,7 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages monitoring)
  #:use-module (gnu packages mpi)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages onc-rpc)
  #:use-module (gnu packages oneapi)
@@ -328,7 +328,7 @@ PostScript, and PDF.  Additional tools include the @command{man} viewer, and
 (define-public man-pages
  (package
    (name "man-pages")
-    (version "6.18")
+    (version "6.16")
    (source
     (origin
       (method url-fetch)
@@ -338,7 +338,7 @@ PostScript, and PDF.  Additional tools include the @command{man} viewer, and
              (string-append "mirror://kernel.org/linux/docs/man-pages/Archive/"
                             "man-pages-" version ".tar.xz")))
       (sha256
-        (base32 "1l949fvqikf88qjxbp1wny185prd3mcgcd3s49l8qx2rigfgld69"))))
+        (base32 "18yp64vb8br49d44jmq47dc901n7p20nqs88zsf8106dfnypl94f"))))
    (build-system gnu-build-system)
    (arguments
     (list
@@ -125,7 +125,6 @@
  #:use-module (gnu packages benchmark)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages boost)
-  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages calendar)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cmake)
@@ -177,6 +176,7 @@
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages netpbm)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages onc-rpc)
  #:use-module (gnu packages oneapi)
@@ -184,7 +184,7 @@ asyncio_mode = auto")))))
           python-attrs
           python-cachetools
           python-click
-           python-dbus
+           python-dbus-1.2
           python-janus
           python-keyring
           python-logbook
@@ -3857,15 +3857,11 @@ follows a traditional multi-track tape recorder control paradigm.")
     (list
      #:phases
      '(modify-phases %standard-phases
-         (add-after 'unpack 'python3.12-compatibility
+         (add-after 'unpack 'python3.11-compatibility
           (lambda _
             (substitute* '("waflib/Context.py"
                            "waflib/ConfigSet.py")
-               (("'rU'") "'r'"))
-             (substitute* "waflib/Context.py"
-               (("imp.new_module") "types.ModuleType")
-               (("import os, re, imp, sys")
-                "import os, re, types, sys"))))
+               (("'rU'") "'r'"))))
         (add-after 'unpack 'remove-sse-flags
           (lambda* (#:key system #:allow-other-keys)
             (unless (or (string-prefix? "x86_64" system)
@@ -1006,11 +1006,11 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
    (home-page "https://nng.nanomsg.org/")
    (license license:expat)))

-(define-public nng-1.11
+(define-public nng-1.10
  (package
    (inherit nng)
    (name "nng")
-    (version "1.11")
+    (version "1.10.1")
    (source
     (origin
       (method git-fetch)
@@ -1019,12 +1019,9 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1l4rxwnc9knndwmy7xg53adyrm17ld7c5gxwm7vgfmgfy0my4zy8"))))
+        (base32 "13nmz1p8qd12gyj7wm8fz1ccap47qh41sxz4jqdhj8gnd0kiy5h4"))))
    (arguments
     (list
-      ;; At least on aarch64-linux, running tests in parallel leads to ports
-      ;; being unavailable in later tests, which then fail.
-      #:parallel-tests? #false
      #:configure-flags
      '(list "-DNNG_ENABLE_COVERAGE=ON"
             "-DNNG_ENABLE_TLS=ON"
@@ -1038,7 +1035,6 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
               (("add_nng_test1\\(httpclient 60 NNG_SUPP_HTTP\\)") "")
               (("add_nng_test\\(tls 60\\)") ""))
             (substitute* "src/platform/CMakeLists.txt"
-               ;; This test only seems to fail on aarch64-linux
               (("nng_test\\(platform_test\\)") "")
               (("nng_test\\(resolver_test\\)") ""))
             (substitute* "src/sp/transport/tcp/CMakeLists.txt"
@@ -3691,7 +3687,7 @@ can be whipped up with little effort.")
    (build-system gnu-build-system)
    (native-inputs (list pkg-config))
    (inputs
-     (list jansson ncurses))
+     (list jansson libcap ncurses))
    (arguments
     `(#:tests? #f))                    ; tests require network access
    (home-page "https://www.bitwizard.nl/mtr/")
@@ -5,7 +5,6 @@
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2025 Maxim Cournoyer <maxim@guixotic.coop>
-;;; Copyright © 2026 Luca Kredel <luca.kredel@web.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,17 +22,127 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

 (define-module (gnu packages ninja)
-  #:use-module (gnu packages build-tools)
-  #:use-module (guix deprecation))
+  #:use-module ((guix licenses) #:select (asl2.0 expat))
+  #:use-module (guix gexp)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system trivial)
+  #:use-module (guix utils)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages bash)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages re2c)
+  #:use-module (srfi srfi-1))

-(define-deprecated/public-alias ninja/pinned
-  (@ (gnu packages build-tools) ninja/pinned))
+(define-public ninja/pinned
+  (hidden-package
+   (package
+     (name "ninja")
+     (version "1.13.2")
+     (source (origin
+               (method git-fetch)
+               (uri (git-reference
+                     (url "https://github.com/ninja-build/ninja")
+                     (commit (string-append "v" version))))
+               (file-name (git-file-name name version))
+               (sha256
+                (base32
+                 "0lp9dmxbjyjwv089i8mgq3nvnhpbnsn01ifm05m9s47w7cifrl8g"))))
+     (build-system gnu-build-system)
+     (inputs (list python-wrapper re2c))
+     (arguments
+      '(; Tests now require googletest, which is a circular dependency.
+        #:tests? #f
+        #:phases
+        (modify-phases %standard-phases
+          (replace 'configure
+            (lambda _
+              (substitute* "src/subprocess-posix.cc"
+                (("/bin/sh") (which "sh")))
+              (substitute* "src/subprocess_test.cc"
+                (("/bin/echo") (which "echo")))))
+          (replace 'build
+            (lambda _
+              (invoke "./configure.py" "--bootstrap")))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "./configure.py")
+                (invoke "./ninja" "ninja_test")
+                (invoke "./ninja_test"))))
+          (replace 'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (bin (string-append out "/bin"))
+                     (doc (string-append out "/share/doc/ninja")))
+                (install-file "ninja" bin)
+                (install-file "doc/manual.asciidoc" doc)))))))
+     (home-page "https://ninja-build.org/")
+     (synopsis "Small build system")
+     (description
+      "Ninja is a small build system with a focus on speed.  It differs from
+other build systems in two major respects: it is designed to have its input
+files generated by a higher-level build system, and it is designed to run
+builds as fast as possible.")
+    (license asl2.0))))

-(define-deprecated/public-alias ninja
-  (@ (gnu packages build-tools) ninja))
+(define-public ninja
+  (package/inherit ninja/pinned
+    (properties (alist-delete 'hidden? (package-properties ninja/pinned)))))

-(define-deprecated/public-alias samurai
-  (@ (gnu packages build-tools) samurai))
+(define-public samurai
+  (package
+    (name "samurai")
+    (version "1.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/michaelforney/samurai")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "04iw18hgkm72yrl83a2xh1jc47w9rilpb95kwick0j37b4q3gxj4"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:tests? #f                  ;no test suite
+           #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
+                                (string-append "PREFIX=" #$output))
+           #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'patch-/bin/sh
+                          (lambda* (#:key inputs #:allow-other-keys)
+                            (substitute* "build.c"
+                              (("/bin/sh")
+                               (search-input-file inputs "bin/sh")))))
+                        (delete 'configure))))
+    (inputs (list bash-minimal))
+    (home-page "https://github.com/michaelforney/samurai")
+    (synopsis "Ninja-compatible build tool written in C")
+    (description "@code{samurai} is a ninja-compatible build tool written in
+C99 with a focus on simplicity, speed, and portability.  It is
+feature-complete and supports most of the same options as ninja.  This package
+provides the command @command{samu}.  For a @command{ninja} command
+replacement, use the @code{samu-as-ninja-wrapper} package.")
+    (license (list asl2.0               ;for the most part
+                   expat))))            ;htab.h, htab.c and tree.c

