gnu: python-dill: Update to 0.4.1.

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

Change-Id: Ifd949babdc06ed4e33cdadae6f392c224f53197a

.dir-locals.el

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

Makefile.am

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

doc/guix.texi

@@ -53,7 +53,7 @@ Copyright @copyright{} 2017, 2019--2026 Maxim Cournoyer@*
 Copyright @copyright{} 2017–2022 Tobias Geerinckx-Rice@*
 Copyright @copyright{} 2017 George Clemmer@*
 Copyright @copyright{} 2017 Andy Wingo@*
-Copyright @copyright{} 2017, 2018, 2019, 2020, 2023, 2024, 2025, 2026 Arun Isaac@*
+Copyright @copyright{} 2017, 2018, 2019, 2020, 2023, 2024, 2025 Arun Isaac@*
 Copyright @copyright{} 2017 nee@*
 Copyright @copyright{} 2018 Rutger Helling@*
 Copyright @copyright{} 2018, 2021, 2023, 2025, 2026 Oleg Pykhalov@*
@@ -77,7 +77,7 @@ Copyright @copyright{} 2020 Damien Cassou@*
 Copyright @copyright{} 2020 Jakub Kądziołka@*
 Copyright @copyright{} 2020 Jack Hill@*
 Copyright @copyright{} 2020 Naga Malleswari@*
-Copyright @copyright{} 2020, 2021, 2025 Brice Waegeneire@*
+Copyright @copyright{} 2020, 2021 Brice Waegeneire@*
 Copyright @copyright{} 2020 R Veera Kumar@*
 Copyright @copyright{} 2020, 2021, 2022 Pierre Langlois@*
 Copyright @copyright{} 2020 pinoaffe@*
@@ -36741,16 +36741,13 @@ The Mumi package to use.
 Data directory to store Debbugs data from upstream Debbugs instance.
 
 @item @code{rsync-remote}
-Remote rsync path from which to download Debbugs data.
+Remote rsync path from which to download Debbugs data.  The remote is
+polled every 5 minutes, unless a previous instance of rsync is already
+running.
 
 @item @code{rsync-flags} (default: @code{'()})
 Additional flags to pass to @command{rsync}.
 
-@item @code{rsync-and-index-event} (default: @code{#~(calendar-event #:minutes '#$(iota 12 0 5))})
-Shepherd calendar event to run the rsync and indexing timer at.  By
-default, this is once every 5 minutes.  The timer job is not run if an
-earlier instance of it is still running.
-
 @item @code{mailer?} (default: @code{#true})
 Whether to enable or disable the mailer component.
 
@@ -52979,8 +52976,7 @@ subset of applications.  This field will be ignored if @code{layout} is set
 to @code{'plain}.
 
 @item @code{excluded} (default: @code{'(".*~" ".*\\.swp" "/\\.git/.*" "\\.gitignore")}) (type: list-of-strings)
-The list of file patterns (including directories)
+The list of file patterns @code{home-dotfiles-service-type} will exclude
-@code{home-dotfiles-service-type} will exclude
 while visiting each one of the @code{directories}.
 
 @end table
@@ -54396,69 +54392,6 @@ Where the service will write its logs.  If unset, it defaults to
 @end table
 @end deftp
 
-@node XDG Home Services
-@subsection XDG Home Services
-
-The @code{(gnu home services xdg)} module provides services related to
-XDG specifications for the desktop.
-
-@subsubheading XDG User Directories
-
-@defvar{home-xdg-user-directories-service-type}
-
-This service sets the names of default user directories such as
-@samp{Downloads} and @samp{Documents}.  These settings are respected by
-most applications via @var{xdg-user-dirs}.
-
-To disable a directory, set it to @code{"$HOME"}.
-
-@end defvar
-
-@c %start of fragment
-
-@deftp {Data Type} home-xdg-user-directories-configuration
-Available @code{home-xdg-user-directories-configuration} fields are:
-
-@table @asis
-@item @code{desktop} (default: @code{"$HOME/Desktop"}) (type: string)
-Default @samp{Desktop} directory, this is what you see on your
-background when using a desktop environment, e.g.  KDE.
-
-@item @code{documents} (default: @code{"$HOME/Documents"}) (type: string)
-Default directory to put documents like PDFs.
-
-@item @code{download} (default: @code{"$HOME/Downloads"}) (type: string)
-Default directory downloaded files, this is where your Web-broser will
-put downloaded files in.
-
-@item @code{music} (default: @code{"$HOME/Music"}) (type: string)
-Default directory for audio files.
-
-@item @code{pictures} (default: @code{"$HOME/Pictures"}) (type: string)
-Default directory for pictures and images.
-
-@item @code{projects} (default: @code{"$HOME/Projects"}) (type: string)
-Default directory for projects.
-
-@item @code{publicshare} (default: @code{"$HOME/Public"}) (type: string)
-Default directory for shared files, which can be accessed by other users
-on local machine or via network.
-
-@item @code{templates} (default: @code{"$HOME/Templates"}) (type: string)
-Default directory for templates.  They can be used by graphical file
-manager or other apps for creating new files with some pre-populated
-content.
-
-@item @code{videos} (default: @code{"$HOME/Videos"}) (type: string)
-Default directory for videos.
-
-@end table
-
-@end deftp
-
-@c %end of fragment
-
-
 @node Guix Home Services
 @subsection Guix Home Services
 

etc/git/commit-msg

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

gnu/home/services/dotfiles.scm

@@ -1,7 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2024 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2024, 2026 Giacomo Leidi <therewasa@fishinthecalculator.me>
-;;; Copyright © 2025 Brice Waegeneire <brice@waegenei.re>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -127,21 +126,18 @@ user's home directory, excluding files that match any of the patterns in EXCLUDE
 
 (define (home-dotfiles-configuration->files config)
   "Return a list of objects compatible with @code{home-files-service-type}'s
-value, excluding files and directories that match any of the patterns configured."
+value, excluding files that match any of the patterns configured."
   (define stow? (eq? (home-dotfiles-configuration-layout config) 'stow))
   (define excluded
     (home-dotfiles-configuration-excluded config))
   (define exclusion-rx
     (make-regexp (string-append "^.*(" (string-join excluded "|") ")$")))
-  (define* (excluded-file? file stat #:optional result)
-    (not (regexp-exec exclusion-rx file)))
 
   (define* (directory-contents directory #:key (packages #f))
     (define (filter-files directory)
       (find-files directory
-                  excluded-file?
+                  (lambda (file stat)
-                  #:enter?
+                    (not (regexp-exec exclusion-rx file)))))
-                  excluded-file?))
     (if (and stow? packages (maybe-value-set? packages))
         (append-map filter-files
                     (map (lambda (pkg)

gnu/home/services/xdg.scm

@@ -204,8 +204,9 @@ for example).")))
 (define-configuration home-xdg-user-directories-configuration
   (desktop
    (string "$HOME/Desktop")
-   "Default @samp{Desktop} directory, this is what you see on your background
+   "Default ``desktop'' directory, this is what you see on your
-when using a desktop environment, e.g. KDE.")
+desktop when using a desktop environment,
+e.g. GNOME (@pxref{XWindow,,,guix.info}).")
   (documents
    (string "$HOME/Documents")
    "Default directory to put documents like PDFs.")
@@ -219,9 +220,6 @@ will put downloaded files in.")
   (pictures
    (string "$HOME/Pictures")
    "Default directory for pictures and images.")
-  (projects
-   (string "$HOME/Projects")
-   "Default directory for projects.")
   (publicshare
    (string "$HOME/Public")
    "Default directory for shared files, which can be accessed by other

gnu/local.mk

@@ -1174,6 +1174,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/cube-nocheck.patch			\
   %D%/packages/patches/cups-relax-root-ownership-check.patch		\
   %D%/packages/patches/cura-engine-gcc-14.patch			\
+  %D%/packages/patches/curl-CVE-2024-8096.patch			\
   %D%/packages/patches/curl-use-ssl-cert-env.patch		\
   %D%/packages/patches/curlftpfs-fix-error-closing-file.patch	\
   %D%/packages/patches/curlftpfs-fix-file-names.patch		\
@@ -1831,6 +1832,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libtgvoip-disable-webrtc.patch 		\
   %D%/packages/patches/libtheora-config-guess.patch		\
   %D%/packages/patches/libtiff-CVE-2022-34526.patch		\
+  %D%/packages/patches/libtirpc-CVE-2021-46828.patch		\
   %D%/packages/patches/libtirpc-hurd.patch			\
   %D%/packages/patches/libtool-grep-compat.patch		\
   %D%/packages/patches/libtool-skip-tests2.patch		\
@@ -1965,7 +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		\
@@ -2003,6 +2005,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/nss-getcwd-nonnull.patch			\
   %D%/packages/patches/nss-increase-test-timeout.patch		\
   %D%/packages/patches/nss-3.56-pkgconfig.patch			\
+  %D%/packages/patches/nss-disable-broken-tests.patch           \
   %D%/packages/patches/nss-3.115-disable-broken-tests.patch     \
   %D%/packages/patches/nss-3.115-disable-pkix-ocsp-tests.patch  \
   %D%/packages/patches/ntp-fix-dereferencing-the-wrong-variable.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/aspell.scm

@@ -52,7 +52,7 @@
 (define-public aspell
   (package
     (name "aspell")
-    (version "0.60.8.2")
+    (version "0.60.8.1")
     (source
      (origin
       (method url-fetch)
@@ -60,7 +60,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "06b9szgm9cj1zh58r7sbl5fbi3vi9fs7b1as4ir8y176x9ilizjp"))
+        "06yjhwlgpcvbrl5g83qjrpzjwjx7hka5lhsfc3x5gm229nri5nnn"))
       (patches (search-patches "aspell-default-dict-dir.patch"))))
     (build-system gnu-build-system)
     (arguments

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)
@@ -276,7 +276,9 @@ has strong support for macros.")
      '(#:parallel-tests? #f))           ; Some tests fail
                                         ; non-deterministically when run in
                                         ; parallel
-    (inputs (list python-wrapper xmlto))
+    (inputs
+     `(("python" ,python-wrapper)
+       ("xmlto" ,xmlto)))
     (home-page "https://yasm.tortall.net/")
     (synopsis "Rewrite of the NASM assembler")
     (description

