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.
2026-07-07 23:04:05 +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
119 changed files with 5727 additions and 7042 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.

@@ -876,8 +876,8 @@ and the maven-build-system."
        "The plasma desktop environment, and KDE Applications."
        #:scope (list (make-regexp* "^gnu/packages/(kde)(-.+|)\\.scm$"))))

-(define-team linux-libre
-  (team 'linux-libre
+(define-team kernel
+  (team 'kernel
        #:name "Linux-libre kernel team"
        #:scope (list "gnu/build/linux-modules.scm"
                      (make-regexp* "^gnu/packages/aux-files/linux-libre.*$")
@@ -1298,7 +1298,7 @@ the \"texlive\" importer."
 (define-member (person "Leo Famulari"
                       "leo@famulari.name"
                       "lfam")
-  linux-libre)
+  kernel)

 (define-member (person "Efraim Flashner"
                       "efraim@flashner.co.il"
@@ -1383,7 +1383,7 @@ the \"texlive\" importer."
 (define-member (person "Vagrant Cascadian"
                       "vagrant@debian.org"
                       "vagrantc")
-  debian embedded linux-libre)
+  debian embedded kernel)

 (define-member (person "Vagrant Cascadian"        ;XXX: duplicate
                       "vagrant@reproducible-builds.org"
@@ -1537,7 +1537,7 @@ the \"texlive\" importer."
 (define-member (person "Rodion Goritskov"
                       "rodion@goritskov.com"
                       "rodion-goritskov")
-  games java kde linux-libre release)
+  games java kde kernel release)

 (define-member (person "Jason Conroy"
                       "jconroy@tscripta.net"
@@ -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"
@@ -1622,7 +1622,7 @@ the \"texlive\" importer."
 (define-member (person "Wilko Meyer"
                       "w@wmeyer.eu"
                       "theesm")
-  linux-libre perl)
+  kernel perl)

 (define-member (person "Untrusem"
                       "mysticmoksh@riseup.net"
@@ -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			\
@@ -1881,7 +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			\
@@ -2368,8 +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	\
@@ -2454,7 +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			\
@@ -2489,7 +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)
@@ -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)
@@ -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.
@@ -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,
@@ -94,16 +94,13 @@
  #:use-module (gnu packages gnome)
  #:use-module (gnu packages golang-build)
  #:use-module (gnu packages golang-xyz)
-  #:use-module (gnu packages gstreamer)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages graphics)
  #:use-module (gnu packages haskell-xyz)
  #:use-module (gnu packages image)
  #:use-module (gnu packages image-processing)
  #:use-module (gnu packages imagemagick)
-  #:use-module (gnu packages kde-frameworks)
  #:use-module (gnu packages linux)
-  #:use-module (gnu packages logging)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages pdf)
@@ -111,7 +108,6 @@
  #:use-module (gnu packages perl-check)
  #:use-module (gnu packages photo)
  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages pretty-print)
  #:use-module (gnu packages profiling)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
@@ -124,8 +120,6 @@
  #:use-module (gnu packages sqlite)
  #:use-module (gnu packages suckless)
  #:use-module (gnu packages stb)
-  #:use-module (gnu packages tbb)
-  #:use-module (gnu packages tls)
  #:use-module (gnu packages terminals)
  #:use-module (gnu packages upnp)
  #:use-module (gnu packages version-control)
@@ -1292,84 +1286,6 @@ workspaces.
 (define-deprecated-package python-ueberzug
  ueberzug)