-(define-deprecated/public-alias samu-as-ninja-wrapper
-  (@ (gnu packages build-tools) samu-as-ninja-wrapper))
+(define-public samu-as-ninja-wrapper
+  (package/inherit samurai
+    (name "samu-as-ninja-wrapper")
+    (build-system trivial-build-system)
+    (arguments
+     (list #:builder
+           (with-imported-modules '((guix build utils))
+             #~(begin
+                 (use-modules (guix build utils))
+                 (let ((bindir (string-append #$output "/bin"))
+                       (samu (string-append #$(this-package-input "samurai")
+                                            "/bin/samu")))
+                   (mkdir-p bindir)
+                   (symlink samu (string-append bindir "/ninja")))))))
+    (inputs (list samurai))
+    (description "This package provides the @command{ninja} command,
+implemented as a symbolic link to the @command{samu} command of @code{samurai}
+package.")))
@@ -109,6 +109,7 @@
  #:use-module (gnu packages markup)
  #:use-module (gnu packages nettle)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages node)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages patchutils)
@@ -304,12 +304,6 @@ human.")
                        ruby-asciidoctor/minimal))
               #~'()
               #~(list "-DWITH_XC_DOCS=NO")))
-      ;; Entries have recently become sorted per the locale, and
-      ;; causes testentrymodel to fail when using the C locale (see:
-      ;; https://github.com/keepassxreboot/keepassxc/issues/11813).
-      ;; testClip runs 'xclip', which hangs in the container,
-      ;; perhaps because it lacks a TTY.
-      #:test-exclude "testentrymodel|testcli"
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'record-clipboard-programs
@@ -333,7 +327,17 @@ human.")
                  "\")")))
              (substitute* "src/gui/Clipboard.cpp"
                (("\"wl-copy\"")
-                 (format #f "~s" (search-input-file inputs "bin/wl-copy")))))))))
+                 (format #f "~s" (search-input-file inputs "bin/wl-copy"))))))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                ;; Entries have recently become sorted per the locale, and
+                ;; causes testentrymodel to fail when using the C locale (see:
+                ;; https://github.com/keepassxreboot/keepassxc/issues/11813).
+                ;; testClip runs 'xclip', which hangs in the container,
+                ;; perhaps because it lacks a TTY.
+                (invoke "ctest" "--exclude-regex"
+                        "testentrymodel|testcli")))))))
    (native-inputs
     (append
      (list qttools-5)
@@ -1,26 +0,0 @@
-Remove nonfree tile data.
-
-Note this does not remove the directories; ensure they are snippeted out separately.
-
-Patch by bdunahu <bdunahu@operationnull.com>.
-
-diff --git a/lib/tiles/list.txt b/lib/tiles/list.txt
-index 3677ba45e..eb2592c9f 100644
--- a/lib/tiles/list.txt
-+++ b/lib/tiles/list.txt
-@@ -54,15 +48,3 @@
- size:16:16:8x16.png
- pref:graf-nmd.prf
- extra:0:0:0
-
-name:5:Shockbolt Dark
-directory:shockbolt
-size:64:64:64x64.png
-pref:graf-shb-dark.prf
-extra:1:27:31
-
-name:6:Shockbolt Light
-directory:shockbolt
-size:64:64:64x64.png
-pref:graf-shb-light.prf
-extra:1:27:31
@@ -1,58 +0,0 @@
-From 4617d2682738aeaece613ea61390dd47447c2d9f Mon Sep 17 00:00:00 2001
-From: Potato Hatsue <1793913507@qq.com>
-Date: Fri, 12 Sep 2025 06:07:02 -0700
-Subject: [PATCH] Allow QuickCheck 2.15.0
-
---
- Test/Chell/QuickCheck.hs | 8 ++++++++
- chell-quickcheck.cabal   | 2 +-
- 2 files changed, 9 insertions(+), 1 deletion(-)
-
-diff --git a/Test/Chell/QuickCheck.hs b/Test/Chell/QuickCheck.hs
-index ea1c488..3227b8e 100644
--- a/Test/Chell/QuickCheck.hs
-+++ b/Test/Chell/QuickCheck.hs
-@@ -1,3 +1,4 @@
-+{-# LANGUAGE CPP #-}
- module Test.Chell.QuickCheck (property) where
- 
- import Test.Chell qualified as Chell
-@@ -30,7 +31,12 @@ property name prop = Chell.test name $ \opts -> Text.withNullTerminal $ \term ->
-             { State.terminal = term,
-               State.maxSuccessTests = QuickCheck.maxSuccess args,
-               State.maxDiscardedRatio = QuickCheck.maxDiscardRatio args,
-+#if MIN_VERSION_QuickCheck(2,15,0)
-+              State.replayStartSize = Nothing,
-+              State.maxTestSize = QuickCheck.maxSize args,
-+#else
-               State.computeSize = computeSize (QuickCheck.maxSize args) (QuickCheck.maxSuccess args),
-+#endif
-               State.numSuccessTests = 0,
-               State.numDiscardedTests = 0,
-               State.classes = mempty,
-@@ -59,6 +65,7 @@ property name prop = Chell.test name $ \opts -> Text.withNullTerminal $ \term ->
-         Test.GaveUp {} -> Chell.TestAborted notes output
-         Test.NoExpectedFailure {} -> Chell.TestFailed notes [failure]
- 
-+#if !MIN_VERSION_QuickCheck(2,15,0)
- -- copied from quickcheck-2.4.1.1/src/Test/QuickCheck/Test.hs
- computeSize :: Int -> Int -> Int -> Int -> Int
- computeSize maxSize maxSuccess n d
-@@ -79,3 +86,4 @@ computeSize maxSize maxSuccess n d
- 
- roundTo :: Int -> Int -> Int
- roundTo n m = (n `div` m) * m
-+#endif
-diff --git a/chell-quickcheck.cabal b/chell-quickcheck.cabal
-index e854412..1f3a1d9 100644
--- a/chell-quickcheck.cabal
-+++ b/chell-quickcheck.cabal
-@@ -34,7 +34,7 @@ library
-     build-depends:
-       , base ^>= 4.16 || ^>= 4.17 || ^>= 4.18 || ^>= 4.19 || ^>= 4.20 || ^>= 4.21
-       , chell ^>= 0.5
-      , QuickCheck ^>= 2.14.2
-+      , QuickCheck ^>= 2.14.2 || ^>= 2.15.0
-       , random ^>= 1.2.1 || ^>= 1.3.0
- 
-     exposed-modules:
@@ -4,7 +4,7 @@
 	# number of sections)
 	'$(TEST_HC)' $(TEST_HC_OPTS) Generate.hs
 	./Generate > ManySections.s
-+	echo '.section .note.GNU-stack,"",@progbits' >> ManySections.s
+	echo '.section .note.GNU-stack,"",@progbits' > ManySections.s
 	echo 'main = putStrLn "Running main..."' > Main.hs
 	'$(TEST_HC)' $(TEST_HC_OPTS) -c ManySections.s
 	'$(TEST_HC)' $(TEST_HC_OPTS) --make -O Main.hs ManySections.o
@@ -1,50 +0,0 @@
-Change Lua to use GUIX_LUA_PATH and GUIX_LUA_CPATH to construct the default
-LUA_PATH and LUA_CPATH, instead of using hard-coded paths that Guix doesn't
-populate.
-
-These paths don't use Lua's usual '?' path wildcard, and thus are compatible
-with Guix's search-paths mechanism.
-
-This patch uses functions defined in lua-5.x-search-path-helpers.patch.
-
--- a/src/loadlib.c
-+++ b/src/loadlib.c
-@@ -280,7 +280,9 @@
-   if (path == NULL)  /* no versioned environment variable? */
-     path = getenv(envname);  /* try unversioned name */
-   if (path == NULL || noenv(L))  /* no environment variable? */
-    lua_pushexternalstring(L, dft, strlen(dft), NULL, NULL);  /* use default */
-+    /* Copy our constructed default string onto the Lua stack.
-+     * Otherwise the location might be reused for another string and case us problems! */
-+    lua_pushstring(L, dft);  /* use default */
-   else if ((dftmark = strstr(path, LUA_PATH_SEP LUA_PATH_SEP)) == NULL)
-     lua_pushstring(L, path);  /* nothing to change */
-   else {  /* path contains a ";;": insert default path in its place */
-@@ -721,14 +729,25 @@
- }
- 
-
-+#include "./guixpaths.c"
-+
-+
- LUAMOD_API int luaopen_package (lua_State *L) {
-   luaL_getsubtable(L, LUA_REGISTRYINDEX, CLIBS);  /* create CLIBS table */
-   lua_pop(L, 1);  /* will not use it now */
-   luaL_newlib(L, pk_funcs);  /* create 'package' table */
-   createsearcherstable(L);
-+
-   /* set paths */
-+  /* Calculate default LUA_PATH and LUA_CPATH values from their
-+     corresponding GUIX_ environment variables */
-+  const char* default_path = guix_path(L); // push default_path
-+  const char* default_cpath = guix_cpath(L); // push default_cpath
-+  lua_pushvalue(L, -3); // copy the old head of the stack back to the top
-  setpath(L, "path", LUA_PATH_VAR, LUA_PATH_DEFAULT);
-  setpath(L, "cpath", LUA_CPATH_VAR, LUA_CPATH_DEFAULT);
-+  setpath(L, "path", LUA_PATH_VAR, default_path);
-+  setpath(L, "cpath", LUA_CPATH_VAR, default_cpath);
-+  lua_pop(L, 3); // pop our three working values back off the stack
-+
-   /* store config information */
-   lua_pushliteral(L, LUA_DIRSEP "\n" LUA_PATH_SEP "\n" LUA_PATH_MARK "\n"
-                      LUA_EXEC_DIR "\n" LUA_IGMARK "\n");
@@ -0,0 +1,513 @@
+This patch shas been backported from the development version or Biostrings.
+
+From 100602242840322b5f6c267faaf8198c1a5aa2af Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
+Date: Thu, 5 Mar 2026 22:36:30 -0800
+Subject: [PATCH] Biostrings 2.79.5: Get rid of never-used SparseMIndex and
+ SparseList classes
+
+This also eliminates the non-API calls to R.
+---
+ DESCRIPTION                 |   3 +-
+ NAMESPACE                   |   2 -
+ R/MIndex-class.R            |  79 -------------------------
+ R/SparseList-class.R        |  80 -------------------------
+ man/Biostrings-internals.Rd |   9 ---
+ src/Biostrings.h            |  41 -------------
+ src/MIndex_class.c          |  67 ---------------------
+ src/R_init_Biostrings.c     |   1 -
+ src/SparseList_utils.c      | 113 ------------------------------------
+ 9 files changed, 1 insertion(+), 394 deletions(-)
+ delete mode 100644 R/SparseList-class.R
+ delete mode 100644 src/SparseList_utils.c
+
+diff --git a/DESCRIPTION b/DESCRIPTION
+index a5d027cc..dbc323ea 100644
+--- a/DESCRIPTION
+++ b/DESCRIPTION
+@@ -76,3 +76,3 @@ Collate: utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R GENETIC_CODE.R
+         injectHardMask.R padAndClip.R strsplit-methods.R misc.R
+-        SparseList-class.R MIndex-class.R lowlevel-matching.R
+        MIndex-class.R lowlevel-matching.R
+         match-utils.R matchPattern.R maskMotif.R matchLRPatterns.R
+diff --git a/NAMESPACE b/NAMESPACE
+index ba1e3bfa..cf14db67 100644
+--- a/NAMESPACE
+++ b/NAMESPACE
+@@ -206,7 +206,6 @@ exportMethods(
+ ### ==========================================================================
+ ### STRING MATCHING
+ ### --------------------------------------------------------------------------
+-###   SparseList-class.R
+ ###   MIndex-class.R
+ ###   lowlevel-matching.R
+ ###   match-utils.R
+@@ -220,7 +219,6 @@ exportMethods(
+ ###   matchPDict.R
+ 
+ exportClasses(
+-    #SparseList,
+     MIndex, ByPos_MIndex,
+     PreprocessedTB, Twobit, ACtree2,
+     PDict3Parts,
+diff --git a/R/MIndex-class.R b/R/MIndex-class.R
+index 022f6746..f50f215e 100644
+--- a/R/MIndex-class.R
+++ b/R/MIndex-class.R
+@@ -218,82 +218,3 @@ ByPos_MIndex.combine <- function(mi_list)
+     new("ByPos_MIndex", width0=ans_width0, NAMES=ans_names, ends=ans_ends)
+ }
+ 
+-
+-### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+-### The "SparseMIndex" class (DISABLED FOR NOW).
+-### 
+-### Slot description:
+-###
+-###   ends_envir: a key-value list (environment) where the values are integer
+-###       vectors containing the ending positions of the pattern whose
+-###       position in the original dictionary is given by the key (the keys are
+-###       strings representing positive integers).
+-### 
+-
+-if (FALSE) {
+-
+-  setClass("SparseMIndex",
+-    contains="MIndex",
+-    representation(
+-        ends_envir="environment"
+-    )
+-  )
+-
+-  setMethod("show", "SparseMIndex",
+-    function(object)
+-    {
+-        cat("Sparse MIndex object of length ", length(object), "\n", sep="")
+-    }
+-  )
+-
+-  setMethod("[[", "SparseMIndex",
+-    function(x, i, j, ...)
+-    {
+-        i <- normalizeDoubleBracketSubscript(i, x)
+-        ans_end <- x@ends_envir[[formatC(i, width=10, format="d", flag="0")]]
+-        if (is.null(ans_end))
+-            ans_end <- integer(0)
+-        ans_width <- rep.int(x@width0[i], length(ans_end))
+-        ans_start <- ans_end - x@width0[i] + 1L
+-        new2("IRanges", start=ans_start, width=ans_width, check=FALSE)
+-    }
+-  )
+-
+-  ### An example of a SparseMIndex object of length 5 where only the
+-  ### 2nd pattern has matches:
+-  ###   > width0 <- c(9L, 10L, 8L, 4L, 10L)
+-  ###   > ends_envir <- new.env(hash=TRUE, parent=emptyenv())
+-  ###   > ends_envir[['0000000002']] <- c(199L, 402L)
+-  ###   > mindex <- new("SparseMIndex", width0=width0, NAMES=letters[1:5], ends_envir=ends_envir)
+-  ###   > mindex[[1]]
+-  ###   > mindex[[2]]
+-  ###   > mindex[[6]] # Error in mindex[[6]] : subscript out of bounds
+-  ###   > names(mindex)
+-  ###   > mindex[["a"]]
+-  ###   > mindex[["b"]]
+-  ###   > mindex[["aa"]] # Error in mindex[["aa"]] : pattern name ‘aa’ not found
+-  ###   > startIndex(mindex)
+-  ###   > endIndex(mindex)
+-  ###   > elementNROWS(mindex)
+-  ###
+-  setMethod("startIndex", "SparseMIndex",
+-    function(x)
+-    {
+-        all.names <- TRUE
+-        .Call2("SparseMIndex_endIndex",
+-              x@ends_envir, x@width0, x@NAMES, all.names,
+-              PACKAGE="Biostrings")
+-    }
+-  )
+-  setMethod("endIndex", "SparseMIndex",
+-    function(x)
+-    {
+-        all.names <- TRUE
+-        .Call2("SparseMIndex_endIndex",
+-              x@ends_envir, NULL, x@NAMES, all.names,
+-              PACKAGE="Biostrings")
+-    }
+-  )
+-
+-}
+-
+diff --git a/R/SparseList-class.R b/R/SparseList-class.R
+deleted file mode 100644
+index 8295fd0f..00000000
+--- a/R/SparseList-class.R
+++ /dev/null
+@@ -1,80 +0,0 @@
+-### =========================================================================
+-### SparseList objects
+-### -------------------------------------------------------------------------
+-###
+-
+-setClass("SparseList",
+-    representation(
+-        length="integer",
+-        env="environment"
+-    )
+-)
+-
+-### Typical use:
+-###   env <- new.env(hash=TRUE, parent=emptyenv())
+-###   key <- formatC(98L, width=10, format="d", flag="0")
+-###   value <- 3:-2
+-###   assign(key, value, envir=env)
+-###   x <- new("SparseList", length=100L, env=env)
+-###   length(x)
+-###   ls(x)
+-###   ls(x, all.names=TRUE)
+-###   as.list(x)
+-###   as.list(x, all.names=TRUE)
+-###   x[[1]]
+-###   x[[98]
+-###   x[[101]]]
+-###
+-
+-setMethod("length", "SparseList", function(x) x@length)
+-
+-### 'pos', 'envir' and 'pattern' args are ignored
+-setMethod("ls", signature(name="SparseList"),
+-    function(name, pos, envir, all.names=FALSE, pattern)
+-    {
+-        if (!all.names)
+-            return(ls(name@env, all.names=TRUE))
+-        seq_len(length(name))
+-    }
+-)
+-
+-setMethod("as.list", "SparseList",
+-    function(x, all.names=FALSE, ...)
+-    {
+-        if (!all.names)
+-            return(as.list(x@env, all.names=TRUE))
+-        ans <- vector(mode="list", length=length(x))
+-        symbols <- ls(x)
+-        for (symb in symbols)
+-            ans[[as.integer(symb)]] <- get(symb, envir=x@env)
+-        ans
+-    }
+-)
+-
+-### Supported 'i' types: character or numeric vector of length 1.
+-setMethod("[[", "SparseList",
+-    function(x, i, j, ...)
+-    {
+-        if (!missing(j) || length(list(...)) > 0)
+-            stop("invalid subsetting")
+-        if (missing(i))
+-            stop("subscript is missing")
+-        if (!is.character(i) && !is.numeric(i))
+-            stop("invalid subscript type")
+-        if (length(i) < 1L)
+-            stop("attempt to select less than one element")
+-        if (length(i) > 1L)
+-            stop("attempt to select more than one element")
+-        if (is.na(i))
+-            stop("subscript cannot be NA")
+-        if (is.character(i))
+-            return(get(i, envir=x@env))
+-        if (!is.integer(i))
+-            i <- as.integer(i)
+-        if (i < 1L || i > length(x))
+-            stop("subscript out of bounds")
+-        i <- formatC(i, width=10, format="d", flag="0")
+-        get(i, envir=x@env)
+-    }
+-)
+-
+diff --git a/man/Biostrings-internals.Rd b/man/Biostrings-internals.Rd
+index 791b0870..609b7694 100644
+--- a/man/Biostrings-internals.Rd
+++ b/man/Biostrings-internals.Rd
+@@ -26,15 +26,6 @@
+ \alias{make_XStringSet_from_strings}
+ \alias{make_XStringSet_from_strings,XStringSet-method}
+ 
+-% SparseList class and methods:
+-\alias{class:SparseList}
+-\alias{SparseList-class}
+-\alias{SparseList}
+-
+-\alias{length,SparseList-method}
+-%\alias{ls,SparseList-method}
+-\alias{as.list,SparseList-method}
+-\alias{[[,SparseList-method}
+ 
+ \title{Biostrings internals}
+ 
+diff --git a/src/Biostrings.h b/src/Biostrings.h
+index 6e725bd5..e86d0ff2 100644
+--- a/src/Biostrings.h
+++ b/src/Biostrings.h
+@@ -446,40 +446,6 @@ SEXP XStringSetList_unstrsplit(
+ );
+ 
+ 
+-/* SparseList_utils.c */
+-
+-SEXP _SparseList_int2symb(int symb_as_int);
+-
+-int _SparseList_symb2int(SEXP symbol);
+-
+-SEXP _get_val_from_env(
+-	SEXP symbol,
+-	SEXP env,
+-	int error_on_unbound_value
+-);
+-
+-SEXP _get_val_from_SparseList(
+-	int symb_as_int,
+-	SEXP env,
+-	int error_on_unbound_value
+-);
+-
+-int _get_int_from_SparseList(
+-	int symb_as_int,
+-	SEXP env
+-);
+-
+-void _set_env_from_IntAE(
+-	SEXP env,
+-	const IntAE *int_ae
+-);
+-
+-void _set_env_from_IntAEAE(
+-	SEXP env,
+-	const IntAEAE *int_aeae
+-);
+-
+-
+ /* match_reporting.c */
+ 
+ int _get_match_storing_code(const char *ms_mode);
+@@ -558,13 +524,6 @@ SEXP ByPos_MIndex_endIndex(
+ 	SEXP x_width0
+ );
+ 
+-SEXP SparseMIndex_endIndex(
+-	SEXP x_ends_envir,
+-	SEXP x_width0,
+-	SEXP x_names,
+-	SEXP all_names
+-);
+-
+ SEXP ByPos_MIndex_combine(SEXP ends_listlist);
+ 
+ 
+diff --git a/src/MIndex_class.c b/src/MIndex_class.c
+index 00212fe9..dd6ad546 100644
+--- a/src/MIndex_class.c
+++ b/src/MIndex_class.c
+@@ -157,73 +157,6 @@ SEXP ByPos_MIndex_endIndex(SEXP x_high2low, SEXP x_ends, SEXP x_width0)
+ 	return ans;
+ }
+ 
+-/*
+- * --- .Call ENTRY POINT ---
+- * All the keys in 'x_ends_envir' must be representing integers left-padded with 0s
+- * so they have the same length. This works properly:
+-     library(Biostrings)
+-     ends_envir <- new.env(parent=emptyenv())
+-     ends_envir[['0000000010']] <- -2:1
+-     ends_envir[['0000000004']] <- 9:6
+-     .Call("SparseMIndex_endIndex",
+-           ends_envir, NULL, letters[1:10], TRUE,
+-           PACKAGE="Biostrings")
+-     .Call("SparseMIndex_endIndex",
+-           ends_envir, NULL, letters[1:10], FALSE,
+-           PACKAGE="Biostrings")
+- * but this doesn't:
+-     ends_envir[['3']] <- 33L
+-     .Call("SparseMIndex_endIndex",
+-           ends_envir, NULL, letters[1:10], FALSE,
+-           PACKAGE="Biostrings")
+- */
+-SEXP SparseMIndex_endIndex(SEXP x_ends_envir, SEXP x_width0, SEXP x_names, SEXP all_names)
+-{
+-	SEXP ans, ans_elt, ans_names, symbols, end;
+-	int nelt, i, j;
+-	IntAE *poffsets, *poffsets_order;
+-
+-	PROTECT(symbols = R_lsInternal(x_ends_envir, 1));
+-	poffsets = new_IntAE_from_CHARACTER(symbols, -1);
+-	nelt = IntAE_get_nelt(poffsets);
+-	if (LOGICAL(all_names)[0]) {
+-		PROTECT(ans = NEW_LIST(LENGTH(x_names)));
+-		for (i = 0; i < nelt; i++) {
+-			j = poffsets->elts[i];
+-			end = _get_val_from_env(STRING_ELT(symbols, i), x_ends_envir, 1);
+-			PROTECT(ans_elt = duplicate(end));
+-			if (x_width0 != R_NilValue)
+-				add_val_to_INTEGER(ans_elt, 1 - INTEGER(x_width0)[j]);
+-			SET_ELEMENT(ans, j, ans_elt);
+-			UNPROTECT(1);
+-		}
+-		SET_NAMES(ans, duplicate(x_names));
+-		UNPROTECT(1);
+-	} else {
+-		//poffsets_order = new_IntAE(nelt, 0, 0);
+-		//get_order_of_int_array(poffsets->elts, nelt, 0, 0,
+-		//		       poffsets_order->elts, 0);
+-		//IntAE_set_nelt(poffsets_order) = nelt; /* = poffsets_order->_buflength */
+-		PROTECT(ans = NEW_LIST(nelt));
+-		PROTECT(ans_names = NEW_CHARACTER(nelt));
+-		for (i = 0; i < nelt; i++) {
+-			//j = poffsets_order->elts[i];
+-			j = i;
+-			end = _get_val_from_env(STRING_ELT(symbols, j), x_ends_envir, 1);
+-			PROTECT(ans_elt = duplicate(end));
+-			if (x_width0 != R_NilValue)
+-				add_val_to_INTEGER(ans_elt, 1 - INTEGER(x_width0)[i]);
+-			SET_ELEMENT(ans, i, ans_elt);
+-			UNPROTECT(1);
+-			SET_STRING_ELT(ans_names, i, duplicate(STRING_ELT(x_names, poffsets->elts[j])));
+-		}
+-		SET_NAMES(ans, ans_names);
+-		UNPROTECT(2);
+-	}
+-	UNPROTECT(1);
+-	return ans;
+-}
+-
+ /*
+  * --- .Call ENTRY POINT ---
+  */
+diff --git a/src/R_init_Biostrings.c b/src/R_init_Biostrings.c
+index 4d2943f8..c1410dbd 100644
+--- a/src/R_init_Biostrings.c
+++ b/src/R_init_Biostrings.c
+@@ -88,7 +88,6 @@ static const R_CallMethodDef callMethods[] = {
+ 
+ /* MIndex_class.c */
+ 	CALLMETHOD_DEF(ByPos_MIndex_endIndex, 3),
+-	CALLMETHOD_DEF(SparseMIndex_endIndex, 4),
+ 	CALLMETHOD_DEF(ByPos_MIndex_combine, 1),
+ 
+ /* lowlevel_matching.c */
+diff --git a/src/SparseList_utils.c b/src/SparseList_utils.c
+deleted file mode 100644
+index 18597b55..00000000
+--- a/src/SparseList_utils.c
+++ /dev/null
+@@ -1,113 +0,0 @@
+-/****************************************************************************
+- *                        Fast SparseList utilities                         *
+- *                            Author: H. Pag\`es                            *
+- ****************************************************************************/
+-#include "Biostrings.h"
+-#include "S4Vectors_interface.h"
+-
+-
+-SEXP _SparseList_int2symb(int symb_as_int)
+-{
+-	char symbbuf[11];
+-
+-	snprintf(symbbuf, sizeof(symbbuf), "%010d", symb_as_int);
+-	return mkChar(symbbuf); /* UNPROTECTED! */
+-}
+-
+-int _SparseList_symb2int(SEXP symbol)
+-{
+-	int symb_as_int;
+-
+-	sscanf(CHAR(symbol), "%d", &symb_as_int);
+-	return symb_as_int;
+-}
+-
+-/* 'symbol' must be a CHARSXP */
+-SEXP _get_val_from_env(SEXP symbol, SEXP env, int error_on_unbound_value)
+-{
+-	SEXP ans;
+-
+-	/* The following code was inspired by R's do_get() code.
+-	 * Note that do_get() doesn't use PROTECT at all and so do we...
+-	 */
+-	ans = findVar(install(translateChar(symbol)), env);
+-	if (ans == R_UnboundValue) {
+-		if (error_on_unbound_value)
+-			error("Biostrings internal error in _get_val_from_env(): "
+-			      "unbound value");
+-		return R_UnboundValue;
+-	}
+-	if (TYPEOF(ans) == PROMSXP)
+-		ans = eval(ans, env);
+-	if (ans != R_NilValue && NAMED(ans) == 0)
+-		SET_NAMED(ans, 1);
+-	return ans;
+-}
+-
+-SEXP _get_val_from_SparseList(int symb_as_int, SEXP env, int error_on_unbound_value)
+-{
+-	SEXP symbol, ans;
+-
+-	PROTECT(symbol = _SparseList_int2symb(symb_as_int));
+-	ans = _get_val_from_env(symbol, env, error_on_unbound_value);
+-	UNPROTECT(1);
+-	return ans;
+-}
+-
+-int _get_int_from_SparseList(int symb_as_int, SEXP env)
+-{
+-	SEXP value;
+-	int val;
+-
+-	value = _get_val_from_SparseList(symb_as_int, env, 0);
+-	if (value == R_UnboundValue)
+-		return NA_INTEGER;
+-	if (LENGTH(value) != 1)
+-		error("Biostrings internal error in _get_int_from_SparseList(): "
+-		      "value is not a single integer");
+-	val = INTEGER(value)[0];
+-	if (val == NA_INTEGER)
+-		error("Biostrings internal error in _get_int_from_SparseList(): "
+-		      "value is NA");
+-	return val;
+-}
+-
+-void _set_env_from_IntAE(SEXP env, const IntAE *int_ae)
+-{
+-	int nelt, symb_as_int, elt;
+-	SEXP symbol, value;
+-
+-	nelt = IntAE_get_nelt(int_ae);
+-	for (symb_as_int = 1; symb_as_int <= nelt; symb_as_int++)
+-	{
+-		elt = int_ae->elts[symb_as_int - 1];
+-		if (elt == NA_INTEGER)
+-			continue;
+-		PROTECT(symbol = _SparseList_int2symb(symb_as_int));
+-		PROTECT(value = ScalarInteger(elt));
+-		defineVar(install(translateChar(symbol)), value, env);
+-		UNPROTECT(2);
+-	}
+-	return;
+-}
+-
+-void _set_env_from_IntAEAE(SEXP env, const IntAEAE *int_aeae)
+-{
+-	int nelt, symb_as_int;
+-	IntAE *ae;
+-	SEXP symbol, value;
+-
+-	nelt = IntAEAE_get_nelt(int_aeae);
+-	for (symb_as_int = 1; symb_as_int <= nelt; symb_as_int++)
+-	{
+-		ae = int_aeae->elts[symb_as_int - 1];
+-		if (IntAE_get_nelt(ae) == 0)
+-			continue;
+-		PROTECT(symbol = _SparseList_int2symb(symb_as_int));
+-		PROTECT(value = new_INTEGER_from_IntAE(ae));
+-		defineVar(install(translateChar(symbol)), value, env);
+-		UNPROTECT(2);
+-	}
+-	return;
+-}
+-
@@ -0,0 +1,142 @@
+From 7fe34542bff0183c3a6a35a62df9035a71698eb2 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
+Date: Fri, 6 Mar 2026 15:54:23 -0800
+Subject: [PATCH] h5mread 1.3.2: Get rid of non-API calls to R
+
+---
+ DESCRIPTION                |  2 +-
+ R/H5File-class.R           | 27 ++++++++++++++++-----------
+ src/h5mread_index.c        |  5 +++--
+ src/h5mread_startscounts.c |  3 ++-
+ 4 files changed, 22 insertions(+), 15 deletions(-)
+
+diff --git a/R/H5File-class.R b/R/H5File-class.R
+index 2735166..6aeb80f 100644
+--- a/R/H5File-class.R
+++ b/R/H5File-class.R
+@@ -73,19 +73,23 @@
+     }
+ }
+ 
+-.h5openfile <- function(filepath, s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
+.h5openfile <- function(filepath, readonly=TRUE,
+                        s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
+ {
+     if (!isSingleString(filepath))
+         stop(wmsg("'filepath' must be a single string specifying ",
+                   "the path or URL to an HDF5 file"))
+    if (!isTRUEorFALSE(readonly))
+        stop(wmsg("'readonly' must be TRUE or FALSE"))
+     if (!isTRUEorFALSE(s3))
+         stop(wmsg("'s3' must be TRUE or FALSE"))
+-
+    if (s3 && !readonly)
+        stop(wmsg("'readonly' must be set to TRUE when 's3' is TRUE"))
+     if (s3) {
+         ID <- .h5openS3file(filepath, s3credentials=s3credentials,
+                                       use.rhdf5=use.rhdf5)
+     } else {
+-        ID <- .h5openlocalfile(filepath, readonly=TRUE, use.rhdf5=use.rhdf5)
+        ID <- .h5openlocalfile(filepath, readonly=readonly, use.rhdf5=use.rhdf5)
+     }
+     ID
+ }
+@@ -136,16 +140,16 @@
+ 
+ .ID_is_closed <- function(ID) { is.null(ID) || is.na(ID) }
+ 
+-.open_H5FileID_xp <- function(xp, filepath, s3=FALSE, s3credentials=NULL,
+-                                            use.rhdf5=FALSE)
+.open_H5FileID_xp <- function(xp, filepath, readonly=TRUE,
+                              s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
+ {
+     ID <- .get_H5FileID_xp_ID(xp)
+     if (!.ID_is_closed(ID)) {
+         ## H5FileID object is already open.
+         return(FALSE)
+     }
+-    ID <- .h5openfile(filepath, s3=s3, s3credentials=s3credentials,
+-                                use.rhdf5=use.rhdf5)
+    ID <- .h5openfile(filepath, readonly=readonly,
+                      s3=s3, s3credentials=s3credentials, use.rhdf5=use.rhdf5)
+     .set_H5FileID_xp_ID(xp, ID)
+     TRUE
+ }
+@@ -183,10 +187,11 @@ close.H5FileID <- function(con, ...)
+     .close_H5FileID_xp(con@xp, ..., use.rhdf5=con@from_rhdf5)
+ }
+ 
+-H5FileID <- function(filepath, s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
+H5FileID <- function(filepath, readonly=TRUE,
+                     s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
+ {
+-    ID <- .h5openfile(filepath, s3=s3, s3credentials=s3credentials,
+-                                use.rhdf5=use.rhdf5)
+    ID <- .h5openfile(filepath, readonly=readonly,
+                      s3=s3, s3credentials=s3credentials, use.rhdf5=use.rhdf5)
+     xp <- .new_H5FileID_xp(ID)
+     reg.finalizer(xp,
+                   function(e) .close_H5FileID_xp(e, use.rhdf5=use.rhdf5),
+@@ -272,7 +277,7 @@ H5File <- function(filepath, s3=FALSE, s3credentials=NULL, .no_rhdf5_h5id=FALSE)
+         rhdf5_h5id <- new("H5FileID")
+     } else {
+         rhdf5_h5id <- H5FileID(filepath, s3=s3, s3credentials=s3credentials,
+-                                         use.rhdf5=TRUE)
+                               use.rhdf5=TRUE)
+     }
+     if (!s3)
+         filepath <- file_path_as_absolute(filepath)
+diff --git a/src/h5mread_index.c b/src/h5mread_index.c
+index 7284815..ec93c25 100644
+--- a/src/h5mread_index.c
+++ b/src/h5mread_index.c
+@@ -9,6 +9,7 @@
+ #include "h5mread_helpers.h"
+ #include "TouchedChunks.h"
+ 
+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
+ #include <stdlib.h>  /* for malloc, free */
+ #include <string.h>  /* for memcmp */
+ //#include <time.h>
+@@ -444,7 +445,7 @@ static int read_chunk_data_4_5(const H5DSetDescriptor *h5dset,
+ 		const size_t *Rarray_dim, SEXP Rarray,
+ 		int method, int use_H5Dread_chunk)
+ {
+-	void *out = DATAPTR(Rarray);
+	void *out = DATAPTR_RW(Rarray);
+ 	if (out == NULL)
+ 		return -1;
+ 
+@@ -874,7 +875,7 @@ static int read_data_6(const AllTChunks *all_tchunks,
+ 	size_t *inner_nchip_buf = R_alloc0_size_t_array(ndim);
+ 	LLongAEAE *inner_breakpoint_bufs = new_LLongAEAE(ndim, ndim);
+ 
+-	void *out = DATAPTR(Rarray);
+	void *out = DATAPTR_RW(Rarray);
+ 	if (out == NULL) {
+ 		_destroy_TChunkIterator(&tchunk_iter);
+ 		return -1;
+diff --git a/src/h5mread_startscounts.c b/src/h5mread_startscounts.c
+index de57fd5..959014f 100644
+--- a/src/h5mread_startscounts.c
+++ b/src/h5mread_startscounts.c
+@@ -8,6 +8,7 @@
+ #include "uaselection.h"
+ #include "h5mread_helpers.h"
+ 
+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
+ #include <stdlib.h>  /* for malloc, free */
+ //#include <time.h>
+ 
+@@ -402,7 +403,7 @@ SEXP _h5mread_startscounts(const H5DSetDescriptor *h5dset,
+ 	SEXP ans = PROTECT(allocVector(h5dset->h5type->Rtype, ans_len));
+ 
+ 	if (ans_len != 0) {
+-		void *mem = DATAPTR(ans);
+		void *mem = DATAPTR_RW(ans);
+ 		if (mem == NULL)
+ 			goto on_error;
+ 
+-- 
+2.52.0
+
@@ -0,0 +1,67 @@
+From a827c9fdeb77edefe6cca81bdb9e0344bc8d3742 Mon Sep 17 00:00:00 2001
+From: Sebastian Gibb <mail@sebastiangibb.de>
+Date: Sat, 13 Dec 2025 23:06:12 +0100
+Subject: [PATCH] fix: non-API call to R: SETLENGTH by using lengthgets
+
+---
+ DESCRIPTION  |  2 +-
+ NEWS.md      |  6 ++++++
+ src/join.c   | 12 ++++--------
+ src/reduce.c |  6 ++----
+ 4 files changed, 13 insertions(+), 13 deletions(-)
+
+diff --git a/src/join.c b/src/join.c
+index f13a703..3849fdf 100644
+--- a/src/join.c
+++ b/src/join.c
+@@ -111,12 +111,10 @@ SEXP C_join_inner(SEXP x, SEXP y, SEXP tolerance, SEXP nomatch) {
+             ++j;
+         }
+     }
+-    SETLENGTH(rx, j);
+-    SETLENGTH(ry, j);
+     SEXP out = PROTECT(allocVector(VECSXP, 2));
+     SEXP nms = PROTECT(allocVector(STRSXP, 2));
+-    SET_VECTOR_ELT(out, 0, rx);
+-    SET_VECTOR_ELT(out, 1, ry);
+    SET_VECTOR_ELT(out, 0, lengthgets(rx, j));
+    SET_VECTOR_ELT(out, 1, lengthgets(ry, j));
+     SET_STRING_ELT(nms, 0, mkChar("x"));
+     SET_STRING_ELT(nms, 1, mkChar("y"));
+     setAttrib(out, R_NamesSymbol, nms);
+@@ -201,12 +199,10 @@ SEXP C_join_outer(SEXP x, SEXP y, SEXP tolerance, SEXP nomatch) {
+         ++i;
+     }
+ 
+-    SETLENGTH(rx, i);
+-    SETLENGTH(ry, i);
+     SEXP out = PROTECT(allocVector(VECSXP, 2));
+     SEXP nms = PROTECT(allocVector(STRSXP, 2));
+-    SET_VECTOR_ELT(out, 0, rx);
+-    SET_VECTOR_ELT(out, 1, ry);
+    SET_VECTOR_ELT(out, 0, lengthgets(rx, i));
+    SET_VECTOR_ELT(out, 1, lengthgets(ry, i));
+     SET_STRING_ELT(nms, 0, mkChar("x"));
+     SET_STRING_ELT(nms, 1, mkChar("y"));
+     setAttrib(out, R_NamesSymbol, nms);
+diff --git a/src/reduce.c b/src/reduce.c
+index 5f87966..8e48058 100644
+--- a/src/reduce.c
+++ b/src/reduce.c
+@@ -66,11 +66,9 @@ SEXP C_reduce(SEXP start, SEXP end, SEXP check) {
+         }
+     }
+ 
+-    SETLENGTH(rs, pos + 1);
+-    SETLENGTH(re, pos + 1);
+     SEXP out = PROTECT(allocVector(VECSXP, 2));
+-    SET_VECTOR_ELT(out, 0, rs);
+-    SET_VECTOR_ELT(out, 1, re);
+    SET_VECTOR_ELT(out, 0, lengthgets(rs, pos + 1));
+    SET_VECTOR_ELT(out, 1, lengthgets(re, pos + 1));
+ 
+     UNPROTECT(4);
+ 
+-- 
+2.52.0
+
@@ -0,0 +1,114 @@
+From 57dc6579d8b53af9e633016705fa9a1cbe58c8c8 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
+Date: Fri, 6 Mar 2026 16:48:20 -0800
+Subject: [PATCH] Rsamtools 2.27.1: Get rid of non-API calls to R
+
+---
+ DESCRIPTION     | 2 +-
+ src/utilities.h | 3 +--
+ 2 files changed, 2 insertions(+), 3 deletions(-)
+
+diff --git a/src/utilities.h b/src/utilities.h
+index bffb98f7..f9d5e09f 100644
+--- a/src/utilities.h
+++ b/src/utilities.h
+@@ -51,8 +51,7 @@ SEXP find_mate_within_groups(SEXP group_sizes,
+ /* call-building macros */
+ 
+ #define NEW_CALL(S, T, NAME, ENV, N)            \
+-    PROTECT(S = T = allocList(N));              \
+-    SET_TYPEOF(T, LANGSXP);                     \
+    PROTECT(S = T = LCONS(R_NilValue, allocList(N-1))); \
+     SETCAR(T, findFun(install(NAME), ENV));     \
+     T = CDR(T)
+ #define CSET_CDR(T, NAME, VALUE)                \
+
+From 8cdec143023e8348a4f8bdc310acd609d14fe493 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
+Date: Fri, 6 Mar 2026 16:59:42 -0800
+Subject: [PATCH] oops, forgot to also get rid of non-API call to FORMALS()
+
+---
+ src/pileupbam.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/pileupbam.c b/src/pileupbam.c
+index f3256ba..7725628 100644
+--- a/src/pileupbam.c
+++ b/src/pileupbam.c
+@@ -655,7 +655,7 @@ SEXP apply_pileups(SEXP files, SEXP names, SEXP regions, SEXP param,
+     if (R_NilValue == regions)
+         Rf_error("'NULL' regions not (yet) supported");
+     _checkparams(regions, R_NilValue, R_NilValue);
+-    if (!Rf_isFunction(callback) || 1L != Rf_length(FORMALS(callback)))
+    if (!Rf_isFunction(callback) || 1L != Rf_length(R_ClosureFormals(callback)))
+         Rf_error("'callback' must be a function of 1 argument");
+     call = PROTECT(Rf_lang2(callback, R_NilValue));
+ 
+
+From ee01a1f13f3b012b0717247d1f21580225b6f3a0 Mon Sep 17 00:00:00 2001
+From: vjcitn <stvjc@channing.harvard.edu>
+Date: Wed, 8 Apr 2026 14:04:26 -0400
+Subject: [PATCH] API solutions
+
+---
+ DESCRIPTION     |  2 +-
+ src/tabixfile.c |  4 ++++
+ src/utilities.c | 13 ++++++++++---
+ 3 files changed, 15 insertions(+), 4 deletions(-)
+
+diff --git a/src/tabixfile.c b/src/tabixfile.c
+index 230a381..6f96568 100644
+--- a/src/tabixfile.c
+++ b/src/tabixfile.c
+@@ -187,8 +187,12 @@ SEXP index_tabix(SEXP filename, SEXP format, SEXP seq, SEXP begin, SEXP end,
+         LOGICAL(zeroBased)[0] == TRUE)
+         conf.preset |= TBX_UCSC;
+ 
+/* following is deprecated in HTSLIB with no precise replacement proposed */
+/* seems unimportant */
+/*
+     if (bgzf_is_bgzf(fn) != 1)
+         Rf_error("file does not appear to be bgzip'd");
+*/
+     if (tbx_index_build(fn, 0, &conf) == -1)
+         Rf_error("index build failed");
+ 
+diff --git a/src/utilities.c b/src/utilities.c
+index e224f91..d15c1d1 100644
+--- a/src/utilities.c
+++ b/src/utilities.c
+@@ -5,6 +5,13 @@
+ #include "XVector_interface.h"
+ #include <htslib/khash.h>
+ 
+#include <Rversion.h>
+
+#if R_VERSION < R_Version(4, 6, 0)
+# define R_getVar(x,y,z) findVar(x,y)
+#endif
+
+
+ void *_Rs_Realloc_impl(void *p, size_t n, size_t t)
+ {
+     /* R_Realloc(p, 0, *) fails inappropriately */
+@@ -30,7 +37,7 @@ SEXP _get_namespace(const char *pkg)
+ void _as_strand(SEXP vec)
+ {
+     SEXP nmspc = PROTECT(_get_namespace("Rsamtools"));
+-    SEXP lvls = PROTECT(eval(findVar(install(".STRAND_LEVELS"), nmspc), nmspc));
+    SEXP lvls = PROTECT(eval(R_getVar(install(".STRAND_LEVELS"), nmspc, TRUE), nmspc));
+     _as_factor_SEXP(vec, lvls);
+     UNPROTECT(2);
+ }
+@@ -38,8 +45,8 @@ void _as_strand(SEXP vec)
+ void _as_nucleotide(SEXP vec)
+ {
+     SEXP nmspc = PROTECT(_get_namespace("Rsamtools"));
+-    SEXP lvls = PROTECT(eval(findVar(install(".PILEUP_NUCLEOTIDE_LEVELS"),
+-                                     nmspc), nmspc));
+    SEXP lvls = PROTECT(eval(R_getVar(install(".PILEUP_NUCLEOTIDE_LEVELS"),
+                                     nmspc, TRUE), nmspc));
+     _as_factor_SEXP(vec, lvls);
+     UNPROTECT(2);
+ }
@@ -0,0 +1,103 @@
+From e39852a54312bbc6ba435848890cc2a7f612357c Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
+Date: Fri, 6 Mar 2026 17:04:19 -0800
+Subject: [PATCH] ShortRead 1.69.3: Get rid of non-API calls to R
+
+---
+ DESCRIPTION |  2 +-
+ src/call.h  |  3 +--
+ src/io.c    | 10 +++++-----
+ 3 files changed, 7 insertions(+), 8 deletions(-)
+
+diff --git a/src/call.h b/src/call.h
+index e15bb5e..e72bbd6 100644
+--- a/src/call.h
+++ b/src/call.h
+@@ -6,8 +6,7 @@ extern "C" {
+ #endif
+ 
+ #define NEW_CALL(S, T, NAME, ENV, N)				\
+-    PROTECT((S) = (T) = allocList((N)));			\
+-    SET_TYPEOF((T), LANGSXP);                                   \
+    PROTECT((S) = (T) = LCONS(R_NilValue, allocList((N)-1)));	\
+     SETCAR((T), findFun(install((NAME)), (ENV)));               \
+     (T) = CDR((T))
+ #define CSET_CDR(T, NAME, VALUE)				\
+diff --git a/src/io.c b/src/io.c
+index 25a0111..9cf4bf8 100644
+--- a/src/io.c
+++ b/src/io.c
+@@ -46,9 +46,9 @@ SEXP write_fastq(SEXP id, SEXP sread, SEXP quality,
+                  SEXP fname, SEXP fmode, SEXP full, SEXP compress,
+                  SEXP max_width)
+ {
+-    if (!(IS_S4_OBJECT(id) && strcmp(get_classname(id), "BStringSet") == 0))
+    if (!(Rf_isS4(id) && strcmp(get_classname(id), "BStringSet") == 0))
+         Rf_error("'%s' must be '%s'", "id", "BStringSet");
+-    if (!(IS_S4_OBJECT(sread) &&
+    if (!(Rf_isS4(sread) &&
+           strcmp(get_classname(sread), "DNAStringSet") == 0))
+         Rf_error("'%s' must be '%s'", "sread", "DNAStringSet");
+     /* check in R -- C-level R_check_super... is not adequate */
+@@ -693,14 +693,14 @@ int _solexa_export_make_id(SEXP result)
+         *x = INTEGER(VECTOR_ELT(result, SLX_X)),
+         *y = INTEGER(VECTOR_ELT(result, SLX_Y)), *pairedReadNumber = NULL;
+     const SEXP
+-        * run = STRING_PTR(VECTOR_ELT(result, SLX_RUN)),
+        * run = STRING_PTR_RO(VECTOR_ELT(result, SLX_RUN)),
+         *multiplexIndex = NULL,
+-        *machine = STRING_PTR(VECTOR_ELT(result, SLX_MACHINE));
+        *machine = STRING_PTR_RO(VECTOR_ELT(result, SLX_MACHINE));
+     const Rboolean
+         withMultiplexIndex = R_NilValue != VECTOR_ELT(result, SLX_MULTIPLEX),
+         withPairedReadNumber = R_NilValue != VECTOR_ELT(result, SLX_PAIRID);
+     if (withMultiplexIndex)
+-        multiplexIndex = STRING_PTR(VECTOR_ELT(result, SLX_MULTIPLEX));
+        multiplexIndex = STRING_PTR_RO(VECTOR_ELT(result, SLX_MULTIPLEX));
+     if (withPairedReadNumber)
+         pairedReadNumber = INTEGER(VECTOR_ELT(result, SLX_PAIRID));
+ 
+-- 
+2.52.0
+
+
+From 2e3368a35e3955a0a92b7f3e2c8dface6709d135 Mon Sep 17 00:00:00 2001
+From: vjcitn <stvjc@channing.harvard.edu>
+Date: Thu, 16 Apr 2026 16:54:15 +0000
+Subject: [PATCH] fixapi
+
+---
+ src/util.c | 10 +++++++++-
+ 1 file changed, 9 insertions(+), 1 deletion(-)
+
+diff --git a/src/util.c b/src/util.c
+index 4a10a90..59c089b 100644
+--- a/src/util.c
+++ b/src/util.c
+@@ -6,6 +6,14 @@ unsigned char _bDecode(char);
+ unsigned char _dnaDecode(char);
+ unsigned char _rnaDecode(char);
+ 
+
+#include <Rversion.h>
+
+#if R_VERSION < R_Version(4, 6, 0)
+# define R_getVar(x,y,z) findVar(x,y)
+#endif
+
+
+ /*
+  * Encode / decode XString wrappers
+  */
+@@ -80,7 +88,7 @@ SEXP _get_namespace(const char *pkg)
+ SEXP _get_strand_levels()
+ {
+     SEXP nmspc = PROTECT(_get_namespace("ShortRead"));
+-    SEXP ans = eval(findVar(install(".STRAND_LEVELS"), nmspc), nmspc);
+    SEXP ans = eval(R_getVar(install(".STRAND_LEVELS"), nmspc, TRUE), nmspc);
+     UNPROTECT(1);
+     return ans;
+ }
+-- 
+2.52.0
+
@@ -0,0 +1,412 @@
+From 803cda41994a22890e0a6e379e6588084d4bc91b Mon Sep 17 00:00:00 2001
+From: vjcitn <stvjc@channing.harvard.edu>
+Date: Fri, 13 Mar 2026 04:04:59 -0400
+Subject: [PATCH 1/2] fixed non-API except for IS_S4_OBJECT
+
+---
+ src/bind.c             |  8 ++++----
+ src/glm_test_R.c       | 20 ++++++++++----------
+ src/imputation.c       |  8 ++++----
+ src/input.c            |  2 +-
+ src/plink.c            |  2 +-
+ src/read_uncertain.c   |  4 ++--
+ src/readped.c          |  2 +-
+ src/single_snp_tests.c |  8 ++++----
+ src/snp_summary.c      |  8 ++++----
+ src/snpmpy.c           |  8 ++++----
+ src/structure.c        |  4 ++--
+ src/subset.c           |  2 +-
+ src/switch.c           |  2 +-
+ src/tdt.c              |  8 ++++----
+ src/testBig.c          |  2 +-
+ 15 files changed, 44 insertions(+), 44 deletions(-)
+
+diff --git a/src/bind.c b/src/bind.c
+index 44b1536..fa87e7c 100644
+--- a/src/bind.c
+++ b/src/bind.c
+@@ -19,7 +19,7 @@ SEXP snp_rbind(SEXP args) {
+     const SEXP This = CAR(args);
+     Class = getAttrib(This, R_ClassSymbol);
+     if (TYPEOF(Class) != STRSXP) {
+-      Class = R_data_class(This, FALSE);
+      Class = R_class(This);
+     }
+     const char *cli = CHAR(STRING_ELT(Class, 0));
+     if(!IS_S4_OBJECT(This)) {
+@@ -66,7 +66,7 @@ SEXP snp_rbind(SEXP args) {
+   SEXP Result, Rnames, Dnames, Diploid = R_NilValue;
+   PROTECT(Result = allocMatrix(RAWSXP, nr, nc));
+   classgets(Result, duplicate(Class));
+-  SET_S4_OBJECT(Result);
+  Rf_asS4(Result, TRUE, 0);
+   PROTECT(Rnames = allocVector(STRSXP, nr));
+   PROTECT(Dnames = allocVector(VECSXP, 2));
+   SET_VECTOR_ELT(Dnames, 0, Rnames);
+@@ -148,7 +148,7 @@ SEXP snp_cbind(SEXP args) {
+     SEXP This = CAR(args);
+     Class = getAttrib(This, R_ClassSymbol);
+     if (TYPEOF(Class) != STRSXP) {
+-      Class = R_data_class(This, FALSE);
+      Class = R_class(This);
+     }
+     const char *cli = CHAR(STRING_ELT(Class, 0));
+     if(!IS_S4_OBJECT(This)) {
+@@ -205,7 +205,7 @@ SEXP snp_cbind(SEXP args) {
+   SEXP Result, Cnames, Dnames;
+   PROTECT(Result = allocMatrix(RAWSXP, nr, nc));
+   classgets(Result, duplicate(Class));
+-  SET_S4_OBJECT(Result);
+  Rf_asS4(Result, TRUE, 0);
+   PROTECT(Dnames = allocVector(VECSXP, 2));
+   setAttrib(Result, R_DimNamesSymbol, Dnames);
+   PROTECT(Cnames = allocVector(STRSXP, nc));
+diff --git a/src/glm_test_R.c b/src/glm_test_R.c
+index d865182..dc8ebef 100644
+--- a/src/glm_test_R.c
+++ b/src/glm_test_R.c
+@@ -19,8 +19,8 @@ SEXP snp_lhs_score(const SEXP Y, const SEXP X, const SEXP Stratum,
+ 
+   /* Y should be a SnpMatrix or an XSnpMatrix */
+   const char *classY = NULL;
+-  if (TYPEOF(R_data_class(Y, FALSE)) == STRSXP) {
+-    classY = CHAR(STRING_ELT(R_data_class(Y, FALSE), 0));
+  if (TYPEOF(R_class(Y)) == STRSXP) {
+    classY = CHAR(STRING_ELT(R_class(Y), 0));
+   } else {
+     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
+   }
+@@ -431,8 +431,8 @@ SEXP snp_rhs_score(SEXP Y, SEXP family, SEXP link,
+   /* Z should be a SnpMatrix or an XSnpMatrix */
+ 
+   const char *classZ = NULL;
+-  if (TYPEOF(R_data_class(Z, FALSE)) == STRSXP) {
+-    classZ = CHAR(STRING_ELT(R_data_class(Z, FALSE), 0));
+  if (TYPEOF(R_class(Z)) == STRSXP) {
+    classZ = CHAR(STRING_ELT(R_class(Z), 0));
+   } else {
+     classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
+   }
+@@ -1003,8 +1003,8 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
+ 
+   /* Y should be a SnpMatrix or an XSnpMatrix */
+   const char *classY = NULL;
+-  if (TYPEOF(R_data_class(Y, FALSE)) == STRSXP) {
+-    classY = CHAR(STRING_ELT(R_data_class(Y, FALSE), 0));
+  if (TYPEOF(R_class(Y)) == STRSXP) {
+    classY = CHAR(STRING_ELT(R_class(Y), 0));
+   } else {
+     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
+   }
+@@ -1286,7 +1286,7 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
+   LOGICAL(Lhs)[0] = 1;
+   setAttrib(Estimates, install("snpLHS"), Lhs);
+   UNPROTECT(6);
+-  SET_S4_OBJECT(Estimates);
+  Rf_asS4(Estimates, TRUE, 0);
+   return(Estimates);
+ }
+ 
+@@ -1360,8 +1360,8 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
+ /* Z should be a SnpMatrix or an XSnpMatrix */
+ 
+   const char *classZ = NULL;
+-  if (TYPEOF(R_data_class(Z, FALSE)) == STRSXP) {
+-    classZ = CHAR(STRING_ELT(R_data_class(Z, FALSE), 0));
+  if (TYPEOF(R_class(Z)) == STRSXP) {
+    classZ = CHAR(STRING_ELT(R_class(Z), 0));
+   } else {
+     classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
+   }
+@@ -1724,7 +1724,7 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
+ 
+   UNPROTECT(gen_names? 7: 6);
+ 
+-  SET_S4_OBJECT(Estimates);
+  Rf_asS4(Estimates, TRUE, 0);
+   return(Estimates);
+   
+ }
+diff --git a/src/imputation.c b/src/imputation.c
+index ff9403b..d796c1b 100644
+--- a/src/imputation.c
+++ b/src/imputation.c
+@@ -77,7 +77,7 @@ SEXP snp_impute(const SEXP X, const SEXP Y, const SEXP Xord, const SEXP Yord,
+   int *diploid = NULL;
+   SEXP cl = GET_CLASS(X);
+   if (TYPEOF(cl) != STRSXP) {
+-    cl = R_data_class(X, FALSE); /* S4 way of getting class attribute */
+    cl = R_class(X); /* S4 way of getting class attribute */
+   }
+   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
+     SEXP Diploid = R_do_slot(X, mkString("diploid"));
+@@ -395,7 +395,7 @@ SEXP snp_impute(const SEXP X, const SEXP Y, const SEXP Xord, const SEXP Yord,
+   PROTECT(Maxpred = allocVector(INTSXP, 1));
+   INTEGER(Maxpred)[0] = maxpred;
+   setAttrib(Result, install("Max.predictors"), Maxpred);
+-  SET_S4_OBJECT(Result);
+  Rf_asS4(Result, TRUE, 0);
+ 
+   /* Tidy up */
+ 
+@@ -701,7 +701,7 @@ SEXP impute_snps(const SEXP Rules, const SEXP Snps, const SEXP Subset,
+   int *diploid_in=NULL, *diploid=NULL;
+   SEXP cl = GET_CLASS(Snps);
+   if (TYPEOF(cl) != STRSXP) {
+-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+    cl = R_class(Snps); /* S4 way of getting class attribute */
+   }
+   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
+     SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
+@@ -753,7 +753,7 @@ SEXP impute_snps(const SEXP Rules, const SEXP Snps, const SEXP Subset,
+     SET_STRING_ELT(Package, 0, mkChar("snpStats"));
+     setAttrib(Class, install("package"), Package);
+     classgets(Result, Class);
+-    SET_S4_OBJECT(Result);
+    Rf_asS4(Result, TRUE, 0);
+   }
+   PROTECT(Dimnames = allocVector(VECSXP, 2));
+   SET_VECTOR_ELT(Dimnames, 0, VECTOR_ELT(names, 0));
+diff --git a/src/input.c b/src/input.c
+index 1d2a95b..60cdad8 100644
+--- a/src/input.c
+++ b/src/input.c
+@@ -330,7 +330,7 @@ SEXP insnp_new(const SEXP Filenames, const SEXP Sample_id, const SEXP Snp_id,
+   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
+   setAttrib(Class, install("package"), Package);
+   classgets(Result, Class);
+-  SET_S4_OBJECT(Result);
+  Rf_asS4(Result, TRUE, 0);
+   unsigned char *result = RAW(Result);
+   memset(result, 0x00, Nsample*Nsnp);
+ 
+diff --git a/src/plink.c b/src/plink.c
+index a413440..9095c2d 100644
+--- a/src/plink.c
+++ b/src/plink.c
+@@ -59,7 +59,7 @@ SEXP readbed(SEXP Bed, SEXP Id, SEXP Snps, SEXP Rsel, SEXP Csel) {
+   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
+   setAttrib(Class, install("package"), Package);
+   classgets(Result, Class);
+-  SET_S4_OBJECT(Result);
+  Rf_asS4(Result, TRUE, 0);
+   
+   unsigned char *result = RAW(Result); 
+   R_xlen_t ncell = (R_xlen_t)nrow*(R_xlen_t)ncol;
+diff --git a/src/read_uncertain.c b/src/read_uncertain.c
+index 2e3b901..fd82617 100644
+--- a/src/read_uncertain.c
+++ b/src/read_uncertain.c
+@@ -137,7 +137,7 @@ SEXP read_mach(const SEXP Filename, const SEXP Colnames, const SEXP Nsubject) {
+   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
+   setAttrib(Class, install("package"), Package);
+   classgets(Result, Class);
+-  SET_S4_OBJECT(Result);
+  Rf_asS4(Result, TRUE, 0);
+   UNPROTECT(2);
+  
+   /* Read in data */
+@@ -278,7 +278,7 @@ SEXP read_impute(const SEXP Filename, const SEXP Rownames, const SEXP Nsnp,
+   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
+   setAttrib(Class, install("package"), Package);
+   classgets(Result, Class);
+-  SET_S4_OBJECT(Result);
+  Rf_asS4(Result, TRUE, 0);
+   UNPROTECT(2);
+ 
+   char buffer[BUFFERSIZE];
+diff --git a/src/readped.c b/src/readped.c
+index 4e8563e..020d05f 100644
+--- a/src/readped.c
+++ b/src/readped.c
+@@ -327,7 +327,7 @@ SEXP readped(SEXP filename, SEXP snp_names, SEXP missing, SEXP X, SEXP sep) {
+   else
+     SET_STRING_ELT(SMClass, 0, mkChar("SnpMatrix"));
+   classgets(Smat, SMClass);
+-  SET_S4_OBJECT(Smat);
+  Rf_asS4(Smat, TRUE, 0);
+   PROTECT(DimNames = allocVector(VECSXP, 2));
+   SET_VECTOR_ELT(DimNames, 0, duplicate(Rnames));
+   protected += 2;
+diff --git a/src/single_snp_tests.c b/src/single_snp_tests.c
+index a242e17..08bd098 100644
+--- a/src/single_snp_tests.c
+++ b/src/single_snp_tests.c
+@@ -53,8 +53,8 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
+   /* SNPs ---- should be a SnpMatrix or an XSnpMatrix */
+ 
+   const char *classS = NULL;
+-  if (TYPEOF(R_data_class(Snps, FALSE)) == STRSXP) {
+-    classS = CHAR(STRING_ELT(R_data_class(Snps, FALSE), 0));
+  if (TYPEOF(R_class(Snps)) == STRSXP) {
+    classS = CHAR(STRING_ELT(R_class(Snps), 0));
+   } else {
+     classS = CHAR(STRING_ELT(getAttrib(Snps, R_ClassSymbol), 0));
+   }
+@@ -108,8 +108,8 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
+   index_db name_index;
+   if (!isNull(Rules)) {
+     const char *classR = NULL;
+-    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
+-      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
+    if (TYPEOF(R_class(Rules)) == STRSXP) {
+      classR = CHAR(STRING_ELT(R_class(Rules), 0));
+     } else {
+       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
+     }
+diff --git a/src/snp_summary.c b/src/snp_summary.c
+index 9b53693..6f181c9 100644
+--- a/src/snp_summary.c
+++ b/src/snp_summary.c
+@@ -47,8 +47,8 @@ SEXP X_snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
+   SEXP ruleNames = R_NilValue;
+   if (!isNull(Rules)) {
+     const char *classR = NULL;
+-    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
+-      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
+    if (TYPEOF(R_class(Rules)) == STRSXP) {
+      classR = CHAR(STRING_ELT(R_class(Rules), 0));
+     } else {
+       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
+     }
+@@ -321,8 +321,8 @@ SEXP snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
+   SEXP ruleNames = R_NilValue;
+   if (!isNull(Rules)) {
+     const char *classR = NULL;
+-    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
+-      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
+    if (TYPEOF(R_class(Rules)) == STRSXP) {
+      classR = CHAR(STRING_ELT(R_class(Rules), 0));
+     } else {
+       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
+     }
+diff --git a/src/snpmpy.c b/src/snpmpy.c
+index 2447048..56b84d9 100644
+--- a/src/snpmpy.c
+++ b/src/snpmpy.c
+@@ -34,7 +34,7 @@ SEXP snp_pre(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
+   int *ifdiploid = NULL;
+   SEXP cl = GET_CLASS(Snps);
+   if (TYPEOF(cl) != STRSXP) {
+-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+    cl = R_class(Snps); /* S4 way of getting class attribute */
+   }
+   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
+     SEXP diploid = R_do_slot(Snps, mkString("diploid"));
+@@ -55,7 +55,7 @@ SEXP snp_pre(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
+ 
+   cl = GET_CLASS(Mat);
+   if (TYPEOF(cl) != STRSXP) {
+-    cl = R_data_class(Mat, FALSE); /* S4 way of getting class attribute */
+    cl = R_class(Mat); /* S4 way of getting class attribute */
+   }
+   if (strcmp(CHAR(STRING_ELT(cl, 0)), "matrix"))
+     error("Argument error - Mat wrong type");
+@@ -161,7 +161,7 @@ SEXP snp_post(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
+   int *ifdiploid = NULL;
+   SEXP cl = GET_CLASS(Snps);
+   if (TYPEOF(cl) != STRSXP) {
+-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+    cl = R_class(Snps); /* S4 way of getting class attribute */
+   }
+   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
+     SEXP diploid = R_do_slot(Snps, mkString("diploid"));
+@@ -182,7 +182,7 @@ SEXP snp_post(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
+ 
+   cl = GET_CLASS(Mat);
+   if (TYPEOF(cl) != STRSXP) {
+-    cl = R_data_class(Mat, FALSE); /* S4 way of getting class attribute */
+    cl = R_class(Mat); /* S4 way of getting class attribute */
+   }
+   if (strcmp(CHAR(STRING_ELT(cl, 0)), "matrix"))
+     error("Argument error - Mat wrong type");
+diff --git a/src/structure.c b/src/structure.c
+index 2a05635..1f9b62e 100644
+--- a/src/structure.c
+++ b/src/structure.c
+@@ -66,7 +66,7 @@ SEXP xxt(const SEXP Snps, const SEXP Strata, const SEXP Correct_for_missing,
+   int *ifDiploid = NULL;
+   SEXP cl = GET_CLASS(Snps);
+   if (TYPEOF(cl) != STRSXP) {
+-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+    cl = R_class(Snps); /* S4 way of getting class attribute */
+   }
+   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
+     SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
+@@ -409,7 +409,7 @@ SEXP ibs_count(const SEXP Snps, const SEXP Uncertain) {
+   int *ifDiploid = NULL;
+   SEXP cl = GET_CLASS(Snps);
+   if (TYPEOF(cl) != STRSXP) {
+-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+    cl = R_class(Snps); /* S4 way of getting class attribute */
+   }
+   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
+     SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
+diff --git a/src/subset.c b/src/subset.c
+index cc7992d..4c2e2c4 100644
+--- a/src/subset.c
+++ b/src/subset.c
+@@ -55,7 +55,7 @@ SEXP subset(SEXP X, SEXP Rows, SEXP Cols) {
+   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
+   setAttrib(Rclass, install("package"), Package);
+   setAttrib(Result, R_ClassSymbol, Rclass);
+-  SET_S4_OBJECT(Result);
+  Rf_asS4(Result, TRUE, 0);
+   PROTECT(Rdim = allocVector(INTSXP, 2));
+   int *rdim = INTEGER(Rdim);
+   rdim[0] = nrows;
+diff --git a/src/switch.c b/src/switch.c
+index 60f7e6c..e2a3287 100644
+--- a/src/switch.c
+++ b/src/switch.c
+@@ -16,7 +16,7 @@ SEXP test_switch(const SEXP Snps, const SEXP Snps2, const SEXP Split,
+   int *female = NULL;
+   SEXP cl = GET_CLASS(Snps);
+   if (TYPEOF(cl) != STRSXP) {
+-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+    cl = R_class(Snps); /* S4 way of getting class attribute */
+   }
+   SEXP diploid = NULL;
+   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
+diff --git a/src/tdt.c b/src/tdt.c
+index cece0d9..000d1c7 100644
+--- a/src/tdt.c
+++ b/src/tdt.c
+@@ -43,8 +43,8 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
+   /* SNPs ---- should be a SnpMatrix or an XSnpMatrix */
+ 
+   const char *classS = NULL;
+-  if (TYPEOF(R_data_class(Snps, FALSE)) == STRSXP) {
+-    classS = CHAR(STRING_ELT(R_data_class(Snps, FALSE), 0));
+  if (TYPEOF(R_class(Snps)) == STRSXP) {
+    classS = CHAR(STRING_ELT(R_class(Snps), 0));
+   } else {
+     classS = CHAR(STRING_ELT(getAttrib(Snps, R_ClassSymbol), 0));
+   }
+@@ -84,8 +84,8 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
+   GTYPE **gt2ht = NULL;
+   if (!isNull(Rules)) {
+     const char *classR = NULL;
+-    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
+-      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
+    if (TYPEOF(R_class(Rules)) == STRSXP) {
+      classR = CHAR(STRING_ELT(R_class(Rules), 0));
+     } else {
+       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
+     }
+diff --git a/src/testBig.c b/src/testBig.c
+index a6eb76f..3dca1da 100644
+--- a/src/testBig.c
+++ b/src/testBig.c
+@@ -18,7 +18,7 @@ SEXP snp_big(SEXP nrow, SEXP ncol) {
+   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
+   setAttrib(Class, install("package"), Package);
+   classgets(Result, Class);
+-  SET_S4_OBJECT(Result);
+  Rf_asS4(Result, TRUE, 0);
+ 
+   PROTECT(Dnames = allocVector(VECSXP, 2));
+   setAttrib(Result, R_DimNamesSymbol, Dnames);
+-- 
+2.52.0
+
@@ -0,0 +1,149 @@
+From a505297e347aa72510ecfc83e7009668693e1260 Mon Sep 17 00:00:00 2001
+From: vjcitn <stvjc@channing.harvard.edu>
+Date: Fri, 13 Mar 2026 04:06:37 -0400
+Subject: [PATCH 2/2] fixed IS_S4_OBJECT
+
+---
+ src/bind.c             | 4 ++--
+ src/fst.c              | 2 +-
+ src/glm_test_R.c       | 8 ++++----
+ src/single_snp_tests.c | 2 +-
+ src/snp_summary.c      | 6 +++---
+ src/tdt.c              | 2 +-
+ 6 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/src/bind.c b/src/bind.c
+index fa87e7c..b3ef928 100644
+--- a/src/bind.c
+++ b/src/bind.c
+@@ -22,7 +22,7 @@ SEXP snp_rbind(SEXP args) {
+       Class = R_class(This);
+     }
+     const char *cli = CHAR(STRING_ELT(Class, 0));
+-    if(!IS_S4_OBJECT(This)) {
+    if(!Rf_isS4(This)) {
+       warning("rbinding SnpMatrix object without S4 object bit");
+     }
+     int nci = ncols(This);
+@@ -151,7 +151,7 @@ SEXP snp_cbind(SEXP args) {
+       Class = R_class(This);
+     }
+     const char *cli = CHAR(STRING_ELT(Class, 0));
+-    if(!IS_S4_OBJECT(This)) {
+    if(!Rf_isS4(This)) {
+       warning("cbinding SnpMatrix object without S4 object bit");
+     }
+     SEXP Di = R_NilValue;
+diff --git a/src/fst.c b/src/fst.c
+index bbc39c0..5451a51 100644
+--- a/src/fst.c
+++ b/src/fst.c
+@@ -23,7 +23,7 @@ SEXP Fst(SEXP Snps, SEXP Group, SEXP HapMap) {
+     ifX = 0; /* to avoid warning message */
+     error("Argument error - class(Snps)");
+   }
+-  if(!IS_S4_OBJECT(Snps)) {
+  if(!Rf_isS4(Snps)) {
+     error("Argument error - Snps is not S4 object");
+   }
+ 
+diff --git a/src/glm_test_R.c b/src/glm_test_R.c
+index dc8ebef..fe9d9c8 100644
+--- a/src/glm_test_R.c
+++ b/src/glm_test_R.c
+@@ -24,7 +24,7 @@ SEXP snp_lhs_score(const SEXP Y, const SEXP X, const SEXP Stratum,
+   } else {
+     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
+   }
+-  if(!IS_S4_OBJECT(Y)) {
+  if(!Rf_isS4(Y)) {
+     error("Y in snp_lhs_score is missing S4 Object bit");
+   }
+   int ifX = 0;
+@@ -443,7 +443,7 @@ SEXP snp_rhs_score(SEXP Y, SEXP family, SEXP link,
+     ifX = 1;
+   else 
+     error("Argument error - class(Z)");
+-  if (!IS_S4_OBJECT(Z)) {
+  if (!Rf_isS4(Z)) {
+     error("Z in snp_rhs_score is missing S4 Object bit");
+   }
+  
+@@ -1008,7 +1008,7 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
+   } else {
+     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
+   }
+-  if(!IS_S4_OBJECT(Y)) {
+  if(!Rf_isS4(Y)) {
+     error("Y in snp_lhs_score is missing S4 Object bit");
+   }
+   int ifX = 0;
+@@ -1365,7 +1365,7 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
+   } else {
+     classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
+   }
+-  if(!IS_S4_OBJECT(Z)) {
+  if(!Rf_isS4(Z)) {
+     error("Z in snp_rhs_score is missing S4 Object bit");
+   }
+   int ifX = 0;
+diff --git a/src/single_snp_tests.c b/src/single_snp_tests.c
+index 08bd098..b577300 100644
+--- a/src/single_snp_tests.c
+++ b/src/single_snp_tests.c
+@@ -67,7 +67,7 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
+     ifX = 0; /* to avoid warning message */
+     error("Argument error - class(Snps)");
+   }
+-  if(!IS_S4_OBJECT(Snps)) {
+  if(!Rf_isS4(Snps)) {
+     error("Argument error - Snps is not S4 object");
+   }
+ 
+diff --git a/src/snp_summary.c b/src/snp_summary.c
+index 6f181c9..c2f1c73 100644
+--- a/src/snp_summary.c
+++ b/src/snp_summary.c
+@@ -24,7 +24,7 @@ SEXP X_snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
+   if (Snps == R_NilValue) {
+     error("Argument error - Snps = NULL");
+   }
+-  if(!IS_S4_OBJECT(Snps)) {
+  if(!Rf_isS4(Snps)) {
+     error("Argument error - Snps is not S4 object");
+   }
+   const unsigned char *snps = RAW(Snps);
+@@ -298,7 +298,7 @@ SEXP snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
+   if (Snps == R_NilValue) {
+     error("Argument error - Snps = NULL");
+   }
+-  if(!IS_S4_OBJECT(Snps)) {
+  if(!Rf_isS4(Snps)) {
+     error("Argument error - Snps is not S4 object");
+   }
+   const unsigned char *snps = RAW(Snps);
+@@ -538,7 +538,7 @@ SEXP row_summary(const SEXP Snps) {
+   if (Snps == R_NilValue) {
+     error("Argument error - Snps = NULL");
+   }
+-  if(!IS_S4_OBJECT(Snps)) {
+  if(!Rf_isS4(Snps)) {
+     error("Argument error - Snps is not S4 object");
+   }
+   const unsigned char *snps = RAW(Snps);
+diff --git a/src/tdt.c b/src/tdt.c
+index 000d1c7..634e1b3 100644
+--- a/src/tdt.c
+++ b/src/tdt.c
+@@ -57,7 +57,7 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
+     ifX = 0; /* to avoid warning message */
+     error("Argument error - class(Snps)");
+   }
+-  if(!IS_S4_OBJECT(Snps)) {
+  if(!Rf_isS4(Snps)) {
+     error("Argument error - Snps is not S4 object");
+   }
+ 
+-- 
+2.52.0
+
@@ -0,0 +1,259 @@
+From 633aa6e3f671e9b58b3508b3944ff0dd45f34f8a Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
+Date: Thu, 5 Mar 2026 14:58:23 -0800
+Subject: [PATCH] SparseArray 1.11.11: Get rid of non-API calls to R
+
+From 65383c02f986832b1416c6ad39da800d8ced05df Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
+Date: Tue, 31 Mar 2026 11:38:20 -0700
+Subject: [PATCH] SparseArray 1.11.13: Use R_getVar() instead of findVar() when
+ R >= 4.6.0
+
+---
+ DESCRIPTION                     |  2 +-
+ src/Makevars                    |  1 +
+ src/Rvector_utils.c             | 15 ++++++++-------
+ src/SparseArray_aperm.c         |  2 +-
+ src/SparseArray_matrixStats.c   |  5 +++--
+ src/SparseArray_subassignment.c |  6 +++---
+ src/SparseVec.h                 |  3 ++-
+ src/leaf_utils.c                |  5 +++--
+ src/test.c                      |  3 +++
+ 9 files changed, 25 insertions(+), 17 deletions(-)
+
+diff --git a/src/Makevars b/src/Makevars
+index 0ee3615..1c5b86e 100644
+--- a/src/Makevars
+++ b/src/Makevars
+@@ -1,2 +1,3 @@
+## See https://cran.r-project.org/doc/manuals/r-release/R-exts.html#OpenMP-support
+ PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
+ PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
+diff --git a/src/Rvector_utils.c b/src/Rvector_utils.c
+index ad80168..7e61ac1 100644
+--- a/src/Rvector_utils.c
+++ b/src/Rvector_utils.c
+@@ -4,6 +4,7 @@
+  ****************************************************************************/
+ #include "Rvector_utils.h"
+ 
+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
+ #include <string.h>  /* for memset() and memcpy() */
+ 
+ 
+@@ -242,7 +243,7 @@ void _fill_Rvector_block_with_val(SEXP Rvector,
+ 				     (const SEXP) val);
+ 		return;
+ 	}
+-	_set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector),
+	_set_elts_to_val(TYPEOF(Rvector), DATAPTR_RW(Rvector),
+ 			 block_offset, block_len, val);
+ }
+ 
+@@ -260,7 +261,7 @@ void _fill_Rvector_block_with_zeros(SEXP Rvector,
+ 				     R_NilValue);
+ 		return;
+ 	}
+-	_set_elts_to_zero(Rtype, DATAPTR(Rvector), block_offset, block_len);
+	_set_elts_to_zero(Rtype, DATAPTR_RW(Rvector), block_offset, block_len);
+ 	return;
+ }
+ 
+@@ -268,7 +269,7 @@ void _fill_Rvector_block_with_zeros(SEXP Rvector,
+ void _fill_Rvector_block_with_ones(SEXP Rvector,
+ 		R_xlen_t block_offset, R_xlen_t block_len)
+ {
+-	_set_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
+	_set_elts_to_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
+ 			 block_offset, block_len);
+ 	return;
+ }
+@@ -277,7 +278,7 @@ void _fill_Rvector_block_with_ones(SEXP Rvector,
+ void _fill_Rvector_block_with_minus_one(SEXP Rvector,
+ 		R_xlen_t block_offset, R_xlen_t block_len)
+ {
+-	_set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR(Rvector),
+	_set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
+ 			 block_offset, block_len);
+ 	return;
+ }
+@@ -293,7 +294,7 @@ void _fill_Rvector_block_with_NA(SEXP Rvector,
+ 					  NA_STRING);
+ 		return;
+ 	}
+-	_set_elts_to_NA(Rtype, DATAPTR(Rvector), block_offset, block_len);
+	_set_elts_to_NA(Rtype, DATAPTR_RW(Rvector), block_offset, block_len);
+ 	return;
+ }
+ 
+@@ -460,7 +461,7 @@ void _fill_Rvector_subset_with_zeros(SEXP Rvector,
+ 				R_NilValue);
+ 		return;
+ 	}
+-	_set_selected_elts_to_zero(Rtype, DATAPTR(Rvector),
+	_set_selected_elts_to_zero(Rtype, DATAPTR_RW(Rvector),
+ 				selection, selection_len, selection_offset);
+ 	return;
+ }
+@@ -470,7 +471,7 @@ void _fill_Rvector_subset_with_ones(SEXP Rvector,
+ 		const int *selection, int selection_len,
+ 		R_xlen_t selection_offset)
+ {
+-	_set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
+	_set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
+ 				  selection, selection_len, selection_offset);
+ 	return;
+ }
+diff --git a/src/SparseArray_aperm.c b/src/SparseArray_aperm.c
+index 0bd092e..bbeaf2c 100644
+--- a/src/SparseArray_aperm.c
+++ b/src/SparseArray_aperm.c
+@@ -721,7 +721,7 @@ static SEXP REC_grow_output_tree(const int *dim, int ndim,
+ 	const type *nzvals_p = NULL;  /* -Wmaybe-uninitialized */	\
+ 	type v;								\
+ 	if (nzvals != R_NilValue) {  /* standard leaf */		\
+-		nzvals_p = (const type *) DATAPTR(nzvals);		\
+		nzvals_p = DATAPTR_RO(nzvals);				\
+ 	} else {  /* lacunar leaf */					\
+ 		v = type ## 1;						\
+ 	}								\
+diff --git a/src/SparseArray_matrixStats.c b/src/SparseArray_matrixStats.c
+index b626553..debacf6 100644
+--- a/src/SparseArray_matrixStats.c
+++ b/src/SparseArray_matrixStats.c
+@@ -16,6 +16,7 @@
+ #include "leaf_utils.h"
+ #include "SparseArray_summarization.h"
+ 
+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
+ #include <string.h>  /* for memcpy() and memset() */
+ 
+ 
+@@ -272,7 +273,7 @@ SEXP C_colStats_SVT(SEXP x_dim, SEXP x_dimnames, SEXP x_type,
+ 	int warn = 0;
+ 	REC_colStats_SVT(x_SVT, x_bg_is_na, INTEGER(x_dim), LENGTH(x_dim),
+ 			 &summarize_op,
+-			 DATAPTR(ans), ans_Rtype,
+			 DATAPTR_RW(ans), ans_Rtype,
+ 			 out_incs, ans_ndim, pardim,
+ 			 &warn);
+ 	if (warn)
+@@ -1175,7 +1176,7 @@ SEXP C_rowStats_SVT(SEXP x_dim, SEXP x_dimnames, SEXP x_type,
+ 		SVT_rowMinsMaxs(x_SVT, x_Rtype, x_bg_is_na,
+ 			INTEGER(x_dim), LENGTH(x_dim),
+ 			opcode, narm,
+-			DATAPTR(ans), LENGTH(ans), ans_Rtype,
+			DATAPTR_RW(ans), LENGTH(ans), ans_Rtype,
+ 			out_incs, ans_ndim, nstrata);
+ 		break;
+ 	    case SUM_OPCODE:
+diff --git a/src/SparseArray_subassignment.c b/src/SparseArray_subassignment.c
+index 4cf1c3d..c3b2d5e 100644
+--- a/src/SparseArray_subassignment.c
+++ b/src/SparseArray_subassignment.c
+@@ -966,13 +966,13 @@ static inline int next_coords0(NindexIterator *Nindex_iter)
+ 		midx_p++;
+ 		coords0_p++;
+ 	}
+-	printf("coords0: ");
+	//printf("coords0: ");
+ 	coords0_p = Nindex_iter->coords0_buf;
+ 	for (along = Nindex_iter->margin; along < Nindex_iter->ndim; along++) {
+-		printf(" %3d", *coords0_p);
+		//printf(" %3d", *coords0_p);
+ 		coords0_p++;
+ 	}
+-	printf("\n");
+	//printf("\n");
+ 	return 1;
+ }
+ 
+diff --git a/src/SparseVec.h b/src/SparseVec.h
+index 894709b..73cd841 100644
+--- a/src/SparseVec.h
+++ b/src/SparseVec.h
+@@ -5,6 +5,7 @@
+ 
+ #include "Rvector_utils.h"
+ 
+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
+ #include <limits.h>  /* for INT_MAX */
+ 
+ 
+@@ -122,7 +123,7 @@ static inline SparseVec toSparseVec(SEXP nzvals, SEXP nzoffs,
+ 		if (IS_STRSXP_OR_VECSXP(Rtype)) {
+ 			sv.nzvals = nzvals;
+ 		} else {
+-			sv.nzvals = DATAPTR(nzvals);
+			sv.nzvals = DATAPTR_RW(nzvals);
+ 		}
+ 	}
+ 	sv.nzoffs = INTEGER(nzoffs);
+diff --git a/src/leaf_utils.c b/src/leaf_utils.c
+index e8066c3..c5ff3aa 100644
+--- a/src/leaf_utils.c
+++ b/src/leaf_utils.c
+@@ -10,6 +10,7 @@
+ #include "SparseVec_subsetting.h"
+ #include "SparseVec_subassignment.h"
+ 
+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
+ #include <string.h>  /* for memcpy() */
+ 
+ 
+@@ -129,7 +130,7 @@ SEXP _make_leaf_from_two_arrays(SEXPTYPE Rtype,
+ 			return ans;
+ 		}
+ 		ans_nzvals = PROTECT(allocVector(Rtype, nzcount));
+-		memcpy(DATAPTR(ans_nzvals), nzvals_p, Rtype_size * nzcount);
+		memcpy(DATAPTR_RW(ans_nzvals), nzvals_p, Rtype_size * nzcount);
+ 	}
+ 	SEXP ans = zip_leaf(ans_nzvals, ans_nzoffs, 0);
+ 	UNPROTECT(2);
+@@ -156,7 +157,7 @@ static SEXP make_leaf_from_Rvector_subset(SEXP Rvector,
+ 
+ 	if (avoid_copy_if_all_selected &&
+ 	    selection_offset == 0 && selection_len == XLENGTH(Rvector) &&
+-	    ATTRIB(Rvector) == R_NilValue)
+	    !ANY_ATTRIB(Rvector))
+ 	{
+ 		/* The full 'Rvector' is selected so can be reused as-is
+ 		   with no need to copy the selected elements to a new SEXP. */
+diff --git a/src/test.c b/src/test.c
+index 493538f..2205fa2 100644
+--- a/src/test.c
+++ b/src/test.c
+@@ -111,6 +111,9 @@ SEXP C_simple_omp_parallel_for_loop(SEXP nloop)
+ 	for (int i = 0; i < INTEGER(nloop)[0]; i++) {
+ #ifdef _OPENMP
+ 		int thread_num = omp_get_thread_num();
+		/* Can't use Rprintf() here because it's not thread-safe (it
+		   can trigger R's garbage collector which itself is not
+		   thread-safe). */
+ 		printf("thread_num = %d\n", thread_num);
+ #endif
+ 	}
+diff --git a/src/readSparseCSV.c b/src/readSparseCSV.c
+index a3d8da0..de1cb95 100644
+--- a/src/readSparseCSV.c
+++ b/src/readSparseCSV.c
+@@ -11,6 +11,7 @@
+ #include "ExtendableJaggedArray.h"
+ 
+ #include <R_ext/Connections.h>
+#include <Rversion.h>
+ 
+ #include <string.h>  /* for memcpy() */
+ 
+@@ -111,7 +112,11 @@ static SEXP dump_env_as_list_or_R_NilValue(SEXP env, int ans_len)
+ 	is_empty = 1;
+ 	for (i = 0; i < ans_len; i++) {
+ 		key = PROTECT(idx0_to_key(i));
+#if R_VERSION < R_Version(4, 6, 0)
+ 		ans_elt = findVar(install(translateChar(key)), env);
+#else
+		ans_elt = R_getVar(install(translateChar(key)), env, FALSE);
+#endif
+ 		UNPROTECT(1);
+ 		if (ans_elt == R_UnboundValue)
+ 			continue;
@@ -1,46 +0,0 @@
-From 1654599ea228efdd7b378ff44ed4e19d547641e0 Mon Sep 17 00:00:00 2001
-From: Bradley Lowekamp <blowekamp@mail.nih.gov>
-Date: Wed, 29 Apr 2026 16:22:49 +0000
-Subject: [PATCH 1/8] BUG: Replace removed CLOENV with R_ClosureEnv for R 4.6.0
- compatibility
-
-R 4.6.0 removed the non-API macro CLOENV from its public headers.
-The replacement R_ClosureEnv() was added in R 4.5.0. Add a version-
-guarded backport so that builds against older R versions (< 4.5.0)
-continue to work.
-
-Fixes #2574
---
- Wrapping/R/sitkRCommand.cxx | 7 ++++++-
- 1 file changed, 6 insertions(+), 1 deletion(-)
-
-diff --git a/Wrapping/R/sitkRCommand.cxx b/Wrapping/R/sitkRCommand.cxx
-index 216a9327b8..c3a62bead9 100644
--- a/Wrapping/R/sitkRCommand.cxx
-+++ b/Wrapping/R/sitkRCommand.cxx
-@@ -19,10 +19,15 @@
- // The python header defines _POSIX_C_SOURCE without a preceding #undef
- #include <iostream>
- #include <Rinternals.h>
-+#include <Rversion.h>
- 
- #include "sitkRCommand.h"
- #include "sitkExceptionObject.h"
- 
-+// R_ClosureEnv was added in R 4.5.0, CLOENV was removed in R 4.6.0
-+#if R_VERSION < R_Version(4, 5, 0)
-+#  define R_ClosureEnv(x) CLOENV(x)
-+#endif
- 
- namespace itk
- {
-@@ -86,7 +91,7 @@ RCommand::SetFunctionClosure(SEXP FN)
-     // element
-     R_fcall = PROTECT(Rf_lang1(this->m_FunctionClosure));
-     this->SetCallbackRCallable(R_fcall);
-    this->SetCallbackREnviron(CLOENV(this->m_FunctionClosure));
-+    this->SetCallbackREnviron(R_ClosureEnv(this->m_FunctionClosure));
-     UNPROTECT(1);
-   }
- }
-
@@ -1,171 +0,0 @@
-From 494259f19b3ca4ad0b11c858bc3ba9b587fa2ed5 Mon Sep 17 00:00:00 2001
-From: Bradley Lowekamp <blowekamp@mail.nih.gov>
-Date: Thu, 30 Apr 2026 16:09:54 +0000
-Subject: [PATCH 1/2] [R] Fix compilation with R 4.6.0 which removed non-API
- macros #3407
-
-R 4.6.0 (April 2025) removed the non-API macro SET_S4_OBJECT and made
-CHARACTER_POINTER return a const pointer, breaking compilation of SWIG
-generated R code.
-
-Replace with proper R API equivalents:
- SET_S4_OBJECT(x) -> x = Rf_asS4(x, TRUE, 0)  (3 sites in rrun.swg)
- CHARACTER_POINTER(v)[i] = ... -> SET_STRING_ELT(v, i, ...)  (2 sites in std_vector.i)
- CHARACTER_POINTER() via pstr -> STRING_ELT(, i) directly  (argcargv.i)
-
-All replacement APIs have been available since R 2.x so no version
-guards are required.
---
- CHANGES.current    | 6 ++++++
- Lib/r/argcargv.i   | 4 +---
- Lib/r/rrun.swg     | 6 +++---
- Lib/r/std_vector.i | 4 ++--
- 4 files changed, 12 insertions(+), 8 deletions(-)
-
-diff --git a/Lib/r/argcargv.i b/Lib/r/argcargv.i
-index 73380f4e2c9..af7aa14d66c 100644
--- a/Lib/r/argcargv.i
-+++ b/Lib/r/argcargv.i
-@@ -14,7 +14,6 @@
- %}
- %typemap(in) (int ARGC, char **ARGV) {
-   $1_ltype i;
-  SEXP *pstr;
-   if ($input == R_NilValue) {
-     /* Empty array */
-     $1 = 0;
-@@ -22,14 +21,13 @@
-     SWIG_exception_fail(SWIG_RuntimeError, "Wrong array type.");
-   } else {
-     $1 = Rf_length($input);
-    pstr = CHARACTER_POINTER($input);
-   }
-   $2 = ($2_ltype) malloc(($1+1)*sizeof($*2_ltype));
-   if ($2 == NULL) {
-     SWIG_exception_fail(SWIG_MemoryError, "Memory allocation failed.");
-   }
-   for (i = 0; i < $1; i++) {
-    $2[i] = ($*2_ltype)STRING_VALUE(pstr[i]);
-+    $2[i] = ($*2_ltype)STRING_VALUE(STRING_ELT($input, i));
-   }
-   $2[i] = NULL;
- }
-diff --git a/Lib/r/rrun.swg b/Lib/r/rrun.swg
-index 4c03d5884d7..5dee391f32f 100644
--- a/Lib/r/rrun.swg
-+++ b/Lib/r/rrun.swg
-@@ -267,7 +267,7 @@ SWIG_MakePtr(void *ptr, const char *typeName, int flags)
-     R_RegisterCFinalizer(external, R_SWIG_ReferenceFinalizer);
- 
-   r_obj = SET_SLOT(r_obj, Rf_mkString((char *) "ref"), external);
-  SET_S4_OBJECT(r_obj);
-+  r_obj = Rf_asS4(r_obj, TRUE, 0);
-   Rf_unprotect(2);
- 
-   return(r_obj);
-@@ -285,7 +285,7 @@ R_SWIG_create_SWIG_R_Array(const char *typeName, SEXP ref, int len)
-    Rf_protect(arr = R_do_slot_assign(arr, Rf_mkString("dims"), Rf_ScalarInteger(len)));
- 
-    Rf_unprotect(3); 			   
-   SET_S4_OBJECT(arr);	
-+   arr = Rf_asS4(arr, TRUE, 0);
-    return arr;
- }
- 
-@@ -308,7 +308,7 @@ SWIG_R_NewPointerObj(void *ptr, swig_type_info *type, int flags) {
-   }
-   rptr = R_MakeExternalPtr(ptr, 
-   R_MakeExternalPtr(type, R_NilValue, R_NilValue), R_NilValue); 
-  SET_S4_OBJECT(rptr);
-+  rptr = Rf_asS4(rptr, TRUE, 0);
-   return rptr;
- }
- 
-diff --git a/Lib/r/std_vector.i b/Lib/r/std_vector.i
-index 6b32c9f6fc2..7db6d3814ac 100644
--- a/Lib/r/std_vector.i
-+++ b/Lib/r/std_vector.i
-@@ -203,7 +203,7 @@
-          PROTECT(result = Rf_allocVector(STRSXP, val->size()));
-          for (unsigned pos = 0; pos < val->size(); pos++)
-            {
-             CHARACTER_POINTER(result)[pos] = Rf_mkChar(((*val)[pos]).c_str());
-+             SET_STRING_ELT(result, pos, Rf_mkChar(((*val)[pos]).c_str()));
-            }
-         UNPROTECT(1);
-         return(result);
-@@ -669,7 +669,7 @@
-             // Fill the R vector
-             for (unsigned vpos = 0; vpos < val->at(pos).size(); ++vpos)
-               {
-                CHARACTER_POINTER(VECTOR_ELT(result, pos))[vpos] = Rf_mkChar(val->at(pos).at(vpos).c_str());
-+                SET_STRING_ELT(VECTOR_ELT(result, pos), vpos, Rf_mkChar(val->at(pos).at(vpos).c_str()));
-               }
-           }
-         UNPROTECT(1);
-
-From 77d8826b46a967af158e982d56008aea2c8f6cb1 Mon Sep 17 00:00:00 2001
-From: Erez Geva <ErezGeva2@gmail.com>
-Date: Fri, 1 May 2026 18:47:42 +0200
-Subject: [PATCH 2/2] Add versioned `R` testing
-
-Signed-off-by: Erez Geva <ErezGeva2@gmail.com>
---
- .github/workflows/linux.yml |  7 +++++++
- Tools/CI-linux-install.sh   | 20 +++++++++++++++++++-
- configure.ac                | 11 +++++++++++
- 3 files changed, 37 insertions(+), 1 deletion(-)
-
-diff --git a/Tools/CI-linux-install.sh b/Tools/CI-linux-install.sh
-index ad74ad3f21f..8f459899906 100644
--- a/Tools/CI-linux-install.sh
-+++ b/Tools/CI-linux-install.sh
-@@ -181,7 +181,25 @@ case "$SWIGLANG" in
- 		fi
- 		;;
- 	"r")
-		$RETRY sudo apt-get -qq install r-base
-+		if [[ -n "$VER" ]]; then
-+			# Should helps with old version, but do not work
-+			#$RETRY sudo apt-get -qq remove r-base r-base-core r-base-dev r-base-html r-doc-html r-recommended
-+			sudo sed -i 's%^# deb-src %deb-src %' /etc/apt/sources.list
-+			sudo sed -i 's%^Types: deb$%Types: deb deb-src%' /etc/apt/sources.list.d/*
-+			$RETRY sudo apt-get -qq update
-+			$RETRY sudo apt-get -qq build-dep r-base
-+			r_build=`mktemp -d`
-+			r_tarball=R-$VER.tar.gz
-+			URL=https://cran.r-project.org/src/base/R-${VER:0:1}
-+			$RETRY wget $URL/$r_tarball
-+			tar -xf "$r_tarball" --strip-components=1 -C "$r_build"
-+			cd "$r_build"
-+			./configure
-+			make
-+			sudo make install
-+		else
-+			$RETRY sudo apt-get -qq install r-base
-+		fi
- 		;;
- 	"ruby")
- 		if [[ "$VER" ]]; then
-diff --git a/configure.ac b/configure.ac
-index e113f4b877c..e309b36ff45 100644
--- a/configure.ac
-+++ b/configure.ac
-@@ -2292,6 +2292,17 @@ else
- if test "x$RBIN" = xyes; then
-    AC_PATH_PROG(RBIN, R)
- fi
-+if test -n "$RBIN" && test -x "$RBIN"; then
-+   r_min_version=2.4.0
-+   AC_MSG_CHECKING([for R version])
-+   r_version=`R --version | grep 'R version' | sed 's%^R version %%;s% (.*%%'`
-+   AS_VERSION_COMPARE(["$r_version"], ["$r_min_version"],
-+                  [AC_MSG_RESULT([older then $r_min_version])
-+                   AS_UNSET([RBIN])],        dnl bellow r_min_version
-+                  [AC_MSG_RESULT([$r_version])],   dnl equal r_min_version
-+                  [AC_MSG_RESULT([$r_version])])   dnl above r_min_version
-+fi
-+
- fi
- 
- AC_SUBST(RBIN)
@@ -98,6 +98,7 @@
  #:use-module (gnu packages lua)
  #:use-module (gnu packages man)
  #:use-module (gnu packages markup)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages ocr)
@@ -47,6 +47,7 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages noweb)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
@@ -55,6 +55,7 @@
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages protobuf)
  #:use-module (gnu packages pkg-config)
@@ -237,7 +237,7 @@ it.")
 (define-public trealla
  (package
    (name "trealla")
-    (version "2.100.15")
+    (version "2.100.6")
    (source
     (origin
       (method git-fetch)
@@ -246,7 +246,7 @@ it.")
          (url "https://github.com/trealla-prolog/trealla")
          (commit (string-append "v" version))))
       (sha256
-        (base32 "1fr3h0hqk5bbzr8n415pd24n2nvxhyaxi03hn5s78q1yklynw13f"))
+        (base32 "0iy8477l9sf8p2jks8dlk5irssh1m4yyj7rflwvirbv19maaaghg"))
       (file-name (git-file-name name version))))
    (build-system gnu-build-system)
    (inputs
@@ -41,7 +41,7 @@
 ;;; Copyright © 2025 Matthew Elwin <elwin@northwestern.edu>
 ;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez@gmail.com>
-;;; Copyright © 2025 Zheng Junjie <z572@z572.online>
+;;; Copyright © 2025 Zheng Junjie <z572@z572.online> 
 ;;; Copyright © 2026 Nguyễn Gia Phong <cnx@loang.net>
 ;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
 ;;;
@@ -66,7 +66,6 @@
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
-  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages check)
@@ -78,6 +77,7 @@
  #:use-module (gnu packages jupyter)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages openstack)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
@@ -40,13 +40,13 @@
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system pyproject)
  #:use-module (gnu packages)
-  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages libffi)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages check)
  #:use-module (gnu packages machine-learning)
  #:use-module (gnu packages maths)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
@@ -40,7 +40,6 @@
 ;;; Copyright © 2025 Ghislain Vaillant <ghislain.vaillant@inria.fr>
 ;;; Copyright © 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2026 Reza Housseini <reza@housseini.me>
-;;; Copyright © 2026 Spencer King <spencer.king@wustl.edu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -88,6 +87,7 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages perl)
@@ -535,42 +535,6 @@ setting up, manipulating, running, visualizing and analyzing atomistic
 simulations.")
    (license license:lgpl2.1+)))

