gnu: node-lts: Update to 24.14.1.

* gnu/packages/node.scm (node-lts): Update to 24.14.1.

Change-Id: I60457e8e8e05e0102feb450655113ba410bd7667

.forgejo/pull_request_template.md

@@ -28,7 +28,13 @@ Tick a box by changing it from [ ] to [x].
   - [ ] i586-gnu
 
 - Package **update**
-  - Closure size increase after update (`./pre-inst-env guix size PACKAGE`).
+  - Closure size increase.
+```console
+$ guix size PACKAGE | tail -n1 # before
+total: ...
+$ ./pre-inst-env guix size PACKAGE | tail -n1 # after
+total: ...
+```
   - Build status of direct dependents (`./pre-inst-env guix build -k -P1 PACKAGE ...`):
 ```text
 

.guix-authorizations

@@ -23,6 +23,8 @@
    (name "cbaines"))
   ("3CE4 6455 8A84 FDC6 9DB4  0CFB 090B 1199 3D9A EBB5"
    (name "civodul"))
+  ("838A FE0D 55DC 074E 360F  943A 84B6 9CE6 F3F6 B767"
+   (name "cnx"))
   ("CCB8 1842 F9D7 058E CD67  377A BF5C DF4D F6BF 6682"
    (name "csantosb"))
   ("510A 8628 E2A7 7678 8F8C  709C 4BC0 2592 5FF8 F4D3"

CODEOWNERS

@@ -347,7 +347,6 @@ guix/scripts/import/pypi\.scm                      @guix/python
 tests/import/pypi\.scm                             @guix/python
 tests/toml\.scm                                    @guix/python
 
-gnu/ci\.scm                                        @guix/qa-packages
 gnu/packages/benchmark\.scm                        @guix/qa-packages
 gnu/packages/check\.scm                            @guix/qa-packages
 gnu/packages/ci\.scm                               @guix/qa-packages

NEWS

@@ -17,6 +17,7 @@ Please send Guix bug reports to bug-guix@gnu.org.
 * Changes in 1.6.0 (since 1.5.0)
 ** Distribution
 *** GNOME updated to version 48
+*** New service for Fossil SCM
 
 * Changes in 1.5.0 (since 1.4.0)
 ** Package management

doc/guix.texi

@@ -2658,9 +2658,11 @@ bootloaders.
 
 Once you are done partitioning the target hard disk drive, you have to
 create a file system on the relevant partition(s)@footnote{Currently
-Guix System only supports ext4, btrfs, JFS, F2FS, and XFS file systems.  In
-particular, code that reads file system UUIDs and labels only works for these
-file system types.}.  For the ESP, if you have one and assuming it is
+Guix System supports only ext4, btrfs, bcachefs, JFS, F2FS, and XFS
+file systems.  In particular, code that reads file system UUIDs and
+labels works only for these file system types.  For bcachefs, also add
+the @code{bcachefs-linux-module} to your @code{operating-system}'s
+@code{initrd-modules}.}.  For the ESP, if you have one and assuming it is
 @file{/dev/sda1}, run:
 
 @example
@@ -27015,6 +27017,32 @@ Deprecated option.
 @end deftp
 
 
+@c %end of fragment
+
+@defvar gardenhostd-service-type
+Type for the service that runs gardenhostd, a partial implementation of
+the systemd-hostnamed daemon.  It provides the org.freedesktop.hostname1
+D-Bus interface, which helps applications like gnome-control-center
+retrieve and modify the system’s hostname, as well as set a pretty
+hostname for display.
+
+The value for this service is a @code{<gardenhostd-configuration>} object.
+@end defvar
+
+@c %start of fragment
+
+@deftp {Data Type} gardenhostd-configuration
+Available @code{gardenhostd-configuration} fields are:
+
+@table @asis
+@item @code{gardenhostd} (default: @code{gardenhostd}) (type: package)
+The gardenhostd package to use.
+
+@end table
+
+@end deftp
+
+
 @c %end of fragment
 
 @defvar accountsservice-service-type
@@ -36561,13 +36589,14 @@ in @code{Nginx}.  It is used to generate cat avatar from a seed, for instance
 the hash of a user's email address.
 
 @deffn {Procedure} cat-avatar-generator-service @
-       [#:cache-dir "/var/cache/cat-avatar-generator"] @
+       [#:cache-dir "/var/cache/cat-avatar-generator/"] @
        [#:package cat-avatar-generator] @
        [#:configuration (nginx-server-configuration)]
 Returns an nginx-server-configuration that inherits @code{configuration}.  It
 extends the nginx configuration to add a server block that serves @code{package},
 a version of cat-avatar-generator.  During execution, cat-avatar-generator will
-be able to use @code{cache-dir} as its cache directory.
+be able to use @code{cache-dir} as its cache directory, which must end
+with a slash, be created manually, and be writable by php-fpm.
 @end deffn
 
 A simple setup for cat-avatar-generator can look like this:
@@ -44243,10 +44272,11 @@ behind a reverse proxy and serve repositories from a custom location.
 (service fossil-service-type
          (fossil-configuration
           (repository "/srv/museum")
-          (repo-list? #t)
+          (list-repositories? #t)
           (base-url "https://museum.example")
-          (socket-file "/var/run/fossil.sock")
-          (compress? #f)))
+          (compress? #f)
+          (https? #t)
+          (socket-file "/var/run/fossil.sock")))
 @end lisp
 
 @deftp {Data Type} fossil-configuration

etc/news.scm

@@ -46,7 +46,8 @@
  (entry (commit "a7c8e68dc51144a6d3981b770aca9c4897fc7c0c")
         (title
          (en "Records can refer to inherited values of thunked fields")
-         (de "Vererbung in Verbundsobjekten erlaubt Verweise auf geerbte Werte verzögert ausgewerteter Felder"))
+         (de "Vererbung in Verbundsobjekten erlaubt Verweise auf geerbte Werte verzögert ausgewerteter Felder")
+         (pt "Registros podem referir-se a valores herdados de campos ainda não evaluados (thunks)"))
         (body
          (en "A new feature has been added to records—the facility used when
 defining packages, services, operating systems, and many other things—that,
@@ -114,7 +115,42 @@ Verbundstypen aus, die mit @code{define-record-type*} erstellt wurden:
 und so weiter.
 
 Hinweis: das ist eine inkompatible Änderung. Die neu eingeführte Bindung –
-@code{inputs} im obigen Beispiel – kann gleichnamige Bindungen überschatten.")))
+@code{inputs} im obigen Beispiel – kann gleichnamige Bindungen überschatten.")
+         (pt "Um novo recurso foi adicionado aos registros - a ferramenta
+usada quando se definem pacotes, serviços, sistemas operacionais, e muitas
+outras coisas - que, quando herdados de outro registro, te permitem referir
+aos valores de campos herdados.  Durante a definição de variantes de pacotes,
+você pode encontrar este padrão:
+
+@lisp
+(package
+  (inherit gdb)
+  (inputs (modify-inputs (package-inputs gdb)
+            (delete \"guile\"))))
+@end lisp
+
+Agora isto pode ser escrito desta forma:
+
+@lisp
+(package
+  (inherit gdb)
+  (inputs (modify-inputs inputs ;<- Note a modificação
+            (delete \"guile\"))))
+@end lisp
+
+Dentro do corpo de @code{inputs}, o identificador @code{inputs} agora está
+atrelado ao @dfn{valor herdado} - id est, ap valor que este campo herda de
+@code{gdb}.  O mesmo mecanismo pode ser empregado ao modificar outros campos
+da entrada ou ao campo @code{arguments}.  É menos verboso mas também
+@uref{https://issues.guix.gnu.org/50335, é mais preciso}.
+
+Esta mudança se aplica aos campos \"thunk-ados\" de todos os tipos de registro
+produzidos por @code{define-record-type*}: @code{package}, @code{origin},
+@code{operating-system}, @code{home-environment}, e assim por diante.
+
+Note que esta é uma modificação incompatível: as ligações introduzidas
+recentemente - @code{inputs} no exemplo acima - podem sombrear ligações de
+mesmo nome.")))
 
  (entry (commit "b52ce9041ad58aeababd2d50d3e72bc23dffff60")
         (title

etc/teams.scm

@@ -991,8 +991,7 @@ perl-build-system as well as the rakudo-build-system."
         #:description
         "Quality assurance software (CI/CD, testing, analysis;
 no direct relation to Guix's QA)."
-        #:scope (list "gnu/ci.scm"
-                      "gnu/packages/benchmark.scm"
+        #:scope (list "gnu/packages/benchmark.scm"
                       "gnu/packages/check.scm"
                       "gnu/packages/ci.scm"
                       "gnu/packages/code.scm"

gnu/build/file-systems.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014-2018, 2020-2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014-2018, 2020-2022, 2026 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
@@ -1455,9 +1455,14 @@ corresponds to the symbols listed in FLAGS."
                (raise c)))
             ((system-error? c)
              (format (current-error-port)
-                     "could not mount partition ~a: ~a~%"
+                     "could not mount partition '~a': ~a~%"
                      (file-system-device fs)
-                     (exception-message c))
+                     (string-trim-both
+                      (call-with-output-string
+                        (lambda (port)
+                          (print-exception port #f
+                                           (exception-kind c)
+                                           (exception-args c))))))
              (unless (file-system-mount-may-fail? fs)
                (raise c))))
       (let* ((type    (file-system-type fs))

gnu/home/services/niri.scm

@@ -19,6 +19,7 @@
 (define-module (gnu home services niri)
   #:use-module (gnu home services)
   #:use-module (gnu home services shepherd)
+  #:use-module (gnu home services desktop)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages glib)
@@ -40,14 +41,15 @@
 
 (define (home-niri-shepherd-service config)
   "Return a shepherd service that runs Niri, a scrollable tiling Wayland
-compositor.  The service starts Niri in a DBus session with appropriate
-environment variables set for a Wayland desktop session."
+compositor.  The service starts Niri with appropriate environment variables
+set for a Wayland desktop session."
   (list (shepherd-service
           (documentation "Run Niri scrollable tiling Wayland compositor.")
           (provision '(niri))
+          (requirement '(dbus))
           (start #~(make-forkexec-constructor
                     (list #$(file-append bash "/bin/bash") "-l"
-                          "-c" "exec dbus-run-session niri --session")
+                          "-c" "exec niri --session")
                     #:environment-variables
                     (append (list #$@(niri-configuration-environment-variables config))
                             '("DESKTOP_SESSION=niri"
@@ -66,6 +68,8 @@ environment variables set for a Wayland desktop session."
    (extensions
     (list (service-extension home-shepherd-service-type
                              home-niri-shepherd-service)
+          (service-extension home-dbus-service-type
+                             (const '()))
           (service-extension home-profile-service-type
                              (lambda (config)
                                (list dbus

gnu/local.mk

@@ -1754,6 +1754,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch\
   %D%/packages/patches/laby-make-install.patch			\
   %D%/packages/patches/laby-use-tmpdir-from-runtime.patch	\
+  %D%/packages/patches/ldc-i686-int128-alignment.patch 		\
   %D%/packages/patches/ldns-drill-examples.patch		\
   %D%/packages/patches/leela-zero-gtest.patch			\
   %D%/packages/patches/less-hurd-path-max.patch			\
@@ -1856,7 +1857,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/lirc-reproducible-build.patch		\
   %D%/packages/patches/llvm-13-gcc-14.patch			\
   %D%/packages/patches/lm-sensors-hwmon-attrs.patch		\
-  %D%/packages/patches/lsof-compat-linux-6.9.patch		\
   %D%/packages/patches/lsof-fatal-test-failures.patch		\
   %D%/packages/patches/lua-CVE-2014-5461.patch                      \
   %D%/packages/patches/lua-pkgconfig.patch                      \
@@ -1976,13 +1976,13 @@ dist_patch_DATA =						\
   %D%/packages/patches/netsurf-y2038-tests.patch		\
   %D%/packages/patches/netsurf-longer-test-timeout.patch	\
   %D%/packages/patches/nhc98-c-update.patch			\
+  %D%/packages/patches/nheko-0-12-1-fix-rendering-replies.patch	\
   %D%/packages/patches/nix-dont-build-html-doc.diff		\
   %D%/packages/patches/nfs4-acl-tools-0.3.7-fixpaths.patch	\
   %D%/packages/patches/network-manager-plugin-ownership.patch	\
   %D%/packages/patches/network-manager-plugin-path.patch	\
   %D%/packages/patches/newlib-getentropy.patch			\
   %D%/packages/patches/nginx-socket-cloexec.patch		\
-  %D%/packages/patches/nickle-man-release-date.patch		\
   %D%/packages/patches/nlopt_CMake-Assume-working-c-compiler-597.patch \
   %D%/packages/patches/nnpack-system-libraries.patch		\
   %D%/packages/patches/nsis-env-passthru.patch			\
@@ -2469,6 +2469,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/t4k-common-libpng16.patch		\
   %D%/packages/patches/tao-add-missing-headers.patch		\
   %D%/packages/patches/tao-fix-parser-types.patch		\
+  %D%/packages/patches/tao-synth-include-string-you-use.patch		\
   %D%/packages/patches/tar-remove-wholesparse-check.patch	\
   %D%/packages/patches/tar-skip-unreliable-tests.patch		\
   %D%/packages/patches/taskwarrior-link-taskchampion-cpp-with-sqlite3.patch \

gnu/packages.scm

@@ -518,8 +518,9 @@ return its return value."
                 (location->string (package-location pkg))))
      (match (package-superseded pkg)
        ((? package? new)
-        (info (G_ "package '~a' has been superseded by '~a'~%")
-              (package-name pkg) (package-name new))
+        (unless (assoc-ref (package-properties pkg) 'supress-supersession-info?)
+          (info (G_ "package '~a' has been superseded by '~a'~%")
+                (package-name pkg) (package-name new)))
         new)
        (#f
         pkg)))

gnu/packages/admin.scm

@@ -4988,16 +4988,16 @@ Python loading in HPC environments.")
   (let ((real-name "inxi"))
     (package
       (name "inxi-minimal")
-      (version "3.3.31-2")
+      (version "3.3.40-1")
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/smxi/inxi")
+               (url "https://codeberg.org/smxi/inxi")
                (commit version)))
          (file-name (git-file-name real-name version))
          (sha256
-          (base32 "1fca5minalpmizbxh5kmjiv8xrl7k6g91zn8d84fxmbhsk8vn3kk"))))
+          (base32 "0ivj0dcx7d2hmmkhyql156sb08385rzw640z9kyq4cv1n8ndz58s"))))
       (build-system trivial-build-system)
       (inputs
        (list bash-minimal
@@ -5023,8 +5023,8 @@ Python loading in HPC environments.")
            (copy-recursively (assoc-ref %build-inputs "source")
                              ,(string-append real-name "-" version))
            (with-directory-excursion ,(string-append real-name "-" version)
-             (with-fluids ((%default-port-encoding #f))
-               (substitute* "inxi" (("/usr/bin/env perl") (which "perl"))))
+             (patch-shebang "inxi" (list (dirname (search-input-file
+                                                    %build-inputs "bin/perl"))))
              (let ((bin (string-append %output "/bin")))
                (install-file "inxi" bin)
                (wrap-program (string-append bin "/inxi")
@@ -5039,7 +5039,8 @@ Python loading in HPC environments.")
                                    ((member name '("util-linux"))
                                     (string-append (store-append "/bin") ":"
                                                    (store-append "/sbin")))
-                                   ((member name '("dmidecode" "iproute2"))
+                                   ((member name '("dmidecode" "iproute2" "lvm2"
+                                                   "mdadm"))
                                     (store-append "/sbin"))
                                    (else (store-append "/bin")))))))
                            %build-inputs)))
@@ -5067,6 +5068,7 @@ support forum.  It runs with the @code{/exec} command in most IRC clients.")
     (name "inxi")
     (inputs
      `(("dmidecode" ,dmidecode)
+       ("eudev" ,eudev)
        ("file" ,file)
        ("bind:utils" ,isc-bind "utils") ; dig
        ("gzip" ,gzip)
@@ -5092,11 +5094,14 @@ support forum.  It runs with the @code{/exec} command in most IRC clients.")
        ("perl-time-hires" ,perl-time-hires)
        ("lvm2" ,lvm2)                   ; lvs
        ("mdadm" ,mdadm)
+       ("wayland-utils" ,wayland-utils)
        ;; TODO: Add more inputs:
        ;; ipmi-sensors
        ;; hddtemp
        ;; perl-xml-dumper
        ;; ipmitool
+       ;; wlr-randr
+       ;; vulkan-tools
        ,@(package-inputs inxi-minimal)))))
 
 (define-public pscircle
@@ -5602,69 +5607,61 @@ representation to stdout.")
 (define-public hosts
   (package
     (name "hosts")
-    (version "3.6.3")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/xwmx/hosts")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1ni4z89kxzgwm26hhx908g04f2h0fypy7lgfa0rvsz8d0wslgcsn"))))
-    (build-system trivial-build-system)
+    (version "3.6.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/xwmx/hosts")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1kzd4lxlflam87dhbx1jx7bj6v6sa4f2024mfxj2768kp9qapraj"))))
+    (build-system copy-build-system)
+    (native-inputs
+     (list bats)) ;for tests
     (inputs
-     `(("bats" ,bats) ;for test
-       ("awk" ,gawk)
-       ("bash" ,bash)
-       ("coreutils" ,coreutils)
-       ("diffutils" ,diffutils)
-       ("grep" ,grep)
-       ("ncurses" ,ncurses) ;tput
-       ("sed" ,sed)))
+     (list gawk
+           bash-minimal
+           coreutils
+           diffutils
+           grep
+           ncurses ;for tput
+           sed))
     (arguments
-     `(#:modules ((guix build utils))
-       #:builder
-       (begin
-         (use-modules (guix build utils))
-         ;; copy source
-         (copy-recursively (assoc-ref %build-inputs "source") ".")
-         ;; patch-shebang phase
-         (setenv "PATH"
-                 (string-append (assoc-ref %build-inputs "bash") "/bin"
-                                ":" (assoc-ref %build-inputs "awk") "/bin"
-                                ":" (assoc-ref %build-inputs "coreutils") "/bin"
-                                ":" (assoc-ref %build-inputs "diffutils") "/bin"
-                                ":" (assoc-ref %build-inputs "grep") "/bin"
-                                ":" (assoc-ref %build-inputs "ncurses") "/bin"
-                                ":" (assoc-ref %build-inputs "sed") "/bin"
-                                ":" "/run/privileged/bin"
-                                ":" (getenv "PATH")))
-         (substitute* "hosts"
-           (("#!/usr/bin/env bash")
-            (string-append "#!" (which "bash")
-                           "\nPATH=" (getenv "PATH"))))
-         ;; check phase
-         (setenv "TERM" "linux") ;set to tty for test
-         (invoke (search-input-file %build-inputs "/bin/bats")
-                 "test")
-         ;; install phase
-         (install-file "hosts" (string-append %output "/bin"))
-         (let ((bash-completion
-                (string-append %output "/etc/bash_completion.d")))
-           (mkdir-p bash-completion)
-           (copy-file "etc/hosts-completion.bash"
-                      (string-append bash-completion "/hosts")))
-         (let ((zsh-completion
-                (string-append %output "/share/zsh/site-functions")))
-           (mkdir-p zsh-completion)
-           (copy-file "etc/hosts-completion.zsh"
-                      (string-append zsh-completion "/_hosts")))
-         (let ((doc (string-append %output "/share/doc/" ,name "-" ,version)))
-           (mkdir-p doc)
-           (install-file "LICENSE" doc)
-           (install-file "README.md" doc))
-         #t)))
+     (list
+      #:install-plan
+      #~'(("hosts" "bin/hosts")
+          ("etc/hosts-completion.bash" "/etc/bash_completion.d/hosts")
+          ("etc/hosts-completion.zsh" "/share/zsh/site-functions/_hosts")
+          ("README.md"
+           #$(string-append "/share/doc/" name "-" version "/README.md")))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-hosts
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* "test/test_helper.bash"
+                (("export _HOSTS=.*")
+                 (string-append "export _HOSTS=" #$output "/bin/hosts")))
+              (substitute* (cons* "hosts"
+                            ;; *.bash and *.bats.
+                            (find-files "test" "\\.bat?sh?.*$"))
+                (("\\btput\\b") (search-input-file inputs "bin/tput"))
+                (("\\bsed\\b") (search-input-file inputs "bin/sed"))
+                (("\\bawk\\b") (search-input-file inputs "bin/awk"))
+                (("\\bgrep\\b") (search-input-file inputs "bin/grep"))
+                (("\\bdiff\\b") (search-input-file inputs "bin/diff"))
+                (("\\bcp\\b") (search-input-file inputs "bin/cp"))
+                (("\\bchmod\\b") (search-input-file inputs "bin/chmod")))))
+          (add-after 'install 'check
+            (lambda* (#:key tests? inputs #:allow-other-keys)
+              (if tests?
+                  (begin
+                    (delete-file "hosts") ;Ensure installed hosts is checked.
+                    (setenv "PATH" "") ;Ensure substitutions were correct.
+                    (setenv "TERM" "linux") ;Set to tty for test.
+                    (invoke (search-input-file inputs "/bin/bats")
+                            "test"))))))))
     (home-page "https://github.com/xwmx/hosts/")
     (synopsis "Script for editing a foreign distro's @file{/etc/hosts} file")
     (description "Hosts is a command line program for managing

gnu/packages/adns.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019, 2021 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2026 Anderson Torres <anderson.torres.8519@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,49 +22,51 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages adns)
-  #:use-module (guix gexp)
-  #:use-module (guix licenses)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix utils)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (gnu packages m4)
+  #:use-module (gnu packages pkg-config)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
-  #:use-module (gnu packages m4)
-  #:use-module (gnu packages pkg-config))
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix gexp)
+  #:use-module (guix packages)
+  #:use-module (guix utils))
 
 (define-public adns
   (package
     (name "adns")
     (version "1.6.1")
-    (source (origin
-              (method url-fetch)
-              (uri (list (string-append "mirror://gnu/adns/adns-"
-                                        version ".tar.gz")
-                         (string-append
-                           "https://www.chiark.greenend.org.uk/~ian/adns/ftp/adns-"
-                           version ".tar.gz")))
-              (sha256
-               (base32
-                "1k81sjf0yzv6xj35vcxp0ccajxrhhmyly7a57xlbs1kmkdwb6f3i"))))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "git://git.chiark.greenend.org.uk/~ianmdlvl/adns.git")
+              (commit (string-append "adns-" version))))
+       (sha256
+        (base32
+         "0ln3l5j7wb1xazrzl76p9xar52p6l2k1cwy7jazxw1acl71k9h5n"))))
     (build-system gnu-build-system)
     (arguments
-     ;; Make sure the programs under bin/ fine libadns.so.
-     '(#:configure-flags (list (string-append "LDFLAGS=-Wl,-rpath -Wl,"
-                                              (assoc-ref %outputs "out")
-                                              "/lib"))
-
-       ;; XXX: Tests expect real name resolution to work.
-       #:tests? #f))
+     (list
+      ;; INFO: Tests expect real name resolution to work.
+      #:tests? #f
+      #:configure-flags
+      #~(list
+         ;; Make sure the programs under bin/ find libadns.so.
+         (string-append "LDFLAGS=-Wl,-rpath -Wl,"
+                        #$output:out
+                        "/lib"))))
     (native-inputs
      (list m4))
     (home-page "https://www.gnu.org/software/adns/")
     (synopsis "Asynchronous DNS client library and utilities")
     (description
-     "GNU adns is a C library that provides easy-to-use DNS resolution
-functionality.  The library is asynchronous, allowing several concurrent
-calls.  The package also includes several command-line utilities for use in
-scripts.")
-    (license gpl3+)))
+     "GNU adns is a C library that provides easy-to-use @acronym{DNS, Domain
+Name System} resolution functionality.  The library is asynchronous, allowing
+several concurrent calls.  The package also includes several command-line
+utilities for use in scripts.")
+    (license license:gpl3+)))
 
 (define-public c-ares
   (package
@@ -146,7 +149,7 @@ asynchronously.  It is intended for applications which need to perform DNS
 queries without blocking, or need to perform multiple DNS queries in parallel.
 The primary examples of such applications are servers which communicate with
 multiple clients and programs with graphical user interfaces.")
-    (license (x11-style "https://c-ares.haxx.se/license.html"))))
+    (license (license:x11-style "https://c-ares.haxx.se/license.html"))))
 
 (define-public c-ares-for-node-lts
   (hidden-package c-ares))

gnu/packages/audio.scm

@@ -42,7 +42,7 @@
 ;;; Copyright © 2022 Andy Tai <atai@atai.org>
 ;;; Copyright © 2023 Sergiu Ivanov <sivanov@colimite.fr>
 ;;; Copyright © 2023 David Thompson <dthompson2@worcester.edu>
-;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2023, 2025-2026 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2023 Gabriel Wicki <gabriel@erlikon.ch>
 ;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2023 Parnikkapore <poomklao@yahoo.com>
@@ -2316,13 +2316,13 @@ object library.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1jds2l3cb96b02jxd7lmrjjl9s7mylnrvg6fpw0j8c141bk8vyg3"))))
+                  "1jds2l3cb96b02jxd7lmrjjl9s7mylnrvg6fpw0j8c141bk8vyg3"))
+                (patches
+                 (search-patches "tao-synth-include-string-you-use.patch"))))
       (build-system cmake-build-system)
       (arguments (list #:tests? #false))  ;there are no tests
       (inputs
        (list glfw freeglut))
-      (native-inputs
-       (list gcc-7))
       (home-page "https://github.com/lucasw/tao_synth")
       (synopsis "Sound synthesis with physical models")
       (description "Tao is a software package for sound synthesis using physical
@@ -6358,6 +6358,59 @@ It is currently fairly complete for PCM devices, and has some support for
 mixers.")
     (license license:psfl)))
 
+(define-public python-pyo
+  (package
+    (name "python-pyo")
+    (version "1.0.6")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/belangeo/pyo")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1igz75kv94dav28rzz19gckgfgdli05q5ghadlvm03ia7xd9l5zm"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+     ;; TODO: collecting ... Fatal Python error: Segmentation fault
+      #:tests? #f
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'sanity-check 'set-HOME
+            (lambda _
+              (setenv "HOME" "/tmp"))))))
+    (native-inputs
+     (list python-pytest
+           python-setuptools))
+    (inputs
+     (list liblo
+           libsndfile
+           portaudio
+           portmidi))
+    (propagated-inputs
+     (list python-wxpython))
+    (home-page "https://github.com/belangeo/pyo")
+    (synopsis "Python module to build digital signal processing program")
+    (description
+     "pyo is a Python module containing classes for a wide variety of audio
+signal processing types.
+
+With pyo, user will be able to include signal processing chains directly in
+Python scripts or projects, and to manipulate them in real time through the
+interpreter.  Tools in pyo module offer primitives, like mathematical
+operations on audio signal, basic signal processing (filters, delays,
+synthesis generators, etc.), but also complex algorithms to create sound
+granulation and others creative audio manipulations.
+
+pyo supports OSC protocol (Open Sound Control), to ease communications between
+softwares, and MIDI protocol, for generating sound events and controlling
+process parameters.  pyo allows creation of sophisticated signal processing
+chains with all the benefits of a mature, and widely used, general programming
+language.")
+    (license license:lgpl3+)))
+
 (define-public ldacbt
   (package
     (name "ldacbt")
@@ -8120,7 +8173,7 @@ and DSD streams.")
 (define-public qpwgraph
   (package
     (name "qpwgraph")
-    (version "0.9.9")
+    (version "1.0.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -8129,7 +8182,7 @@ and DSD streams.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "03001pvcbvr206k00751232gm50x1icf086z8c5hiakl2ym79gwl"))))
+                "0l3fflfpwkqy4iif8ifzzr3yy39ahzqdixx5g3rhj3zzbaysj73h"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f))                ; no tests

gnu/packages/bioconductor.scm

@@ -3436,14 +3436,14 @@ the @code{HorvathMethylChip40} (Mammal40) array.")
 (define-public r-systempiperdata
   (package
     (name "r-systempiperdata")
-    (version "2.14.5")
+    (version "2.14.6")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeRdata" version
                               'experiment))
        (sha256
-        (base32 "1yrq1vyc0pmp3iv621cvdsavlarcca3z4bbxfzbg0ny3fyqp67pb"))))
+        (base32 "1j7h40hcm0gyahmlilvlb83ddmwrarqn319qwpnrgwcji8fm92jd"))))
     (properties `((upstream-name . "systemPipeRdata")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocgenerics r-biostrings r-jsonlite r-remotes))
@@ -4552,15 +4552,9 @@ these biases and construct statistically consistent estimators.")
