gnu: linux-libre: Update default version to 7.0.

* gnu/packages/linux.scm (linux-libre-version, linux-libre-gnu-revision,
linux-libre-pristine-source, linux-libre-source, linux-libre,
linux-libre-arm64-mnt-reform): Update to 7.0.

.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
-                         ;; #8545 (issues), !8545 (PRs), guix/guix#8545 and
-                         ;; guix/guix!8545
-                         (rx (group (seq (? "guix/guix") (or "#" "!"))
-                                    (group (one-or-more digit))))))
+     (eval . (setq-local
+              ;; #8545, guix/guix#8545, guix/guix!8545, but not !8545
+              bug-reference-bug-regexp
+              (rx (group (or (seq (zero-or-more "guix/guix") "#")
+                             (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"))

CODEOWNERS

@@ -292,12 +292,12 @@ guix/build-system/julia\.scm                       @guix/julia
 
 gnu/packages/(kde)(-.+|)\.scm$                     @guix/kde
 
-gnu/build/linux-modules\.scm                       @guix/linux-libre
-gnu/packages/aux-files/linux-libre.*$              @guix/linux-libre
-gnu/packages/linux\.scm                            @guix/linux-libre
-gnu/tests/linux-modules\.scm                       @guix/linux-libre
-guix/build/linux-module-build-system\.scm          @guix/linux-libre
-guix/build-system/linux-module\.scm                @guix/linux-libre
+gnu/build/linux-modules\.scm                       @guix/kernel
+gnu/packages/aux-files/linux-libre.*$              @guix/kernel
+gnu/packages/linux\.scm                            @guix/kernel
+gnu/tests/linux-modules\.scm                       @guix/kernel
+guix/build/linux-module-build-system\.scm          @guix/kernel
+guix/build-system/linux-module\.scm                @guix/kernel
 
 gnu/packages/lisp(-.+|)\.scm$                      @guix/lisp
 guix/build/asdf-build-system\.scm                  @guix/lisp

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 \

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
-  echo "cannot strip comments from $1"
-  exit 1
+if ! cat "$1" | sed -e '/>8/q' | git stripspace --strip-comments > "${dest}" ; then
+   echo "cannot strip comments from $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

etc/teams.scm

@@ -876,8 +876,8 @@ and the maven-build-system."
         "The plasma desktop environment, and KDE Applications."
         #:scope (list (make-regexp* "^gnu/packages/(kde)(-.+|)\\.scm$"))))
 
-(define-team linux-libre
-  (team 'linux-libre
+(define-team kernel
+  (team 'kernel
         #:name "Linux-libre kernel team"
         #:scope (list "gnu/build/linux-modules.scm"
                       (make-regexp* "^gnu/packages/aux-files/linux-libre.*$")
@@ -1298,7 +1298,7 @@ the \"texlive\" importer."
 (define-member (person "Leo Famulari"
                        "leo@famulari.name"
                        "lfam")
-  linux-libre)
+  kernel)
 
 (define-member (person "Efraim Flashner"
                        "efraim@flashner.co.il"
@@ -1383,7 +1383,7 @@ the \"texlive\" importer."
 (define-member (person "Vagrant Cascadian"
                        "vagrant@debian.org"
                        "vagrantc")
-  debian embedded linux-libre)
+  debian embedded kernel)
 
 (define-member (person "Vagrant Cascadian"        ;XXX: duplicate
                        "vagrant@reproducible-builds.org"
@@ -1537,7 +1537,7 @@ the \"texlive\" importer."
 (define-member (person "Rodion Goritskov"
                        "rodion@goritskov.com"
                        "rodion-goritskov")
-  games java kde linux-libre release)
+  games java kde kernel release)
 
 (define-member (person "Jason Conroy"
                        "jconroy@tscripta.net"
@@ -1622,7 +1622,7 @@ the \"texlive\" importer."
 (define-member (person "Wilko Meyer"
                        "w@wmeyer.eu"
                        "theesm")
-  linux-libre perl)
+  kernel perl)
 
 (define-member (person "Untrusem"
                        "mysticmoksh@riseup.net"

gnu/local.mk

@@ -1527,6 +1527,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gnumach-version.patch			\
   %D%/packages/patches/gnupg-default-pinentry.patch		\
   %D%/packages/patches/gnupg-1-build-with-gcc10.patch		\
+  %D%/packages/patches/gnutls-no-which.patch			\
   %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \
   %D%/packages/patches/gobject-introspection-cc.patch		\
   %D%/packages/patches/gobject-introspection-girepository.patch	\
@@ -1966,7 +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		\
@@ -2116,6 +2117,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-clarabel-blas.patch		\
   %D%/packages/patches/python-daemon-relax-lockfile.patch	\
   %D%/packages/patches/python-docrepr-fix-tests.patch		\
+  %D%/packages/patches/python-gpg-setup-72.patch                \
   %D%/packages/patches/python-hdmedians-replace-nose.patch	\
   %D%/packages/patches/python-jinja2-fragments-modify-conftest-py.patch	\
   %D%/packages/patches/python-louvain-fix-test.patch		\
@@ -2366,8 +2368,16 @@ dist_patch_DATA =						\
   %D%/packages/patches/renpy-fix-integer-slots.patch			\
   %D%/packages/patches/reposurgeon-add-missing-docbook-files.patch	\
   %D%/packages/patches/rdkit-unbundle-external-dependencies.patch	\
+  %D%/packages/patches/r-biostrings-r4.6.0-compat.patch		\
+  %D%/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch \
   %D%/packages/patches/r-httpuv-1.6.6-unvendor-libuv.patch	\
+  %D%/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch \
+  %D%/packages/patches/r-rsamtools-r-4.6.0-compat.patch		\
+  %D%/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch \
+  %D%/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch \
   %D%/packages/patches/r-sapa-lapack.patch			\
+  %D%/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch \
+  %D%/packages/patches/r-sparsearray-r-4.6.0-compat.patch	\
   %D%/packages/patches/ripperx-missing-file.patch		\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
   %D%/packages/patches/rtosc-0.3.1-fix-invalid-comparison-operator.patch	\
@@ -2452,7 +2462,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/shared-mime-info-xdgmime-path.patch	\
   %D%/packages/patches/sharutils-CVE-2018-1000097.patch		\
   %D%/packages/patches/showtime-python-3.11-compat.patch        \
-  %D%/packages/patches/simpleitk-r-4.6.0.patch			\
   %D%/packages/patches/sipwitch-fix-build-with-exosip5.patch	\
   %D%/packages/patches/slim-config.patch			\
   %D%/packages/patches/slim-gcc-14.patch			\
@@ -2487,7 +2496,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/swift-corelibs-libdispatch-5.7.3-modulemap.patch	\
   %D%/packages/patches/swift-llvm-5.7.3-linux.patch	\
   %D%/packages/patches/swig-support-gcc-12.patch		\
-  %D%/packages/patches/swig-support-r-4.6.0.patch		\
   %D%/packages/patches/swish-e-search.patch			\
   %D%/packages/patches/swish-e-format-security.patch		\
   %D%/packages/patches/t1lib-CVE-2010-2642.patch		\

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)
@@ -2135,17 +2135,7 @@ envelope follower, distortion effects, tape effects and more.")
 	        (base32
                  "01hnx4hhbz3ap3bw15s42q4q1mw1mhdjwygq4550wvjfg6k4ga8w"))))
       (build-system waf-build-system)
-      (arguments
-       (list
-        #:tests? #false ;There are no tests.
-        #:phases
-        '(modify-phases %standard-phases
-           (add-after 'unpack 'python3.12-compatibility
-             (lambda _
-               (substitute* "waflib/Context.py"
-                 (("imp.new_module") "types.ModuleType")
-                 (("import os, re, imp, sys")
-                  "import os, re, types, sys")))))))
+      (arguments (list #:tests? #false)) ;There are no tests.
       (inputs (list lv2))
       (native-inputs (list pkg-config))
       (home-page "https://git.drobilla.net/cgit.cgi/omins.lv2.git/")

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)
@@ -1430,86 +1430,33 @@ within this package are the 3000 bone marrow cells used for vignettes.")
       (license license:gpl3))))
 
 (define-public r-pizzarr
-  (package
-    (name "r-pizzarr")
-    (version "0.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/keller-mark/pizzarr")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1m38c57pfliycxkhb3mwgh01cl2q76r1jhd3vnk07dbfhqdbqai6"))))
-    (properties `((upstream-name . "pizzarr")))
-    (build-system cargo-build-system)
-    (arguments
-     (list
-      #:imported-modules
-      (append %cargo-build-system-modules
-              %r-build-system-modules)
-      #:modules
-      '((guix build cargo-build-system)
-        ((guix build r-build-system) #:prefix r:)
-        (guix build utils))
-      #:cargo-build-flags
-      '(list "--target-dir=./target" "--release")
-      #:phases
-      #~(append (modify-phases %standard-phases
-                  (add-after 'unpack 'patch-Makevars
-                    (lambda _
-                      ;; At this point we've already built the Rust parts.
-                      (substitute* "src/Makevars.in"
-                        (("^all:.*") "all:")
-                        (("^\\$\\(STATLIB\\):") "NOBODYCARES:")
-                        (("@PKG_LIBS_EXTRA@") "@PKG_LIBS_EXTRA@ -lzstd -lz"))))
-                  (add-after 'patch-Makevars 'chdir
-                    (lambda _ (chdir "src/rust")))
-                  (add-after 'chdir 'patch-rust-dependency
-                    (lambda _
-                      (setenv "RUSTFLAGS" "--print=native-static-libs")
-                      (substitute* "Cargo.toml"
-                        (("extendr-api = \\{ git.* \\}") "extendr-api = \"0.8.1\""))))
-                  (add-after 'package 'chdir-back
-                    (lambda _ (chdir "../..")))
-                  (delete 'install)
-                  (delete 'check))
-                (modify-phases (@ (guix build r-build-system) %standard-phases)
-                  (delete 'unpack)
-                  (replace 'patch-tests
-                    (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-                      ((assoc-ref (@ (guix build r-build-system) %standard-phases)
-                                  'patch-tests)
-                       #:skipped-tests
-                       ;; These files contain tests that require Internet access.
-                       '("test-compat.R" "test-get.R"
-                         ;; HttpStore requires the crul package
-                         ("test-zarrs-dispatch.R" "can_use_zarrs_create returns FALSE for HttpStore")
-                         ("test-zarrs-store-cache.R" "HttpStore get_store_identifier returns URL")))))
-                  (replace 'check
-                    (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-                      ((assoc-ref (@ (guix build r-build-system) %standard-phases)
-                                  'check)
-                       #:test-target "tests"
-                       #:test-types #false
-                       #:inputs inputs
-                       #:outputs outputs
-                       #:tests? tests?)))))))
-    (propagated-inputs (list r-jsonlite r-memoise r-qs2 r-r6 r-stringr))
-    (inputs
-     (cons* openssl zlib `(,zstd "lib")
-            (cargo-inputs 'r-pizzarr)))
-    (native-inputs
-     (list pkg-config
-           r-minimal r-pbapply r-testthat r-vcr))
-    (home-page "https://github.com/keller-mark/pizzarr")
-    (synopsis "Slice into Zarr arrays in R")
-    (description
-     "This package provides an implementation of chunked, compressed,
+  (let ((commit "5f4705789ba29344dcb97023f290a26a7f7abd0c")
+        (revision "2"))
+    (package
+      (name "r-pizzarr")
+      (version (git-version "0.1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/keller-mark/pizzarr")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "17pd6bk8kvnrvvyfqvm8q47kzghlfyfjdd9b7cwiazc5xr4vz6f0"))))
+      (properties `((upstream-name . "pizzarr")))
+      (build-system r-build-system)
+      ;; Some tests require Internet access.
+      (arguments (list #:tests? #false))
+      (propagated-inputs (list r-jsonlite r-memoise r-qs r-r6 r-stringr))
+      (native-inputs (list r-pbapply r-testthat r-vcr))
+      (home-page "https://github.com/keller-mark/pizzarr")
+      (synopsis "Slice into Zarr arrays in R")
+      (description
+       "This package provides an implementation of chunked, compressed,
 N-dimensional arrays for R, Zarr specification version 2 (2024)
 <doi:10.5281/zenodo.11320255>.")
-    (license license:expat)))
+      (license license:expat))))
 
