gnu: python-dill: Update to 0.4.1.

* gnu/packages/python-xyz.scm (python-dill): Update to 0.4.1.
[source]: Switch to git-fetch.
[arguments] <test-backend, test-flags>: Use 'custom backend instead of
overwriting test phase.
<phases>: Use default 'check.
[native-inputs]: Remove python-wheel.
[home-page]: Update to URL to http://dill.rtfd.io/.

Change-Id: Ifd949babdc06ed4e33cdadae6f392c224f53197a

.dir-locals.el

@@ -42,11 +42,12 @@
      ;; For use with 'bug-reference-prog-mode'.  Extra bug-reference
      ;; configuration should be done in your Emacs user configuration file;
      ;; refer to (info (guix) The Perfect Setup).
-     (eval . (setq-local bug-reference-bug-regexp
+     (eval . (setq-local
-                         ;; #8545 (issues), !8545 (PRs), guix/guix#8545 and
+              ;; #8545, guix/guix#8545, guix/guix!8545, but not !8545
-                         ;; guix/guix!8545
+              bug-reference-bug-regexp
-                         (rx (group (seq (? "guix/guix") (or "#" "!"))
+              (rx (group (or (seq (zero-or-more "guix/guix") "#")
-                                    (group (one-or-more digit))))))
+                             (seq (one-or-more "guix/guix") "!"))
+                         (group (one-or-more digit))))))
      (bug-reference-url-format . "https://codeberg.org/guix/guix/issues/%s")
 
      (eval . (add-to-list 'completion-ignored-extensions ".go"))

Makefile.am

@@ -1281,14 +1281,6 @@ $(GIT_HOOKS_DIR):
 $(GIT_HOOKS_DIR)/%: etc/git/% | $(GIT_HOOKS_DIR)/
 	if [ -n "$(GIT_HOOKS_DIR)" ]; then cp "$<" "$@"; fi
 
-# Special-case the pre-push hook installation, to ensure it is always
-# up-to-date with its source.
-.PHONY: $(GIT_HOOKS_DIR)/pre-push
-$(GIT_HOOKS_DIR)/pre-push: etc/git/pre-push | $(GIT_HOOKS_DIR)
-	@if [ -n "$(GIT_HOOKS_DIR)" ]; then \
-	  cmp "--silent" "$<" "$@" || cp "$<" "$@"; \
-	fi
-
 $(GIT_CONFIG_FILE): etc/git/gitconfig
 	if [ -n "$(GIT_CONFIG_FILE)" ]; then \
 	  git config --fixed-value --replace-all include.path \

doc/guix.texi

@@ -53,7 +53,7 @@ Copyright @copyright{} 2017, 2019--2026 Maxim Cournoyer@*
 Copyright @copyright{} 2017–2022 Tobias Geerinckx-Rice@*
 Copyright @copyright{} 2017 George Clemmer@*
 Copyright @copyright{} 2017 Andy Wingo@*
-Copyright @copyright{} 2017, 2018, 2019, 2020, 2023, 2024, 2025, 2026 Arun Isaac@*
+Copyright @copyright{} 2017, 2018, 2019, 2020, 2023, 2024, 2025 Arun Isaac@*
 Copyright @copyright{} 2017 nee@*
 Copyright @copyright{} 2018 Rutger Helling@*
 Copyright @copyright{} 2018, 2021, 2023, 2025, 2026 Oleg Pykhalov@*
@@ -124,7 +124,7 @@ Copyright @copyright{} 2023 Thomas Ieong@*
 Copyright @copyright{} 2023 Saku Laesvuori@*
 Copyright @copyright{} 2023 Graham James Addis@*
 Copyright @copyright{} 2023-2025 Tomas Volf@*
-Copyright @copyright{} 2024-2026 Herman Rimm@*
+Copyright @copyright{} 2024, 2025 Herman Rimm@*
 Copyright @copyright{} 2024 Matthew Trzcinski@*
 Copyright @copyright{} 2024 Richard Sent@*
 Copyright @copyright{} 2024 Dariqq@*
@@ -16124,10 +16124,6 @@ the tag name for separating the numbers of the version.
 pre-releases; to make it also look for pre-releases, set the this
 property to @code{#t}.
 
-@item @code{stable-version-regexp}: a regular expression for matching the
-version string, if specified the updater will pick the latest version from
-matching ones when the @option{--target-version} option is omitted.
-
 @end itemize
 
 @lisp
@@ -16714,12 +16710,6 @@ guix lint @var{options} @var{package}@dots{}
 @end example
 
 If no package is given on the command line, then all packages are checked.
-To check packages in particular source files, the syntax is:
-
-@example
-guix lint @var{options} --whole-file @var{file}@dots{}
-@end example
-
 The @var{options} may be zero or more of the following:
 
 @table @code
@@ -16757,23 +16747,9 @@ Only enable the checkers that do not depend on Internet access.
 Add @var{directory} to the front of the package module search path
 (@pxref{Package Modules}).
 
-@item --whole-file
+This allows users to define their own packages and make them visible to
-@itemx -f
+the command-line tools.
-Check the top-level package definitions in the given files; subsequent
-arguments are treated as file names rather than package names.  This
-option also enables a special checker which checks if a package
-alphabetically succeeds the one above it.
 
-For example, to check if the packages in @file{gnu/packages/matrix.scm}
-are sorted alphabetically, and if the package names therein follow
-established conventions, run:
-
-@example
-guix lint -c name -f gnu/packages/matrix.scm
-@end example
-
-The previous two options allow users to define their own packages and
-make them visible to the command-line tools.
 @end table
 
 @node Invoking guix size
@@ -36765,16 +36741,13 @@ The Mumi package to use.
 Data directory to store Debbugs data from upstream Debbugs instance.
 
 @item @code{rsync-remote}
-Remote rsync path from which to download Debbugs data.
+Remote rsync path from which to download Debbugs data.  The remote is
+polled every 5 minutes, unless a previous instance of rsync is already
+running.
 
 @item @code{rsync-flags} (default: @code{'()})
 Additional flags to pass to @command{rsync}.
 
-@item @code{rsync-and-index-event} (default: @code{#~(calendar-event #:minutes '#$(iota 12 0 5))})
-Shepherd calendar event to run the rsync and indexing timer at.  By
-default, this is once every 5 minutes.  The timer job is not run if an
-earlier instance of it is still running.
-
 @item @code{mailer?} (default: @code{#true})
 Whether to enable or disable the mailer component.
 

etc/git/commit-msg

@@ -1,4 +1,5 @@
 #!/bin/sh
+# From Gerrit Code Review 3.11.1.
 #
 # Part of Gerrit Code Review (https://www.gerritcodereview.com/)
 #
@@ -69,9 +70,9 @@ dest="$1.tmp.${random}"
 
 trap 'rm -f "$dest" "$dest-2"' EXIT
 
-if ! sed -e '/>8/q' "$1" | git stripspace --strip-comments > "${dest}" ; then
+if ! cat "$1" | sed -e '/>8/q' | git stripspace --strip-comments > "${dest}" ; then
-  echo "cannot strip comments from $1"
+   echo "cannot strip comments from $1"
-  exit 1
+   exit 1
 fi
 
 if test ! -s "${dest}" ; then
@@ -90,7 +91,7 @@ else
   pattern=".*"
 fi
 
-if git interpret-trailers --no-divider --parse < "$1" | grep -q "^$token: $pattern$" ; then
+if git interpret-trailers --parse < "$1" | grep -q "^$token: $pattern$" ; then
   exit 0
 fi
 
@@ -98,7 +99,6 @@ fi
 # sentinel at the end to make sure there is one.
 # Avoid the --in-place option which only appeared in Git 2.8
 if ! git interpret-trailers \
-         --no-divider \
          --trailer "Signed-off-by: SENTINEL" < "$1" > "$dest-2" ; then
   echo "cannot insert Signed-off-by sentinel line in $1"
   exit 1
@@ -110,7 +110,6 @@ fi
 # Avoid the --in-place option which only appeared in Git 2.8
 # Avoid the --where option which only appeared in Git 2.15
 if ! git -c trailer.where=before interpret-trailers \
-         --no-divider \
          --trailer "Signed-off-by: $token: $value" < "$dest-2" |
      sed -e "s/^Signed-off-by: \($token: \)/\1/" \
          -e "/^Signed-off-by: SENTINEL/d" > "$dest" ; then

gnu/local.mk

@@ -1967,7 +1967,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/mswebrtc-cmake.patch			\
   %D%/packages/patches/mtools-mformat-uninitialized.patch	\
   %D%/packages/patches/mupen64plus-ui-console-notice.patch	\
-  %D%/packages/patches/musl-CVE-2026-40200.patch		\
+  %D%/packages/patches/musl-cross-locale.patch			\
   %D%/packages/patches/mutt-store-references.patch		\
   %D%/packages/patches/m17n-lib-1.8.0-use-pkg-config-for-freetype.patch	\
   %D%/packages/patches/nanosvg-prusa-slicer.patch		\
@@ -1993,7 +1993,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/nhc98-c-update.patch			\
   %D%/packages/patches/nheko-0-12-1-fix-rendering-replies.patch	\
   %D%/packages/patches/nix-dont-build-html-doc.diff		\
-  %D%/packages/patches/nlohmann_json_fix_char8_t.patch		\
   %D%/packages/patches/nfs4-acl-tools-0.3.7-fixpaths.patch	\
   %D%/packages/patches/neovim-tree-sitter-grammar-path.patch	\
   %D%/packages/patches/network-manager-plugin-ownership.patch	\
@@ -2024,6 +2023,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ocaml-4.07-dynamically-allocate-signal-stack.patch	\
   %D%/packages/patches/ocaml-4.09-dynamically-allocate-signal-stack.patch	\
   %D%/packages/patches/ocaml-4.09-multiple-definitions.patch	\
+  %D%/packages/patches/ogs-6.5.7-netcdfconverter.patch \
   %D%/packages/patches/omake-fix-non-determinism.patch	\
   %D%/packages/patches/oneko-remove-nonfree-characters.patch	\
   %D%/packages/patches/onetbb-other-arches.patch	\
@@ -2628,7 +2628,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/x265-arm-flags.patch			\
   %D%/packages/patches/x265-4-arm-flags.patch			\
   %D%/packages/patches/xdg-desktop-portal-wlr-harcoded-length.patch\
-  %D%/packages/patches/xdmf-3.0.0-hdf5.patch \
   %D%/packages/patches/xf86-video-siliconmotion-fix-ftbfs.patch \
   %D%/packages/patches/xfig-Enable-error-message-for-missing-libraries.patch		\
   %D%/packages/patches/xfig-Fix-double-free-when-requesting-MediaBox.patch		\

gnu/packages/admin.scm

@@ -144,7 +144,7 @@
   #:use-module (gnu packages elf)
   #:use-module (gnu packages file)
   #:use-module (gnu packages file-systems)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gawk)
@@ -2979,7 +2979,7 @@ system is under heavy load.")
 (define-public stress-ng
   (package
     (name "stress-ng")
-    (version "0.21.01")
+    (version "0.20.01")
     (source
      (origin
        (method git-fetch)
@@ -2988,7 +2988,7 @@ system is under heavy load.")
              (commit (string-append "V" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "11w8xjm53lgnxfvg286lavqjh0il3bfr1fsgyk915167r4vlabqq"))))
+        (base32 "1jkinrxh9ppv7xfii9xlisnd2679wnj4ljq12h8y0nvwrm8fkm0b"))))
     (build-system gnu-build-system)
     (arguments
      ;; XXX The test suite seems to cause instability on the VisionFive 2
@@ -4434,7 +4434,7 @@ buffers.")
 (define-public igt-gpu-tools
   (package
     (name "igt-gpu-tools")
-    (version "2.4")
+    (version "2.3")
     (source
      (origin
        (method git-fetch)
@@ -4443,7 +4443,7 @@ buffers.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0ijvfa5wamihzbl8l29sc27ml0kmgzlld83jm5mln6bb4bvny4gs"))))
+        (base32 "1vyqrsvxraib98r4i6cjmxq7nis480s2ns95v78dscygcci42i8a"))))
     (build-system meson-build-system)
     (arguments
      `(#:tests? #f              ; many of the tests try to load kernel modules
@@ -4461,7 +4461,6 @@ buffers.")
            libdrm
            libpciaccess
            libunwind
-           pciutils
            procps
            python))
     (native-inputs
@@ -7072,7 +7071,7 @@ network, which causes enabled computers to power on.")
 (define-public witr
   (package
     (name "witr")
-    (version "0.3.2")
+    (version "0.3.1")
     (source
      (origin
        (method git-fetch)
@@ -7081,7 +7080,7 @@ network, which causes enabled computers to power on.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "06vxrgd0j2v6s4snmyviwpp66hm5zai7xca9318inhyg4jw3ngg5"))))
+        (base32 "03v9n4mdvqm0knqjl4s64321i5clqpmlrlkkdb87glzb9p28sg00"))))
     (build-system go-build-system)
     (arguments
      (list
@@ -7228,38 +7227,6 @@ has a focus on performance.  It can be used as a greeter by starting
 it from @file{~/.bashrc} for example.")
     (license license:agpl3+)))
 
-(define-public zeptofetch
-  (package
-    (name "zeptofetch")
-    (version "1.21")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://gitlab.archlinux.org/gurov/zeptofetch")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1f1dm9nrp0z0prqy90csrkbk98ixp0jx76ax473qb0qsbb7ys4g7"))))
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:tests? #f ; No tests available.
-      #:make-flags
-      #~(list (string-append "PREFIX="
-                             #$output))
-      #:phases
-      #~(modify-phases %standard-phases
-          (delete 'configure)))) ; No configure script.
-    (home-page "https://gitlab.archlinux.org/gurov/zeptofetch")
-    (synopsis
-     "Fast, minimal system information tool for Linux.")
-    (description
-     "This package provides a system fetch tool, similar to
-@command{neofetch}, @command{fastfetch}, etc.  It is lightweight and
-has a focus on performance.")
-    (license license:gpl3+)))
-
 (define-public zzz
   (package
     (name "zzz")

gnu/packages/algebra.scm

@@ -52,7 +52,7 @@
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages documentation)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fltk)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)

gnu/packages/apparmor.scm

@@ -22,7 +22,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages dejagnu)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages linux)

gnu/packages/assembly.scm

@@ -50,7 +50,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages image)
   #:use-module (gnu packages linux)

gnu/packages/astronomy.scm

@@ -66,7 +66,7 @@
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages documentation)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages fortran-xyz)
   #:use-module (gnu packages freedesktop)

gnu/packages/audio.scm

@@ -103,7 +103,7 @@
   #:use-module (gnu packages elf)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fltk)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)

gnu/packages/bioinformatics.scm

@@ -96,7 +96,7 @@
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages dlang)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gd)
@@ -6710,20 +6710,20 @@ meso, or continuum scale.")
                 "09693dmf1scdac5pyq6qyn8b4mcipvnmc370k9a5z41z81m3dcsj"))))
     (build-system gnu-build-system)
     (arguments
-     (list
+     `(#:test-target "test"
-       #:test-target "test"
        #:tests? #f ; tests require access to the web
        #:make-flags
-       #~(list "CC=gcc"
+       ,#~(list "CC=gcc"
-               (string-append "prefix=" #$output))
+                (string-append "prefix=" #$output))
        #:phases
-       #~(modify-phases %standard-phases
+       (modify-phases %standard-phases
          (delete 'configure))))
     (inputs
      (list zlib curl))
     (native-inputs
-     (list doxygen
+     `(("doxygen" ,doxygen)
-           python)) ;for tests
+       ;; Need for tests
+       ("python" ,python-2)))
     (home-page "https://github.com/dpryan79/libBigWig")
     (synopsis "C library for handling bigWig files")
     (description
@@ -17839,99 +17839,94 @@ once.  This package provides tools to perform Drop-seq analyses.")
     (license license:expat)))
 