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)
@@ -1858,9 +1858,18 @@ R. Seaman's protocol}
          (file-name (git-file-name name version))
          (sha256
           (base32 "0n2jzlpwvjgj8ydg7hsqxnvy8s9pdi5z96id0231kgi87pyfkh7s"))
-         (modules '((guix build utils)))
+         (modules '((guix build utils)
+                    (ice-9 ftw)
+                    (srfi srfi-26)))
          (snippet
           #~(begin
+              ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+              (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-all-but "thirdparty" "thirdparty.cmake")))))
       (build-system cmake-build-system)
       (arguments

gnu/packages/audio.scm

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

gnu/packages/avahi.scm

@@ -98,24 +98,24 @@
                  (cut patch-shebang <> path)
                  (find-files (string-append #$output "/etc/avahi"))))))))
     (inputs
-     (cons* bash-minimal
+     `(("bash-minimal" ,bash-minimal)
-            dbus
+       ("dbus" ,dbus)
-            expat
+       ("expat" ,expat)
-            gdbm
+       ("gdbm" ,gdbm)
-            glib
+       ("glib" ,glib)
-            libdaemon
+       ;; Do not use libcap when cross-compiling since it's not quite
-            libevent
+       ;; cross-compilable; and use it only for supported systems.
-            ;; Do not use libcap when cross-compiling since it's not quite
+       ,@(if (and (not (%current-target-system))
-            ;; cross-compilable; and use it only for supported systems.
+                  (member (%current-system)
-            (if (and (not (%current-target-system))
+                          (package-supported-systems libcap)))
-                     (member (%current-system)
+             `(("libcap" ,libcap))   ;to enable chroot support in avahi-daemon
-                             (package-supported-systems libcap)))
+             '())
-                (list libcap)        ;to enable chroot support in avahi-daemon
+       ("libdaemon" ,libdaemon)
-                (list))))
+       ("libevent" ,libevent)))
     (native-inputs
-     (list gettext-minimal
+     `(("gettext" ,gettext-minimal)
-           (list glib "bin")
+       ("glib" ,glib "bin")
-           pkg-config))
+       ("pkg-config" ,pkg-config)))
     (synopsis "Implementation of mDNS/DNS-SD protocols")
     (description
      "Avahi is a system which facilitates service discovery on a local

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)
@@ -3864,13 +3864,20 @@ familiar to anyone with experience of scikit-learn or scipy.")
       (file-name (git-file-name name version))
       (sha256
        (base32 "0hznpj15kx2sla16wlmcqz21n2vi2qb1493v30vz75hnm1m4iwm1"))
-      (modules '((guix build utils)))
+      (modules '((guix build utils)
+                 (ice-9 ftw)))
       (snippet
        #~(begin
            ;; Delete everything except for examples directory:
-           (delete-all-but ".""pysnptools" "tests")
+           (define (delete-except exceptions)
-           (delete-all-but "pysnptools" "examples")
+             (lambda (file)
-           (delete-all-but "tests" "datasets"))))))
+               (unless (member file `("." ".." ,@exceptions))
+                 (delete-file-recursively file))))
+           (for-each (delete-except '("pysnptools" "tests")) (scandir "."))
+           (with-directory-excursion "pysnptools"
+             (for-each (delete-except '("examples")) (scandir ".")))
+           (with-directory-excursion "tests"
+             (for-each (delete-except '("datasets")) (scandir "."))))))))
 
 (define-public python-pysnptools
   (package
@@ -6703,20 +6710,20 @@ meso, or continuum scale.")
                 "09693dmf1scdac5pyq6qyn8b4mcipvnmc370k9a5z41z81m3dcsj"))))
     (build-system gnu-build-system)
     (arguments
-     (list
+     `(#:test-target "test"
-       #:test-target "test"
        #:tests? #f ; tests require access to the web
        #:make-flags
-       #~(list "CC=gcc"
+       ,#~(list "CC=gcc"
-               (string-append "prefix=" #$output))
+                (string-append "prefix=" #$output))
        #:phases
-       #~(modify-phases %standard-phases
+       (modify-phases %standard-phases
          (delete 'configure))))
     (inputs
      (list zlib curl))
     (native-inputs
-     (list doxygen
+     `(("doxygen" ,doxygen)
-           python)) ;for tests
+       ;; Need for tests
+       ("python" ,python-2)))
     (home-page "https://github.com/dpryan79/libBigWig")
     (synopsis "C library for handling bigWig files")
     (description
@@ -17832,99 +17839,94 @@ once.  This package provides tools to perform Drop-seq analyses.")
     (license license:expat)))
 
 (define-public pigx-rnaseq
-  (let ((commit "1605b541da090e13d58dae6fed38ae8dda09f002"))
+  (package
-    (package
+    (name "pigx-rnaseq")
-      (name "pigx-rnaseq")
+    (version "0.1.1")
-      (version (git-version "0.1.1" "0" commit))
+    (source (origin
-      (source (origin
+              (method url-fetch)
-                (method git-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
-                (uri (git-reference
+                                  "releases/download/v" version
-                       (url "https://github.com/BIMSBbioinfo/pigx_rnaseq/")
+                                  "/pigx_rnaseq-" version ".tar.gz"))
-                       (commit commit)
+              (sha256
-                       (recursive? #true)))
+               (base32
-                (file-name (git-file-name name version))
+                "0mlas0srl04mvgsyydm67gg5syijf1k2f6dy7bdqqxc70fywfd08"))))
-                (sha256
+    (build-system gnu-build-system)
-                 (base32
+    (arguments
-                  "1j5c0wlasmxvz9z64yga56m2hhbybl149kknsrpvmq0v2gl31rn5"))))
+     `(#:parallel-tests? #f             ; not supported
-      (build-system gnu-build-system)
+       #:phases
-      (arguments
+       (modify-phases %standard-phases
-       (list
+         ;; "test.sh" runs the whole pipeline, which takes a long time and
-        #:parallel-tests? #f             ; not supported
+         ;; might fail due to OOM.  The MultiQC is also resource intensive.
-        #:phases
+         (add-after 'unpack 'disable-resource-intensive-test
-        '(modify-phases %standard-phases
+           (lambda _
-           ;; "test.sh" runs the whole pipeline, which takes a long time and
+             (substitute* "Makefile.in"
-           ;; might fail due to OOM.  The MultiQC is also resource intensive.
+               (("^  tests/test_multiqc/test.sh") "")
-           (add-after 'unpack 'disable-resource-intensive-test
+               (("^  test.sh") ""))))
-             (lambda _
+         (add-before 'bootstrap 'autoreconf
-               (substitute* "Makefile.am"
+           (lambda _
-                 (("^  tests/test_multiqc/test.sh.*") "")
+             (invoke "autoreconf" "-vif")))
-                 (("^  tests/test_hisat2/test.sh.*") "  tests/test_hisat2/test.sh\n")
+         (add-before 'configure 'set-PYTHONPATH
-                 (("^  test.sh") ""))))
+           (lambda _
-           (add-before 'bootstrap 'autoreconf
+             (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
-             (lambda _
+         (add-before 'check 'set-timezone
-               (invoke "autoreconf" "-vif")))
+           ;; The readr package is picky about timezones.
-           (add-before 'configure 'set-PYTHONPATH
+           (lambda* (#:key inputs #:allow-other-keys)
-             (lambda _
+             (setenv "TZ" "UTC+1")
-               (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
+             (setenv "TZDIR"
-           (add-before 'check 'set-timezone
+                     (search-input-directory inputs
-             ;; The readr package is picky about timezones.
+                                             "share/zoneinfo"))))
-             (lambda* (#:key inputs #:allow-other-keys)
+         (add-before 'check 'pre-check
-               (setenv "TZ" "UTC+1")
+           (lambda _
-               (setenv "TZDIR"
+             ;; Needed for tests
-                       (search-input-directory inputs
+             (setenv "HOME" "/tmp"))))))
-                                               "share/zoneinfo"))))
+    (inputs
-           (add-before 'check 'pre-check
+     (list coreutils
-             (lambda _
+           sed
-               ;; Needed for tests
+           gzip
-               (setenv "HOME" "/tmp"))))))
+           snakemake-7
-      (inputs
+           megadepth
-       (list coreutils
+           multiqc
-             sed
+           star-for-pigx
-             gzip
+           hisat2
-             snakemake
+           fastp
-             megadepth
+           htseq
-             multiqc
+           samtools
-             star-for-pigx
+           r-minimal
-             hisat2
+           r-rmarkdown
-             fastp
+           r-genomeinfodb
-             htseq
+           r-ggplot2
-             samtools
+           r-ggpubr
-             r-minimal
+           r-ggrepel
-             r-rmarkdown
+           r-gprofiler2
-             r-genomeinfodb
+           r-deseq2
-             r-ggplot2
+           r-dt
-             r-ggpubr
+           r-knitr
-             r-ggrepel
+           r-pheatmap
-             r-gprofiler2
+           r-corrplot
-             r-deseq2
+           r-reshape2
-             r-dt
+           r-plotly
-             r-knitr
+           r-scales
-             r-pheatmap
+           r-summarizedexperiment
-             r-corrplot
+           r-crosstalk
-             r-reshape2
+           r-tximport
-             r-plotly
+           r-rtracklayer
-             r-scales
+           r-rjson
-             r-summarizedexperiment
+           salmon
-             r-crosstalk
+           pandoc
-             r-tximport
+           python-wrapper
-             r-rtracklayer
+           python-deeptools
-             r-rjson
+           python-pyyaml))
-             salmon
+    (native-inputs
-             pandoc
+     (list tzdata automake autoconf))
-             python-wrapper
+    (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
-             python-deeptools
+    (synopsis "Analysis pipeline for RNA sequencing experiments")
-             python-pyyaml))
+    (description "PiGX RNAseq is an analysis pipeline for preprocessing and
-      (native-inputs
-       (list tzdata automake autoconf))
-      (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
-      (synopsis "Analysis pipeline for RNA sequencing experiments")
-      (description "PiGX RNAseq is an analysis pipeline for preprocessing and
 reporting for RNA sequencing experiments.  It is easy to use and produces high
 quality reports.  The inputs are reads files from the sequencing experiment,
 and a configuration file which describes the experiment.  In addition to
 quality control of the experiment, the pipeline produces a differential
 expression report comparing samples in an easily configurable manner.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public pigx-chipseq
   (package
@@ -18130,7 +18132,7 @@ methylation and segmentation.")
            python-loompy
            pandoc
            samtools
-           snakemake-6
+           snakemake-5
            star-for-pigx
            r-minimal
            r-argparser