 (define-public r-rhtslib12
   (let ((commit "ee186daf04876969c7f31c16a0e0fda8e7c16a30")
@@ -4625,11 +4572,8 @@ into separate processes; and more.")
      (list
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'python3.12-compatibility
+          (add-after 'unpack 'python3.11-compatibility
             (lambda _
-              ;; This was removed in Python 3.12
-              (substitute* "Bio/Align/_aligners.c"
-                (("case PyUnicode_WCHAR_KIND:") ""))
               ;; Py_TYPE was changed to an inline static function in Python
               ;; 3.11, so it cannot be used on the left-hand side.
               (substitute* "Bio/triemodule.c"
@@ -6710,20 +6654,20 @@ 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"
-               (string-append "prefix=" #$output))
+       ,#~(list "CC=gcc"
+                (string-append "prefix=" #$output))
        #:phases
-       #~(modify-phases %standard-phases
+       (modify-phases %standard-phases
          (delete 'configure))))
     (inputs
      (list zlib curl))
     (native-inputs
-     (list doxygen
-           python)) ;for tests
+     `(("doxygen" ,doxygen)
+       ;; Need for tests
+       ("python" ,python-2)))
     (home-page "https://github.com/dpryan79/libBigWig")
     (synopsis "C library for handling bigWig files")
     (description
@@ -14046,20 +13990,33 @@ of scRNA-seq data.")
 (define-public r-misha
   (package
     (name "r-misha")
-    (version "5.6.23")
+    (version "4.1.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/tanaylab/misha")
-             (commit (string-append "v" version))))
+             (commit version)))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1k973j04iq02dy4f7qgi3cmp3rcx5yinyx0m7vyag54rqanird8x"))))
+         "0bgivx3lzjh3173jsfrhb5kvhjsn53br0n4hmyx7i3dwy2cnnp2p"))
+       ;; Delete bundled executable.
+       (snippet
+        '(delete-file "exec/bigWigToWig"))))
     (build-system r-build-system)
-    (propagated-inputs (list r-curl r-digest r-magrittr r-ps r-yaml))
-    (native-inputs (list r-knitr r-testthat))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-use-bundled-bigWigToWig
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "R/misha.R"
+               (("get\\(\".GLIBDIR\"\\), \"/exec/bigWigToWig")
+                (string-append "\""
+                               (assoc-ref inputs "kentutils")
+                               "/bin/bigWigToWig"))))))))
+    (inputs
+     (list kentutils))
     (home-page "https://github.com/tanaylab/misha")
     (synopsis "Toolkit for analysis of genomic data")
     (description "This package is intended to help users to efficiently
@@ -17839,99 +17796,94 @@ once.  This package provides tools to perform Drop-seq analyses.")
     (license license:expat)))
 
 (define-public pigx-rnaseq
-  (let ((commit "1605b541da090e13d58dae6fed38ae8dda09f002"))
-    (package
-      (name "pigx-rnaseq")
-      (version (git-version "0.1.1" "0" commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/BIMSBbioinfo/pigx_rnaseq/")
-                       (commit commit)
-                       (recursive? #true)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "1j5c0wlasmxvz9z64yga56m2hhbybl149kknsrpvmq0v2gl31rn5"))))
-      (build-system gnu-build-system)
-      (arguments
-       (list
-        #:parallel-tests? #f             ; not supported
-        #:phases
-        '(modify-phases %standard-phases
-           ;; "test.sh" runs the whole pipeline, which takes a long time and
-           ;; might fail due to OOM.  The MultiQC is also resource intensive.
-           (add-after 'unpack 'disable-resource-intensive-test
-             (lambda _
-               (substitute* "Makefile.am"
-                 (("^  tests/test_multiqc/test.sh.*") "")
-                 (("^  tests/test_hisat2/test.sh.*") "  tests/test_hisat2/test.sh\n")
-                 (("^  test.sh") ""))))
-           (add-before 'bootstrap 'autoreconf
-             (lambda _
-               (invoke "autoreconf" "-vif")))
-           (add-before 'configure 'set-PYTHONPATH
-             (lambda _
-               (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
-           (add-before 'check 'set-timezone
-             ;; The readr package is picky about timezones.
-             (lambda* (#:key inputs #:allow-other-keys)
-               (setenv "TZ" "UTC+1")
-               (setenv "TZDIR"
-                       (search-input-directory inputs
-                                               "share/zoneinfo"))))
-           (add-before 'check 'pre-check
-             (lambda _
-               ;; Needed for tests
-               (setenv "HOME" "/tmp"))))))
-      (inputs
-       (list coreutils
-             sed
-             gzip
-             snakemake
-             megadepth
-             multiqc
-             star-for-pigx
-             hisat2
-             fastp
-             htseq
-             samtools
-             r-minimal
-             r-rmarkdown
-             r-genomeinfodb
-             r-ggplot2
-             r-ggpubr
-             r-ggrepel
-             r-gprofiler2
-             r-deseq2
-             r-dt
-             r-knitr
-             r-pheatmap
-             r-corrplot
-             r-reshape2
-             r-plotly
-             r-scales
-             r-summarizedexperiment
-             r-crosstalk
-             r-tximport
-             r-rtracklayer
-             r-rjson
-             salmon
-             pandoc
-             python-wrapper
-             python-deeptools
-             python-pyyaml))
-      (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
+  (package
+    (name "pigx-rnaseq")
+    (version "0.1.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
+                                  "releases/download/v" version
+                                  "/pigx_rnaseq-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0mlas0srl04mvgsyydm67gg5syijf1k2f6dy7bdqqxc70fywfd08"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:parallel-tests? #f             ; not supported
+       #:phases
+       (modify-phases %standard-phases
+         ;; "test.sh" runs the whole pipeline, which takes a long time and
+         ;; might fail due to OOM.  The MultiQC is also resource intensive.
+         (add-after 'unpack 'disable-resource-intensive-test
+           (lambda _
+             (substitute* "Makefile.in"
+               (("^  tests/test_multiqc/test.sh") "")
+               (("^  test.sh") ""))))
+         (add-before 'bootstrap 'autoreconf
+           (lambda _
+             (invoke "autoreconf" "-vif")))
+         (add-before 'configure 'set-PYTHONPATH
+           (lambda _
+             (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
+         (add-before 'check 'set-timezone
+           ;; The readr package is picky about timezones.
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "TZ" "UTC+1")
+             (setenv "TZDIR"
+                     (search-input-directory inputs
+                                             "share/zoneinfo"))))
+         (add-before 'check 'pre-check
+           (lambda _
+             ;; Needed for tests
+             (setenv "HOME" "/tmp"))))))
+    (inputs
+     (list coreutils
+           sed
+           gzip
+           snakemake-7
+           megadepth
+           multiqc
+           star-for-pigx
+           hisat2
+           fastp
+           htseq
+           samtools
+           r-minimal
+           r-rmarkdown
+           r-genomeinfodb
+           r-ggplot2
+           r-ggpubr
+           r-ggrepel
+           r-gprofiler2
+           r-deseq2
+           r-dt
+           r-knitr
+           r-pheatmap
+           r-corrplot
+           r-reshape2
+           r-plotly
+           r-scales
+           r-summarizedexperiment
+           r-crosstalk
+           r-tximport
+           r-rtracklayer
+           r-rjson
+           salmon
+           pandoc
+           python-wrapper
+           python-deeptools
+           python-pyyaml))
+    (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
@@ -18137,7 +18089,7 @@ methylation and segmentation.")
            python-loompy
            pandoc
            samtools
-           snakemake-6
+           snakemake-5
            star-for-pigx
            r-minimal
            r-argparser
@@ -18864,28 +18816,26 @@ activity prediction from transcriptomics data, and its R implementation
       (build-system r-build-system)
       (arguments
        (list
-        #:skipped-tests
-        ;; These tests attempt to connect to the Internet.
-        '(("test-liana_utils.R" "Test liana pipe")
-          ("test-liana_tensor.R"
-           ".*Test tensor wrapper.*"
-           ".*Test decompose_tensor.*")
-          ;; XXX: This test returns a data.frame instead of an error.
-          ("test-liana_cytotalk.R" ".*Test Cytotalk Wrap.*"))
         #:phases
         '(modify-phases %standard-phases
            ;; This is needed to find ~/.config/OmnipathR/omnipathr.yml
            (add-after 'unpack 'set-HOME
              (lambda _ (setenv "HOME" "/tmp")))
-           (add-after 'unpack 'seurat-compatibility
+           (add-after 'unpack 'disable-bad-tests
              (lambda _
-               ;; The `slot` argument of `GetAssayData()` was deprecated in
-               ;; SeuratObject 5.0.0.
-               (substitute* '("R/cellchat_pipe.R"
-                              "R/sca_pipe.R"
-                              "R/liana_prep.R"
-                              "R/natmi_pipe.R")
-                 (("slot =") "layer =")))))))
+               ;; These tests attempt to connect to the Internet.
+               (substitute* "tests/testthat/test-liana_utils.R"
+                 ((".*Test liana pipe.*" m)
+                  (string-append m "skip('guix')\n")))
+               (substitute* "tests/testthat/test-liana_tensor.R"
+                 ((".*Test tensor wrapper.*" m)
+                  (string-append m "skip('guix')\n"))
+                 ((".*Test decompose_tensor.*" m)
+                  (string-append m "skip('guix')\n")))
+               ;; XXX: This test returns a data.frame instead of an error.
+               (substitute* "tests/testthat/test-liana_cytotalk.R"
+                 ((".*Test Cytotalk Wrap.*" m)
+                  (string-append m "skip('guix')\n"))))))))
       (propagated-inputs
        (list r-basilisk
              r-basilisk-utils
@@ -21750,6 +21700,70 @@ want to explore e.g.: the function of a set of differentially expressed
 genes.")
       (license license:gpl3))))
 