 (define-public pigx-rnaseq
-  (let ((commit "1605b541da090e13d58dae6fed38ae8dda09f002"))
+  (package
-    (package
+    (name "pigx-rnaseq")
-      (name "pigx-rnaseq")
+    (version "0.1.1")
-      (version (git-version "0.1.1" "0" commit))
+    (source (origin
-      (source (origin
+              (method url-fetch)
-                (method git-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
-                (uri (git-reference
+                                  "releases/download/v" version
-                       (url "https://github.com/BIMSBbioinfo/pigx_rnaseq/")
+                                  "/pigx_rnaseq-" version ".tar.gz"))
-                       (commit commit)
+              (sha256
-                       (recursive? #true)))
+               (base32
-                (file-name (git-file-name name version))
+                "0mlas0srl04mvgsyydm67gg5syijf1k2f6dy7bdqqxc70fywfd08"))))
-                (sha256
+    (build-system gnu-build-system)
-                 (base32
+    (arguments
-                  "1j5c0wlasmxvz9z64yga56m2hhbybl149kknsrpvmq0v2gl31rn5"))))
+     `(#:parallel-tests? #f             ; not supported
-      (build-system gnu-build-system)
+       #:phases
-      (arguments
+       (modify-phases %standard-phases
-       (list
+         ;; "test.sh" runs the whole pipeline, which takes a long time and
-        #:parallel-tests? #f             ; not supported
+         ;; might fail due to OOM.  The MultiQC is also resource intensive.
-        #:phases
+         (add-after 'unpack 'disable-resource-intensive-test
-        '(modify-phases %standard-phases
+           (lambda _
-           ;; "test.sh" runs the whole pipeline, which takes a long time and
+             (substitute* "Makefile.in"
-           ;; might fail due to OOM.  The MultiQC is also resource intensive.
+               (("^  tests/test_multiqc/test.sh") "")
-           (add-after 'unpack 'disable-resource-intensive-test
+               (("^  test.sh") ""))))
-             (lambda _
+         (add-before 'bootstrap 'autoreconf
-               (substitute* "Makefile.am"
+           (lambda _
-                 (("^  tests/test_multiqc/test.sh.*") "")
+             (invoke "autoreconf" "-vif")))
-                 (("^  tests/test_hisat2/test.sh.*") "  tests/test_hisat2/test.sh\n")
+         (add-before 'configure 'set-PYTHONPATH
-                 (("^  test.sh") ""))))
+           (lambda _
-           (add-before 'bootstrap 'autoreconf
+             (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
-             (lambda _
+         (add-before 'check 'set-timezone
-               (invoke "autoreconf" "-vif")))
+           ;; The readr package is picky about timezones.
-           (add-before 'configure 'set-PYTHONPATH
+           (lambda* (#:key inputs #:allow-other-keys)
-             (lambda _
+             (setenv "TZ" "UTC+1")
-               (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
+             (setenv "TZDIR"
-           (add-before 'check 'set-timezone
+                     (search-input-directory inputs
-             ;; The readr package is picky about timezones.
+                                             "share/zoneinfo"))))
-             (lambda* (#:key inputs #:allow-other-keys)
+         (add-before 'check 'pre-check
-               (setenv "TZ" "UTC+1")
+           (lambda _
-               (setenv "TZDIR"
+             ;; Needed for tests
-                       (search-input-directory inputs
+             (setenv "HOME" "/tmp"))))))
-                                               "share/zoneinfo"))))
+    (inputs
-           (add-before 'check 'pre-check
+     (list coreutils
-             (lambda _
+           sed
-               ;; Needed for tests
+           gzip
-               (setenv "HOME" "/tmp"))))))
+           snakemake-7
-      (inputs
+           megadepth
-       (list coreutils
+           multiqc
-             sed
+           star-for-pigx
-             gzip
+           hisat2
-             snakemake
+           fastp
-             megadepth
+           htseq
-             multiqc
+           samtools
-             star-for-pigx
+           r-minimal
-             hisat2
+           r-rmarkdown
-             fastp
+           r-genomeinfodb
-             htseq
+           r-ggplot2
-             samtools
+           r-ggpubr
-             r-minimal
+           r-ggrepel
-             r-rmarkdown
+           r-gprofiler2
-             r-genomeinfodb
+           r-deseq2
-             r-ggplot2
+           r-dt
-             r-ggpubr
+           r-knitr
-             r-ggrepel
+           r-pheatmap
-             r-gprofiler2
+           r-corrplot
-             r-deseq2
+           r-reshape2
-             r-dt
+           r-plotly
-             r-knitr
+           r-scales
-             r-pheatmap
+           r-summarizedexperiment
-             r-corrplot
+           r-crosstalk
-             r-reshape2
+           r-tximport
-             r-plotly
+           r-rtracklayer
-             r-scales
+           r-rjson
-             r-summarizedexperiment
+           salmon
-             r-crosstalk
+           pandoc
-             r-tximport
+           python-wrapper
-             r-rtracklayer
+           python-deeptools
-             r-rjson
+           python-pyyaml))
-             salmon
+    (native-inputs
-             pandoc
+     (list tzdata automake autoconf))
-             python-wrapper
+    (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
-             python-deeptools
+    (synopsis "Analysis pipeline for RNA sequencing experiments")
-             python-pyyaml))
+    (description "PiGX RNAseq is an analysis pipeline for preprocessing and
-      (native-inputs
-       (list tzdata automake autoconf))
-      (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
-      (synopsis "Analysis pipeline for RNA sequencing experiments")
-      (description "PiGX RNAseq is an analysis pipeline for preprocessing and
 reporting for RNA sequencing experiments.  It is easy to use and produces high
 quality reports.  The inputs are reads files from the sequencing experiment,
 and a configuration file which describes the experiment.  In addition to
 quality control of the experiment, the pipeline produces a differential
 expression report comparing samples in an easily configurable manner.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public pigx-chipseq
   (package
@@ -18002,7 +17997,7 @@ expression report comparing samples in an easily configurable manner.")
            fastqc
            bowtie
            idr
-           snakemake
+           snakemake-7
            samtools
            bedtools
            kentutils))
@@ -18020,87 +18015,80 @@ in an easily configurable manner.")
     (license license:gpl3+)))
 
 (define-public pigx-bsseq
-  (let ((commit "1b3a69bd5363fa882af4193215de7fb475bae066"))
+  (package
-    (package
+    (name "pigx-bsseq")
-      (name "pigx-bsseq")
+    (version "0.1.10")
-      (version (git-version "0.1.10" "0" commit))
+    (source (origin
-      (source (origin
+              (method url-fetch)
-                (method git-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
-                (uri (git-reference
+                                  "releases/download/v" version
-                       (url "https://github.com/BIMSBbioinfo/pigx_bsseq/")
+                                  "/pigx_bsseq-" version ".tar.gz"))
-                       (commit commit)
+              (sha256
-                       (recursive? #true)))
+               (base32
-                (file-name (git-file-name name version))
+                "1vy3mhbrfdnjbhikwg3mgkfnwnzk96a1n27cxrr7gsffpmz9q6wa"))))
-                (sha256
+    (build-system gnu-build-system)
-                 (base32
+    (arguments
-                  "0r0gjfycgh1hqba7ma03bwxlvr2kz68yzclx5iba3wrxxqmivil6"))))
+     (list
-      (build-system gnu-build-system)
+      ;; TODO: tests currently require 12+GB of RAM.  See
-      (arguments
+      ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/164
-       (list
+      #:tests? #f
-        ;; TODO: tests currently require 12+GB of RAM.  See
+      #:phases
-        ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/164
+      '(modify-phases %standard-phases
-        #:tests? #f
+         (add-before 'configure 'set-PYTHONPATH
-        #:phases
+           (lambda _
-        '(modify-phases %standard-phases
+             (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
-           ;; This file is meant for development, but it interferes with
+         (add-before 'check 'set-timezone
-           ;; Makefile.
+           ;; The readr package is picky about timezones.
-           (add-after 'unpack 'delete-GNUmakefile
+           (lambda* (#:key inputs #:allow-other-keys)
-             (lambda _ (delete-file "GNUmakefile")))
+             (setenv "TZ" "UTC+1")
-           (add-before 'configure 'set-PYTHONPATH
+             (setenv "TZDIR"
-             (lambda _
+                     (search-input-directory inputs
-               (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
+                                             "share/zoneinfo"))))
-           (add-before 'check 'set-timezone
+         (add-before 'check 'pre-check
-             ;; The readr package is picky about timezones.
+           (lambda _
-             (lambda* (#:key inputs #:allow-other-keys)
+             ;; Needed for tests
-               (setenv "TZ" "UTC+1")
+             (setenv "HOME" "/tmp"))))))
-               (setenv "TZDIR"
+    (native-inputs
-                       (search-input-directory inputs
+     (list tzdata-for-tests))
-                                               "share/zoneinfo"))))
+    (inputs
-           (add-before 'check 'pre-check
+     (list coreutils
-             (lambda _
+           sed
-               ;; Needed for tests
+           grep
-               (setenv "HOME" "/tmp"))))))
+           r-minimal
-      (native-inputs
+           r-annotationhub
-       (list tzdata-for-tests autoconf automake))
+           r-dt
-      (inputs
+           r-genomation
-       (list coreutils
+           r-ggbio
-             sed
+           r-ggrepel
-             grep
+           r-matrixstats
-             r-minimal
+           r-methylkit
-             r-annotationhub
+           r-reshape2
-             r-dt
+           r-rtracklayer
-             r-genomation
+           r-rmarkdown
-             r-ggbio
+           r-bookdown
-             r-ggrepel
+           r-ggplot2
-             r-matrixstats
+           r-ggbio
-             r-methylkit
+           pandoc
-             r-reshape2
+           python-wrapper
-             r-rtracklayer
+           python-pyyaml
-             r-rmarkdown
+           snakemake-7
-             r-bookdown
+           bismark
-             r-ggplot2
+           bowtie
-             r-ggbio
+           bwa-meth
-             pandoc
+           fastqc
-             python-wrapper
+           methyldackel
-             python-pyyaml
+           multiqc
-             snakemake
+           trim-galore
-             bismark
+           cutadapt
-             bowtie
+           samblaster
-             bwa-meth
+           samtools))
-             fastqc
+    (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
-             methyldackel
+    (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
-             multiqc
+    (description "PiGx BSseq is a data processing pipeline for raw fastq read
-             trim-galore
-             cutadapt
-             samblaster
-             samtools))
-      (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
-      (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
-      (description "PiGx BSseq is a data processing pipeline for raw fastq read
 data of bisulfite experiments; it produces reports on aggregate methylation
 and coverage and can be used to produce information on differential
 methylation and segmentation.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public pigx-scrnaseq
   (package
@@ -18144,7 +18132,7 @@ methylation and segmentation.")
            python-loompy
            pandoc
            samtools
-           snakemake-6
+           snakemake-5
            star-for-pigx
            r-minimal
            r-argparser
@@ -18273,7 +18261,7 @@ based methods.")
            r-tidyr
            r-viridis
            samtools
-           snakemake
+           snakemake-7
            wget))
     (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
     (synopsis "Analysis pipeline for wastewater sequencing")

gnu/packages/bison.scm

@@ -28,7 +28,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages m4)
   #:use-module (gnu packages perl)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (srfi srfi-1))
 
 (define-public bison

gnu/packages/bootloaders.scm

@@ -55,7 +55,7 @@
   #:use-module (gnu packages cross-base)
   #:use-module (gnu packages disk)
   #:use-module (gnu packages firmware)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)

gnu/packages/build-tools.scm

@@ -76,7 +76,7 @@
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages re2c)
   #:use-module (gnu packages regex)
   #:use-module (gnu packages rpc)
   #:use-module (gnu packages serialization)

gnu/packages/c.scm

@@ -63,6 +63,7 @@
   #:use-module (gnu packages bison)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages perl)

gnu/packages/cdrom.scm

@@ -52,7 +52,7 @@
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages docbook)

gnu/packages/chemistry.scm

@@ -46,7 +46,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages documentation)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages fortran-xyz)

gnu/packages/chicken.scm

@@ -20,113 +20,65 @@
 
 (define-module (gnu packages chicken)
   #:use-module (gnu packages)
-  #:use-module (gnu packages bash)
-  #:use-module (guix gexp)
   #:use-module (guix packages)
-  #:use-module (guix utils)
   #:use-module (guix build-system chicken)
   #:use-module (guix build-system gnu)
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix svn-download)
   #:use-module ((guix licenses)
-                #:prefix license:)
+                #:prefix license:))
-  #:use-module (srfi srfi-1))
 
-;; This package is build from pre-built C source code, provided in the CHICKEN
-;; release tarball.  Based on this bootstrap compiler, we build CHICKEN from
-;; the Scheme source, thus enabling us to (at least) patch it.
-;;
-;; See <https://issues.guix.gnu.org/22366>.
-(define-public chicken-bootstrap
-  (hidden-package
-   (package
-     (name "chicken-bootstrap")
-     (version "5.4.0")
-     (source (origin
-               (method url-fetch)
-               (uri (string-append "https://code.call-cc.org/releases/"
-                                   version "/chicken-" version ".tar.gz"))
-               (sha256
-                (base32
-                 "0pzcrnzkjw2sa44vy59wbygvlc3nva8zisprkdnvyrqi3jk4lp9w"))))
-     (build-system gnu-build-system)
-     (arguments
-      `(#:modules ((guix build gnu-build-system)
-                   (guix build utils)
-                   (srfi srfi-1))
-
-        ;; No `configure' script; run "make check" after "make install" as
-        ;; prescribed by README.
-        #:phases
-        (modify-phases %standard-phases
-          (delete 'configure)
-          (delete 'check)
-          (add-after 'install 'check
-            (assoc-ref %standard-phases 'check)))
-
-        #:make-flags (let ((out (assoc-ref %outputs "out")))
-                       (list "PLATFORM=linux"
-                             (string-append "PREFIX=" out)
-                             (string-append "VARDIR=" out "/var/lib")))
-
-        ;; Parallel builds are not supported, as noted in README.
-        #:parallel-build? #f))
-     (native-search-paths
-      (list (search-path-specification
-             (variable "CHICKEN_REPOSITORY_PATH")
-             ;; TODO extract binary version into a module level definition.
-             (files (list "var/lib/chicken/11")))))
-     ;; Reference gcc-toolchain lazily to avoid circular module dependency
-     ;; problems.
-     (propagated-inputs (list (module-ref (resolve-interface
-                                           '(gnu packages commencement))
-                                          'gcc-toolchain)))
-     (home-page "https://www.call-cc.org/")
-     (synopsis "R5RS Scheme implementation that compiles native code via C")
-     (description
-      "CHICKEN is a compiler for the Scheme programming language.  CHICKEN
-pr oduces portable and efficient C, supports almost all of the R5RS Scheme
-la nguage standard, and includes many enhancements and extensions.")
-     (license license:bsd-3))))
-
-;; The CHICKEN compiler is itself written in CHICKEN, the CHICKEN release
-;; tarballs includes auto-generated C code to mitigate the compiler
-;; bootstrapping problem.  To be able to patch the original Scheme source,
-;; we compile from this Scheme source here using the chicken-bootstrap
-;; compiler obtained from the autogenerated C code.
-;;
-;; See <https://issues.guix.gnu.org/22366>.
 (define-public chicken
   (package
-    (inherit chicken-bootstrap)
     (name "chicken")
+    (version "5.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://code.call-cc.org/releases/"
+                                  version "/chicken-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0pzcrnzkjw2sa44vy59wbygvlc3nva8zisprkdnvyrqi3jk4lp9w"))))
+    (build-system gnu-build-system)
     (arguments
-     (substitute-keyword-arguments (package-arguments chicken-bootstrap)
+     `(#:modules ((guix build gnu-build-system)
-       ((#:phases phases)
+                  (guix build utils)
-        #~(modify-phases #$phases
+                  (srfi srfi-1))
-            ;; CHICKEN contains auto-generated C code, remove it and
+
-            ;; compile from the Scheme source using chicken-bootstrap.
+       ;; No `configure' script; run "make check" after "make install" as
-            (add-after 'unpack 'remove-auto-generated-code
+       ;; prescribed by README.
-              (lambda _
+       #:phases
-                (invoke "make" "spotless")))
+       (modify-phases %standard-phases
-            ;; Invoke commands by name, not by path.
+         (delete 'configure)
-            ;;
+         (delete 'check)
-            ;; See <https://codeberg.org/guix/guix/issues/8471>.
+         (add-after 'install 'check
-            (add-after 'unpack 'fix-paths
+           (assoc-ref %standard-phases 'check)))
-              (lambda* (#:key inputs #:allow-other-keys)
+
-                (let ((sh (search-input-file inputs "/bin/sh"))
+       #:make-flags (let ((out (assoc-ref %outputs "out")))
-                      (cp (search-input-file inputs "/bin/cp")))
+                      (list "PLATFORM=linux"
-                  (substitute* "egg-compile.scm"
+                            (string-append "PREFIX=" out)
-                    (("/bin/sh") sh)
+                            (string-append "VARDIR=" out "/var/lib")))
-                    (("\"cp\"") (string-append "\"" cp "\"")))
+
-                  (substitute* "posixunix.scm"
+       ;; Parallel builds are not supported, as noted in README.
-                    (("/bin/sh") sh))
+       #:parallel-build? #f))
-                  (substitute* "chicken-install.scm"
+    (native-search-paths
-                    (("\"sh \"") (string-append "\"" sh " \""))))))))))
+     (list (search-path-specification
-    (inputs (list chicken-bootstrap))
+            (variable "CHICKEN_REPOSITORY_PATH")
-    (properties
+            ;; TODO extract binary version into a module level definition.
-     (alist-delete 'hidden? (package-properties chicken-bootstrap)))))
+            (files (list "var/lib/chicken/11")))))
+    ;; Reference gcc-toolchain lazily to avoid circular module dependency
+    ;; problems.
+    (propagated-inputs (list (module-ref (resolve-interface
+                                          '(gnu packages commencement))
+                                         'gcc-toolchain)))
+    (home-page "https://www.call-cc.org/")
+    (synopsis "R5RS Scheme implementation that compiles native code via C")
+    (description
+     "CHICKEN is a compiler for the Scheme programming language.  CHICKEN
+produces portable and efficient C, supports almost all of the R5RS Scheme
+language standard, and includes many enhancements and extensions.")
+    (license license:bsd-3)))
 
 (define-public chicken-compile-file
   (package

gnu/packages/clojure.scm

@@ -23,24 +23,19 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages clojure)
+  #:use-module (gnu packages)
   #:use-module (gnu packages base)
-  #:use-module (gnu packages golang-build)
-  #:use-module (gnu packages golang-check)
-  #:use-module (gnu packages golang-xyz)
-  #:use-module (gnu packages golang)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages java)
   #:use-module (gnu packages maven)
-  #:use-module (gnu packages)
-  #:use-module (guix build-system ant)
-  #:use-module (guix build-system clojure)
-  #:use-module (guix build-system copy)
-  #:use-module (guix build-system go)
-  #:use-module (guix download)
   #:use-module (guix gexp)
-  #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages))
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system ant)
+  #:use-module (guix build-system copy)
+  #:use-module (guix build-system clojure))
 