-(define-public python-autoray
-  (package
-    (name "python-autoray")
-    (version "0.8.10")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/jcmgray/autoray")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1gqfkpdng09l804xm9r1r098w10gr1bc5ax2xmhrpz9niybv71f5"))))
-    (build-system pyproject-build-system)
-    ;; tests: 1758 passed, 1483 skipped, 96 xfailed, 4 warnings
-    (native-inputs
-     (list python-hatch-vcs
-           python-hatchling
-           python-pytest))
-    (propagated-inputs
-     (list python-dask
-           python-matplotlib
-           python-networkx
-           python-numpy
-           python-opt-einsum
-           python-scipy
-           python-sparse))
-    (home-page "https://github.com/jcmgray/autoray")
-    (synopsis "Library for abstracting tensor operations")
-    (description
-     "This package provides a lightweight Python library for
-abstracting tensor operations.  It provides an automatic dispatch mechanism
-that means you can write backend agnostic code that works for any library
-that provides a @code{numpy} compatible API.")
-    (license license:asl2.0)))
-
 (define-public python-baycomp
  (package
    (name "python-baycomp")
@@ -1151,93 +1115,6 @@ computing in Python.  It extends both the @code{concurrent.futures} and
@code{dask} APIs to moderate sized clusters.")
    (license license:bsd-3)))