+(define-public r-seurat-utils
+  (let ((commit "c0374cc9e25ce391ba8013fda0f8c7babbb9201d")
+        (revision "1"))
+    (package
+      (name "r-seurat-utils")
+      (version (git-version "2.5.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/Seurat.utils")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "15l86b43q245gzz7gsr5rhs4sir74lc14d64yqxfqcb0zrb2bzzd"))))
+      (properties `((upstream-name . "Seurat.utils")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-codeandroll2
+                               r-cowplot
+                               r-databaselinke-r
+                               r-dplyr
+                               r-enhancedvolcano
+                               r-foreach
+                               r-ggcorrplot
+                               r-ggexpress
+                               r-ggplot2
+                               r-ggpubr
+                               r-ggrepel
+                               r-hgnchelper
+                               r-htmlwidgets
+                               r-job
+                               r-magrittr
+                               r-markdownhelpers
+                               r-markdownreports
+                               r-matrix
+                               r-matrixstats
+                               r-pheatmap
+                               r-plotly
+                               r-princurve
+                               r-qs
+                               r-r-utils
+                               r-readr
+                               r-readwriter
+                               r-reshape2
+                               r-rstudioapi
+                               r-scales
+                               r-seurat
+                               r-soupx
+                               r-sparsematrixstats
+                               r-stringendo
+                               r-stringr
+                               r-tibble
+                               r-tictoc
+                               r-tidyverse
+                               r-vroom))
+      (home-page "https://github.com/vertesy/Seurat.utils")
+      (synopsis "Collection of utility functions for Seurat")
+      (description
+       "This is a collection of utility functions for Seurat.  These functions
+allow the automation and multiplexing of plotting, 3D plotting, visualization
+of statistics & QC, interaction with the Seurat object.  Some functionalities
+require functions from CodeAndRoll and MarkdownReports libraries.")
+      (license license:gpl3))))
+
 (define-public r-seuratextend
   (let ((commit "5dacd7c1e1da3bc0e78ab81d60056f6d7da3d386")
         (revision "1"))
@@ -22464,39 +22478,38 @@ frames with arbitrary sets of columns.")
       (license license:expat))))
 
 (define-public r-imagearray
-  (package
-    (name "r-imagearray")
-    (version "1.0.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ImageArray" version))
-       (sha256
-        (base32 "07zq5fcw2dsvm4qaksaj4gy9gj5lxcgq82l497c5kgvl4wba049c"))))
-    (properties `((upstream-name . "ImageArray")))
-    (build-system r-build-system)
-    (arguments
-     (list
-      #:skipped-tests
-      ;; RBiomFormats is not installed.
-      '(("test-array.R" "check indexing \\(BFArray\\)"))))
-    (propagated-inputs (list r-delayedarray
-                             r-ebimage
-                             r-hdf5array
-                             r-magick
-                             r-rarr
-                             r-rhdf5
-                             r-s4arrays
-                             r-s4vectors
-                             r-zarrarray))
-    (native-inputs (list r-ggplot2 r-knitr r-testthat))
-    (home-page "https://github.com/BIMSBbioinfo/ImageArray")
-    (synopsis "Framework for on-disk and in-memory image arrays")
-    (description
-     "@code{ImageArray} provides a framework for on-disk and in-memory image
-arrays, specifically for pyramidal images stored in HDF5, Zarr and life
-sciences image file formats (OME Bio-Formats).")
-    (license license:expat)))
+  (let ((commit "2f90694fa33ed8320a6a2f7e0ad5c8a1796cbfc6")
+        (revision "1"))
+    (package
+      (name "r-imagearray")
+      (version (git-version "0.99.6" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/BIMSBbioinfo/ImageArray")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1mf68b007dc5wdzdva4vkjgkavgagjk45qv05f7vahbpi24yjj4n"))))
+      (properties `((upstream-name . "ImageArray")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-delayedarray
+                               r-ebimage
+                               r-hdf5array
+                               r-magick
+                               r-rarr
+                               r-rhdf5
+                               r-s4arrays
+                               r-s4vectors))
+      (native-inputs (list r-knitr r-testthat))
+      (home-page "https://github.com/BIMSBbioinfo/ImageArray")
+      (synopsis "Framework for on-disk and in-memory image arrays")
+      (description
+       "@code{ImageArray} provides a framework for on-disk and in-memory image
+arrays, specifically for pyramidal images stored in either HDF5 files or Zarr
+stores.")
+      (license license:expat))))
 
 (define-public r-velocyto
   (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350")
@@ -22580,7 +22593,7 @@ dependencies of @code{VoltRon} package.")
 (define-public r-voltron
   (package
     (name "r-voltron")
-    (version "0.2.6")
+    (version "0.2.5")
     (source
      (origin
        (method git-fetch)
@@ -22589,7 +22602,7 @@ dependencies of @code{VoltRon} package.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "00fl5dmyd9ad4hd0cblgi0415sf6q4q67wh04r7fws828vs5vaj1"))))
+        (base32 "057n4yipkq3gnlyrb63l2ryi78nlmaas02avargm352g5ra1xl9s"))))
     (properties `((upstream-name . "VoltRon")))
     (build-system r-build-system)
     (arguments
@@ -22653,15 +22666,18 @@ guix_python <- \"~a\";"
                              r-irlba
                              r-magick
                              r-matrix
+                             r-pizzarr
                              r-rann
                              r-rcdt
                              r-rcpp
                              r-rcppannoy
                              r-rcpparmadillo
+                             r-reshape2
+                             r-reticulate
+                             r-rhdf5
                              r-rjson
                              r-rlang
                              r-s4arrays
-                             r-s4vectors
                              r-shiny
                              r-shinyjs
                              r-sp
@@ -22714,8 +22730,8 @@ spots, cells and even molecules.")
     (license license:expat)))
 
 (define-public r-zarrdataframe
-  (let ((commit "f5f671521934b2afc3c511f8c09181bc7bb789a4")
-        (revision "3"))
+  (let ((commit "84c7db2f6f5f84b4a4308f8eb72bedc131fb68bc")
+        (revision "2"))
     (package
       (name "r-zarrdataframe")
       (version (git-version "0.0.0" revision commit))
@@ -22727,13 +22743,13 @@ spots, cells and even molecules.")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "0klp2njn6qsa8n6c01v1z2dfaa93lhbzhwhbyhl23h8gg7d28yc1"))))
+          (base32 "1idrvdlzbwyixlg830sn19vfdn3n3irmlyr4ncf7dpk72r08g3hw"))))
       (properties
        '((upstream-name . "ZarrDataFrame")
          (updater-extra-native-inputs . ("r-testthat"))))
       (build-system r-build-system)
       (propagated-inputs (list r-biocgenerics r-delayedarray r-rarr
-                               r-s4vectors r-zarrarray))
+                               r-s4vectors))
       (native-inputs (list r-knitr r-testthat))
       (home-page "https://github.com/BIMSBbioinfo/ZarrDataFrame")
       (synopsis "Bioconductor-friendly Bindings for Zarr")
@@ -22745,35 +22761,39 @@ frames with arbitrary sets of columns.")
       (license license:expat))))
 
 (define-public r-zarrarray
-  (package
-    (name "r-zarrarray")
-    (version "1.0.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ZarrArray" version))
-       (sha256
-        (base32 "1ny91qg257kgb1hz2h4jvb0rna9cwyw7fqyj5axv52r3b98xn040"))))
-    (properties `((upstream-name . "ZarrArray")))
-    (build-system r-build-system)
-    (propagated-inputs (list r-biocgenerics
-                             r-delayedarray
-                             r-iranges
-                             r-rarr
-                             r-s4arrays
-                             r-s4vectors
-                             r-sparsearray))
-    (native-inputs (list r-knitr r-testthat))
-    (home-page "https://bioconductor.org/packages/ZarrArray")
-    (synopsis "Bring Zarr datasets in R as DelayedArray objects")
-    (description
-     "The @code{ZarrArray} package leverages the Rarr package to bring Zarr
-datasets in R as @code{DelayedArray} objects.  The main class in the package
-is the @code{ZarrArray} class.  A @code{ZarrArray} object is an array-like
-object that represents a Zarr dataset in R. @code{ZarrArray} objects are
-@code{DelayedArray} derivatives and therefore support all operations (delayed
-or block-processed) supported by @code{DelayedArray} objects.")
-    (license license:artistic2.0)))
+  (let ((commit "3cc3e6acf986074dfaece2ad23f9b56962054625")
+        (revision "2"))
+    (package
+      (name "r-zarrarray")
+      (version (git-version "1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/BIMSBbioinfo/ZarrArray")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1qjj92cpxpm3zh05vf60h5gmcn1qady0s38hibb0l57iwdhlhrb3"))))
+      (properties
+       '((upstream-name . "ZarrArray")
+         (updater-extra-native-inputs . ("r-testthat"))))
+      (build-system r-build-system)
+      ;; The tests seem to be outdated.
+      (arguments (list #:tests? #false))
+      (propagated-inputs (list r-biocgenerics
+                               r-delayedarray
+                               r-iranges
+                               r-matrix
+                               r-rarr
+                               r-s4arrays
+                               r-s4vectors
+                               r-sparsearray))
+      (native-inputs (list r-testthat))
+      (home-page "https://github.com/BIMSBbioinfo/ZarrArray")
+      (synopsis "Zarr backend for DelayedArray objects")
+      (description "Zarr backend for @code{DelayedArray} objects.")
+      (license license:expat))))
 
 (define-public methyldackel
   (package
@@ -24411,77 +24431,79 @@ It also handles cell type-specific differential expression.")
       (license license:gpl3))))
 