 (define-public clojure-spec-alpha
   (package
@@ -1258,44 +1253,3 @@ an operation on the service. invoke takes a map and returns a map, and works
 the same way for every operation on every service.")
     (home-page "https://github.com/cognitect-labs/aws-api")
     (license license:asl2.0)))
-
-(define-public let-go
-  (package
-    (name "let-go")
-    (version "1.7.4")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/nooga/let-go")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "139a129fw3w9a4bcfgms60ll90vy2vmqinbmjn44zmgx4fr2adif"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:go go-1.26
-      #:install-source? #f
-      #:import-path "github.com/nooga/let-go"))
-    (native-inputs
-     (list go-github-com-davecgh-go-spew
-           go-github-com-alimpfard-line
-           go-github-com-hashicorp-go-uuid
-           go-github-com-kr-pretty
-           go-github-com-pmezard-go-difflib
-           go-github-com-stretchr-testify
-           go-github-com-zeebo-bencode
-           go-golang-org-x-sys
-           go-gopkg-in-check-v1
-           go-gopkg-in-yaml-v3))
-    (home-page "https://nooga.github.io/let-go")
-    (synopsis "Clojure dialect written in Go")
-    (description
-     "let-go is a Clojure dialect with a bytecode compiler and a stack virtual
-machine, written in the Go programming language.
-
-It is not a drop-in replacement for Clojure JVM.  It does not load JARs and
-does not aim to.  Most idiomatic Clojure code runs unmodified, but a real
-project with library dependencies will need adjustments.")
-    (license license:expat)))

gnu/packages/cluster.scm

@@ -32,7 +32,7 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages docbook)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages linux)

gnu/packages/cobol.scm

@@ -25,7 +25,7 @@
   #:use-module (guix gexp)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages dbm)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)

gnu/packages/code.scm

@@ -66,7 +66,7 @@
   #:use-module (gnu packages curl)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages emacs)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages golang-build)

gnu/packages/commencement.scm

@@ -42,7 +42,7 @@
   #:use-module (gnu packages m4)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages bison)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages multiprecision)

gnu/packages/compiler-tools.scm

@@ -1,11 +1,8 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012-2014, 2019, 2022 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2024-2025 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017, 2020, 2021 Sergei Trofimovich <slyfox@inbox.ru>
-;;; Copyright © 2018, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
-;;; Copyright © 2024 Janneke Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2022 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2025 Alexey Abramov <levenson@mmer.org>
+;;; Copyright © 2022 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2024-2025 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2025 Anderson Torres <anderson.torres.8519@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -25,21 +22,14 @@
 
 (define-module (gnu packages compiler-tools)
   #:use-module (gnu packages autotools)
-  #:use-module (gnu packages bison)
   #:use-module (gnu packages gawk)
-  #:use-module (gnu packages m4)
-  #:use-module (gnu packages man)
-  #:use-module (gnu packages python)
-  #:use-module (gnu packages)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial)
   #:use-module (guix download)
   #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
+  #:use-module (guix packages))
-  #:use-module (guix utils)
-  #:use-module (srfi srfi-1))
 
 (define-public byacc
   (package
@@ -75,59 +65,6 @@ consist of a set of LALR(1) parsing tables and a driver routine written in the
 C programming language.")
     (license license:public-domain)))
 
-(define-public flex
-  (package
-    (name "flex")
-    (version "2.6.4")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/westes/flex"
-             "/releases/download/v" version "/"
-             "flex-" version ".tar.gz"))
-       (sha256
-        (base32
-         "15g9bv236nzi665p9ggqjlfn4dwck5835vf0bbw2cz7h5c1swyp8"))))
-    (build-system gnu-build-system)
-    (arguments
-     (if (%current-target-system)
-         (list #:configure-flags
-               #~'("ac_cv_func_malloc_0_nonnull=yes"
-                   "ac_cv_func_realloc_0_nonnull=yes"))
-         '()))
-    (native-inputs
-     (list help2man
-           ;; m4 is not present in PATH when cross-building
-           m4))
-    (inputs
-     (list
-      (package
-        (inherit bison)
-        (arguments
-         ;; Disable tests, since they require flex.
-         (substitute-keyword-arguments arguments
-           ((#:tests? _ #f) #f)))
-        (inputs (modify-inputs inputs
-                  (delete "flex"))))))
-    (propagated-inputs (list m4))
-    (home-page "https://github.com/westes/flex")
-    (synopsis "Fast lexical analyser generator")
-    (description
-     "Flex is a tool for generating scanners.  A scanner, sometimes
-called a tokenizer, is a program which recognizes lexical patterns in
-text.  The flex program reads user-specified input files, or its standard
-input if no file names are given, for a description of a scanner to
-generate.  The description is in the form of pairs of regular expressions
-and C code, called rules.  Flex generates a C source file named,
-\"lex.yy.c\", which defines the function yylex().  The file \"lex.yy.c\"
-can be compiled and linked to produce an executable.  When the executable
-is run, it analyzes its input for occurrences of text matching the
-regular expressions for each rule.  Whenever it finds a match, it
-executes the corresponding C code.")
-    (license (license:non-copyleft "file://COPYING"
-                                   "See COPYING in the distribution."))))
-
 (define-public oyacc
   (package
     (name "oyacc")
@@ -175,42 +112,3 @@ besides libc.")
     (description
      "This package provides the @command{yacc} command, implemented as a
 symbolic link to the @command{oyacc} command from the same-named package.")))
-
-(define-public re2c
-  (package
-    (name "re2c")
-    (version "4.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/skvadrik/" name
-                           "/releases/download/" version "/"
-                           name "-" version ".tar.xz"))
-       (sha256
-        (base32
-         "07ysqgdm0h566a8lwnpdgycp93vz7zskzihsgah3bla0ycj2pp69"))))
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:tests?
-      (not (or (%current-target-system)
-               ;; TODO: run_tests.py hangs
-               (system-hurd?)))
-      #:phases
-      (if (target-arm32?)
-          #~(modify-phases %standard-phases
-              (add-after 'unpack 'patch-sources
-                (lambda _
-                  (invoke "patch" "-p1" "--force" "--input"
-                          #$(local-file (search-patch
-                                         "re2c-Use-maximum-alignment.patch"))))))
-          #~%standard-phases)))
-    (native-inputs
-     (list python))             ; for the test driver
-    (home-page "https://re2c.org/")
-    (synopsis "Lexer generator")
-    (description
-     "@code{re2c, Regular Expressions to Code} is a flexible lexical analyser.
-Instead of using traditional table-driven approaches, it encodes a finite
-state machine directly in the code in the form of jumps and comparisons.")
-    (license license:public-domain)))

gnu/packages/compression.scm

@@ -42,7 +42,6 @@
 ;;; Copyright © 2024 David Elsing <david.elsing@posteo.net>
 ;;; Copyright © 2024 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2024, 2025 Zheng Junjie <873216071@qq.com>
-;;; Copyright © 2026 Jake Forster <jakecameron.forster@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3192,33 +3191,3 @@ exported by the zlib library.")
 ratio at the cost of high CPU/memory usage.")
     (home-page "https://github.com/byronknoll/cmix")
     (license license:gpl3)))
-
-(define-public zlib-ng
-  (package
-    (name "zlib-ng")
-    (version "2.3.3")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/zlib-ng/zlib-ng")
-                     (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0g4pxy7gc1slw9n6j583hzps32mml30f08gmmg1adsq4y3dl2cny"))))
-    (build-system cmake-build-system)
-    (native-inputs (list googletest))
-    (home-page "https://github.com/zlib-ng/zlib-ng")
-    (synopsis "Fork of the zlib data compression library")
-    (description
-     "zlib-ng is a @code{zlib} replacement with optimizations for next
-generation systems.")
-    (license license:zlib)))
-
-(define-public zlib-ng-compat
-  (package/inherit zlib-ng
-    (name "zlib-ng-compat")
-    (arguments
-     (substitute-keyword-arguments arguments
-       ((#:configure-flags flags #~(list))
-        #~(cons "-DZLIB_COMPAT=ON" #$flags))))))

gnu/packages/coq.scm

@@ -35,7 +35,7 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages emacs)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ocaml)

gnu/packages/coreboot.scm

@@ -23,7 +23,7 @@
 (define-module (gnu packages coreboot)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages pciutils)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system cargo)

gnu/packages/cpp.scm

@@ -53,7 +53,6 @@
 ;;; Copyright © 2025 Murilo <murilo@disroot.org>
 ;;; Copyright © 2026 Justin Veilleux <terramorpha@cock.li>
 ;;; Copyright © 2026 Daniel Littlewood <dan@danielittlewood.xyz>
-;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1434,9 +1433,6 @@ data transfer object.")
 (define-public nlohmann-json
   (package
     (name "nlohmann-json")
-    ;; XXX: Merge related package `nlohmann-json-no-char8-t' back into here when
-    ;; updating from 3.12.0, as the unique patch it applies will already be
-    ;; incorporated in.
     (version "3.12.0")
     (home-page "https://github.com/nlohmann/json")
     (source
@@ -1510,46 +1506,6 @@ intuitive syntax and trivial integration.")
 (define-deprecated-package json-modern-cxx
   nlohmann-json)
 
-(define-public nlohmann-json-no-char8-t
-  (package
-    ;; XXX: Version 3.12.0 does not work without char8_t support.
-    ;; OpenRCT2 compiles with -fno-char8_t, and thus requires this patch.
-    ;; See https://github.com/nlohmann/json/pull/4736
-    (inherit nlohmann-json)
-    (name "nlohmann-json-no-char8-t")
-    (version "3.12.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference (url "https://github.com/nlohmann/json")
-                           (commit (string-append "v" version))))
-       (sha256
-        (base32 "09nqq56ighr3lghhn3fs399lkllghz717j0xyp87x0giw86ayh3h"))
-       (file-name (git-file-name name version))
-       (modules '((guix build utils)))
-       (snippet
-        #~(begin
-            ;; Delete bundled software.  Preserve doctest_compatibility.h, which
-            ;; is a wrapper library added by this package.
-            (install-file "./tests/thirdparty/doctest/doctest_compatibility.h"
-                          "/tmp")
-            (delete-file-recursively "./tests/thirdparty")
-            (install-file "/tmp/doctest_compatibility.h"
-                          "./tests/thirdparty/doctest")
-
-            ;; Adjust for the unbundled fifo_map and doctest.
-            (substitute* (find-files "./tests/" "\\.h(pp)?")
-              (("#include \"doctest\\.h\"") "#include <doctest/doctest.h>")
-              (("#include <doctest\\.h>") "#include <doctest/doctest.h>"))
-            (with-directory-excursion "tests/src"
-              (let ((files (find-files "." "\\.cpp$")))
-                (substitute* files
-                  (("#include ?\"(fifo_map.hpp)\"" all fifo-map-hpp)
-                   (string-append
-                    "#include <fifo_map/" fifo-map-hpp ">")))))))
-       (patches
-        (search-patches "nlohmann_json_fix_char8_t.patch"))))))
-
 (define-public jthread
   (let ((commit "0fa8d394254886c555d6faccd0a3de819b7d47f8")
         (revision "0"))
@@ -4524,29 +4480,6 @@ file name and location, as well as filters with friendly names (such as
        "This package provides a simple S-Expression parser for C++.")
       (license license:gpl3+))))
 
-(define-public sfl-library
-  (package
-    (name "sfl-library")
-    (version "2.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/slavenf/sfl-library")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1ngy86b9y1b8a4j37c14m1jrg0q5b12jj8b0gdnpl5sjb1r2fljk"))))
-    (build-system cmake-build-system)
-    (arguments (list #:tests? #f))              ;no tests
-    (home-page "https://github.com/slavenf/sfl-library")
-    (synopsis "Header-only C++11/20 container library")
-    (description "sfl-library provides many STL-like (Standard Template Library)
-containers including vectors, associative containers, and unordered containers
-based on hash tables.  These containers are designed for C++11 and C++20
-constant expression usage.")
-    (license license:zlib)))
-
 (define-public string-view-lite
   (package
     (name "string-view-lite")

gnu/packages/databases.scm

@@ -32,7 +32,7 @@
 ;;; Copyright © 2017 Kristofer Buffington <kristoferbuffington@gmail.com>
 ;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
-;;; Copyright © 2018, 2021-2023, 2026 Maxim Cournoyer <maxim@guixotic.coop>
+;;; Copyright © 2018, 2021, 2022, 2023 Maxim Cournoyer <maxim@guixotic.coop>
 ;;; Copyright © 2019 Jack Hill <jackhill@jackhill.us>
 ;;; Copyright © 2019 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2019 Gábor Boskovits <boskovits@gmail.com>
@@ -109,7 +109,7 @@
   #:use-module (gnu packages dbm)
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages emacs)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
@@ -131,7 +131,6 @@
   #:use-module (gnu packages guile-xyz)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages jemalloc)
-  #:use-module (gnu packages kerberos)
   #:use-module (gnu packages language)
   #:use-module (gnu packages libedit)
   #:use-module (gnu packages libevent)
@@ -148,7 +147,6 @@
   #:use-module (gnu packages networking)
   #:use-module (gnu packages node)
   #:use-module (gnu packages onc-rpc)
-  #:use-module (gnu packages openldap)
   #:use-module (gnu packages openstack)
   #:use-module (gnu packages pantheon)
   #:use-module (gnu packages parallel)
@@ -177,7 +175,6 @@
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages ruby-check)
   #:use-module (gnu packages ruby-xyz)
-  #:use-module (gnu packages security-token)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages ssh)
@@ -1186,81 +1183,50 @@ autocompletion and syntax highlighting.")
 auto-completion and syntax highlighting.")
     (license license:bsd-3)))
 
+;; XXX When updating, check whether boost-for-mysql is still needed.
+;; It might suffice to patch ‘cmake/boost.cmake’ as done in the past.
 (define-public mysql
   (package
     (name "mysql")
-    (version "9.7.0")
+    (version "5.7.33")
     (source (origin
               (method url-fetch)
               (uri (list (string-append
-                          "https://cdn.mysql.com/Downloads/MySQL-"
+                          "https://dev.mysql.com/get/Downloads/MySQL-"
                           (version-major+minor version) "/"
+                          name "-" version ".tar.gz")
+                         (string-append
+                          "https://downloads.mysql.com/archives/get/file/"
                           name "-" version ".tar.gz")))
               (sha256
                (base32
-                "0v9hc8yzp0f5pwl4kr1a8k7lwyf62g95klxb6avfrc2npjx79dbl"))
+                "1bb343mf7n0qg2qz497gxjsqprygrjz1q1pbz76hgqxnsy08sfxd"))))
-              (modules '((guix build utils)
-                         (ice-9 ftw)
-                         (srfi srfi-26)))
-              (snippet
-               #~(begin
-                   (define (delete-all-but directory . preserve)
-                     (with-directory-excursion directory
-                       (let* ((pred (negate (cut member <>
-                                                 (cons* "." ".." preserve))))
-                              (items (scandir "." pred)))
-                         (for-each (cut delete-file-recursively <>) items))))
-
-                   ;; Delete bundled source libraries.
-                   (delete-all-but "extra"
-                                   ;; XXX: The build system doesn't currently
-                                   ;; support unbundling these.
-                                   "json" ;used by bundled opentelemetry
-                                   "libbacktrace"
-                                   "libcno"
-                                   "opentelemetry-cpp"
-                                   "opentelemetry-proto"
-                                   "rapidjson"
-                                   "unordered_dense"
-                                   "xxhash")))))
     (build-system cmake-build-system)
     (arguments
      (list
-      #:tests? #f          ;FIXME: teach build system to use system googletest
       #:configure-flags
       #~(list "-DBUILD_CONFIG=mysql_release"
-              "-DWITH_AUTHENTICATION_LDAP=ON"
+              "-DWITH_SSL=system"
-              "-DWITH_AUTHENTICATION_WEBAUTHN=ON"
+              "-DWITH_ZLIB=system"
-              "-DWITH_BENCHMARK=OFF"
+              "-DDEFAULT_CHARSET=utf8"
-              ;; XXX: BUILD_ID is disabled so that the INFO_BIN target is not
+              "-DDEFAULT_COLLATION=utf8_general_ci"
-              ;; run; this target relies on running mysqld before it is
-              ;; installed, which fails in our case.
-              "-DWITH_BUILD_ID=OFF"
-              "-DWITH_FIDO=system"
-              "-DWITH_SYSTEM_LIBS=ON"
-              "-DWITH_UNIT_TESTS=OFF"   ;avoid bundled googletest
-              "-DREPRODUCIBLE_BUILD=ON"
               "-DMYSQL_DATADIR=/var/lib/mysql"
               "-DMYSQL_UNIX_ADDR=/run/mysqld/mysqld.sock"
-              "-DINSTALL_INFODIR=share/info"
+              "-DINSTALL_INFODIR=share/mysql/docs"
               "-DINSTALL_MANDIR=share/man"
               "-DINSTALL_PLUGINDIR=lib/mysql/plugin"
+              "-DINSTALL_SCRIPTDIR=bin"
               "-DINSTALL_INCLUDEDIR=include/mysql"
               "-DINSTALL_DOCREADMEDIR=share/mysql/docs"
               "-DINSTALL_SUPPORTFILESDIR=share/mysql"
               "-DINSTALL_MYSQLSHAREDIR=share/mysql"
-              "-DINSTALL_MYSQLTESTDIR=OFF"
               "-DINSTALL_DOCDIR=share/mysql/docs"
-              "-DINSTALL_SHAREDIR=share/mysql")
+              "-DINSTALL_SHAREDIR=share/mysql"
+              ;; Get rid of test data.
+              "-DINSTALL_MYSQLTESTDIR="
+              "-DINSTALL_SQLBENCHDIR=")
       #:phases
       #~(modify-phases %standard-phases
-          (add-before 'configure 'disable-broken-abi-check
-            (lambda _
-              ;; The ABI check started failing with MySQL 9.7.0 for unknown
-              ;; reasons.
-              (substitute* "cmake/abi_check.cmake"
-                (("RUN_ABI_CHECK 1")
-                 "RUN_ABI_CHECK 0"))))
           (add-after 'install 'remove-extra-binaries
             (lambda _
               ;; Remove the 3 *_embedded files, which weigh in at
@@ -1287,51 +1253,35 @@ auto-completion and syntax highlighting.")
                            (dirname coreutils)
                            (dirname grep)
                            (dirname ps)
-                           (dirname sed)))))))
+                           (dirname sed))))))))))
-          (add-after 'install 'fix-permissions
-            ;; XXX: Otherwise, the guix daemon reports: "suspicious ownership
-            ;; or permission on `/gnu/store/...-mysql-9.7.0'; rejecting this
-            ;; build output".
-            (lambda _
-              (chmod #$output #o755))))))
     (native-inputs
      (list bison perl pkg-config))
     (inputs
      (list bash-minimal
-           boost
+           boost-for-mysql
            coreutils
-           curl
-           cyrus-sasl
            gawk
            grep
-           icu4c
            libaio
-           libedit
-           libfido2
            libtirpc
-           lz4
-           mit-krb5
            ncurses
-           openldap
+           openssl-1.1
-           openssl
-           protobuf
            procps
            rpcsvc-proto                 ; rpcgen
            sed
-           zlib
+           zlib))
-           `(,zstd "lib")))
     (home-page "https://www.mysql.com/")
     (synopsis "Fast, easy to use, and popular database")
     (description
      "MySQL is a fast, reliable, and easy to use relational database
 management system that supports the standardized Structured Query
 Language.")
-    (license license:gpl2)))    ;v2 only -- see 'Election of GPLv2' in LICENSE
+    (license license:gpl2)))
 