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/boost.scm

@@ -271,8 +271,7 @@ across a broad spectrum of applications.")
                 "0yrgn6syk260ckq9ld44vjv1bl6bamhy3jbp10kikcipcv0d5na6"))))))
 
 (define-public boost-1.83
-  (package
+  (hidden-package (package (inherit boost)
-    (inherit boost)
     (name "boost")
     (version "1.83.0")
     (source (origin
@@ -283,7 +282,7 @@ across a broad spectrum of applications.")
               (patches
                  (list (boost-patch
                         "0001-unordered-fix-copy-assign.patch" version
-                        "0l520lqh2vxdlyzvpki6hy2ylqimag8v18n2sdbmliifxiiha4gl")))
+                        "09j61m5xh7099k5na9i43x5rra51znf7vm2nyh89yqpizcll9q66")))
               (patch-flags '("-p2"))
               (sha256
                (base32
@@ -313,7 +312,7 @@ across a broad spectrum of applications.")
                             (else
                              #~())))
                      ;; Not cross-compiling.
-                     #~())))))))
+                     #~()))))))))
 
 (define-deprecated-package boost-with-python3
   boost)

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/check.scm

@@ -1139,7 +1139,8 @@ Anything Protocol} compliant programs can also be executed through Kyua.")
     (arguments
      `(#:tests? #f
        #:configure-flags '("-DBUILD_SHARED_LIBS=ON")))
-    (native-inputs (list python-wrapper))
+    (native-inputs
+     `(("python" ,python-wrapper)))
     (home-page "https://github.com/google/googletest/")
     (synopsis "Test discovery and XUnit test framework")
     (description "Google Test features an XUnit test framework, automated test

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/cluster.scm

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

gnu/packages/cobol.scm

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

gnu/packages/code.scm

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

gnu/packages/commencement.scm

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

gnu/packages/compiler-tools.scm

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

gnu/packages/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/curl.scm

@@ -68,15 +68,16 @@
 (define-public curl
   (package
     (name "curl")
-    (version "8.20.0")
+    (version "8.6.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://curl.se/download/curl-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "15mqw8y9vdxlz9cpr2z7q9r6552wgs7q7vr2k7lfl35s930jvzk3"))
+                "05fv468yjrb7qwrxmfprxkrcckbkij0myql0vwwnalgr3bcmbk9w"))
-              (patches (search-patches "curl-use-ssl-cert-env.patch"))))
+              (patches (search-patches "curl-use-ssl-cert-env.patch"
+                                       "curl-CVE-2024-8096.patch"))))
     (outputs '("out"
                "doc"))                  ;1.2 MiB of man3 pages
     (build-system gnu-build-system)
@@ -105,20 +106,36 @@
               (mkdir-p (string-append #$output:doc "/share/man"))
               (rename-file (string-append #$output "/share/man/man3")
                            (string-append #$output:doc "/share/man/man3"))))
-          (add-after 'unpack 'patch-runtests
+          (replace 'check
-            (lambda _
+            (lambda* (#:key tests? parallel-tests? make-flags #:allow-other-keys)
               (substitute* "tests/runtests.pl"
-                (("/bin/sh") (which "sh")))))
+                (("/bin/sh") (which "sh")))
-          #$@(if (or (target-arm32?)
+              (when tests?
-                     (target-aarch64?))
+                (let* ((job-count (string-append
-                 #~((add-after 'unpack 'skip-tests
+                                   "-j"
-                      (lambda _
+                                   (if parallel-tests?
-                        (let ((port (open-file "tests/data/DISABLED" "a")))
+                                       (number->string (parallel-job-count))
-                          (display "1474\n" port)
+                                       "1")))
-                          (close port)))))
+                       ;; Ignore test 1477 due to a missing file in the 8.5.0
-                 #~())
+                       ;; release.  See
+                       ;; <https://github.com/curl/curl/issues/12462>.
+                       (arguments `("-C" "tests" "test"
+                                    ,@make-flags
+                                    ,(if #$(or (system-hurd?)
+                                               (target-arm32?)
+                                               (target-aarch64?))
+                                         ;; protocol FAIL
+                                         (string-append "TFLAGS=~1474 "
+                                                        "!1477 "
+                                                        job-count)
+                                         (string-append "TFLAGS=\"~1477 "
+                                                        job-count "\"")))))
+                  ;; The top-level "make check" does "make -C tests quiet-test", which
+                  ;; is too quiet.  Use the "test" target instead, which is more
+                  ;; verbose.
+                  (apply invoke "make" arguments)))))
           #$@(if (system-hurd?)
-                 #~((add-after 'unpack 'skip-tests/hurd
+                 #~((add-after 'unpack 'skip-tests
                       (lambda _
                         (let ((port (open-file "tests/data/DISABLED" "a")))
                           (display "526\n" port)
@@ -130,20 +147,11 @@
                           (display "564\n" port)
                           (display "575\n" port)
                           (display "1021\n" port)
-                          (display "1474\n" port)
                           (display "1501\n" port)
                           (close port)))))
-                 #~())
+                 #~()))))
-          (add-after 'install 'sanitize-libcurl.pc
-            (lambda _
-              ;; The pkgconfig file has all dependencies in Requires.private
-              ;; which is unnecessary for our shared library use and would
-              ;; require propagating them.
-              (substitute* (string-append #$output "/lib/pkgconfig/libcurl.pc")
-                (("^Requires.private:.*") "")))))))
     (native-inputs
-     (list nghttp2 perl pkg-config python-minimal-wrapper
+     (list nghttp2 perl pkg-config python-minimal-wrapper))
-           openssl))                    ;for tests
     (inputs
      (list gnutls libidn libpsl mit-krb5 `(,nghttp2 "lib") zlib))
     (native-search-paths

gnu/packages/databases.scm

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

gnu/packages/datalog.scm

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

gnu/packages/debug.scm

@@ -58,7 +58,7 @@
   #:use-module (gnu packages code)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages digest)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gdb)
@@ -1112,9 +1112,17 @@ to aid in debugging.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256 (base32 "0ppx8r9isc772y0ahpgl8g5b3yxka7ffqzlcsa920aib5nj39lrg"))
-       (modules '((guix build utils)))
+       (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))))
             (substitute* "pyproject.toml"
               ;; Python is linked with GNU readline on all Guix targets.
               ((".*gnureadline.*") "")

gnu/packages/dictionaries.scm

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

gnu/packages/django.scm

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

gnu/packages/dns.scm

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

gnu/packages/documentation.scm

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

gnu/packages/dotnet.scm

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

gnu/packages/education.scm

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

gnu/packages/electronics.scm

@@ -90,7 +90,7 @@
   #:use-module (gnu packages elf)
   #:use-module (gnu packages embedded)
   #:use-module (gnu packages engineering)
-  #:use-module (gnu packages compiler-tools)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gawk)
@@ -1750,21 +1750,31 @@ exploration and optimization.")
               (commit version)
               (recursive? #t)))
        (file-name (git-file-name name version))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
        (snippet
-        #~(delete-all-but "libs"
+        #~(begin
-            "delaunay-triangulation"
+            ;; XXX: 'delete-all-but' is copied from the turbovnc package.
-            "dxflib"
+            (define (delete-all-but directory . preserve)
-            ;; "fontobene-qt"
+              (with-directory-excursion directory
-            ;; "googletest"
+                (let* ((pred (negate (cut member <>
-            ;; "hoedown"
+                                          (cons* "." ".." preserve))))
-            "librepcb"
+                       (items (scandir "." pred)))
-            ;; "muparser"
+                  (for-each (cut delete-file-recursively <>) items))))
-            "optional"
+            (delete-all-but "libs"
-            "parseagle"
+                            "delaunay-triangulation"
-            ;; "polyclipping"
+                            "dxflib"
-            ;; "quazip"
+                            ;; "fontobene-qt"
-            "type_safe"))
+                            ;; "googletest"
+                            ;; "hoedown"
+                            "librepcb"
+                            ;; "muparser"
+                            "optional"
+                            "parseagle"
+                            ;; "polyclipping"
+                            ;; "quazip"
+                            "type_safe")))
        (sha256
         (base32 "1g3k2g2p5yy7zk971bg7qh4k38p30aydp27c5bfb02gn7djknz7w"))))
     (build-system cmake-build-system)
@@ -2348,9 +2358,18 @@ layout of a circuit corresponds to the desired netlists.")
               ;; no longer have their original upstream.
               (recursive? #t)))
        (file-name (git-file-name name version))
-       (modules '((guix build utils)))
        (snippet
         #~(begin
+            (use-modules (guix build utils)
+                         (ice-9 ftw)
+                         (srfi srfi-26))
+            ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+            (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-all-but "3rdparty"
                             ;; The following sources have all been patched, so
                             ;; cannot easily be unbundled.