 (define-public r-spectre
-  (package
-    (name "r-spectre")
-    (version "1.3.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/ImmuneDynamics/Spectre")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "15g9w08x0pz2ia9qfalhcg3z5z2zx2085mfbr8gx9w5yxnw475ld"))))
-    (properties `((upstream-name . "Spectre")))
-    (build-system r-build-system)
-    (propagated-inputs
-     (list r-biobase
-           r-biocmanager
-           r-caret
-           r-class
-           r-colorramps
-           r-data-table
-           r-dendsort
-           r-devtools
-           r-dplyr
-           r-exactextractr
-           r-factoextra
-           r-flowcore
-           r-flowsom
-           r-flowviz
-           r-fnn
-           r-ggplot2
-           r-ggpointdensity
-           r-ggpubr
-           r-ggraph
-           r-ggthemes
-           r-gridextra
-           r-gridextra
-           r-gtools
-           r-hdf5array
-           r-irlba
-           r-patchwork
-           r-pheatmap
-           r-plyr
-           r-qs2
-           r-raster
-           r-rcolorbrewer
-           r-rhdf5
-           r-rstudioapi
-           r-rsvd
-           r-rtsne
-           r-s2
-           r-scales
-           r-scattermore
-           r-sf
-           r-sp
-           r-stars
-           r-stringr
-           r-tidygraph
-           r-tidyr
-           r-tidyr
-           r-tiff
-           r-umap
-           r-uwot))
-    (home-page "https://github.com/ImmuneDynamics/Spectre")
-    (synopsis "High-dimensional cytometry and imaging analysis")
-    (description
-     "This package provides a computational toolkit in R for the
+  (let ((commit "ff5314fd5b3f29121e52f948d91e222a19dd4d25")
+        (revision "1"))
+    (package
+      (name "r-spectre")
+      (version "1.2.0")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/ImmuneDynamics/Spectre")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0hziqlaq6mnkxi4bwp5xilxy90yh1vz1j1n117d38vmchvclx9yq"))))
+      (properties `((upstream-name . "Spectre")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-biobase
+             r-biocmanager
+             r-caret
+             r-class
+             r-colorramps
+             r-data-table
+             r-dendsort
+             r-devtools
+             r-dplyr
+             r-exactextractr
+             r-factoextra
+             r-flowcore
+             r-flowsom
+             r-flowviz
+             r-fnn
+             r-ggplot2
+             r-ggpointdensity
+             r-ggpubr
+             r-ggraph
+             r-ggthemes
+             r-gridextra
+             r-gridextra
+             r-gtools
+             r-hdf5array
+             r-irlba
+             r-patchwork
+             r-pheatmap
+             r-plyr
+             r-qs
+             r-raster
+             r-rcolorbrewer
+             r-rhdf5
+             r-rstudioapi
+             r-rsvd
+             r-rtsne
+             r-s2
+             r-scales
+             r-scattermore
+             r-sf
+             r-sp
+             r-stars
+             r-stringr
+             r-tidygraph
+             r-tidyr
+             r-tidyr
+             r-tiff
+             r-umap
+             r-uwot))
+      (home-page "https://github.com/ImmuneDynamics/Spectre")
+      (synopsis "High-dimensional cytometry and imaging analysis")
+      (description
+       "This package provides a computational toolkit in R for the
 integration, exploration, and analysis of high-dimensional single-cell
 cytometry and imaging data.")
-    (license license:expat)))
+      (license license:expat))))
 
 (define-public r-compgenomrdata
   (let ((commit "24484cb77631e1123ead6c329b9d62c160e600c6")

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/chez.scm

@@ -302,7 +302,7 @@ will name the threaded machine type unless THREADS? is provided as #f."
     (name "chez-scheme-for-racket")
     ;; The version should match `(scheme-version #t)`.
     ;; See s/cmacros.ss c. line 360.
-    (version "10.4.0-pre-release.1-1") ; expect a chez-nanopass-bootstrap update
+    (version "10.3.0-pre-release.2") ; expect a chez-nanopass-bootstrap update
     (source #f)
     (build-system gnu-build-system)
     (inputs `(,@(if (nix-system->native-chez-machine-type)
@@ -507,7 +507,7 @@ version of Chez Scheme.")
     (name "chez-scheme")
     ;; The version should match `(scheme-version-number #t)`.
     ;; See s/cmacros.ss c. line 360.
-    (version "10.4.0") ; expect a chez-nanopass-bootstrap update
+    (version "10.2.0") ; expect a chez-nanopass-bootstrap update
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -515,7 +515,7 @@ version of Chez Scheme.")
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "079vlkl27qdvsg1rsynmd828m42n98c2dnldkhsxf2slfsqd9kv5"))
+                "14iv4kfkyvrkigr1n2prf71n2l3vs0sf0549rvh6y4x2faa2l329"))
               (file-name (git-file-name name version))
               (patches (search-patches "chez-scheme-bin-sh.patch"))
               (snippet #~(begin
@@ -840,9 +840,9 @@ User's Guix}, among other documents.")
 (define-public chez-nanopass-bootstrap
   (hidden-package
    (package
-     (name "chez-nanopass-bootstrap")
-     (version "1.9.4")
-     (properties '((chez-nanopass-release-date . "December 29, 2025")))
+     (name "chez-nanopass")
+     (version "1.9.2")
+     (properties `((chez-nanopass-release-date . "October 18, 2020")))
      (source
       (origin
         (method git-fetch)
@@ -850,7 +850,7 @@ User's Guix}, among other documents.")
               (url "https://github.com/nanopass/nanopass-framework-scheme")
               (commit (string-append "v" version))))
         (sha256
-         (base32 "1qq0vnbrvcialgjgnblfq3qp1ilqg94h0kg896ksd9v4g7ipj9v0"))
+         (base32 "16vjsik9rrzbabbhbxbaha51ppi3f9n8rk59pc6zdyffs0vziy4i"))
         (file-name (git-file-name "nanopass-framework-scheme" version))
         (snippet
          #~(begin
@@ -929,9 +929,10 @@ create compilers, making them easier to understand and maintain.")
 (define-public chez-nanopass
   (package
     (inherit chez-nanopass-bootstrap)
-    (name "chez-nanopass")
-    (version "1.9.4")
-    (properties '((chez-nanopass-release-date . "December 29, 2025")))
+    ;; This release has a significant bug fix.  Expect the next releases of
+    ;; chez-scheme{,-for-racket} to want this for chez-nanopass-bootstrap.
+    (version "1.9.3")
+    (properties '((chez-nanopass-release-date . "August 24, 2025")))
     (source
      (let ((bootstrap-origin (package-source chez-nanopass-bootstrap)))
        (origin
@@ -940,7 +941,7 @@ create compilers, making them easier to understand and maintain.")
                 (url (git-reference-url (origin-uri bootstrap-origin)))
                 (commit (string-append "v" version))))
          (sha256
-          (base32 "1qq0vnbrvcialgjgnblfq3qp1ilqg94h0kg896ksd9v4g7ipj9v0"))
+          (base32 "0757x3a3b4kcd3jk52h4ikqzv7cc1mvphlw592f0r5pz99bkxiin"))
          (file-name (git-file-name "nanopass-framework-scheme" version)))))
     (native-inputs (list chez-scheme stex))))
 

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 © 2025 Alexey Abramov <levenson@mmer.org>
+;;; Copyright © 2022 Ludovic Courtès <ludo@gnu.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 utils)
-  #:use-module (srfi srfi-1))
+  #:use-module (guix packages))
 
 (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

@@ -34,7 +34,7 @@
 ;;; Copyright © 2021 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021, 2024-2025 Maxim Cournoyer <maxim@guixotic.coop>
-;;; Copyright © 2021, 2026 Ahmad Jarara <ajarara@fastmail.com>
+;;; Copyright © 2021 Ahmad Jarara <git@ajarara.io>
 ;;; Copyright © 2022 Greg Hogan <code@greghogan.com>
 ;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com>
 ;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
@@ -3005,13 +3005,17 @@ can append files to the end of such compressed archives.")
           "00ibddiy62kbs9wl52c35j0hbqanx6pi7lvzkpzmbsizkj8mhp1p"))))
     (build-system cmake-build-system)
     (arguments
-     (list
-      #:configure-flags
-      #~'("-DWITH_TESTS=ON"
-          "-DBUILD_SHARED_LIBS=ON")))
+     '(#:tests? #f
+       #:configure-flags
+       (let* ((out (assoc-ref %outputs "out"))
+              (lib (string-append out "/lib")))
+         (list
+          "-DCMAKE_BUILD_TYPE=Release"
+          "-DBUILD_SHARED_LIBS=ON"
+          "-DCBOR_CUSTOM_ALLOC=ON"
+          (string-append "-DCMAKE_INSTALL_LIBDIR=" lib)
+          (string-append "-DCMAKE_INSTALL_RPATH=" lib)))))
     (synopsis "The C library for parsing and generating CBOR")
-    (native-inputs
-     (list cmocka))
     (description
      "@acronym{CBOR, The Concise Binary Object Representation} is a data format
 whose design goals include the possibility of extremely small code size, fairly

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/crypto.scm

@@ -1009,7 +1009,7 @@ SHA-1, SHA-2, and SHA-3, yet is at least as secure as SHA-3.")
 (define-public rhash
   (package
     (name "rhash")
-    (version "1.4.6")
+    (version "1.4.3")
     (source
      (origin
        (method url-fetch)
@@ -1018,7 +1018,7 @@ SHA-1, SHA-2, and SHA-3, yet is at least as secure as SHA-3.")
        (file-name (string-append "rhash-" version ".tar.gz"))
        (sha256
         (base32
-         "0ylkxhkj4nzmb0iampn2lv7v4yw59x7dl8mdcxqcx2mfxv7ijq4z"))))
+         "0glaghjvwh9ziiqf599v0fdr6jrgc7lcnriq0h7r41k3jrkglh0y"))))
     (build-system gnu-build-system)
     (arguments
      (list #:configure-flags

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"))
-              (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")))))
+                "1bb343mf7n0qg2qz497gxjsqprygrjz1q1pbz76hgqxnsy08sfxd"))))
     (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_AUTHENTICATION_WEBAUTHN=ON"
-              "-DWITH_BENCHMARK=OFF"
-              ;; XXX: BUILD_ID is disabled so that the INFO_BIN target is not
-              ;; 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"
+              "-DWITH_SSL=system"
+              "-DWITH_ZLIB=system"
+              "-DDEFAULT_CHARSET=utf8"
+              "-DDEFAULT_COLLATION=utf8_general_ci"
               "-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)))))))
-          (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))))))
+                           (dirname sed))))))))))
     (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
-           protobuf
+           openssl-1.1
            procps
            rpcsvc-proto                 ; rpcgen
            sed
-           zlib
-           `(,zstd "lib")))
+           zlib))
     (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)
@@ -5665,7 +5645,7 @@ with integrated support for finding required rows quickly.")
 (define-public apache-arrow
   (package
     (name "apache-arrow")
-    (version "24.0.0")
+    (version "23.0.1")
     (source
      (origin
        (method git-fetch)
@@ -5675,7 +5655,7 @@ with integrated support for finding required rows quickly.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1j3gs5ffa9gx2y2nggmi2zn5rj0bsnjnxrzfnipx6050jz6n8dx9"))))
+         "1qn7wgavi3kiz4d6w1naqj5631bg87fnj6gbhaxmpmynm5hi9wm7"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -5843,8 +5823,6 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
            pkg-config
            python-cython
            python-pytest
-           python-pytest-runner
-           python-scikit-build-core
            python-setuptools-scm
            python-setuptools))
     (outputs '("out"))

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/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)
@@ -1314,7 +1314,7 @@ package.")
        #:tests? #f)) ;no test suite
     (native-inputs (list asciidoc
                          gettext-minimal
-                         git-minimal/pinned
+                         git-minimal
                          perl
                          perl-unicode-linebreak
                          perl-yaml-tiny

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")
@@ -23872,8 +23831,8 @@ actually changing the buffer's text.")
 