 (define-public mysql-connector-python
   (package
     (name "mysql-connector-python")
-    (version "9.7.0")
+    (version "8.3.0")
     (source
      (origin
        (method git-fetch)
@@ -1340,23 +1290,66 @@ Language.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0zdm35apj1cfraxwlqfmr04pm87qpw73ilb8p88cn08zsa8q11hg"))))
+        (base32 "18jvpnnwmfrn961rvqmsygp7dw3spf3swhxhal4hhj5hqddckj5f"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      ;; tests: 1371 passed
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'compatibility
+            (lambda _
+              (substitute* "src/mysql_capi.c"
+                (("res = mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
+                 "res = 0;")
+                (("mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
+                 "")
+                (("mysql_options\\(&self->session, MYSQL_OPT_TLS_CIPHERSUITES.*")
+                 "")
+                ;; The C API does not have mysql_bind_param, so we produce an
+                ;; error here.
+                (("status = mysql_bind_param.*") "status = 1;")
+                (("#include \"mysql_capi_conversion\\.h\"" all)
+                 (string-append all "\n" "#include <stdbool.h>")))))
           (add-after 'unpack 'chdir
             (lambda _
-              ;; Our protobuf is too old for the mysqlx dev API, so use the
-              ;; classic one without the C modules.
               (chdir "mysql-connector-python")))
+          (add-before 'build 'prepare-build
+            (lambda _
+              (setenv "MYSQL_CAPI" #$(this-package-input "mysql"))))
           (replace 'check
             (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
                 ;; Some of these tests might be failing due to the build
                 ;; container's restrictions, others are due to the version
                 ;; mismatch.
+                (substitute* "tests/cext/test_cext_api.py"
+                  (("def test_change_user") "def _do_not_test_change_user")
+                  (("def test_get_character_set_info")
+                   "def _do_not_test_get_character_set_info"))
+                (substitute* "tests/test_bugs.py"
+                  (("def test_change_user") "def _do_not_test_change_user")
+                  (("def test_lost_connection") "def _do_not_test_lost_connection")
+                  (("def test_kill_query") "def _do_not_test_kill_query")
+                  ;; These all fail because of expired certificates.
+                  (("def test_cext_verify_server_certificate")
+                   "def _do_not_test_cext_verify_server_certificate")
+                  (("def test_pure_verify_server_certificate")
+                   "def _do_not_test_pure_verify_server_certificate")
+                  (("def test_verify_server_name_cext_cnx")
+                   "def _do_not_test_verify_server_name_cext_cnx")
+                  (("def test_verify_server_name_pure_cnx")
+                   "def _do_not_test_verify_server_name_pure_cnx"))
+                (substitute* '("tests/test_connection.py"
+                               "tests/test_aio_connection.py")
+                  (("def test_allow_local_infile_in_path")
+                   "def _do_not_test_allow_local_infile_in_path")
+                  ;; This fails because of expired certificates.
+                  (("def test_connect_with_unix_socket")
+                   "def _do_not_test_connect_with_unix_socket"))
+                (substitute* "tests/test_constants.py"
+                  (("def test_deprecated")
+                   "def _do_not_test_deprecated"))
                 (mkdir-p "/tmp/datadir")
                 (invoke "python3" "unittests.py"
                         "--verbosity=3"
@@ -1364,8 +1357,9 @@ Language.")
                         "--keep"
                         "--mysql-topdir=/tmp/datadir"
                         "--unix-socket=/tmp/datadir")))))))
+    (propagated-inputs (list python-protobuf))
+    (inputs (list mysql protobuf-3.20 openssl-1.1 zlib))
     (native-inputs (list python-setuptools))
-    (inputs (list mysql openssl zlib `(,zstd "lib")))
     (home-page "https://dev.mysql.com/doc/connector-python/en/index.html")
     (synopsis "MySQL driver written in Python")
     (description "MySQL Connector/Python enables Python programs to access
@@ -1672,14 +1666,14 @@ and high-availability (HA).")
 (define-public postgresql-17
   (package
     (name "postgresql")
-    (version "17.10")
+    (version "17.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "144cb40gn1lasvz0jvz4i72mda8k7pm1bx6azq2vggfddm8h72h7"))
+                "1dg9labqgph2idaypb8khdvbag29pr3h4bqv5w8k7kgc08rk97pg"))
               (patches (search-patches
                         "postgresql-disable-normalize_exec_path.patch"))))
     (build-system gnu-build-system)
@@ -1742,14 +1736,14 @@ pictures, sounds, or video.")
   (package
     (inherit postgresql-17)
     (name "postgresql")
-    (version "16.14")
+    (version "16.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "0w9lgsn03m4k0v3m622v7fk3gqbfbjvwv34mrrc0i4ip4wa7gl7n"))
+                "0hib575m9x3z8c71gkcv9jsyq77d3qk7q2zgzvfy6clwrvs8b16y"))
               (patches (search-patches
                         "postgresql-disable-normalize_exec_path.patch"))))
     (arguments
@@ -1773,14 +1767,14 @@ pictures, sounds, or video.")
   (package
     (inherit postgresql-16)
     (name "postgresql")
-    (version "15.18")
+    (version "15.15")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "1d13qckpslfqamdmp23q3rbzxlp1rqwszylilyllpsp3gzwhvpqi"))
+                "1ais46b2ij38y75i1w336as03pybyndsd2pp2q8gdjq9igmsllsp"))
               (patches (search-patches
                         "postgresql-disable-resolve_symlinks.patch"))))
     (native-inputs (modify-inputs native-inputs
@@ -1793,7 +1787,6 @@ pictures, sounds, or video.")
     (inherit postgresql-15)
     (name "postgresql")
     (version "14.20")
-    (replacement postgresql-14.23)
     (source (origin
               (inherit (package-source postgresql-15))
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
@@ -1802,19 +1795,6 @@ pictures, sounds, or video.")
                (base32
                 "0sv45dsmyplfys6dfdjdwmrczl46s82x35xdh311nxj02q7z29vm"))))))
 
-(define-public postgresql-14.23
-  (package
-    (inherit postgresql-14)
-    (name "postgresql")
-    (version "14.23")
-    (source (origin
-              (inherit (package-source postgresql-14))
-              (uri (string-append "https://ftp.postgresql.org/pub/source/v"
-                                  version "/postgresql-" version ".tar.bz2"))
-              (sha256
-               (base32
-                "19clihp73ak2p5di90jhg50lqjkkr0iy349gkki30qsl5f11cwnc"))))))
-
 (define-deprecated/public postgresql-13 #f
   (package
     (inherit postgresql-14)

gnu/packages/datalog.scm

@@ -20,7 +20,7 @@
   #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages python)

gnu/packages/debug.scm

@@ -58,7 +58,7 @@
   #:use-module (gnu packages code)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages digest)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gdb)

gnu/packages/dictionaries.scm

@@ -56,7 +56,7 @@
   #:use-module (gnu packages curl)
   #:use-module (gnu packages education)
   #:use-module (gnu packages emacs)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fribidi)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)

gnu/packages/django.scm

@@ -105,7 +105,7 @@ prefixing to determine WebSocket endpoints versus HTTP endpoints.")
 (define-public python-channels
   (package
     (name "python-channels")
-    (version "4.2.2")
+    (version "4.3.2")
     (source
      (origin
        (method git-fetch) ; no tests in PyPI
@@ -114,8 +114,14 @@ prefixing to determine WebSocket endpoints versus HTTP endpoints.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0x7w29qpj2acrzf8hcgymsyr5gk3aj2wkbvlwcr01ygd6as8h7hz"))))
+        (base32 "0lxq5l0729ms4xzbn1rq968qpi7ipa9aj1wjvzrpdxd3mmlg2618"))))
     (build-system pyproject-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'delete-selenium-tests
+           (lambda* _
+             (delete-file "tests/sample_project/tests/test_selenium.py"))))))
     (propagated-inputs (list python-asgiref python-django))
     ;; Channels develops and maintains Daphne but any other ASGI server can be
     ;; used, so keep it in native-inputs for tests.
@@ -200,13 +206,13 @@ your project into different processes.")
 (define-public python-django
   (package
     (name "python-django")
-    (version "5.2.13")
+    (version "6.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "django" version))
        (sha256
-        (base32 "1i1vlffzhwbzp6r6y8ycvwklc45diy4c6i897z379l48a7dqj5d3"))))
+        (base32 "0saj5w1pmfl2bf6smmbx2h8v6b9n9djdsbp46v468a4ax5r6hvdw"))))
     (build-system pyproject-build-system)
     (arguments
      '(#:test-flags
@@ -374,28 +380,27 @@ and adapters that are useful for non-trivial configuration scenarios.")
 (define-public python-django-extensions
   (package
     (name "python-django-extensions")
-    (version "4.1")
+    (properties '((commit . "32ddfb0499bec7f39f9fbb44568d2781cecd1f32")
+                  (revision . "0")))
+    (version (git-version "4.1"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
     (source
      (origin
        (method git-fetch)
        ;; Fetch from the git repository, so that the tests can be run.
        (uri (git-reference
              (url "https://github.com/django-extensions/django-extensions")
-             (commit version)))
+             (commit (assoc-ref properties 'commit))))
        (file-name (string-append name "-" version))
        (sha256
-        (base32 "1qayan9za7ylvzkwp6p0l0735gavnzd1kdjsfc178smq6xnby0ss"))))
+        (base32 "09gk82rsmqgaz4pqk0xvb4mgfprls8h1wm24p74d0ykdi7li2plg"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       ;; The 5 tests in test_dumbscript.py fail (OperationalError).
       #:test-flags
-      #~(list "--ignore" "tests/test_dumpscript.py"
+      #~(list "--ignore" "tests/test_dumpscript.py")))
-              "-k" (string-append
-                    ;; These fail for unknown reasons.
-                    "not test_do_export_emails_format_vcard_start"
-                    " and not test_initialize_runserver_plus"
-                    " and not test_should_highlight_python_syntax_with_name"))))
     (propagated-inputs
      (list python-django))
     (native-inputs
@@ -406,6 +411,8 @@ and adapters that are useful for non-trivial configuration scenarios.")
            python-pytest-django
            python-setuptools
            python-shortuuid
+           python-vobject
+           python-werkzeug
            tzdata-for-tests))
     (home-page "https://github.com/django-extensions/django-extensions")
     (synopsis "Custom management extensions for Django")

gnu/packages/dns.scm

@@ -56,7 +56,7 @@
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages elf)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages glib)

gnu/packages/documentation.scm

@@ -57,7 +57,7 @@
   #:use-module (gnu packages bison)
   #:use-module (gnu packages kde-frameworks)
   #:use-module (gnu packages docbook)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gettext)

gnu/packages/dotnet.scm

@@ -29,7 +29,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages base)

gnu/packages/education.scm

@@ -42,7 +42,7 @@
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages django)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)

gnu/packages/electronics.scm

@@ -90,7 +90,7 @@
   #:use-module (gnu packages elf)
   #:use-module (gnu packages embedded)
   #:use-module (gnu packages engineering)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gawk)
@@ -1021,7 +1021,7 @@ files.")
 (define-public klayout
   (package
     (name "klayout")
-    (version "0.30.9")
+    (version "0.30.8")
     (source
      (origin (method git-fetch)
              (uri (git-reference
@@ -1030,7 +1030,7 @@ files.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-               "1v5ddw7xixvdc3qshd0lkrc3ayk2q5wkk1zbhvsidq0kzlqbr2z5"))))
+               "0aw0y5k27pslql9pir6nplapj6ml6fkhzd815s13rlnw3bm0fcs6"))))
     (build-system copy-build-system)
     (arguments
      (list
@@ -2207,7 +2207,7 @@ which allows one to install the M8 firmware on any Teensy.")
 (define-public magic
   (package
     (name "magic")
-    (version "8.3.652")
+    (version "8.3.644")
     (source
      (origin
        (method git-fetch)
@@ -2216,7 +2216,7 @@ which allows one to install the M8 firmware on any Teensy.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "07q2lldcq6zb1apa5d3paciha92r6jlp7xny8pc31f56k5s9jnmz"))))
+        (base32 "0qp1alm4pczfm77r8lxwgzrwh02ihvfmk9sbwjlfbrixg1dn85xb"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -2312,7 +2312,7 @@ coverage.")
 (define-public netgen
   (package
     (name "netgen")
-    (version "1.5.320")
+    (version "1.5.319")
     (source
      (origin
        (method git-fetch)
@@ -2321,7 +2321,7 @@ coverage.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "11mvf0nrsfc1lxbgqhmczi0maw4n10lib2xqnhpkyy73ci489147"))))
+        (base32 "16xd2xcsny1bb6yk4lz34jfpwfb5xi2i9izxjymmalnzhg32i9cz"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -4376,7 +4376,7 @@ input and outputs an XML dataset.")
 (define-public qucs-s
   (package
     (name "qucs-s")
-    (version "26.1.1")                  ;update qucsator-rf accordingly
+    (version "26.1.0")                  ;update qucsator-rf accordingly
     (source
      (origin
        (method git-fetch)
@@ -4386,7 +4386,7 @@ input and outputs an XML dataset.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "009siqmn76r2l17hnjqmr6ap8nw969hd5fyqigb4p3i8cvjq7gmx"))))
+         "0aiyrcrxln4v6qm2dmigb54wl0mj499q3g18pz87m1s2lfgicpb1"))))
     (build-system qt-build-system)
     (arguments
      (list

gnu/packages/emacs-xyz.scm

@@ -4547,6 +4547,43 @@ boilerplate code from defining new Flymake backend functions.")
     (description "This package adds Clojure syntax checker clj-kondo.")
     (license license:gpl3+)))
 
+(define-public emacs-flymake-shellcheck
+  ;; No tag, version grabbed from source .el file.
+  (let ((commit "ac534e9ef15c82ac86ae65fe5004d29dbc8c92c7")
+        (revision "1"))
+    (package
+      (name "emacs-flymake-shellcheck")
+      (version (git-version "0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/federicotdn/flymake-shellcheck")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "04yfb4sy41spjzk9mhm4gy0h8vnjx09p2g6nm1yzgd9a5ph9sqgl"))))
+      (build-system emacs-build-system)
+      (arguments
+       '(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'substitute-shellcheck-path
+             (lambda* (#:key inputs #:allow-other-keys)
+               (make-file-writable "flymake-shellcheck.el")
+               (emacs-substitute-sexps "flymake-shellcheck.el"
+                 ("defcustom flymake-shellcheck-path"
+                  `(or (executable-find "shellcheck")
+                       ,(search-input-file inputs "bin/shellcheck")))))))))
+      (inputs
+       (list shellcheck))
+      (home-page "https://github.com/federicotdn/flymake-shellcheck")
+      (synopsis "Flymake backend for Bash/Sh powered by ShellCheck")
+      (description
+       "This package provides a backend for Flymake to use the
+tool ShellCheck for static analyzing @command{bash} and @command{sh}
+scripts.")
+      (license license:gpl3+))))
+
 (define-public emacs-a
   (package
     (name "emacs-a")
@@ -5266,39 +5303,6 @@ to prevent advertisers from tracking you when you open URLs (or listen to
 podcasts) in Emacs.")
       (license (list license:gpl3+)))))
 
-(define-public emacs-emcp
-  (let ((commit "a91016452ef73813ea4a7e84cde233176d87a97f")
-        (revision "0"))
-    (package
-      (name "emacs-emcp")
-      (version (git-version "0.1.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-                (url "https://codeberg.org/martenlienen/emcp")
-                (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "08wbpj95l38fsdihxhgryb74psl11agw5n9swnpf1j3qyhwa13cn"))))
-      (build-system emacs-build-system)
-      (arguments
-       (list
-        #:test-command
-        #~(list "emacs" "-Q" "-batch"
-                "-l" "emcp-tests.el"
-                "-f"
-                "ert-run-tests-batch-and-exit")))
-      (propagated-inputs
-       (list emacs-elisp-refs emacs-magit emacs-http-server))
-      (home-page "https://codeberg.org/martenlienen/emcp")
-      (synopsis "Emacs MCP client")
-      (description
-       "@code{emacs-emcp} is an Emacs client for the @acronym{Model Context
-Protocol, MCP}, designed to connect LLM agents directly to Emacs.")
-      (license license:gpl3+))))
-
 (define emacs-emms-print-metadata
   (package
     (name "emacs-emms-print-metadata")
@@ -16790,51 +16794,6 @@ line program.")
 requests library that uses the url library.")
       (license license:gpl2+))))
 