-(define-public ueberzugpp
-  (package
-    (name "ueberzugpp")
-    (version "2.9.10")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-              (url "https://github.com/jstkdng/ueberzugpp")
-              (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "1jac2sca4pmcxp8xcvaxhf6j15phyc85gb5n9ymajbahnd4hbcv2"))))
-    (build-system cmake-build-system)
-    (arguments
-     (list #:tests? #f    ; no tests
-           #:configure-flags
-           #~(list "-DENABLE_OPENCV=ON"
-                   "-DENABLE_X11=ON"
-                   "-DENABLE_WAYLAND=ON")))
-    (native-inputs
-     (list extra-cmake-modules
-           gobject-introspection
-           pkg-config))
-    (inputs
-     (list cairo
-           chafa
-           cli11
-           expat
-           fftw
-           fmt
-           imagemagick
-           imath
-           lcms
-           libexif
-           libgsf
-           librsvg
-           libsixel
-           libwebp
-           libxcb
-           matio
-           nlohmann-json
-           opencv
-           openexr
-           openssl
-           orc
-           pango
-           poppler
-           range-v3
-           spdlog
-           tbb
-           vips
-           wayland
-           wayland-protocols
-           xcb-util-image))
-    (home-page "https://github.com/jstkdng/ueberzugpp")
-    (synopsis "Drop in replacement for ueberzug written in C++")
-    (description "Überzug++ is a command line utility written in C++ which
-allows to draw images on terminals by using X11/Wayland child windows, sixels,
- kitty and iterm2.
-
-Advantages over @command{w3mimgdisplay}:
-@itemize
-@item Support for Wayland: Sway, Hyprland, niri and Wayfire
-@item No race conditions as a new window is created to display images
-@item Expose events will be processed, so images will be redrawn on switch
-workspaces
-@item Tmux support on X11, Sway and Hyprland
-@item Terminals without the @env{WINDOWID} environment variable are supported
-@item Chars are used as position - and size unit
-@item No memory leak (usage of smart pointers)
-@item A lot of image formats supported (through OpenCV and libvips).
-@item GIF and animated WEBP support on X11, Sixel, Sway and hyprland
-@item Fast image downscaling (through OpenCV and OpenCL)
-@item Cache resized images for faster viewing
-@end itemize")
-    (license license:gpl3)))
-
 (define-public vv
  (package
    (name "vv")
@@ -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
@@ -1,50 +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
@@ -25,7 +25,6 @@
  #:use-module (guix build-system cmake)
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
-  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages compression)
@@ -35,6 +34,7 @@
  #:use-module (gnu packages libffi)
  #:use-module (gnu packages linux)
  #: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)
@@ -88,9 +88,7 @@ you tailor the wrapping process to suit your application.")
                                 name "-" version ".tar.gz"))
              (sha256
               (base32
-                "1kqz533599d00rrz0g2ryf8w2ynb25ayylpx10nmkxsndiq2l5j0"))
-              (patches
-               (search-patches "swig-support-r-4.6.0.patch"))))
+                "1kqz533599d00rrz0g2ryf8w2ynb25ayylpx10nmkxsndiq2l5j0"))))
    (native-inputs (list boost
                         pcre2 ; for pcre2-config
                         ;; The following are for tests and examples:
@@ -31008,7 +31008,7 @@ dissertation in LaTeX.")
    (license license:lppl1.2+)))

 (define-public texlive-neoschool
-  (let ((revision 79141))             ;release 1.3.9
+  (let ((revision 79027))             ;release 1.3.7
    (package
      (name "texlive-neoschool")
      (version (string-append "2026.1-" (number->string revision)))
@@ -31022,7 +31022,7 @@ dissertation in LaTeX.")
                                 "tex/latex/neoschool/"))))
         (file-name (git-file-name name version))
         (sha256
-          (base32 "1jafxp187i2y8wci0b8rsa661l57b71pyf41xrsfz41c7ky7m0gs"))))
+          (base32 "08rv34syx6r4j3cfsfhd9409fhqfvh35vp4jb3ixmd1f03idzmmx"))))
      (outputs '("out" "doc"))
      (build-system texlive-build-system)
      (home-page "https://ctan.org/pkg/neoschool")
@@ -115,16 +115,16 @@ Firefox locales.")