 (define-public emacs-diff-hl
   ;; No new tags or releases since 2024.
-  (let ((commit "7d873b2f58908de1ea2f499da9bf993e088953d7")
-        (revision "1"))
+  (let ((commit "e79aa49ad3cbbe85379cf6646db3aaacd3b04708")
+        (revision "0"))
     (package
       (name "emacs-diff-hl")
       (version (git-version "1.10.0" revision commit))
@@ -23885,7 +23844,7 @@ actually changing the buffer's text.")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "15a9cjlpjsfcb2hxqbb123389qhiqs06mn01pas2l0jqhc2p86v9"))))
+          (base32 "0fvxngcbx36vqj72fllfp5iqwihcqd1dfhmqr3m1284191q83na3"))))
       (build-system emacs-build-system)
       (arguments
        (list
@@ -23908,7 +23867,7 @@ actually changing the buffer's text.")
                 (invoke "git" "init")
                 (invoke "git" "add" ".")
                 (invoke "git" "commit" "-m" "Commit all."))))))
-      (native-inputs (list git-minimal/pinned))
+      (native-inputs (list git-minimal))
       (home-page "https://github.com/dgutov/diff-hl")
       (synopsis "Highlight uncommitted changes using VC")
       (description
@@ -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 deprecation))
+  #:use-module (guix licenses)
+  #: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-deprecated/public-alias flex
-  (@ (gnu packages compiler-tools) flex))
+(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)
+    (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)
-       (uri (string-append
-             "https://github.com/rsms/inter/releases/download/"
-             "v" version "/Inter-" version ".zip"))
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/rsms/inter")
+              (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")
@@ -4311,7 +4287,7 @@ typographical palette.")
 (define-public font-mona-sans
   (package
     (name "font-mona-sans")
-    (version "2.0.27")
+    (version "2.0.26")
     (source
      (origin
        (method git-fetch)
@@ -4321,7 +4297,7 @@ typographical palette.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "10xbs857d21zrfx0cpzcsyyk76j921qq68qpz5r2kl4jr3gz541z"))))
+         "09b6apxq659y4dkkm5swy683q6hviibv1cd48ragm5rd1376hsaz"))))
     (build-system font-build-system)
     (outputs '("out" "ttf" "woff"))
     (home-page "https://github.com/mona-sans")

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)
@@ -6959,7 +6959,7 @@ tactics.")
 (define-public widelands
   (package
     (name "widelands")
-    (version "1.3.1")
+    (version "1.3")
     (source
      (origin
        (method git-fetch)
@@ -6968,7 +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)

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

@@ -27,7 +27,6 @@
 ;;; Copyright © 2025 Antoine Côté <antoine.cote@posteo.net>
 ;;; Copyright © 2026 Luis Guilherme Coelho <lgcoelho@disroot.org>
 ;;; Copyright © 2026 Daniel Littlewood <dan@danielittlewood.xyz>
-;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -83,7 +82,6 @@
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages)
-  #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
@@ -239,7 +237,7 @@ generation.")
 (define-public libassuan
   (package
     (name "libassuan")
-    (version "3.0.2")
+    (version "3.0.1")
     (source
      (origin
       (method url-fetch)
@@ -247,7 +245,7 @@ generation.")
                           version ".tar.bz2"))
       (sha256
        (base32
-        "1xin9h3vhx94j5w9p7xi3csmw1a6yfif2w4r1x8k7rk6sbd1r4yj"))))
+        "1ccly6aqyxv3hgshhls6qw177salcrawp0x4lsqs9ph3c4pg9w68"))))
     (build-system gnu-build-system)
     (arguments (if (%current-target-system)
                    (list #:configure-flags
@@ -269,7 +267,7 @@ provided.")
 (define-public libksba
   (package
     (name "libksba")
-    (version "1.8.0")
+    (version "1.6.7")
     (source
      (origin
       (method url-fetch)
@@ -278,7 +276,7 @@ provided.")
             version ".tar.bz2"))
       (sha256
        (base32
-        "14lj3ld4nxf916kq01z0203x36nhgymxf0j222mg4jap16wrssr9"))))
+        "0qxpmadxggx5808326i9g4ya0xrnv14mfxpg7rlvckmviq5m2wng"))))
     (build-system gnu-build-system)
     (propagated-inputs
      (list libgpg-error))
@@ -436,16 +434,16 @@ libskba (working with X.509 certificates and CMS data).")
                (substitute* "checks/Makefile.in"
                  (("/bin/sh") (which "sh"))))))))))
 
-(define-public gpgme-2
+(define-public gpgme
   (package
     (name "gpgme")
-    (version "2.1.0")
+    (version "1.24.1")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://gnupg/gpgme/gpgme-" version ".tar.bz2"))
       (sha256
-       (base32 "0azrddb51c423il7xdqcrahvi8fyhblvvs7hzgs5jqn27yjmw744"))))
+       (base32 "0px87fbp90xp8vf1wms02flk14zmrqsfr135f5his1kiiqjx01ga"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -457,7 +455,7 @@ libskba (working with X.509 certificates and CMS data).")
     (propagated-inputs
      ;; As required by the pkg-config's Requires.private.
      (list libgpg-error libassuan))
-    (home-page "https://gnupg.org/software/gpgme/index.html")
+    (home-page "https://www.gnupg.org/related_software/gpgme/")
     (synopsis "Library providing simplified access to GnuPG functionality")
     (description
      "GnuPG Made Easy (GPGME) is a library designed to make access to GnuPG
@@ -471,107 +469,57 @@ instead.  This way bug fixes or improvements can be done at a central place
 and every application benefits from this.")
     (license license:lgpl2.1+)))
 
-(define-public gpgme-1
-  (package
-    (inherit gpgme-2)
-    (version "1.24.1")
-    (source
-     (origin
-      (method url-fetch)
-      (uri (string-append "mirror://gnupg/gpgme/gpgme-" version ".tar.bz2"))
-      (sha256
-       (base32 "0px87fbp90xp8vf1wms02flk14zmrqsfr135f5his1kiiqjx01ga"))))))
-
-(define-public gpgme gpgme-1)
-
-(define-public gpgmepp
-  (package
-    (name "gpgmepp")
-    (version "2.1.0")
-    (source
-     (origin
-      (method url-fetch)
-      (uri (string-append "mirror://gnupg/gpgmepp/gpgmepp-" version ".tar.xz"))
-      (sha256
-       (base32 "1qhn583cbi67694m3bg77ckb892in2f16src2x5m0102ix309y2p"))))
-    (build-system cmake-build-system)
-    (arguments
-     (list
-      ;; FIXME: BUILD_TESTING variable is enabled by deault, but still no tests
-      ;; are found.
-      #:tests? #f))
-    (propagated-inputs
-     ;; As required by the pkg-config's Requires.private.
-     (list gpgme-2 libgpg-error))
-    (home-page "https://gnupg.org/software/gpgme/index.html")
-    (synopsis "C++ bindings/wrapper for GPGME")
-    (description
-     "GPGME++ is a C++ wrapper (or C++ bindings) for the GnuPG project's
-@acronym{GPGME, GnuPG Made Easy} library.")
-    (license license:lgpl2.1+)))
-
 (define-public qgpgme-qt5
   (package
+    (inherit gpgme)
     (name "qgpgme-qt5")
-    (version "2.0.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "mirror://gnupg/qgpgme/qgpgme-" version ".tar.xz"))
-       (sha256
-        (base32 "1bb198dk49bd7yx4cf4w07acjhllilx1nczdna7139ncflj5nr0m"))))
-    (build-system qt-build-system)
     (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'check-setup
-            (lambda _
-              (setenv "HOME" (getcwd))
-              (invoke "gpg-agent" "--daemon"))))))
-    (propagated-inputs
-     (list gpgme-2        ;for FindGpgme.cmake and QGpgmeQt6Config.cmake
-           gpgmepp        ;for QGpgmeQt6Config.cmake
-           libgpg-error)) ;for FindLibGpgError.cmake and QGpgmeQt6Config.cmake
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'chdir-and-symlink
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((gpgme (assoc-ref inputs "gpgme")))
+               (symlink (string-append gpgme "/lib/libgpgmepp.la")
+                        "lang/cpp/src/libgpgmepp.la")
+               (symlink (string-append gpgme "/lib/libgpgme.la")
+                        "src/libgpgme.la"))
+             (chdir "lang/qt"))))))
+    (propagated-inputs (list gpgme))    ;required by QGpgmeConfig.cmake
     (native-inputs
-     (list gnupg        ;for tests
-           pkg-config))
-    (home-page "https://gnupg.org/software/gpgme/index.html")
+     (modify-inputs native-inputs
+       (prepend pkg-config)))
+    (inputs
+     (modify-inputs inputs
+       (prepend qtbase-5)))
     (synopsis "Qt API bindings for gpgme")
     (description "QGpgme provides a very high level Qt API around GpgMEpp.
 