-(define-public python-dvc-data
-  (package
-    (name "python-dvc-data")
-    (version "3.16.12")
-    (home-page "https://github.com/iterative/dvc-data")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "dvc_data" version))
-              (sha256
-               (base32
-                "156iwdn7v5jhwbpwz92n28qiasgcbmcqv9vxg8xbvdfxzlzw0b7r"))))
-    (build-system pyproject-build-system)
-    (propagated-inputs
-     (list python-attrs
-           python-dictdiffer
-           python-diskcache
-           python-dvc-objects
-           python-fsspec
-           python-funcy-1.14
-           python-orjson
-           python-pygtrie
-           python-sqltrie
-           python-tqdm))
-    (native-inputs
-     (list python-click
-           python-pytest
-           python-pytest-benchmark
-           python-pytest-mock
-           ;; python-pytest-servers is not packaged in Guix yet
-           python-setuptools
-           python-setuptools-scm
-           python-typer
-           python-wheel))
-    (arguments
-     (list
-      #:test-flags
-      ;; TODO: package python-pytest-server with its transitive dependencies
-      #~(list "--ignore=tests/hashfile/test_db.py"
-              "--ignore=tests/hashfile/test_db_index.py"
-              "--ignore=tests/hashfile/test_obj.py"
-              "--ignore=tests/index/test_build.py"
-              "--ignore=tests/index/test_checkout.py"
-              "--ignore=tests/index/test_fs.py"
-              "--ignore=tests/index/test_index.py"
-              "--ignore=tests/index/test_storage.py")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'patch-pyproject
-            (lambda _
-              ;; setuptools cannot handle both license and license-files
-              (substitute* "pyproject.toml"
-                (("^license = .*") "license = {text = \"Apache-2.0\"}\n")
-                (("^license-files = .*") "")))))))
-    (synopsis "DVC's data management subsystem")
-    (description "Dvc data is DVC's data management subsystem.")
-    (license license:asl2.0)))
-
-(define-public python-dvc-objects
-  (package
-    (name "python-dvc-objects")
-    (version "5.1.1")
-    (home-page "https://github.com/iterative/dvc-objects")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "dvc_objects" version))
-       (sha256
-        (base32 "1amx5z8k2v2hbsajg0dcd5dxmmlv9bnbchpas95s8sj86cm8yc4y"))))
-    (build-system pyproject-build-system)
-    (propagated-inputs (list python-fsspec
-                             python-funcy-1.14))
-    (native-inputs
-     (list python-mypy
-           python-pytest
-           python-pytest-asyncio
-           python-pytest-benchmark
-           python-pytest-mock
-           python-pytest-sugar
-           python-reflink
-           python-setuptools
-           python-setuptools-scm
-           python-wheel))
-    (synopsis "Filesystem and object-db level abstractions for DVC")
-    (description "Dvc objects provides a filesystem and object-db level
-abstractions to use in dvc and dvc-data.")
-    (license license:asl2.0)))
-
 (define-public python-ecos
  (package
    (name "python-ecos")
@@ -1284,47 +1161,6 @@ numerical software for solving convex second-order cone programs (SOCPs).")
 which uncovers hidden structures in categorical data")
    (license license:expat)))