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")
@@ -16148,9 +16152,18 @@ placed at the margin of the minibuffer for your completion candidates.")
                (url "https://github.com/Fuco1/smartparens")
                (commit commit)))
          (file-name (git-file-name name version))
-         (modules '((guix build utils)))
+         (modules '((guix build utils)
+                    (ice-9 ftw)
+                    (srfi srfi-26)))
          (snippet
           '(begin
+             ;; Taken from nextpnr package.
+             (define (delete-all-but directory . preserve)
+               (with-directory-excursion directory
+                 (let* ((pred
+                         (negate (cut member <> (append '("." "..") preserve))))
+                        (items (scandir "." pred)))
+                   (for-each delete-file items))))
              ;; Only activate basic tests.
              (delete-all-but "test"
                              "test-helper.el"
@@ -16781,51 +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")
@@ -42111,7 +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
@@ -42120,7 +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)
@@ -464,6 +464,13 @@ It aims to support Nintendo DSi and 3DS as well.")
                     (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))))
+
               ;; Clean up the source from bundled libraries we don't need.
               (delete-all-but "Externals"
                               ;; XXX: The build system is currently hard-coded
@@ -653,6 +660,14 @@ turbo speed, networked multiplayer, and graphical enhancements.")
                     (srfi srfi-26)))
          (snippet
           #~(begin
+              ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+              (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))))
+
               ;; Clean up the source from bundled libraries we don't need.
               (delete-all-but "Externals"
                               ;; XXX: The build system is currently hard-coded
@@ -1068,9 +1083,17 @@ The following systems are supported:
          (sha256
           (base32
            "0dfsz4dsh49dc9xx9rjhfzfkg4h91i2ksgp2inlr9yhgldw9q8h3"))
-         (modules '((guix build utils)))
+         (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-all-but "src/third-party"
                               "blip_buf"
                               "inih")))))
@@ -2301,9 +2324,42 @@ physical device and the RetroPad virtual controller.")
          (modules '((guix build utils)))
          (snippet
           '(begin
+             (use-modules (guix build utils)
+                          (ice-9 ftw)
+                          (srfi srfi-1)
+                          (srfi srfi-26))
+             (define (delete-all-but . preserve)
+               ;; Walk the file tree and delete everything except the paths
+               ;; listed in PRESERVE.  Directories listed PRESERVE will cause
+               ;; their whole contents to be preserved.
+               (let ((preserve (map (compose (cut string-trim-right <> #\/)
+                                             (cut string-append "./" <>))
+                                    preserve)))
+                 (file-system-fold
+                  (lambda (path stat result) ;enter
+                    (or (any (lambda (x)
+                               (or (string-prefix? path x)
+                                   (string-prefix? x path)))
+                             preserve)
+                        (begin
+                          (delete-file-recursively path)
+                          #f)))
+                  (lambda (path stat result) ;leaf (file)
+                    (unless (any (cut string-prefix? <> path) preserve)
+                      (delete-file path)))
+                  (const #t)                 ;down (directory)
+                  (const #t)                 ;up (directory)
+                  (lambda (path stat result) ;skip
+                    (when (file-exists? path)
+                      (error "could not enter unreadable directory" path)))
+                  (lambda (path stat errno result) ;error
+                    (error "error processing" path (strerror errno)))
+                  0
+                  ".")))
+
              ;; This is an allow-list of the shaders explicitly licensed as
              ;; free software.
-             (delete-all-but "."
+             (delete-all-but
               "anamorphic/shaders/anamorphic.slang" ;expat
               "anamorphic/anamorphic.slangp"
               "annotated_passthru.slang" ;public license
@@ -2960,7 +3016,16 @@ GLSL (@file{.slang}) shaders for use with RetroArch.")
              (commit (string-append "v" version))))
        (snippet
         #~(begin
-            (use-modules (guix build utils))
+            (use-modules (guix build utils)
+                         (ice-9 ftw)
+                         (srfi srfi-26))
+            ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+            (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))))
             ;; Remove as much bundled sources as possible, shaving off about
             ;; 65 MiB.
             (delete-all-but "deps"
@@ -3769,14 +3834,24 @@ de-interlacing patches for use with PCSX2.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0nr53cjifqwnz3icxsj01yd3aw1vfsfxga4zz5zi8aqr175mvq27"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
        (snippet
         #~(begin
             (substitute* "cmake/Pcsx2Utils.cmake"
               (("(PCSX2_GIT_REV \")Unknown" _ prefix)
                (string-append prefix #$version "-guix")))
             (delete-file "3rdparty/include/Packet32.h") ;"not open source"
-            (delete-all-but "3rdparty"
+            ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+            (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-all-but
+             "3rdparty"
              ;; asl2.0 and cc0
              "glad"                     ;Is tailored.
              ;; bsd-3

gnu/packages/engineering.scm

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

gnu/packages/esolangs.scm

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

gnu/packages/fabric-management.scm

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

gnu/packages/file-systems.scm

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

gnu/packages/finance.scm

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

gnu/packages/firmware.scm

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

gnu/packages/flashing-tools.scm

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

gnu/packages/flex.scm

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

gnu/packages/fltk.scm

@@ -23,6 +23,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages fltk)
+  #:use-module ((guix licenses) #:select (lgpl2.0 lgpl2.0+))
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages build-tools)
@@ -34,10 +35,8 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
-  #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
+  #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system waf)
@@ -57,63 +56,63 @@
       (sha256
        (base32 "0pnifyhhvcqfjd6iaa4m14kvfyqhjjdw0aqbcizcdhhqrl6q4pjg"))))
    (build-system gnu-build-system)
+   (native-inputs
+    (list autoconf
+          automake
+          pkg-config))
+   (inputs
+    `(("libjpeg" ,libjpeg-turbo)
+      ("libpng" ,libpng)
+      ("libx11" ,libx11)
+      ("libxft" ,libxft)
+      ("mesa" ,mesa)
+      ("zlib" ,zlib)))
     (arguments
-     (list
+     `(#:tests? #f                      ;TODO: compile programs in "test" dir
-      #:tests? #f ;TODO: compile programs in "test" dir
+       #:configure-flags
-      #:configure-flags
+       (list "--enable-shared"
-      #~(list "--enable-shared"
+             (string-append "DSOFLAGS=-Wl,-rpath=" %output "/lib"))
-              (string-append "DSOFLAGS=-Wl,-rpath=" %output "/lib"))
+       #:phases
-      #:phases
+       (modify-phases %standard-phases
-      #~(modify-phases %standard-phases
+         (add-before 'configure 'patch-makeinclude
-          (add-before 'configure 'patch-makeinclude
+           (lambda _
-            (lambda _
+             (substitute* "makeinclude.in"
-              (substitute* "makeinclude.in"
+               (("/bin/sh") (which "sh")))
-                (("/bin/sh")
+             #t))
-                 (which "sh")))))
+         (add-after 'install 'patch-config
-          (add-after 'install 'patch-config
+           ;; Provide -L flags for image libraries when querying fltk-config to
-            ;; Provide -L flags for image libraries when querying fltk-config to
+           ;; avoid propagating inputs.
-            ;; avoid propagating inputs.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
-            (lambda* (#:key inputs #:allow-other-keys)
+             (let ((conf (string-append (assoc-ref outputs "out")
-              (let ((conf (string-append #$output "/bin/fltk-config"))
+                                        "/bin/fltk-config"))
-                    (libjpeg-so (search-input-file inputs "lib/libjpeg.so"))
+                   (jpeg (assoc-ref inputs "libjpeg"))
-                    (libpng-so (search-input-file inputs "lib/libpng.so"))
+                   (png  (assoc-ref inputs "libpng"))
-                    (libz-so (search-input-file inputs "lib/libz.so")))
+                   (zlib (assoc-ref inputs "zlib")))
-                (substitute* conf
+               (substitute* conf
-                  (("-ljpeg")
+                 (("-ljpeg") (string-append "-L" jpeg "/lib -ljpeg"))
-                   (string-append "-L" (dirname libjpeg-so) " -ljpeg"))
+                 (("-lpng") (string-append "-L" png "/lib -lpng"))
-                  (("-lpng")
+                 (("-lz") (string-append "-L" zlib "/lib -lz"))))
-                   (string-append "-L" (dirname libpng-so) " -lpng"))
+             #t)))))
-                  (("-lz")
-                   (string-append "-L" (dirname libz-so) " -lz")))))))))
-    (native-inputs (list autoconf automake pkg-config))
-    (inputs
-     (list libjpeg-turbo
-           libpng
-           libx11
-           libxft
-           mesa
-           zlib))
     (home-page "https://www.fltk.org")
     (synopsis "3D C++ GUI library")
-    (description
+    (description "FLTK is a C++ GUI toolkit providing modern GUI functionality
-     "FLTK is a C++ GUI toolkit providing modern GUI functionality without the
+without the bloat.  It supports 3D graphics via OpenGL and its built-in GLUT
-bloat.  It supports 3D graphics via OpenGL and its built-in GLUT emulation.
+emulation.  FLTK is designed to be small and modular enough to be statically
-FLTK is designed to be small and modular enough to be statically linked, but
+linked, but works fine as a shared library.  FLTK also includes an excellent
-works fine as a shared library.  FLTK also includes an excellent UI builder
+UI builder called FLUID that can be used to create applications in minutes.")
-called FLUID that can be used to create applications in minutes.")
+    (license lgpl2.0))) ; plus certain additional permissions
-    (license license:lgpl2.0))) ; plus certain additional permissions
 
 (define-public fltk
   (package
     (inherit fltk-1.3)
-    (version "1.4.5")
+    (version "1.4.4")
     (source (origin
       (method git-fetch)
       (uri (git-reference
               (url "https://github.com/fltk/fltk")
               (commit (string-append "release-" version))))
       (sha256
-       (base32 "19bl0ryarg31wkhw01ryilp9iwwh6vwnsq9mnzmarzm0dkwhjc7c"))))))
+       (base32 "1nfl37c9yplp4gxjjlajysfj2vsr47xjlcq78ambd7im4wbjgj76"))))))
 
 
 (define-public ntk
@@ -163,4 +162,4 @@ called FLUID that can be used to create applications in minutes.")
 library, adding improved graphics rendering via Cairo, a streamlined and
 enhanced widget set, and other features designed to improve the appearance and
 performance of the Non applications.")
-    (license license:lgpl2.0+))) ; plus certain additional permissions
+    (license lgpl2.0+))) ; plus certain additional permissions

gnu/packages/fonts.scm

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

gnu/packages/fontutils.scm

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

gnu/packages/freedesktop.scm

@@ -792,16 +792,16 @@ the freedesktop.org XDG Base Directory specification.")
 (define-public elogind
   (package
     (name "elogind")
-    (version "255.22")
+    (version "255.17")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/elogind/elogind")
-                    (commit (string-append "V" version))))
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0hnzks8f0jl2hkf954pqky5490zacqaipz20k38qvzl5g8i1if5l"))))
+                "0cb6p559281dzh24is91v6d4v4kz45yhyizibi4sfql9nign865h"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags
@@ -2733,20 +2733,18 @@ Rendering Manager devices.")
 (define-public xdg-user-dirs
   (package
     (name "xdg-user-dirs")
-    (version "0.20")
+    (version "0.17")
     (source (origin
-              (method git-fetch)
+              (method url-fetch)
-              (uri (git-reference
+              (uri (string-append "http://user-dirs.freedesktop.org/releases/"
-                     (url "https://gitlab.freedesktop.org/xdg/xdg-user-dirs.git")
+                                    name "-" version ".tar.gz"))
-                     (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
               (sha256
-               (base32
+               (base32 "13216b8rfkzak5k6bvpx6jvqv3cnbgpijnjwj8a8d3kq4cl0a1ra"))))
-                "1s235wp6z0d94z5qhwf408ppli1p3s3zah8rynm9ljh3hmmv0p2g"))))
+    (build-system gnu-build-system)
-    (build-system meson-build-system)
     (native-inputs
      (list gettext-minimal
            docbook-xsl
+           docbook-xml-4.3
            libxslt))
     (home-page "https://www.freedesktop.org/wiki/Software/xdg-user-dirs/")
     (synopsis "Tool to help manage \"well known\" user directories")

gnu/packages/game-development.scm

@@ -1181,9 +1181,17 @@ It is capable of creating games for SCUMM version 6 and partially version 7.")
        (sha256
         (base32
          "12f1d45995qf5sazjmmfdydllcd6alhqs1s4xwv3jiq1fw66hcy9"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
        (snippet
         '(begin
+           ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+           (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-all-but "extlibs/headers"
                            "glad")))))  ;pre-generated headers
     (build-system cmake-build-system)