 QGpgME was originally developed as part of libkleo and incorporated into
 gpgpme starting with version 1.7.")
-    (license license:gpl2+)))
+    (license license:gpl2+))) ;; Note: this differs from gpgme
 
 (define-public qgpgme
   (package
+    (inherit gpgme)
     (name "qgpgme")
-    (version "2.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "mirror://gnupg/qgpgme/qgpgme-" version ".tar.xz"))
-       (sha256
-        (base32 "024gdw8i5ibmq0bjjf6znhxw93chh1j21dr25m0gk9z4xsrzwcjv"))))
-    (build-system qt-build-system)
     (arguments
-     (list
-      #:qtbase qtbase
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'check-setup
-            (lambda _
-              (setenv "HOME" (getcwd))
-              (invoke "gpg-agent" "--daemon"))))))
-    (propagated-inputs
-     (list gpgme-2        ;for FindGpgme.cmake and QGpgmeQt6Config.cmake
-           gpgmepp        ;for QGpgmeQt6Config.cmake
-           libgpg-error)) ;for FindLibGpgError.cmake and QGpgmeQt6Config.cmake
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'chdir-and-symlink
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((gpgme (assoc-ref inputs "gpgme")))
+               (symlink (string-append gpgme "/lib/libgpgmepp.la")
+                        "lang/cpp/src/libgpgmepp.la")
+               (symlink (string-append gpgme "/lib/libgpgme.la")
+                        "src/libgpgme.la"))
+             (chdir "lang/qt"))))))
+    (propagated-inputs (list gpgme))    ;required by QGpgmeConfig.cmake
     (native-inputs
-     (list gnupg        ;for tests
-           pkg-config))
-    (home-page "https://gnupg.org/software/gpgme/index.html")
+     (modify-inputs native-inputs
+       (prepend pkg-config)))
+    (inputs
+     (modify-inputs inputs
+       (prepend qtbase)))
     (synopsis "Qt API bindings for gpgme")
     (description "QGpgme provides a very high level Qt API around GpgMEpp.")
     (license license:gpl2+)))
@@ -635,20 +583,21 @@ interface (FFI) of Guile.")
 (define-public python-gpg
   (package
     (name "python-gpg")
-    (version "2.0.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "gpg" version))
+              (patches (search-patches "python-gpg-setup-72.patch"))
               (sha256
                (base32
-                "0f2l0iyc8gp49i604c5wpliaa1dsyj0i0p9xc9zfj4z7fwaavdsf"))))
+                "1ji3ynhp36m1ccx7bmaq75dhij9frpn19v9mpi4aajn8csl194il"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:tests? #f ; No test suite.
       #:phases
       #~(modify-phases %standard-phases
-          (add-before 'build 'patch-setup.py
+          (add-before 'build 'set-environment
             (lambda _
               ;; GPGME is built with large file support, so we need to set
               ;; _FILE_OFFSET_BITS to 64 in all users of the GPGME library.
@@ -658,16 +607,9 @@ interface (FFI) of Guile.")
                            "extra_macros = { \"_FILE_OFFSET_BITS\": 64 }")))
                      #~())
               (substitute* "setup.py"
-                (("cc") (which "gcc"))
-                (("\\/usr\\/lib\\/x86_64-linux-gnu( -lgpg-error)" _ keep)
-                 (string-append #$(this-package-input "libgpg-error") "/lib"
-                                keep))
-                (("\\/usr\\/lib\\/x86_64-linux-gnu( -lgpgme)" _ keep)
-                 (string-append #$(this-package-input "gpgme") "/lib" keep))
-                (("\\/usr\\/local(', 'include', 'gpgme\\.h')" _ keep)
-                 (string-append #$(this-package-input "gpgme") keep))))))))
+                (("cc") (which "gcc"))))))))
     (inputs
-     (list gpgme-2 libgpg-error))
+     (list gpgme))
     (native-inputs
      (list swig-4.0 python-setuptools))
     (home-page (package-home-page gpgme))
@@ -751,14 +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))
@@ -822,7 +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)
@@ -832,7 +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
@@ -846,57 +788,56 @@ parties.")
                   perl-net-idn-encode
                   libmd))
     (arguments
-     (list #:tests? #f                      ; no test suite
-           #:phases
-           #~(modify-phases %standard-phases
-               (replace 'configure
-                 (lambda _
-                   (substitute* "keyanalyze/Makefile"
-                     (("LDLIBS")
-                      (string-append "CC=" (which "gcc") "\nLDLIBS")))
-                   (substitute* "keyanalyze/Makefile"
-                     (("\\./configure")
-                      (string-append "./configure --prefix=" #$output)))
-                   (substitute* "gpgwrap/Makefile"
-                     (("\\} clean")
-                      (string-append
-                       "} clean\ninstall:\n\tinstall -D bin/gpgwrap "
-                       #$output "/bin/gpgwrap\n")))
-                   (substitute* '("gpgsigs/Makefile" "keyanalyze/Makefile"
-                                  "keylookup/Makefile" "sig2dot/Makefile"
-                                  "springgraph/Makefile")
-                     (("/usr") #$output))
-                   (setenv "CONFIG_SHELL" (which "sh"))))
-               (replace 'install
-                 (lambda* (#:key #:allow-other-keys #:rest args)
-                   (let ((install (assoc-ref %standard-phases 'install)))
-                     (apply install args)
-                     (for-each
-                      (lambda (dir file)
-                        (copy-file (string-append dir "/" file)
-                                   (string-append #$output "/bin/" file)))
-                      '("caff" "caff" "caff" "gpgdir" "gpg-key2ps"
-                        "gpglist" "gpg-mailkeys" "gpgparticipants")
-                      '("caff" "pgp-clean" "pgp-fixkey" "gpgdir" "gpg-key2ps"
-                        "gpglist" "gpg-mailkeys" "gpgparticipants"))
-                     (for-each
-                      (lambda (dir file)
-                        (copy-file
-                         (string-append dir "/" file)
-                         (string-append #$output "/share/man/man1/" file)))
-                      '("caff" "caff" "caff" "gpgdir"
-                        "gpg-key2ps" "gpglist" "gpg-mailkeys"
-                        "gpgparticipants" "gpgsigs" "gpgwrap/doc"
-                        "keyanalyze" "keyanalyze/pgpring" "keyanalyze")
-                      '("caff.1" "pgp-clean.1" "pgp-fixkey.1" "gpgdir.1"
-                        "gpg-key2ps.1" "gpglist.1" "gpg-mailkeys.1"
-                        "gpgparticipants.1" "gpgsigs.1" "gpgwrap.1"
-                        "process_keys.1" "pgpring.1" "keyanalyze.1")))))
-               (add-after 'install 'wrap-programs
-                 (lambda _
-                   (wrap-program
-                       (string-append #$output "/bin/caff")
-                     `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))))))))
+     `(#:tests? #f                      ; no test suite
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (substitute* "keyanalyze/Makefile"
+                 (("LDLIBS") (string-append "CC=" (which "gcc") "\nLDLIBS")))
+               (substitute* "keyanalyze/Makefile"
+                 (("\\./configure") (string-append "./configure --prefix=" out)))
+               (substitute* "gpgwrap/Makefile"
+                 (("\\} clean")
+                  (string-append "} clean\ninstall:\n\tinstall -D bin/gpgwrap "
+                                 out "/bin/gpgwrap\n")))
+               (substitute* '("gpgsigs/Makefile" "keyanalyze/Makefile"
+                              "keylookup/Makefile" "sig2dot/Makefile"
+                              "springgraph/Makefile")
+                 (("/usr") out))
+               (setenv "CONFIG_SHELL" (which "sh")))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys #:rest args)
+             (let ((out (assoc-ref outputs "out"))
+                   (install (assoc-ref %standard-phases 'install)))
+               (apply install args)
+               (for-each
+                (lambda (dir file)
+                  (copy-file (string-append dir "/" file)
+                             (string-append out "/bin/" file)))
+                '("caff" "caff" "caff" "gpgdir" "gpg-key2ps"
+                  "gpglist" "gpg-mailkeys" "gpgparticipants")
+                '("caff" "pgp-clean" "pgp-fixkey" "gpgdir" "gpg-key2ps"
+                  "gpglist" "gpg-mailkeys" "gpgparticipants"))
+               (for-each
+                (lambda (dir file)
+                  (copy-file (string-append dir "/" file)
+                             (string-append out "/share/man/man1/" file)))
+                '("caff" "caff" "caff" "gpgdir"
+                  "gpg-key2ps" "gpglist" "gpg-mailkeys"
+                  "gpgparticipants" "gpgsigs" "gpgwrap/doc"
+                  "keyanalyze" "keyanalyze/pgpring" "keyanalyze")
+                '("caff.1" "pgp-clean.1" "pgp-fixkey.1" "gpgdir.1"
+                  "gpg-key2ps.1" "gpglist.1" "gpg-mailkeys.1"
+                  "gpgparticipants.1" "gpgsigs.1" "gpgwrap.1"
+                  "process_keys.1" "pgpring.1" "keyanalyze.1")))))
+         (add-after 'install 'wrap-programs
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out")))
+               (wrap-program
+                   (string-append out "/bin/caff")
+                 `("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,
@@ -1208,24 +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")
-           #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'install 'wrap-program
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   (let ((gnupg (assoc-ref inputs "gnupg")))
-                     (wrap-program (string-append #$output "/bin/gpa")
-                       `("PATH" ":" prefix (,(string-append gnupg "/bin"))))))))))
+     `(#:make-flags '("CFLAGS=-Wno-implicit-function-declaration")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'wrap-program
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (gnupg (assoc-ref inputs "gnupg")))
+               (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-check.scm

@@ -2151,57 +2151,6 @@ testing and improve the efficiency of unit test writing.")
 testing of time-sensitive code.")
     (license license:expat)))
 
-(define-public go-github-com-josharian-mapfs
-  (package
-    (name "go-github-com-josharian-mapfs")
-    (version "0.0.0-20210615234106-095c008854e6")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/josharian/mapfs")
-             (commit (go-version->git-ref version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "09i6shqwacx8nm6jfyhc1zvry8fcb3ddd98m96skzybv9lckq7h4"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/josharian/mapfs"))
-    (home-page "https://github.com/josharian/mapfs")
-    (synopsis "Fork of Go std's testing/fstest.MapFS")
-    (description
-     "This is a fork of the @code{MapFS} component of the Go standard
-library's testing/fstest package.")
-    (license license:bsd-3)))
-
-(define-public go-github-com-josharian-txtarfs
-  (package
-    (name "go-github-com-josharian-txtarfs")
-    (version "0.0.0-20240408113805-5dc76b8fe6bf")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/josharian/txtarfs")
-              (commit (go-version->git-ref version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "129rf6hviw46rxcnnkc8jb1k579798rrhnh1k3nn7npi260ia44m"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/josharian/txtarfs"))
-    (propagated-inputs
-     (list go-github-com-josharian-mapfs
-           go-golang-org-x-tools))
-    (home-page "https://github.com/josharian/txtarfs")
-    (synopsis "Convert a txtar to an io.FS")
-    (description
-     "This package turns a @url{https://pkg.go.dev/golang.org/x/tools/txtar,
- txtar} into an @url{https://pkg.go.dev/io/fs, fs.FS}.")
-    (license license:expat)))
-
 (define-public go-github-com-joshdk-go-junit
   (package
     (name "go-github-com-joshdk-go-junit")
@@ -2713,56 +2662,6 @@ error messages, preserving the order of @code{have} (actual result) before
 @code{want} (expected result) to minimize confusion.")
     (license license:asl2.0)))
 
-(define-public go-github-com-newmo-oss-go-caller
-  (package
-    (name "go-github-com-newmo-oss-go-caller")
-    (version "0.1.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/newmo-oss/go-caller")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1hn0wj2v6yvn83lpilbcb9xpa36fmcbv83rk6fhr2rwckp2dxy8p"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/newmo-oss/go-caller"))
-    (native-inputs
-     (list go-github-com-google-go-cmp))
-    (home-page "https://github.com/newmo-oss/go-caller")
-    (synopsis "Collect stack traces at runtime")
-    (description
-     "This package provides a library for collecting stack traces at runtime.")
-    (license license:expat)))
-
-(define-public go-github-com-newmo-oss-gotestingmock
-  (package
-    (name "go-github-com-newmo-oss-gotestingmock")
-    (version "0.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/newmo-oss/gotestingmock")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1flgmarj961k4vl6d7i2740snrdfjiv4aigb87v5aznvi8bwa5d3"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/newmo-oss/gotestingmock"))
-    (propagated-inputs
-     (list go-github-com-newmo-oss-go-caller))
-    (home-page "https://github.com/newmo-oss/gotestingmock")
-    (synopsis "Mocking utilities for Go")
-    (description
-     "This package provides mocking utilities for unit tests in Go.")
-    (license license:expat)))
-
 (define-public go-github-com-onsi-ginkgo
   (package
     (name "go-github-com-onsi-ginkgo")
@@ -3368,84 +3267,6 @@ and CLI tool.")
 such as readers and writers that fail after N consecutive reads/writes.")
     (license license:expat)))
 