-(define-public python-einops
-  (package
-    (name "python-einops")
-    (version "0.8.1")
-    (source
-     (origin
-       (method git-fetch) ;PyPI misses .ipynb files required for tests
-       (uri (git-reference
-             (url "https://github.com/arogozhnikov/einops")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "07xd5a4sya3mr003f17hxykcbq3zf3mnr51qagv7fy55qcnbkn97"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      ;; Skip optional dependency on Jupyter during tests.
-      #~(list "--ignore=scripts/test_notebooks.py")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'set-backend
-            (lambda _
-              ;; Einops supports different backends, but we test
-              ;; only NumPy for availability and simplicity.
-              (setenv "EINOPS_TEST_BACKENDS" "numpy"))))))
-    (native-inputs
-     (list python-hatchling
-           python-nbconvert
-           python-nbformat
-           python-parameterized
-           python-pytest))
-    (propagated-inputs
-     (list python-numpy))
-    (home-page "https://einops.rocks/")
-    (synopsis "Tensor operations for different backends")
-    (description
-     "Einops provides a set of tensor operations for NumPy and multiple deep
-learning frameworks.")
-    (license license:expat)))
-
 (define-public python-fast-histogram
  (package
    (name "python-fast-histogram")
@@ -1397,35 +1233,6 @@ clustering schemes efficiently.  The package is made with two interfaces to
 standard software: R and Python.")
    (license license:bsd-2)))