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

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

gnu/packages/golang-apps.scm

@@ -192,9 +192,17 @@ definitions in Go programs.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0c1rxbj3v3m0fqb8q96xlbawxm9scyx6vvr8pddkiwp7zkx4ajym"))
-       (modules '((guix build utils)))
+       (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-all-but "cmd" "godoc")
             (delete-all-but "." "cmd")))))
     (build-system go-build-system)

gnu/packages/golang-build.scm

@@ -1535,9 +1535,17 @@ Go programming language.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0sjvngpahkb5x573i855fjlb1fdmr6n269nmb5xxnbabjb27mnvg"))
-       (modules '((guix build utils)))
+       (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-all-but "go" "expect")
             (delete-all-but "." "go")))))
     (build-system go-build-system)
@@ -1567,9 +1575,17 @@ Go source code (including go.mod and go.work files) as test expectations.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0sjvngpahkb5x573i855fjlb1fdmr6n269nmb5xxnbabjb27mnvg"))
-       (modules '((guix build utils)))
+       (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-all-but "go" "packages")
             (delete-all-but "go/packages" "packagestest")
             (delete-all-but "." "go")))))
@@ -1602,9 +1618,18 @@ tools on.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "1blk22apy424j9v58lfy4pxnrgh93yqchqhxsnf78dmx4vx5yi9r"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
        (snippet
-        #~(begin (delete-all-but "." "godoc")))))
+        #~(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-all-but "." "godoc")))))
     (build-system go-build-system)
     (arguments
      (list

gnu/packages/golang-xyz.scm

@@ -1304,8 +1304,26 @@ may be interactive or produce standard formats such as SVG or PDF.")
          (file-name (git-file-name name version))
          (sha256
           (base32 "1np11if704xzyhsx9mqhz7djx23g6wnz62r1v9ra6xaz91yfic0n"))
-         (modules '((guix build utils)))
+         (modules '((guix build utils)
-         (snippet #~(delete-all-but "." "generate"))))
+                    (ice-9 ftw)
+                    (srfi srfi-26)))
+         (snippet
+          #~(begin
+              ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+              (define (delete-all-but directory . preserve)
+                (define (directory? x)
+                  (and=> (stat x #f)
+                         (compose (cut eq? 'directory <>) stat:type)))
+                (with-directory-excursion directory
+                  (let* ((pred
+                          (negate (cut member <> (append '("." "..") preserve))))
+                         (items (scandir "." pred)))
+                    (for-each (lambda (item)
+                                (if (directory? item)
+                                    (delete-file-recursively item)
+                                    (delete-file item)))
+                              items))))
+              (delete-all-but "." "generate")))))
       (build-system go-build-system)
       (arguments
        (list
@@ -5047,8 +5065,18 @@ and multi-selects with a focus on user experience and aesthetics.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "1nr09574rdrgnsj7c2z11233zljl3gcqax0jb3na6v4ixl7gnhq2"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
-       (snippet #~(delete-all-but "." "ansi"))))
+                  (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-all-but "." "ansi")))))
     (build-system go-build-system)
     (arguments
      (list
@@ -5085,7 +5113,14 @@ ECMA-48} specs.")
                   (ice-9 ftw)
                   (srfi srfi-26)))
        (snippet
-        #~(begin (delete-all-but "." "cellbuf")))))
+        #~(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-all-but "." "cellbuf")))))
     (build-system go-build-system)
     (arguments
      (list
@@ -5143,8 +5178,18 @@ ECMA-48} specs.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "088786ak8jsgvssbb5y16z066vfq9f6078sjc7iv766knfr2i0x2"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
-       (snippet #~(delete-all-but "." "errors"))))
+                  (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-all-but "." "errors")))))
     (build-system go-build-system)
     (arguments
      (list
@@ -5296,9 +5341,18 @@ package provides an API for comparing Golden files.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "1shw55110fnn4xz80wmgr18czmiil6z1j064m90iw8c7j9llfzn5"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
        (snippet
-        #~(begin (delete-all-but "." "term")))))
+        #~(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-all-but "." "term")))))
     (build-system go-build-system)
     (arguments
      (list
@@ -5386,8 +5440,21 @@ package provides an API for comparing Golden files.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0blpb8vpl7sc6pb43h0730wdcwrkvnhly6qhik6wljrzn2nqz5g2"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
-       (snippet #~(delete-all-but "." "xpty"))))
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+            ;; Consider implementing it as a reusable procedure in
+            ;; guix/build/utils or guix/build-system/go.
+            (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-all-but "." "xpty")))))
     (build-system go-build-system)
     (arguments
      (list
@@ -6470,8 +6537,21 @@ packages.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0afaljkkd388f6igr3f2vjnd14yr8h20fcfzglw8j5q1q7a1cvik"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
-       (snippet #~(delete-all-but "." "pkg"))))
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+            ;; Consider implementing it as a reusable procedure in
+            ;; guix/build/utils or guix/build-system/go.
+            (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-all-but "." "pkg")))))
     (build-system go-build-system)
     (arguments
      (list
@@ -16056,9 +16136,18 @@ Twisted's manhole library} .")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0xj782ghf0iv8r2xxmg2vrh72b02h216y4yfyi60y9z0691lrsip"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
        (snippet
-        #~(begin (delete-all-but "." "tools")))))
+        #~(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-all-but "." "tools")))))
     (build-system go-build-system)
     (arguments
      (list
@@ -19843,9 +19932,18 @@ publish–subscribe pattern}.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0an8ypp8v9gfxbbb71mpimb1g9labl4v7lgazcphysn6c5smgmiw"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
        (snippet
-        #~(begin (delete-all-but "." "atomicwriter")))))
+        #~(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-all-but "." "atomicwriter")))))
     (build-system go-build-system)
     (arguments
      (list
@@ -19900,9 +19998,18 @@ https://github.com/syndtr/gocapability.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "1nh1disclgydvq7k10awzks6k8kw9cjj3q19f83ksi4b76p5l475"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
        (snippet
-        #~(begin (delete-all-but "." "mount")))))
+        #~(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-all-but "." "mount")))))
     (build-system go-build-system)
     (arguments
      (list
@@ -30960,8 +31067,21 @@ when they'd prefer a more familiar, loosely typed API.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "05i15278swdmpif3p6g18sy0sn7rnfdl3m2rj5p30cnyb0j29vig"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
-       (snippet #~(delete-all-but "." "exp"))))
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+            ;; Consider implementing it as a reusable procedure in
+            ;; guix/build/utils or guix/build-system/go.
+            (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-all-but "." "exp")))))
     (build-system go-build-system)
     (arguments
      (list
@@ -32442,9 +32562,18 @@ code.")
     (name "go-modernc-org-ccgo-v4")
     (source (origin
               (inherit (package-source go-modernc-org-ccgo-v3))
-              (modules '((guix build utils)))
+              (modules '((guix build utils)
+                         (ice-9 ftw)
+                         (srfi srfi-26)))
               (snippet
-               #~(begin (delete-all-but "." "v4")))))
+               #~(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-all-but "." "v4")))))
     (arguments
      (substitute-keyword-arguments
          (package-arguments go-modernc-org-ccgo-v3)
@@ -33400,9 +33529,20 @@ unmarshaling functions based on @code{encoding/json} @code{Unmarshal()}.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "12n8ij4gisah5mvxcgq263iic61gjpxdj3ml03826zckzn7wlv46"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
        (snippet
         #~(begin
+            ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+            ;; Consider implementing it as a reusable procedure in
+            ;; guix/build/utils or guix/build-system/go.
+            (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-all-but "." "cmd")
             (delete-all-but "cmd" "config")))))
     (build-system go-build-system)