-(define-public go-github-com-tenntenn-golden
-  (package
-    (name "go-github-com-tenntenn-golden")
-    (version "0.5.5")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/tenntenn/golden")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "09w3h7c4z930z91dg7bfs9m680pw9zgqyyikw88gisv1z86y3qlz"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/tenntenn/golden"))
-    (native-inputs
-     (list go-github-com-google-go-cmp))
-    (propagated-inputs
-     (list go-github-com-josharian-txtarfs
-           go-golang-org-x-tools))
-    (home-page "https://github.com/tenntenn/golden")
-    (synopsis "Utilities for golden file tests")
-    (description "This package provides utilities for golden file tests.")
-    (license license:expat)))
-
-(define-public go-github-com-tenntenn-modver
-  (package
-    (name "go-github-com-tenntenn-modver")
-    (version "1.0.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/tenntenn/modver")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1p4402lizz5ny0l49yxa65ryhx09wm8g13lx4pw0nw0s4r06rw3g"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/tenntenn/modver"))
-    (native-inputs
-     (list go-github-com-google-go-cmp))
-    (propagated-inputs
-     (list go-github-com-hashicorp-go-version))
-    (home-page "https://github.com/tenntenn/modver")
-    (synopsis "Utility for Go modules")
-    (description "This package provides utilities for Go modules.")
-    (license license:expat)))
-
-(define-public go-github-com-tenntenn-text-transform
-  (package
-    (name "go-github-com-tenntenn-text-transform")
-    (version "0.0.0-20250402111347-ba836492e880")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/tenntenn/text")
-              (commit (go-version->git-ref version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "19f302js8pxyqnl189992zp6pl169b4gpgn6wywpdir77vm56pih"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/tenntenn/text/transform"
-      #:unpack-path "github.com/tenntenn/text"))
-    (propagated-inputs
-     (list go-golang-org-x-text))
-    (home-page "https://github.com/tenntenn/text")
-    (synopsis "Text transformation utilities")
-    (description "This package provides text transformation utilities in Go.")
-    (license license:expat)))
-
 (define-public go-github-com-tj-assert
   (package
     (name "go-github-com-tj-assert")
@@ -3728,34 +3549,6 @@ goroutine leaks and understanding goroutine lifecycles.")
 based on Go @code{testing} library procedures.")
     (license license:cc0)))
 
-(define-public go-gitlab-com-bosi-decorder
-  (package
-    (name "go-gitlab-com-bosi-decorder")
-    (version "0.4.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://gitlab.com/bosi/decorder")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0g9x5f7mhvdzwki57902qgb4ih2gipkg255nf9hjv30flfnl2294"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "gitlab.com/bosi/decorder"
-      #:test-flags #~(list "-vet=off")))
-    (propagated-inputs
-     (list go-golang-org-x-tools))
-    (home-page "https://gitlab.com/bosi/decorder")
-    (synopsis "Declaration order and number linter for golang")
-    (description
-     "This package provides a declaration order linter for Go.  In case of
-this tool declarations are @code{type}, @code{const}, @code{var} and
-@code{func}.")
-    (license license:expat)))
-
 (define-public go-go-abhg-dev-requiredfield
   (package
     (name "go-go-abhg-dev-requiredfield")
@@ -3864,60 +3657,6 @@ and restore them afterwards.")
 of @url{https://github.com/wadey/gocovmerge}.")
     (license license:bsd-2)))
 
-(define-public go-go-simpler-org-assert
-  (package
-    (name "go-go-simpler-org-assert")
-    (version "0.9.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/go-simpler/assert")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0pg3yhicggby978n8war9n5zzigr95mvnsipnk6zgsjn6gyvjdm5"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "go-simpler.org/assert"))
-    (home-page "https://go-simpler.org/assert")
-    (synopsis "Assertions for the standard testing package")
-    (description
-     "This package implements assertions for the standard @code{testing}
-package, and is a minimalistic replacement for the @code{stretchr/testify}
-package.")
-    (license license:mpl2.0)))
-
-(define-public go-go-simpler-org-musttag
-  (package
-    (name "go-go-simpler-org-musttag")
-    (version "0.14.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/go-simpler/musttag")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "15kvnppc2q8ay1m8lhag0bmdx08kc68lzv78699qkyi6bcw68ajf"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "go-simpler.org/musttag"
-      #:test-flags #~(list "-skip" "TestAnalyzer")))
-    (native-inputs
-     (list go-go-simpler-org-assert))
-    (propagated-inputs
-     (list go-golang-org-x-tools))
-    (home-page "https://go-simpler.org/musttag")
-    (synopsis "Enforce field tags in (un)marshaled structs")
-    (description
-     "This package checks that exported fields of a struct passed to a
-@code{Marshal}-like function are annotated with the relevant tag.")
-    (license license:mpl2.0)))
-
 (define-public go-go-simpler-org-sloglint
   (package
     (name "go-go-simpler-org-sloglint")

gnu/packages/golang-xyz.scm

@@ -4683,7 +4683,7 @@ contexts (e.g. testing).")
 (define-public go-github-com-charlievieth-fastwalk
   (package
     (name "go-github-com-charlievieth-fastwalk")
-    (version "1.0.14")
+    (version "1.0.8")
     (source
      (origin
        (method git-fetch)
@@ -4692,7 +4692,7 @@ contexts (e.g. testing).")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0ab90pdqgnd0a6ylmq35zca0imj2pp4pxz2bcmg2zx0szv3910im"))))
+        (base32 "17zy17q31p8b93bf703rr0xqafp02bb0slkrgpxb8r0aaxz3zg4y"))))
     (build-system go-build-system)
     (arguments
      (list

gnu/packages/graph.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017-2026 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017-2025 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018, 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2021, 2022, 2024 Efraim Flashner <efraim@flashner.co.il>
@@ -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)
@@ -227,7 +227,7 @@ more.")
    (package
      (inherit igraph)
      (name "igraph")
-     (version "1.0.1")
+     (version "0.10.15")
      (source
       (origin
         (inherit (package-source igraph))
@@ -239,39 +239,7 @@ more.")
         (file-name (git-file-name name version))
         (sha256
          (base32
-          "01mynhbl2ph0gkc0zr5klwqvczwcimfs2kdn6didwg4k8gsrcxlr"))
-        (modules '((guix build utils)
-                   (ice-9 ftw)
-                   (srfi srfi-26)))
-        ;; We need the vendored versions of qhull and cxsparse.
-        (snippet '(begin
-                    (delete-file-recursively "src/isomorphism/bliss")
-                    (substitute* '("src/CMakeLists.txt"
-                                   "etc/cmake/benchmark_helpers.cmake")
-                      ;; Remove extraneous bundling related variables.
-                      ((".*_IS_VENDORED.*") "")
-                      ((".*add_sub.*isomorphism/bliss.*") "")
-                      (("(.*TARGETS.*)bliss(.*)pcg(.*)"
-                        _ part1 part2 part3)
-                       (string-append part1 part2 part3))
-                      ((" pcg ") " pcg_random "))))))
-     (arguments
-      (substitute-keyword-arguments (package-arguments igraph)
-        ((#:phases phases '%standard-phases)
-         #~(modify-phases #$phases
-             ;; We have to use the bundled version because it has been
-             ;; modified from upstream.
-             (delete 'patch-suitesparse)))
-        ((#:configure-flags flags)
-         #~(list "-DBUILD_SHARED_LIBS=ON"
-                 "-DIGRAPH_INFOMAP_SUPPORT=OFF"
-                 "-DCMAKE_C_FLAGS=-Wno-error=incompatible-pointer-types"
-                 ;; Use the same integer width as suitesparse-cxsparse, which
-                 ;; uses int64_t in SuiteSparse v6.0.0 and later.
-                 "-DIGRAPH_INTEGER_SIZE=64"))))
-     (inputs
-      (modify-inputs (package-inputs igraph)
-        (delete "suitesparse-cxsparse"))))))
+          "0z9jqvl65j4z6brrjlfyykba2bs10az6dx6m8g41snlfnx21a82d")))))))
 
 (define-public python-igraph
   (package

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.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/ibus.scm

@@ -36,7 +36,6 @@
   #:use-module (guix licenses)
   #:use-module (guix packages)
   #:use-module (guix gexp)
-  #:use-module (guix deprecation)
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system cmake)
@@ -947,42 +946,37 @@ traditional Chinese output.")
 hanja dictionary and small hangul character classification.")
     (license lgpl2.1+)))
 
-(define-public ibus-hangul
+(define-public ibus-libhangul
   (package
-    (name "ibus-hangul")
-    (version "1.5.5")
+    (name "ibus-libhangul")
+    (version "1.5.3")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/libhangul/ibus-hangul")
-             (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (string-append "https://github.com/libhangul/ibus-hangul/"
+                           "releases/download/" version
+                           "/ibus-hangul-" version ".tar.gz"))
        (sha256
-        (base32 "0wsbh6ii223wdai2qwcwy6sj5jr9zzma7511fhkfq4m2qxdhwsn7"))))
+        (base32
+         "1400ba2p34vr9q285lqvjm73f6m677cgfdymmjpiwyrjgbbiqrjy"))))
     (build-system gnu-build-system)
     (arguments
-     (list
-      #:make-flags
-      #~'("DISABLE_GUI_TESTS=ibus-hangul")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'install 'wrap
-            (lambda* (#:key inputs #:allow-other-keys)
-              (wrap-program (string-append #$output
-                                           "/libexec/ibus-setup-hangul")
-                `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH")))
-                `("LD_LIBRARY_PATH" ":" prefix
-                  (,(dirname (search-input-file inputs "lib/libhangul.so"))))
-                `("GI_TYPELIB_PATH" ":" prefix
-                  (,(getenv "GI_TYPELIB_PATH")))))))))
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'wrap
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (wrap-program (string-append (assoc-ref outputs "out")
+                                          "/libexec/ibus-setup-hangul")
+               `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH")))
+               `("LD_LIBRARY_PATH" ":" prefix
+                 (,(string-append (assoc-ref inputs "libhangul") "/lib")))
+               `("GI_TYPELIB_PATH" ":" prefix
+                 (,(getenv "GI_TYPELIB_PATH"))))
+             #t)))))
     (native-inputs
-     (list autoconf
-           automake
-           gettext-minimal
-           `(,glib "bin")
-           libtool
-           pkg-config))
+     `(("pkg-config" ,pkg-config)
+       ("gettext" ,gettext-minimal)
+       ("glib:bin" ,glib "bin")))
     (inputs
      (list bash-minimal
            ibus
@@ -997,9 +991,6 @@ hanja dictionary and small hangul character classification.")
      "ibus-hangul is a Korean input method engine for IBus.")
     (license gpl2+)))
 