-(define-public emacs-http-server
-  (let ((commit "00e746baf4a622a7545b4af5c5237a55d51f801b")
-        (revision "0"))
-    (package
-      (name "emacs-http-server")
-      (version (git-version "0.1.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-                (url "https://codeberg.org/martenlienen/http-server.el")
-                (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "0j7ls15ljk22qxy6hs2qzcjnbdfvrq4qwly8s6kfbczi74mw5iji"))))
-      (build-system emacs-build-system)
-      (arguments
-       (list
-        #:test-command
-        #~(list "emacs" "-Q" "-batch"
-                "-l" "http-server.el"
-                "-l" "http-server-ws.el"
-                "-l" "http-server-tests.el"
-                "-l" "http-server-ws-tests.el"
-                "--eval"
-                (string-append
-                 "(ert-run-tests-batch-and-exit "
-                 "'(and (not http-server-accepts-extra-methods)
-                        (not http-server-rejects-unsupported-methods)))"))
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-after 'unpack 'build-info-manual
-              (lambda _
-                (invoke "makeinfo" "--no-split"
-                        "-o" "http-server.info" "docs/http-server.texi"))))))
-      (native-inputs
-       (list emacs-package-lint emacs-plz emacs-websocket texinfo))
-      (home-page "https://codeberg.org/martenlienen/http-server.el")
-      (synopsis "Emacs HTTP server")
-      (description
-       "This library implements an HTTP server inside of Emacs to communicate
-with the user or other external programs.")
-      (license license:gpl3+))))
-
 (define-public emacs-rtfm-mode
   (package
    (name "emacs-rtfm-mode")
@@ -42120,7 +42079,7 @@ add popup descriptions to existing keymaps
 (define-public emacs-forgejo
   (package
     (name "emacs-forgejo")
-    (version "0.2.3")
+    (version "0.2.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -42129,7 +42088,7 @@ add popup descriptions to existing keymaps
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1c8s8a0hwb44jddxsrd74bh8rwaz8z5mn9ga8jmwxy7w045xfln1"))))
+                "0hf4sckxdygxa84g3pi3m2qy16ngx76jsrf192q5l4fppsyirnws"))))
     (build-system emacs-build-system)
     (arguments
      (list #:lisp-directory "lisp"

gnu/packages/embedded.scm

@@ -57,7 +57,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cross-base)
   #:use-module (gnu packages dejagnu)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gdb)
   #:use-module (gnu packages guile)

gnu/packages/emulators.scm

@@ -81,7 +81,7 @@
   #:use-module (gnu packages engineering)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages file-systems)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fltk)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)

gnu/packages/engineering.scm

@@ -113,7 +113,7 @@
   #:use-module (gnu packages emacs-build)
   #:use-module (gnu packages emacs-xyz)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gawk)

gnu/packages/esolangs.scm

@@ -24,7 +24,7 @@
 (define-module (gnu packages esolangs)
   #:use-module (gnu packages)
   #:use-module (gnu packages bison)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)

gnu/packages/fabric-management.scm

@@ -30,7 +30,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages bison)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages linux)

gnu/packages/file-systems.scm

@@ -78,7 +78,7 @@
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gettext)

gnu/packages/finance.scm

@@ -99,7 +99,7 @@
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages emacs-xyz)
   #:use-module (gnu packages dbm)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)

gnu/packages/firmware.scm

@@ -68,7 +68,7 @@
   #:use-module (gnu packages elf)
   #:use-module (gnu packages embedded)
   #:use-module (gnu packages flashing-tools)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gawk)

gnu/packages/flashing-tools.scm

@@ -72,7 +72,7 @@
   #:use-module (gnu packages electronics)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages embedded)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang-xyz)

gnu/packages/flex.scm

@@ -1,5 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2026 Anderson Torres <anderson.torres.8519@gmail.com>
+;;; Copyright © 2012, 2013, 2014, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2024 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -17,9 +19,65 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages flex)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (guix licenses)
-  #:use-module (guix deprecation))
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix gexp)
+  #:use-module (guix utils)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages m4)
+  #:use-module (gnu packages man)
+  #:use-module (gnu packages bison)
+  #:use-module (srfi srfi-1))
 
-;; XXX: Deprecated on 2026-05-28.
+(define-public flex
-(define-deprecated/public-alias flex
+  (package
-  (@ (gnu packages compiler-tools) flex))
+    (name "flex")
+    (version "2.6.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/westes/flex"
+                    "/releases/download/v" version "/"
+                    "flex-" version ".tar.gz"))
+              (sha256
+               (base32
+                "15g9bv236nzi665p9ggqjlfn4dwck5835vf0bbw2cz7h5c1swyp8"))))
+    (build-system gnu-build-system)
+    (inputs
+     (let ((bison-for-tests
+            (package
+              (inherit bison)
+              (arguments
+               ;; Disable tests, since they require flex.
+               (substitute-keyword-arguments arguments
+                 ((#:tests? _ #f) #f)))
+              (inputs (alist-delete "flex" (package-inputs bison))))))
+       `(("bison" ,bison-for-tests))))
+    (arguments
+     (if (%current-target-system)
+         (list #:configure-flags
+               #~'("ac_cv_func_malloc_0_nonnull=yes"
+                   "ac_cv_func_realloc_0_nonnull=yes"))
+         '()))
+    ;; m4 is not present in PATH when cross-building
+    (native-inputs
+     (list help2man m4))
+    (propagated-inputs (list m4))
+    (home-page "https://github.com/westes/flex")
+    (synopsis "Fast lexical analyser generator")
+    (description
+     "Flex is a tool for generating scanners.  A scanner, sometimes
+called a tokenizer, is a program which recognizes lexical patterns in
+text.  The flex program reads user-specified input files, or its standard
+input if no file names are given, for a description of a scanner to
+generate.  The description is in the form of pairs of regular expressions
+and C code, called rules.  Flex generates a C source file named,
+\"lex.yy.c\", which defines the function yylex().  The file \"lex.yy.c\"
+can be compiled and linked to produce an executable.  When the executable
+is run, it analyzes its input for occurrences of text matching the
+regular expressions for each rule.  Whenever it finds a match, it
+executes the corresponding C code.")
+    (license (non-copyleft "file://COPYING"
+                           "See COPYING in the distribution."))))

gnu/packages/fonts.scm

@@ -335,14 +335,14 @@ mediums.")
     (version "4.1")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append
+       (uri (git-reference
-             "https://github.com/rsms/inter/releases/download/"
+              (url "https://github.com/rsms/inter")
-             "v" version "/Inter-" version ".zip"))
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "07miarbl5ain7pg7sxlrb2j4m9prbriacyqpv1mvckwxlkagv0wq"))))
+        (base32 "1g54vl3jkpan0s1mzrb1s8zjqzy9787ffjg9sfy6yjy4k3qg8xhx"))))
     (build-system font-build-system)
-    (outputs '("out" "ttf" "woff"))
     (home-page "https://rsms.me/inter")
     (synopsis "Variable font family optimized for screen readability")
     (description
@@ -400,30 +400,6 @@ Lisnoti is available in regular, italic, bold and bold-italic
 variants.")
       (license license:silofl1.1))))
 
-(define-public font-literata
-  (package
-    (name "font-literata")
-    (version "3.103")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/googlefonts/literata")
-                     (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1nnr5y6fz7da06ihinmna2a1g79q8l41bgr62l6jpl43p1dw93dn"))))
-    (build-system font-build-system)
-    (outputs (list "out" "woff"))
-    (home-page "https://github.com/googlefonts/literata")
-    (synopsis "Contemporary serif typeface for long-form reading")
-    (description
-     "Literata is a serif screen font family.  It was conceived for intensive
-editorial use, especially on screens of all sorts.  Its main potential is in
-digital publishing, whether on the web, electronic press, or mobile
-applications.")
-    (license license:silofl1.1)))
-
 (define-public font-inconsolata
   (package
     (name "font-inconsolata")

gnu/packages/fontutils.scm

@@ -52,7 +52,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages docbook)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages fribidi)

gnu/packages/games.scm

@@ -144,7 +144,7 @@
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages emulators)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fltk)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
@@ -6148,22 +6148,39 @@ have a steep learning curve.")))
 (define-public openrct2-title-sequences
   (package
    (name "openrct2-title-sequences")
-   (version "0.4.26")
+   (version "0.1.2")
    (source
     (origin
      (method url-fetch)
-     (uri (string-append "https://github.com/OpenRCT2/title-sequences"
+     (uri (string-append "https://github.com/OpenRCT2/title-sequences/releases/download/v"
-                         "/releases/download/v" version
+                         version "/title-sequence-v" version ".zip"))
-                         "/title-sequences.zip"))
      (file-name (string-append name "-" version ".zip"))
      (sha256
       (base32
-       "0n680llpcyzl22bbphp9diz4m86gz2rn97yxlky44qspn63rgfys"))))
+       "0qbyxrsw8hlgaq0r5d7lx7an3idy4qbfv7yiw9byhldk763n9cfw"))))
-   (build-system copy-build-system)
+   (build-system trivial-build-system)
+   (native-inputs
+    `(("bash" ,bash)
+      ("coreutils" ,coreutils)
+      ("unzip" ,unzip)))
    (arguments
-    (list #:install-plan #~'(("." "/share/openrct2/title-sequences"))))
+    `(#:modules ((guix build utils))
-   (native-inputs (list unzip))
+      #:builder
-   (home-page "https://openrct2.io")
+      (begin
+        (use-modules (guix build utils))
+        (let* ((out (assoc-ref %outputs "out"))
+               (openrct2-title-sequences (string-append out
+                                         "/share/openrct2/title-sequences"))
+               (source (assoc-ref %build-inputs "source"))
+               (unzip (search-input-file %build-inputs "/bin/unzip")))
+          (copy-file source (string-append ,name "-" ,version ".zip"))
+          (invoke unzip (string-append ,name "-" ,version ".zip"))
+          (delete-file (string-append ,name "-" ,version ".zip"))
+          (mkdir-p openrct2-title-sequences)
+          (copy-recursively "."
+                            openrct2-title-sequences)
+          #t))))
+   (home-page "https://github.com/OpenRCT2/OpenRCT2")
    (synopsis "Title sequences for OpenRCT2")
    (description
     "openrct2-title-sequences is a set of title sequences for OpenRCT2.")
@@ -6173,22 +6190,38 @@ have a steep learning curve.")))
 (define-public openrct2-objects
   (package
    (name "openrct2-objects")
-   (version "1.7.9")
+   (version "1.0.20")
    (source
     (origin
      (method url-fetch)
-     (uri (string-append "https://github.com/OpenRCT2/objects"
+     (uri (string-append "https://github.com/OpenRCT2/objects/releases/download/v"
-                         "/releases/download/v" version "/objects.zip"))
+                         version "/objects.zip"))
      (file-name (string-append name "-" version ".zip"))
      (sha256
-      (base32 "1mpa4vpgs4m9izak8h5rkfcn80jbcm2di717k97g30kf1k91wijm"))))
+      (base32 "1q7a38kcwrfijav6app1gf253yfv8b0rljbkah8040y6i7snw9mw"))))
-   (build-system copy-build-system)
+   (build-system trivial-build-system)
+   (native-inputs
+    `(("bash" ,bash)
+      ("coreutils" ,coreutils)
+      ("unzip" ,unzip)))
    (arguments
-    ;; zip has multiple top-level directories to install.
+    `(#:modules ((guix build utils))
-    (list #:install-plan #~'((".." "/share/openrct2/objects"
+      #:builder
-                              #:exclude ("environment-variables")))))
+      (begin
-   (native-inputs (list unzip))
+        (use-modules (guix build utils))
-   (home-page "https://openrct2.io")
+        (let* ((out (assoc-ref %outputs "out"))
+               (openrct2-objects (string-append out
+                                         "/share/openrct2/objects"))
+               (source (assoc-ref %build-inputs "source"))
+               (unzip (search-input-file %build-inputs "/bin/unzip")))
+          (copy-file source (string-append ,name "-" ,version ".zip"))
+          (invoke unzip (string-append ,name "-" ,version ".zip"))
+          (delete-file (string-append ,name "-" ,version ".zip"))
+          (mkdir-p openrct2-objects)
+          (copy-recursively "."
+                            openrct2-objects)
+          #t))))
+   (home-page "https://github.com/OpenRCT2/OpenRCT2")
    (synopsis "Objects for OpenRCT2")
    (description
     "openrct2-objects is a set of objects for OpenRCT2.")
@@ -6284,7 +6317,7 @@ that follows two aliens who come to Earth in search of a stolen artifact.")
 (define-public openrct2
   (package
     (name "openrct2")
-    (version "0.5.0")
+    (version "0.3.3")
     (source
      (origin
        (method git-fetch)
@@ -6293,88 +6326,53 @@ that follows two aliens who come to Earth in search of a stolen artifact.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0pxlk3a8akl0ghcbqqq5xw8chmxss7kwbvi52ixfqri68n46srxh"))
+        (base32 "01nanpbz5ycdhkyd46fjfvj18sw729l4vk7xg12600f9rjngjk76"))))
-       (modules '((guix build utils)))
-       (snippet
-        #~(begin
-            (with-directory-excursion "src/thirdparty"
-              (for-each delete-file-recursively
-                        '("quickjs-ng" "sfl")))
-            (substitute* "src/openrct2/CMakeLists.txt"
-              ;; use sys quickjs for scripting features
-              (("if \\(ENABLE_SCRIPTING\\)") "if (false)")
-              (("add_library\\(OpenRCT2[^\n]+" all)
-               (string-join
-                `(,all
-                  "find_library(QJS_L NAMES qjs REQUIRED)"
-                  "find_path(QJS_I NAMES quickjs.h REQUIRED)"
-                  "target_link_libraries(libopenrct2 ${QJS_L})"
-                  "target_include_directories(libopenrct2 SYSTEM PRIVATE ${QJS_I})")
-                "\n")))))))
     (build-system cmake-build-system)
     (arguments
-     (list
+     `(#:configure-flags (list "-DDOWNLOAD_OBJECTS=OFF"
-      #:configure-flags #~(list "-DDOWNLOAD_OBJECTS=OFF"
+                               "-DDOWNLOAD_TITLE_SEQUENCES=OFF")
-                                "-DDOWNLOAD_TITLE_SEQUENCES=OFF"
+       #:tests? #f                      ; tests require network access
-                                "-DDOWNLOAD_OPENSFX=OFF"
+       #:phases
-                                "-DDOWNLOAD_OPENMUSIC=OFF"
+       (modify-phases %standard-phases
-                                "-DDISABLE_DISCORD_RPC=ON"
+         (add-after 'unpack 'fix-usr-share-paths&add-data
-                                "-DDISABLE_VERSION_CHECKER=ON")
+           (lambda* (#:key inputs outputs #:allow-other-keys)
-      ;; many issues such as https://github.com/OpenRCT2/OpenRCT2/issues/12719
+             (let ((titles (assoc-ref inputs "openrct2-title-sequences"))
-      #:tests? #f
+                   (objects (assoc-ref inputs "openrct2-objects")))
-      #:phases
+               ;; Fix some references to /usr/share.
-      #~(modify-phases %standard-phases
+               (substitute* "src/openrct2/platform/Platform.Linux.cpp"
-          (add-after 'unpack 'fix-usr-share-paths&add-data
+                 (("/usr/share")
-            ;; TODO: OpenRCT2 can optionally use free music and sounds!
+                  (string-append (assoc-ref %outputs "out") "/share")))
-            ;; https://github.com/OpenRCT2/OpenMusic
+               (copy-recursively
-            ;; https://github.com/OpenRCT2/OpenSoundEffects
+                (string-append titles "/share/openrct2/title-sequences")
-            ;; ideally we package these instead of the ones the user is supposed
+                "data/title")
-            ;; to supply.
+               (copy-recursively
-            (lambda* (#:key inputs #:allow-other-keys)
+                (string-append objects "/share/openrct2/objects")
-              (let ((titles (assoc-ref inputs "openrct2-title-sequences"))
+                "data/object"))))
-                    (objects (assoc-ref inputs "openrct2-objects"))
+         (add-before 'configure 'get-rid-of-errors
-                    (sfl (assoc-ref inputs "sfl-library")))
+           (lambda _
-                ;; Fix some references to /usr/share.
+             ;; Don't treat warnings as errors.
-                (substitute* "src/openrct2/platform/Platform.Linux.cpp"
+             (substitute* "CMakeLists.txt"
-                  (("/usr/share")
+               (("-Werror") ""))
-                   (string-append #$output "/share")))
+             #t)))))
-                (copy-recursively
+    (inputs `(("curl" ,curl)
-                 (string-append titles "/share/openrct2/title-sequences")
+              ("duktape" ,duktape)
-                 "data/title")
+              ("fontconfig" ,fontconfig)
-                (copy-recursively
+              ("freetype" ,freetype)
-                 (string-append objects "/share/openrct2/objects")
+              ("icu4c" ,icu4c)
-                 "data/object")
+              ("jansson" ,jansson)
-                (copy-recursively
+              ("nlohmann-json" ,nlohmann-json)
-                 (string-append sfl "/include")
+              ("libpng" ,libpng)
-                 "src/thirdparty"))))
+              ("libzip" ,libzip)
-          (add-before 'configure 'get-rid-of-errors
+              ("mesa" ,mesa)
-            (lambda _
+              ("openrct2-objects" ,openrct2-objects)
-              ;; Don't treat warnings as errors.
+              ("openrct2-title-sequences" ,openrct2-title-sequences)
-              (substitute* "CMakeLists.txt"
+              ("openssl" ,openssl)
-                (("-Werror") "")))))))
+              ("sdl2" ,sdl2)
-    (inputs
+              ("speexdsp" ,speexdsp)
-     (list curl
+              ("zlib" ,zlib)))
-           flac
+    (native-inputs
-           fontconfig
+     (list pkg-config))
-           freetype
+    (home-page "https://github.com/OpenRCT2/OpenRCT2")
-           icu4c
-           jansson
-           libpng
-           libvorbis
-           libzip
-           mesa
-           nlohmann-json-no-char8-t
-           openrct2-objects
-           openrct2-title-sequences
-           openssl
-           quickjs-ng
-           sdl2
-           sfl-library
-           speexdsp
-           zlib
-           (list zstd "lib")))
-    (native-inputs (list pkg-config))
-    (home-page "https://openrct2.io")
     (synopsis "Free software re-implementation of RollerCoaster Tycoon 2")
     (description "OpenRCT2 is a free software re-implementation of
 RollerCoaster Tycoon 2 (RCT2).  The gameplay revolves around building and
@@ -6382,8 +6380,8 @@ maintaining an amusement park containing attractions, shops and facilities.
 