 ;; We copy the official build id, which is defined at
 ;; tor-browser-build/rbm.conf (browser_release_date).
-(define %torbrowser-build-date "20260518170000")
+(define %torbrowser-build-date "20260507142516")

 ;; To find the last version, look at https://www.torproject.org/download/.
-(define %torbrowser-version "15.0.14")
+(define %torbrowser-version "15.0.13")

 ;; To find the last Firefox version, browse
 ;; https://archive.torproject.org/tor-package-archive/torbrowser/<%torbrowser-version>
 ;; There should be only one archive that starts with
 ;; "src-firefox-tor-browser-".
-(define %torbrowser-firefox-version "140.11.0esr-15.0-1-build3")
+(define %torbrowser-firefox-version "140.10.2esr-15.0-1-build1")

 ;; See tor-browser-build/rbm.conf for the list.
 (define %torbrowser-locales (list "ar" "be" "bg" "ca" "cs" "da" "de" "el" "es-ES" "fa"
@@ -139,11 +139,11 @@ Firefox locales.")
    (method git-fetch)
    (uri (git-reference
          (url "https://gitlab.torproject.org/tpo/translation.git")
-          (commit "6749f7ce29126312167aee8e07cd45a4aa4acb9d")))
+          (commit "bca639ef183dba065e6f9dc0bab86aedb03f9335")))
    (file-name "translation-base-browser")
    (sha256
     (base32
-      "1ancjf85is34yi2zbpdmasfyfin6pfmiqlmcnjqqqbk5k6zj2scy"))))
+      "0h1vp8qkbbydkii7a1hfgrgzyyrfax4gkv24g50xrx34r7qjhjcl"))))

 ;; See tor-browser-build/projects/translation/config.
 (define torbrowser-translation-specific
@@ -151,11 +151,11 @@ Firefox locales.")
    (method git-fetch)
    (uri (git-reference
          (url "https://gitlab.torproject.org/tpo/translation.git")
-          (commit "a2e92e2c255377898a72be2fc0d073766a7ee4ed")))
+          (commit "56f475a6c10e509aaff0657b9d864463d387cea7")))
    (file-name "translation-tor-browser")
    (sha256
     (base32
-      "1y0x4wgy5prz0q817mdvs7pdbr8k14ap55jikyv8nyx3an13vhhp"))))
+      "1g723zzdl23lgfbik3pzhyqznzg7csn32n2ndra4bvnrbnrvm39y"))))

 (define torbrowser-assets
  ;; This is a prebuilt Torbrowser from which we take the assets we need.
@@ -171,7 +171,7 @@ Firefox locales.")
         version "/tor-browser-linux-x86_64-" version ".tar.xz"))
       (sha256
        (base32
-         "03pmcdriwnb1azrn0jsxl453x947yq088c0cjhzwrfxbnqv6s54k"))))
+         "09a9mnbbq01l4j7c0r3qbmzdwwn40c4nvwihbgvzh42s5az6jvdz"))))
    (arguments
     (list
      #:install-plan
@@ -212,7 +212,7 @@ Browser.")
         ".tar.xz"))
       (sha256
        (base32
-         "0wmrq1w5kmxm6ganr7ppf0rblcpi18gsk8fv68nf65sjpxk0gf6w"))))
+         "1xnd4s0m66q9ij3xf1n5lym4k0pvgd8m4lrj5dn30g7pfzjgwnss"))))
    (build-system mozilla-build-system)
    (inputs
     (list lyrebird
@@ -789,17 +789,17 @@ attacks on the privacy of Tor users.")