-;; XXX: Deprecated on 2026-05-26.
-(define-deprecated-package ibus-libhangul ibus-hangul)
-
 (define-public ibus-table
   (package
     (name "ibus-table")

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)
@@ -1923,7 +1923,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
 (define-public simpleitk
   (package
     (name "simpleitk")
-    (version "2.5.4")
+    (version "2.5.3")
     (source
      (origin
        (method git-fetch)
@@ -1932,9 +1932,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1bzj5naqbgv2b31iqgz7qqk9rixsvjqycjz6l7w3gm7v1aj14jpb"))
-       (patches
-        (search-patches "simpleitk-r-4.6.0.patch"))))
+        (base32 "0fvacjfq0p8v7r2cmzwwh7bxb6ayavznhj0m81dah463x472qkd2"))))
     (build-system cmake-build-system)
     (outputs '("out" "python" "r"))
     (arguments
@@ -2034,7 +2032,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
                    version "/SimpleITKData-" version ".tar.gz"))
              (sha256
               (base32
-               "0hryvi9fgqac00ng1bfhw3lm0al1dh0ka6jglba2q368nls428nx")))))
+               "0i4f87g1rh6xxisw06gwwyi8f216qqs6ih3gghi3k49vsl0h4g5d")))))
     (synopsis "Simplified interface to @acronym{ITK, Insight Toolkit}")
     (description
      "SimpleITK is an image analysis toolkit built on top of @acronym{ITK,

gnu/packages/image-viewers.scm

@@ -39,7 +39,6 @@
 ;;; Copyright © 2025 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2025 Igorj Gorjaĉev <igor@goryachev.org>
 ;;; Copyright © 2026 Daniel Littlewood <dan@danielittlewood.xyz>
-;;; Copyright © 2026 Luis Guilherme Coelho <lgcoelho@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -95,16 +94,13 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-xyz)
-  #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages graphics)
   #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages image)
   #:use-module (gnu packages image-processing)
   #:use-module (gnu packages imagemagick)
-  #:use-module (gnu packages kde-frameworks)
   #:use-module (gnu packages linux)
-  #:use-module (gnu packages logging)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pdf)
@@ -112,7 +108,6 @@
   #:use-module (gnu packages perl-check)
   #:use-module (gnu packages photo)
   #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages profiling)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
@@ -125,8 +120,6 @@
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages suckless)
   #:use-module (gnu packages stb)
-  #:use-module (gnu packages tbb)
-  #:use-module (gnu packages tls)
   #:use-module (gnu packages terminals)
   #:use-module (gnu packages upnp)
   #:use-module (gnu packages version-control)
@@ -1293,84 +1286,6 @@ workspaces.
 (define-deprecated-package python-ueberzug
   ueberzug)
 
-(define-public ueberzugpp
-  (package
-    (name "ueberzugpp")
-    (version "2.9.10")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-              (url "https://github.com/jstkdng/ueberzugpp")
-              (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "1jac2sca4pmcxp8xcvaxhf6j15phyc85gb5n9ymajbahnd4hbcv2"))))
-    (build-system cmake-build-system)
-    (arguments
-     (list #:tests? #f    ; no tests
-           #:configure-flags
-           #~(list "-DENABLE_OPENCV=ON"
-                   "-DENABLE_X11=ON"
-                   "-DENABLE_WAYLAND=ON")))
-    (native-inputs
-     (list extra-cmake-modules
-           gobject-introspection
-           pkg-config))
-    (inputs
-     (list cairo
-           chafa
-           cli11
-           expat
-           fftw
-           fmt
-           imagemagick
-           imath
-           lcms
-           libexif
-           libgsf
-           librsvg
-           libsixel
-           libwebp
-           libxcb
-           matio
-           nlohmann-json
-           opencv
-           openexr
-           openssl
-           orc
-           pango
-           poppler
-           range-v3
-           spdlog
-           tbb
-           vips
-           wayland
-           wayland-protocols
-           xcb-util-image))
-    (home-page "https://github.com/jstkdng/ueberzugpp")
-    (synopsis "Drop in replacement for ueberzug written in C++")
-    (description "Überzug++ is a command line utility written in C++ which
-allows to draw images on terminals by using X11/Wayland child windows, sixels,
- kitty and iterm2.
-
-Advantages over @command{w3mimgdisplay}:
-@itemize
-@item Support for Wayland: Sway, Hyprland, niri and Wayfire
-@item No race conditions as a new window is created to display images
-@item Expose events will be processed, so images will be redrawn on switch
-workspaces
-@item Tmux support on X11, Sway and Hyprland
-@item Terminals without the @env{WINDOWID} environment variable are supported
-@item Chars are used as position - and size unit
-@item No memory leak (usage of smart pointers)
-@item A lot of image formats supported (through OpenCV and libvips).
-@item GIF and animated WEBP support on X11, Sixel, Sway and hyprland
-@item Fast image downscaling (through OpenCV and OpenCL)
-@item Cache resized images for faster viewing
-@end itemize")
-    (license license:gpl3)))
-
 (define-public vv
   (package
     (name "vv")

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)
@@ -4540,7 +4540,7 @@ to separate the structure of documents from the data they contain.")
     (native-inputs
      (list extra-cmake-modules kdoctools pkg-config))
     (inputs
-     (list gpgme-2
+     (list gpgme
            kauth
            kcodecs
            kconfig
@@ -4585,7 +4585,7 @@ the passwords on KDE work spaces.")
     (native-inputs
      (list extra-cmake-modules kdoctools-5))
     (inputs
-     (list gpgme-2
+     (list gpgme
            kauth-5
            kcodecs-5
            kconfig-5

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)
@@ -581,7 +581,7 @@ PIM data into Akonadi for use in KDE PIM applications.")
            akonadi-mime
            boost
            breeze-icons
-           gpgme-2
+           gpgme
            grantleetheme
            kcmutils
            kcontacts
@@ -785,7 +785,7 @@ information.")
            akonadi-mime
            akonadi-search
            boost
-           gpgme-2
+           gpgme
            grantleetheme
            kcalendarcore
            kcmutils
@@ -1552,7 +1552,7 @@ protocol for querying and modifying directory services running over TCP/IP.")
            kdoctools))
     (inputs
      (list boost
-           gpgme-2
+           gpgme
            kcmutils
            kcodecs
            kconfig
@@ -1614,7 +1614,7 @@ and retrieving certificates from LDAP servers.")
            akonadi-mime
            akonadi-search
            boost
-           gpgme-2
+           gpgme
            grantleetheme
            kaddressbook
            kbookmarks
@@ -1788,7 +1788,7 @@ KMail.")
     (inputs
      (list akonadi-contacts
            boost
-           gpgme-2
+           gpgme
            grantleetheme
            karchive
            kcodecs
@@ -1972,7 +1972,7 @@ using a Qt/KMime C++ API.")
      (list akonadi-contacts
            akonadi-search
            boost
-           gpgme-2
+           gpgme
            grantleetheme
            karchive
            kcalendarcore
@@ -2634,7 +2634,7 @@ various Google services.")
      (list extra-cmake-modules kdoctools qttools))
     (inputs
      (list boost
-           gpgme-2
+           gpgme
            kcodecs
            kcompletion
            kconfig
@@ -2648,7 +2648,7 @@ various Google services.")
            kpimtextedit
            qgpgme))
     (propagated-inputs
-     (list gpgme-2 qgpgme))
+     (list gpgme qgpgme))
     (arguments
      (list
       #:qtbase qtbase

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/kde-utils.scm

@@ -344,7 +344,7 @@ your computer.")
                 "02g9k51srrqslapjxzcymnmy9v1frv9pkgg8wmf6d0607hwkaff5"))))
     (build-system qt-build-system)
     (native-inputs (list extra-cmake-modules))
-    (inputs (list gpgme-2
+    (inputs (list gpgme
                   kauth
                   karchive
                   kcoreaddons

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/libidn.scm

@@ -60,14 +60,14 @@ Java libraries.")
 (define-public libidn2
   (package
     (name "libidn2")
-    (version "2.3.8")
+    (version "2.3.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/libidn/" name "-" version
                                   ".tar.gz"))
               (sha256
                (base32
-                "0ykqq39yacg9vvf2alyl5sskbfr531dmzwrgyzhj25hpyqdr2mzm"))))
+                "0r3xzmmrx4hsc53jdncd5yqmkwzjgc4vh4hfkndm3f8hns8sf8ac"))))
     (inputs
      (list libunistring))
     (build-system gnu-build-system)

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"
-      #:librewolf-hash "0fm11phcpp2xggwdhdl044f4a015adg8bplw4cj0in5hq1zqkbi2"
+      #:firefox-hash "1h440pkdqkx3085ij9nz9n9h1b6c2p92bg3lf983my6b711f62m8"
+      #: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)
@@ -1218,6 +1218,12 @@ 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-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
@@ -1234,12 +1240,6 @@ 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-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
@@ -1979,6 +1979,8 @@ 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-7.0)
+
 (define-public linux-libre-arm64-mnt-reform-6.19
   ;; Kernel for use on the MNT/Reform systems
   ;; https://mntre.com/reform.html
@@ -2315,8 +2317,6 @@ 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-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
-       (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")))))
+      (inputs (list ggml openssl))
       (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)

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)
@@ -3857,15 +3857,11 @@ follows a traditional multi-track tape recorder control paradigm.")
      (list
       #:phases
       '(modify-phases %standard-phases
-         (add-after 'unpack 'python3.12-compatibility
+         (add-after 'unpack 'python3.11-compatibility
            (lambda _
              (substitute* '("waflib/Context.py"
                             "waflib/ConfigSet.py")
-               (("'rU'") "'r'"))
-             (substitute* "waflib/Context.py"
-               (("imp.new_module") "types.ModuleType")
-               (("import os, re, imp, sys")
-                "import os, re, types, sys"))))
+               (("'rU'") "'r'"))))
          (add-after 'unpack 'remove-sse-flags
            (lambda* (#:key system #:allow-other-keys)
              (unless (or (string-prefix? "x86_64" system)

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"))
-              (patches
-               (search-patches "musl-CVE-2026-40200.patch"))))
+                "1r3mgky9d19b2285s274qxzlgs7sncx8plm01vd691sdx2xii8d9"))))
     (build-system gnu-build-system)
     (arguments
      (list #:tests? #f                      ; musl has no tests