     (build-system r-build-system)
     (arguments
      (list
-      #:phases
-      '(modify-phases %standard-phases
-         (add-after 'unpack 'skip-bad-tests
-           (lambda _
-             ;; This test needs Internet access.
-             (with-directory-excursion "tests/testthat"
-               (substitute* "test-examples.R"
-                 ((".*find_taxonomy\\(\\) is working.*" m)
-                  (string-append m "skip('guix')\n")))))))))
+      #:skipped-tests
+      ;; This test needs Internet access.
+      '(("test-examples.R" ".*find_taxonomy\\(\\) is working.*"))))
     (propagated-inputs
      (list r-ape
            r-assertthat
@@ -4611,13 +4605,13 @@ to understand their data better and discover new insights.")
 (define-public r-anndatar
   (package
     (name "r-anndatar")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anndataR" version))
        (sha256
-        (base32 "1vi9aqgdjy0nlbsk7628sz12jsxd9bfb79yxhh0ngijpxj9sxd4p"))))
+        (base32 "1gn1yyfs08a77zrl4cidahxim3kgcvpbsrgfxxnhhrka57xcylld"))))
     (properties `((upstream-name . "anndataR")))
     (build-system r-build-system)
     (arguments
@@ -4670,14 +4664,13 @@ directly access various slots (e.g. X, obs, var), or convert the data into
     (build-system r-build-system)
     (arguments
      (list
+      #:test-directory "inst/unitTests"
+      ;; These tests require internet access.
+      #:skipped-tests
+      '("test_recipe.R"
+        "test_webAccessFunctions.R")
       #:phases
       '(modify-phases %standard-phases
-         (add-after 'unpack 'delete-bad-tests
-           (lambda _
-             ;; These tests require internet access.
-             (for-each delete-file
-                       '("inst/unitTests/test_recipe.R"
-                         "inst/unitTests/test_webAccessFunctions.R"))))
          (add-before 'install 'set-home
            (lambda _ (setenv "HOME" "/tmp"))))))
     (propagated-inputs
@@ -5244,13 +5237,13 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
 (define-public r-arrayqualitymetrics
   (package
     (name "r-arrayqualitymetrics")
-    (version "3.64.0")
+    (version "3.66.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "arrayQualityMetrics" version))
               (sha256
                (base32
-                "1kz2d40wx2ksy9dz1z3wylcj7y7ad9z8xphsnz39j02m4g5mbvlp"))))
+                "0y9k81vwqq74zfdrc2hvx7mg0l7572hvrsby00m20z034j7f9pmi"))))
     (properties
      '((upstream-name . "arrayQualityMetrics")
        ;; We don't need these.
@@ -5272,7 +5265,7 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
                              r-svglite
                              r-vsn
                              r-xml))
-    (native-inputs (list r-knitr))
+    (native-inputs (list r-biocstyle r-knitr))
     (home-page "https://bioconductor.org/packages/arrayQualityMetrics")
     (synopsis "Quality metrics report for microarray data sets")
     (description
@@ -6110,10 +6103,8 @@ retrieval analyses, or similar technologies.")
     (build-system r-build-system)
     (arguments
      (list
-      #:phases
-      '(modify-phases %standard-phases
-         (add-after 'unpack 'disable-bad-tests
-           (lambda _ (delete-file "tests/testthat/test-download.R"))))))
+      ;; This requires internet access.
+      #:skipped-tests '("test-download.R")))
     (propagated-inputs (list cmake r-dir-expiry))
     (native-inputs (list r-knitr r-testthat))
     (home-page "https://github.com/LTLA/biocmake")
@@ -6421,17 +6412,6 @@ objects.")
         (base32 "189akh4lpbp0dzgflb3nb3vi94bhmsj7qkcl597dnnzxqz00hsb2"))))
     (properties `((upstream-name . "CoreGx")))
     (build-system r-build-system)
-    (arguments
-     (list
-      #:phases
-      '(modify-phases %standard-phases
-         (add-after 'unpack 'disable-bad-tests
-           (lambda _
-             ;; It is unclear why 3 tests fail.
-             (with-directory-excursion "tests/testthat"
-               (substitute* "test-LongTable-utils.R"
-                 ((".*doesn't miss assay observations.*" m)
-                  (string-append m "skip('guix')\n")))))))))
     (propagated-inputs
      (list r-bench
            r-biobase
@@ -7900,13 +7880,13 @@ Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
 (define-public r-isva
   (package
     (name "r-isva")
-    (version "1.9")
+    (version "1.10")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "isva" version))
               (sha256
                (base32
-                "05qx9q0kg4ma23v4abhihw0vz017nq6hv2jzsiqx4d20ngh1dl4z"))))
+                "1im1bwbf6l88m4bwwwr0z2x8bvw927s3fqbwc06s5240wc8syjpl"))))
     (properties `((upstream-name . "isva")))
     (build-system r-build-system)
     (propagated-inputs (list r-fastica r-jade r-qvalue))
@@ -8673,13 +8653,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.66.1")
+    (version "2.66.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "1cmzay4z9s183dc001rxfa81ql67la9y8m0p0wsn2iwzxzx94n8g"))))
+                "1awsfklcs35vrmjkc12bk5ys9w7ib0799i3d0k138y44a0837pph"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -10337,13 +10317,13 @@ Enrichment Analysis} (GSEA).")
 (define-public r-gsva
   (package
     (name "r-gsva")
-    (version "2.4.6")
+    (version "2.4.8")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GSVA" version))
               (sha256
                (base32
-                "08i2s5zlm75mr7zl357cic2zxcy7aqqfv67xb0w67n48cw016ri6"))))
+                "0p9awi85dbmmyplhdfz0in4nhaavb58gpf48kqyp30rcc3v5a8h0"))))
     (properties `((upstream-name . "GSVA")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase
@@ -10738,6 +10718,54 @@ nucleotide sequence analysis.  The package is primarily useful to developers
 of other R packages who wish to make use of HTSlib.")
     (license license:lgpl2.0+)))
 
+(define-public r-rliger
+  (package
+    (name "r-rliger")
+    (version "2.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/welch-lab/liger")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1w849km9b347m56qwr5lr6ymdk7wv22hr224riscm0zrnx402yb3"))))
+    (properties `((upstream-name . "rliger")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-cli
+                             r-delayedarray
+                             r-dplyr
+                             r-ggplot2
+                             r-hdf5array
+                             r-hdf5r
+                             r-leidenalg
+                             r-lifecycle
+                             r-magrittr
+                             r-matrix
+                             r-patchwork
+                             r-rann
+                             r-rcpp
+                             r-rcpparmadillo
+                             r-rcppplanc
+                             r-rcppprogress
+                             r-rlang
+                             r-s4vectors
+                             r-scales
+                             r-uwot))
+    (native-inputs
+     (list r-circlize r-complexheatmap r-knitr r-testthat r-viridis))
+    (home-page "https://github.com/welch-lab/liger")
+    (synopsis "Linked inference of genomic experimental relationships")
+    (description
+     "LIGER is a package for integrating and analyzing multiple single-cell
+datasets. It relies on integrative non-negative matrix factorization to
+identify shared and dataset-specific factors.")
+    (license license:gpl3)))
+
+(define-deprecated-package r-liger
+  r-rliger)
+
 (define-public r-rnbeads
   (package
     (name "r-rnbeads")
@@ -11117,13 +11145,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-maaslin2
   (package
     (name "r-maaslin2")
-    (version "1.22.0")
+    (version "1.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Maaslin2" version))
        (sha256
-        (base32 "10hdjhi1ykk513hzvs0bi6avzghqmkqns8knhz3ycv7bj3ynp70x"))))
+        (base32 "0z8vfx6db6xfvqdhg6n8jx3fmgwvq22facsacq6ym867kw2jafiz"))))
     (properties `((upstream-name . "Maaslin2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11311,17 +11339,6 @@ high distances can be flagged as potentially low-quality.")
        ;; Avoid dependency cycle.
        (updater-ignored-native-inputs . ("r-spectra"))))
     (build-system r-build-system)
-    (arguments
-     (list
-      #:phases
-      '(modify-phases %standard-phases
-         ;; This test uses a deprecated procedure that has since been removed
-         ;; from testthat.
-         (add-after 'unpack 'testthat-compatibility
-           (lambda _
-             (substitute* "tests/testthat/test_zzz.R"
-               ((".*.onLoad works.*" m)
-                (string-append m "skip('guix')\n"))))))))
     (propagated-inputs (list r-biocparallel r-mscoreutils))
     (native-inputs (list r-callr r-knitr r-microbenchmark r-robustbase
                          r-testthat))
@@ -11528,13 +11545,13 @@ time-series data (including a graphical user interface).")
 (define-public r-mmuphin
   (package
     (name "r-mmuphin")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MMUPHin" version))
        (sha256
-        (base32 "0d8i9b6pjwz409jd46fm1n9h21hzg8zgzpvchywpyc1k896fvz4l"))
+        (base32 "1zdk9ffa996w4acnhbs7grbji5s3plwhcl6m21yajrlck2i9y3cw"))
        ;; Delete generated files.
        (snippet
         '(for-each delete-file
@@ -14298,13 +14315,13 @@ level.")
 (define-public r-tcgautils
   (package
     (name "r-tcgautils")
-    (version "1.30.2")
+    (version "1.30.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "TCGAutils" version))
               (sha256
                (base32
-                "1zwzx7mfp4s0v1rdjsyxj4l9w360g4qm3am8yf5lsd0biciqqh93"))))
+                "1nppp70675y3ds76jf61rhfis2lgkxqjhz48b367qa55g3q2ah61"))))
     (properties `((upstream-name . "TCGAutils")))
     (build-system r-build-system)
     (arguments
@@ -15024,14 +15041,14 @@ unmodeled, or latent sources of noise.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "2.16.3")
+    (version "2.16.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "0maixi0hwqzkpiq60hf60x4q3gv3hkvmrqh3ygv0fk63g1k9f6cj"))))
+         "1zrk6ky58f30wvaxph5dc2wr418qfpwc7d8pkxpl5dhb5g7vgn8r"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     ;; Tests fail because genWorkenvir fails to set up the environment.
@@ -15398,13 +15415,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.")
 (define-public r-xllim
   (package
     (name "r-xllim")
-    (version "2.3")
+    (version "2.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xLLiM" version))
        (sha256
-        (base32 "08v6acn6vpn8asn61ldqdryjz0xk5zyd2v63aqrc5xximpqwrp7d"))))
+        (base32 "1h2z6a3j3yi7rj5lyk7gb1iyp2vf516fgmk7wr333gfkvk522n2r"))))
     (properties `((upstream-name . "xLLiM")))
     (build-system r-build-system)
     (propagated-inputs (list r-abind
@@ -16304,14 +16321,14 @@ signals directly in the Bruker format.")
 (define-public r-codedepends
   (package
     (name "r-codedepends")
-    (version "0.6.6")
+    (version "0.6.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "CodeDepends" version))
        (sha256
         (base32
-         "0msq5ksjqp2pjzl6f1vizw53gdf5lz520bpdr5dbjwz5mc1mp0bz"))))
+         "02sj40qxq5vywgqay9q9vpv3s6j3jjr46kc8q3v1yw2vbsmlvrz0"))))
     (properties `((upstream-name . "CodeDepends")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17382,14 +17399,14 @@ data.")
 (define-public r-ggtree
   (package
     (name "r-ggtree")
-    (version "4.0.4")
+    (version "4.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggtree" version))
        (sha256
         (base32
-         "1qi5nispv0cirfayijybnn1nr8l6sb2adnic3y37qm3yv91w6s6z"))))
+         "0w9hqc3m35mrdqy5iwcm201pzpbl8jw6rd3wyzwp6f53wbbm2lbh"))))
     (properties `((upstream-name . "ggtree")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18703,13 +18720,13 @@ standardization of the analyses and the development of best practices.")
 (define-public r-microbiomestat
   (package
     (name "r-microbiomestat")
-    (version "1.3")
+    (version "1.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "MicrobiomeStat" version))
               (sha256
                (base32
-                "02xg8l4d0z5wrdrm5dj5a0q51vsbhf3f6z2lk8294c4d85s09dhl"))))
+                "0in28lzds3sv1xa25vs8q5mmm1ax78s2axhq7mi23njqip5xmsr1"))))
     (properties
      '((upstream-name . "MicrobiomeStat")
        (updater-extra-inputs . ("nlopt"))
@@ -18717,23 +18734,21 @@ standardization of the analyses and the development of best practices.")
     (build-system r-build-system)
     (inputs (list nlopt))
     (native-inputs (list pkg-config))
-    (propagated-inputs (list r-bbmisc
+    (propagated-inputs (list r-bbotk
                              r-dplyr
                              r-foreach
                              r-ggplot2
                              r-ggrepel
-                             r-lhs
                              r-lmertest
                              r-mass
                              r-matrix
                              r-matrixstats
-                             r-mlr
-                             r-mlrmbo
+                             r-mlr3
+                             r-mlr3mbo
                              r-modeest
-                             r-paramhelpers
+                             r-paradox
                              r-rcpp
                              r-rcpparmadillo
-                             r-smoof
                              r-statmod))
     (home-page "https://cran.r-project.org/package=MicrobiomeStat")
     (synopsis "Statistical methods for microbiome compositional data")
@@ -19637,14 +19652,14 @@ correspondence between different data sources.")
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.30.4")
+    (version "1.30.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "080q91ll8rvqf93hcmxc7kjbmmihyh0vrpxck2pqrwglbqxm4xll"))))
+         "12c6xwp29mmalvxp3asliv2hlha5vv8l37prmmcgpdi4nghfic3b"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aplot
@@ -22889,14 +22904,14 @@ expression space.")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.28.0")
+    (version "1.28.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "1ibxynw77a8mqv9av7z828wcazjpm4sfp83hd412f2rmgkls895x"))))
+         "016wpficnbricf4f7sgq8j53cl178f1332fh9zvlx7q560489zf1"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -23528,14 +23543,14 @@ populations, splice site strength, conservation, etc.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.40.1")
+    (version "1.40.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "1xqy4jl8im7i4kd4iwn8hvhy172fzsadyn90kprihmvccmpd5cr3"))))
+         "0k2rcgg4ll06b9j7999d4l60wpmi3vnjaqiy5ay8ppd1z0m38ygf"))))
     (properties
      '((upstream-name . "variancePartition")
        (updater-extra-native-inputs . ("r-rfast"))))
@@ -23876,30 +23891,26 @@ rate} (FDR).")
 (define-public r-activedriverwgs
   (package
     (name "r-activedriverwgs")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActiveDriverWGS" version))
        (sha256
         (base32
-         "0xnplgwxd197a4d422bsxg753q158i12ils16awd1cw30wafdxkk"))))
+         "1v6lnzbaksqpc33q3bp4mwij6rrfbqhi5wk1qx32h2wr2hr4208y"))))
     (properties
      `((upstream-name . "ActiveDriverWGS")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biostrings
            r-bsgenome
-           r-bsgenome-hsapiens-ucsc-hg19
-           r-bsgenome-hsapiens-ucsc-hg38
-           r-bsgenome-mmusculus-ucsc-mm9
-           r-bsgenome-mmusculus-ucsc-mm10
            r-genomeinfodb
            r-genomicranges
            r-iranges
            r-s4vectors))
     (native-inputs
-     (list r-knitr r-testthat))
+     (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat))
     (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
     (synopsis "Driver discovery tool for cancer whole genomes")
     (description
@@ -24759,13 +24770,13 @@ functionality.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.78.0")
+    (version "1.78.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1dfsfj4dm9wnh4qr1sqdrwzccl3pgw58j17vr3i1bvxkrq31p1ws"))))
+                "1qw3xwsffdqfwpmwrpzg8rnjwv9l45lkjz8bf5272hkhgjc7b1a8"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -24878,14 +24889,14 @@ db and resource files to AWS S3 buckets.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.36.1")
+    (version "1.36.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "09jwnwiq4vx7cmzq5va3rh7npjyhi1p5p344c4n0h9nr55mxzjiw"))))
+         "0bhr51c58vdfvly0bh3hgr397qkq45yw8221rpr38cah7dbzvrba"))))
     (properties
      '((upstream-name . "MultiAssayExperiment")
        (updater-extra-native-inputs
@@ -25954,13 +25965,13 @@ provided for direct creation of an in-memory tatami matrix from a HDF5 file.")
 (define-public r-beadarray
   (package
     (name "r-beadarray")
-    (version "2.58.0")
+    (version "2.60.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "beadarray" version))
               (sha256
                (base32
-                "0m9hmy4xn7q2v4ra95b9h08d0qh5qmjgqmg96vabyv46gn5i7qp4"))))
+                "1bcirbg10ai6jpa8a5ppq4450r5h2bwizb98qn0z0hmm1mm4ww9r"))))
     (properties `((upstream-name . "beadarray")))
     (build-system r-build-system)
     (propagated-inputs (list r-annotationdbi
@@ -26390,13 +26401,13 @@ of other packages.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.38.0")
+    (version "1.38.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "1qwygk8fg8nharrkmjs65fcl3lsdi232f2383s5j8vm1qil5gghd"))))
+                "1p8dzjphrcqai1f8wh56jfv377dqzdfnx2sl9sn73axbsr41swa7"))))
     (build-system r-build-system)
     (properties
      '((updater-extra-native-inputs
@@ -26501,13 +26512,13 @@ variable and significantly correlated genes.")
 (define-public r-sparsearray
   (package
     (name "r-sparsearray")
-    (version "1.10.8")
+    (version "1.10.10")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SparseArray" version))
        (sha256
-        (base32 "1bjxljwfrv787ikp61xl29wx3k6624qz75gl1kzfif62vys7vgf0"))))
+        (base32 "19c1dfa5wizq7k53a43i5dwwaqs44prclxbf1k0i3awx5wz6qlbw"))))
     (properties `((upstream-name . "SparseArray")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocgenerics
@@ -27161,14 +27172,14 @@ with your data.")
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.42.0")
+    (version "2.42.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "1v5z4fmwgs3swvpa09y986sracz0nsggq8s9hp1nmwb9a9grw8px"))))
+         "0djrd63nsqpy46acblg5k8pq6ldqccr35r6h0sf4xridpkqm78b1"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -27183,7 +27194,6 @@ with your data.")
            r-readr
            r-s4vectors
            r-seqinfo
-           r-snpstats
            r-tibble
            r-variantannotation))
     (native-inputs
@@ -27644,16 +27654,6 @@ visualizations for publication-quality multi-panel figures.")
          "1c7vy10ga3cswsqwxljbgqlsjg0d2lx9srfknbjy4fkbyrjci15k"))))
     (properties `((upstream-name . "ballgown")))
     (build-system r-build-system)
-    (arguments
-     (list
-      #:phases
-      '(modify-phases %standard-phases
-         ;; These deprecated procedures have been removed in testthat.
-         (add-after 'unpack 'testthat-compatibility
-           (lambda _
-             (substitute* "tests/testthat/test-annotation.R"
-               (("is_true\\(\\)") "expect_true")
-               (("is_false\\(\\)") "expect_false")))))))
     (propagated-inputs
      (list r-biobase
            r-genomicranges
@@ -28409,28 +28409,18 @@ separate published packages.")
 (define-public r-biomformat
   (package
     (name "r-biomformat")
-    (version "1.38.0")
+    (version "1.38.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomformat" version))
        (sha256
         (base32
-         "1ydcgifdrgg48y7qxg0gw30h332y3yk3k3n17fajkv58mlvyx1yc"))))
+         "0b0w0mfx448ph8fla3nb4i50mvpnv498kxip7rnh14xwas9rhdd7"))))
     (properties `((upstream-name . "biomformat")))
     (build-system r-build-system)
-    (arguments
-     (list
-      #:phases
-      '(modify-phases %standard-phases
-         ;; These deprecated procedures have been removed in testthat.
-         (add-after 'unpack 'testthat-compatibility
-           (lambda _
-             (substitute* "tests/testthat/test-IO.R"
-               (("is_true\\(\\)") "expect_true")
-               (("is_false\\(\\)") "expect_false")))))))
     (propagated-inputs
-     (list r-jsonlite r-matrix r-plyr r-rhdf5))
+     (list r-jsonlite r-matrix r-rhdf5))
     (native-inputs (list r-knitr r-testthat))
     (home-page "https://github.com/joey711/biomformat/")
     (synopsis "Interface package for the BIOM file format")
@@ -29188,25 +29178,15 @@ reproducibility.")
 (define-public r-phyloseq
   (package
     (name "r-phyloseq")
-    (version "1.54.1")
+    (version "1.54.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "phyloseq" version))
        (sha256
-        (base32 "1zivxag6b2bjh32k1mpn7hlvalap97rp90x3cbfynqrk6933f4bq"))))
+        (base32 "106zwzzwzvb5x0lz9i68wshh2nsa2rf5rmkqjqsvr4smxq6hknlj"))))
     (properties `((upstream-name . "phyloseq")))
     (build-system r-build-system)
-    (arguments
-     (list
-      #:phases
-      '(modify-phases %standard-phases
-         ;; These deprecated procedures have been removed in testthat.
-         (add-after 'unpack 'testthat-compatibility
-           (lambda _
-             (substitute* (find-files "tests/testthat" "\\.R$")
-               (("is_true\\(\\)") "expect_true")
-               (("is_false\\(\\)") "expect_false")))))))
     (propagated-inputs
      (list r-ade4
            r-ape

gnu/packages/bioinformatics.scm

@@ -922,7 +922,10 @@ suite native in R.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12h1di45fg06nhsliii7v0h1z567pkpis1xm4ar1qr8ns1n8iljw"))))
+        (base32 "12h1di45fg06nhsliii7v0h1z567pkpis1xm4ar1qr8ns1n8iljw"))
+       (modules '((guix build utils)))
+       (snippet
+        '(delete-file-recursively "r/src/vendor/highway"))))
     (properties `((upstream-name . "BPCells")))
     (build-system r-build-system)
     (arguments
@@ -930,7 +933,11 @@ suite native in R.")
       #:phases
       '(modify-phases %standard-phases
          (add-after 'unpack 'chdir
-           (lambda _ (chdir "r"))))))
+           (lambda _
+             (substitute* "r/configure"
+               (("tools/hwy-test.cpp" m)
+                (string-append m " $HWY_LIBS $HWY_CFLAGS")))
+             (chdir "r"))))))
     (propagated-inputs
      (list r-dplyr
            r-ggplot2
@@ -957,7 +964,7 @@ suite native in R.")
            r-igraph
            r-iranges
            r-matrixstats))
-    (inputs (list hdf5 zlib))
+    (inputs (list hdf5 google-highway zlib))
     (native-inputs (list pkg-config))
     (home-page "https://github.com/bnprks/BPCells")
     (synopsis "Single cell counts matrices to PCA")

gnu/packages/build-tools.scm

@@ -26,6 +26,7 @@
 ;;; Copyright © 2025 Josep Bigorra <jjbigorra@gmail.com>
 ;;; Copyright © 2025 John Kehayias <john.kehayias@protonmail.com>
 ;;; Copyright © 2026 Nemin <bergengocia@protonmail.com>
+;;; Copyright © 2026 Nguyễn Gia Phong <cnx@loang.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -100,6 +101,7 @@
   #:use-module (gnu packages rpc)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages tcl)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages unicode)
   #:use-module (gnu packages version-control)
@@ -139,6 +141,48 @@ Bourne shell script instead of m4.")
     (home-page "https://github.com/radareorg/acr")
     (license license:gpl2)))
 
+(define-public autosetup
+  (package
+    (name "autosetup")
+    (version "0.7.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/msteveb/autosetup")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256 (base32 "002b380073cpxlqziia2gvngywrb37b08p9k0zk9vlxn2p174hc6"))
+       (modules '((guix build utils)))
+       (snippet
+        #~(begin
+            (delete-file "jimsh0.c")
+            (substitute* "Makefile"
+              (("^.*tclsh8\\..*")       ;tests run with specific Tcl versions
+               ""))))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:test-target "test"
+           #:phases
+           #~(modify-phases %standard-phases
+               (delete 'configure)
+               (delete 'build)
+               (replace 'install
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   (substitute* "sys-find-tclsh"
+                     (("jimsh tclsh")
+                      (search-input-file inputs "bin/tclsh")))
+                   (invoke "tclsh" "autosetup"
+                           (string-append "--sysinstall=" #$output)))))))
+    (inputs (list tcl))
+    (home-page "https://msteveb.github.io/autosetup/")
+    (synopsis "Build environment auto-configurator")
+    (description
+     "@command{autosetup} is a tool, similar to @command{autoconf},
+to configure a build system for the appropriate environment,
+according to the system capabilities and the user-selected options.")
+    (license license:bsd-2)))
+
 (define-public bam
   (package
     (name "bam")

gnu/packages/containers.scm

@@ -375,7 +375,7 @@ contents, and discovering ways to shrink the size of Docker/OCI image.")
 (define-public guix-compose
   (package
     (name "guix-compose")
-    (version "0.1.1")
+    (version "0.2.0")
     (source
      (origin
        (method git-fetch)
@@ -384,7 +384,7 @@ contents, and discovering ways to shrink the size of Docker/OCI image.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ij6rfs5pfykk8c53q029sl2qx3k572dqdfb6pn5s569l6697ci1"))))
+        (base32 "1dy48qkz3ifxagijpvwg7rmq7hz3pikhdcfral6djyc9ppmz8mbm"))))
     (build-system guile-build-system)
     (arguments
      (list
@@ -426,7 +426,7 @@ contents, and discovering ways to shrink the size of Docker/OCI image.")
                  "guile" "-L" "./modules" "-s" "tests/test-compose.scm")))))))
     (native-inputs (list guile-3.0))
     ;; Avoid setting propagated so that we use the user’s profile.
-    (inputs (list guix guile-yamlpp))
+    (inputs (list guix guile-dotenv guile-yamlpp))
     (native-search-paths
      (list $GUIX_EXTENSIONS_PATH))
     (synopsis "Guix' docker compose compatibility layer")

gnu/packages/crypto.scm

@@ -1688,14 +1688,14 @@ structure.  However CryFS is not considered stable yet by the developers.")
 (define-public b3sum
   (package
     (name "b3sum")
-    (version "1.8.2")
+    (version "1.8.4")
     (source
       (origin
         (method url-fetch)
         (uri (crate-uri "b3sum" version))
         (file-name (string-append name "-" version ".tar.gz"))
         (sha256
-         (base32 "06qc6iv574km4j1ja4qhxyai680jkll58qzpz4mb79c0rk750dpd"))))
+         (base32 "0pkra5zh680cl9q92hpzmg9flz99b06bhpg7jyhymg1nkm0anw7a"))))
     (build-system cargo-build-system)
     (arguments
      (list

gnu/packages/distributed.scm

@@ -51,7 +51,7 @@
 (define-public boinc-client
   (package
     (name "boinc-client")
-    (version "8.2.8")
+    (version "8.2.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -62,7 +62,7 @@
               (file-name (git-file-name "boinc" version))
               (sha256
                (base32
-                "1ppcf57p6dkv9dv5k90fj3xhbv9di2d3yjkg2flfv5d45s82lay8"))))
+                "0ik9423ii6kal29jdn907pxy8w86zpi8n158qx1gcsh8lsaif1v5"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/django.scm

@@ -709,13 +709,13 @@ your code.")
 (define-public python-django-filter
   (package
     (name "python-django-filter")
-    (version "25.1")
+    (version "25.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "django_filter" version))
               (sha256
                (base32
-                "0lvi82f3dnj89ip8hry8fq8w7x632r5p84dlr451rnm8izsfxj8y"))))
+                "08wgzqirabxzcdhh0wvv45hqr6dqxy3ifm7mjv86hi0zjd59h3kn"))))
     (build-system pyproject-build-system)
     (arguments
      '(#:phases

gnu/packages/dlang.scm

@@ -75,7 +75,8 @@
        (uri (string-append "https://github.com/ldc-developers/ldc/releases"
                            "/download/v" version "/ldc-" version "-src.tar.gz"))
        (sha256
-        (base32 "13pkg69wjj4ali4ikijicccpg8y6f2hghhb70z9lrqr2w3pkhqna"))))
+        (base32 "13pkg69wjj4ali4ikijicccpg8y6f2hghhb70z9lrqr2w3pkhqna"))
+       (patches (search-patches "ldc-i686-int128-alignment.patch"))))
     (build-system cmake-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -372,6 +373,7 @@ integration tests...\n")
               ;; Do not build the shared libphobos2.so library, to avoid
               ;; retaining a reference to gcc:lib.