 Note that this package does @emph{not} provide the game assets (sounds,
 images, etc.)")
-    ;; See bottom of:
+    ;; See <https://github.com/OpenRCT2/OpenRCT2/wiki/Required-RCT2-files>
-    ;; https://github.com/OpenRCT2/OpenRCT2/blob/develop/distribution/readme.txt
+    ;; regarding assets.
     (license license:gpl3+)))
 
 (define-public openriichi
@@ -6961,7 +6959,7 @@ tactics.")
 (define-public widelands
   (package
     (name "widelands")
-    (version "1.3.1")
+    (version "1.3")
     (source
      (origin
        (method git-fetch)
@@ -6970,7 +6968,7 @@ tactics.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0ab9s1imqdq1krfwlba1ipx3pwnvy91aqqzr15ssfzixy4wj5mww"))
+        (base32 "1j288rkflqmzxbacrrx35y8qm4mvbvd30c03cmkvh8b29jkgz3gp"))
        (modules '((guix build utils)))
        (snippet
         #~(delete-file-recursively "src/third_party/minizip"))))

gnu/packages/gcc.scm

@@ -51,7 +51,7 @@
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages elf)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages perl)
   #:use-module (guix packages)
   #:use-module (guix download)

gnu/packages/gdb.scm

@@ -31,7 +31,7 @@
   #:use-module (gnu packages bison)
   #:use-module (gnu packages cross-base)
   #:use-module (gnu packages dejagnu)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages hurd)
   #:use-module (gnu packages llvm)

gnu/packages/geo.scm

@@ -91,7 +91,7 @@
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages elf)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
@@ -807,7 +807,7 @@ OpenGeoSys")
 (define-public ogs-serial
   (package
     (name "ogs-serial")
-    (version "6.5.8")
+    (version "6.5.7")
     (source
      (origin
        (method git-fetch)
@@ -816,7 +816,9 @@ OpenGeoSys")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "037il6jw2j1g7bvrwvbp20yf0cnz7c7f3wmszxfv5ay7l54sffqg"))))
+        (base32 "1wflgkbcsa4sr8g63img0ld6h4jm1b7hjzsa2m4gsbzc6j7kd41w"))
+       ;; Remove patch on next release, likely 6.5.8
+       (patches (search-patches "ogs-6.5.7-netcdfconverter.patch"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -871,7 +873,6 @@ OpenGeoSys")
            tclap
            tfel
            vtk
-           xdmf
            xmlpatch
            zlib))
     (propagated-inputs

gnu/packages/gl.scm

@@ -50,7 +50,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages elf)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)

gnu/packages/glib.scm

@@ -56,7 +56,7 @@
   #:use-module (gnu packages elf)
   #:use-module (gnu packages enlightenment)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gnome)

gnu/packages/gnome.scm

@@ -136,7 +136,7 @@
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages enchant)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages file-systems)
   #:use-module (gnu packages firmware)

gnu/packages/gnucash.scm

@@ -324,7 +324,7 @@ applications and libraries.  It is used by AqBanking.")
 (define-public aqbanking
   (package
     (name "aqbanking")
-    (version "6.9.2")
+    (version "6.8.5")
     (source
      (origin
        (method git-fetch)
@@ -333,7 +333,7 @@ applications and libraries.  It is used by AqBanking.")
               (commit version)))
        (sha256
         (base32
-         "1n1867vdml71p9dbcx70rmf10b12l7l0vq847bbizrkq7b0ha8w0"))
+         "1xqhhxhr1azqvdn47389h469d3srl5l3n1nx82jx2djbx9sdzdq9"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments

gnu/packages/gnupg.scm

@@ -693,14 +693,14 @@ and signature functionality from Python programs.")
 (define-public perl-gnupg-interface
   (package
     (name "perl-gnupg-interface")
-    (version "1.06")
+    (version "1.05")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/B/BP/BPS/"
                                   "GnuPG-Interface-" version ".tar.gz"))
               (sha256
                (base32
-                "07946rsmz0ibasd53l4qiwg0dl1h65p8byja4d7fiflxsklxccs4"))))
+                "0ig0ra2s1v2rw2ikm1hd0iwf2phhcr8kbc90jhr8kdpvlkymshsl"))))
     (build-system perl-build-system)
     (inputs
      (list gnupg))
@@ -764,7 +764,7 @@ parties.")
 (define-public signing-party
   (package
     (name "signing-party")
-    (version "2.12")
+    (version "2.11")
     (home-page "https://salsa.debian.org/signing-party-team/signing-party")
     (source (origin
               (method git-fetch)
@@ -774,7 +774,7 @@ parties.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1a4x02rcs5ryvfnhb6naiwc5jsil5k1fh8b01fkijkbzbh54qjc5"))))
+                "1aig5ssabzbk4mih7xd04vgr931bw0flbi8dz902wlr610gyv5s5"))))
     (build-system gnu-build-system)
     (native-inputs
      ;; autoconf-wrapper is required due to the non-standard
@@ -788,57 +788,56 @@ parties.")
                   perl-net-idn-encode
                   libmd))
     (arguments
-     (list #:tests? #f                      ; no test suite
+     `(#:tests? #f                      ; no test suite
-           #:phases
+       #:phases
-           #~(modify-phases %standard-phases
+       (modify-phases %standard-phases
-               (replace 'configure
+         (replace 'configure
-                 (lambda _
+           (lambda* (#:key outputs #:allow-other-keys)
-                   (substitute* "keyanalyze/Makefile"
+             (let ((out (assoc-ref outputs "out")))
-                     (("LDLIBS")
+               (substitute* "keyanalyze/Makefile"
-                      (string-append "CC=" (which "gcc") "\nLDLIBS")))
+                 (("LDLIBS") (string-append "CC=" (which "gcc") "\nLDLIBS")))
-                   (substitute* "keyanalyze/Makefile"
+               (substitute* "keyanalyze/Makefile"
-                     (("\\./configure")
+                 (("\\./configure") (string-append "./configure --prefix=" out)))
-                      (string-append "./configure --prefix=" #$output)))
+               (substitute* "gpgwrap/Makefile"
-                   (substitute* "gpgwrap/Makefile"
+                 (("\\} clean")
-                     (("\\} clean")
+                  (string-append "} clean\ninstall:\n\tinstall -D bin/gpgwrap "
-                      (string-append
+                                 out "/bin/gpgwrap\n")))
-                       "} clean\ninstall:\n\tinstall -D bin/gpgwrap "
+               (substitute* '("gpgsigs/Makefile" "keyanalyze/Makefile"
-                       #$output "/bin/gpgwrap\n")))
+                              "keylookup/Makefile" "sig2dot/Makefile"
-                   (substitute* '("gpgsigs/Makefile" "keyanalyze/Makefile"
+                              "springgraph/Makefile")
-                                  "keylookup/Makefile" "sig2dot/Makefile"
+                 (("/usr") out))
-                                  "springgraph/Makefile")
+               (setenv "CONFIG_SHELL" (which "sh")))))
-                     (("/usr") #$output))
+         (replace 'install
-                   (setenv "CONFIG_SHELL" (which "sh"))))
+           (lambda* (#:key outputs #:allow-other-keys #:rest args)
-               (replace 'install
+             (let ((out (assoc-ref outputs "out"))
-                 (lambda* (#:key #:allow-other-keys #:rest args)
+                   (install (assoc-ref %standard-phases 'install)))
-                   (let ((install (assoc-ref %standard-phases 'install)))
+               (apply install args)
-                     (apply install args)
+               (for-each
-                     (for-each
+                (lambda (dir file)
-                      (lambda (dir file)
+                  (copy-file (string-append dir "/" file)
-                        (copy-file (string-append dir "/" file)
+                             (string-append out "/bin/" file)))
-                                   (string-append #$output "/bin/" file)))
+                '("caff" "caff" "caff" "gpgdir" "gpg-key2ps"
-                      '("caff" "caff" "caff" "gpgdir" "gpg-key2ps"
+                  "gpglist" "gpg-mailkeys" "gpgparticipants")
-                        "gpglist" "gpg-mailkeys" "gpgparticipants")
+                '("caff" "pgp-clean" "pgp-fixkey" "gpgdir" "gpg-key2ps"
-                      '("caff" "pgp-clean" "pgp-fixkey" "gpgdir" "gpg-key2ps"
+                  "gpglist" "gpg-mailkeys" "gpgparticipants"))
-                        "gpglist" "gpg-mailkeys" "gpgparticipants"))
+               (for-each
-                     (for-each
+                (lambda (dir file)
-                      (lambda (dir file)
+                  (copy-file (string-append dir "/" file)
-                        (copy-file
+                             (string-append out "/share/man/man1/" file)))
-                         (string-append dir "/" file)
+                '("caff" "caff" "caff" "gpgdir"
-                         (string-append #$output "/share/man/man1/" file)))
+                  "gpg-key2ps" "gpglist" "gpg-mailkeys"
-                      '("caff" "caff" "caff" "gpgdir"
+                  "gpgparticipants" "gpgsigs" "gpgwrap/doc"
-                        "gpg-key2ps" "gpglist" "gpg-mailkeys"
+                  "keyanalyze" "keyanalyze/pgpring" "keyanalyze")
-                        "gpgparticipants" "gpgsigs" "gpgwrap/doc"
+                '("caff.1" "pgp-clean.1" "pgp-fixkey.1" "gpgdir.1"
-                        "keyanalyze" "keyanalyze/pgpring" "keyanalyze")
+                  "gpg-key2ps.1" "gpglist.1" "gpg-mailkeys.1"
-                      '("caff.1" "pgp-clean.1" "pgp-fixkey.1" "gpgdir.1"
+                  "gpgparticipants.1" "gpgsigs.1" "gpgwrap.1"
-                        "gpg-key2ps.1" "gpglist.1" "gpg-mailkeys.1"
+                  "process_keys.1" "pgpring.1" "keyanalyze.1")))))
-                        "gpgparticipants.1" "gpgsigs.1" "gpgwrap.1"
+         (add-after 'install 'wrap-programs
-                        "process_keys.1" "pgpring.1" "keyanalyze.1")))))
+           (lambda* (#:key outputs #:allow-other-keys)
-               (add-after 'install 'wrap-programs
+             (let* ((out (assoc-ref outputs "out")))
-                 (lambda _
+               (wrap-program
-                   (wrap-program
+                   (string-append out "/bin/caff")
-                       (string-append #$output "/bin/caff")
+                 `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB"))))))))))
-                     `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))))))))
     (synopsis "Collection of scripts for simplifying gnupg key signing")
     (description
      "Signing-party is a collection for all kinds of PGP/GnuPG related things,
@@ -1150,24 +1149,25 @@ however, pgpdump produces more detailed and easier to understand output.")
 (define-public gpa
   (package
     (name "gpa")
-    (version "0.11.1")
+    (version "0.11.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnupg/gpa/"
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "02sx9my3s4yjxzxzs8pfif8wvpjrjsh75wwa5mxd0h867v6v5i8b"))))
+                "1k1kvxffyb4nm83yp3mnx9bfmcciwb7vfw8c3xscnh85yxdzma16"))))
     (build-system gnu-build-system)
     (arguments
-     (list #:make-flags #~(list "CFLAGS=-Wno-implicit-function-declaration")
+     `(#:make-flags '("CFLAGS=-Wno-implicit-function-declaration")
-           #:phases
+       #:phases
-           #~(modify-phases %standard-phases
+       (modify-phases %standard-phases
-               (add-after 'install 'wrap-program
+         (add-after 'install 'wrap-program
-                 (lambda* (#:key inputs #:allow-other-keys)
+           (lambda* (#:key inputs outputs #:allow-other-keys)
-                   (let ((gnupg (assoc-ref inputs "gnupg")))
+             (let ((out (assoc-ref outputs "out"))
-                     (wrap-program (string-append #$output "/bin/gpa")
+                   (gnupg (assoc-ref inputs "gnupg")))
-                       `("PATH" ":" prefix (,(string-append gnupg "/bin"))))))))))
+               (wrap-program (string-append out "/bin/gpa")
+                 `("PATH" ":" prefix (,(string-append gnupg "/bin"))))))))))
     (native-inputs (list pkg-config))
     (inputs
      (list bash-minimal

gnu/packages/golang-crypto.scm

@@ -4293,7 +4293,7 @@ purpose of improving obfs4proxy's meek_lite transport.")
 (define-public go-go-mau-fi-libsignal
   (package
     (name "go-go-mau-fi-libsignal")
-    (version "0.2.1")
+    (version "0.1.2")
     (source
      (origin
        (method git-fetch)
@@ -4309,7 +4309,7 @@ purpose of improving obfs4proxy's meek_lite transport.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0jwqhaaqjf5fb322karppisbg5s1la459a0cwvhbii899nzyd59k"))))
+        (base32 "1pd2kijza7dr5nbgfw176ca1r3rmgpx8h22gqjp557awxqhw9lzr"))))
     (build-system go-build-system)
     (arguments
      (list

gnu/packages/golang-graphics.scm

@@ -1,6 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
-;;; Copyright © 2026 orahcio <orahcio@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -250,88 +249,3 @@ multiple return values, Go's native multiple return values are used instead.
 Whenever a native GTK call could return an unexpected NULL pointer, an
 additional error is returned in the Go binding.")
     (license license:isc)))
-
-(define-public go-github-com-jackmordaunt-icns-v3
-  (package
-    (name "go-github-com-jackmordaunt-icns-v3")
-    (version "3.0.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/JackMordaunt/icns")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "04wnxv79b1xbca16kgz98zc929q60lwcgcc6q784lkz2a1clh2z2"))
-       (modules '((guix build utils)))
-       (snippet
-        #~(begin
-            ;; Submodules with their own go.mod files and packaged separately:
-            (delete-file-recursively "cmd")))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/jackmordaunt/icns/v3"
-      #:test-flags #~(list "-vet=off")))
-    (propagated-inputs
-     (list go-github-com-nfnt-resize))
-    (home-page "https://github.com/jackmordaunt/icns")
-    (synopsis "Easily create .icns files")
-    (description
-     "This package provides Go library to easily convert @code{.jpg} and
-@code{.png} to @code{.icns}, or to convert from any @code{image.Image} to
-@code{.icns}.")
-    (license license:expat)))
-
-(define-public go-github-com-sergeymakinen-go-bmp
-  (package
-    (name "go-github-com-sergeymakinen-go-bmp")
-    (version "1.0.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/sergeymakinen/go-bmp")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0bglvxqmjvgclcfjpkznxyifj5r0bh837c2iw6x1vylc7lqcq07h"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/sergeymakinen/go-bmp"))
-    (home-page "https://github.com/sergeymakinen/go-bmp")
-    (synopsis "BMP image decoder and encoder")
-    (description "Package bmp implements a BMP image decoder and encoder.")
-    (license license:bsd-3)))
-
-(define-public go-github-com-sergeymakinen-go-ico
-  (package
-    (name "go-github-com-sergeymakinen-go-ico")
-    (version "1.0.0-beta.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/sergeymakinen/go-ico")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "115fgnhn1j91zvkigl1x03jkc2dn6vx7qvfmm6l59d24qkfv6cwn"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/sergeymakinen/go-ico"))
-    (propagated-inputs
-     (list go-github-com-sergeymakinen-go-bmp))
-    (home-page "https://github.com/sergeymakinen/go-ico")
-    (synopsis "ICO and CUR file decoders and encoders")
-    (description "Package ico implements an ICO file decoder and encoder.")
-    (license license:bsd-3)))
-
-;;;
-;;; Avoid adding new packages to the end of this file. To reduce the chances
-;;; of a merge conflict, place them above in alphabetic order:
-;;; guix import --insert=gnu/packages/golang-graphics.scm pypi <package-name>.
-;;;

gnu/packages/golang-web.scm

@@ -3724,51 +3724,6 @@ lookups.  It implements looking up the following records:
 Storage}.")
     (license license:asl2.0)))
 