 ;; We copy the official build id, which can be found there:
 ;; https://cdn.mullvad.net/browser/update_responses/update_1/release.
-(define %mullvadbrowser-build-date "20260518170000")
+(define %mullvadbrowser-build-date "20260506160000")

 ;; To find the last version, look at
 ;; https://mullvad.net/en/download/browser/linux.
-(define %mullvadbrowser-version "15.0.14")
+(define %mullvadbrowser-version "15.0.12")

 ;; To find the last Firefox version, browse
 ;; https://archive.torproject.org/tor-package-archive/mullvadbrowser/<%mullvadbrowser-version>
 ;; There should be only one archive that starts with
 ;; "src-firefox-mullvad-browser-".
-(define %mullvadbrowser-firefox-version "140.11.0esr-15.0-1-build2")
+(define %mullvadbrowser-firefox-version "140.10.2esr-15.0-1-build1")

 ;; See tor-browser-build/projects/translation/config.
 (define mullvadbrowser-translation-base
@@ -807,11 +807,11 @@ attacks on the privacy of Tor users.")
    (method git-fetch)
    (uri (git-reference
          (url "https://gitlab.torproject.org/tpo/translation.git")
-          (commit "6749f7ce29126312167aee8e07cd45a4aa4acb9d")))
+          (commit "bca639ef183dba065e6f9dc0bab86aedb03f9335")))
    (file-name "translation-base-browser")
    (sha256
     (base32
-      "1ancjf85is34yi2zbpdmasfyfin6pfmiqlmcnjqqqbk5k6zj2scy"))))
+      "0h1vp8qkbbydkii7a1hfgrgzyyrfax4gkv24g50xrx34r7qjhjcl"))))

 ;; See tor-browser-build/projects/translation/config.
 (define mullvadbrowser-translation-specific
@@ -839,7 +839,7 @@ attacks on the privacy of Tor users.")
         version "/mullvad-browser-linux-x86_64-" version ".tar.xz"))
       (sha256
        (base32
-         "02f6hcp7391s7vcqvqngidrj0zmz9aqhmm0bi0hw26ckfz0vdyhk"))))
+         "0qd285awd2pslw8q05s0mqfjclcjmwra0bcs5bvbpqdazpsxm9sf"))))
    (arguments
     (list
      #:install-plan
@@ -882,7 +882,7 @@ Mullvad Browser.")
         %mullvadbrowser-firefox-version ".tar.xz"))
       (sha256
        (base32
-         "0y4qx3hvizm5zigdq9c17l6kzs2h74hyi22syjm9bh1cfpvl2pym"))))
+         "0nwbcdqcyr5a9w233gmfjy0ych8frhx5am1zszyl84i7miykqads"))))
    (arguments
     (substitute-keyword-arguments arguments
       ((#:phases phases)
@@ -36,8 +36,7 @@
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages gdb)
-  #:use-module (gnu packages perl)
-  #:use-module (gnu packages python))
+  #:use-module (gnu packages perl))

 (define-public valgrind/pinned
  (package
@@ -112,7 +111,5 @@ also use Valgrind to build new tools.")
  (package/inherit valgrind
    (inputs
     ;; GDB is needed to provide a sane default for `--db-command'.
-     (list gdb
-           `(,(canonical-package (libc-for-target)) "debug")
-           python))                     ;for cg_* shebangs
+     (list gdb `(,(canonical-package (libc-for-target)) "debug")))
    (properties '())))
@@ -1180,7 +1180,7 @@ provides an integration with GitHub and GitLab.")
 (define-public got
  (package
    (name "got")
-    (version "0.125")
+    (version "0.124")
    (source (origin
              (method url-fetch)
              (uri
@@ -1189,7 +1189,7 @@ provides an integration with GitHub and GitLab.")
                version ".tar.gz"))
              (sha256
               (base32
-                "1b5saas4ywfknsxski52w34x1h36ib2pns41xcm3fr3k2201kmmd"))))
+                "0i4w1njqggdqdxw3mismyqy0kjhnr4gsrd9b2p2awhwk1ac8xwwg"))))
    (inputs
     (list libevent
           `(,util-linux "lib")
@@ -3533,6 +3533,7 @@ modification time.")
       (uri (fossil-reference
             (uri "https://fossil.wanderinghorse.net/r/libfossil")
             (check-in version)))
+       (file-name (fossil-file-name name version))
       (sha256
        (base32 "0haaczpjnjpkiikf0q70nfabm2csdk6dl9rh80j0sh90wfvkyqwm"))
       (modules '((guix build utils)
@@ -4844,52 +4845,6 @@ git commands for repository metrics and summarization, commit and log editing,
 developer workflow, and project and release management.")
    (license license:expat)))