               "SHARED=0"
+              "DIFFABLE=1"              ;constant timestamp
               "VERBOSE=1")
       #:modules
       `(,@%default-gnu-modules
@@ -476,6 +478,15 @@ integration tests...\n")
               (phase-in-sub-dir 'build "dmd"))
             (add-after 'build 'build-phobos
               (phase-in-sub-dir 'build "phobos"))
+            (add-after 'build-phobos 'build-man
+              (lambda* (#:key make-flags #:allow-other-keys)
+                (with-directory-excursion "dmd/compiler/docs"
+                  (let ((dmd (or (which "gdmd")
+                                 (which "dmd"))))
+                    ((assoc-ref %standard-phases 'build)
+                     #:make-flags (cons
+                                   (string-append "DMD=" dmd)
+                                   make-flags))))))
             (replace 'check
               (phase-in-sub-dir 'check "dmd"))
             (add-after 'check 'check-phobos
@@ -501,7 +512,7 @@ integration tests...\n")
                       (for-each (cut install-file <> lib-lib)
                                 (find-files "." "^libdruntime\\.so[.0-9]*$")))
                     (copy-recursively "druntime/import" out-include)
-                    (copy-recursively "compiler/docs/man" out-man))
+                    (copy-recursively "generated/docs/man" out-man))
                   (with-directory-excursion "phobos"
                     (with-directory-excursion build-sub-dir
                       (install-file "libphobos2.a" out-lib)
@@ -676,6 +687,7 @@ needed.")
                  (lambda* (#:key tests? #:allow-other-keys)
                    (when tests?
                      (invoke "bin/rdmd" "rdmd_test.d" "bin/rdmd"
+                             "-m" (if #$(target-64bit?) "64" "32")
                              "--rdmd-default-compiler" "ldmd2"))))
                (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)

gnu/packages/dns.scm

@@ -295,35 +295,37 @@ prompt the user with the option to go with insecure DNS only.")
 (define-public dnsmasq
   (package
     (name "dnsmasq")
-    (version "2.90")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "http://www.thekelleys.org.uk/dnsmasq/dnsmasq-"
-                    version ".tar.xz"))
-              (sha256
-               (base32
-                "1r09l537vi867hlpv6vl7nvqhscvq1kf04m896bfrgrpv2dk0l4f"))))
+    (version "2.92")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "http://thekelleys.org.uk/git/dnsmasq.git")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "055gn5kigz0m9y09vig97s1g257hnlkhw4wv9d9wdficnsxcbwwm"))))
     (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f ;no tests
+      #:make-flags
+      #~(list (string-append "PREFIX=" #$output)
+              (string-append "CC=" #$(cc-for-target))
+              (string-append "PKG_CONFIG=" #$(pkg-config-for-target))
+              "COPTS=\"-DHAVE_DBUS\"")
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure) ;no configure
+          (add-after 'install 'install-dbus
+            (lambda _
+              (install-file "dbus/dnsmasq.conf"
+                            (string-append #$output "/etc/dbus-1/system.d")))))))
     (native-inputs
      (list pkg-config))
     (inputs
      (list dbus))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (delete 'configure)
-         (add-after 'install 'install-dbus
-           (lambda _
-             (install-file "dbus/dnsmasq.conf"
-                           (string-append %output "/etc/dbus-1/system.d")))))
-
-       #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
-                          (string-append "CC=" ,(cc-for-target))
-                          (string-append "PKG_CONFIG=" ,(pkg-config-for-target))
-                          "COPTS=\"-DHAVE_DBUS\"")
-       #:tests? #f))                    ; no ‘check’ target
-    (home-page "https://www.thekelleys.org.uk/dnsmasq/doc.html")
+    (home-page "https://thekelleys.org.uk/dnsmasq/doc.html")
     (synopsis "Small caching DNS proxy and DHCP/TFTP server")
     (description
      "Dnsmasq is a light-weight DNS forwarder and DHCP server.  It is designed

gnu/packages/duckdb.scm

@@ -148,13 +148,13 @@ system.")
 (define-public r-duckdb
   (package
     (name "r-duckdb")
-    (version "1.4.4")
+    (version "1.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "duckdb" version))
        (sha256
-        (base32 "1hch36v3lsymnx30lv3cjy12gs3v3mhd44ha97l7w9mwp9wbzmxl"))
+        (base32 "177621m08whqqk4yhj3zrr08l3d9hhlqh3gm9jzhi5cplg47cksq"))
        ;; This package bundles the duckdb sources and builds a custom variant
        ;; of duckdb.  I'd be happy to link it with our duckdb library instead,
        ;; but it does not seem possible to do that.
@@ -179,10 +179,12 @@ system.")
                          r-dplyr
                          r-remotes
                          r-rlang
+                         r-sf
                          r-testthat
                          r-tibble
                          r-vctrs
                          r-withr
+                         r-wk
                          tzdata-for-tests))
     (home-page "https://r.duckdb.org/")
     (synopsis "DBI package for the DuckDB database management system")

gnu/packages/emacs-xyz.scm

@@ -15153,6 +15153,27 @@ exporter already existing in Org mode.  It supports the Github flavored
 markdown features.")
     (license license:gpl3+)))
 
+(define-public emacs-grip-mode
+  (package
+    (name "emacs-grip-mode")
+    (version "2.5.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/seagle0128/grip-mode")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1mrpmzcxgc9hkv55d6kv79f8y6ldqrf5b48f0a4fy30qlgby2wyz"))))
+    (arguments (list #:tests? #f)) ;no tests
+    (build-system emacs-build-system)
+    (home-page "https://github.com/seagle0128/grip-mode")
+    (synopsis "Instant GitHub-flavored Markdown/Org preview")
+    (description "Instant GitHub-flavored Markdown/Org preview using
+@code{grip}, @code{mdopen} or @code{go-grip}.")
+    (license license:gpl3)))
+
 (define-public emacs-2048-game
   (package
     (name "emacs-2048-game")
@@ -16975,6 +16996,35 @@ called.  If there are more, each window will have its first character
 highlighted.  Pressing that character will switch to that window.")
     (license license:gpl3+)))
 
+(define-public emacs-spatial-window
+  (package
+    (name "emacs-spatial-window")
+    (version "0.9.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/lewang/spatial-window")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "19whlw6p2q6ma20ifkr6iyrhj5l99vj1hv06s7j6j6pvgah27lm4"))))
+    (build-system emacs-build-system)
+    (arguments
+     (list
+      #:test-command
+      #~(list "emacs" "-Q" "-batch" "-L"  "."
+              "-l" "spatial-window-geometry-test.el"
+              "-l" "spatial-window-test.el"
+              "-f" "ert-run-tests-batch-and-exit")))
+    (propagated-inputs (list emacs-posframe))
+    (home-page "https://github.com/lewang/spatial-window")
+    (synopsis "Jump to windows by spatial position")
+    (description
+     "Jump to Emacs windows by pressing keys that match their spatial position
+on your keyboard.")
+    (license license:gpl3+)))
+
 (define-public emacs-windsize
   ;; There is no proper release.  The base version is extracted from the
   ;; "Version" keyword in the main file.
@@ -17721,6 +17771,29 @@ etc), but also compiling languages (C, C++, Go, Java etc) and markup
 languages.")
     (license license:gpl3+)))
 
+(define-public emacs-quotable
+  (package
+    (name "emacs-quotable")
+    (version "1.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/coopi/emacs-quotable")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "00359yljynmk6bqifvfrrradm4na9ap76isibi2d6s4i810szixh"))))
+    (build-system emacs-build-system)
+    (home-page "https://codeberg.org/coopi/emacs-quotable")
+    (synopsis "Emacs Lisp client for the Quotable API")
+    (description
+     "This package provides a programmatic interface for the
+@uref{https://github.com/lukePeavey/quotable, Quotable @acronym{API,
+Application Programming Interface}}, a free and open-source quotations
+@acronym{API}.")
+    (license license:agpl3+)))
+
 (define-public emacs-pkg-info
   (package
     (name "emacs-pkg-info")
@@ -24436,11 +24509,9 @@ conflicts.")
             (lambda* (#:key inputs native-inputs #:allow-other-keys)
               (substitute* "xelb-gen"
                 (("/usr/bin/env") (which "env")))
-              (let ((xcb-proto #$(this-package-native-input "xcb-proto"))
-                    (emacs (search-input-file (or native-inputs inputs)
-                                              "/bin/emacs")))
-                (invoke "make"
-                        (format #f "PROTO_PATH=~a/share/xcb" xcb-proto))))))))
+              (invoke "make"
+                      (format #f "PROTO_PATH=~a/share/xcb"
+                              #$(this-package-native-input "xcb-proto"))))))))
     (native-inputs (list xcb-proto))
     (propagated-inputs (list emacs-compat))
     (home-page "https://github.com/emacs-exwm/xelb")
@@ -24537,7 +24608,8 @@ of XELB.")
     (name "emacs-exwm-no-x-toolkit")
     (synopsis "Emacs X window manager (without an X toolkit)")
     (propagated-inputs
-     (list emacs-xelb-no-x-toolkit))
+     (modify-inputs propagated-inputs
+       (replace "emacs-xelb" emacs-xelb-no-x-toolkit)))
     (arguments
      (substitute-keyword-arguments arguments
        ((#:emacs emacs) `,emacs-no-x-toolkit)))))
@@ -28071,7 +28143,7 @@ match and total match information in the mode-line in various search modes.")
 (define-public emacs-pg
   (package
     (name "emacs-pg")
-    (version "0.62")
+    (version "0.63")
     (source (origin
               (method git-fetch)
               (uri (git-reference (url "https://github.com/emarsden/pg-el")
@@ -28079,7 +28151,7 @@ match and total match information in the mode-line in various search modes.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0fjzrn5b4s00km71ya98vwwfyvd4rvcywxdxqzy5xfrv8crm92w6"))))
+                "19hh45mlb4j6a3ys3wvivj0bm5xy5vjwscnvn68b656b5jk5himh"))))
     (build-system emacs-build-system)
     (propagated-inputs (list emacs-peg))
     (home-page "https://github.com/emarsden/pg-el")
@@ -28095,7 +28167,7 @@ end users.")
 (define-public emacs-pgmacs
   (package
     (name "emacs-pgmacs")
-    (version "0.42")
+    (version "0.30")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -28104,7 +28176,7 @@ end users.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0pf8y64hka1fl47dphmh4xgxiwfsd0g4q2fazq5yc48zwr9nsf02"))))
+                "0f4mbamk2n9l7qwhi2n1kwvng6wa9yp6k2w1qn6yc07pri2mb6yc"))))
     (build-system emacs-build-system)
     (propagated-inputs
      (list emacs-pg))
@@ -28113,6 +28185,12 @@ end users.")
     (home-page "https://github.com/emarsden/pgmacs")
     (license license:gpl3+)))
 
+(define-public emacs-pgmacs-0.42
+  (package
+    (inherit emacs-pgmacs)
+    (version "0.42")
+    (properties `((superseded . ,emacs-pgmacs)))))
+
 (define-public emacs-finalize
   (package
   (name "emacs-finalize")

gnu/packages/embedded.scm

@@ -1505,7 +1505,8 @@ hardware.  The utility support USB and UART as serial link.")
                  (apply (assoc-ref cargo:%standard-phases phase)
                         #:cargo-target #$(cargo-triplet)
                         args))
-               '(unpack-rust-crates
+               '(prepare-rust-crates
+                 unpack-rust-crates
                  configure
                  check-for-pregenerated-files
                  patch-cargo-checksums)))))))

gnu/packages/engineering.scm

@@ -135,6 +135,7 @@
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages javascript)
   #:use-module (gnu packages jupyter)
+  #:use-module (gnu packages icu4c)
   #:use-module (gnu packages kde-frameworks)
   #:use-module (gnu packages libcanberra)
   #:use-module (gnu packages libevent)
@@ -2720,16 +2721,17 @@ dynamics is used by FreeCAD 1.0.0 for its new Assembly workbench.")
 (define-public freecad
   (package
     (name "freecad")
-    (version "1.0.2")
+    (version "1.1.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/FreeCAD/FreeCAD")
-             (commit version)))
+             (commit version)
+             (recursive? #t)))          ;needed for the AddonManager
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1zyz473fzrz9h073wp4k65qq4bkhqsp245nsv6nv186sl78l99xa"))
+        (base32 "029ndw1dypx0xhs4fyiinf7gpk8am0vm9b24idvdsx9x7ghrqz4j"))
        (snippet
         #~(begin
             (use-modules (guix build utils))
@@ -2746,7 +2748,7 @@ dynamics is used by FreeCAD 1.0.0 for its new Assembly workbench.")
       #:configure-flags
       #~(list
          "-DBUILD_FLAT_MESH:BOOL=ON"
-         "-DBUILD_ENABLE_CXX_STD:STRING=C++17"
+         "-DBUILD_ENABLE_CXX_STD:STRING=C++20"  ; FreeCAD 1.1 requires C++20
          "-DENABLE_DEVELOPER_TESTS=OFF"  ;; see the above: #:tests? comment
          "-DFREECAD_QT_VERSION=6"  ;; Build with Qt6
          "-DFREECAD_USE_EXTERNAL_ONDSELSOLVER=ON"  ;; unbundle ondsel-solver
@@ -2768,12 +2770,13 @@ dynamics is used by FreeCAD 1.0.0 for its new Assembly workbench.")
      (list c++-gsl
            doxygen
            graphviz
+           pybind11
            qttools
            pkg-config
-           swig-4.0))
+           swig-4.4))
     (inputs
      (list bash-minimal
-           boost-1.83
+           boost
            coin3d
            double-conversion
            eigen
@@ -2783,6 +2786,7 @@ dynamics is used by FreeCAD 1.0.0 for its new Assembly workbench.")
            gl2ps
            glew
            hdf5-1.10
+           icu4c
            jsoncpp
            libarea
            libjpeg-turbo
@@ -2805,13 +2809,11 @@ dynamics is used by FreeCAD 1.0.0 for its new Assembly workbench.")
            python-ply
            python-pyside-6
            python-pyyaml
-           python-shiboken-6
            python-wrapper
            qtsvg
            qtwebchannel
            qtwebengine
            qtwayland
-           qtx11extras
            sqlite
            onetbb                       ;same version as opencascade-occt
            vtk-9.5

gnu/packages/file-systems.scm

@@ -88,6 +88,7 @@
   #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
   #:use-module (gnu packages golang-crypto)
+  #:use-module (gnu packages golang-web)
   #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages haskell-xyz)
@@ -761,7 +762,7 @@ from a mounted file system.")
   ;; completions by running a native bcachefs binary at build time.
   (package
     (name "bcachefs-tools-minimal")
-    (version "1.35.1")
+    (version "1.37.4")
     (source
      (origin
        (method git-fetch)
@@ -770,7 +771,7 @@ from a mounted file system.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1jn7fqlvhr0iazfx31wamvmf3qmgrzlf9ghvz8qazk8b6ipv77fn"))))
+        (base32 "17041jphzbg0ppxlc1acr3d73zyn02spjvi5my30wak8xh9n6nan"))))
     (build-system cargo-build-system)
     (arguments
      (list
@@ -968,20 +969,13 @@ minimal bcachefs-tools package.  It is meant to be used in initrds.")
 (define-public bcachefs-linux-module
   (package
     (name "bcachefs-linux-module")
-    (version "1.35.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://evilpiepirate.org/git/bcachefs-tools.git")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1jn7fqlvhr0iazfx31wamvmf3qmgrzlf9ghvz8qazk8b6ipv77fn"))))
+    (version (package-version bcachefs-tools-minimal))
+    (source (package-source bcachefs-tools-minimal))
     (build-system linux-module-build-system)
     (arguments
      (list
-      #:tests? #f ;no 'check' target
+      #:make-flags #~(list "BCACHEFS_DKMS=1")
+      #:tests? #f                       ;no 'check' target
       #:source-directory "build/src/fs/bcachefs"
       #:phases
       #~(modify-phases %standard-phases
@@ -990,18 +984,14 @@ minimal bcachefs-tools package.  It is meant to be used in initrds.")
               (with-output-to-file ".version"
                 (lambda ()
                   (display #$version)))))
-          (add-after 'unpack 'patch-source
-            (lambda _
-              (substitute* "Makefile"
-                ;; Remove unnecessary dependencies
-                (("^.*PKG_CONFIG.*$")
-                 ""))))
-          (add-before 'configure 'prepare-build-dir
-            (lambda _
-              (invoke "make" "install_dkms"
-                      (string-append "DESTDIR="
-                                     (getcwd) "/") "DKMSDIR=build/"))))))
-    (home-page (package-home-page bcachefs-tools-minimal/static))
+          (add-before 'configure 'prepare-build-directory
+            (lambda* (#:key make-flags #:allow-other-keys)
+              (apply invoke "make" "install_dkms"
+                     (string-append "DESTDIR="
+                                    (getcwd) "/")
+                     "DKMSDIR=build/"
+                     make-flags))))))
+    (home-page (package-home-page bcachefs-tools-minimal))
     (synopsis "Bcachefs Linux kernel module")
     (description
      "This package provides the Linux kernel module for Bcachefs.
@@ -2140,6 +2130,75 @@ the XDG directory specification from @file{~/.@var{name}} to
 @file{~/.config/@var{name}}.")
       (license license:gpl2+))))
 
+(define-public s5cmd
+  (package
+    (name "s5cmd")
+    (version "2.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/peak/s5cmd")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1y1bwma6f68j00jfdjxvw5flp9l4cdys7dgkrr0yvfz68lk9a17v"))
+       (snippet
+        #~(begin (use-modules (guix build utils))
+                 (delete-file-recursively "vendor")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:install-source? #f
+      #:import-path "github.com/peak/s5cmd/v2"
+      #:test-flags
+      #~(list "-vet=off"
+              ;; cp_test.go:74: assertion failed: text/plain; charset=utf-8
+              ;; (tc.expectedContentType string) != text/html; charset=utf-8
+              ;; (string)
+              "-skip" "TestGuessContentType")
+      #:test-subdirs
+      ;; build flag -mod=vendor only valid when using modules
+      ;; /<...>/peak/s5cmd/v2/e2e/util_test.go:417 +0x3b9
+      ;; /<...>/peak/s5cmd/v2/e2e/main_test.go:12 +0x65
+      #~(list "command/..."
+              "orderedwriter/..."
+              "progressbar/..."
+              "storage/..."
+              "storage/url/..."
+              "strutil/...")
+      #:phases
+      #~(modify-phases %standard-phases
+	  (add-after 'install 'rename-binaries
+	    (lambda _
+	      (rename-file
+	       (string-append #$output "/bin/v2")
+	       (string-append #$output "/bin/s5cmd")))))))
+    (native-inputs
+     (list go-github-com-aws-aws-sdk-go
+           go-github-com-cheggaaa-pb-v3
+           go-github-com-google-go-cmp
+           go-github-com-hashicorp-go-multierror
+           go-github-com-iancoleman-strcase
+           go-github-com-igungor-gofakes3
+           go-github-com-karrick-godirwalk
+           go-github-com-kballard-go-shellquote
+           go-github-com-lanrat-extsort-1.0.2
+           go-github-com-termie-go-shutil
+           go-github-com-urfave-cli-v2
+           go-go-uber-org-mock
+           go-gotest-tools-v3
+           go-honnef-co-go-tools
+           go-mvdan-cc-unparam))
+    (home-page "https://github.com/peak/s5cmd")
+    (synopsis "Parallel S3 and local filesystem execution tool")
+    (description
+     "@code{s5cmd} is a fast S3 and local filesystem execution tool.  It comes
+with support for a multitude of operations including tab completion and
+wildcard support for files, which can be handy for object storage workflow
+while working with large number of files.")
+    (license license:expat)))
+
 (define-public squashfuse
   (package
     (name "squashfuse")

gnu/packages/finance.scm

@@ -766,7 +766,7 @@ require Coincurve.")
 (define-public electrum
   (package
     (name "electrum")
-    (version "4.7.1")
+    (version "4.7.2")
     (source
      (origin
        (method git-fetch)
@@ -775,7 +775,7 @@ require Coincurve.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "171jbap3khzwkyxg730sasfj01qiip396sgyiwr1i6yq5fxd23pi"))))
+        (base32 "05y3w9jhpfxd7frzlilqvsfggrgfzcml2spc2qb5xx9j4q62hnmx"))))
     (build-system pyproject-build-system)
     (arguments
      (list

gnu/packages/freedesktop.scm

@@ -1150,6 +1150,60 @@ GNOME Shell.  The @command{localectl} command-line tool allows you to interact
 with localed.  This package is extracted from the broader systemd package.")
     (license license:lgpl2.1+)))
 
+(define-public gardenhostd
+  (package
+   (name "gardenhostd")
+   (version "1.1")
+   (source (origin
+            (method git-fetch)
+            (uri (git-reference
+                  (url "https://codeberg.org/axtlos/gardenhostd.git")
+                  (commit (string-append "v" version))))
+            (file-name (git-file-name name version))
+            (sha256
+             (base32
+              "1q0pdh0imc2ggb26cddl62hx6fmz6z4hqj2352a4k9wxyn5kfiam"))))
+   (build-system meson-build-system)
+   (arguments
+    (list
+     #:imported-modules `(,@%meson-build-system-modules
+                          ,@%pyproject-build-system-modules)
+     #:modules '(((guix build pyproject-build-system) #:prefix pyproject:)
+                 (guix build meson-build-system)
+                 (guix build utils))
+     #:phases
+     #~(modify-phases %standard-phases
+         (add-after 'install 'remove-extra-files
+           (lambda _
+             (with-directory-excursion #$output
+               (delete-file-recursively "etc/init.d")
+               (rmdir "etc"))))
+         ;; See <https://codeberg.org/guix/guix/issues/7579>.
+         (add-after 'install 'wrap-search-paths
+           (lambda _
+             (wrap-program (string-append #$output "/libexec/gardenhostd")
+               `("GUIX_PYTHONPATH" prefix
+                 ,(map
+                   (lambda (package)
+                     (string-append
+                      package "/lib/python"
+                      (pyproject:python-version #$(this-package-input "python"))
+                      "/site-packages"))
+                   ;; Avoids references to meson’s libraries.
+                   (list #$(this-package-input "python")
+                         #$(this-package-input "python-pygobject"))))))))))
+   (inputs
+    (list bash-minimal
+          python
+          python-pygobject))
+   (home-page "https://codeberg.org/axtlos/gardenhostd")
+   (synopsis "Minimal Python implementation of systemd-hostnamed")
+   (description "This package is a partial implementation of the
+systemd-hostnamed daemon.  It provides the @code{org.freedesktop.hostname1}
+D-Bus interface, which helps applications like GNOME Settings retrieve and
+modify the system’s hostname, as well as set a pretty hostname for display.")
+   (license license:gpl3+)))
+
 (define-public packagekit
   (package
     (name "packagekit")
@@ -2862,7 +2916,7 @@ to the C library @code{uchardet} to increase performance.")
 (define-public udiskie
   (package
     (name "udiskie")
-    (version "2.6.1")
+    (version "2.6.2")
     (source
      (origin
        (method git-fetch)
@@ -2871,7 +2925,7 @@ to the C library @code{uchardet} to increase performance.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0ngr8sdzd32mxamzfh82ar8m40z52lx91339b7dq3in0cr5r1ynp"))))
+        (base32 "0zc23yf2sw1m21xkfbpfjzbp7xykqjwq56fr2nxzlc02n7g6iqgk"))))
     (build-system pyproject-build-system)
     (arguments
      (list

gnu/packages/games.scm

@@ -3964,7 +3964,7 @@ that beneath its ruins lay buried an ancient evil.")
 (define-public angband
   (package
     (name "angband")
-    (version "4.2.5")
+    (version "4.2.6")
     (source
      (origin
        (method git-fetch)
@@ -3973,7 +3973,7 @@ that beneath its ruins lay buried an ancient evil.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0kg6npbfy42mhggsqvs04khc8198i980z52xm59pws29698qazaw"))
+        (base32 "0hgzdvlh0j42w4q9kch9xvhnbvcrypac01xhpksw35gj9my887cp"))
        (modules '((guix build utils)))
        (snippet
         ;; So, some of the sounds/graphics/tilesets are under different
@@ -3989,12 +3989,55 @@ that beneath its ruins lay buried an ancient evil.")
            (substitute* "lib/Makefile"
              ;; And don't try to invoke makefiles in the directories we removed.
              (("gamedata customize help screens fonts tiles sounds icons user")
-              "gamedata customize help screens user"))))))
+              "gamedata customize help screens user"))
+           ;; Remove nonfree .dll files too.
+           (delete-file-recursively "src/win")))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f                      ; no check target
-       #:configure-flags (list (string-append "--bindir=" %output "/bin"))))
-    (native-inputs (list autoconf automake))
+     `(#:configure-flags (list (string-append "--bindir=" %output "/bin"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'fix-infinite-loop-on-sighup
+           ;; XXX Release 4.2.6 has a major bug where sending the process a
+           ;; SIGHUP when closing the terminal causes it to infinite loop
+           ;; waiting for input: https://github.com/angband/angband/issues/6558
+           ;; Reevaluate for future versions.
+           (lambda _
+             (substitute* "src/ui-signals.c"
+               (("(SIGHUP, )SIG_IGN" _ first)
+                (string-append first "handle_signal_abort")))))
+         (add-before 'check 'skip-failing-tests
+           (lambda _
+             (let ((to-skip '(;; some of these may be fixable, but most try to
+                              ;; create a directory in the user's home directory.
+                              ;; Rather than reading environment variables, they
+                              ;; lookup the username using getpwnam(3) and manually
+                              ;; construct the string.
+                              ;; Generic "Suite died":
+                              "game/basic"
+                              "game/mage"
+                              ;; "Cannot create '//.angband/Angband'":
+                              "effects/chain"
+                              "effects/destruction"
+                              "effects/earthquake"
+                              "object/info"
+                              "object/slays"
+                              "player/calc-inventory"
+                              "player/combine-pack"
+                              "player/digging"
+                              "player/inven-carry-num"
+                              "player/inven-wield"
+                              "player/timed"
+                              ;; This file likes to read /etc/passwd
+                              "z-file/path-normalize")))
+               (substitute* "src/tests/Makefile"
+                 (("include \\$\\(SUITES\\)" all)
+                  (string-append all "\nTESTPROGS := $(filter-out "
+                                 (string-join to-skip " ")
+                                 ", $(TESTPROGS))")))))))))
+    (native-inputs (list autoconf
+                         automake
+                         perl)) ;for tests
     (inputs (list ncurses))
     (home-page "https://rephial.org/")
     (synopsis "Dungeon exploration roguelike")
@@ -4905,7 +4948,7 @@ Protocol).")
 (define-public extremetuxracer
   (package
     (name "extremetuxracer")
-    (version "0.8.2")
+    (version "0.8.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4913,7 +4956,7 @@ Protocol).")
                     version "/etr-" version ".tar.xz"))
               (sha256
                (base32
-                "0knd22lzhzqih1w92y6m7yxha376c6ydl22wy4xm6jg2x5jlk1qw"))))
+                "1rbk8zqfzzk90znf3f5lqqa12j0n6pm2qgwzabzmlnkm1k68acps"))))
     (build-system gnu-build-system)
     (native-inputs
      (list pkg-config))

gnu/packages/gimp.scm

@@ -398,7 +398,8 @@ that is extensible via a plugin system.")
                         ;; environment, as it could cause Gimp to crash (see
                         ;; bug#77921).
                         `("GI_TYPELIB_PATH" prefix
-                          (,(getenv "GI_TYPELIB_PATH")))
+                          (,(getenv "GI_TYPELIB_PATH")
+                           ,(string-append #$output "/lib/girepository-1.0")))
                         `("GUIX_PYTHONPATH" prefix
                           (,(getenv "GUIX_PYTHONPATH")))
                         `("GDK_PIXBUF_MODULE_FILE" =

gnu/packages/gnome-circle.scm

@@ -524,7 +524,8 @@ like automatic language detection, text-to-speech and clipboard buttons.")
                             #:vendor-dir "vendor"
                             #:cargo-target #$(cargo-triplet)
                             args))
-                   '(unpack-rust-crates
+                   '(prepare-rust-crates
+                     unpack-rust-crates
                      configure
                      check-for-pregenerated-files
                      patch-cargo-checksums))))))))
@@ -595,7 +596,8 @@ Transmission, and can be used to control remote Transmission instances.")
                         #:vendor-dir "vendor"
                         #:cargo-target #$(cargo-triplet)
                         args))
-               '(unpack-rust-crates
+               '(prepare-rust-crates
+                 unpack-rust-crates
                  configure
                  check-for-pregenerated-files
                  patch-cargo-checksums)))))))

gnu/packages/gnuzilla.scm

@@ -604,6 +604,7 @@ in the case of Firefox, it is browser/locales/all-locales."
     "zh-CN"
     "zh-TW"))
 
+;;; Please keep these versions in sync with icedove.