-(define-public go-github-com-beeper-argo-go
-  (package
-    (name "go-github-com-beeper-argo-go")
-    (version "1.1.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/beeper/argo-go")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1c11aqbap9yxpnc8bvzjiy5cg53brhc47hw2q24xjvbw5d90r2ff"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/beeper/argo-go"
-      #:embed-files #~(list "prelude.graphql")
-      #:test-flags
-      #~(list "-vet=off"
-              "-skip" (string-join
-                       ;; These test groups fail with panic by similar error:
-                       ;; UnsignedDecode failed for 10000000000000000000000:
-                       ;; varint: varint too large for 64-bit. Encoded:
-                       ;; 80808092abb7b2f099bc08.
-                       (list "TestUnsignedRoundTrip"
-                             "TestQueriesEquivalence"
-                             "TestStarWarsEquivalence"
-                             "TestZigZagRoundTrip"
-                             ;; UnsignedDecode error mismatch for too long
-                             ;; varint.
-                             "TestUnsignedDecodeTooLong")
-                       "|"))))
-    (native-inputs
-     (list go-github-com-stretchr-testify))
-    (propagated-inputs
-     (list go-github-com-elliotchance-orderedmap-v3
-           go-github-com-vektah-gqlparser-v2))
-    (home-page "https://github.com/beeper/argo-go")
-    (synopsis "Go implementation of Argo for GraphQL")
-    (description
-     "Go implementation of Argo, a compact and compressible binary
-serialization format for GraphQL.")
-    (license license:expat)))
-
 (define-public go-github-com-beevik-ntp
   (package
     (name "go-github-com-beevik-ntp")
@@ -20917,30 +20872,28 @@ state machine.  See @url{https://raft.github.io/raft.pdf} for more info.")
 (define-public go-go-mau-fi-whatsmeow
   (package
     (name "go-go-mau-fi-whatsmeow")
-    (version "0.0.0-20260529101937-a7ea56383ec4")
+    (version "0.0.0-20241215104421-68b0856cce22")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-              (url "https://github.com/tulir/whatsmeow")
+             (url "https://github.com/tulir/whatsmeow")
-              (commit (go-version->git-ref version))))
+             (commit (go-version->git-ref version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0i6vcn6l5sf0wsyr3k856xiz5pq3ivl9a7xd1bzqzlq74jmivivc"))))
+        (base32 "1y3h132g3w6ihc8jn587wvyha9xm3sinjlr0znqq7krvynz3z8id"))))
     (build-system go-build-system)
     (arguments
      (list
       #:import-path "go.mau.fi/whatsmeow"))
     (propagated-inputs
-     (list go-github-com-beeper-argo-go
+     (list go-github-com-google-uuid
-           go-github-com-coder-websocket
+           go-github-com-gorilla-websocket
-           go-github-com-google-uuid
            go-github-com-rs-zerolog
            go-go-mau-fi-libsignal
            go-go-mau-fi-util
            go-golang-org-x-crypto
            go-golang-org-x-net
-           go-golang-org-x-sync
            go-google-golang-org-protobuf))
     (home-page "https://go.mau.fi/whatsmeow")
     (synopsis "Go library for the WhatsApp web multidevice API")
@@ -23390,16 +23343,16 @@ the code or routes.")
 (define-public go-maunium-net-go-mautrix
   (package
     (name "go-maunium-net-go-mautrix")
-    (version "0.28.0")
+    (version "0.22.1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-              (url "https://github.com/mautrix/go")
+             (url "https://github.com/mautrix/go")
-              (commit (string-append "v" version))))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "09isb4q876mkcwm2yk7vgzwhd3yw1n0s78qvdb7wpmab6vvxjnlf"))))
+        (base32 "0msqbs3qc9ljckj41hgvp16p0sbfzm25wzldb68av9svimscwnmm"))))
     (build-system go-build-system)
     (arguments
      (list
@@ -23415,32 +23368,27 @@ the code or routes.")
          ;; golang.org/x/net/publicsuffix/table.go:33:12: pattern data/text:
          ;; cannot embed irregular file data/text
          "text")
-      #:test-flags
+    #:test-flags
-      #~(list "-skip" (string-join
+    #~(list "-skip" (string-join
-                       ;; Network access is required for the tets.
+                     ;; Network access is required for the tets.
-                       (list "TestCrossSignVerification_ScanQRAndConfirmScan"
+                     (list "TestClient_Version"
-                             "TestSelfVerification_Accept_QRContents"
+                           "TestResolveServerName/RM_Step_3B"
-                             "TestSelfVerification_ScanQRAndConfirmScan"
+                           "TestResolveServerName/RM_Step_3C"
-                             "TestSelfVerification_ScanQRTransactionIDCorrup"
+                           "TestResolveServerName/RM_Step_3C_MSC4040"
-                             "TestSelfVerification_ScanQRKeyCorrupted"
+                           "TestResolveServerName/RM_Step_3D"
-                             "TestVerification_SAS"
+                           "TestResolveServerName/RM_Step_4"
-                             "TestVerification_SAS_BothCallStart"
+                           "TestResolveServerName/RM_Step_4_MSC4040"
-                             "TestVerification_Start"
+                           "TestResolveServerName/maunium")
-                             "TestVerification_StartThenCancel"
+                     "|")
-                             "TestVerification_Accept_NoSupportedMethods"
+            "-vet=off")))
-                             "TestVerification_Accept_CorrectMethodsPresented"
+    ;; XXX: The final application needs a "libolm" package.
-                             "TestVerification_Accept_CancelOnNonParticipati"
+    (native-inputs
-                             "TestVerification_ErrorOnDoubleAccept"
+     (list olm))
-                             "TestVerification_CancelOnDoubleStart"
-                             "TestClient_Version"
-                             "TestResolveServerName"
-                             "TestServerKeyResponse_VerifySelfSignature"
-                             "TestServerKeyResponse_FailWithFilter")
-                       "|"))))
     (propagated-inputs
      (list go-filippo-io-edwards25519
            go-github-com-chzyer-readline
-           go-github-com-coder-websocket
+           go-github-com-gorilla-mux
+           go-github-com-gorilla-websocket
            go-github-com-lib-pq
            go-github-com-mattn-go-sqlite3
            go-github-com-rs-xid
@@ -23457,9 +23405,7 @@ the code or routes.")
            go-golang-org-x-net
            go-golang-org-x-sync
            go-gopkg-in-yaml-v3
-           go-maunium-net-go-mauflag
+           go-maunium-net-go-mauflag))
-           ;; XXX: The final application needs a "libolm" package.
-           olm))
     (home-page "https://maunium.net/go/mautrix")
     (synopsis "Golang Matrix framework")
     (description

gnu/packages/golang-xyz.scm

@@ -78,7 +78,6 @@
 ;;; Copyright © 2026 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2026 Daniel Littlewood <dan@danielittlewood.xyz>
 ;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
-;;; Copyright © 2026 orahcio <orahcio@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -114,7 +113,6 @@
   #:use-module (gnu packages golang-check)
   #:use-module (gnu packages golang-compression)
   #:use-module (gnu packages golang-crypto)
-  #:use-module (gnu packages golang-graphics)
   #:use-module (gnu packages golang-maths)
   #:use-module (gnu packages golang-vcs)
   #:use-module (gnu packages golang-web)
@@ -445,33 +443,6 @@ a human-readable byte format.")
 time dependencies in tests.")
     (license license:asl2.0)))
 
-(define-public go-code-rocketnine-space-tslocum-cbind
-  (package
-    (name "go-code-rocketnine-space-tslocum-cbind")
-    (version "0.1.5")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://codeberg.org/tslocum/cbind.git")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0a0gpzapm3jsivdf5h6lvlxhzngrmyj7xp5fdk20l8r4yba7yqsy"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "code.rocketnine.space/tslocum/cbind"
-      #:test-flags #~(list "--skip" "TestConfiguration")))
-    (propagated-inputs
-     (list go-github-com-gdamore-tcell-v2))
-    (home-page "https://codeberg.org/tslocum/cbind")
-    (synopsis "Key event handling library for tcell")
-    (description
-     "Package cbind provides a tcell key event encoding, decoding and handling
-as human-readable strings.")
-    (license license:expat)))
-
 (define-public go-codeberg-org-anaseto-gruid
   (package
     (name "go-codeberg-org-anaseto-gruid")
@@ -1869,33 +1840,6 @@ software (based on Python's
 @uref{https://github.com/pycontribs/tendo, tendo}).")
     (license license:expat)))
 
-(define-public go-github-com-alimpfard-line
-  (package
-    (name "go-github-com-alimpfard-line")
-    (version "0.0.0-20230131232016-03b4e7dee324")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/alimpfard/line")
-              (commit (go-version->git-ref version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0swjy1z7hqy4xgq2hfa457rs7p9d7fw5lmdh0zaf3n25rqv10ds1"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/alimpfard/line"))
-    (propagated-inputs
-     (list go-golang-org-x-sys))
-    (home-page "https://github.com/alimpfard/line")
-    (synopsis "Terminal line editor")
-    (description
-     "This package provides a full reimplementation of SerenityOS's LibLine in
-Go language.  It supports flexible autocompletion, live prompt, buffer update
-and stylisation, multiline editing and more.")
-    (license license:bsd-2)))
-
 (define-public go-github-com-alsm-ioprogress
   (package
     (name "go-github-com-alsm-ioprogress")
@@ -9826,37 +9770,6 @@ O(1) for @code{Set}, @code{Get}, @code{Delete} and @code{Len}.")
         #~(modify-phases %standard-phases
             (delete 'remove-submodule)))))))
 
-(define-public go-github-com-elliotchance-orderedmap-v3
-  (package
-    (name "go-github-com-elliotchance-orderedmap-v3")
-    (version "3.1.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/elliotchance/orderedmap")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1w681qsybcf34g0wn9hm6nnzc9jcdv59ahjiqdq9hs22xq0qgnjj"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      ;; Projects includes v1, v2 and v3 in the same source tree.
-      #:import-path "github.com/elliotchance/orderedmap/v3"
-      #:unpack-path "github.com/elliotchance/orderedmap"))
-    (native-inputs
-     (list go-github-com-stretchr-testify))
-    (home-page "https://github.com/elliotchance/orderedmap")
-    (synopsis "Ordered map in with amortized O(1) for Set, Get, Delete and Len")
-    (description
-     "An @code{*OrderedMap} is a high performance ordered map that maintains
-amortized O(1) for @code{Set}, @code{Get}, @code{Delete} and @code{Len}.
-Internally an @code{*OrderedMap} uses the composite type
-@url{https://go.dev/blog/maps, map} combined with a trimmed down linked list
-to maintain the order.")
-    (license license:expat)))
-
 (define-public go-github-com-elliotwutingfeng-asciiset
   (package
     (name "go-github-com-elliotwutingfeng-asciiset")
@@ -10189,36 +10102,6 @@ and @code{io.ReadCloser}) with overwrites
                     "  This package is a fork of dlclark/regexp2 providing a
 more similar API to regexp."))))
 
-(define-public go-github-com-esiqveland-notify
-  (package
-    (name "go-github-com-esiqveland-notify")
-    (version "0.13.3")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/esiqveland/notify")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "03d27a8rl55j6dqclg3233dj3j7v0i0p9cda06f9c4a21djamrfb"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/esiqveland/notify"))
-    (native-inputs
-     (list go-github-com-stretchr-testify))
-    (propagated-inputs
-     (list go-github-com-godbus-dbus-v5))
-    (home-page "https://github.com/esiqveland/notify")
-    (synopsis "Delivering desktop notifications over DBus")
-    (description
-     "Notify is a Go library for interacting with the DBus notification
-service defined by freedesktop.org at
-@url{https://developer.gnome.org/notification-spec/}.  Notify can deliver
-desktop notifications over DBus, ala how @code{libnotify} does it.")
-    (license license:bsd-3)))
-
 (define-public go-github-com-ettle-strcase
   (package
     (name "go-github-com-ettle-strcase")
@@ -11010,37 +10893,6 @@ library in go standard library.")
      "Go library that pluralizes and singularizes English nouns.")
     (license license:bsd-2)))
 
-(define-public go-github-com-gen2brain-beeep
-  (package
-    (name "go-github-com-gen2brain-beeep")
-    (version "0.11.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/gen2brain/beeep")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0jvfspz941r93djf83gsjqw8w9v34fa9dys1465iwbq769ayizmw"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/gen2brain/beeep"
-      #:test-flags #~(list "--skip" "TestAlert|TestNotify")))
-    (propagated-inputs
-     (list go-github-com-esiqveland-notify
-           go-github-com-godbus-dbus-v5
-           go-github-com-jackmordaunt-icns-v3
-           go-github-com-sergeymakinen-go-ico
-           go-golang-org-x-sys))
-    (home-page "https://github.com/gen2brain/beeep")
-    (synopsis "Sending desktop notifications, alerts and beeps")
-    (description
-     "Package beeep provides a cross-platform library for sending desktop
-notifications and beeps.")
-    (license license:bsd-2)))
-
 (define-public go-github-com-ghemawat-stream
   (package
     (name "go-github-com-ghemawat-stream")
@@ -29913,31 +29765,6 @@ utilities for cty Golang module.")
      "Package yaml can marshal and unmarshal cty values in YAML format.")
     (license license:asl2.0)))
 
-(define-public go-github-com-zeebo-bencode
-  (package
-    (name "go-github-com-zeebo-bencode")
-    (version "1.0.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/zeebo/bencode")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0c6bw1if1vbcr9l4684a4jdri8z31m8msjpp7z6y2p9s1jqjhkrp"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/zeebo/bencode"))
-    (home-page "https://github.com/zeebo/bencode")
-    (synopsis "Bencode marshal and unmarshal library")
-    (description
-     "This library implements encoding and decoding of
-@url{https://wiki.theory.org/BitTorrentSpecification#Bencoding, bencoded}
-objects.")
-    (license license:expat)))
-
 (define-public go-github-com-zeebo-errs
   (package
     (name "go-github-com-zeebo-errs")
@@ -30251,31 +30078,6 @@ connections.")
       "This package provides a pretty printing library for Golang values.")
     (license license:expat)))
 
-(define-public go-github-com-zyedidia-clipboard
-  (package
-    (name "go-github-com-zyedidia-clipboard")
-    (version "1.0.4")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/zyedidia/clipboard")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1nrs2ll6dh31wyzxh2zbykwvpavhlpzysfk6qgfj5s4rz6ck8glz"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:tests? #f      ;requires clipboard (xclip or xsel)
-      #:import-path "github.com/zyedidia/clipboard"))
-    (home-page "https://github.com/zyedidia/clipboard")
-    (synopsis "Clipboard for Golang")
-    (description
-     "Package clipboard read/write on clipboard.  It's an alternative fork of
-@url{https://github.com/atotto/clipboard}.")
-    (license license:bsd-3)))
-
 (define-public go-github-com-zyedidia-clipper
   (package
     (name "go-github-com-zyedidia-clipper")
@@ -30784,7 +30586,7 @@ Identifier (RFC3986) specification in Go.")
 (define-public go-go-mau-fi-util
   (package
     (name "go-go-mau-fi-util")
-    (version "0.9.9")
+    (version "0.8.4")
     (source
      (origin
        (method git-fetch)
@@ -30793,7 +30595,7 @@ Identifier (RFC3986) specification in Go.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1d6365n4j5hx172mi5f9rk49l7cgcbf8qvi721b0l34j2m036rsy"))))
+        (base32 "0zzkrbwgbxfppsxjck8qgj4xxzpiq25sx4p3zwjh6s1yz3kfb97p"))))
     (build-system go-build-system)
     (arguments
      (list

gnu/packages/graph.scm

@@ -55,7 +55,7 @@
   #:use-module (gnu packages cran)
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages docbook)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gd)
   #:use-module (gnu packages graphics)

gnu/packages/graphics.scm

@@ -78,7 +78,7 @@
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages documentation)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)

gnu/packages/groff.scm

@@ -37,7 +37,7 @@
   #:use-module (gnu packages bash)
   #:use-module (gnu packages ruby-xyz)
   #:use-module (gnu packages bison)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages netpbm)
   #:use-module (gnu packages perl)

gnu/packages/gstreamer.scm

@@ -56,7 +56,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages elf)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages ghostscript)

gnu/packages/guile-xyz.scm

@@ -4019,38 +4019,6 @@ with documentation.
     ;; details.
     (license license:gpl3+)))
 