-;; XXX: Not maintained since 2019. The project was archived by the owner on
-;; Nov 2, 2020. It is now read-only.
-(define-public python-fbpca
-  (package
-    (name "python-fbpca")
-    (version "1.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "fbpca" version))
-              (sha256
-               (base32
-                "1lbjqhqsdmqk86lb86q3ywf7561zmdny1dfvgwqkyrkr4ij7f1hm"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      ;; TypeError: 'dia_matrix' object is not subscriptable
-      #~(list "--deselect=fbpca.py::TestPCA::test_sparse"
-              "fbpca.py")))
-    (native-inputs (list python-pytest python-setuptools))
-    (propagated-inputs
-     (list python-numpy python-scipy))
-    (home-page "https://fbpca.readthedocs.io/")
-    (synopsis "Functions for principal component analysis and accuracy checks")
-    (description
-     "This package provides fast computations for @dfn{principal component
-analysis} (PCA), SVD, and eigendecompositions via randomized methods")
-    (license license:bsd-3)))
-
 (define-public python-fgivenx
  (package
    (name "python-fgivenx")
@@ -4820,6 +4627,76 @@ changed, it made sense to abstract away the nuisance of having to re-learn
 them.")
  (license license:bsd-3)))

+;; XXX: Not maintained since 2019. The project was archived by the owner on
+;; Nov 2, 2020. It is now read-only.
+(define-public python-fbpca
+  (package
+    (name "python-fbpca")
+    (version "1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "fbpca" version))
+              (sha256
+               (base32
+                "1lbjqhqsdmqk86lb86q3ywf7561zmdny1dfvgwqkyrkr4ij7f1hm"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; TypeError: 'dia_matrix' object is not subscriptable
+      #~(list "--deselect=fbpca.py::TestPCA::test_sparse"
+              "fbpca.py")))
+    (native-inputs (list python-pytest python-setuptools))
+    (propagated-inputs
+     (list python-numpy python-scipy))
+    (home-page "https://fbpca.readthedocs.io/")
+    (synopsis "Functions for principal component analysis and accuracy checks")
+    (description
+     "This package provides fast computations for @dfn{principal component
+analysis} (PCA), SVD, and eigendecompositions via randomized methods")
+    (license license:bsd-3)))
+
+(define-public python-einops
+  (package
+    (name "python-einops")
+    (version "0.8.1")
+    (source
+     (origin
+       (method git-fetch) ;PyPI misses .ipynb files required for tests
+       (uri (git-reference
+             (url "https://github.com/arogozhnikov/einops")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "07xd5a4sya3mr003f17hxykcbq3zf3mnr51qagv7fy55qcnbkn97"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; Skip optional dependency on Jupyter during tests.
+      #~(list "--ignore=scripts/test_notebooks.py")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-backend
+            (lambda _
+              ;; Einops supports different backends, but we test
+              ;; only NumPy for availability and simplicity.
+              (setenv "EINOPS_TEST_BACKENDS" "numpy"))))))
+    (native-inputs
+     (list python-hatchling
+           python-nbconvert
+           python-nbformat
+           python-parameterized
+           python-pytest))
+    (propagated-inputs
+     (list python-numpy))
+    (home-page "https://einops.rocks/")
+    (synopsis "Tensor operations for different backends")
+    (description
+     "Einops provides a set of tensor operations for NumPy and multiple deep
+learning frameworks.")
+    (license license:expat)))
+
 (define-public python-uhi
  (package
    (name "python-uhi")
@@ -6390,6 +6267,93 @@ well as key metadata and SIRENE database containing data on all French
 compagnies.")
    (license license:expat)))

+(define-public python-dvc-objects
+  (package
+    (name "python-dvc-objects")
+    (version "5.1.1")
+    (home-page "https://github.com/iterative/dvc-objects")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "dvc_objects" version))
+       (sha256
+        (base32 "1amx5z8k2v2hbsajg0dcd5dxmmlv9bnbchpas95s8sj86cm8yc4y"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-fsspec
+                             python-funcy-1.14))
+    (native-inputs
+     (list python-mypy
+           python-pytest
+           python-pytest-asyncio
+           python-pytest-benchmark
+           python-pytest-mock
+           python-pytest-sugar
+           python-reflink
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
+    (synopsis "Filesystem and object-db level abstractions for DVC")
+    (description "Dvc objects provides a filesystem and object-db level
+abstractions to use in dvc and dvc-data.")
+    (license license:asl2.0)))
+
+(define-public python-dvc-data
+  (package
+    (name "python-dvc-data")
+    (version "3.16.12")
+    (home-page "https://github.com/iterative/dvc-data")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "dvc_data" version))
+              (sha256
+               (base32
+                "156iwdn7v5jhwbpwz92n28qiasgcbmcqv9vxg8xbvdfxzlzw0b7r"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-attrs
+           python-dictdiffer
+           python-diskcache
+           python-dvc-objects
+           python-fsspec
+           python-funcy-1.14
+           python-orjson
+           python-pygtrie
+           python-sqltrie
+           python-tqdm))
+    (native-inputs
+     (list python-click
+           python-pytest
+           python-pytest-benchmark
+           python-pytest-mock
+           ;; python-pytest-servers is not packaged in Guix yet
+           python-setuptools
+           python-setuptools-scm
+           python-typer
+           python-wheel))
+    (arguments
+     (list
+      #:test-flags
+      ;; TODO: package python-pytest-server with its transitive dependencies
+      #~(list "--ignore=tests/hashfile/test_db.py"
+              "--ignore=tests/hashfile/test_db_index.py"
+              "--ignore=tests/hashfile/test_obj.py"
+              "--ignore=tests/index/test_build.py"
+              "--ignore=tests/index/test_checkout.py"
+              "--ignore=tests/index/test_fs.py"
+              "--ignore=tests/index/test_index.py"
+              "--ignore=tests/index/test_storage.py")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-pyproject
+            (lambda _
+              ;; setuptools cannot handle both license and license-files
+              (substitute* "pyproject.toml"
+                (("^license = .*") "license = {text = \"Apache-2.0\"}\n")
+                (("^license-files = .*") "")))))))
+    (synopsis "DVC's data management subsystem")
+    (description "Dvc data is DVC's data management subsystem.")
+    (license license:asl2.0)))
+
 (define-public python-pyqtgraph
  (package
    (name "python-pyqtgraph")
@@ -268,6 +268,7 @@
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages node)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages openstack)
@@ -17626,14 +17627,6 @@ should be stored on various operating systems.")
       (sha256
        (base32 "0vm1r1jlaiagj0l9yf7j6zn9w3733dr2169911c0svgrr3gwiwn9"))))
    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      '(modify-phases %standard-phases
-         (add-after 'unpack 'fix-tests
-           (lambda _
-             (substitute* "pasta/augment/inline_test.py"
-               (("assertRaisesRegexp") "assertRaisesRegex")))))))
    (propagated-inputs (list python-six))
    (native-inputs (list python-pytest python-setuptools))
    (home-page "https://github.com/google/pasta")
@@ -18311,21 +18304,9 @@ is binding LibSass.")
       (sha256
        (base32 "1fj4zkcnx3mk7kbnf4d6pjgv331n17wzpphpwdnmr498ghbsph9k"))))
    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:tests? #f  ;circular dependency with python-aiohttp
-      #:phases
-      '(modify-phases %standard-phases
-         (add-after 'unpack 'python3.12-compatibility
-           (lambda _
-             (substitute* '("idna_ssl.py"
-                            "tests/test_base.py")
-               (("import ssl")
-                "import ssl\nimport urllib3")
-               (("ssl.match_hostname")
-                "urllib3.util.ssl_match_hostname")))))))
+    (arguments (list #:tests? #f))  ;circular dependency with python-aiohttp
    (native-inputs (list python-setuptools))
-    (propagated-inputs (list python-idna python-urllib3))
+    (propagated-inputs (list python-idna))
    (home-page "https://github.com/aio-libs/idna-ssl")
    (synopsis "Support Unicode(idna) domains for Python's @code{ssl} module")
    (description
@@ -39767,31 +39748,6 @@ progress, among other things.")
 for linkify-it-py projects.")
    (license license:expat)))

-(define-public python-udapi
-  (package
-    (name "python-udapi")
-    (version "0.5.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/udapi/udapi-python")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1z9nyj0jmd2yk58c5kag4fkfb7y478di859xi56xc7fhvmyjf7nj"))))
-    (build-system pyproject-build-system)
-    (native-inputs
-     (list python-pytest python-setuptools))
-    (propagated-inputs
-     (list python-colorama python-termcolor))
-    (home-page "http://udapi.readthedocs.io")
-    (synopsis "Framework for processing Universal Dependencies data")
-    (description
-     "This package is a Python library providing an API for processing
-Universal Dependencies data.")
-    (license license:gpl3+)))
-
 (define-public python-ujson
  (package
    (name "python-ujson")
@@ -1255,7 +1255,7 @@ base, via the @file{pythoncapi_compat.h} header file.")
 (define-public micropython
  (package
    (name "micropython")
-    (version "1.28.0")
+    (version "1.26.1")
    (source
      (origin
        (method url-fetch)
@@ -1263,7 +1263,7 @@ base, via the @file{pythoncapi_compat.h} header file.")
                            "releases/download/v" version
                            "/micropython-" version ".tar.xz"))
        (sha256
-         (base32 "05d2gd3g8v3paxf4fin4cv5scgnc4yl0jdahpjs37nmqaybcahsf"))
+         (base32 "165c8g60f5zf82gw2d94snyjmcgn999jn4i8ngyc0wk2vwa6bghj"))
      (modules '((guix build utils)))
      (snippet
       '(begin
@@ -74,7 +74,6 @@
  #:use-module (gnu packages bash)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bison)
-  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages crypto)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cmake)
@@ -113,6 +112,7 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages markup)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages node)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages pciutils)
@@ -179,9 +179,9 @@ official project.")
    (home-page "https://github.com/oclero/qtappinstancemanager")
    (license license:expat)))

-(define-public qcoro-qt6
+(define-public qcoro-qt5
  (package
-    (name "qcoro-qt6")
+    (name "qcoro-qt5")
    (version "0.11.0")
    (source
     (origin
@@ -194,18 +194,31 @@ official project.")
        (base32 "0g9laaw1mkp5ynpp3c7aingndcmgncbacslq3p6bzwjisdd6xr5m"))))
    (build-system qt-build-system)
    (arguments
-     (list #:qtbase qtbase
-           #:configure-flags
+     (list #:configure-flags
           #~(list "-DCMAKE_CXX_FLAGS=-fPIC"
-                   "-DUSE_QT_VERSION=6")))
+                   (string-append "-DUSE_QT_VERSION="
+                                  #$(version-major
+                                     (package-version
+                                      (this-package-input "qtbase")))))))
    (native-inputs (list dbus))         ;for tests
-    (inputs (list qtdeclarative qtwebsockets libxkbcommon))
+    (inputs (list qtbase-5 qtdeclarative-5 qtwebsockets-5))
    (home-page "https://qcoro.dvratil.cz/")
-    (synopsis "C++ Coroutine Library for Qt6")
+    (synopsis "C++ Coroutine Library for Qt5")
    (description "QCoro is a C++ library that provide set of tools to make use
 of C++20 coroutines in connection with certain asynchronous Qt actions.")
    (license license:expat)))

+(define-public qcoro-qt6
+  (package
+    (inherit qcoro-qt5)
+    (name "qcoro-qt6")
+    (synopsis "C++ Coroutine Library for Qt6")
+    (inputs (modify-inputs inputs
+              (replace "qtbase" qtbase)
+              (replace "qtdeclarative" qtdeclarative)
+              (replace "qtwebsockets" qtwebsockets)
+              (append libxkbcommon)))))
+
 (define-public qlementine
  (package
    (name "qlementine")
@@ -1661,6 +1674,13 @@ from within Qt 5.")))
 XLSX document format.")
     (license license:expat)))

+(define-public qxlsx-qt5
+  (package/inherit qxlsx
+    (name "qxlsx-qt5")
+    (inputs
+     (list qtbase-5))
+    (synopsis "Qt5 build for the qxlsx library")))
+
 (define-public qtxmlpatterns-5
  (package (inherit qtsvg-5)
    (name "qtxmlpatterns")
@@ -6445,9 +6465,9 @@ handles the authentication process of an account and securely stores the
 credentials and service-specific settings.")
    (license license:lgpl2.1+)))

-(define-public packagekit-qt6
+(define-public packagekit-qt5
  (package
-    (name "packagekit-qt6")
+    (name "packagekit-qt5")
    (version "1.1.2")
    (source (origin
              (method git-fetch)
@@ -6459,18 +6479,30 @@ credentials and service-specific settings.")
               (base32
                "1nx8xfhz9v4pc0mz1ir0pq47skpc3w3yj8wqa4m5yky87ib5xcxc"))))
    (build-system cmake-build-system)
-    (arguments
-      (list
-        #:tests? #f          ;no test suite
-        #:configure-flags #~(list "-DBUILD_WITH_QT6=ON")))
-    (inputs (list packagekit qtbase))
+    (arguments '(#:tests? #f))          ;no test suite
+    (native-inputs (list pkg-config))
+    (inputs (list packagekit qtbase-5))
    (home-page "https://www.freedesktop.org/software/PackageKit/pk-intro.html")
-    (synopsis "Qt6 bindings for PackageKit")
-    (description "Provides Qt6 bindings to PackageKit which is a DBUS
+    (synopsis "Qt5 bindings for PackageKit")
+    (description "Provides Qt5 bindings to PackageKit which is a DBUS
 abstraction layer that allows the session user to manage packages in
 a secure way.")
    (license license:lgpl2.1+)))

+(define-public packagekit-qt6
+  (package
+    (inherit packagekit-qt5)
+    (name "packagekit-qt6")
+    (arguments (substitute-keyword-arguments arguments
+                 ((#:configure-flags flags #~'())
+                  #~(cons "-DBUILD_WITH_QT6=ON" #$flags))))
+    (inputs (modify-inputs inputs
+              (replace "qtbase" qtbase)))
+    (synopsis "Qt6 bindings for PackageKit")
+    (description "Provides Qt6 bindings to PackageKit which is a DBUS
+abstraction layer that allows the session user to manage packages in
+a secure way.")))
+
 ;; fork for support qt6
 (define-public signond-qt6
  (let ((commit "c8ad98249af541514ff7a81634d3295e712f1a39")
@@ -202,7 +202,7 @@
 ;;
 ;; CODE:

-(define %racket-version "9.1") ; Remember to update chez-scheme-for-racket!
+(define %racket-version "8.18") ; Remember to update chez-scheme-for-racket!
 (define %racket-commit
  (string-append "v" %racket-version))
 (define %racket-origin
@@ -212,7 +212,7 @@
          (url "https://github.com/racket/racket")
          (commit %racket-commit)))
    (sha256
-     (base32 "1yc6lkydg32998ajnqws83zakksmbp3hb21spq0sfaq4v7wg2ng6"))
+     (base32 "0m38im7a3b3w7sdl15vpsrx7dxw5iz22f1zzffy1bkbbqz45pm87"))
    (file-name (git-file-name "racket" %racket-version))
    (patches (search-patches "racket-chez-scheme-bin-sh.patch"
                             "racket-launcher-config-dir.patch"
@@ -695,7 +695,6 @@ DrRacket IDE, are not included.")
         ("net-lib" "pkgs/net-lib")
         ("racket-doc" "pkgs/racket-doc")
         ("racket-index" "pkgs/racket-index")
-         ("racket-index-exe" "pkgs/racket-index-exe")
         ("scheme-doc" "pkgs/scheme-doc")
         ("sandbox-lib" "pkgs/sandbox-lib")
         ("sequence-tools-lib" "pkgs/sequence-tools-lib")
@@ -707,10 +706,10 @@ DrRacket IDE, are not included.")
       "class-iop" (base32 "08z57q83cr7wnh6g8ah3hdhmsmf9zp1jfs7yvxv188l3hzvygy5l")
       '("class-iop-lib"))
      (simple-racket-origin
-       "compatibility" (base32 "0q5k4p44sf2y4gl69js11qvicyzqwy16ry74bvj1vrn8i8xws55b")
+       "compatibility" (base32 "1d1py9wizi4jnzak7b6d0p9filxv1x9mlx5gsp3yhcjajigq182p")
       '("compatibility" "compatibility-doc" "compatibility-lib"))
      (simple-racket-origin
-       "contract-profile" (base32 "068z8flwcznqg0bjk227i2qapqbciyrckgqf8mvk57gxmr6zh3d3")
+       "contract-profile" (base32 "1xm2z8g0dpv5d9h2sg680vx1a8ix9gbsdpxxb8qv1w7akp73paj3")
       '(("contract-profile" ".")))
      (simple-racket-origin
       "data" (base32 "11ai6c9h0brbblc6xn045ajj4gyrvbjpk1pqcqm1m0dy9q2rzd4a")
@@ -719,7 +718,7 @@ DrRacket IDE, are not included.")
       "datalog" (base32 "0nf6cy4djpyhfvgpa6yn72apbz9s83gp0qg95pzjd0az4v6qwq1s")
       '(("datalog" ".")))
      (simple-racket-origin
-       "db" (base32 "09f2wysqmgs46nbzmwrhbn6jqnkpj6bsabm6s6kw8qmp6azca9q2")
+       "db" (base32 "0qwl8gyd71sm56kcs021g99cpw5bibaycvk1x7ng69jhkylg6q6f")
       '("db" "db-doc" "db-lib"))
      (simple-racket-origin
       "deinprogramm" (base32 "1zkasf94gzp97q0fhrd065d56zv10h0j0ncmaghzglkmjj8c3vvx")
@@ -732,10 +731,10 @@ DrRacket IDE, are not included.")
       "distributed-places" (base32 "1dajpkj9balqcpv6cdk9hwjz592h1vq8rrx5vncariiac4vbdpa0")
       '("distributed-places" "distributed-places-doc" "distributed-places-lib"))
      (simple-racket-origin
-       "draw" (base32 "157r861rx2avbjpqhrrxwdqxwf5ksvw38km3pw7rxiwvwh9nys8k")
+       "draw" (base32 "1nny22h0hnd40qs3ndkhfrgg793y6f4gl9jpdz1g2k0cpr3818rg")
       '("draw" "draw-doc" "draw-lib"))
      (simple-racket-origin
-       "drracket" (base32 "17sszhx5nd549w7kj6pd3c3cyjps2swbp7rmg36yaxm71pli5gs5")
+       "drracket" (base32 "07qh9dzgd2xhd0375z78vcsf32za08cacj4s2mcrhilcvcgw9s0j")
       '("drracket"
         "drracket-core"
         "drracket-core-lib"
@@ -754,7 +753,7 @@ DrRacket IDE, are not included.")
       "eopl" (base32 "0qihajdpwf2q7hbs6fsw6mmmzy57kgzgry3vyp9z8w7ay8df3w15")
       '(("eopl" ".")))
      (simple-racket-origin
-       "errortrace" (base32 "02z80khr4kqhcpq1k3djz7jgkwa31vnacid4qx8naab9dkbcp5x8")
+       "errortrace" (base32 "0l9k2rx6z4jkid7kxhbs763s66pxbzvfrgxajykbrmqkv77lhb3w")
       '("errortrace" "errortrace-doc" "errortrace-lib"))
      (simple-racket-origin
       "expeditor" (base32 "1nk88jq0blzcw45fr8nwp024cysplayi3paaay4z824lkn1smzaa")
@@ -771,13 +770,13 @@ DrRacket IDE, are not included.")
       "games" (base32 "13z7fnbr48s98lmfxc0nbfhbqkd4hphymy2r63hqm783xzn6ylzi")
       '(("games" ".")))
      (simple-racket-origin
-       "gui" (base32 "1c47622y5cf1p7nnbycaf53m8vakf55lqzv8byqzj7zcvcsh8s16")
+       "gui" (base32 "0qkxa8cq0cblriamd7x502g918kjvq4348l6c8qmqdpn9cw9mg2h")
       '("gui" "gui-doc" "gui-lib" "tex-table"))
      (simple-racket-origin
-       "gui-pkg-manager" (base32 "1f0ssg37kdk3xn9js616ns345565q39j9h51wzd99753iqd45m92")
+       "gui-pkg-manager" (base32 "024880k3wmvkqhjc954prrkavwv3bgafcw00ajz7h2llygh0aqpl")
       '("gui-pkg-manager-lib"))
      (simple-racket-origin
-       "htdp" (base32 "02a5zny1njys40jfsi2spw82ar0kkbfddpk10al822ajs1manhak")
+       "htdp" (base32 "14bdv86zxs87rvvvbwvq3x0sqpg1hj16whjcv20r96c26b1xxj36")
       '("htdp" "htdp-doc" "htdp-lib"))
      (simple-racket-origin
       "html" (base32 "18n1jnjgzfknc8nv8dppi85nb8q08gqdwkg6hfjk08x0p00anx2x")
@@ -792,16 +791,16 @@ DrRacket IDE, are not included.")
       "lazy" (base32 "0rn8kd0ih7aw6fj1g7jdvi5978a6q4hyd6gbh89nb6j5ijvlgn43")
       '(("lazy" ".")))
      (simple-racket-origin
-       "macro-debugger" (base32 "08qmkrvm3qvac4829izmlwl9qrlsc1f6y8yqiradibhm05k7rwg7")
+       "macro-debugger" (base32 "133b74pxavbafcsmp34kgvwmx1l6xx4bykzvgwwjg3kg2fa5bg1g")
       '("macro-debugger" "macro-debugger-text-lib"))
      (simple-racket-origin
-       "main-distribution" (base32 "0gk7wrwy0r1yllk827h8awfswngl1lhlq765d6s42y841v33jn0i")
+       "main-distribution" (base32 "0m2n9s32s8a4a2gn4ywrm9l8jycdm5ayi5w9kh5wchhrrw7qzq7y")
       '(("main-distribution" ".")))
      (simple-racket-origin
       "make" (base32 "10852fj30bz5r46c3d99s37fkgy5yh44gb01j29sf3kxnhi0g2sa")
       '(("make" ".")))
      (simple-racket-origin
-       "math" (base32 "1mgqxx9lbwhd8if3mxz7ji2wryvihjmq5imn2316skkvr16yy8mx")
+       "math" (base32 "1399mynmcrybipjsy2ikzs600jjxda0lah653w3vx2lfspsn31if")
       '("math" "math-doc" "math-lib"))
      (simple-racket-origin
       "mysterx" (base32 "11p9jzrafw0hizhl0cs4sxx7rv281185q8hryic2rpk0kzjdyr48")
@@ -810,7 +809,7 @@ DrRacket IDE, are not included.")
       "mzcom" (base32 "0rc9pfj7gwm5azghqvcibz6si1x5s2v8mr2yngk7ssq9gzfbi6a4")
       '(("mzcom" ".")))
      (simple-racket-origin
-       "mzscheme" (base32 "0p7bp8rmzw7k12sjxdqlxf31d8ama4wv9qz6ryvnmjn2qyhrr3d1")
+       "mzscheme" (base32 "04kyrhznq46mklacf7pms4fv47zsimqqk3948r3w2ym9n04fhjsx")
       '("mzscheme" "mzscheme-doc" "mzscheme-lib"))
      (racket-packages-origin
       "net-cookies" (origin
@@ -819,7 +818,7 @@ DrRacket IDE, are not included.")
                             (url "https://github.com/RenaissanceBug/racket-cookies")
                             (commit %racket-commit)))
                       (sha256 (base32
-                                "0v6lbpv8ly4jwpjr3rk0q6izpsnfp45ysgrhngpw7jshkjc5wgyd"))
+                                "1fbl717w5801bydx3nzwxddd1rh1cc0gxwpjc7ka9zh5ak09sb0w"))
                       (file-name
                        (git-file-name "RenaissanceBug-racket-cookies" %racket-version)))
       '("net-cookies" "net-cookies-doc" "net-cookies-lib"))
@@ -839,16 +838,16 @@ DrRacket IDE, are not included.")
       "option-contract" (base32 "1914dcxy6qzpg3cpnzdm9lj0kwyw8xdb85mwiamqfkbg0xlyyhpa")
       '("option-contract" "option-contract-doc" "option-contract-lib"))
      (simple-racket-origin
-       "parser-tools" (base32 "0dp99d1a47kqyg2iqdijm5781qnd571iwvg85dvrjc76ab4pccgd")
+       "parser-tools" (base32 "0i822p7ik6q03l7mrlf0qb63xdxvx06yl5lg1g1qri5wmi5xj0pb")
       '("parser-tools" "parser-tools-doc" "parser-tools-lib"))
      (simple-racket-origin
       "pconvert" (base32 "0xw9f9692v2qp16fwmwmwmrb118kpz259vmx8cq6s9vsw0112zpq")
       '("pconvert-lib" "pconvert-doc"))
      (simple-racket-origin
-       "pict" (base32 "1xs1k98nr052p5v30abn7kl8pm1rdwj8xqvrghw8b62bvhhb072a")
+       "pict" (base32 "17pldgiifmwi968dwlk23c1wnrlks0x7aj5jdmdfsf9xgq31wkb5")
       '("pict" "pict-doc" "pict-lib"))
      (simple-racket-origin
-       "pict-snip" (base32 "1qrqbigw6arhccqgqzblfqqcpsdy15dwb0y22axwxgpw1ax0ki6f")
+       "pict-snip" (base32 "081nwiy4a0n4f7xws16hqbhf0j3kz5alizndi3nnyr3chm4kng6x")
       '("pict-snip" "pict-snip-doc" "pict-snip-lib"))
      (simple-racket-origin
       "picturing-programs" (base32 "1a3d6nw9n827b4711nvgrnw7w47k4fxvk8c2a8br6a1l748kxkwy")
@@ -866,7 +865,7 @@ DrRacket IDE, are not included.")
       "preprocessor" (base32 "1p5aid58ifnjy4xl0ysh85cq39k25661v975jrpk182z3k5621mg")
       '(("preprocessor" ".")))
      (simple-racket-origin
-       "profile" (base32 "1n6jlhkq0zs2sd132k92nvw08qscadjz3d6p2r5pjlcdawkmkik0")
+       "profile" (base32 "10lv3iz58hqk043llnbqrkmjnm1pbvr4j1j188g85zg798rqyjzs")
       '("profile" "profile-doc" "profile-lib"))
      (racket-packages-origin
       "quickscript" (origin
@@ -896,7 +895,7 @@ DrRacket IDE, are not included.")
                         (git-file-name "jeapostrophe-racket-cheat" %racket-version)))
       '(("racket-cheat" ".")))
      (simple-racket-origin
-       "racklog" (base32 "0i2jnghb5vqmk2f0cppgggyp73zy1q0dlhpvxrzdxw39skmhmgkc")
+       "racklog" (base32 "0fr8xij0sssfnmwn6dfdi4jj3l62f2yj3jrjljv13kaycrfls032")
       '(("racklog" ".")))
      (simple-racket-origin
       "rackunit" (base32 "191x4lgxg1bbkimdndg6j562zyxq48l0g21f9j2ln2hmh9s1v065")
@@ -915,7 +914,7 @@ DrRacket IDE, are not included.")
       "realm" (base32 "0rlvwyd6rpyl0zda4a5p8dp346fvqzc8555dgfnrhliymkxb6x4g")
       '(("realm" ".")))
      (simple-racket-origin
-       "redex" (base32 "1gg36wpd5kw01dwz353j5xvd2c673aws5l3jn2h2rzqlslk49dw7")
+       "redex" (base32 "1h60mhaaiiwqcnmskqfrl6jhg4d97xjdcxnhw9krm4aysa9b9bwf")
       '("redex"
         "redex-benchmark"
         "redex-doc"
@@ -930,7 +929,7 @@ DrRacket IDE, are not included.")
       "scheme-lib" (base32 "0pcf0y8rp4qyjhaz5ww5sr5diq0wpcdfrrnask7zapyklzx1jx8x")
       '(("scheme-lib" ".")))
      (simple-racket-origin
-       "scribble" (base32 "1h6rkkbvxa6fwcpv6y5n14y984z4bxlhn04hhv8r7398a6jsldg6")
+       "scribble" (base32 "0pg8brgyyziw3y8fp6ls6ii7i02cmm5168i4zmqfxjzywswljf17")
       '("scribble"
         "scribble-doc"
         "scribble-html-lib"
@@ -956,13 +955,13 @@ DrRacket IDE, are not included.")
       "slatex" (base32 "0pkm2isbbdk63slrbsxcql7rr0wdrw5kapw1xq4ps5k8dhlzv8x0")
       '(("slatex" ".")))
      (simple-racket-origin
-       "slideshow" (base32 "1aprcapyj0362lfh2pbcyxf4r2k01zmp6yy9ppag0xbz0jw437im")
+       "slideshow" (base32 "0dyg20qs40s2d6ha28zb9h5x4v7phkddinqm446b4jishyrg7dqc")
       '("slideshow" "slideshow-doc" "slideshow-exe" "slideshow-lib" "slideshow-plugin"))
      (simple-racket-origin
-       "snip" (base32 "10727bi2ybn2ahlkpikdknwfzfsppaw5wkvjmzd380jp1fw91q67")
+       "snip" (base32 "1jpy5728w9bszgsjczlzrjjxsvqlcn4ah6gd3rp0plp8zzk9mq0s")
       '("snip" "snip-lib"))
      (simple-racket-origin
-       "typed-racket" (base32 "1cmp3065fp9lm6rsfml7x5bvnilh1fs9k0511l11qdismz2sndpy")
+       "typed-racket" (base32 "00d5pb5h34066q4prb9v5s5m9ggbby31f3anshd9vfsrzhd38p4n")
       '("source-syntax"
         "typed-racket"
         "typed-racket-compatibility"
@@ -973,7 +972,7 @@ DrRacket IDE, are not included.")
       "srfi" (base32 "07q7wdgnf88z1rq0bfpn4b41abhfswa38c0s2hkn325blk53k4a6")
       '("srfi" "srfi-doc" "srfi-lib" "srfi-lite-lib"))
      (simple-racket-origin
-       "string-constants" (base32 "085anm6s5ghg5bfggavknpr52py1a72qwjihvp0rnxpkf181sn8c")
+       "string-constants" (base32 "0llalgdncn18ix5xnx82yyms221g47xh7s3w6inch53ip3yc6ksr")
       '("string-constants" "string-constants-doc" "string-constants-lib"))
      (simple-racket-origin
       "swindle" (base32 "1q8vdxpzczzwdw2mys2caab45yvadmqkixsr29k8pl03n8dsg8j9")
@@ -985,16 +984,16 @@ DrRacket IDE, are not included.")
       "trace" (base32 "1zx0kfbacidg5rllbvx842x949ra22n004irs3vm1hqmwmixy3is")
       '(("trace" ".")))
      (simple-racket-origin
-       "unix-socket" (base32 "039r2aqc6xc4b3x95ggjg4ab1pfiff6pavi4d40662zgwbi61pwk")
+       "unix-socket" (base32 "02dfwas5ynbpyz74w9kwb4wgb37y5wys7svrlmir8k0n9ph9vq0y")
       '("unix-socket" "unix-socket-doc" "unix-socket-lib"))
      (simple-racket-origin
-       "web-server" (base32 "0v66z9dklf02lc0g357h4rnfq5pnk87d1qz59sfrlzz24phxg9g6")
+       "web-server" (base32 "0ry5vwjd06ml9hmspgrwci8c99syx7zhp9sgldmhwwfvf5m1g29d")
       '("web-server" "web-server-doc" "web-server-lib"))
      (simple-racket-origin
       "wxme" (base32 "1qp5gr9gqsakiq3alw6m4yyv5vw4i3hp4y4nhq8vl2nkjmirvn0b")
       '("wxme" "wxme-lib"))
      (simple-racket-origin
-       "xrepl" (base32 "1kkcm68qyck2d6mp56h1j5fnfbx938a15dnyn1cf5yqpj9cc637m")
+       "xrepl" (base32 "0sw531zvd8xqckmrh5da4fiq0sfjyg1nj5d508l7bl3azn35khil")
       '("xrepl" "xrepl-doc" "xrepl-lib"))))
    (build-system gnu-build-system)
    (arguments
@@ -31,7 +31,7 @@
 ;;; Copyright © 2022-2025 Remco van 't Veer <remco@remworks.net>
 ;;; Copyright © 2022 Taiju HIGASHI <higashi@taiju.info>
 ;;; Copyright © 2023 Yovan Naumovski <yovan@gorski.stream>
-;;; Copyright © 2023, 2024, 2025, 2026 gemmaro <gemmaro.dev@gmail.com>
+;;; Copyright © 2023, 2024, 2025 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023, 2024 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2023, 2024 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2023-2025 Hartmut Goebel <h.goebel@crazy-compilers.com>
@@ -8201,27 +8201,19 @@ differences (added or removed nodes) between two XML/HTML documents.")
 (define-public ruby-racc
  (package
    (name "ruby-racc")
-    (version "1.8.1")
+    (version "1.5.2")
    (source
     (origin
-       (method git-fetch) ;for tests
-       (uri (git-reference
-             (url "https://github.com/ruby/racc")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (rubygems-uri "racc" version))
       (sha256
        (base32
-         "1sg2mqp6yxdxrn9kbbsxkd6930fxvm4yjl8knsc0wq6fkipnhm8q"))))
+         "178k7r0xn689spviqzhvazzvxfq6fyjldxb3ywjbgipbfi4s8j1g"))))
    (build-system ruby-build-system)
    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'build 'compile
-            (lambda _
-              (invoke "rake" "compile"))))))
+     `(#:tests? #f))            ; Fails while parsing test instructions.
    (native-inputs
-     (list ruby-rake-compiler ruby-test-unit-ruby-core))
+     (list ruby-hoe ruby-rake-compiler))
    (synopsis "LALR(1) parser generator for Ruby")
    (description
     "Racc is a LALR(1) parser generator.  It is written in Ruby itself, and
@@ -116,6 +116,7 @@
  #:use-module (gnu packages lua)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages shells)
  #:use-module (gnu packages ssh)
  #:use-module (gnu packages pcre)
@@ -4211,14 +4212,14 @@ background agent taking care of maintaining the necessary state.")
 (define-public rust-cargo-c
  (package
    (name "rust-cargo-c")
-    (version "0.10.20+cargo-0.94.0")
+    (version "0.10.22+cargo-0.96.0")
    (source
      (origin
        (method url-fetch)
        (uri (crate-uri "cargo-c" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-         (base32 "0q1198xlkcd50nxx722s18lpm6hacnvzqqacb0xdld8ll9z3m5ay"))))
+         (base32 "1j5122hla12v6xjpvsvzv10gzvm80dbf65b2cy6669kcpjvlk1v0"))))
    (build-system cargo-build-system)
    (arguments (list #:install-source? #f))
    (native-inputs
@@ -37,8 +37,6 @@
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
-  #:use-module (gnu packages rust)
-  #:use-module (gnu packages statistics)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages virtualization))

@@ -248,48 +246,6 @@ transliterating them.  It supports Emoji and Chinese.")
       ;; checkout and does not need a cargo input.
       (inputs (cargo-inputs 'rust-deunicode-1.6.2.cfb8552))))))

-;; Workspace dependency of r-pizzarr.
-(define-public rust-extendr-0.8.1.93d7244
-  (let ((commit "93d7244e3145d94186bc2f35258ad0ef25a28908")
-        (revision "1"))
-    (hidden-package
-     (package
-       (name "rust-extendr")
-       (version (git-version "0.8.1" revision commit))
-       (source (origin
-                 (method git-fetch)
-                 (uri (git-reference
-                        (url "https://github.com/extendr/extendr")
-                        (commit commit)))
-                 (file-name (git-file-name name version))
-                 (sha256
-                  (base32
-                   "03d16y7f1r0y1s8gwzw7wzn5yhcqr1wn0vga9dvdjxpbga372vx7"))))
-       (build-system cargo-build-system)
-       (arguments
-        (list
-         #:cargo-package-crates
-         ;; Note that the order matters!
-         '(list "extendr-ffi"
-                "extendr-macros"
-                "extendr-api"
-                "extendr-engine")
-         #:phases
-         #~(modify-phases %standard-phases
-             (add-after 'unpack 'set-R_HOME
-               (lambda _
-                 (delete-file-recursively ".cargo")
-                 (setenv "R_HOME"
-                         (string-append
-                          #$(this-package-input "r-minimal")
-                          "/lib/R")))))))
-       (inputs (cons r-minimal (cargo-inputs 'extendr)))
-       (home-page "https://extendr.rs/")
-       (synopsis "R extension library for Rust")
-       (description "This library allows you to extend R with Rust.  It can be
-used to write R packages that link with Rust libraries.")
-       (license license:expat)))))
-
 ;; Workspace dependency of zed.
 ;;
 ;; Cargo side: Cargo unifies dependency versions across zed's
@@ -620,6 +576,40 @@ for Rust.")
 UTF-32 support.")
     (license (list license:expat license:unlicense)))))

+(define-public rust-pipewire-0.8.0.fd3d8f7
+  (let ((commit "fd3d8f7861a29c2eeaa4c393402e013578bb36d9")
+        (revision "0"))
+    (hidden-package
+     (package
+       (name "rust-pipewire")
+       (version (git-version "0.8.0" revision commit))
+       (source
+        (origin
+          (method git-fetch)
+          (uri (git-reference
+                (url "https://gitlab.freedesktop.org/pipewire/pipewire-rs.git")
+                (commit commit)))
+          (file-name (git-file-name name version))
+          (sha256
+           (base32 "1hzyhz7xg0mz8a5y9j6yil513p1m610q3j9pzf6q55vdh5mcn79v"))))
+       (build-system cargo-build-system)
+       (arguments
+        (list #:skip-build? #t
+              #:cargo-package-crates
+              ''("libspa-sys" "libspa" "pipewire-sys" "pipewire")
+              #:phases
+              #~(modify-phases %standard-phases
+                  ;; Avoid circular dependency.
+                  (add-after 'unpack 'remove-dev-dependencies
+                    (lambda _
+                      (substitute* "libspa/Cargo.toml"
+                        (("^pipewire.*") "")))))))
+       (inputs (cargo-inputs 'rust-pipewire-0.8.0.fd3d8f7))
+       (home-page "https://pipewire.org/")
+       (synopsis "Rust bindings for PipeWire")
+       (description "This package provides Rust bindings for PipeWire.")
+       (license license:expat)))))
+
 ;; Workspace dependency of zed.
 ;;
 ;; Cargo side: Cargo unifies dependency versions across zed's
@@ -127,11 +127,15 @@
    (arguments
     (substitute-keyword-arguments (package-arguments base-rust)
       ((#:disallowed-references _ '())
-        (list (this-package-native-input "rustc-bootstrap")))))
+        (list (this-package-native-input "rust")
+              ;; Refer to cargo as #$rustc:cargo.
+              (gexp-input (this-package-native-input "rust") "cargo")))))
    (native-inputs
-     (modify-inputs native-inputs
-       (replace "rustc-bootstrap" base-rust)
-       (replace "cargo-bootstrap" (list base-rust "cargo"))))))
+     (list pkg-config
+           python-minimal-wrapper
+           python-setuptools-bootstrap
+           base-rust
+           `(,base-rust "cargo")))))