 (define %icecat-base-version "140.9.0")
 (define %icecat-version (string-append %icecat-base-version "-gnu1"))
 (define %icecat-build-id "20260324000000") ;must be of the form YYYYMMDDhhmmss
@@ -1248,24 +1249,29 @@ testing.")
        (cpe-name . "firefox_esr")
        (cpe-version . ,(first (string-split version #\-)))))))
 
-(define %icedove-build-id "20260224000000") ;must be of the form YYYYMMDDhhmmss
+(define %icedove-build-id "20260324000000") ;must be of the form YYYYMMDDhhmmss
 ;;; See <https://product-details.mozilla.org/1.0/thunderbird_versions.json>
 ;;; for the source of truth regarding Thunderbird releases.
-(define %icedove-version "140.8.0")
+;;; Please keep these version numbers in sync with icecat.
+;;; Please also update thunderbird-comm-source and thunderbird-comm-l10n to
+;;; the icedove version.
+(define %icedove-version "140.9.0")
 
 ;; Provides the "comm" folder which is inserted into the icecat source.
 ;; Avoids the duplication of Icecat's source tarball.  Pick the changeset that
 ;; matches the most recent tag of the form 'THUNDERBIRD_140_2_0esr_RELEASE'.
+;; Please also update the commit of thunderbird-comm-l10n to match the
+;; changeset used by thunderbird-comm-source.
 (define thunderbird-comm-source
   (origin
     (method hg-fetch)
     (uri (hg-reference
           (url "https://hg.mozilla.org/releases/comm-esr140")
-          (changeset "aa377fbf351e6b10b053e6afa421755c82d5fcf7")))
+          (changeset "8be9f2d3072c225a1e5f153745a18984c2babf8f")))
     (file-name (string-append "thunderbird-" %icedove-version "-checkout"))
     (sha256
      (base32
-      "0595jg1qbwclzi9qssljqkisrm2dn99rzxzaz2mcfi7b1kvbfaki"))
+      "04j35957x03m5x7mhh8zxa86mwjy0is2vb614sr4inkvvz4rs2hg"))
     (patches (search-patches "icedove-observer-fix.patch"))))
 
 ;;; To regenerate, see the `format-locales' helper defined above.
@@ -1342,7 +1348,8 @@ testing.")
   ;; The commit to use can be found in the mail/locales/l10n-changesets.json
   ;; file in Thunderbird's source (e.g.:
   ;; <https://hg-edge.mozilla.org/releases/comm-esr140/file/efb07defaa2d56105675dc1d936af581ebfd8ffa/mail/locales/l10n-changesets.json>)
-  (let* ((commit "b6fd3d6c75ba35d91fe131a654df76ca86f35ac5")
+  ;; where the hash in the URL is the changeset from thunderbird-comm-source.
+  (let* ((commit "7c86eab97e77f00ca7ed8f224d38338a3ed46693")
          (revision "0")
          (version (git-version %icedove-version revision commit)))
     (origin
@@ -1353,7 +1360,7 @@ testing.")
       (file-name (git-file-name "thunderbird-l10n" version))
       (sha256
        (base32
-        "0n4df6kv70a6mxxsqwc83nhj8vl7acv9bcbf07nkcsjjxh3szvqc")))))
+        "1navma2gwcgbbiwcwrc5lrx2jk3qmrnrc6i8pvhb8156pz4cg5nd")))))
 
 (define icedove-source
   (let ((name (string-append "icedove-" %icedove-version)))

gnu/packages/golang-check.scm

@@ -3342,6 +3342,33 @@ and restore them afterwards.")
 @url{http://www.freebsd.org/cgi/man.cgi?query=fail,failpoints} for Golang.")
     (license license:asl2.0)))
 
+(define-public go-go-shabbyrobe-org-gocovmerge
+  (package
+    (name "go-go-shabbyrobe-org-gocovmerge")
+    (version "0.0.0-20230507111327-fa4f82cfbf4d")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://git.sr.ht/~shabbyrobe/gocovmerge")
+              (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0sbr6i1m5hjbnlfad8cl8w30949r02c66l85hcmyyd9ka30mqr23"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "go.shabbyrobe.org/gocovmerge"))
+    (propagated-inputs
+     (list go-golang-org-x-tools))
+    (home-page "https://go.shabbyrobe.org/gocovmerge")
+    (synopsis "gocovmerge")
+    (description
+     "Package gocovmerge takes the results from multiple @code{go test
+-coverprofile} runs and merges them into one profile.  It is a maintained fork
+of @url{https://github.com/wadey/gocovmerge}.")
+    (license license:bsd-2)))
+
 (define-public go-go-simpler-org-sloglint
   (package
     (name "go-go-simpler-org-sloglint")

gnu/packages/golang-web.scm

@@ -3404,6 +3404,41 @@ pattern.")
 @code{net/rpc}.")
     (license license:expat)))
 
+(define-public go-github-com-cevatbarisyilmaz-ara
+  (package
+    (name "go-github-com-cevatbarisyilmaz-ara")
+    (version "0.0.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/cevatbarisyilmaz/ara")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0512nlqqv9bnsplphiw7q9s80icl63wgl88b7m6m4vsvn5ghphc8"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/cevatbarisyilmaz/ara"
+      #:test-flags
+      ;; ialer_test.go:46: lookup google.com on [::1]:53: read udp
+      ;; [::1]:39632->[::1]:53: read: connection refused
+      #~(list "-skip" "TestDialer|TestNewCustomResolver")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-examples
+            (lambda* (#:key import-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" import-path)
+                (delete-file "example_test.go")))))))
+    (home-page "https://github.com/cevatbarisyilmaz/ara")
+    (synopsis "Dialer with customizable resolver")
+    (description
+     "Package ara provides a dialer with customizable resolver.  It can be
+used with @code{http.Client} and @code{http.Transport} to alter host
+lookups.")
+    (license license:expat)))
+
 (define-public go-github-com-chris-ramon-douceur
   (package
     (name "go-github-com-chris-ramon-douceur")
@@ -5277,7 +5312,8 @@ for Go.")
     (home-page "https://github.com/emersion/go-sasl")
     (synopsis "SASL library written in Go")
     (description
-     "This package provides a SASL library written in Go.")
+     "This package provides a @acronym{Simple Authentication and Security
+Layer, SASL} library written in Go.")
     (license license:expat)))
 
 (define-public go-github-com-emersion-go-smtp
@@ -8630,6 +8666,40 @@ protocol) - used to discover UPnP services on a network
  by the IBM Cloud @code{OpenAPI} SDK Generator (openapi-sdkgen).")
     (license license:asl2.0)))
 
+(define-public go-github-com-igungor-gofakes3
+  (package
+    (name "go-github-com-igungor-gofakes3")
+    (version "0.0.18")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/igungor/gofakes3")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "136wvgz8d1982ns3vqqlvk3r7cbns7b0givwcrala562sd87yqka"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/igungor/gofakes3"))
+    (propagated-inputs
+     (list go-github-com-aws-aws-sdk-go
+           go-github-com-ryszard-goskiplist
+           go-github-com-shabbyrobe-gocovmerge
+           go-github-com-spf13-afero
+           go-go-etcd-io-bbolt
+           go-golang-org-x-tools
+           go-gopkg-in-mgo-v2))
+    (home-page "https://github.com/igungor/gofakes3")
+    (synopsis "Simple fake AWS S3 object storage")
+    (description
+     "AWS S3 fake server and testing library for extensive S3 test integrations.
+Either by running a test-server, e.g. for testing of AWS Lambda functions
+accessing S3.  Or, to have a simple and convencience S3 mock- and test-server.
+It's an alternative fork of @url{https://github.com/johannesboyne/gofakes3}.")
+    (license license:expat)))
+
 (define-public go-github-com-inetaf-tcpproxy
   (package
     (name "go-github-com-inetaf-tcpproxy")
@@ -9144,6 +9214,48 @@ described in @url{https://www.rfc-editor.org/rfc/rfc959,RFC 959}.")
 transforms one JSON document into another through a JMESPath expression.")
     (license license:asl2.0)))
 
+(define-public go-github-com-johannesboyne-gofakes3
+  (package
+    (name "go-github-com-johannesboyne-gofakes3")
+    (version "0.0.0-20260208201424-4c385a1f6a73")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/johannesboyne/gofakes3")
+              (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "14h4wrryrn4darp2vg2kyh2rwz0p93y99plv7lyql9i50h351895"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/johannesboyne/gofakes3"))
+    (native-inputs
+     (list go-github-com-stretchr-testify
+           go-go-shabbyrobe-org-gocovmerge))
+    (propagated-inputs
+     (list go-github-com-aws-aws-sdk-go-v2
+           go-github-com-aws-aws-sdk-go-v2-config
+           go-github-com-aws-aws-sdk-go-v2-credentials
+           go-github-com-aws-aws-sdk-go-v2-feature-s3-manager
+           go-github-com-aws-aws-sdk-go-v2-service-s3
+           go-github-com-aws-smithy-go
+           go-github-com-cevatbarisyilmaz-ara
+           go-github-com-ryszard-goskiplist
+           go-github-com-spf13-afero
+           go-go-etcd-io-bbolt
+           go-golang-org-x-tools
+           go-gopkg-in-mgo-v2))
+    (home-page "https://github.com/johannesboyne/gofakes3")
+    (synopsis "Simple fake AWS S3 object storage")
+    (description
+     "AWS S3 fake server and testing library for extensive S3 test
+integrations.  Either by running a test-server, e.g. for testing of AWS Lambda
+functions accessing S3.  Or, to have a simple and convencience S3 mock- and
+test-server.")
+    (license license:expat)))
+
 (define-public go-github-com-jsimonetti-rtnetlink
   (package
     (name "go-github-com-jsimonetti-rtnetlink")

gnu/packages/golang-xyz.scm

@@ -16158,6 +16158,27 @@ in memory.  The library operates on channels and uses temporary disk storage
 to handle datasets larger than available RAM.")
     (license license:asl2.0)))
 
+;; For s5cmd@2.3.0, remove when a fresh version is released.
+(define-public go-github-com-lanrat-extsort-1.0.2
+  (hidden-package
+   (package
+     (inherit go-github-com-lanrat-extsort)
+     (name "go-github-com-lanrat-extsort")
+     (version "1.0.2")
+     (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/lanrat/extsort")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0blsif4qzmmlqxhgc6dyl7rn9zws7mvlc6ckjj43cxlp517ravk8"))))
+     (arguments
+      (list
+       #:tests? #f
+       #:import-path "github.com/lanrat/extsort")))))
+
 (define-public go-github-com-layeh-gopher-luar
   (package
     (name "go-github-com-layeh-gopher-luar")
@@ -24807,6 +24828,34 @@ standard library.")
      "This package provides XOR bitwise code engine.")
     (license license:expat)))
 
+(define-public go-github-com-termie-go-shutil
+  (package
+    (name "go-github-com-termie-go-shutil")
+    (version "0.0.0-20140729215957-bcacb06fecae")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/termie/go-shutil")
+              (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0xwdx3qiqxm1bmlzqlf1cgdmrkmmahhdm2piikyhw8cbl3wdih82"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/termie/go-shutil"
+      #:test-flags
+      ;; shutil_test.go:101: open test/testfile3: permission denied
+      #~(list "-skip" "TestCopy")))
+    (home-page "https://github.com/termie/go-shutil")
+    (synopsis "Golang port of Python's shutil")
+    (description
+     "This package implements a direct port of a few of the functions from
+Python's @url{https://docs.python.org/3/library/shutil.html, shutil} package
+for high-level filesystem operations.")
+    (license license:expat)))
+
 (define-public go-github-com-texttheater-golang-levenshtein
   (package
     (name "go-github-com-texttheater-golang-levenshtein")
@@ -29351,6 +29400,57 @@ decimal arithmetic.")
     (description "Go library for ini files")
     (license license:asl2.0)))
 
+(define-public go-gopkg-in-mgo-v2
+  ;; XXX: Upstream note - UNMAINTAINED
+  ;; Suggested alternatives:
+  ;; - https://github.com/globalsign/mgo
+  ;;   Community supported fork of mgo.
+  ;; - https://github.com/coreos/bbolt
+  ;;   Single file in-memory document database for Go.
+  ;; - https://github.com/dgraph-io/badger
+  ;;   Fast in-memory document database for Go.
+  ;; - https://github.com/dgraph-io/dgraph
+  ;;   Distributed graph database on top of Badger.
+  ;; - https://github.com/lib/pq
+  ;;   PostgreSQL driver in pure Go.
+  (package
+    (name "go-gopkg-in-mgo-v2")
+    (version "2016.08.01")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/go-mgo/mgo")
+             (commit (string-append "r" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0rwbi1z63w43b0z9srm8m7iz1fdwx7bq7n2mz862d6liiaqa59jd"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "gopkg.in/mgo.v2"
+      #:test-flags
+      #~(list "-vet=off"
+              ;; Panic: runtime error: invalid memory address or nil pointer
+              ;; dereference (PC=0x47ADB1)
+              "-skip" "TestAll")
+    #:test-subdirs
+    ;; internal/sasl/sasl.go needs <sasl/sasl.h> header.
+    #~(list "internal/json/..."
+            "internal/scram/...")))
+    (native-inputs
+     (list go-gopkg-in-check-v1
+           go-gopkg-in-yaml-v2))
+    (propagated-inputs
+     (list go-gopkg-in-tomb-v2))
+    (home-page "https://labix.org/mgo")
+    (synopsis "Rich MongoDB driver for Go")
+    (description
+     "@command{mgo} (pronounced as mango) is a MongoDB driver for the Go
+language that implements a rich and well tested selection of features under a
+very simple API following standard Go idioms.")
+    (license license:expat)))
+
 (define-public go-gopkg-in-natefinch-lumberjack-v2
   (package
     (name "go-gopkg-in-natefinch-lumberjack-v2")
@@ -29418,6 +29518,25 @@ decimal arithmetic.")
 termination.")
     (license license:bsd-3)))
 
+(define-public go-gopkg-in-tomb-v2
+  (package
+    (inherit go-gopkg-in-tomb-v1)
+    (name "go-gopkg-in-tomb-v2")
+    (version "2.0.0-20161208151619-d5d1b5820637")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/go-tomb/tomb")
+              (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1sv15sri99szkdz1bkh0ir46w9n8prrwx5hfai13nrhkawfyfy10"))))
+    (build-system go-build-system)
+    (arguments
+     (substitute-keyword-arguments arguments
+       ((#:import-path _) "gopkg.in/tomb.v2")))))
+
 (define-public go-gopkg-in-validator-v2
   (package
     (name "go-gopkg-in-validator-v2")

gnu/packages/guile-xyz.scm

@@ -918,7 +918,7 @@ generate API documentation for GNU Guile projects.")
 (define-public guile-dotenv
   (package
    (name "guile-dotenv")
-   (version "0.2.1")
+   (version "0.3.1")
     (source
      (origin
        (method git-fetch)
@@ -927,7 +927,7 @@ generate API documentation for GNU Guile projects.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1zgc9xwpz6w64rbndvl8c73lsx935byin921209acyw54j52g706"))))
+        (base32 "0j2m9nnjp7096gdy2b038p7wrx93hgw6i6rfy4gh9hkvk4q43b1m"))))
    (build-system gnu-build-system)
    (arguments
     (list
@@ -948,7 +948,6 @@ generate API documentation for GNU Guile projects.")
           pkg-config
           texinfo))
    (inputs (list guile-3.0))
-   (propagated-inputs (list nyacc))
    (synopsis "Read environment variables specifications from @code{.env} files")
    (description "This package provides a simple Guile interface to @code{.env}
 (or dotenv) files.  It implements parsing of files and setting environment
@@ -990,8 +989,7 @@ variables from them.")
                                              (assoc-ref inputs input)
                                              path))
                                           (list "guile-config"
-                                                "guile-dotenv"
-                                                "nyacc"))))))
+                                                "guile-dotenv"))))))
                       (bin (string-append (ungexp output) "/bin/")))
                  (wrap-program (string-append bin "dotenv")
                    (dep-path "GUILE_LOAD_PATH" site)

gnu/packages/guile.scm

@@ -900,7 +900,7 @@ type system, elevating types to first-class status.")
 (define-public guile-git
   (package
     (name "guile-git")
-    (version "0.10.0")
+    (version "0.11.0")
     (home-page "https://gitlab.com/guile-git/guile-git.git")
     (source (origin
               (method git-fetch)
@@ -910,7 +910,7 @@ type system, elevating types to first-class status.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "01scznpg7356ygdlgn1f2892bwg6fsvp37hbmsk4gsg0g49aj4la"))))
+                "1yjyil6z4k80pjdps8v6h6lxikwxmjxvrslf2jrmq2rrfnajschz"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags '("GUILE_AUTO_COMPILE=0")       ; to prevent guild warnings

gnu/packages/image-viewers.scm

@@ -96,6 +96,7 @@
   #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages graphics)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages image)
   #:use-module (gnu packages image-processing)
   #:use-module (gnu packages imagemagick)
@@ -116,6 +117,7 @@
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
+  #:use-module (gnu packages sqlite)
   #:use-module (gnu packages suckless)
   #:use-module (gnu packages stb)
   #:use-module (gnu packages terminals)
@@ -1051,6 +1053,67 @@ synchronization of multiple instances.")
     (home-page "https://nomacs.org/")
     (license license:gpl3+)))
 
+(define-public timg
+  (package
+    (name "timg")
+    (version "1.6.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/hzeller/timg")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0xr3g6my2n9ry5mqiw1qvf7m0lpmj20h2xsnh75653ha83wqxmhm"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Remove bundled sources
+        #~(begin
+            (delete-file-recursively "third_party") #t))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~'("-Wno-dev" "-DWITH_OPENSLIDE_SUPPORT=ON")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'configure 'fix-stb-path
+            ;; This package expects stb-image to be at stb/stb_image.h, but
+            ;; Guix puts it at stb_image.h instead
+            (lambda _
+              (substitute* "src/CMakeLists.txt"
+                (("stb/stb")
+                 "stb"))
+              (substitute* "src/stb-image-source.cc"
+                (("#include \"stb/stb_image.h\"")
+                 "#include \"stb_image.h\"")))))
+      #:tests? #f)) ;No tests
+    (inputs (list cairo
+                  ffmpeg
+                  graphicsmagick
+                  libdeflate
+                  libdicom
+                  libexif
+                  libjpeg-turbo
+                  librsvg
+                  libsixel
+                  libxml2
+                  openjpeg
+                  openslide
+                  poppler
+                  qoi
+                  sqlite
+                  stb-image))
+    (native-inputs (list git pandoc pkg-config))
+    (home-page "https://timg.sh/")
+    (synopsis "Terminal image and video viewer")
+    (description
+     "This package provides a user-friendly terminal image viewer that uses
+graphic capabilities of terminals (Sixel, Kitty or iterm2), or 24-Bit color
+capabilities and unicode character blocks if these are not available.")
+    (license license:gpl2)))
+
 (define-public xzgv
   (package
     (name "xzgv")

gnu/packages/image.scm

@@ -74,6 +74,7 @@
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages datastructures)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
@@ -106,6 +107,7 @@
   #:use-module (gnu packages qt)
   #:use-module (gnu packages ragel)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages sqlite)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages video)
@@ -245,6 +247,29 @@ code is Valgrind-clean and unit tested.")
     (home-page "https://sourceforge.net/projects/iqa/")
     (license license:bsd-4)))
 
+(define-public libdicom
+  (package
+    (name "libdicom")
+    (version "1.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ImagingDataCommons/libdicom")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0l1z8riv7lrw65nswq8lvyvnxn5vc06gydwc96gj3ywb1gcqv831"))))
+    (build-system meson-build-system)
+    (inputs (list check uthash))
+    (native-inputs (list pkg-config))
+    (home-page "https://github.com/ImagingDataCommons/libdicom")
+    (synopsis "C library for reading DICOM files")
+    (description
+     "This package is a C library and a set of command-line tools for reading
+DICOM WSI files.")
+    (license license:expat)))
+
 (define-public libpng
   (package
    (name "libpng")
@@ -1109,6 +1134,41 @@ JPEG 2000 Reference Software.")
     (home-page "https://github.com/uclouvain/openjpeg")
     (license license:bsd-2)))
 
+(define-public openslide
+  (package
+    (name "openslide")
+    (version "4.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/openslide/openslide")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "00gc530g0lxm2lhwq249w97021w1v1y9ybqs2z5l1z922s15rhl2"))))
+    (build-system meson-build-system)
+    (inputs (list cairo
+                  gdk-pixbuf
+                  glib
+                  libdicom
+                  libjpeg-turbo
+                  libpng
+                  libtiff
+                  libxml2
+                  openjpeg
+                  sqlite
+                  zlib
+                  zstd))
+    (native-inputs (list pkg-config))
+    (home-page "https://openslide.org/")
+    (synopsis "C library for reading slide image files")
+    (description
+     "OpenSlide is a C library for reading whole slide image files (also known
+as virtual slides).  It provides a consistent and simple API for reading files
+from multiple vendors.")
+    (license license:lgpl2.1)))
+
 (define-public giflib
   (package
     (name "giflib")
@@ -1968,6 +2028,34 @@ possible, all formats supported by the PNG standard are represented.")
 use, copy, modify and distribute these images for any purpose and without fee
 is hereby granted."))))
 
+(define-public qoi
+  (let ((commit "6fff9b70dd79b12f808b0acc5cb44fde9998725e")
+        (revision "0"))
+    (package
+      (name "qoi")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/phoboslab/qoi")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "078zasncyylgnwx6br82nkjssl82wygz6fh8zm65fbfpadzfa3x7"))))
+      (build-system copy-build-system)
+      (arguments
+       (list
+        #:install-plan
+        #~'(("qoi.h" "include/"))
+        #:tests? #f)) ;No tests
+      (home-page "https://qoiformat.org")
+      (synopsis "Library for the QOI image format")
+      (description
+       "This package provides a library for the QOI image format, offering
+fast, lossless image compression.")
+      (license license:expat))))
+
 (define-public libjpeg-turbo
   (package
     (name "libjpeg-turbo")

gnu/packages/irc.scm

@@ -14,7 +14,7 @@
 ;;; Copyright © 2022 Jai Vetrivelan <jaivetrivelan@gmail.com>
 ;;; Copyright © 2022 jgart <jgart@dismail.de>
 ;;; Copyright © 2023, 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
-;;; Copyright © 2024, 2025 Ashish SHUKLA <ashish.is@lostca.se>
+;;; Copyright © 2024-2026 Ashish SHUKLA <ashish.is@lostca.se>
 ;;; Copyright © 2024 Christian Miller <christian.miller@dadoes.de>
 ;;; Copyright © 2024 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2025 Zheng Junjie <z572@z572.online>
@@ -348,7 +348,7 @@ Conferencing} and @acronym{ICB, Internet Citizen's Band}.")
 (define-public weechat
   (package
     (name "weechat")
-    (version "4.8.2")
+    (version "4.9.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -357,7 +357,7 @@ Conferencing} and @acronym{ICB, Internet Citizen's Band}.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "06lmbd27fdj7z7v6m096csswp73354516z64apfyz8lr5kh140wq"))))
+                "1pwayhpnyd6nq1sph4hqi43xwqgq6vj6fr8q0xqn0jx5zzjlyx8c"))))
     (build-system cmake-build-system)
     (outputs '("out" "doc"))
     (native-inputs
@@ -393,12 +393,13 @@ Conferencing} and @acronym{ICB, Internet Citizen's Band}.")
            #~(modify-phases %standard-phases
                #$@(if (target-x86?)
                       #~((add-after 'install 'move-doc
-                           (lambda* (#:key outputs #:allow-other-keys)
-                             (let* ((out (assoc-ref outputs "out"))
-                                    (doc (assoc-ref outputs "doc"))
-                                    (from (string-append out "/share/doc/weechat"))
-                                    (to (string-append doc "/share/doc/weechat")))
-                               (mkdir-p (string-append doc "/share/doc"))
+                           (lambda _
+                             (let ((from (string-append #$output
+                                                        "/share/doc/weechat"))
+                                   (to (string-append #$output:doc
+                                                      "/share/doc/weechat")))
+                               (mkdir-p (string-append #$output:doc
+                                                       "/share/doc"))
                                (rename-file from to)))))
                       #~()))))
     (synopsis "Extensible chat client")

gnu/packages/kde-pim.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2022 Brendan Tildesley <mail@brendan.scot>
 ;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com>
-;;; Copyright © 2023-2025 Sughosha <sughosha@disroot.org>
+;;; Copyright © 2023-2026 Sughosha <sughosha@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -70,6 +70,7 @@
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages video)
   #:use-module (gnu packages wget)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xml))
@@ -2104,6 +2105,83 @@ information in non-ASCII character sets.")
 application \"Parts\" to be embedded as a Kontact component (or plugin).")
     (license license:lgpl2.0+)))
 
+(define-public kalarm
+  (package
+    (name "kalarm")
+    (version "25.12.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://kde/stable/release-service/" version
+                           "/src/kalarm-" version ".tar.xz"))
+       (sha256
+        (base32 "0g8frgnpzbr2npx7i28271yfcv7yqx4h6bzmkgxip1chhycjwps5"))))
+    (build-system qt-build-system)
+    (arguments
+     (list #:qtbase qtbase
+           ;; There are only 2 tests, kadatetimetest and kaeventtest, which
+           ;; fail due to be unable to determine system time zone.
+           #:tests? #f
+           #:configure-flags
+           #~(list "-DENABLE_LIBVLC=OFF"))) ;Use only mpv
+    (native-inputs
+     (list extra-cmake-modules kdoctools pkg-config))
+    (inputs
+     (list akonadi
+           akonadi-contacts
+           akonadi-mime
+           grantleetheme
+           kauth
+           kcalendarcore
+           kcalutils
+           kcodecs
+           kcompletion
+           kconfig
+           kconfigwidgets
+           kcontacts
+           kcrash
+           kdbusaddons
+           kglobalaccel
+           kguiaddons
+           kholidays
+           ki18n
+           kiconthemes
+           kidentitymanagement
+           kio
+           kitemmodels
+           kitemviews
+           kjobwidgets
+           kmailtransport
+           kmime
+           knotifications
+           knotifyconfig
+           kpimtextedit
+           kservice
+           kstatusnotifieritem
+           ktextaddons
+           ktextwidgets
+           kwidgetsaddons
+           kwindowsystem
+           kxmlgui
+           mpv))
+    (home-page "https://apps.kde.org/kalarm/")
+    (synopsis "Alarm manager for KDE")
+    (description "Kalarm is a personal alarm message, command and email
+scheduler application for KDE.
+
+It features:
+@itemize
+@item displaying alarms using your own text message, the text generated by a
+ command, or a text or image file,
+@item audible alarm using a sound file,
+@item recurring alarm on an hours/minutes, daily, weekly, monthly or annual
+ basis, or set it to trigger every time you log in,
+@item display alarms color and font customization, and
+@item support for multiple alarm calendars, which for example enables you to
+ share alarms between a laptop and desktop computer.
+@end itemize")
+    (license license:gpl2+)))
+
 (define-public korganizer
   (package
     (name "korganizer")

gnu/packages/kde-plasma.scm

@@ -2426,6 +2426,7 @@ integration of Qt applications when running on a KDE Plasma workspace.")
                   knotifications
                   kirigami
                   libplasma
+                  lz4
                   mobile-broadband-provider-info
                   modemmanager-qt
                   network-manager
@@ -2439,6 +2440,7 @@ integration of Qt applications when running on a KDE Plasma workspace.")
                   ksvg
                   qcoro-qt6
                   openconnect
+                  qtwebengine
                   qtdeclarative))
     (synopsis "Plasma applet for managing network connections")
     (description "This package provides Plasma applet for managing network

gnu/packages/language.scm

@@ -282,16 +282,18 @@ Random Cage Fighting Birds, Cool Music etc.")
 (define-public libchewing
   (package
     (name "libchewing")
-    (version "0.9.1")
+    (version "0.11.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/chewing/libchewing")
-             (commit (string-append "v" version))))
+             (commit (string-append "v" version))
+             ;; Also libchewing-data
+             (recursive? #t)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0gh64wvrk5pn0fhmpvj1j99d5g7f7697rk96zbkc8l72yjr819z5"))))
+        (base32 "08734i3xyq3wv5vimki7cz438v56ywk3x3assgfjlrngj1ijw0y8"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -875,7 +877,7 @@ noun phrases, verb phrases, etc.).")