gnu/packages/graph.scm

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

gnu/packages/graphics.scm

@@ -44,7 +44,6 @@
 ;;; Copyright © 2025 James Smith <jsubuntuxp@disroot.org>
 ;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
 ;;; Copyright © 2026 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
-;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -79,7 +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)
@@ -1533,71 +1532,77 @@ frames per second (FPS), temperatures, CPU/GPU load and more.")
 (define-public openexr
   (package
     (name "openexr")
-    (version "3.4.11")
+    (version "3.2.4")
-    (source
+    (source (origin
-     (origin
+              (method git-fetch)
-       (method git-fetch)
+              (uri (git-reference
-       (uri (git-reference
+                    (url
-             (url "https://github.com/AcademySoftwareFoundation/openexr")
+                     "https://github.com/AcademySoftwareFoundation/openexr")
-             (commit (string-append "v" version))))
+                    (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
+              (file-name (git-file-name name version))
-       (sha256 (base32 "0c0l62s42i4jxp6bsf47fqlmdrazpk783jfpgj4jnprsm2spdp75"))
+              (sha256
-       (modules '((guix build utils)))
+               (base32
-       ;; Unbundle third party libraries.
+                "00s1a05kggk71vfbnsvykyjc2j7y6yyzgl63sy4yiddshz2k2mcr"))))
-       (snippet #~(with-directory-excursion "external"
-                    (for-each delete-file-recursively
-                      '("deflate" "OpenJPH"))))))
     (build-system cmake-build-system)
     (arguments
-     (list
+     (list #:configure-flags
-      #:configure-flags
+           #~(list #$@(match (%current-system)
-      #~(list #$@(match (%current-system)
+                        ;; A test explicitly checks for SSE2 (would fail on
-                   ;; A test explicitly checks for SSE2 (would fail on
+                        ;; i686-linux), so make sure it is enabled for both C
-                   ;; i686-linux), so make sure it is enabled for both C
+                        ;; and CPP.
-                   ;; and CPP.
+                        ((or "x86_64-linux" "i686-linux")
-                   ((or "x86_64-linux" "i686-linux")
+                         '("-DCMAKE_CXX_FLAGS=-mfpmath=sse -msse2"
-                    '("-DCMAKE_CXX_FLAGS=-mfpmath=sse -msse2"
+                           "-DCMAKE_C_FLAGS=-mfpmath=sse -msse2"))
-                      "-DCMAKE_C_FLAGS=-mfpmath=sse -msse2"))
+                        (_ '())))
-                   (_ '())))
+           #:phases
-      #:phases
+           #~(modify-phases %standard-phases
-      #~(modify-phases %standard-phases
+               (add-after 'unpack 'patch-test-directory
-          (add-after 'unpack 'patch-test-directory
+                 (lambda _
-            (lambda _
+                   (substitute* (list
-              (substitute* '("src/test/OpenEXRTest/tmpDir.h"
+                                 "src/test/OpenEXRTest/tmpDir.h"
-                             "src/test/OpenEXRCoreTest/main.cpp")
+                                 "src/test/OpenEXRCoreTest/main.cpp")
-                (("/var/tmp") "/tmp"))))
+                     (("/var/tmp")
-          ;; Disable tests that fail at least on i686-linux.
+                      "/tmp"))))
-          #$@(if (target-32bit?)
+               #$@(if (target-32bit?)
-                 #~((add-after 'patch-test-directory 'disable-broken-tests
+                      #~((add-after 'patch-test-directory 'disable-broken-tests
-                      (lambda _
+                           (lambda _
-                        (substitute* "src/test/OpenEXRCoreTest/main.cpp"
+                             ;; Disable tests that fail at least on i686-linux.
-                          ((".*testNoCompression, .*") "")
+                             (substitute* '("src/test/OpenEXRCoreTest/main.cpp"
-                          ((".*testRLECompression, .*") "")
+					    "src/test/OpenEXRTest/main.cpp")
-                          ((".*testZIPCompression, .*") "")
+                               (("TEST \\(testCompression, \"basic\"\\);")
-                          ((".*testZIPSCompression, .*") "")
+                                "")
-                          ((".*testB44Compression, .*") "")
+                               (("TEST\\( testNoCompression, \"core_compression\" \\);")
-                          ((".*testB44ACompression, .*") ""))
+                                "")
-                        (substitute* "src/test/OpenEXRTest/main.cpp"
+                               (("TEST\\( testRLECompression, \"core_compression\" \\);")
-                          ((".*testCompression, .*") "")
+                                "")
-                          ((".*testOptimizedInterleavePatterns, .*") "")))))
+                               (("TEST\\( testZIPCompression, \"core_compression\" \\);")
-                 #~())
+                                "")
-          ;; Disable tests known to fail on aarch64.  Remove once
+                               (("TEST\\( testZIPSCompression, \"core_compression\" \\);")
-          ;; https://github.com/AcademySoftwareFoundation/openexr/issues/1460
+                                "")
-          ;; is fixed.
+                               (("TEST\\( testB44Compression, \"core_compression\" \\);")
-          #$@(if (target-aarch64?)
+                                "")
-                 #~((add-after 'patch-test-directory 'disable-broken-tests
+                               (("TEST\\( testB44ACompression, \"core_compression\" \\);")
-                      (lambda _
+                                "")
-                        (substitute* '("src/test/OpenEXRCoreTest/main.cpp")
+                               (("TEST \\(testOptimizedInterleavePatterns, \"basic\"\\);")
-                          (("TEST \\(testDWAACompression, \"core_compression\"\\);")
+                                "")))))
-                           "")
+                      #~())
-                          (("TEST \\(testDWABCompression, \"core_compression\"\\);")
+               #$@(if (target-aarch64?)
-                           "")))))
+                      #~((add-after 'patch-test-directory 'disable-broken-aarch64-tests
-                 #~()))))
+                           ;; Disable tests known to fail on aarch64. Remove once
+                           ;; https://github.com/AcademySoftwareFoundation/openexr/issues/1460
+                           ;; is fixed.
+                           (lambda _
+                             (substitute* '("src/test/OpenEXRCoreTest/main.cpp")
+                               (("TEST \\(testDWAACompression, \"core_compression\"\\);")
+                                "")
+                               (("TEST \\(testDWABCompression, \"core_compression\"\\);")
+                                "")))))
+                      #~()))))
+    (inputs (list imath))
     (propagated-inputs
-     (list libdeflate ;marked as Requires.private in OpenEXR.pc
+     (list libdeflate ; Marked as Requires.private in OpenEXR.pc.
-           imath      ;marked as Requires in OpenEXR.pc
+           imath)) ; Marked as Requires in OpenEXR.pc.
-           openjph))  ;marked as Requires.private in OpenEXR.pc
+    (home-page "https://www.openexr.com/")
-    (home-page "https://openexr.com")
     (synopsis "High-dynamic-range file format library")
     (description
      "OpenEXR provides the specification and reference implementation of the

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)
@@ -47,13 +47,13 @@
 (define-public groff
   (package
    (name "groff")
-   (version "1.24.0")
+   (version "1.22.4")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/groff/groff-" version
                                 ".tar.gz"))
             (sha256 (base32
-                     "0w3mf9jb5j1gbw1160lr5498q4ayl5i3jpf5g8721l1yzzcbr6z7"))))
+                     "14q2mldnr1vx0l9lqp9v2f6iww24gj28iyh4j2211hyynx67p3p7"))))
    (build-system gnu-build-system)
    (outputs '("out"
               "doc"))                    ;12MiB of PS, PDF, HTML, and examples

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)
@@ -713,7 +713,7 @@ exec ${system}/rc \"$@\"
        ("libpciaccess" ,libpciaccess-static)
 
        ;; For NFS support
-       ("libtirpc" ,libtirpc)
+       ("libtirpc" ,libtirpc/hurd)
 
        ;; Tools for the /libexec/* scripts.
        ("bash-minimal" ,bash-minimal)

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)
@@ -600,16 +600,24 @@ different data arrays similar to those available in the numdiff software.")
               (file-name (git-file-name name version))
               (snippet
                #~(begin
-                   (use-modules (guix build utils))
+                   (use-modules (guix build utils)
+                                (ice-9 ftw)
+                                (srfi srfi-26))
                    ;; Delete any bundled .jar files.
                    (for-each delete-file (find-files "." "\\.jar$"))
+                   (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-all-but "3rdparty"
-                     "fastcv"           ;TODO: Unbundle these
+                                   "fastcv"     ;TODO: Unbundle these
-                     "libspng"
+                                   "libspng"
-                     "libtim-vx"
+                                   "libtim-vx"
-                     "orbbecsdk"
+                                   "orbbecsdk"
-                     "quirc"
+                                   "quirc"
-                     "zlib-ng")))
+                                   "zlib-ng")))
               (sha256
                (base32
                 "15w4fqjqv5k1yw70jbjsnlgiky39mqpy05rvmm2fbyjrif4kbgkl"))))

gnu/packages/image.scm

@@ -2987,101 +2987,86 @@ by AOM, including with alpha.")
 Format) file format decoder and encoder.")
     (license license:lgpl3+)))
 