-(define-public git-quick-stats
-  (package
-    (name "git-quick-stats")
-    (version "2.11.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/git-quick-stats/git-quick-stats")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1sx6idfl0s88xx5wd39cg1540hzkh7p6yad0l56qnf9v2i38hra1"))))
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:test-target "test"
-      #:tests? #f ;Tests require interactive terminal
-      #:make-flags #~(list (string-append "PREFIX=" #$output))
-      #:phases
-      #~(modify-phases %standard-phases
-          (delete 'configure)
-          (add-after 'install 'wrap-program
-            (lambda _
-              (wrap-program (string-append #$output "/bin/git-quick-stats")
-                '("PATH" ":" prefix
-                  #$(map (lambda (x)
-                          (file-append (cadr x) "/bin"))
-                        (package-inputs this-package)))))))))
-    (native-inputs (list which))
-    (inputs (list bash-minimal
-                  coreutils-minimal
-                  gawk
-                  git-minimal/pinned
-                  grep
-                  ncurses
-                  util-linux))
-    (home-page "https://git-quick-stats.sh")
-    (synopsis "Access various statistics in git repositories")
-    (description
-     "Any git repository may contain tons of information about commits,
-contributors, and files.  Extracting this information is not always trivial,
-mostly because there are a gazillion options to a gazillion git commands.
-This package provides a cleaner interface to access this information.")
-    (license license:expat)))
-
 (define-public hut
  (package
    (name "hut")
@@ -196,6 +196,7 @@
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages nettle)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages ocr)
  #:use-module (gnu packages openkinect)
  #:use-module (gnu packages pcre)
@@ -4234,7 +4235,7 @@ be used for realtime video capture via Linux-specific APIs.")
                "-DENABLE_QSV11=OFF"
                "-DENABLE_NVENC=OFF"
                ;; Requires a custom version of websocketpp in inputs, that's
-                ;; patched to be compatible with recent versions of Boost 
+                ;; patched to be compatible with recent versions of Boost
                "-DENABLE_WEBSOCKET=ON"
                ;; Browser plugin requires cef, but it is not packaged yet.
                ;; <https://bitbucket.org/chromiumembedded/cef/src/master/>
@@ -6502,7 +6503,7 @@ and audio capture, network stream playback, and many more.")
 (define-public dav1d
  (package
    (name "dav1d")
-    (version "1.5.1")
+    (version "1.5.3")
    (source
      (origin
        (method git-fetch)
@@ -6511,7 +6512,7 @@ and audio capture, network stream playback, and many more.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-         (base32 "1n0b5m4srdjsqg15plc9fng5kjv14ygqahjxy8863fbzhr13vjx9"))))
+         (base32 "0x19r721gf91a37xqm70j7qcpadyd3m9lcf1lasxq73wnby5lxqk"))))
    (build-system meson-build-system)
    (native-inputs
     (if (target-x86?)
@@ -6793,63 +6794,59 @@ result in several formats:
 (define-public rav1e
  (package
    (name "rav1e")
-    (version "0.7.1")
+    (version "0.8.1")
    (source
     (origin
       (method url-fetch)
       (uri (crate-uri "rav1e" version))
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
-        (base32 "1sawva6nmj2fvynydbcirr3nb7wjyg0id2hz2771qnv6ly0cx1yd"))))
+        (base32 "0axk3ji3jmlr81svmsy5zvj8shmhpp8lz5nyghkq752xx1bdvdj3"))))
    (build-system cargo-build-system)
    (arguments
-     `(#:install-source? #f
+     (list
+       #:install-source? #f
+       #:modules '((guix build cargo-build-system)
+                   (guix build utils)
+                   (ice-9 match))
       #:phases
-       (modify-phases %standard-phases
-         (replace 'build
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (invoke "cargo" "cinstall" "--release"
-                       ;; Only build the dynamic library.
-                       "--library-type" "cdylib"
-                       (string-append "--prefix=" out)))))