 (define-public praat
   (package
     (name "praat")
-    (version "6.4.61")
+    (version "6.4.62")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -884,7 +886,7 @@ noun phrases, verb phrases, etc.).")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0lxg0h07cgz5fjhpsihvf8dk6g03fp4a7ar8x70pm2s5lbfr1amy"))))
+                "0jplas35yrhh1csdiw2mim4cgmj5iz5c3b87908smd0r528v75a6"))))
     (build-system gnu-build-system)
     (arguments
      (list #:make-flags #~(list (string-append "CC="

gnu/packages/lean.scm

@@ -70,7 +70,7 @@
            python-wrapper
            tzdata-for-tests))
     (inputs
-     (list cadical gmp libuv llvm))
+     (list cadical-2.1 gmp libuv llvm))
     (arguments
      (list
       #:make-flags

gnu/packages/libevent.scm

@@ -164,14 +164,14 @@ resolution, asynchronous file system operations, and threading primitives.")
   (package
     (inherit libuv)
     (name "libuv")
-    (version "1.49.2")
+    (version "1.51.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://dist.libuv.org/dist/v" version
                                   "/libuv-v" version ".tar.gz"))
               (sha256
                (base32
-                "1a75p8wp4l43y2ffj1szs1ssm6nzjad7k51bqi2r04ngs9mp044c"))))
+                "1szqivvs7izbhw1a3nd1ipbk012yvqqkjg0sjmqxw1hi1fwmf1az"))))
     (properties '((hidden? . #t)))))
 
 (define-public libuv-for-r-httpuv

gnu/packages/linux.scm

@@ -531,7 +531,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; The current "stable" kernels. That is, the most recently released major
 ;; versions that are still supported upstream.
 
-(define-public linux-libre-6.19-version "6.19.9")
+(define-public linux-libre-6.19-version "6.19.10")
 (define-public linux-libre-6.19-gnu-revision "gnu")
 (define deblob-scripts-6.19
   (linux-libre-deblob-scripts
@@ -541,12 +541,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "05jpciyypvmy6byaxjl49b1fvzxcnlhknf0xabrdj5152iznrzkh")))
 (define-public linux-libre-6.19-pristine-source
   (let ((version linux-libre-6.19-version)
-        (hash (base32 "1gsmklhqpx5k9wca3gr8j439q8khr9byy7ivxqyr9qqjmyinhq61")))
+        (hash (base32 "072s76238rnf87yhdy15nbxfyq7x3ch7p2v14dq4pq551qd48va6")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.19)))
 
-(define-public linux-libre-6.18-version "6.18.19")
+(define-public linux-libre-6.18-version "6.18.20")
 (define-public linux-libre-6.18-gnu-revision "gnu")
 (define deblob-scripts-6.18
   (linux-libre-deblob-scripts
@@ -556,7 +556,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "0qlih8w8wg4v5cwbmd34rbhb6mjgbx69i9rx3s2vxw7h42q9l0ai")))
 (define-public linux-libre-6.18-pristine-source
   (let ((version linux-libre-6.18-version)
-        (hash (base32 "0309xd8ifsy9pa19s8qnsyxkmcqq4z3p16jckjnnhz6h3hkpibza")))
+        (hash (base32 "0lrm76rdlr92kjq3g410qdff9v49mpdf400lmsh7hq74k2ymlyl3")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.18)))
@@ -565,47 +565,47 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; Here are the support timelines:
 ;; <https://www.kernel.org/category/releases.html>
 
-(define-public linux-libre-6.12-version "6.12.77")
+(define-public linux-libre-6.12-version "6.12.79")
 (define-public linux-libre-6.12-gnu-revision "gnu")
 (define deblob-scripts-6.12
   (linux-libre-deblob-scripts
    linux-libre-6.12-version
    linux-libre-6.12-gnu-revision
    (base32 "168aykyvyyp34549hqhlprl0n052q8wdb2y3vyxqw40wpf2vw3ln")
-   (base32 "1v6glxf94p9z0yq5m102jwcpyh6anpbp3h8wwff9hxlfy2wdlzzk")))
+   (base32 "1x48hpmvajz7v5wn1vdd7l5r14mq4ngzh5npz3pj81z4f1g61i0a")))
 (define-public linux-libre-6.12-pristine-source
   (let ((version linux-libre-6.12-version)
-        (hash (base32 "0rzz5hdixa5xmr99gja3xr9nxgpmrpxyg4llmvkl3vyawpmkd21m")))
+        (hash (base32 "02vrl0m5iw4jiyhpcni2l8kcfzq279s69yagrdz5sany6cgpbyjb")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.12)))
 
-(define-public linux-libre-6.6-version "6.6.129")
+(define-public linux-libre-6.6-version "6.6.130")
 (define-public linux-libre-6.6-gnu-revision "gnu")
 (define deblob-scripts-6.6
   (linux-libre-deblob-scripts
    linux-libre-6.6-version
    linux-libre-6.6-gnu-revision
    (base32 "0y3lawljby2rl0mb0yjdyaasci4pl935y8xa0dnmbzff23knkxlw")
-   (base32 "0z47f6mkllk1fgpq04x73djl5gh3mj50bxj2rpg4jlzm0rcirrag")))
+   (base32 "0xp9b2vkrb0g0rn4i33b59rhp4sgh1dbwzk28vwz7kwac6l5rcpi")))
 (define-public linux-libre-6.6-pristine-source
   (let ((version linux-libre-6.6-version)
-        (hash (base32 "12j42awg44w97zq8fzifpm300jm9q9ya7qkpn7xbnkr2480qz86a")))
+        (hash (base32 "139480lyi3if8pd2j3yld5a01lk7113kbcn2kxpzyk29p5kslq14")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.6)))
 
-(define-public linux-libre-6.1-version "6.1.166")
+(define-public linux-libre-6.1-version "6.1.167")
 (define-public linux-libre-6.1-gnu-revision "gnu")
 (define deblob-scripts-6.1
   (linux-libre-deblob-scripts
    linux-libre-6.1-version
    linux-libre-6.1-gnu-revision
    (base32 "10gcbkd5jxfspa712kvb3qmsjgsapd9cz47pmpfk03bbfzf8ydlv")
-   (base32 "1jiwwl5sgpc16x0v6phbknv94mc46gvwgc2z8s4pdgn4j54yrd8v")))
+   (base32 "1w5pfws6l39dpc3lzazs1n6r4m96f6rdf6vb2scy5fhmrd933ldc")))
 (define-public linux-libre-6.1-pristine-source
   (let ((version linux-libre-6.1-version)
-        (hash (base32 "0jcl12gjlfdf9pwqg1m84rzwnrj3grxxgk5blrq8zlaq45sgr3c1")))
+        (hash (base32 "1jwqwp2fg3wdsh9w663rbnbv1rvsvksv1pj4bzns8swp0wy0a618")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.1)))
@@ -2690,7 +2690,7 @@ and should be used with caution, especially on untested models.")
 (define-public corefreq
   (package
     (name "corefreq")
-    (version "1.98.4")
+    (version "2.1.0")
     (source
      (origin
        (method git-fetch)
@@ -2699,7 +2699,7 @@ and should be used with caution, especially on untested models.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0mxp5h23y09674syaj5gpdifr53zvgjv7g7hargwg6897883qfln"))))
+        (base32 "054rnrwvkbfmy2maxjk928fh1p346313ixhkbjwcq7qjz3idjixl"))))
     ;; The upstream Makefile is now such a proprietary mess that standard builds
     ;; as performed by our linux-module-build-system are more or less impossible
     ;; without heavy patching.  However, we still keep it as the main build
@@ -2731,14 +2731,12 @@ and should be used with caution, especially on untested models.")
                         (string-append = dir "\n"))
                        (("^([[:space:]]+)(.* modules_install.*)"
                          _ indent command)
-                        (string-append indent "@echo skipping " command))))))
+                        (string-append indent "echo skipping " command))))))
                (add-before 'build 'prepare
-                 (lambda* (#:key source-directory make-flags #:allow-other-keys)
+                 (lambda* (#:key source-directory #:allow-other-keys)
                    ;; Lazily fix another mismatch between what the kernel module
                    ;; build system expects and what this package provides.
-                   (symlink "source/build" source-directory) ;$(BUILD)
-                   ;; Set up symbolic links inside $(BUILD), for some reason.
-                   (apply invoke "make" "prepare" make-flags)))
+                   (symlink "source/build" source-directory)))
                (replace 'build (assoc-ref gnu:%standard-phases 'build))
                (add-before 'install 'resolve-symlink
                  ;; The build system silently fails to install from a symlink.
@@ -6021,7 +6019,7 @@ devices that can inject events directly into the input subsystem.")
 (define-public interception-dual-function-keys
   (package
     (name "interception-dual-function-keys")
-    (version "1.4.0")
+    (version "1.5.0")
     (home-page "https://gitlab.com/interception/linux/plugins/dual-function-keys")
     (source (origin
               (method git-fetch)
@@ -6031,7 +6029,7 @@ devices that can inject events directly into the input subsystem.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0s49vbg3j4rwh78i8rx8qr7myql09p7b3lhrjl0p7dd98xp6ann6"))))
+                "17jc02wh45yk427qryb0ydyim16607i31wyghbsahahd6mrh9ylv"))))
     (build-system gnu-build-system)
     (inputs
      (list libevdev yaml-cpp))
@@ -11011,30 +11009,28 @@ compatible with Python's ConfigParser style of .INI files, including RFC
     (license license:bsd-3)))
 
 (define-public simpleini
-  (let ((commit "6048871ea9ee0ec24be5bd099d161a10567d7dc2")
-        (revision "1"))
-    (package
-      (name "simpleini")
-      (version (git-version "4.22" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/brofield/simpleini")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "1szaflnrzw1zx9v5g6mbbiaf9wfglp4n4jjq2793k9ryz3qxil9j"))))
-      (build-system cmake-build-system)
-      (arguments
-       (list #:configure-flags #~(list "-DSIMPLEINI_USE_SYSTEM_GTEST=ON")))
-      (native-inputs (list googletest))
-      (home-page "https://github.com/brofield/simpleini")
-      (synopsis "Simple API to read and write INI-style files")
-      (description
-       "SimpleIni provides a simple API to read and write INI-style
+  (package
+    (name "simpleini")
+    (version "4.25")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/brofield/simpleini")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1v9s0kr5ca1gdbnlkdz7chzypy0wz95f09l0r6jnmff4qy6db56l"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list #:configure-flags #~(list "-DSIMPLEINI_USE_SYSTEM_GTEST=ON")))
+    (native-inputs (list googletest))
+    (home-page "https://github.com/brofield/simpleini")
+    (synopsis "Simple API to read and write INI-style files")
+    (description
+     "SimpleIni provides a simple API to read and write INI-style
 configuration files.  It supports data files in ASCII, MBCS and Unicode.")
-      (license license:expat))))
+    (license license:expat)))
 
 (define-public xfsprogs
   (package

gnu/packages/llvm.scm

@@ -1412,7 +1412,11 @@ Library.")
      (substitute-keyword-arguments arguments
        ((#:configure-flags flags)
         #~(append #$flags
-                  (list "-DLLVM_TARGETS_TO_BUILD=AMDGPU;X86"
+                  (list #$(string-append
+                           "-DLLVM_TARGETS_TO_BUILD=AMDGPU;X86"
+                           (if (string=? "X86" (system->llvm-target))
+                               ""
+                               (string-append ";" (system->llvm-target))))
                         "-DLLVM_VERSION_SUFFIX=")))))
     (properties `((hidden? . #t)
                   ,@(package-properties llvm-base)))

gnu/packages/lsof.scm

@@ -37,7 +37,7 @@
 (define-public lsof
   (package
     (name "lsof")
-    (version "4.99.3")
+    (version "4.99.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -46,8 +46,7 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1v32407al4j0hhcph95lv4xvr9h012lii29iyq41iwj39zwfavax"))
-              (patches (search-patches "lsof-compat-linux-6.9.patch"))))
+                "08p0c0wci9vam6b29ym7z7sip8gd0j0dz7zy4f0b32dw51rb3z9k"))))
     (build-system gnu-build-system)
     (native-inputs (list automake
                          autoconf
@@ -57,27 +56,6 @@
                          pkg-config
                          procps ;for ps
                          util-linux)) ;for unshare
-    (arguments
-     (list #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'unpack 'fix-configure-ac-version
-                 ;; see https://github.com/lsof-org/lsof/commit/932a0b3b1992497e23fd9b8d31116b9ca9b0f98d
-                 ;; to fix tests/case-01-version.bash test fail.
-                 (lambda _
-                   (substitute* "configure.ac"
-                     (("4\\.99\\.0")
-                      "4.99.3"))))
-               (add-before 'bootstrap 'disable-failing-tests
-                 (lambda _
-                   (substitute* "Makefile.am"
-                     ;; Fails with ‘ERROR!!! client gethostbyaddr() failure’.
-                     (("(TESTS \\+=.*) tests/LTsock" _ prefix)
-                      prefix)
-                     ;; Fails on CoW filesystems (eg. btrfs)
-                     (("tests/LTlock") "")
-                     ;; Fails because /proc not mounted in sandbox
-                     (("\tdialects/linux/tests/case-20-epoll.bash \\\\")
-                      "\\")))))))
     (synopsis "Display information about open files")
     (description
      "Lsof stands for LiSt Open Files, and it does just that.

gnu/packages/lua.scm

@@ -26,6 +26,7 @@
 ;;; Copyright © 2025 Zheng Junjie <z572@z572.online>
 ;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
 ;;; Copyright © 2025 Aaron Boyd <aaron.boyd.org@gmail.com>
+;;; Copyright © 2026 Nguyễn Gia Phong <cnx@loang.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1201,6 +1202,105 @@ on numbers.")
 (define-public lua5.1-bitop
   (make-lua-bitop "lua5.1-bitop" lua-5.1))
 
+(define (make-lua-djot name lua)
+  (package
+    (name name)
+    (version "0.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/jgm/djot.lua")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256 (base32 "0kivx4yyj2zhj23d93h5rr0ab7gkazd3z7r7aqv1bgmigcw47pj2"))
+       (modules '((guix build utils)))
+       (snippet #~(begin
+                    (delete-file-recursively "clib")
+                    (delete-file-recursively "doc/api")
+                    (delete-file "doc/djot.1")))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-makefile
+            (lambda _
+              (substitute* "Makefile"
+                (("^all: .*") "all:\n"))))
+          (delete 'configure)
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "lua" "test.lua"))))
+          (replace 'install
+            (lambda _
+              (let ((lua-path
+                     (string-append
+                      #$output
+                      "/share/lua/"
+                      #$(version-major+minor (package-version lua)))))
+                (install-file "djot.lua" lua-path)
+                (copy-recursively "djot" (string-append lua-path "/djot"))))))))
+    (native-inputs (list lua))
+    (home-page "https://github.com/jgm/djot.lua")
+    (synopsis "Lua parser for the djot light markup language")
+    (description
+     "This package provides a Lua parser for djot, a light markup syntax.
+It can produce an AST, rendered HTML, or a stream of match tokens
+that identify elements by source position, which could be used
+for syntax highlighting or a linting tool.")
+    (license license:expat)))
+
+(define-public lua5.4-djot
+  (make-lua-djot "lua5.4-djot" lua-5.4))
+
+(define-public lua-djot
+  (make-lua-djot "lua-djot" lua))
+
+(define-public lua5.2-djot
+  (make-lua-djot "lua5.2-djot" lua-5.2))
+
+(define-public lua5.1-djot
+  (make-lua-djot "lua5.1-djot" lua-5.1))
+
+(define-public djot
+  (package
+    (inherit lua5.1-djot)
+    (name "djot")
+    (arguments
+     (substitute-keyword-arguments (package-arguments lua5.1-djot)
+       ((#:phases phases)
+        #~(modify-phases #$phases
+            (replace 'patch-makefile
+              (lambda _
+                (substitute* "Makefile"
+                  (("^all: .*") "all: doc/djot.1\n"))))
+            (replace 'check
+              (lambda* (#:key tests? #:allow-other-keys)
+                (when tests?
+                  (invoke "luajit" "test.lua"))))
+            (add-after 'install 'install-bin-and-man
+              (lambda* (#:key inputs #:allow-other-keys)
+                (let ((out-lua (string-append #$output "/share/lua/5.1"))
+                      (out-bin (string-append #$output "/bin/djot")))
+                  (copy-file "bin/main.lua" "bin/djot")
+                  (substitute* "bin/djot"
+                    (("^local djot = require" all)
+                     (string-append
+                      "#!"
+                      (search-input-file inputs "bin/luajit")
+                      "\n"
+                      all)))
+                  (install-file "bin/djot" (string-append #$output "/bin"))
+                  (chmod out-bin #o755)
+                  (wrap-program out-bin
+                    `("GUIX_LUA_PATH" ";" = (,out-lua))))
+                (install-file "doc/djot.1"
+                              (string-append #$output "/share/man/man1"))))))))
+    (native-inputs (list pandoc))
+    (inputs (list luajit))))
+
 (define-public lutok
   (package
     (name "lutok")

gnu/packages/mail.scm

@@ -67,6 +67,7 @@
 ;;; Copyright © 2025 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2026 Sergey Trofimov <sarg@sarg.org.ru>
+;;; Copyright © 2026 Nguyễn Gia Phong <cnx@loang.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -93,6 +94,7 @@
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages build-tools)
   #:use-module (gnu packages c)
   #:use-module (gnu packages calendar)
   #:use-module (gnu packages check)
@@ -767,7 +769,7 @@ operating systems.")
 (define-public neomutt
   (package
     (name "neomutt")
-    (version "20250404")
+    (version "20260105")
     (source
      (origin
        (method git-fetch)
@@ -776,8 +778,21 @@ operating systems.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32
-          "1w53g6l98cd3x2a6m0q245fm5gln95vzpgskvg4dz9yysmbki9az"))))
+        (base32 "1sg6ifabci7xyp3zds1w906vx6jsmyjlfr6bqld7m7hj07by9ndd"))
+       (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 "autosetup"
+              "mutt-gettext.tcl"
+              "mutt-iconv.tcl")))))
     (build-system gnu-build-system)
     (inputs
      (list cyrus-sasl
@@ -793,19 +808,19 @@ operating systems.")
            libxml2
            lmdb
            notmuch
+           sqlite
            `(,zstd "lib")))
     (native-inputs
      `(("automake" ,automake)
+       ("autosetup" ,autosetup)
        ("gettext-minimal" ,gettext-minimal)
        ("pkg-config" ,pkg-config)
        ("docbook-xsl" ,docbook-xsl)
        ("docbook-xml" ,docbook-xml-4.2)
        ("w3m" ,w3m)
-       ("tcl" ,tcl)
-
        ;; Test file data for the unit tests included in the neomutt source.
        ("neomutt-test-files"
-        ,(let ((commit "8629adab700a75c54e8e28bf05ad092503a98f75"))
+        ,(let ((commit "c769cdefd45bcdfc4a72664821bd7f67ad4d5f6c"))
            (origin
              (method git-fetch)
              (uri (git-reference
@@ -814,69 +829,62 @@ operating systems.")
              (file-name (git-file-name "neomutt-test-files" commit))
              (sha256
               (base32
-                "1ci04nqkab9mh60zzm66sd6mhsr6lya8wp92njpbvafc86vvwdlr")))))))
+               "0jvy9z2hmpvcxa10k7f68l2lqdxrppj36c4v8nmjrldkwgpkdaq3")))))))
     (arguments
-     `(#:test-target "test"
-       #:configure-flags
-       (list "--gpgme"
+     (list
+      #:test-target "test"
+      #:configure-flags
+      #~(list "--enable-autocrypt"
+              "--gpgme"
+              ;; Database, implies header caching.
+              "--disable-tokyocabinet"
+              "--disable-qdbm"
+              "--disable-bdb"
+              "--lmdb"
+              "--kyotocabinet"
 
-             ;; Database, implies header caching.
-             "--disable-tokyocabinet"
-             "--disable-qdbm"
-             "--disable-bdb"
-             "--lmdb"
-             "--kyotocabinet"
+              "--gdbm"
 
-             "--gdbm"
+              "--gnutls"
+              "--sasl"
+              (string-append "--with-sasl="
+                             #$(this-package-input "cyrus-sasl"))
 
-             "--gnutls"
-             "--ssl=1"
-             "--sasl"
-             (string-append "--with-sasl="
-                            (assoc-ref %build-inputs "cyrus-sasl"))
+              "--smime"
+              "--notmuch"
+              (string-append "--with-notmuch="
+                             #$(this-package-input "notmuch"))
 
-             "--smime"
-             "--notmuch"
-             (string-append "--with-notmuch="
-                            (assoc-ref %build-inputs "notmuch"))
+              "--idn2"
 
-             "--idn2"
-
-             ;; If we do not set this, neomutt wants to check
-             ;; whether the path exists, which it does not
-             ;; in the chroot.
-             "--with-mailpath=/var/mail"
-
-             (string-append "--with-ncurses="
-                            (assoc-ref %build-inputs "ncurses"))
-             (string-append "--prefix="
-                            (assoc-ref %outputs "out"))
-             "--zstd=1")
-       #:phases
-       (modify-phases %standard-phases
-         ;; TODO: autosetup is meant to be included in the source,
-         ;; but we should package autosetup and use our own version of it.
-         (replace 'configure
-           (lambda* (#:key outputs inputs configure-flags #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (flags `(,@configure-flags))
-                    (bash (which "bash")))
-               (setenv "SHELL" bash)
-               (setenv "CONFIG_SHELL" bash)
-               (apply invoke bash
-                      (string-append (getcwd) "/configure")
-                      flags))))
-         (add-before 'check 'prepare-test-files
-           (lambda* (#:key inputs #:allow-other-keys)
-             (copy-recursively (assoc-ref inputs "neomutt-test-files") "tests")
-             ;; FIXME: investigate why tests are failing, Nix is also disabling one
-             (substitute* "test/main.c"
-                          (("NEOMUTT_TEST_ITEM\\(test_expando_filter\\)") "")
-                           (("NEOMUTT_TEST_ITEM\\(test_mutt_sig_exit_handler\\)") "")
-                           (("NEOMUTT_TEST_ITEM\\(test_mutt_path_tilde\\)") ""))
-             (with-directory-excursion "tests"
-               (setenv "NEOMUTT_TEST_DIR" (getcwd)) ; must be absolute
-               (invoke "bash" "setup.sh")))))))
+              ;; If we do not set this, neomutt wants to check
+              ;; whether the path exists, which it does not
+              ;; in the chroot.
+              "--with-mailpath=/var/mail"
+              (string-append "--with-ncurses="
+                             #$(this-package-input "ncurses"))
+              (string-append "--prefix=" #$output)
+              "--zstd=1")
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'configure
+            (lambda* (#:key configure-flags #:allow-other-keys)
+              (apply invoke "autosetup"
+                     (string-append "--prefix=" #$output)
+                     configure-flags)))
+          (add-before 'check 'prepare-test-files
+            (lambda _
+              (copy-recursively
+               #$(this-package-native-input "neomutt-test-files")
+               "tests")
+              ;; FIXME: investigate why tests are failing, Nix also disables
+              ;; (a different) one: test_expando_node_padding.
+              (substitute* "test/main.c"
+                (("NEOMUTT_TEST_ITEM\\(test_expando_filter\\)") "")
+                (("NEOMUTT_TEST_ITEM\\(test_mutt_path_tilde\\)") ""))
+              (with-directory-excursion "tests"
+                (setenv "NEOMUTT_TEST_DIR" (getcwd)) ; must be absolute
+                (invoke "bash" "setup.sh")))))))
     (home-page "https://neomutt.org/")
     (synopsis "Command-line mail reader based on Mutt")
     (description
@@ -1411,22 +1419,25 @@ attachments, create new maildirs, and so on.")
 (define-public alot
   (package
     (name "alot")
-    (version "v0.12")
+    (version "0.12")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
               (url "https://github.com/pazz/alot")
-              (commit version)))
+              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
         (base32 "018zqpjrl3cggj1myysjj04a054mg890khhdh1qjmd70k8l3w1di"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 334 passed, 4 deselected, 9 xfailed, 29 warnings, 11 subtests
+      ;; tests: 299 passed, 39 deselected, 9 xfailed, 29 warnings, 11 subtests
       #:test-flags
       #~(list
+         ;; Randomly fails with FileNotFoundError; does not happen
+         ;; in git checkout though, so no upstream issue.
+         "--deselect=tests/test_crypto.py"
          "-k" (string-join
                ;; alot.settings.errors.ConfigError: failed to read notmuch
                ;; config with command ...

gnu/packages/maths.scm

@@ -9895,19 +9895,19 @@ also included.")
 (define-public cadical
   (package
     (name "cadical")
-    (version "2.0.0")
+    (version "2.2.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/arminbiere/cadical")
                     (commit (string-append "rel-" version))))
               (file-name (git-file-name name version))
-              (patches (search-patches "cadical-add-shared-library.patch"))
               (sha256
-               (base32 "1dzjah3z34v89ka48hncwqkxrwl4xqn9947p0ipf39lxshrq91xa"))))
+               (base32 "09p4nm8jyvhnsgpmbawzlk8b932k33s922a2rxm77sy8s31mm13m"))))
     (build-system gnu-build-system)
     (arguments
      (list #:test-target "test"
+           #:configure-flags #~(list "-shared")
            #:modules `(((guix build copy-build-system) #:prefix copy:)
                        (guix build gnu-build-system)
                        (guix build utils)
@@ -9917,16 +9917,7 @@ also included.")
            #~(modify-phases %standard-phases
                (replace 'configure
                  (lambda* (#:key configure-flags #:allow-other-keys)
-                   (setenv "CXXFLAGS" "-DPIC -fPIC")
                    (apply invoke "./configure" configure-flags)))
-               (replace 'check
-                 (lambda args
-                   ;; Tests are incorrectly linked upstream.
-                   ;; Since we don't install them, just work around this in the
-                   ;; check phase.
-                   (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/build"))
-                   (apply (assoc-ref %standard-phases 'check) args)
-                   (unsetenv "LD_LIBRARY_PATH")))
                (replace 'install
                  (lambda args
                    (apply
@@ -9944,6 +9935,39 @@ also included.")
 clause learning.")
     (license license:expat)))
 
+(define-public cadical-2.1
+  (package
+    (inherit cadical)
+    (name "cadical")
+    (version "2.1.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/arminbiere/cadical")
+                    (commit (string-append "rel-" version))))
+              (file-name (git-file-name name version))
+              (patches (search-patches "cadical-add-shared-library.patch"))
+              (sha256 (base32
+                       "1gl0xd6zyxb127w8k0mps9m2izaqb7im7j91by4lkknmm7xhwyav"))))
+    (arguments (substitute-keyword-arguments (package-arguments cadical)
+                 ((#:configure-flags _)
+                  #~(list))
+                 ((#:phases phases)
+                  #~(modify-phases #$phases
+                      (add-before 'configure 'set-shared-flags
+                        (lambda _
+                          (setenv "CXXFLAGS" "-DPIC -fPIC")))
+                      (replace 'check
+                        (lambda args
+                          ;; Tests are incorrectly linked upstream.
+                          ;; Since we don't install them, just work around this in the
+                          ;; check phase.
+                          (setenv "LD_LIBRARY_PATH"
+                                  (string-append (getcwd) "/build"))
+                          (apply (assoc-ref %standard-phases
+                                            'check) args)
+                          (unsetenv "LD_LIBRARY_PATH")))))))))
+
 (define-public cadiback
   (let ((commit "789329d8fcda851085ed72f1b07d8c3f46243b8a")
         (revision "1"))
@@ -10058,7 +10082,20 @@ true in all models.")
                  (add-after 'unpack 'no-tune-native
                    (lambda _
                      (substitute* "CMakeLists.txt"
-                       (("-mtune=native") "")))))))
+                       (("-mtune=native") ""))))
+                 ;; Refer to the library in ${LOUVAIN_COMMUNITIES_LIBRARIES} by
+                 ;; full path.  This ensures that we find references to it in
+                 ;; software using this library via CMake.
+                 ;;
+                 ;; CMake expects module to set this variable to a full path.
+                 ;; See <https://cmake.org/cmake/help/v4.3/module/SelectLibraryConfigurations.html#command:select_library_configurations>.
+                 (add-after 'unpack 'cmake-lib-full-path
+                   (lambda* (#:key outputs #:allow-other-keys)
+                     (substitute* "louvain_communitiesConfig.cmake.in"
+                       (("louvain_communities")
+                        (string-append
+                          (assoc-ref outputs "out")
+                          "/lib/liblouvain_communities.so"))))))))
       (native-inputs (list python))
       (home-page "https://github.com/meelgroup/louvain-community")
       (synopsis "Multi-criteria community detection")

gnu/packages/matrix.scm

@@ -437,7 +437,8 @@ fetch and store media in Amazon S3.")