-(define libjxl-testdata
-  (origin
-    (method git-fetch)
-    (uri (git-reference
-          (url "https://github.com/libjxl/testdata")
-          (commit "ff8d743aaba05b3014f17e5475e576242fa979fc")))
-    (sha256
-     (base32 "05nba2h0m74n5f9jzl3vzvnj74fj3si09ncwk2dqg41qdc49d1ng"))))
-
 (define-public libjxl
   (package
     (name "libjxl")
-    (version "0.11.2")
+    (version "0.11.1")
     (outputs (list "out" "pixbuf-loader"))
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/libjxl/libjxl")
-             (commit (string-append "v" version))))
+             (commit (string-append "v" version))
+             (recursive? #t)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0a6fg2v81rqsbrzi97x1d7wadcikh2fizr64rsza668cwvsk631q"))))
+        (base32 "1wfxzrhj8a19z6x47ib1qbmgyg56jsxjs955xcvqhdkrx8l2271r"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Delete the bundles that will not be used.
+        '(begin
+           (for-each (lambda (directory)
+                       (delete-file-recursively
+                        (string-append "third_party/" directory)))
+                     '("brotli" "googletest" "highway" "lcms" "libjpeg-turbo"
+                       "libpng" "zlib"))))))
     (build-system cmake-build-system)
     (arguments
-     (list
+     `(#:modules ((guix build cmake-build-system)
-      #:configure-flags
+                  (guix build utils)
-      #~'("-DJPEGXL_FORCE_SYSTEM_GTEST=true"
+                  (srfi srfi-26))
-          "-DJPEGXL_FORCE_SYSTEM_BROTLI=true"
+       #:configure-flags
-          "-DJPEGXL_FORCE_SYSTEM_LCMS2=true"
+       (list "-DJPEGXL_FORCE_SYSTEM_GTEST=true"
-          "-DJPEGXL_FORCE_SYSTEM_HWY=true"
+             "-DJPEGXL_FORCE_SYSTEM_BROTLI=true"
-          "-DJPEGXL_BUNDLE_LIBPNG=false"
+             "-DJPEGXL_FORCE_SYSTEM_LCMS2=true"
-          "-DJPEGXL_ENABLE_PLUGINS=true")
+             "-DJPEGXL_FORCE_SYSTEM_HWY=true"
-      #:phases
+             "-DJPEGXL_BUNDLE_LIBPNG=false"
-      #~(modify-phases %standard-phases
+             "-DJPEGXL_ENABLE_PLUGINS=true")
-          #$@(cond
+       #:phases
-               ((target-riscv64?)
+       (modify-phases %standard-phases
-                #~((add-after 'unpack 'fix-atomic
+         ,@(cond
-                     (lambda _
+             ((target-riscv64?)
-                       (substitute* "lib/jxl/enc_xyb.cc"
+              '((add-after 'unpack 'fix-atomic
-                         (("#include \"lib/jxl/enc_xyb.h\"" a)
+                  (lambda _
-                          (string-append a "\n#include <atomic>")))))))
+                    (substitute* "lib/jxl/enc_xyb.cc"
-               ((target-x86-32?)
+                      (("#include \"lib/jxl/enc_xyb.h\"" a)
-                #~((add-after 'unpack 'loosen-test-parameter
+                       (string-append a "\n#include <atomic>")))))))
-                     (lambda _
+             ((target-x86-32?)
-                       ;; This test fails likely due to a floating point
+              '((add-after 'unpack 'loosen-test-parameter
-                       ;; rounding difference.
+                  (lambda _
-                       (substitute* "lib/jxl/color_management_test.cc"
+                    ;; This test fails likely due to a floating point
-                         (("8\\.7e-4") "8.7e-3"))))))
+                    ;; rounding difference.
-               (#t
+                    (substitute* "lib/jxl/color_management_test.cc"
-                #~()))
+                      (("8\\.7e-4") "8.7e-3"))))))
-         (add-after 'unpack 'patch-dependencies
+             (#t '()))
-           (lambda* (#:key inputs #:allow-other-keys)
-             (with-directory-excursion "third_party"
-               ;; HACK: Create dummy files to pretend the bundled sjpeg and
-               ;; skcms exist.
-               (apply invoke "touch"
-                      '("sjpeg/CMakeLists.txt"
-                        "sjpeg/COPYING"
-                        "skcms/skcms.h"
-                        "skcms/LICENSE"))
-               (substitute* "CMakeLists.txt"
-                 (("include\\(skcms\\.cmake\\)")
-                  "find_library(SKCMS_LIB NAMES skcms REQUIRED)")
-                 (("include\\(sjpeg\\.cmake\\)")
-                  "find_package(sjpeg REQUIRED)")))
-             (with-directory-excursion "lib"
-               (substitute* "jxl_cms.cmake"
-                 (("target_link_skcms\\(jxl_cms\\)")
-                  "target_link_libraries(jxl_cms PRIVATE ${SKCMS_LIB})"))
-               (substitute* "jxl_extras.cmake"
-                 (("\\.\\.\\/third_party\\/sjpeg\\/src")
-                  (dirname (search-input-file inputs "src/sjpegi.h")))))))
-         (add-after 'unpack 'unpack-testdata
-           (lambda _
-             (rmdir "testdata")
-             (copy-recursively #$libjxl-testdata "testdata")))
          (add-after 'install 'split
-           (lambda _
+           (lambda* (#:key outputs #:allow-other-keys)
-             (for-each
+              (let* ((out            (assoc-ref outputs "out"))
-              (lambda (path)
+                     (out:pixbuf     (assoc-ref outputs "pixbuf-loader"))
-                (let ((old (string-append #$output path))
+                     (thumbnailer    (string-append
-                      (new (string-append #$output:pixbuf-loader path)))
+                                      out
-                  (install-file old (dirname new))
+                                      "/share/thumbnailers/jxl.thumbnailer"))
-                  (delete-file old)
+                     (thumbnailer*   (string-append
-                  (chmod new #o555)))
+                                      out:pixbuf
-              '("/lib/gdk-pixbuf-2.0/2.10.0/loaders/libpixbufloader-jxl.so"
+                                      "/share/thumbnailers/jxl.thumbnailer"))
-                "/share/thumbnailers/jxl.thumbnailer")))))))
+                     (pixbuf-loader  (string-append
+                                      out
+                                      "/lib/gdk-pixbuf-2.0/2.10.0/loaders/"
+                                      "libpixbufloader-jxl.so"))
+                     (pixbuf-loader* (string-append
+                                      out:pixbuf
+                                      "/lib/gdk-pixbuf-2.0/2.10.0/loaders/"
+                                      "libpixbufloader-jxl.so")))
+
+                (for-each (lambda (old new)
+                            (install-file old (dirname new))
+                            (delete-file old)
+                            (chmod new #o555))
+                          (list thumbnailer pixbuf-loader)
+                          (list thumbnailer* pixbuf-loader*))))))))
     (native-inputs
-     (list asciidoc
+     (list asciidoc doxygen googletest pkg-config python))
-           doxygen
-           googletest
-           pkg-config
-           python
-           (package-source sjpeg)))     ;for sjpegi.h
     (inputs
      (list freeglut
            gdk-pixbuf
@@ -3094,8 +3079,6 @@ Format) file format decoder and encoder.")
            libpng
            libwebp
            openexr
-           sjpeg
-           skcms
            zlib))
     ;; These are in Requires.private of libjxl.pc.
     (propagated-inputs

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/ipfs.scm

@@ -1362,9 +1362,21 @@ code prior to it getting merged into @code{go-cid}.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "00lwizzdfdx6kynxddal3all6q9dhwqanpkw0d0vxlwik4nkvxa5"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
        (snippet
-        #~(begin (delete-all-but "." "ipfs")))))
+        #~(begin
+            ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+            ;; Consider to implement it as re-usable procedure in
+            ;; guix/build/utils or guix/build-system/go.
+            (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-all-but "." "ipfs")))))
     (build-system go-build-system)
     (arguments
      (list

gnu/packages/jemalloc.scm

@@ -36,7 +36,7 @@
 (define-public jemalloc
   (package
     (name "jemalloc")
-    (version "5.3.1")
+    (version "5.3.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -44,7 +44,7 @@
                     version "/jemalloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "14kgf0hs864hp5xxqfqh37l1d8wwg57h7wv28rffs8ig4f0bq9iq"))))
+                "1apyxjd1ixy4g8xkr61p0ny8jiz8vyv1j0k4nxqkxpqrf4g2vf1d"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/kde-frameworks.scm

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

gnu/packages/kde-graphics.scm

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

gnu/packages/kde-multimedia.scm

@@ -588,11 +588,14 @@ This package is part of the KDE multimedia module.")
           (add-after 'install 'wrap-executable
             (lambda _
               (let* ((ffmpeg #$(this-package-input "ffmpeg"))
+                     (frei0r #$(this-package-input "frei0r-plugins"))
                      (ladspa #$(this-package-input "ladspa"))
                      (qtbase #$(this-package-input "qtbase")))
                 (wrap-program (string-append #$output "/bin/kdenlive")
                   `("PATH" ":" prefix
                     ,(list (string-append ffmpeg "/bin")))
+                  `("FREI0R_PATH" ":" =
+                    (,(string-append frei0r "/lib/frei0r-1")))
                   `("LADSPA_PATH" ":" =
                     (,(string-append ladspa "/lib/ladspa")))
                   `("QT_QPA_PLATFORM_PLUGIN_PATH" ":" =
@@ -600,12 +603,13 @@ This package is part of the KDE multimedia module.")
                   `("MLT_PREFIX" ":" =
                     (,#$(this-package-input "mlt"))))))))))
     (native-inputs
-     (list extra-cmake-modules frei0r-api kdoctools pkg-config qttools))
+     (list extra-cmake-modules kdoctools pkg-config qttools))
     (inputs
      (list bash-minimal
            breeze                       ; make dark theme available easily
            breeze-icons                 ; recommended icon set
            ffmpeg
+           frei0r-plugins
            imath
            karchive
            kcrash
@@ -634,10 +638,6 @@ This package is part of the KDE multimedia module.")
            qtsvg
            qtwayland
            shared-mime-info))
-    (native-search-paths
-     (list (search-path-specification
-            (variable "FREI0R_PATH")
-            (files (list "lib/frei0r-1")))))
     (home-page "https://kdenlive.org")
     (synopsis "Non-linear video editor")
     (description "Kdenlive is an acronym for KDE Non-Linear Video Editor.

gnu/packages/kde-pim.scm

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

gnu/packages/kde-sdk.scm

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

gnu/packages/kerberos.scm

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

gnu/packages/kubernetes.scm

@@ -92,8 +92,16 @@ tree for exported @acronym{CustomResourceDefinition, CRD} types.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0d9rjyl5h0xm9isgr8b2fz8528wk3pds71rjl8g08fgsmsa5kicb"))
-       (modules '((guix build utils)))
+       (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))))
                     ;; Replace symlinks to tests with file contents
                     (for-each
                      (lambda (f)
@@ -174,8 +182,16 @@ tree for exported @acronym{CustomResourceDefinition, CRD} types.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0d9rjyl5h0xm9isgr8b2fz8528wk3pds71rjl8g08fgsmsa5kicb"))
-       (modules '((guix build utils)))
+       (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-all-but "." "server")
                     (rename-file "server" "server.tmp")
                     (mkdir-p "server/v3")
@@ -249,8 +265,16 @@ system.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0d9rjyl5h0xm9isgr8b2fz8528wk3pds71rjl8g08fgsmsa5kicb"))
-       (modules '((guix build utils)))
+       (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-all-but "." "pkg")
                     (rename-file "pkg" "pkg.tmp")
                     (mkdir-p "pkg/v3")

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/libcanberra.scm

@@ -69,6 +69,17 @@
        (search-patches "libcanberra-sound-theme-freedesktop.patch"
                        "libcanberra-wayland-crash.patch"))))
     (build-system gnu-build-system)
+    (inputs
+     `(("alsa-lib" ,alsa-lib)
+       ("gstreamer" ,gstreamer)
+       ("gtk+" ,gtk+)
+       ("libltdl" ,libltdl)
+       ("libvorbis" ,libvorbis)
+       ("pulseaudio" ,pulseaudio)
+       ("udev" ,eudev)
+       ("sound-theme-freedesktop" ,sound-theme-freedesktop)))
+    (native-inputs
+     (list pkg-config))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -76,21 +87,10 @@
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "src/sound-theme-spec.c"
                (("@SOUND_THEME_DIRECTORY@")
-                (dirname
+                (string-append
-                 (dirname
+                 (assoc-ref inputs "sound-theme-freedesktop")
-                  (search-input-directory inputs
+                 "/share")))
-                                          "share/sounds/freedesktop"))))))))))
+             #t)))))
-    (inputs
-     (list alsa-lib
-           gstreamer
-           gtk+
-           libltdl
-           libvorbis
-           pulseaudio
-           eudev
-           sound-theme-freedesktop))
-    (native-inputs
-     (list pkg-config))
     (home-page "https://0pointer.de/lennart/projects/libcanberra/")
     (synopsis
      "Implementation of the XDG Sound Theme and Name Specifications")