-         (add-after 'install 'install-completions
-           (lambda* (#:key native-inputs outputs #:allow-other-keys)
-             (unless ,(%current-target-system)
-               (let* ((out (assoc-ref outputs "out"))
-                      (share (string-append out "/share"))
-                      (bash-completions-dir
-                        (string-append out "/etc/bash_completion.d"))
-                      (zsh-completions-dir
-                        (string-append share "/zsh/site-functions"))
-                      (fish-completions-dir
-                        (string-append share "/fish/vendor_completions.d"))
-                      (elvish-completions-dir
-                        (string-append share "/elvish/lib"))
-                      (rav1e (string-append out "/bin/rav1e"))
-                      (common-flags '("-" "-o" "-" "advanced" "--completion")))
-                 (mkdir-p bash-completions-dir)
-                 (with-output-to-file
-                   (string-append bash-completions-dir "/rav1e")
-                   (lambda _ (apply invoke rav1e (append common-flags '("bash")))))
-                 (mkdir-p zsh-completions-dir)
-                 ;; This one currently fails to build.
-                 ;(with-output-to-file
-                 ;  (string-append zsh-completions-dir "/_rav1e")
-                 ;  (lambda _ (apply invoke rav1e (append common-flags '("zsh")))))
-                 (mkdir-p fish-completions-dir)
-                 (with-output-to-file
-                   (string-append fish-completions-dir "/rav1e.fish")
-                   (lambda _ (apply invoke rav1e (append common-flags '("fish")))))
-                 (mkdir-p elvish-completions-dir)
-                 (with-output-to-file
-                   (string-append elvish-completions-dir "/rav1e")
-                   (lambda _
-                     (apply invoke rav1e (append common-flags '("elvish"))))))))))))
+       #~(modify-phases %standard-phases
+           (replace 'build
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out")))
+                 (invoke "cargo" "cinstall" "--release"
+                         ;; Only build the dynamic library.
+                         "--library-type" "cdylib"
+                         (string-append "--prefix=" out)))))
+           (add-after 'install 'install-completions
+              (lambda* (#:key native-inputs #:allow-other-keys)
+                (for-each
+                  (match-lambda
+                    ((shell . path)
+                     (mkdir-p (in-vicinity #$output (dirname path)))
+                     (let ((binary
+                             (if #$(%current-target-system)
+                                 (search-input-file native-inputs "bin/rav1e")
+                                 (in-vicinity #$output "bin/rav1e"))))
+                       (with-output-to-file (in-vicinity #$output path)
+                         (lambda _
+                           (invoke binary
+                                   "-" "-o"
+                                   "-" "advanced"
+                                   "--completion" shell))))))
+                  '(("bash" . "share/bash-completion/completions/rav1e")
+                    ("elvish" . "share/elvish/lib/rav1e")
+                    ("fish" . "share/fish/vendor_completions.d/rav1e.fish")
+                    ;; This one currently fails to build.
+                    ;("zsh" . "share/zsh/site-functions/_rav1e")
+                    )))))))
    (native-inputs
     (append (if (target-x86?)
                 (list nasm)
                 '())
+             (if (%current-target-system)
+                 (list this-package)
+                 '())
             (list pkg-config rust-cargo-c)))
    (inputs
     (cons* libgit2-1.9 zlib (cargo-inputs 'rav1e)))
@@ -140,6 +140,7 @@
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages nettle)
  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ninja)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages onc-rpc)
  #:use-module (gnu packages package-management)
--- 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