                  (apply (assoc-ref cargo:%standard-phases phase)
                         #:cargo-target #$(cargo-triplet)
                         args))
-               '(unpack-rust-crates
+               '(prepare-rust-crates
+                 unpack-rust-crates
                  configure
                  check-for-pregenerated-files
                  patch-cargo-checksums))))

gnu/packages/messaging.scm

@@ -1183,7 +1183,7 @@ of xmpppy.")
 (define-public gajim
   (package
     (name "gajim")
-    (version "2.4.4")
+    (version "2.4.5")
     (source
      (origin
        (method url-fetch)
@@ -1191,7 +1191,7 @@ of xmpppy.")
                            (version-major+minor version)
                            "/gajim-" version ".tar.gz"))
        (sha256
-         (base32 "0s2jryg8c0ifgf88pfj7k1ifhl1l2fw4w8w80g7xh3qpk5gj7ml0"))
+         (base32 "1rkxzf1pfd29rip5bw4730fl7b2xk12zpiwnfkyzxlkmbh4j3kp2"))
        (patches
          (search-patches "gajim-honour-GAJIM_PLUGIN_PATH.patch"))))
     (build-system pyproject-build-system)
@@ -1261,7 +1261,7 @@ of xmpppy.")
           ;; FIXME: Cannot use this expression as it would
           ;; introduce a circular dependency at the top level.
           ;; (version-major+minor (package-version python))
-          "3.10"
+          "3.11"
           "/site-packages"))))))
     (native-inputs
      (list gettext-minimal
@@ -2356,7 +2356,11 @@ for the Matrix protocol.  It is built on to of @code{Boost.Asio}.")
        (sha256
         (base32 "098jqccwsfbqkdpnhbych2rd076385wb51fx9qyjfiddidxv2mas"))
        (modules '((guix build utils)))
-       (snippet '(delete-file-recursively "third_party"))))
+       (snippet '(delete-file-recursively "third_party"))
+       ;; Release 0.12.1 has a major bug which prevents replies
+       ;; from rendering: https://github.com/Nheko-Reborn/nheko/issues/1944
+       ;; TODO: revaluate for future versions.
+       (patches (search-patches "nheko-0-12-1-fix-rendering-replies.patch"))))
     (arguments
      (list
       #:tests? #f                       ;no test target

gnu/packages/mpi.scm

@@ -166,70 +166,113 @@ bind processes, and much more.")
 
 (define-public hwloc-2
   (package
-    (inherit hwloc-1)
+    (name "hwloc")
     (version "2.13.0")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://download.open-mpi.org/release/hwloc/v"
-                                  (version-major+minor version)
-                                  "/hwloc-" version ".tar.bz2"))
-              (sha256
-               (base32
-                "1aqdznqp7f18yg95vbr5n6ccxxdiywacygvn3wbhzn7bnspkdsaj"))
-              ;; XXX: Remove after updating package from 2.13.0.
-              (patches (search-patches "hwloc-add-with-opencl.patch"))))
-
-    (native-inputs (modify-inputs native-inputs
-                     (append autoconf)
-                     (append automake)
-                     (append libtool)
-                     (append opencl-headers)
-                     (append bash)))              ;for completion tests
-    (inputs (modify-inputs inputs
-              ;; XXX: rocm-smi requires libdrm/drm.h but doesn't propagate a
-              ;; package providing these. For now, libdrm is used to provide
-              ;; this header.
-              (append libdrm)
-              (append opencl-icd-loader)
-              (append rocm-smi-lib)
-              (delete "numactl")))               ;libnuma is no longer needed.
-    (propagated-inputs (modify-inputs propagated-inputs
-                         ;; hwloc.pc lists libze_loader and libxml2 in
-                         ;; 'Requires.private' in 'hwloc.pc'.
-                         (append level-zero libxml2)))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/open-mpi/hwloc")
+              (commit (string-append "hwloc-" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1l9skkcizlv0qvw2lzmysndbm528xvszhiqq3569da157qpa5xav"))
+       ;; XXX: Remove after updating package from 2.13.0.
+       (patches (search-patches "hwloc-add-with-opencl.patch"))))
+    (build-system gnu-build-system)
+    (outputs '("out"           ;'lstopo' & co., depends on Cairo, libx11, etc.
+               "lib"           ;small closure
+               "doc"           ;400+ section 3 man pages
+               "debug"))
+    (native-inputs
+     (list autoconf automake libtool opencl-headers bash pkg-config))
+    (inputs
+     (append (if (%current-target-system)
+                 '()              ;fewer dependencies when cross-compiling
+                 (list libx11 cairo ncurses expat))
+             (list
+              ;; XXX: rocm-smi requires libdrm/drm.h but doesn't
+              ;; propagate a package providing these. For now, libdrm is
+              ;; used to provide this header.
+              libdrm
+              opencl-icd-loader
+              rocm-smi-lib)))
+    (propagated-inputs
+     ;; hwloc.pc lists libze_loader and libxml2 in
+     ;; 'Requires.private' in 'hwloc.pc'.
+     (list level-zero libpciaccess libxml2))
     (arguments
-     (substitute-keyword-arguments arguments
-       ((#:configure-flags flags '())
-        #~(cons* (string-append "--with-opencl="
-                                #$(this-package-input "opencl-icd-loader"))
-                 "--enable-rsmi"
-                 (string-append "--with-rocm="
-                                #$(this-package-input "rocm-smi-lib"))
-                 #$flags))
-       ((#:phases phases)
-        #~(modify-phases #$phases
-            (add-after 'unpack 'delete-configure
-              (lambda _
-                ;; Remove configure file to generate it with patch.
-                (delete-file "configure")))
-            (replace 'skip-linux-libnuma-test
-              (lambda _
-                ;; Arrange to skip 'tests/hwloc/linux-libnuma', which fails on
-                ;; some machines: <https://github.com/open-mpi/hwloc/issues/213>.
-                (substitute* "tests/hwloc/linux-libnuma.c"
-                  (("numa_available\\(\\)")
-                   "-1"))))
-            (add-before 'check 'skip-tests-that-require-/sys
-              (lambda _
-                ;; 'test-gather-topology.sh' requires /sys as of 2.9.0; skip it.
-                (setenv "HWLOC_TEST_GATHER_TOPOLOGY" "0")))
-            (add-before 'check 'skip-test-that-fails-on-qemu
-              (lambda _
-                ;; Skip test that fails on emulated hardware due to QEMU bug:
-                ;; <https://bugs.gnu.org/40342>.
-                (substitute* "tests/hwloc/hwloc_get_last_cpu_location.c"
-                  (("hwloc_topology_init" all)
-                   (string-append "exit (77);\n" all)))))))))))
+     (list
+      #:configure-flags
+      #~(list
+         (string-append
+          "--with-opencl=" #$(this-package-input "opencl-icd-loader"))
+         "--enable-rsmi"
+         (string-append "--with-rocm=" #$(this-package-input "rocm-smi-lib"))
+         "--localstatedir=/var")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'skip-linux-libnuma-test
+            (lambda _
+              ;; Arrange to skip 'tests/hwloc/linux-libnuma', which fails on
+              ;; some machines: <https://github.com/open-mpi/hwloc/issues/213>.
+              (substitute* "tests/hwloc/linux-libnuma.c"
+                (("numa_available\\(\\)")
+                 "-1"))))
+          (add-after 'install 'refine-libnuma
+            ;; Give -L arguments for libraries to avoid propagation
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let ((out  (assoc-ref outputs "lib"))
+                    (numa (assoc-ref inputs "numactl")))
+                (substitute* (map (lambda (f) (string-append out "/" f))
+                                  '("lib/pkgconfig/hwloc.pc" "lib/libhwloc.la"))
+                  (("-lnuma" lib)
+                   (string-append "-L" numa "/lib " lib))))))
+          (add-after 'install 'avoid-circular-references
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((lib (assoc-ref outputs "lib")))
+                ;; Suppress the 'prefix=' and 'exec_prefix=' lines so that the
+                ;; "lib" output doesn't refer to "out".
+                (substitute* (string-append lib "/lib/pkgconfig/hwloc.pc")
+                  (("^.*prefix=.*$")
+                   "")))))
+          (add-after 'install 'move-man-pages
+            (lambda _
+              ;; Move section 1 and 3 man pages to the "doc" output.
+              (copy-recursively (string-append #$output "/share/man/man1")
+                                (string-append #$output:doc "/share/man/man1"))
+              (copy-recursively (string-append #$output "/share/man/man7")
+                                (string-append #$output:doc "/share/man/man7"))
+              (delete-file-recursively
+               (string-append #$output "/share/man/man1"))
+              (delete-file-recursively
+               (string-append #$output "/share/man/man7"))))
+          (add-before 'check 'skip-tests-that-require-/sys
+            (lambda _
+              ;; 'test-gather-topology.sh' requires /sys as of 2.9.0; skip it.
+              (setenv "HWLOC_TEST_GATHER_TOPOLOGY" "0")))
+          (add-before 'check 'skip-test-that-fails-on-qemu
+            (lambda _
+              ;; Skip test that fails on emulated hardware due to QEMU bug:
+              ;; <https://bugs.gnu.org/40342>.
+              (substitute* "tests/hwloc/hwloc_get_last_cpu_location.c"
+                (("hwloc_topology_init" all)
+                 (string-append "exit (77);\n" all))))))))
+    (home-page "https://www.open-mpi.org/projects/hwloc/")
+    (synopsis "Abstraction of hardware architectures")
+    (description
+     "hwloc provides a portable abstraction (across OS,
+versions, architectures, ...) of the hierarchical topology of modern
+architectures, including NUMA memory nodes, sockets, shared caches, cores and
+simultaneous multithreading.  It also gathers various attributes such as cache
+and memory information.  It primarily aims at helping high-performance
+computing applications with gathering information about the hardware so as to
+exploit it accordingly and efficiently.
+
+hwloc may display the topology in multiple convenient formats.  It also offers
+a powerful programming interface to gather information about the hardware,
+bind processes, and much more.")
+    (license license:bsd-3)))
 
 (define-public hwloc
   ;; The latest stable series of hwloc.

gnu/packages/nickle.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Nikita <nikita@n0.is>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2024 Eric Bavier <bavier@posteo.net>
+;;; Copyright © 2024,2026 Eric Bavier <bavier@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -20,35 +20,42 @@
 
 (define-module (gnu packages nickle)
   #:use-module (gnu packages)
+  #:use-module (gnu packages algebra)
+  #:use-module (gnu packages bison)
+  #:use-module (gnu packages flex)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages readline)
-  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages ruby-xyz)
+  #:use-module (guix build-system meson)
   #:use-module (guix download)
+  #:use-module (guix gexp)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages))
 
 (define-public nickle
   (package
     (name "nickle")
-    (version "2.97")
+    (version "2.107")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nickle.org/release/nickle-"
-                                  version ".tar.gz"))
+                                  version ".tar.xz"))
               (sha256
                (base32
-                "0gqashcs3r0d1yp6rq6q2ayjdwsjxnd8z0ij55ayrbhn296l7mp2"))
-              (patches (search-patches "nickle-man-release-date.patch"))))
-    (build-system gnu-build-system)
-    (inputs (list readline))
+                "1wli8p5fv2ldy51ycc8pcx8rl3ph2wbyiqs21qpjadlvildaaqj0"))))
+    (build-system meson-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-build-date
-           (lambda _
-             ;; Our patch touches Makefile.am, but rather than rebootstrap,
-             ;; make the substitution directly in Makefile.in.
-             (substitute* "Makefile.in"
-               (("BUILD_DATE") "RELEASE_DATE")))))))
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-before 'configure 'disable-benchmarks
+                          ;; Benchmarks would require `gmp` and don't
+                          ;; test anything not already covered by other
+                          ;; tests, so disable them here.
+                          (lambda _
+                            (substitute* "meson.build"
+                              (("^subdir\\('bench'\\)" &)
+                               (string-append "# " &))))))))
+    (native-inputs (list bc bison flex pkg-config ruby-asciidoctor-pdf))
+    (inputs (list readline))
     (synopsis "Numeric oriented programming language")
     (description
      "Nickle is a programming language based prototyping environment with

gnu/packages/node-xyz.scm

@@ -2324,7 +2324,7 @@ a string consisting of a number and a time unit is converted to milliseconds.")
 (define-public node-nan
   (package
     (name "node-nan")
-    (version "2.22.0")
+    (version "2.26.2")
     (source
      (origin
        (method git-fetch)
@@ -2333,7 +2333,7 @@ a string consisting of a number and a time unit is converted to milliseconds.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "02gqm23x26glffvyxrnk610hy3hg0kwh2v58dhnb032l0jhjzqvp"))))
+        (base32 "18xv0m40jgy3sc4pldw95w6p72ms5a5h0x2sm2mimlwlmxmrjlmb"))))
     (build-system node-build-system)
     (arguments
      `(#:phases

gnu/packages/node.scm

@@ -274,7 +274,7 @@
                             (lambda (file stat)
                               (executable-file? file))
                             #:stat lstat)))))
-         (add-after 'install 'install-npmrc
+         (add-after 'install 'fix-node-gyp-reference
            ;; Note: programs like node-gyp only receive these values if
            ;; they are started via `npm` or `npx`.
            ;; See: https://github.com/nodejs/node-gyp#npm-configuration
@@ -482,7 +482,7 @@ Node.js and web browsers.")
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/indutny/llparse-builder.git")
+             (url "https://github.com/nodejs/llparse-builder.git")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
@@ -491,10 +491,6 @@ Node.js and web browsers.")
        (modules '((guix build utils)))
        (snippet
         '(begin
-           ;; FIXME: Unneeded runtime dependency.
-           ;; https://github.com/indutny/llparse-builder/pull/2
-           (substitute* "package.json"
-             (("\"@types/debug.*,") ""))
            ;; Fix imports for esbuild.
            ;; https://github.com/evanw/esbuild/issues/477
            (substitute* '("src/node/invoke.ts"
@@ -521,7 +517,8 @@ Node.js and web browsers.")
          (add-after 'patch-dependencies 'delete-dependencies
            (lambda _
              (modify-json (delete-dependencies
-                           `("@types/mocha"
+                           `("@types/debug"
+                             "@types/mocha"
                              "@types/node"
                              "mocha"
                              "ts-node"
@@ -539,7 +536,7 @@ Node.js and web browsers.")
      (list node-binary-search-bootstrap node-debug-bootstrap))
     (native-inputs
      (list esbuild))
-    (home-page "https://github.com/indutny/llparse-builder#readme")
+    (home-page "https://github.com/nodejs/llparse-builder#readme")
     (properties '((hidden? . #t)))
     (synopsis "Graph builder for consumption by llparse")
     (description "This package builds graphs for consumption by llparse.")
@@ -553,7 +550,7 @@ Node.js and web browsers.")
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/indutny/llparse-frontend.git")
+             (url "https://github.com/nodejs/llparse-frontend.git")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
@@ -602,7 +599,7 @@ Node.js and web browsers.")
      (list node-debug-bootstrap node-llparse-builder-bootstrap))
     (native-inputs
      (list esbuild))
-    (home-page "https://github.com/indutny/llparse-frontend#readme")
+    (home-page "https://github.com/nodejs/llparse-frontend#readme")
     (properties '((hidden? . #t)))
     (synopsis "Frontend for the llparse compiler")
     (description "This package is a frontend for the llparse compiler.")
@@ -611,17 +608,17 @@ Node.js and web browsers.")
 (define-public node-llparse-bootstrap
   (package
     (name "node-llparse")
-    (version "7.1.0")
+    (version "7.3.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/indutny/llparse.git")
+             (url "https://github.com/nodejs/llparse.git")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "10da273iy2if88hp79cwms6c8qpsl1fkgzll6gmqyx5yxv5mkyp6"))
+         "09hqjcynkz5iv7aydzdwgs42r7y2zylplv0ff7w0vkdsgb08j22a"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -645,10 +642,14 @@ Node.js and web browsers.")
          (add-after 'patch-dependencies 'delete-dependencies
            (lambda args
              (modify-json (delete-dependencies
-                           `("@types/debug"
+                           `("@stylistic/eslint-plugin"
+                             "@typescript-eslint/eslint-plugin"
+                             "@typescript-eslint/parser"
+                             "@types/debug"
                              "@types/mocha"
                              "@types/node"
                              "esm"
+                             "eslint"
                              "llparse-test-fixture"
                              "mocha"
                              "ts-node"
@@ -676,7 +677,7 @@ parser definition into a C output.")
 (define-public llhttp-bootstrap
   (package
     (name "llhttp")
-    (version "9.2.1")
+    (version "9.3.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -685,7 +686,7 @@ parser definition into a C output.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0mzg19aqb1am498gms0z75cwd5kmfg9p78b1hhxw67019nsjcbac"))
+                "0yz4ys94pjq2fs2pihpqjvmxj2mbpm8k5prlm445z4qlajzlr4kb"))
               (patches (search-patches "llhttp-ponyfill-object-fromentries.patch"))
               (modules '((guix build utils)))
               (snippet
@@ -747,14 +748,14 @@ source files.")
 (define-public node-lts
   (package
     (inherit node-bootstrap)
-    (version "22.14.0")
+    (version "24.14.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nodejs.org/dist/v" version
                                   "/node-v" version ".tar.gz"))
               (sha256
                (base32
-                "12msprh604s6qdsgwymxw4kl8ivaldbaydf4v37lbp02aznk2kkc"))
+                "1cri5lp3a9jhh34dbd48hq2zyb7xjb9qs6zl36l3q2blawgwz642"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -770,13 +771,17 @@ source files.")
                               "deps/icu-small"
                               "deps/nghttp2"
                               "deps/ngtcp2"
+                              "deps/llhttp"
                               "deps/uv"
-                              "deps/zlib"))))))
+                              "deps/zlib"
+                              "deps/zstd"))))))
     (arguments
      (substitute-keyword-arguments arguments
        ((#:configure-flags configure-flags)
         ''("--shared-cares"
            "--shared-libuv"
+           "--shared-http-parser"
+           "--shared-http-parser-libname=llhttp"
            "--shared-nghttp2"
            "--shared-openssl"
            "--shared-zlib"
@@ -784,6 +789,7 @@ source files.")
            "--with-intl=system-icu"
            "--shared-ngtcp2"
            "--shared-nghttp3"
+           "--shared-zstd"
            ;;Needed for correct snapshot checksums
            "--v8-enable-snapshot-compression"))
        ((#:phases phases)
@@ -846,9 +852,11 @@ source files.")
                (for-each delete-file
                          '("test/parallel/test-https-agent-unref-socket.js"))
 
-               ;; This test is timing-sensitive, and fails sporadically on
+               ;; These tests are timing-sensitive, and fail sporadically on
                ;; slow, busy, or even very fast machines.
-               (delete-file "test/parallel/test-fs-utimes.js")
+               (for-each delete-file
+                         '("test/parallel/test-fs-utimes.js"
+                           "test/sequential/test-performance-eventloopdelay.js"))
 
                ;; FIXME: This test fails randomly:
                ;; https://github.com/nodejs/node/issues/31213
@@ -899,18 +907,6 @@ source files.")
                      "test/parallel/test-http2-invalid-last-stream-id.js")
                  (("client\\.connect\\(address\\)")
                   "client.connect(address.port)"))))
-           (add-after 'delete-problematic-tests 'replace-llhttp-sources
-             (lambda* (#:key inputs #:allow-other-keys)
-               ;; Replace pre-generated llhttp sources
-               (let ((llhttp (assoc-ref inputs "llhttp")))
-                 (copy-file (string-append llhttp "/src/llhttp.c")
-                            "deps/llhttp/src/llhttp.c")
-                 (copy-file (string-append llhttp "/src/api.c")
-                            "deps/llhttp/src/api.c")
-                 (copy-file (string-append llhttp "/src/http.c")
-                            "deps/llhttp/src/http.c")
-                 (copy-file (string-append llhttp "/include/llhttp.h")
-                            "deps/llhttp/include/llhttp.h"))))
            ;; npm installs dependencies by copying their files over a tar
            ;; stream.  A file with more than one hardlink is marked as a
            ;; "Link".  pacote/lib/fetcher.js calls node-tar's extractor with a
@@ -935,30 +931,22 @@ source files.")
            ;;   https://github.com/npm/pacote/issues/285
            (add-after 'install 'ignore-number-of-hardlinks
              (lambda* (#:key outputs #:allow-other-keys)
-               (let ((file (string-append (assoc-ref outputs "out")
-                                          "/lib/node_modules/npm/node_modules"
-                                          "/tar/lib/write-entry.js")))
-                 (substitute* file
+               (let ((dir (string-append (assoc-ref outputs "out")
+                                         "/lib/node_modules/npm/node_modules"
+                                         "/tar/dist")))
+                 (substitute*
+                     (list (string-append dir "/esm/write-entry.js")
+                           (string-append dir "/commonjs/write-entry.js"))
                    (("this.stat.nlink > 1") "false")))))
-           (add-after 'install 'install-node-gyp-wrapper
+           (replace 'fix-node-gyp-reference
              (lambda* (#:key inputs outputs #:allow-other-keys)
-               (let* ((out (assoc-ref outputs "out"))
-                      (dir (string-append out "/lib/node_modules/npm/bin/node-gyp-bin"))
-                      (file (string-append dir "/node-gyp")))
-                 (mkdir-p dir)
-                 ;; See https://github.com/npm/cli/issues/6842
-                 (call-with-output-file file
-                   (lambda (port)
-                     (format port "#!~a/bin/sh
-if [ \"x$npm_config_node_gyp\" = \"x\" ]; then
-  ~a/bin/node \"~a/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js\" \"$@\"
-else
-  \"$npm_config_node_gyp\" \"$@\"
-fi"
-                             (assoc-ref inputs "bash")
-                             out
-                             out)))
-                 (chmod file #o555))))))))
+               (let ((out (assoc-ref outputs "out")))
+                 (for-each
+                  (lambda (spec)
+                    (wrap-program (string-append out spec)
+                      `("npm_package_config_node_gyp_nodedir" = (,out))))
+                  '("/bin/npm"
+                    "/bin/npx")))))))))
     (native-inputs
      (list ;; Runtime dependencies for binaries used as a bootstrap.
            c-ares-for-node-lts
@@ -974,7 +962,8 @@ fi"
            pkg-config
            procps
            python
-           util-linux))
+           util-linux
+           gcc-14))
     (inputs
      (list bash-minimal
            coreutils
@@ -987,7 +976,8 @@ fi"
            nghttp3
            `(,nghttp2 "lib")
            openssl
-           zlib))
+           zlib
+           `(,zstd-1.5.7 "lib")))
     (supported-systems
       (cons "riscv64-linux" (package-supported-systems node-bootstrap)))
     (properties (alist-delete 'hidden? (package-properties node-bootstrap)))))
@@ -1003,6 +993,6 @@ fi"
         `(cons* "--shared" "--without-npm" ,flags))
        ((#:phases phases '%standard-phases)
         `(modify-phases ,phases
-           (delete 'install-npmrc)
+           (delete 'fix-node-gyp-reference)
            (delete 'patch-nested-shebangs)
            (delete 'ignore-number-of-hardlinks)))))))

gnu/packages/nss.scm

@@ -398,7 +398,7 @@ taken from the NSS package and thus ultimately from the Mozilla project.")
 (define-public nsncd
   (package
     (name "nsncd")
-    (version "1.5.1")
+    (version "1.5.2")
     (source
      (origin
        (method git-fetch)
@@ -407,7 +407,7 @@ taken from the NSS package and thus ultimately from the Mozilla project.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1qiphwlwbnni2vfqjbdzv2a1qgqv2ycmygmyrbx8pgaak9gl5hfi"))))
+        (base32 "1kzwd5vlz5paal8k79dkamjqczz7k8azyc8zwjyhalcxzsjkdn0w"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-test-flags

gnu/packages/parallel.scm

@@ -82,7 +82,7 @@
 (define-public parallel
   (package
     (name "parallel")
-    (version "20260222")
+    (version "20260322")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -90,7 +90,7 @@
       (uri (string-append "mirror://gnu/parallel/parallel-"
                           version ".tar.bz2"))
       (sha256
-       (base32 "0j0zmq1klbvpz590vr2di8yvsniwixlhsmir7zfjy3rajx42l9y6"))
+       (base32 "1q7g5f13nlwichgh0dk8w5fqjnfnxvwxk6rjy0fd5l7l6blq0ikn"))
       (snippet
        '(begin
           (use-modules (guix build utils))

gnu/packages/patches/cadical-add-shared-library.patch

@@ -12,10 +12,10 @@ Liliana Marie Prikler <liliana.prikler@gmail.com>:
  1 file changed, 4 insertions(+), 1 deletion(-)
 
 diff --git a/makefile.in b/makefile.in
-index 291cb3e3..d179f591 100644
+index 5e1c1b3a..de3fe975 100644
 --- a/makefile.in
 +++ b/makefile.in
-@@ -34,7 +34,7 @@ COMPILE=$(CXX) $(CXXFLAGS) -I$(DIR) -I$(ROOT)/src
+@@ -38,7 +38,7 @@ COMPILE=$(CXX) $(CXXFLAGS) -I$(DIR) -I../src
  
  #--------------------------------------------------------------------------#
  
@@ -24,26 +24,23 @@ index 291cb3e3..d179f591 100644
  
  #--------------------------------------------------------------------------#
  
-@@ -54,10 +54,10 @@ contrib/%.o: $(ROOT)/contrib/%.cpp $(ROOT)/contrib/%.hpp $(ROOT)/src/*.hpp makef
+@@ -53,14 +53,17 @@ all: libcadical.a cadical mobical
  # tester 'mobical') and the library are the main build targets.
  
- cadical: src/cadical.o libcadical.a makefile
+ cadical: cadical.o libcadical.a makefile
 -	$(COMPILE) -o $@ $< -L. -lcadical $(LIBS)
 +	$(COMPILE) -static -o $@ $< -L. -lcadical $(LIBS)
  
- mobical: src/mobical.o libcadical.a makefile $(LIBS)
+ mobical: mobical.o libcadical.a makefile $(LIBS)
 -	$(COMPILE) -o $@ $< -L. -lcadical
 +	$(COMPILE) -static -o $@ $< -L. -lcadical
  
  libcadical.a: $(OBJ_SOLVER) $(OBJ_CONTRIB) makefile
  	ar rc $@ $(OBJ_SOLVER) $(OBJ_CONTRIB)
-@@ -62,5 +62,8 @@ mobical: src/mobical.o libcadical.a makefile $(LIBS)
- libcadical.a: $(OBJ_SOLVER) $(OBJ_CONTRIB) makefile
- 	ar rc $@ $(OBJ_SOLVER) $(OBJ_CONTRIB)
  
 +libcadical.so: $(OBJ_SOLVER) $(OBJ_CONTRIB) $(LIBS) makefile
 +	$(COMPILE) -shared -o $@ $(OBJ_SOLVER) $(OBJ_CONTRIB) $(LIBS)
 +
  #--------------------------------------------------------------------------#
  
- # Note that 'build.hpp' is generated and resides in the build directory.
+ # Note that 'build.hpp' is generated and resides in the build directory.