-(define-public guile-scriba
-  (package
-    (name "guile-scriba")
-    (version "0.1.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://codeberg.org/jjba23/scriba.git")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1chhbhy21g6zghc3alpqhvb6nizylmzzapjariykv41f47ynhljs"))))
-    (build-system guile-build-system)
-    (arguments
-     (list
-      #:source-directory "src"))
-    (propagated-inputs (list guile-json-4))
-    (inputs (list guile-3.0))
-    (synopsis "Structured logging framework for Guile Scheme")
-    (description
-     "Scriba is a structured logging library for GNU Guile that prioritizes
-flexibility and observability.  It provides modular log routing, formatting,
-and filtering, allowing developers to generate human-readable console logs
-during development and machine-readable JSON logs for production environments.
-Key features include an auto-logger configured via environment variables,
-dynamically scoped log contexts using Scheme parameters, ahead-of-time log
-level filtering, and minimal runtime overhead achieved through memoization
-and compile-time macros.")
-    (home-page "https://codeberg.org/jjba23/scriba")
-    (license license:lgpl3+)))
-
 (define-public guile-simple-iterators
   (let ((commit "50f16a2b2aa57e657e52e19fb3c35bdc182cfa36")
         (revision "0"))
@@ -7558,7 +7526,7 @@ in a large number of randomly generated test cases.")
 (define-public guile-veritas
   (package
     (name "guile-veritas")
-    (version "0.3.0")
+    (version "0.1.6")
     (source
      (origin
        (method git-fetch)
@@ -7567,13 +7535,13 @@ in a large number of randomly generated test cases.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1i64pd5pcx37i25hnks7zj8pbwf1fdy0s5y9ic2sgn800zqq1dxy"))))
+        (base32 "1h4si2p8gj4wfhvn4cshga2kjxf59vd4nwvxkc2i3g5gv3kxhm3k"))))
     (build-system guile-build-system)
     (arguments
      (list
       #:source-directory "src"))
     (native-inputs (list guile-3.0))
-    (propagated-inputs (list guile-fibers guile-json-4))
+    (propagated-inputs (list guile-fibers))
     (home-page "https://codeberg.org/jjba23/veritas")
     (synopsis "Testing framework for Guile")
     (description

gnu/packages/guile.scm

@@ -44,7 +44,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages dbm)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gperf)

gnu/packages/hardware.scm

@@ -61,7 +61,7 @@
   #:use-module (gnu packages debian)
   #:use-module (gnu packages disk)
   #:use-module (gnu packages documentation)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)

gnu/packages/haskell.scm

@@ -52,7 +52,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages ghostscript)

gnu/packages/heads.scm

@@ -33,7 +33,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages m4)

gnu/packages/hurd.scm

@@ -38,7 +38,7 @@
   #:use-module (gnu packages cross-base)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages disk)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages bison)

gnu/packages/image-processing.scm

@@ -72,7 +72,7 @@
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages engineering)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages game-development)
   #:use-module (gnu packages gcc)
@@ -1521,7 +1521,7 @@ libraries designed for computer vision research and implementation.")
                     python
                     onetbb
                     vxl-1
-                    zlib-ng-compat))
+                    zlib))
       (native-inputs
        (list castxml
              git-minimal

gnu/packages/instrumentation.scm

@@ -34,7 +34,7 @@
   #:use-module (gnu packages elf)
   #:use-module (gnu packages engineering)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages glib)

gnu/packages/kde-frameworks.scm

@@ -58,7 +58,7 @@
   #:use-module (gnu packages databases)
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages ebook)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gl)

gnu/packages/kde-graphics.scm

@@ -57,7 +57,7 @@
   #:use-module (gnu packages djvu)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages ebook)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages fribidi)

gnu/packages/kde-pim.scm

@@ -46,7 +46,7 @@
   #:use-module (gnu packages cyrus-sasl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages documentation)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages geo)
   #:use-module (gnu packages glib)

gnu/packages/kde-sdk.scm

@@ -36,7 +36,7 @@
   #:use-module (guix packages)
   #:use-module (gnu packages)
   #:use-module (gnu packages bison)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages apr)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages code)

gnu/packages/kerberos.scm

@@ -36,7 +36,7 @@
   #:use-module (gnu packages bison)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages dbm)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
   #:use-module (gnu packages gettext)

gnu/packages/lego.scm

@@ -27,7 +27,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages qt))
 

gnu/packages/lesstif.scm

@@ -25,7 +25,7 @@
   #:use-module (guix git-download)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages c)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages pkg-config)

gnu/packages/libreoffice.scm

@@ -59,7 +59,7 @@
   #:use-module (gnu packages databases)
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages documentation)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages game-development)

gnu/packages/librewolf.scm

@@ -125,14 +125,14 @@
   ;; ex:
   ;; tar xf /gnu/store/...-firefox-123.4.source.tar.xz -O \
   ;;     firefox-123.4/browser/locales/l10n-changesets.json | grep revision
-  (let ((commit "a867076ab29cc0777b14d0448707629cdb825d81"))
+  (let ((commit "a8799feda04a221a2c552576501975662c5350bb"))
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/mozilla-l10n/firefox-l10n.git")
             (commit commit)))
       (file-name (git-file-name "firefox-l10n" commit))
-      (sha256 (base32 "1j6gzzq1y5nx7iv3p173fmc4b87d5lwb0hnaiq1lmc6ryjnzk3wm")))))
+      (sha256 (base32 "1625rh1w5fdq6nl7fpwgiln29hkqcj0zksmnwcfj34y5cvhwrq2z")))))
 
 (define* (make-librewolf-source #:key version firefox-hash librewolf-hash l10n)
   (let* ((ff-src (firefox-source-origin
@@ -244,17 +244,17 @@
 ;; It's used for cache validation and therefore can lead to strange bugs.
 ;; ex: date '+%Y%m%d%H%M%S'
 ;; or: (format-time-string "%Y%m%d%H%M%S")
-(define %librewolf-build-id "20260527211539")
+(define %librewolf-build-id "20260524201108")
 
 (define-public librewolf
   (package
     (name "librewolf")
-    (version "151.0.2-1")
+    (version "151.0.1-2")
     (source
      (make-librewolf-source
       #:version version
-      #:firefox-hash "1j7q00fwdijvg5b01jmadhqabwmwdcqd15srmkbqsqgjk5vjdi33"
+      #:firefox-hash "1h440pkdqkx3085ij9nz9n9h1b6c2p92bg3lf983my6b711f62m8"
-      #:librewolf-hash "0fm11phcpp2xggwdhdl044f4a015adg8bplw4cj0in5hq1zqkbi2"
+      #:librewolf-hash "1hy4p1336igy8p73hrgvmv7krbr15ap9ain79n340d3sapqkhbg8"
       #:l10n firefox-l10n))
     (build-system gnu-build-system)
     (arguments

gnu/packages/lighting.scm

@@ -29,7 +29,7 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gnunet)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages libftdi)
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages linux)

gnu/packages/linux.scm

@@ -135,7 +135,7 @@
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gawk)
@@ -1218,12 +1218,6 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
                        "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
                      #:configuration-file kernel-config))
 
-(define-public linux-libre-version         linux-libre-7.0-version)
-(define-public linux-libre-gnu-revision    linux-libre-7.0-gnu-revision)
-(define-public linux-libre-pristine-source linux-libre-7.0-pristine-source)
-(define-public linux-libre-source          linux-libre-7.0-source)
-(define-public linux-libre                 linux-libre-7.0)
-
 (define-public linux-libre-6.19
   (make-linux-libre* linux-libre-6.19-version
                      linux-libre-6.19-gnu-revision
@@ -1240,6 +1234,12 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
                        "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
                      #:configuration-file kernel-config))
 
+(define-public linux-libre-version         linux-libre-6.18-version)
+(define-public linux-libre-gnu-revision    linux-libre-6.18-gnu-revision)
+(define-public linux-libre-pristine-source linux-libre-6.18-pristine-source)
+(define-public linux-libre-source          linux-libre-6.18-source)
+(define-public linux-libre                 linux-libre-6.18)
+
 (define-public linux-libre-6.12
   (make-linux-libre* linux-libre-6.12-version
                      linux-libre-6.12-gnu-revision
@@ -1979,8 +1979,6 @@ dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-reform2-dsi.dtb
 dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-reform-next.dtb
 dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-pocket-reform.dtb")))))))))))
 
-(define-public linux-libre-arm64-mnt-reform linux-libre-arm64-mnt-reform-7.0)
-
 (define-public linux-libre-arm64-mnt-reform-6.19
   ;; Kernel for use on the MNT/Reform systems
   ;; https://mntre.com/reform.html
@@ -2317,6 +2315,8 @@ dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-reform2-dsi.dtb
 dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-reform-next.dtb
 dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-pocket-reform.dtb")))))))))))
 
+(define-public linux-libre-arm64-mnt-reform linux-libre-arm64-mnt-reform-6.18)
+
 (define-public linux-libre-arm64-mnt-reform-6.12
   ;; Kernel for use on the MNT/Reform systems
   ;; https://mntre.com/reform.html

gnu/packages/logging.scm

@@ -46,7 +46,7 @@
   #:use-module (gnu packages curl)
   #:use-module (gnu packages cyrus-sasl)
   #:use-module (gnu packages databases)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages geo)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages kerberos)

gnu/packages/lua.scm

@@ -77,7 +77,7 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages rdf)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages re2c)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages rsync)
   #:use-module (gnu packages ssh)

gnu/packages/machine-learning.scm

@@ -210,7 +210,7 @@ representations and sentence classification.")
 (define-public ggml
   (package
     (name "ggml")
-    (version "0.13.0")                  ;sync with llama.cpp
+    (version "0.12.0")                  ;sync with llama.cpp
     (source
      (origin
        (method git-fetch)
@@ -219,12 +219,12 @@ representations and sentence classification.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "089lxkq086s520700hs962i89nvh4j1gr5fdj1md7fixx7v7yiy9"))))
+        (base32 "19y1id0j2slbfrjb4ycjvqisa3sfvpngpc1r3z1bmv3z9kbkj6n6"))))
     (build-system cmake-build-system)
     (arguments
      (list
       #:configure-flags
-      #~(list #$(string-append "-DGGML_BUILD_COMMIT=" version)
+      #~(list #$(string-append "-DGGML_BUILD_NUMBER=" version)
               "-DBUILD_SHARED_LIBS_DEFAULT=ON"
               "-DGGML_BACKEND_DL=ON"
               (string-append "-DGGML_BACKEND_DIR="
@@ -872,7 +872,7 @@ NumPy @code{dtype} extensions used in machine learning libraries, including:
     (license license:asl2.0)))
 
 (define-public llama-cpp
-  (let ((tag "9353"))                  ;sync with ggml and python-gguf
+  (let ((tag "9276"))                  ;sync with ggml and python-gguf
     (package
       (name "llama-cpp")
       (version (string-append "0.0.0-" tag))
@@ -884,7 +884,7 @@ NumPy @code{dtype} extensions used in machine learning libraries, including:
                (commit (string-append "b" tag))))
          (file-name (git-file-name name tag))
          (sha256
-          (base32 "0f942ngvkbk36763kmf3pvfy4hkqy4k806dnhs0mvs2l3gkxw6a1"))))
+          (base32 "07f23yiy2q0xrpfbkcvn9gs2adb3zmqyllih0kqklxa7vvmsmw1r"))))
       (build-system cmake-build-system)
       (arguments
        (list
@@ -897,27 +897,16 @@ NumPy @code{dtype} extensions used in machine learning libraries, including:
         #:configure-flags
         #~(list "-DBUILD_SHARED_LIBS=ON"
                 "-DLLAMA_USE_SYSTEM_GGML=ON"
-                #$(string-append "-DLLAMA_BUILD_NUMBER=" tag))
+                #$(string-append "-DLLAMA_BUILD_NUMBER=" tag)
+                ;; See https://github.com/ggml-org/llama.cpp/issues/23105
+                "-DLLAMA_BUILD_UI=OFF")
         #:phases
         #~(modify-phases %standard-phases
-            ;; See :
-            ;; llama.cpp/issues/23105#issuecomment-4531264818
-            (add-before 'build 'get-ui
-              (lambda _
-                (with-directory-excursion "tools/ui"
-                  (copy-file #$(this-package-input "ui.tar.gz") "ui.tar.gz")
-                  (invoke "tar" "xvf" "ui.tar.gz")
-                  (rename-file "llama-b9353" "dist"))))
             (add-after 'unpack 'fix-tests
               (lambda _
                 ;; test-thread-safety downloads ML model from network,
                 ;; cannot run in Guix build environment
                 (substitute* '("tests/CMakeLists.txt")
-                  (("llama_build_and_test\\(test-save-load-state.cpp.*")
-                   "")
-                  (("set_tests_properties\\(test-save-load-state.*")
-                   "")
-
                   (("llama_build_and_test\\(test-thread-safety.cpp.*")
                    "")
                   (("set_tests_properties\\(test-thread-safety.*")
@@ -957,16 +946,7 @@ NumPy @code{dtype} extensions used in machine learning libraries, including:
                 (for-each delete-file
                           (find-files (string-append #$output "/bin")
                                       "^test-")))))))
-      (inputs
+      (inputs (list ggml openssl))
-       (list ggml openssl
-             (origin
-               (method url-fetch)
-               (uri
-                (format #f "~a/releases/download/b~a/llama-b~a-ui.tar.gz"
-                        "https://github.com/ggml-org/llama.cpp" tag tag))
-               (file-name "ui.tar.gz")
-               (sha256
-                (base32 "1rqgq5nfw0wbym3gz2ivhrpl69b4fpl6my6nnnr1cbdd6x1mvz44")))))
       (native-inputs
        ;; These are only used in the check phase for test-jinja-py
        (list python-minimal-wrapper python-jinja2))

gnu/packages/mail.scm

@@ -117,7 +117,7 @@
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages enchant)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gawk)

gnu/packages/man.scm

@@ -47,7 +47,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages dbm)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gettext)

gnu/packages/maths.scm

@@ -141,7 +141,7 @@
   #:use-module (gnu packages elf)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fltk)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
@@ -11732,35 +11732,3 @@ use the library and researchers to make new capabilities available under a
 common interface.
 ")
     (license license:bsd-3)))
-
-(define-public xdmf
-  (package
-    (name "xdmf")
-    ;; Project does not publish releases / tags
-    (properties '((commit . "04a84bab0eb1568e0f1a27c8fb60c6931efda003")
-                  (revision . "0")))
-    (version (git-version "3.0.0"
-                          (assoc-ref properties 'revision)
-                          (assoc-ref properties 'commit)))
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://gitlab.kitware.com/xdmf/xdmf")
-              (commit (assoc-ref properties 'commit))))
-       (file-name (git-file-name name version))
-       (patches
-        (search-patches "xdmf-3.0.0-hdf5.patch"))
-       (sha256
-        (base32 "06k4vibkvgxlzkn06x470aq5q18p7yhql8awrpdz3czys3z8i288"))))
-    (build-system cmake-build-system)
-    (arguments
-     (list #:tests? #f)) ;has no tests
-    (inputs
-     (list boost hdf5 libxml2))
-    (home-page "https://www.xdmf.org/index.html")
-    (synopsis "XDMF library")
-    (description
-     "This package provides the eXtensible Data Model and Format (XDMF) C++
-library.")
-    (license license:bsd-4)))

gnu/packages/matrix.scm

@@ -11,7 +11,6 @@
 ;;; Copyright © 2025 Arjan Adriaanse <arjan@adriaan.se>
 ;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2026 Zheng Junjie <z572@z572.online>
-;;; Copyright © 2026 orahcio <orahcio@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -60,7 +59,7 @@
 (define-public mautrix-whatsapp
   (package
     (name "mautrix-whatsapp")
-    (version "0.2605.0")
+    (version "0.11.2")
     (source
      (origin
        (method git-fetch)
@@ -69,7 +68,7 @@
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "02gmzby57vn5cc23m2laqcqqkvghlabm08fzjzqfzx8g18cmymas"))))
+        (base32 "0wn9kldhh865w5mbg3cl61m0db9nr7zl1j8lqs2dixsaihv1lbnx"))))
     (build-system go-build-system)
     (arguments
      (list
@@ -106,13 +105,7 @@
          ;; go.mau.fi/webp/webp.go:14:12: pattern internal: cannot embed
          ;; directory internal: contains no embeddable files
          ".*\\.c"
-         ".*\\.h"
+         ".*\\.h")))
-         ;; go.mau.fi/whatsmeow/argo/argo.go:16:13:
-         ;; pattern argo-wire-type-store.argo: cannot embed
-         ".*\\.argo"
-         ;; go.mau.fi/whatsmeow/argo/argo.go:19:13:
-         ;; pattern name-to-queryids.json: cannot embed
-         ".*\\.json")))
     (native-inputs
      (list olm
            go-github-com-gorilla-mux

gnu/packages/messaging.scm

@@ -47,7 +47,6 @@
 ;;; Copyright © 2025 Evgeny Pisemsky <mail@pisemsky.site>
 ;;; Copyright © 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2025 Adrien 'neox' Bourmault <neox@gnu.org>
-;;; Copyright © 2026 orahcio <orahcio@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3460,56 +3459,6 @@ a persistent connection to an IRC server, acting as a proxy and buffer for
 a number of clients.")
     (license license:gpl3+)))
 
-(define-public whatscli
-  (package
-    (name "whatscli")
-    (version "1.1.4")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/normen/whatscli")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0ijp0783h4hivj33qi10azhq1bl512jq1wrva2alpkv7wp4qhnw6"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:install-source? #f
-      #:import-path "github.com/normen/whatscli"
-      #:embed-files #~(list ".*\\.argo" ".*\\.json" ".*\\.sql")))
-    (native-inputs
-     (list go-code-rocketnine-space-tslocum-cbind
-           go-github-com-adrg-xdg
-           go-github-com-gdamore-tcell-v2
-           go-github-com-gen2brain-beeep
-           go-github-com-mattn-go-colorable
-           go-github-com-mattn-go-sqlite3
-           go-github-com-rivo-tview
-           go-github-com-skip2-go-qrcode
-           go-github-com-skratchdot-open-golang
-           go-github-com-zyedidia-clipboard
-           go-go-mau-fi-whatsmeow
-           go-google-golang-org-protobuf
-           go-gopkg-in-ini-v1))
-    (home-page "https://github.com/normen/whatscli")
-    (synopsis "Command line interface for WhatsApp")
-    (description
-     "WhatsCLI is a command-line interface for WhatsApp that connects
-through the Web App API without requiring a browser.  It provides a
-terminal-based user interface built with tview, featuring:
-@itemize
-@item Sending and receiving WhatsApp messages in a terminal
-@item QR code setup for simple authentication
-@item Downloading and opening image, video, audio, and document attachments
-@item Sending images, video, audio, and document attachments
-@item Basic group management capabilities
-@item Desktop notifications support
-@item Color customization options
-@end itemize")
-    (license license:expat)))
-
 (define-public weechat-wee-slack
   (package
     (name "weechat-wee-slack")

gnu/packages/mpi.scm

@@ -46,7 +46,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages fabric-management)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages java)
   #:use-module (gnu packages libevent)

gnu/packages/multiprecision.scm

@@ -32,7 +32,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages bison)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages m4)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages texinfo)

gnu/packages/music.scm

@@ -133,7 +133,7 @@
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fltk)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)

gnu/packages/musl.scm

@@ -31,16 +31,14 @@
 (define-public musl
   (package
     (name "musl")
-    (version "1.2.6")
+    (version "1.2.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.musl-libc.org/releases/"
                                   "musl-" version ".tar.gz"))
               (sha256
                (base32
-                "0ajic0jgiyfk2sk3brn1wsshq0kp9za8x7i4qcgiariwc4xzv1fm"))
+                "1r3mgky9d19b2285s274qxzlgs7sncx8plm01vd691sdx2xii8d9"))))
-              (patches
-               (search-patches "musl-CVE-2026-40200.patch"))))
     (build-system gnu-build-system)
     (arguments
      (list #:tests? #f                      ; musl has no tests