gnu/packages/libreoffice.scm

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

gnu/packages/librewolf.scm

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

gnu/packages/lighting.scm

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

gnu/packages/linux.scm

@@ -86,7 +86,6 @@
 ;;; Copyright © 2025 Mathieu Laparie <mlaparie@disr.it>
 ;;; Copyright © 2025 John Kehayias <john.kehayias@protonmail.com>
 ;;; Copyright © 2025 Arjan Adriaanse <arjan@adriaan.se>
-;;; Copyright © 2025 Dariqq <dariqq@posteo.net>
 ;;; Copyright © 2026 Justin Veilleux <terramorpha@cock.li>
 ;;; Copyright © 2026 Simen Endsjø <contact@simendsjo.me>
 ;;;
@@ -136,7 +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)
@@ -3037,45 +3036,57 @@ which need to be installed separately.")
 (define-public linux-pam
   (package
     (name "linux-pam")
-    (version "1.7.2")
+    (version "1.5.2")
     (source
      (origin
-       (method git-fetch)
+       (method url-fetch)
-       (uri (git-reference
+       (uri (string-append
-              (url "https://github.com/linux-pam/linux-pam")
+             "https://github.com/linux-pam/linux-pam/releases/download/v"
-              (commit (string-append "v" version))))
+             version "/Linux-PAM-" version ".tar.xz"))
-       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1z5apric696zsci28c7651spvdll0zrpfm9z574gcjf45mp22gmi"))
+         "0kgrsj2scv5mx6w925h9hxf11jnqqs9z8s22aw94b90xm4qp3v74"))
        (patches (search-patches "linux-pam-unix_chkpwd.patch"
                                 "linux-pam-no-setfsuid.patch"))))
-    (build-system meson-build-system)
+
-    (outputs '("out" "doc")) ;; 0.8 MiB of html
+    (build-system gnu-build-system)
     (inputs (list libxcrypt))
     (native-inputs
-     (list gettext-minimal
+     (list flex
-           flex bison
+           ;; TODO: optional dependencies
-           ;; manpages
+           ;; ("cracklib" ,cracklib)
-           libxslt
+           ))
-           libxml2
-           docbook-xml
-           docbook-xsl))
     (arguments
      (list
-      #:configure-flags
+      ;; Most users, such as `shadow', expect the headers to be under
-      #~(list
+      ;; `security'.
-         ;; lastlog is deprecated since 1.5.3
+      #:configure-flags #~(list (string-append "--includedir="
-         "-Dpam_lastlog=enabled"
+                                               (assoc-ref %outputs "out")
-         (string-append "-Dvendordir=" #$output "/share/pam")
+                                               "/include/security")
-         (string-append "-Ddocbook-rng="
+                                ;; explicit libdir for pkgconfig files
-                        #$(let ((docbook-xml (this-package-native-input
+                                ;; drop with 1.5.3, which fixes
-                                              "docbook-xml")))
+                                ;; https://github.com/linux-pam/linux-pam/issues/466
-                            (file-append docbook-xml
+                                (string-append "--libdir="
-                                         "/xml/docbook/"
+                                               (assoc-ref %outputs "out")
-                                         (package-version docbook-xml)
+                                               "/lib")
-                                         "/rng/docbookxi.rng")))
+
-         (string-append "-Dhtmldir=" #$output:doc "/share/doc/" #$name "/html"))
+                                ;; XXX: <rpc/rpc.h> is missing from glibc when
+                                ;; cross-compiling, so we have to disable NIS
+                                ;; support altogether.
+                                #$@(if (%current-target-system)
+                                       #~("--disable-nis")
+                                       #~()))
+
+      #:phases (if (target-hurd?)
+                   #~(modify-phases %standard-phases
+                       (add-after 'unpack 'skip-pam-limits
+                         (lambda _
+                           ;; 'pam_limits.c' uses <sys/prctl.h>, which is
+                           ;; Linux-specific.  Skip it on GNU/Hurd.
+                           (substitute* "modules/Makefile.in"
+                             (("pam_limits") "")))))
+                   #~%standard-phases)
+
       ;; XXX: Tests won't run in chroot, presumably because /etc/pam.d
       ;; isn't available.
       #:tests? #f))
@@ -4550,7 +4561,7 @@ that the Ethernet protocol is much simpler than the IP protocol.")
 (define-public iproute
   (package
     (name "iproute2")
-    (version "7.0.0")
+    (version "6.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4558,7 +4569,7 @@ that the Ethernet protocol is much simpler than the IP protocol.")
                     version ".tar.xz"))
               (sha256
                (base32
-                "0kiggxwnjsglxnj43wqkc0rmq0acxf6xqcgk7ddc0qyynpvr0a76"))))
+                "0wm2g70vfhnf8wb6py3zmzwxp4zv1icny1pvkwaxmr67rggbhlac"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -4570,7 +4581,6 @@ that the Ethernet protocol is much simpler than the IP protocol.")
                 "HOSTCC=gcc"
                 (string-append "BASH_COMPDIR=" out
                                "/etc/bash_completion.d")
-                (string-append "PREFIX=" out)
                 (string-append "LIBDIR=" out "/lib")
                 (string-append "HDRDIR=" out "/include")
                 (string-append "SBINDIR=" out "/sbin")
@@ -4595,7 +4605,7 @@ that the Ethernet protocol is much simpler than the IP protocol.")
               (substitute* "Makefile"
                 (("^.*ARPDDIR.*$") "")))))))
     (inputs
-     (list bdb iptables libbpf libcap libelf libmnl libselinux libtirpc))
+     (list bdb iptables libmnl))
     (native-inputs
      (list bison flex pkg-config))
     ;; For tests.
@@ -4624,62 +4634,65 @@ inadequately in modern network environments, and both should be deprecated.")
         (revision "0"))
     (package
       (name "net-tools")
-      (version (string-append "1.60-" revision "."
+      (version (string-append "1.60-" revision "." (string-take commit 7)))
-                              (string-take commit 7)))
+      (source (origin
-      (source
+               (method url-fetch)
-       (origin
+               (uri (string-append "https://sourceforge.net/code-snapshots/git/"
-         (method url-fetch)
+                                   "n/ne/net-tools/code.git/net-tools-code-"
-         (uri (string-append "https://sourceforge.net/code-snapshots/git/"
+                                   commit ".zip"))
-                             "n/ne/net-tools/code.git/net-tools-code-" commit
+               (file-name (string-append name "-" version ".zip"))
-                             ".zip"))
+               (sha256
-         (file-name (string-append name "-" version ".zip"))
+                (base32
-         (sha256
+                 "0hz9fda9d78spp774b6rr5xaxav7cm4h0qcpxf70rvdbrf6qx7vy"))))
-          (base32 "0hz9fda9d78spp774b6rr5xaxav7cm4h0qcpxf70rvdbrf6qx7vy"))))
       (home-page "https://net-tools.sourceforge.net/")
       (build-system gnu-build-system)
       (arguments
-       (list
+       `(#:modules ((guix build gnu-build-system)
-        ;; Binaries that depend on libnet-tools.a don't declare that
-        ;; dependency, making it parallel-unsafe.
-        #:parallel-build? #f
-
-        #:tests? #f ;no test suite
-        #:make-flags
-        #~(list #$(string-append "CC=" (cc-for-target))
-                (string-append "BASEDIR=" #$output)
-                (string-append "INSTALLNLSDIR=" #$output "/share/locale")
-                (string-append "mandir=/share/man"))
-        #:modules `((guix build gnu-build-system)
                     (guix build utils)
                     (srfi srfi-1)
                     (srfi srfi-26))
-        #:phases
+         #:phases
-        #~(modify-phases %standard-phases
+         (modify-phases %standard-phases
-            (replace 'configure
+           (replace 'configure
-              (lambda _
+             (lambda* (#:key outputs #:allow-other-keys)
-                (mkdir-p (string-append #$output "/bin"))
+               (let ((out (assoc-ref outputs "out")))
-                (mkdir-p (string-append #$output "/sbin"))
+                 (mkdir-p (string-append out "/bin"))
+                 (mkdir-p (string-append out "/sbin"))
 
-                ;; Pretend we have everything...
+                 ;; Pretend we have everything...
-                (system "yes | make config")
+                 (system "yes | make config")
 
-                ;; ... except for the things we don't have.
+                 ;; ... except for the things we don't have.
-                ;; HAVE_AFDECnet requires libdnet, which we don't have.
+                 ;; HAVE_AFDECnet requires libdnet, which we don't have.
-                ;; HAVE_HWSTRIP and HAVE_HWTR require kernel headers
+                 ;; HAVE_HWSTRIP and HAVE_HWTR require kernel headers
-                ;; that have been removed.
+                 ;; that have been removed.
-                ;; XXX SELINUX and AFBLUETOOTH are removed for now, but we should
+                 ;; XXX SELINUX and AFBLUETOOTH are removed for now, but we should
-                ;; think about adding them later.
+                 ;; think about adding them later.
-                (substitute* '("config.make" "config.h")
+                 (substitute* '("config.make" "config.h")
-                  (("^.*HAVE_(AFDECnet|HWSTRIP|HWTR|SELINUX|AFBLUETOOTH)[ =]1.*$")
+                   (("^.*HAVE_(AFDECnet|HWSTRIP|HWTR|SELINUX|AFBLUETOOTH)[ =]1.*$")
-                   ""))))
+                    ""))
-            (add-after 'install 'remove-redundant-commands
+                 #t)))
-              (lambda _
+           (add-after 'install 'remove-redundant-commands
-                ;; Remove commands and man pages redundant with Inetutils.
+             (lambda* (#:key outputs #:allow-other-keys)
-                (for-each delete-file
+               ;; Remove commands and man pages redundant with Inetutils.
-                          (append-map (cute find-files #$output <>)
+               (let* ((out (assoc-ref outputs "out"))
-                                      '("^hostname"
+                      (dup (append-map (cut find-files out <>)
-                                        "^(yp|nis|dns)?domainname"))))))))
+                                       '("^hostname"
-      (native-inputs (list gettext-minimal unzip))
+                                         "^(yp|nis|dns)?domainname"))))
+                 (for-each delete-file dup)
+                 #t))))
+         ;; Binaries that depend on libnet-tools.a don't declare that
+         ;; dependency, making it parallel-unsafe.
+         #:parallel-build? #f
+
+         #:tests? #f                                ; no test suite
+         #:make-flags (let ((out (assoc-ref %outputs "out")))
+                        (list ,(string-append "CC=" (cc-for-target))
+                              (string-append "BASEDIR=" out)
+                              (string-append "INSTALLNLSDIR=" out "/share/locale")
+                              (string-append "mandir=/share/man")))))
+      (native-inputs `(("gettext" ,gettext-minimal)
+                       ("unzip" ,unzip)))
       (supported-systems (remove target-hurd? %supported-systems))
       (synopsis "Tools for controlling the network subsystem in Linux")
       (description

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)