gnu/packages/patches/ldc-i686-int128-alignment.patch

@@ -0,0 +1,40 @@
+Description: Adjust int128 alignment
+Author: Walter Bright <WalterBright@users.noreply.github.com>
+Origin: backport, https://github.com/ldc-developers/ldc/commit/f634e2a6542a8b563d9ba1b680afd5337b4c09ea
+Bug: https://github.com/ldc-developers/ldc/issues/1356
+Last-Update: 2024-12-30
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/dmd/common/int128.d
++++ b/dmd/common/int128.d
+@@ -20,7 +20,29 @@
+ alias U = ulong;
+ enum Ubits = uint(U.sizeof * 8);
+ 
+-align(16) struct Cent
++version (DigitalMars)
++{
++    /* The alignment should follow target.stackAlign(),
++     * which is `isXmmSupported() ? 16 : (is64bit ? 8 : 4)
++     */
++    version (D_SIMD)
++        private enum Cent_alignment = 16;
++    else version (X86_64)
++        private enum Cent_alignment = 8;
++    else
++        private enum Cent_alignment = 4;
++}
++else
++{
++    version (LDC) version (X86) version = LDC_X86;
++
++    version (X86_64)       private enum Cent_alignment = 16;
++    // 32-bit x86: need default alignment due to https://github.com/ldc-developers/ldc/issues/1356
++    else version (LDC_X86) private enum Cent_alignment = U.alignof;
++    else                   private enum Cent_alignment = (size_t.sizeof * 2);
++}
++
++align(Cent_alignment) struct Cent
+ {
+     U lo;      // low 64 bits
+     U hi;      // high 64 bits

gnu/packages/patches/lsof-compat-linux-6.9.patch

@@ -1,67 +0,0 @@
-This commit adds the patch that fixes:
-<https://github.com/lsof-org/lsof/issues/317>
-
-The issue was triggering the following error in the `test` phase that
-resulted in a build failure in Linux 6.9 or higher:
-
-    FAIL: lib/dialects/linux/tests/case-20-pidfd-pid.bash
-
-
-From c1678e3f6e4b4d984cb3078b7bf0c9e24bedb8ca Mon Sep 17 00:00:00 2001
-From: Jiajie Chen <c@jia.je>
-Date: Fri, 17 May 2024 15:22:35 +0800
-Subject: [PATCH] [linux] Maintain original output for pidfd in linux 6.9
-
----
- 00DIST                     |  3 +++
- lib/dialects/linux/dproc.c | 13 +++++++++++++
- 2 files changed, 16 insertions(+)
-
-diff --git a/00DIST b/00DIST
-index d5a0349..9a29611 100644
---- a/00DIST
-+++ b/00DIST
-@@ -5605,6 +5605,9 @@ Supplement	Regenerated the 4.04 distribution to correct a non-
- 
- 		[linux] Do not embed kernel version in CFLAGS (#314)
- 
-+		[linux] Linux 6.9 changed the pidfs appearence in procfs. Try
-+		to maintain original output in lsof (#317)
-+
- 
- Vic Abell <abe@purdue.edu>
- July 14, 2018
-diff --git a/lib/dialects/linux/dproc.c b/lib/dialects/linux/dproc.c
-index cb6bb64..3a7a120 100644
---- a/lib/dialects/linux/dproc.c
-+++ b/lib/dialects/linux/dproc.c
-@@ -1273,6 +1273,10 @@ static int process_id(struct lsof_context *ctx, /* context */
- #endif     /* defined(HASEPTOPTS) */
-                 if (rest && rest[0] == '[' && rest[1] == 'p')
-                     fdinfo_mask |= FDINFO_PID;
-+                else if (Lf->ntype == N_REGLR && rest && *rest && strcmp(pbuf, "pidfd") == 0) {
-+                    // https://github.com/lsof-org/lsof/issues/317
-+                    fdinfo_mask |= FDINFO_PID;
-+                }
- 
-                 if ((av = get_fdinfo(ctx, pathi, fdinfo_mask, &fi)) &
-                     FDINFO_POS) {
-@@ -1338,6 +1342,15 @@ static int process_id(struct lsof_context *ctx, /* context */
-                     Lf->sf |= SELPTYINFO;
-                 }
- #endif /* defined(HASEPTOPTS) && defined(HASPTYEPT) */
-+                else if (Lf->ntype == N_REGLR && rest && *rest && Lf->nm &&
-+                         strcmp(Lf->nm, "pidfd") == 0) {
-+                    // https://github.com/lsof-org/lsof/issues/317
-+                    // pidfd since Linux 6.9 becomes a regular file:
-+                    // /proc/PID/fd/FD -> pidfd:[INODE]
-+                    (void)snpf(rest, sizeof(pbuf) - (rest - pbuf),
-+                                "[pidfd:%d]", fi.pid);
-+                    enter_nm(ctx, rest);
-+                }
- 
-                 if (Lf->sf)
-                     link_lfile(ctx);
--- 
-2.45.2
-

gnu/packages/patches/nheko-0-12-1-fix-rendering-replies.patch

@@ -0,0 +1,290 @@
+From 2769642d3c7bd3c0d830b2f18ef6b3bf6a710bf4 Mon Sep 17 00:00:00 2001
+From: Nicolas Werner <nicolas.werner@hotmail.de>
+Date: Sun, 14 Sep 2025 23:43:20 +0200
+Subject: [PATCH] Fix most reply rendering issues with qt 6.9.2
+
+---
+ resources/qml/TimelineBubbleMessageStyle.qml  | 31 ++++----
+ resources/qml/TimelineDefaultMessageStyle.qml | 32 ++++-----
+ resources/qml/TopBar.qml                      |  2 +-
+ resources/qml/delegates/Reply.qml             | 70 ++++++++++---------
+ 4 files changed, 65 insertions(+), 70 deletions(-)
+
+diff --git a/resources/qml/TimelineBubbleMessageStyle.qml b/resources/qml/TimelineBubbleMessageStyle.qml
+index 560cb1338..722718bc4 100644
+--- a/resources/qml/TimelineBubbleMessageStyle.qml
++++ b/resources/qml/TimelineBubbleMessageStyle.qml
+@@ -210,9 +210,10 @@ TimelineEvent {
+ 
+                         AbstractButton {
+                             id: replyRow
+-                            visible: wrapper.reply
++                            visible: wrapper.replyTo
++
++                            leftPadding: Nheko.paddingSmall + 4
+ 
+-                            height: replyLine.height
+                             anchors.left: parent.left
+                             anchors.right: parent.right
+ 
+@@ -225,19 +226,7 @@ TimelineEvent {
+                                 cursorShape: Qt.PointingHandCursor
+                             }
+ 
+-                            contentItem: Row {
+-                                id: replyRowLay
+-
+-                                spacing: Nheko.paddingSmall
+-
+-                                Rectangle {
+-                                    id: replyLine
+-                                    height: Math.min( wrapper.reply?.height, timelineView.height / 10) + Nheko.paddingSmall + replyUserButton.height
+-                                    color: replyRow.userColor
+-                                    width: 4
+-                                }
+-
+-                                Column {
++                            contentItem: Column {
+                                     spacing: 0
+ 
+                                     id: replyCol
+@@ -247,7 +236,7 @@ TimelineEvent {
+ 
+                                         contentItem: Label {
+                                             id: userName_
+-                                            text: wrapper.reply?.userName ?? ''
++                                            text: wrapper.reply?.userName ?? 'missing name'
+                                             color: replyRow.userColor
+                                             textFormat: Text.RichText
+                                             width: wrapper.maxWidth
+@@ -259,12 +248,20 @@ TimelineEvent {
+                                         replyUserButton,
+                                         wrapper.reply,
+                                     ]
+-                                }
+                             }
+ 
+                             background: Rectangle {
+                                 //width: replyRow.implicitContentWidth
+                                 color: Qt.tint(palette.base, Qt.hsla(replyRow.userColor.hslHue, 0.5, replyRow.userColor.hslLightness, 0.1))
++                                Rectangle {
++                                    anchors.top: parent.top
++                                    anchors.bottom: parent.bottom
++                                    anchors.left: parent.left
++
++                                    id: replyLine
++                                    color: replyRow.userColor
++                                    width: 4
++                                }
+                             }
+ 
+                             onClicked: {
+diff --git a/resources/qml/TimelineDefaultMessageStyle.qml b/resources/qml/TimelineDefaultMessageStyle.qml
+index 2bc0171a8..49454ac0b 100644
+--- a/resources/qml/TimelineDefaultMessageStyle.qml
++++ b/resources/qml/TimelineDefaultMessageStyle.qml
+@@ -192,9 +192,9 @@ TimelineEvent {
+ 
+                 AbstractButton {
+                     id: replyRow
+-                    visible: wrapper.reply
++                    visible: wrapper.replyTo
+ 
+-                    height: replyLine.height
++                    leftPadding: Nheko.paddingSmall + 4
+ 
+                     property color userColor: TimelineManager.userColor(wrapper.reply?.userId ?? '', palette.base)
+ 
+@@ -205,19 +205,7 @@ TimelineEvent {
+                         cursorShape: Qt.PointingHandCursor
+                     }
+ 
+-                    contentItem: Row {
+-                        id: replyRowLay
+-
+-                        spacing: Nheko.paddingSmall
+-
+-                        Rectangle {
+-                            id: replyLine
+-                            height: Math.min( wrapper.reply?.height, timelineView.height / 10) + Nheko.paddingSmall + replyUserButton.height
+-                            color: replyRow.userColor
+-                            width: 4
+-                        }
+-
+-                        Column {
++                    contentItem: Column {
+                             spacing: 0
+ 
+                             id: replyCol
+@@ -227,7 +215,7 @@ TimelineEvent {
+ 
+                                 contentItem: Label {
+                                     id: userName_
+-                                    text: wrapper.reply?.userName ?? ''
++                                    text: wrapper.reply?.userName ?? 'missing name'
+                                     color: replyRow.userColor
+                                     textFormat: Text.RichText
+                                     width: wrapper.maxWidth
+@@ -239,12 +227,20 @@ TimelineEvent {
+                                 replyUserButton,
+                                 wrapper.reply,
+                             ]
+-                        }
+                     }
+ 
+                     background: Rectangle {
+-                        //width: replyRow.implicitContentWidth
+                         color: Qt.tint(palette.base, Qt.hsla(replyRow.userColor.hslHue, 0.5, replyRow.userColor.hslLightness, 0.1))
++
++                        Rectangle {
++                            anchors.top: parent.top
++                            anchors.bottom: parent.bottom
++                            anchors.left: parent.left
++
++                            id: replyLine
++                            color: replyRow.userColor
++                            width: 4
++                        }
+                     }
+ 
+                     onClicked: {
+diff --git a/resources/qml/TopBar.qml b/resources/qml/TopBar.qml
+index 900e59e8b..cd20e94ec 100644
+--- a/resources/qml/TopBar.qml
++++ b/resources/qml/TopBar.qml
+@@ -330,7 +330,7 @@ Pane {
+                         ImageButton {
+                             id: deletePinButton
+ 
+-                            Layout.alignment: Qt.AlignTop | Qt.AlignLeft
++                            Layout.alignment: Qt.AlignTop | Qt.AlignRight
+                             Layout.preferredHeight: 16
+                             Layout.preferredWidth: 16
+                             ToolTip.text: qsTr("Unpin")
+diff --git a/resources/qml/delegates/Reply.qml b/resources/qml/delegates/Reply.qml
+index 7ee2a0a14..77cad0f0a 100644
+--- a/resources/qml/delegates/Reply.qml
++++ b/resources/qml/delegates/Reply.qml
+@@ -5,6 +5,7 @@
+ import QtQuick
+ import QtQuick.Controls
+ import QtQuick.Window
++import QtQuick.Layouts
+ import im.nheko
+ import "../"
+ 
+@@ -21,7 +22,11 @@ AbstractButton {
+     property string userId: eventId ? room.dataById(eventId, Room.UserId, "") : ""
+     property string userName: eventId ? room.dataById(eventId, Room.UserName, "") : ""
+     implicitHeight: replyContainer.height
+-    implicitWidth: replyContainer.implicitWidth
++    implicitWidth: replyContainer.implicitWidth + leftPadding + rightPadding
++
++    leftPadding: 4 + Nheko.paddingSmall
++    rightPadding: Nheko.paddingSmall
++
+     required property int maxWidth
+     property bool limitHeight: false
+ 
+@@ -31,14 +36,14 @@ AbstractButton {
+     }
+ 
+     onClicked: {
+-        let link = reply.child.linkAt != undefined && reply.child.linkAt(pressX-colorline.width, pressY - userName_.implicitHeight);
++        let link = timelineEvent.main.linkAt != undefined && timelineEvent.main.linkAt(pressX-colorline.width, pressY - userName_.implicitHeight);
+         if (link) {
+             Nheko.openLink(link)
+         } else {
+             room.showEvent(r.eventId)
+         }
+     }
+-    onPressAndHold: replyContextMenu.show(reply.child.copyText, reply.child.linkAt(pressX-colorline.width, pressY - userName_.implicitHeight), r.eventId)
++    onPressAndHold: replyContextMenu.show(timelineEvent.main.copyText, timelineEvent.main.linkAt(pressX-colorline.width, pressY - userName_.implicitHeight), r.eventId)
+ 
+     contentItem: TimelineEvent {
+         id: timelineEvent
+@@ -51,49 +56,36 @@ AbstractButton {
+         maxWidth: r.maxWidth
+         limitAsReply: r.limitHeight
+ 
+-        //height: replyContainer.implicitHeight
+-        data: Row {
++        data: Column {
+             id: replyContainer
+-
+-            spacing: Nheko.paddingSmall
++            spacing: 0
+ 
+             clip: r.limitHeight
+ 
+             height: r.limitHeight ? Math.min( timelineEvent.main?.height, timelineView.height / 10) + Nheko.paddingSmall + usernameBtn.height : undefined
+ 
+-            Rectangle {
+-                id: colorline
+-
+-                width: 4
+-                height: content.height
+-
+-                color: TimelineManager.userColor(r.userId, palette.base)
+-            }
+-
+-            Column {
+-                id: content
+-                spacing: 0
++            // FIXME: I have no idea, why this name doesn't render in the reply popup on Qt 6.9.2
++            AbstractButton {
++                id: usernameBtn
+ 
+-                AbstractButton {
+-                    id: usernameBtn
++                visible: r.eventId
+ 
+-
+-                    contentItem: Label {
+-                        id: userName_
+-                        text: r.userName
+-                        color: r.userColor
+-                        textFormat: Text.RichText
+-                        width: timelineEvent.main?.width
+-                    }
+-                    onClicked: room.openUserProfile(r.userId)
++                contentItem: Label {
++                    visible: r.eventId
++                    id: userName_
++                    text: r.userName
++                    color: r.userColor
++                    textFormat: Text.RichText
++                    width: timelineEvent.main?.width
+                 }
+-
+-                data: [
+-                    usernameBtn, timelineEvent.main,
+-                ]
++                onClicked: room.openUserProfile(r.userId)
+             }
+ 
++            data: [
++                usernameBtn, timelineEvent.main,
++            ]
+         }
++
+     }
+ 
+     background: Rectangle {
+@@ -103,6 +95,16 @@ AbstractButton {
+         property color userColor: TimelineManager.userColor(r.userId, palette.base)
+         property color bgColor: palette.base
+         color: Qt.tint(bgColor, Qt.hsla(userColor.hslHue, 0.5, userColor.hslLightness, 0.1))
++
++        Rectangle {
++            anchors.top: parent.top
++            anchors.bottom: parent.bottom
++            anchors.left: parent.left
++
++            id: colorline
++            color: backgroundItem.userColor
++            width: 4
++        }
+     }
+ 
+ }

gnu/packages/patches/nickle-man-release-date.patch

@@ -1,41 +0,0 @@
-Submitted close to upstream at
-https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1070162
-
-From 95ff7e9de4ed815e060b1df59b5b2b105307e0d7 Mon Sep 17 00:00:00 2001
-From: Eric Bavier <bavier@posteo.net>
-Date: Mon, 29 Apr 2024 23:34:15 -0500
-Subject: [PATCH] Fixes substitution of REALEASE_DATE in nickle.1
-
-* Makefile.am (nickle.1): 'BUILD_DATE' -> 'RELEASE_DATE'.
-* nickle.1.in: Include version in footer.
----
- Makefile.am | 2 +-
- nickle.1.in | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/Makefile.am b/Makefile.am
-index ba28ec9..5ed56a3 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -96,7 +96,7 @@ RELEASE_FILES = $(TARFILE) $(SIGFILE) $(SRPMFILE) $(RPMFILE)
- 
- nickle.1: nickle.1.in nickle-config.h
- 	sed -e 's,@''VERSION@,$(VERSION),' \
--	    -e 's,@''BUILD_DATE@,$(BUILD_DATE),' \
-+	    -e 's,@''RELEASE_DATE@,$(RELEASE_DATE),' \
- 	    -e 's,@''pkgdatadir@,$(pkgdatadir),' $(top_srcdir)/nickle.1.in > $@
- 	    
- nickle.spec: nickle.spec.in nickle-config.h
-diff --git a/nickle.1.in b/nickle.1.in
-index 4871ac2..1ab9e08 100644
---- a/nickle.1.in
-+++ b/nickle.1.in
-@@ -1,4 +1,4 @@
--.TH NICKLE 1 "@RELEASE_DATE@"
-+.TH NICKLE 1 "@RELEASE_DATE@" "nickle @VERSION@"
- .SH NAME
- nickle \- a desk calculator language
- .SH SYNOPSIS
--- 
-2.41.0
-

gnu/packages/patches/tao-synth-include-string-you-use.patch

@@ -0,0 +1,187 @@
+Upstream-Status: not reported
+
+diff --git a/include/tao/bow.h b/include/tao/bow.h
+index 38c7081..0a35886 100644
+--- a/include/tao/bow.h
++++ b/include/tao/bow.h
+@@ -21,6 +21,7 @@
+ 
+ #include <tao/access_point.h>
+ #include <tao/device.h>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/circle.h b/include/tao/circle.h
+index f3061ae..2f96c68 100644
+--- a/include/tao/circle.h
++++ b/include/tao/circle.h
+@@ -21,6 +21,7 @@
+ 
+ #include <tao/cell.h>
+ #include <tao/instrument.h>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/connector.h b/include/tao/connector.h
+index 0c255f2..1cdcc13 100644
+--- a/include/tao/connector.h
++++ b/include/tao/connector.h
+@@ -21,6 +21,7 @@
+ 
+ #include <tao/access_point.h>
+ #include <tao/device.h>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/device.h b/include/tao/device.h
+index 06d025c..9bb48aa 100644
+--- a/include/tao/device.h
++++ b/include/tao/device.h
+@@ -32,6 +32,7 @@
+ #endif
+ 
+ #include <tao/access_point.h>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/ellipse.h b/include/tao/ellipse.h
+index ac3b849..c05fcf7 100644
+--- a/include/tao/ellipse.h
++++ b/include/tao/ellipse.h
+@@ -21,6 +21,7 @@
+ 
+ #include <tao/cell.h>
+ #include <tao/instrument.h>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/graphics_engine.h b/include/tao/graphics_engine.h
+index bf67425..b2764aa 100644
+--- a/include/tao/graphics_engine.h
++++ b/include/tao/graphics_engine.h
+@@ -23,6 +23,7 @@
+ #include <iomanip>
+ #include <memory>
+ #include <sstream>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/hammer.h b/include/tao/hammer.h
+index 172a8e8..0a4cf2d 100644
+--- a/include/tao/hammer.h
++++ b/include/tao/hammer.h
+@@ -20,6 +20,7 @@
+ #define HAMMER_H
+ 
+ #include <tao/device.h>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/instrument.h b/include/tao/instrument.h
+index 3b23ac7..60cb6e0 100644
+--- a/include/tao/instrument.h
++++ b/include/tao/instrument.h
+@@ -26,6 +26,7 @@ extern "C" {
+ #include <tao/access_point.h>
+ #include <tao/pitch.h>
+ #include <vector>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/output.h b/include/tao/output.h
+index db34e92..03e3224 100644
+--- a/include/tao/output.h
++++ b/include/tao/output.h
+@@ -23,6 +23,7 @@
+ #include <fstream>
+ #include <sstream>
+ #include <vector>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/pitch.h b/include/tao/pitch.h
+index a76f5eb..fa31ab2 100644
+--- a/include/tao/pitch.h
++++ b/include/tao/pitch.h
+@@ -19,6 +19,8 @@
+ #ifndef TAOPITCH_H
+ #define TAOPITCH_H
+ 
++#include <string>
++
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+ #else
+diff --git a/include/tao/rectangle.h b/include/tao/rectangle.h
+index 5c1e77c..0056dcd 100644
+--- a/include/tao/rectangle.h
++++ b/include/tao/rectangle.h
+@@ -21,6 +21,7 @@
+ 
+ #include <tao/cell.h>
+ #include <tao/instrument.h>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/rgb_color.h b/include/tao/rgb_color.h
+index 69259b6..3f8f7b7 100644
+--- a/include/tao/rgb_color.h
++++ b/include/tao/rgb_color.h
+@@ -1,6 +1,8 @@
+ #ifndef TAORGBCOLOR_H
+ #define TAORGBCOLOR_H
+ 
++#include <string>
++
+ /*
+ static struct colors=
+ {
+diff --git a/include/tao/stop.h b/include/tao/stop.h
+index 85a6570..f6868f2 100644
+--- a/include/tao/stop.h
++++ b/include/tao/stop.h
+@@ -23,6 +23,7 @@
+ #include <tao/device.h>
+ #include <tao/pitch.h>
+ #include <tao/strand.h>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/strand.h b/include/tao/strand.h
+index 65a0d30..1fe99a4 100644
+--- a/include/tao/strand.h
++++ b/include/tao/strand.h
+@@ -21,6 +21,7 @@
+ 
+ #include <tao/cell.h>
+ #include <tao/instrument.h>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+diff --git a/include/tao/triangle.h b/include/tao/triangle.h
+index 06d2b2c..9978f94 100644
+--- a/include/tao/triangle.h
++++ b/include/tao/triangle.h
+@@ -21,6 +21,7 @@
+ 
+ #include <tao/cell.h>
+ #include <tao/instrument.h>
++#include <string>
+ 
+ #ifdef WIN32
+ #define DLLEXPORT __declspec(dllexport)
+-- 
+2.52.0
+

gnu/packages/patchutils.scm

@@ -361,7 +361,7 @@ GiB).")
 (define-public meld
   (package
     (name "meld")
-    (version "3.23.0")
+    (version "3.23.1")
     (source
      (origin
        (method url-fetch)
@@ -369,7 +369,7 @@ GiB).")
                            (version-major+minor version)
                            "/meld-" version ".tar.xz"))
        (sha256
-        (base32 "19n273shqs8l5lrlic0hr5iv1mp9223ijf3pkh8a49g08112lg4q"))))
+        (base32 "0x1mhk39g98x2w54w7y82fmgx6ad622q6k57a6scdiv38s92gy3k"))))
     (build-system meson-build-system)
     (native-inputs
      (list desktop-file-utils

gnu/packages/pkg-config.scm

@@ -205,3 +205,28 @@ provides access to most of pkgconf's functionality, to allow other tooling
 such as compilers and IDEs to discover and use libraries configured by
 pkgconf.")
     (license isc)))
+
+(define-public pkgconf-as-pkg-config
+  (package/inherit pkgconf
+    (name "pkgconf-as-pkg-config")
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (delete 'build)
+          (replace 'install
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((pkgconf (search-input-file inputs "bin/pkgconf")))
+                (mkdir-p (string-append #$output "/bin"))
+                (symlink pkgconf (string-append #$output "/bin/pkg-config"))
+                ;; Also make 'pkg.m4' available, some packages might expect it.
+                (mkdir-p (string-append #$output "/share"))
+                (symlink (string-append (dirname (dirname pkgconf))
+                                        "/share/aclocal")
+                         (string-append #$output "/share/aclocal"))))))))
+    (native-inputs '())
+    (inputs (list pkgconf))
+    (propagated-inputs '())))

gnu/packages/prolog.scm

@@ -236,7 +236,7 @@ it.")
 (define-public trealla
   (package
     (name "trealla")
-    (version "2.92.7")
+    (version "2.92.15")
     (source
      (origin
        (method git-fetch)
@@ -245,7 +245,7 @@ it.")
           (url "https://github.com/trealla-prolog/trealla")
           (commit (string-append "v" version))))
        (sha256
-        (base32 "07z2i0bkqzdx0szwr4v98cb9r7a3ghy0vz5jn3xa7zh41yfr33nx"))
+        (base32 "15kmal7pja5y0jxzl7kycr028513gc4y00dlvvs2f7gcviiddbxh"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (inputs

gnu/packages/python-compression.scm

@@ -289,11 +289,13 @@ were a single file.")
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 743 passed, 1 skipped, 1 deselected
+      ;; tests: 742 passed, 1 skipped, 2 deselected
       #:test-flags
       #~(list "--ignore=benchmarks/test_bench.py"
               ;; FIXME: Did not raise cramjam.DecompressionError
-              "--deselect=tests/test_variants.py::test_variants_raise_exception[deflate]")
+              "--deselect=tests/test_variants.py::test_variants_raise_exception[deflate]"
+              ;; This test fails nondeterministically.
+              "--deselect=tests/test_variants.py::test_variants_decompress_into[zlib-Buffer-File]")
       #:imported-modules `(,@%cargo-build-system-modules
                            ,@%pyproject-build-system-modules)
       #:modules '(((guix build cargo-build-system) #:prefix cargo:)
@@ -787,12 +789,11 @@ the LZ4 frame format.")
     (build-system pyproject-build-system)
     (arguments
      (list #:test-backend #~'unittest))
-    (native-inputs
-     (list python-cramjam
-           python-setuptools))
+    (native-inputs (list python-setuptools))
     (inputs
      (list snappy))
-    (home-page "https://github.com/andrix/python-snappy")
+    (propagated-inputs (list python-cramjam))
+    (home-page "https://github.com/intake/python-snappy")
     (synopsis "Python bindings for the Snappy compression library")
     (description
      "@code{python-python-snappy} provides bindings to the Snappy library and

gnu/packages/python-science.scm

@@ -1278,6 +1278,52 @@ dependent on sampled parameters.  It assumes one has a Bayesian posterior
 conditional posterior @code{P(y|x,D,M)} in the @code{(x,y)} plane.")
     (license license:expat)))
 
+(define-public python-flox
+  (package
+    (name "python-flox")
+    (version "0.11.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/xarray-contrib/flox")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0jy1kxk9r0az39zmbmf6md55c35ldkk9q6pcfg8jb4chwi4i34iw"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "--ignore" "tests/test_asv.py" ; ignore benchmark test
+              ;; FIXME: Check why test_cohorts failed.
+              "--ignore" "tests/test_cohorts.py")))
+    (propagated-inputs (list python-numpy
+                             python-numpy-groupies
+                             python-packaging
+                             python-pandas
+                             python-scipy
+                             python-toolz))
+    (native-inputs (list ;; python-cubed ; TODO: package this
+                         python-dask
+                         python-netcdf4
+                         python-numbagg
+                         python-pytest
+                         python-pytest-snapshot
+                         python-pytest-xdist
+                         python-setuptools
+                         python-setuptools-scm
+                         python-sparse
+                         python-xarray))
+    (home-page "https://github.com/xarray-contrib/flox")
+    (synopsis "GroupBy operations for @code{dask.array}")
+    (description "@code{flox} mainly provides strategies for fast GroupBy
+reductions with @code{dask.array}.  It uses the MapReduce paradigm (or a
+\"tree reduction\") to run the GroupBy operation in a parallel-native way
+totally avoiding a sort or shuffle operation.  @code{flox} can use either
+@code{dask} or @code{cubed} as its backend.")
+    (license license:asl2.0)))
+
 (define-public python-formulaic
   (package
     (name "python-formulaic")
@@ -2134,6 +2180,35 @@ The supported distributions are:
 @end itemize")
     (license license:expat)))
 
+(define-public python-numbagg
+  (package
+    (name "python-numbagg")
+    (version "0.9.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/numbagg/numbagg")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1frx10rdyklp0zbd8bckl63i0vmj0z93nkx1i7dylbv99iw27215"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-numba python-numpy))
+    (native-inputs (list python-bottleneck
+                         python-pandas
+                         python-pytest
+                         python-pytest-benchmark ; runs by default
+                         python-setuptools
+                         python-setuptools-scm
+                         python-tabulate))
+    (home-page "https://github.com/numbagg/numbagg")
+    (synopsis "Fast N-dimensional aggregation functions with Numba")
+    (description "Numbagg provides high-performance implementations for moving
+window, aggregation, and grouping functions.  It leverages Numba's JIT
+compilation and is especially performant on multi-core parallelism.")
+    (license license:bsd-3)))
+
 (define-public python-numdifftools
   (package
     (name "python-numdifftools")
@@ -5905,7 +5980,8 @@ science including tools for accessing data sets in Python.")
                  (apply (assoc-ref cargo:%standard-phases phase)
                         #:cargo-target #$(cargo-triplet)
                         args))
-               '(unpack-rust-crates
+               '(prepare-rust-crates
+                 unpack-rust-crates
                  configure
                  check-for-pregenerated-files
                  patch-cargo-checksums)))))))

gnu/packages/qt.scm

@@ -5867,39 +5867,41 @@ color-related widgets.")
      (modify-inputs inputs
        (replace "qtbase" qtbase-5)))))
 
-;; TODO: Split shiboken2 binding generator into a dedicated output.
-;; This executable requires libxml2, libxslt, clang-toolchain at runtime.
-;; The libshiboken library only requires Qt and Python at runtime.
-(define-public python-shiboken-2
+(define-public python-shiboken-6
   (package
-    (name "python-shiboken-2")
-    (version "5.15.16")
+    (name "python-shiboken-6")
+    (version "6.9.2")
     (source (origin
               (method url-fetch)
-              (uri (string-append "mirror://qt/QtForPython/pyside2/PySide2-"
-                                  version "-src/pyside-setup-opensource-src-"
+              (uri (string-append "mirror://qt/QtForPython/pyside6/PySide6-"
+                                  version "-src/pyside-setup-everywhere-src-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0q3ky0fai3wr8kr1q82vdg5byhbn5sfdymmb554afpi72zyxcgkd"))))
+                "0b92b4zi5rqg5acgbb6yan349idvzmc0x8wjwkdwkga2ad38gh4y"))))
     (build-system cmake-build-system)
     (inputs
-     ;; pyside-2 fails with clang>=16, pyside-6 needs llvm>=14.