 ;;; Note: mrustc's only purpose is to be able to bootstrap Rust; it's designed
 ;;; to be used in source form.
@@ -600,40 +604,33 @@ safety and thread safety guarantees.")
             (setenv "PATH" (string-append "/tmp/bin:" (getenv "PATH")))))
         (replace 'configure
           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (gcc (assoc-ref inputs "gcc"))
-                    (python (assoc-ref inputs "python"))
-                    (binutils (assoc-ref inputs "binutils"))
-                    (rustc (assoc-ref inputs "rustc-bootstrap"))
-                    (cargo (assoc-ref inputs "cargo-bootstrap"))
-                    (llvm (assoc-ref inputs "llvm")))
-               (call-with-output-file "config.toml"
-                 (lambda (port)
-                   (display (string-append "
+             (call-with-output-file "config.toml"
+               (lambda (port)
+                 (display (string-append "
 [llvm]
 [build]
-cargo = \"" cargo "/bin/cargo" "\"
-rustc = \"" rustc "/bin/rustc" "\"
+cargo = \"" (search-input-file inputs "bin/cargo") "\"
+rustc = \"" (search-input-file inputs "bin/rustc") "\"
 docs = false
-python = \"" python "/bin/python" "\"
+python = \"" (search-input-file inputs "bin/python") "\"
 vendor = true
 submodules = false
 [install]
-prefix = \"" out "\"
+prefix = \"" (assoc-ref outputs "out") "\"
 sysconfdir = \"etc\"
 [rust]
 debug=false
 jemalloc=false
-default-linker = \"" gcc "/bin/gcc" "\"
+default-linker = \"" (search-input-file inputs "bin/gcc") "\"
 channel = \"stable\"
 rpath = true
 [target." ,(platform-rust-target (lookup-platform-by-system (%current-system))) "]
-llvm-config = \"" llvm "/bin/llvm-config" "\"
-cc = \"" gcc "/bin/gcc" "\"
-cxx = \"" gcc "/bin/g++" "\"
-ar = \"" binutils "/bin/ar" "\"
+llvm-config = \"" (search-input-file inputs "bin/llvm-config") "\"
+cc = \"" (search-input-file inputs "bin/gcc") "\"
+cxx = \"" (search-input-file inputs "bin/g++") "\"
+ar = \"" (search-input-file inputs "bin/ar") "\"
 [dist]
-") port))))))
+") port)))))
         (replace 'build
           ;; The standard library source location moved in this release.
           (lambda* (#:key parallel-build? #:allow-other-keys)
@@ -694,15 +691,15 @@ ar = \"" binutils "/bin/ar" "\"
                 `("LIBRARY_PATH" ":"
                   suffix (,(string-append libc "/lib"))))))))))
    (native-inputs
-     `(("pkg-config" ,pkg-config)
-       ("python" ,python-minimal-wrapper)
-       ("python-setuptools" ,python-setuptools-bootstrap)
-       ("rustc-bootstrap" ,rust-bootstrap-1.54)
-       ("cargo-bootstrap" ,rust-bootstrap-1.54 "cargo")))
+     (list pkg-config
+           python-minimal-wrapper
+           python-setuptools-bootstrap
+           rust-bootstrap-1.54
+           `(,rust-bootstrap-1.54 "cargo")))
    (inputs
-     `(("bash" ,bash-minimal)
-       ("llvm" ,llvm-13)
-       ("openssl" ,openssl)))
+     (list bash-minimal
+           llvm-13
+           openssl))
    ;; rustc invokes gcc, so we need to set its search paths accordingly.
    (native-search-paths
     %gcc-search-paths)
@@ -1155,9 +1152,11 @@ safety and thread safety guarantees.")
           (package-arguments base-rust)))
      (native-inputs
       (if (supported-package? rust-bootstrap-1.74)
-           (modify-inputs native-inputs
-             (replace "cargo-bootstrap" (list rust-bootstrap-1.74 "cargo"))
-             (replace "rustc-bootstrap" rust-bootstrap-1.74))
+           (list pkg-config
+                 python-minimal-wrapper
+                 python-setuptools-bootstrap
+                 rust-bootstrap-1.74
+                 (list rust-bootstrap-1.74 "cargo"))
           (package-native-inputs base-rust)))
      (inputs (modify-inputs inputs
                (replace "llvm" llvm-17))))))
@@ -1174,8 +1173,8 @@ safety and thread safety guarantees.")
             (delete 'add-cc-shim-to-path))))))))

 (define-public rust-1.77
-  (let ((base-rust (rust-bootstrapped-package rust-1.76 "1.77.1"
-                    "18d4ncdzp0nfimmw029xdf7vv1hgh82v30mjnnixnllzar66w47f")))
+  (let ((base-rust (rust-bootstrapped-package rust-1.76 "1.77.2"
+                    "1hrq2r9brhwl77qv18qk4pqrzfgnn9w6fwf7vgykhrjrizpmf566")))
    (package
      (inherit base-rust)
      (arguments
@@ -1622,8 +1621,8 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
 (define-public rust-1.91
  (let ((base-rust
         (rust-bootstrapped-package
-          rust-1.90 "1.91.0"
-          "12iysk87bmhlcdcbr939y8cdfcx0an4z9ixjlbq16c3ma60m4zrj")))
+          rust-1.90 "1.91.1"
+          "08sp8idsymyrqj70sxhfjz5zx7nfl4vl4i7hc495fqczsc2y5p1q")))
    (package
      (inherit base-rust)
      (source
@@ -1772,8 +1771,8 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
 (define-public rust-1.93
  (let ((base-rust
         (rust-bootstrapped-package
-          rust-1.92 "1.93.0"
-          "01d7a1mvyvqmq9khyw5cbnwyngzgb4pxpdwhqgzl669j7kc2n4b9")))
+          rust-1.92 "1.93.1"
+          "07z02gq7x54sdbisbzcigk95h01qz0ckg52hz77g7jfrnd20l8sc")))
    (package
      (inherit base-rust)
      (source
@@ -1916,6 +1915,67 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
                     (copy-recursively "stage2/lib"
                                       (string-append out "/lib")))))))))))))

+(define-public rust-1.95
+  (let ((base-rust
+         (rust-bootstrapped-package
+          rust-1.94 "1.95.0"
+          "05d53hj717ildhvm3rln7821r08nzbbfk72nqcvpb5j67sl856za")))
+    (package
+      (inherit base-rust)
+      (source
+       (origin
+         (inherit (package-source base-rust))
+         (snippet
+          '(begin
+             (for-each delete-file-recursively
+                       '("src/llvm-project"
+                         "vendor/curl-sys-0.4.79+curl-8.12.0/curl"
+                         "vendor/curl-sys-0.4.83+curl-8.15.0/curl"
+                         "vendor/curl-sys-0.4.84+curl-8.17.0/curl"
+                         "vendor/jemalloc-sys-0.5.3+5.3.0-patched/jemalloc"
+                         "vendor/jemalloc-sys-0.5.4+5.3.0-patched/jemalloc"
+                         "vendor/libffi-sys-4.1.0/libffi"
+                         "vendor/libmimalloc-sys-0.1.44/c_src/mimalloc"
+                         "vendor/libz-sys-1.1.21/src/zlib"
+                         "vendor/libz-sys-1.1.23/src/zlib"
+                         "vendor/openssl-src-111.28.2+1.1.1w/openssl"
+                         "vendor/openssl-src-300.5.0+3.5.0/openssl"
+                         "vendor/openssl-src-300.5.4+3.5.4/openssl"
+                         "vendor/tikv-jemalloc-sys-0.5.4+5.3.0-patched/jemalloc"
+                         "vendor/tikv-jemalloc-sys-0.6.1+5.3.0-1-\
+ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
+             ;; Remove vendored dynamically linked libraries.
+             ;; find . -not -type d -executable -exec file {} \+ | grep ELF
+             ;; Also remove the bundled (mostly Windows) libraries.
+             (for-each delete-file
+                       (find-files "vendor" "\\.(a|dll|exe|lib)$"))
+             ;; Use the packaged nghttp2.
+             (for-each
+              (lambda (ver)
+                (let ((vendored-dir
+                       (format #f "vendor/libnghttp2-sys-~a/nghttp2" ver))
+                      (build-rs
+                       (format #f "vendor/libnghttp2-sys-~a/build.rs" ver)))
+                  (delete-file-recursively vendored-dir)
+                  (delete-file build-rs)
+                  (call-with-output-file build-rs
+                    (lambda (port)
+                      (format port "fn main() {~@
+                         println!(\"cargo:rustc-link-lib=nghttp2\");~@
+                         }~%")))))
+              '("0.1.11+1.64.0"))
+             ;; Adjust vendored dependency to explicitly use rustix with libc
+             ;; backend.
+             (substitute* '("vendor/tempfile-3.14.0/Cargo.toml"
+                            "vendor/tempfile-3.16.0/Cargo.toml"
+                            "vendor/tempfile-3.19.1/Cargo.toml"
+                            "vendor/tempfile-3.20.0/Cargo.toml"
+                            "vendor/tempfile-3.21.0/Cargo.toml"
+                            "vendor/tempfile-3.23.0/Cargo.toml"
+                            "vendor/tempfile-3.24.0/Cargo.toml")
+               (("features = \\[\"fs\"" all)
+                (string-append all ", \"use-libc\""))))))))))
+
 (define (make-ignore-test-list strs)
  "Function to make creating a list to ignore tests a bit easier."
  (map (lambda (str)
@@ -1930,7 +1990,7 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
 ;;; Here we take the latest included Rust, make it public, and re-enable tests
 ;;; and extra components such as rustfmt.
 (define-public rust
-  (let ((base-rust rust-1.93))
+  (let ((base-rust rust-1.95))
    (package
      (inherit base-rust)
      (properties (append
@@ -1942,15 +2002,21 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
       (substitute-keyword-arguments
         (strip-keyword-arguments '(#:tests?)
                                  (package-arguments base-rust))
-         ((#:disallowed-references _ '())
-          (list (this-package-native-input "rustc-bootstrap")
-                ;; Refer to cargo-bootstrap as #$rustc-bootstrap:cargo.
-                (gexp-input (this-package-native-input "rustc-bootstrap")
-                            "cargo")))
         ((#:modules modules)
          (cons '(srfi srfi-26) modules))
         ((#:phases phases)
          `(modify-phases ,phases
+             (add-after 'unpack 'patch-shebangs-in-tests
+               (lambda* (#:key inputs #:allow-other-keys)
+                 (with-directory-excursion
+                   "src/tools/rust-analyzer/crates/parser/test_data"
+                   (substitute* '("lexer/ok/shebang_frontmatter.rast"
+                                  "parser/inline/ok/frontmatter.rast")
+                     (("/usr/bin/env cargo")
+                      (search-input-file inputs "bin/cargo")))
+                   (substitute* "lexer/ok/single_line_comments.rast"
+                     (("/usr/bin/env bash")
+                      (search-input-file inputs "bin/bash"))))))
             (add-after 'unpack 'disable-tests-requiring-git
               (lambda _
                 (substitute* "src/tools/cargo/tests/testsuite/publish_lockfile.rs"
@@ -2042,15 +2108,13 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
               (lambda* (#:key inputs #:allow-other-keys)
                 (mkdir-p "src/llvm-project/compiler-rt")
                 (copy-recursively
-                  (string-append (assoc-ref inputs "clang-source")
-                                 "/compiler-rt")
+                  (search-input-directory inputs "/compiler-rt")
                  "src/llvm-project/compiler-rt")))
             (add-after 'unpack 'unpack-libunwind
               (lambda* (#:key inputs #:allow-other-keys)
                 (mkdir-p "src/llvm-project/libunwind")
                 (copy-recursively
-                  (string-append (assoc-ref inputs "clang-source")
-                                 "/libunwind")
+                  (search-input-directory inputs "/libunwind")
                  "src/llvm-project/libunwind")))
             (replace 'patch-cargo-checksums
               (lambda _
@@ -2092,6 +2156,7 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
                           "library/std" ;rustc
                           "src/tools/cargo"
                           "src/tools/clippy"
+                           "src/tools/llvm-bitcode-linker"
                           "src/tools/rust-analyzer"
                           "src/tools/rustfmt"))))
             (replace 'check
@@ -2111,7 +2176,10 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
             (replace 'install
               ;; Phase overridden to also install more tools.
               (lambda* (#:key outputs #:allow-other-keys)
-                 (invoke "./x.py" "install")
+                 ;; Install rustc, std, and llvm-bitcode-linker.
+                 ;; rust-src is handled separately in 'install-rust-src'.
+                 (invoke "./x.py" "install" "compiler/rustc" "library/std"
+                         "llvm-bitcode-linker")
                 (substitute* "config.toml"
                   ;; Adjust the prefix to the 'cargo' output.
                   (("prefix = \"[^\"]*\"")
@@ -2159,7 +2227,7 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
                 (with-directory-excursion
                   (string-append (assoc-ref outputs "rust-src")
                                  "/lib/rustlib/src/rust/src/tools/")
-                   (substitute* (find-files "." "\\.rs$")
+                   (substitute* (find-files "." "\\.(rs|rast)$")
                     (("#!.*/bin/cargo")
                      (string-append "#!" (assoc-ref outputs "cargo")
                                     "/bin/cargo"))))))
@@ -2178,14 +2246,15 @@ exec -a \"$0\" \"~a\" \"$@\""
                                              "/lib/rustlib/src/rust/library")
                               (string-append bin "/.rust-analyzer-real"))))
                   (chmod (string-append bin "/rust-analyzer") #o755))))))))
-      (native-inputs (cons*
-                      ;; Keep in sync with the llvm used to build rust.
-                      `("clang-source" ,(package-source clang-runtime-21))
-                      ;; Add test inputs.
-                      `("gdb" ,gdb/pinned)
-                      `("git-minimal" ,git-minimal/pinned)
-                      `("procps" ,procps)
-                      (package-native-inputs base-rust)))
+      (native-inputs
+       (modify-inputs (package-native-inputs base-rust)
+        (prepend
+          ;; Keep in sync with the llvm used to build rust.
+          (package-source clang-runtime-21)
+          ;; Add test inputs.
+          gdb/pinned
+          git-minimal/pinned
+          procps)))
      (native-search-paths
       (cons*
         ;; For HTTPS access, Cargo reads from a single-file certificate
@@ -244,21 +244,26 @@ This Guix package is built to use the nettle cryptographic library.")
 (define-public sequoia-wot-tools
  (package
    (name "sequoia-wot-tools")
-    (version "0.15.2")
+    (version "0.15.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
-              (url "https://gitlab.com/sequoia-pgp/sequoia-wot.git/")
-              (commit (string-append "sequoia-wot/v" version))))
+              (url "https://gitlab.com/sequoia-pgp/sequoia-wot")
+              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "18v713n36sq5pvd1pbs34v7dly1bi614kwra09qxpsxk0ffp225z"))))
+        (base32 "03wa4l582hx0qq28pkhrf0pagckyx6df01pb4chyngadk49q1xn7"))))
    (build-system cargo-build-system)
    (arguments
     (list
       #:features '(list "sequoia-openpgp/crypto-nettle")
       #:cargo-package-crates ''("tools")
+       #:cargo-test-flags
+       '(list "--"
+              "--skip=gpg_trust_roots"
+              "--skip=backward_propagation::tests::cliques"
+              "--skip=tests::cliques")
       #:install-source? #f
       #:cargo-install-paths ''("tools")
       #:phases
@@ -271,12 +276,11 @@ This Guix package is built to use the nettle cryptographic library.")
                 (for-each (lambda (file)
                             (install-file file man1))
                           (find-files "target/release" "\\.1$"))
-                 (mkdir-p (string-append out "/share/bash-completion/completions"))
+                 (mkdir-p (string-append out "/etc/bash_completion.d"))
                 (mkdir-p (string-append share "/fish/vendor_completions.d"))
                 (mkdir-p (string-append share "/elvish/lib"))
                 (copy-file (car (find-files "target/release" "sq-wot.bash"))
-                            (string-append
-                              out "/share/bash-completion/completions/sq-wot"))
+                            (string-append out "/etc/bash_completion.d/sq-wot"))
                 (copy-file (car (find-files "target/release" "sq-wot.fish"))
                            (string-append
                              share "/fish/vendor_completions.d/sq-wot.fish"))
@@ -288,7 +292,7 @@ This Guix package is built to use the nettle cryptographic library.")
    (inputs
     (cons* nettle openssl sqlite (cargo-inputs 'sequoia-wot-tools)))
    (native-inputs
-     (list clang gnupg pkg-config))
+     (list clang pkg-config))
    (home-page "https://sequoia-pgp.org/")
    (synopsis "Implementation of OpenPGP's web of trust")
    (description
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Efraim Flashner	786fb2a695	gnu: rust-cargo-c: Update to 0.10.22+cargo-0.96.0. * gnu/packages/rust-apps.scm (0.10.22+cargo-0.96.0): Update to 0.10.22+cargo-0.96.0. * gnu/packages/rust-crates.scm (lookup-cargo-inputs)[rust-cargo-c]: Update entry. Change-Id: I8460cb49440e0cd9d7e6e1666ab123f3e877b79d	2026-05-25 14:05:08 +03:00
Efraim Flashner	554a013918	gnu: rust: Update to 1.95. * gnu/packages/rust.scm (rust-1.95): New variable. (rust): Update to 1.95. Change-Id: Id79077ea01bfcc08881c3ff545f3c7bda15c2702	2026-05-25 13:50:50 +03:00
Efraim Flashner	971e70f9b5	gnu: rust-1.93: Update to 1.93.1. * gnu/packages/rust.scm (rust-1.93): Update to 1.93.1. Change-Id: Ifed9036acb1da4bd327f8a76c2f86bcf2ba057a1	2026-05-25 13:50:50 +03:00
Efraim Flashner	e7a2b1c9af	gnu: rust-1.91: Update to 1.91.1. * gnu/packages/rust.scm (rust-1.91): Update to 1.91.1. Change-Id: I67f5005c850d9acce743908df10aa45c8b8f46ba	2026-05-25 13:50:50 +03:00
Efraim Flashner	807a953ed9	gnu: rust-1.77: Update to 1.77.2. * gnu/packages/rust.scm (rust-1.77): Update to 1.77.2. Change-Id: I7d4bf58d0d286672e31a587e3167a36fd4e6b79f	2026-05-25 13:50:50 +03:00
Efraim Flashner	690b843347	gnu: rust: Never refer to previous rust version. * gnu/packages/rust.scm (rust-bootstrapped-package)[arguments]: Adjust the disallowed-references to have the rust and cargo inputs. (rust)[arguments]: Don't override inherited disallowed-references. Change-Id: I467aa47ebb85bce1c05798ac6de9ec8c32037b42	2026-05-25 13:50:50 +03:00
Efraim Flashner	9b5afcb777	gnu: rust: Remove input labels. * gnu/packages/rust.scm (rust)[native-inputs]: Remove input labels. [arguments]: Adjust phases accordingly. Fixes: guix/guix#7889 Change-Id: I05aa5d846b2ee4ed374a62a89d1ae3ab979e236c	2026-05-25 13:50:50 +03:00
Efraim Flashner	e4c5bbf688	gnu: rust-1.55: Remove input labels. * gnu/packages/rust.scm (rust-1.55)[arguments]: Adjust the 'configure phase to not need input labels. [native-inputs]: Remove input labels. [inputs]: Remove input labels. (rust-bootstrapped-package)[arguments]: Adjust for change in name of rust input. [native-inputs]: Rewrite to use explicit inputs. (rust-1.75)[native-inputs]: Rewrite to use explicit inputs. (rust)[arguments]: Adjust for change in name of rust input. Change-Id: I1077d57b359982f5b9641bebb192fa12ec28b8d5	2026-05-25 13:50:47 +03:00
Efraim Flashner	96c7671ca1	gnu: rust-cargo-c: Update to 0.10.21. * gnu/packages/rust-apps.scm (rust-cargo-c): Update to 0.10.21. * gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for rust-cargo-c. Change-Id: Id2c5d0cc1568d0787257ad44e1865adac7c9377e	2026-05-25 13:46:38 +03:00
Efraim Flashner	aa03ba89d9	gnu: rust: Update to 1.94. * gnu/packages/rust.scm (rust): Update to 1.94. [arguments]: Add a phase to patch more files for the test suite. Adjust the 'dont-reference-previous-cargo-version phase for changes in the source. Change-Id: I965e8b3b4046322820be632d01926331fc9afc38	2026-05-25 13:38:47 +03:00
Efraim Flashner	66b8bd3508	gnu: rav1e: Rewrite the install-completions phase. * gnu/packages/video.scm (rav1e)[arguments]: Rewrite the 'install-completions phase to make it cleaner. [native-inputs]: Add rav1e when cross-compiling. Change-Id: I38e1196ea0fb96986ad5c4ae2221facc06fe746d	2026-05-25 13:38:47 +03:00
Efraim Flashner	d3f738137f	gnu: rust-crates: Unbundle more crates. * gnu/packages/rust-crates.scm: Unbundle more rust crates. Change-Id: I93abcf264272b390f526d317fb924941b884376c	2026-05-25 13:38:47 +03:00
Efraim Flashner	65b9ca32e9	gnu: rav1e: Update to 0.8.1. * gnu/packages/video.scm (rav1e): Update to 0.8.1. * gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update the rav1e entry. Change-Id: I376c812e036d87f669aa035191e43f66665ab1cd	2026-05-25 13:38:12 +03:00
Efraim Flashner	c129b7f01e	gnu: dav1d: Update to 1.5.3. * gnu/packages/video.scm (dav1d): Update to 1.5.3. Change-Id: Ia14848b247b5b1cc78c78bdfde083362182792d3	2026-05-25 13:36:14 +03:00
Danny Milosavljevic	af25628e0b	gnu: rust: Install rust-src only once. * gnu/packages/rust.scm (rust)[arguments]<#:phases>{install}: Install rust-src only once. {build}: Explicitly request src/tools/llvm-bitcode-linker (no change). Closes: guix/guix#6671 Change-Id: I9f64c2d115794126ad82aebb87ad192fcf94abd7	2026-05-25 13:36:14 +03:00
Danny Milosavljevic	474c19ec87	build-system/cargo: Work around "cargo package" weirdness. * guix/build/cargo-build-system.scm (package): Modify. Closes: guix/guix#6825 Change-Id: I0ab97662e52d53ca1558c40bd9c1cbd28eae0197	2026-05-25 13:36:10 +03:00