-     (list clang-toolchain-15
+     (list clang-toolchain-18
            libxml2
            libxslt
            python-wrapper
-           qtbase-5
-           qtxmlpatterns-5))
+           qtbase))
+    (properties `((upstream-name . "pyside-setup")))
     (arguments
      (list
       #:tests? #f
       ;; FIXME: Building tests fails
-      #:configure-flags #~(list "-DBUILD_TESTS=off")
+      #:configure-flags #~(list
+                           ;; The RUNPATH of shibokenmodule contains the entry
+                           ;; in build directory instead of install directory.
+                           "-DCMAKE_SKIP_RPATH=TRUE"
+                           (string-append "-DCMAKE_MODULE_LINKER_FLAGS=-Wl,-rpath="
+                                          #$output "/lib")
+                           "-DBUILD_TESTS=off")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'use-shiboken-dir-only
-            (lambda _ (chdir "sources/shiboken2")))
+            (lambda _ (chdir "sources/shiboken6")))
           (add-before 'configure 'make-files-writable-and-update-timestamps
             (lambda _
               ;; The build scripts need to modify some files in
@@ -5914,20 +5916,7 @@ color-related widgets.")
           (add-before 'configure 'set-build-env
             (lambda _
               (let ((llvm #$(this-package-input "clang-toolchain")))
-                (setenv "CLANG_INSTALL_DIR" llvm))))
-          (add-before 'configure 'workaround-importlib-error
-            (lambda _
-              ;; The following hack works around the error
-              ;;   "module 'importlib' has no attribute 'machinery'"
-              ;; when building python-pyside-2, which depends on
-              ;; this package.
-              (substitute* "libshiboken/embed/signature_bootstrap.py"
-                (("import importlib" all)
-                 (string-append
-                  all
-                  "\n        import importlib.machinery as imachi"))
-                (("importlib.machinery.ModuleSpec")
-                 "imachi.ModuleSpec")))))))
+                (setenv "CLANG_INSTALL_DIR" llvm)))))))
     (home-page "https://wiki.qt.io/Qt_for_Python")
     (synopsis
      "Shiboken generates bindings for C++ libraries using CPython source code")
@@ -5941,153 +5930,12 @@ color-related widgets.")
       license:lgpl3
       license:bsd-3))))
 
-(define-public python-shiboken-6
-  (package
-    (inherit python-shiboken-2)
-    (name "python-shiboken-6")
-    (version "6.9.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://qt/QtForPython/pyside6/PySide6-"
-                                  version "-src/pyside-setup-everywhere-src-"
-                                  version ".tar.xz"))
-              (sha256
-               (base32
-                "0b92b4zi5rqg5acgbb6yan349idvzmc0x8wjwkdwkga2ad38gh4y"))))
-    (build-system cmake-build-system)
-    (inputs
-     (modify-inputs inputs
-       (replace "qtbase" qtbase)
-       (delete "qtxmlpatterns")))
-    (arguments
-     (substitute-keyword-arguments arguments
-       ((#:phases p)
-        #~(modify-phases #$p
-            (delete 'workaround-importlib-error)
-            (replace 'use-shiboken-dir-only
-              (lambda _ (chdir "sources/shiboken6")))))
-       ((#:configure-flags flags)
-        #~(cons*
-           ;; The RUNPATH of shibokenmodule contains the entry in build
-           ;; directory instead of install directory.
-           "-DCMAKE_SKIP_RPATH=TRUE"
-           (string-append "-DCMAKE_MODULE_LINKER_FLAGS=-Wl,-rpath="
-                          #$output "/lib")
-           #$flags))))
-    (properties `((upstream-name . "pyside-setup")))))
-
-(define-public python-pyside-2
-  (package
-    (name "python-pyside-2")
-    (version (package-version python-shiboken-2))
-    (source (package-source python-shiboken-2))
-    (build-system cmake-build-system)
-    (inputs
-     (list qtbase-5
-           qtdatavis3d-5
-           qtdeclarative-5
-           qtlocation-5
-           qtmultimedia-5
-           qtquickcontrols-5
-           qtquickcontrols2-5
-           qtscript-5
-           qtscxml-5
-           qtsensors-5
-           qtspeech-5
-           qtsvg-5
-           qttools-5
-           qtwebchannel-5
-           qtwebengine-5
-           qtwebsockets-5
-           qtx11extras
-           qtxmlpatterns-5))
-    (propagated-inputs
-     (list python-shiboken-2))
-    (native-inputs
-     (list python-wrapper))
-    (arguments
-     (list
-      #:tests? #f
-      ;; FIXME: Building tests fail.
-      #:configure-flags
-      #~(list "-DBUILD_TESTS=FALSE"
-              (string-append "-DPYTHON_EXECUTABLE="
-                             (search-input-file %build-inputs
-                                                "/bin/python")))
-      #:modules '((guix build cmake-build-system)
-                  (guix build utils)
-                  (srfi srfi-1))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'go-to-source-dir
-            (lambda _ (chdir "sources/pyside2")))
-          (add-after 'go-to-source-dir 'fix-qt-module-detection
-            (lambda _
-              ;; Activate qt module support even if it not in the same
-              ;; directory as qtbase.
-              (substitute* "../cmake_helpers/helpers.cmake"
-                (("\\(\"\\$\\{found_basepath\\}\" GREATER \"0\"\\)")
-                 "true"))
-              ;; Add include directories for qt modules.
-              (let ((dirs (map (lambda (path)
-                                 (string-append path "/include/qt5"))
-                               (list
-                                #$@(map (lambda (name)
-                                          (this-package-input name))
-                                        '("qtdatavis3d"
-                                          "qtdeclarative"
-                                          "qtlocation"
-                                          "qtmultimedia"
-                                          "qtquickcontrols"
-                                          "qtquickcontrols2"
-                                          "qtscript"
-                                          "qtscxml"
-                                          "qtsensors"
-                                          "qtspeech"
-                                          "qtsvg"
-                                          "qttools"
-                                          "qtwebchannel"
-                                          "qtwebengine"
-                                          "qtwebsockets"
-                                          "qtx11extras"
-                                          "qtxmlpatterns"))))))
-                (substitute* "cmake/Macros/PySideModules.cmake"
-                  (("\\$\\{PATH_SEP\\}\\$\\{core_includes\\}" all)
-                   (fold (lambda (dir paths)
-                           (string-append paths "${PATH_SEP}" dir))
-                         all
-                         dirs)))
-                (setenv "CXXFLAGS" (fold (lambda (dir paths)
-                                           (string-append paths " -I" dir))
-                                         ""
-                                         dirs))))))))
-    (home-page "https://wiki.qt.io/Qt_for_Python")
-    (synopsis
-     "The Qt for Python product enables the use of Qt5 APIs in Python applications")
-    (description
-     "The Qt for Python product enables the use of Qt5 APIs in Python
-applications.  It lets Python developers utilize the full potential of Qt,
-using the PySide2 module.  The PySide2 module provides access to the
-individual Qt modules such as QtCore, QtGui,and so on.  Qt for Python also
-comes with the Shiboken2 CPython binding code generator, which can be used to
-generate Python bindings for your C or C++ code.")
-    (license (list
-              license:lgpl3
-              ;;They state that:
-              ;; this file may be used under the terms of the GNU General
-              ;; Public License version 2.0 or (at your option) the GNU
-              ;; General Public license version 3 or any later version
-              ;; approved by the KDE Free Qt Foundation.
-              ;; Thus, it is currently v2 or v3, but no "+".
-              license:gpl3
-              license:gpl2))))
-
 (define-public python-pyside-6
   (package
-    (inherit python-pyside-2)
     (name "python-pyside-6")
     (version (package-version python-shiboken-6))
     (source (package-source python-shiboken-6))
+    (build-system cmake-build-system)
     ;; TODO: Add more Qt components if available.
     (inputs
      (list qtbase
@@ -6148,6 +5996,7 @@ generate Python bindings for your C or C++ code.")
                                 (string-append "-I" dir))
                               dirs)
                          " "))))))))
+    (home-page "https://wiki.qt.io/Qt_for_Python")
     (synopsis
      "The Qt for Python product enables the use of Qt6 APIs in Python applications")
     (description
@@ -6156,7 +6005,17 @@ applications.  It lets Python developers utilize the full potential of Qt,
 using the PySide6 module.  The PySide6 module provides access to the
 individual Qt modules such as QtCore, QtGui,and so on.  Qt for Python also
 comes with the Shiboken6 CPython binding code generator, which can be used to
-generate Python bindings for your C or C++ code.")))
+generate Python bindings for your C or C++ code.")
+    (license (list
+              license:lgpl3
+              ;;They state that:
+              ;; this file may be used under the terms of the GNU General
+              ;; Public License version 2.0 or (at your option) the GNU
+              ;; General Public license version 3 or any later version
+              ;; approved by the KDE Free Qt Foundation.
+              ;; Thus, it is currently v2 or v3, but no "+".
+              license:gpl3
+              license:gpl2))))
 
 (define-public libqglviewer
   (package

gnu/packages/rdesktop.scm

@@ -223,7 +223,7 @@ of parts of the Windows API.")
 (define-public xrdp
   (package
     (name "xrdp")
-    (version "0.10.4.1")
+    (version "0.10.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -231,7 +231,7 @@ of parts of the Windows API.")
                     version "/xrdp-" version ".tar.gz"))
               (sha256
                (base32
-                "0pwg5zadd788nl2fpls60w3nm557a95ihp4x1ggf0yy5hqzdzsjj"))))
+                "08xikyk5ww9kq5w8jf7k1ij2l19xb783gxgkw901qjyyck8rdg4s"))))
     (build-system gnu-build-system)
     (inputs (list check
                   fuse

gnu/packages/ruby-xyz.scm

@@ -4768,10 +4768,17 @@ temporary files and directories during tests.")
                (base32
                 "0w1m432q3y5v9lkak8yyxadak3z17bsp6afni97i4zjdgfz7niz2"))))
     (build-system ruby-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; This avoids requiring extra dependencies in Rakefile.
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "ruby" "test/run-test.rb")))))))
     (propagated-inputs
      (list ruby-power-assert))
-    (native-inputs
-     (list bundler ruby-packnga ruby-yard))
     (synopsis "Unit testing framework for Ruby")
     (description "@code{Test::Unit} is unit testing framework for Ruby, based
 on xUnit principles.  These were originally designed by Kent Beck, creator of
@@ -4780,15 +4787,9 @@ It allows writing tests, checking results and automated testing in Ruby.")
     (home-page "https://test-unit.github.io/")
     (license (list license:psfl license:ruby))))
 
-(define-public ruby-test-unit/minimal
-  (hidden-package
-   (package
-     (inherit ruby-test-unit)
-     (arguments
-      (ensure-keyword-arguments
-       (package-arguments ruby-test-unit)
-       (list #:tests? #f)))
-     (native-inputs '()))))
+;; XXX: Deprecated on <2026-04-03>.
+(define-deprecated/public-alias ruby-test-unit/minimal
+  ruby-test-unit)
 
 (define-public ruby-test-unit-ruby-core
   (package
@@ -4940,7 +4941,7 @@ HTML, and PDF through LaTeX.")
                                  ,(package-version ruby-test-unit)
                                  "/lib\"")))))))))
     (native-inputs
-     (list bundler ruby-test-unit/minimal))
+     (list bundler ruby-test-unit))
     (synopsis "Ruby library adding metaclass method to all objects")
     (description
      "Metaclass is a Ruby library adding a @code{metaclass} method to all Ruby

gnu/packages/rust-apps.scm

@@ -10,7 +10,7 @@
 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.ccom>
-;;; Copyright © 2021, 2022, 2025 Zheng Junjie <z572@z572.online>
+;;; Copyright © 2021, 2022, 2025, 2026 Zheng Junjie <z572@z572.online>
 ;;; Copyright © 2021 Alexandru-Sergiu Marton <brown121407@posteo.ro>
 ;;; Copyright © 2021, 2023-2025 Maxim Cournoyer <maxim@guixotic.coop>
 ;;; Copyright © 2021, 2022 Petr Hodina <phodina@protonmail.com>
@@ -143,14 +143,14 @@
 (define-public aardvark-dns
   (package
     (name "aardvark-dns")
-    (version "1.14.0")
+    (version "1.17.0")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "aardvark-dns" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "1d2bs5lmijv6s3n71gqc986n1wy7ny9w74741njjix7932a7yd5f"))))
+        (base32 "1i7agi5ivg1399xy2cgcrz2hgg1bgfs68jwvdrxfz5856hc0gcrk"))))
     (build-system cargo-build-system)
     (arguments
      `(#:install-source? #f))
@@ -957,33 +957,36 @@ highlighting tool to ease code review from your terminal.")
 (define-public difftastic
   (package
     (name "difftastic")
-    (version "0.63.0")
+    (version "0.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "difftastic" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32
-         "0md332fch4b87akdvljzxp4m2k5yri7cpkz3n54jc762j7j9qmrz"))))
+        (base32 "012h76wx5jv6czc9j4awfan7vhrc6g5fdgnxrjmzg5q27wn99hn6"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:install-source? #f
-       #:cargo-test-flags
-       `("--release" "--"
-         "--skip=display::side_by_side::tests::test_display_hunks"
-         "--skip=display::style::tests::split_string_cjk"
-         "--skip=display::style::tests::split_string_cjk2"
-         "--skip=display::style::tests::split_string_simple"
-         "--skip=display::style::tests::split_string_unicode"
-         "--skip=display::style::tests::test_combining_char"
-         "--skip=display::style::tests::test_split_and_apply"
-         ,(string-append "--skip=display::style::tests::"
-                         "test_split_and_apply_gap_between_styles_on_wrap_boundary")
-         "--skip=display::style::tests::test_split_and_apply_trailing_text"
-         "--skip=display::style::tests::test_split_and_apply_trailing_text_newline")))
+     (list
+      #:install-source? #f
+      #:cargo-test-flags
+      '(list "--"
+             "--skip=display::side_by_side::tests::test_display_hunks"
+             "--skip=display::style")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; jemalloc needs unbundling for tikv-jemallocator-sys
+          (add-before 'build 'override-jemalloc
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((jemalloc (assoc-ref inputs "jemalloc")))
+                ;; This flag is needed when not using the bundled jemalloc.
+                ;; https://github.com/tikv/jemallocator/issues/19
+                (setenv
+                 "CARGO_FEATURE_UNPREFIXED_MALLOC_ON_SUPPORTED_PLATFORMS" "1")
+                (setenv "JEMALLOC_OVERRIDE"
+                        (string-append jemalloc "/lib/libjemalloc.so"))))))))
     (inputs
-     (cons mimalloc (cargo-inputs 'difftastic)))
+     (cons jemalloc (cargo-inputs 'difftastic)))
     (home-page "https://difftastic.wilfred.me.uk/")
     (synopsis "Structural diff command that understands syntax")
     (description
@@ -2306,6 +2309,37 @@ specified image or color, easing the process of theme creation.")
 @code{cffi} bindings as well as rust binaries as python packages.")
     (license (list license:expat license:asl2.0))))
 
+(define-public mdopen
+  (package
+    (name "mdopen")
+    (properties '((commit . "3858a4d2222ac789b168729ac1ae7b726342526e")))
+    (version (git-version "0.5.0" "0"
+                          (assoc-ref properties
+                                     'commit)))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/immanelg/mdopen")
+             (commit (assoc-ref properties
+                                'commit))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "024pv3wg6dg7yh8acpq3m0rrh046zfmcs940jivkjh8i9a5s2k3b"))))
+    (arguments
+     (list
+      #:install-source? #f
+      #:tests? #f)) ;tests are non-functional
+    (build-system cargo-build-system)
+    (inputs (cons* openssl oniguruma
+                   (cargo-inputs 'mdopen)))
+    (native-inputs (list pkg-config))
+    (home-page "https://github.com/immanelg/mdopen")
+    (synopsis "Markdown preview server")
+    (description "Quickly preview local markdown files in browser with
+GitHub-like look.")
+    (license license:gpl3+)))
+
 (define-public mitm-cache
   (package
     (name "mitm-cache")
@@ -4236,7 +4270,8 @@ Full featured offline client with caching support.")
                  (format #t "Running cargo phase: ~a~%" phase)
                  (apply (assoc-ref cargo:%standard-phases phase)
                         args))
-               '(unpack-rust-crates
+               '(prepare-rust-crates
+                 unpack-rust-crates
                  configure
                  check-for-pregenerated-files
                  patch-cargo-checksums))))
@@ -4318,7 +4353,7 @@ tools.")
 (define-public git-absorb
   (package
     (name "git-absorb")
-    (version "0.7.0")
+    (version "0.9.0")
     (source
      (origin
        ;; crates.io does not include the manual page.
@@ -4328,47 +4363,46 @@ tools.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1cqz9m5w7sh7pgfcirvdpv6i7l7nfaqbgs88zx0wr5sqg5wk2zky"))))
+        (base32 "1xr1bjia3sx2i7hw99r2s950xi4fa996bcg3n7j9arcjmrb7w14c"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:install-source? #f
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'install 'install-manual-page
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (man (string-append out "/share/man/man1")))
-               (with-directory-excursion "Documentation"
-                 (invoke "a2x"
-                         "--no-xmllint"
-                         "--doctype=manpage"
-                         "--format=manpage"
-                         "git-absorb.adoc"))
-               (install-file "Documentation/git-absorb.1" man))))
-         (add-after 'install 'install-completions
-           (lambda* (#:key native-inputs outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (share (string-append out "/share"))
-                    (git-absorb
-                      (if ,(%current-target-system)
-                          (search-input-file native-inputs "/bin/git-absorb")
-                          (string-append out "/bin/git-absorb"))))
-               (mkdir-p (string-append out "/etc/bash_completion.d"))
-               (with-output-to-file
-                 (string-append out "/etc/bash_completion.d/git-absorb")
-                 (lambda _ (invoke git-absorb "--gen-completions" "bash")))
-               (mkdir-p (string-append share "/fish/vendor_completions.d"))
-               (with-output-to-file
-                 (string-append share "/fish/vendor_completions.d/git-absorb.fish")
-                 (lambda _ (invoke git-absorb "--gen-completions" "fish")))
-               (mkdir-p (string-append share "/zsh/site-functions"))
-               (with-output-to-file
-                 (string-append share "/zsh/site-functions/_git-absorb")
-                 (lambda _ (invoke git-absorb "--gen-completions" "zsh")))
-               (mkdir-p (string-append share "/elvish/lib"))
-               (with-output-to-file
-                 (string-append share "/elvish/lib/git-absorb")
-                 (lambda _ (invoke git-absorb "--gen-completions" "elvish")))))))))
+     (list
+      #:install-source? #f
+      #:modules
+      '((guix build cargo-build-system)
+        (guix build utils)
+        (ice-9 match))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'install 'install-manual-page
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (man (string-append out "/share/man/man1")))
+                (with-directory-excursion "Documentation"
+                  (invoke "a2x"
+                          "--no-xmllint"
+                          "--doctype=manpage"
+                          "--format=manpage"
+                          "git-absorb.adoc"))
+                (install-file "Documentation/git-absorb.1" man))))
+          (add-after 'install 'install-completions
+            (lambda* (#:key native-inputs #:allow-other-keys)
+              (for-each
+               (match-lambda
+                 ((shell . path)
+                  (mkdir-p (in-vicinity #$output (dirname path)))
+                  (let ((binary
+                         (if #$(%current-target-system)
+                             (search-input-file native-inputs "bin/git-absorb")
+                             (in-vicinity #$output "bin/git-absorb"))))
+                    (with-output-to-file (in-vicinity #$output path)
+                      (lambda _
+                        (invoke binary "--gen-completions" shell))))))
+               '(("bash"    . "share/bash-completion/completions/git-absorb")
+                 ("elvish"  . "share/elvish/lib/git-absorb")
+                 ("fish"    . "share/fish/vendor_completions.d/git-absorb.fish")
+                 ("nushell" . "share/nushell/vendor/autoload/git-absorb")
+                 ("zsh"     . "share/zsh/site-functions/_git-absorb"))))))))
     (native-inputs
      (append
        (if (%current-target-system)

gnu/packages/scribus.scm

@@ -50,14 +50,14 @@
 (define-public scribus
   (package
     (name "scribus")
-    (version "1.6.4")
+    (version "1.6.5")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/scribus/scribus/"
                            version "/scribus-" version ".tar.gz"))
        (sha256
-        (base32 "1ddsga862wwq2lb12rlsm6009gfx9nxx3s5323jifs53fs1y3knp"))))
+        (base32 "1jj86a2xydkyqfdyhfikcxxl3m4j861mbbcswdd7779q11wysckq"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ;no test target

gnu/packages/statistics.scm

@@ -384,7 +384,7 @@ comparison and diagnostics.")
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "4.5.2")
+    (version "4.5.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -392,7 +392,7 @@ comparison and diagnostics.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "084z6yg4l09hqmwfpwii1645bqyflg8mxsg1cxycssgc0rqzyw8d"))))
+                "1wmqnm813lb58c0vwhjymnkfih3a6mq4cr9xa6n72wiw57a1wp5a"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -1781,60 +1781,6 @@ knowledge integration, designable W and H matrices and multiple forms of
 regularizations.")
       (license license:bsd-2))))
 
-(define-public r-swne
-  (let ((commit "05fc3ee4e09b2c34d99c69d3b97cece4c1c34143")
-        (revision "1"))
-    (package
-      (name "r-swne")
-      (version (git-version "0.6.20" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/yanwu2014/swne")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "0crlpg9kclbv4v8250p3086a3lk6f2hcq79psqkdylc1qnrx3kfx"))))
-      (properties `((upstream-name . "swne")))
-      (build-system r-build-system)
-      (propagated-inputs
-       (list r-fnn
-             r-ggplot2
-             r-ggrepel
-             r-hash
-             r-ica
-             r-igraph
-             r-irlba
-             r-jsonlite
-             r-rliger
-             r-mass
-             r-matrix
-             r-mgcv
-             r-nnlm ;not listed but required at install time
-             r-plyr
-             r-proxy
-             r-rcolorbrewer
-             r-rcpp
-             r-rcpparmadillo
-             r-rcppeigen
-             r-reshape
-             r-reshape2
-             r-snow
-             r-umap
-             r-usedist))
-      (home-page "https://github.com/yanwu2014/swne")
-      (synopsis "Visualize high dimensional datasets")
-      (description
-       "@dfn{Similarity Weighted Nonnegative Embedding} (SWNE) is a method for
-visualizing high dimensional datasets.  SWNE uses Nonnegative Matrix
-Factorization to decompose datasets into latent factors, projects those
-factors onto 2 dimensions, and embeds samples and key features in 2 dimensions
-relative to the factors.  SWNE can capture both the local and global dataset
-structure, and allows relevant features to be embedded directly onto the
-visualization, facilitating interpretation of the data.")
-      (license license:gpl2))))
-
 (define-public r-languageserver
   (let ((commit "004da9388f9b19990f031c8dc9b527fb406378ba")
         (revision "1"))

gnu/packages/syndication.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2019-2025 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2019-2026 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018, 2019, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020, 2023 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
@@ -144,14 +144,14 @@
 (define-public newsboat
   (package
     (name "newsboat")
-    (version "2.41")
+    (version "2.43")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://newsboat.org/releases/" version
                            "/newsboat-" version ".tar.xz"))
        (sha256
-        (base32 "194945xyacrkpwkd3246p50f8y59gw91kjrpp59z9ycrp7dbr61a"))))
+        (base32 "1x9pgmgk90rk9gin3hgy7799j5p69yzhsjc5kwn46k7slnw0fl9j"))))
     (build-system cargo-build-system)
     (native-inputs
      (append

gnu/packages/task-management.scm

@@ -353,7 +353,8 @@ to finish tasks, not organize them.")
                   (format #t "Running cargo phase: ~a~%" phase)
                   (apply (assoc-ref cargo:%standard-phases phase)
                          #:cargo-target #$(cargo-triplet) args))
-                '(unpack-rust-crates
+                '(prepare-rust-crates
+                  unpack-rust-crates
                   configure
                   check-for-pregenerated-files
                   patch-cargo-checksums)))))))

gnu/packages/terminals.scm

@@ -242,14 +242,14 @@ managers.")
 (define-public asciinema
   (package
     (name "asciinema")
-    (version "3.1.0")
+    (version "3.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "asciinema" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "19pszccw536g0ryd4z33ni1lx9a20hi47g9x4xwmg1v4plpr5szr"))))
+        (base32 "1p99rnhp62n50jmlmxlvs8w56si0lvcy505fb1mgxhn1a66i5rqw"))))
     (build-system cargo-build-system)
     (arguments
      (list

gnu/packages/version-control.scm

@@ -53,7 +53,7 @@
 ;;; Copyright © 2023 Steve George <steve@futurile.net>
 ;;; Copyright © 2023 Josselin Poiret <dev@jpoiret.xyz>
 ;;; Copyright © 2024 Hilton Chain <hako@ultrarare.space>
-;;; Copyright © 2023, 2024 Zheng Junjie <873216071@qq.com>
+;;; Copyright © 2023, 2024, 2026 Zheng Junjie <z572@z572.online>
 ;;; Copyright © 2023 Ryan Desfosses <rdesfo@sdf.org>
 ;;; Copyright © 2024 Suhail Singh <suhail@bayesians.ca>
 ;;; Copyright © 2024 Simon Tournier <zimon.toutoune@gmail.com>
@@ -839,6 +839,28 @@ everything from small to very large projects with speed and efficiency.")
         ((#:configure-flags flags #~'())
          (if (%current-target-system) git-cross-configure-flags #~(list)))))))
 
+(define-public mergiraf
+  (package
+    (name "mergiraf")
+    (version "0.16.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "mergiraf" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0b5rsdz1s68kc37rqvjwpgwj2651arigbzgcf7chdspzjc9fkllk"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:install-source? #f))
+    ;; for tests
+    (native-inputs (list git-minimal/pinned))
+    (inputs (cargo-inputs 'mergiraf))
+    (home-page "https://mergiraf.org/")
+    (synopsis "Syntax-aware merge driver for Git")
+    (description "This package provides a syntax-aware merge driver for Git.")
+    (license license:gpl3)))
+
 (define-public python-klaus
   (package
     (name "python-klaus")
@@ -1009,7 +1031,7 @@ desired format.")
 (define-public git-tools
   (package
     (name "git-tools")
-    (version "2022.12")
+    (version "2025.08")
     (source
      (origin
        (method git-fetch)
@@ -1018,7 +1040,7 @@ desired format.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0s8x74ggcr6nqzplr0jfzp3cavq0nmdm35hqywzs2bbq75i1mijd"))))
+        (base32 "1djc40yzyrh4xhj1c717j7sqyhgwapz9mvsn9ja4yph3jxx6zs0f"))))
     (build-system copy-build-system)
     (arguments
      `(#:install-plan '(("git-branches-rename" "bin/git-branches-rename")

gnu/packages/video.scm

@@ -6899,6 +6899,14 @@ can also directly record to WebM or MP4 if you prefer.")
      (list
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-entry-points
+            (lambda _
+              (substitute* "setup.py"
+                ;; main.py is in a "mps_youtube" and not in
+                ;; "mps_youtube/main", see:
+                ;; <https://github.com/mps-youtube/yewtube/pull/1334>.
+                (("yt = mps_youtube:main.main")
+                 "yt = mps_youtube.main:main"))))
           (add-after 'unpack 'relax-requirements
             (lambda _
               (substitute* "mps_youtube/__init__.py"

gnu/packages/vim.scm

@@ -16,6 +16,7 @@
 ;;; Copyright © 2023 Charles Jackson <charles.b.jackson@protonmail.com>
 ;;; Copyright © 2023 Foundation Devices, Inc. <hello@foundationdevices.com>
 ;;; Copyright © 2023, 2024 Nguyễn Gia Phong <cnx@loang.net>
+;;; Copyright © 2025, 2026 Herman Rimm <herman@rimm.ee>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -93,102 +94,104 @@
   (package
     (name "vim")
     (version "9.2.0232")
-    (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                    (url "https://github.com/vim/vim")
-                    (commit (string-append "v" version))))
-             (file-name (git-file-name name version))
-             (sha256
-              (base32
-               "0z5b77qq5rmddf42f8sqd4sbf81y1r8d9i9f0naczb9bz762wx0r"))))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/vim/vim")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0z5b77qq5rmddf42f8sqd4sbf81y1r8d9i9f0naczb9bz762wx0r"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:test-target "test"
+     (list
+       #:test-target "test"
        #:parallel-tests? #f
+       #:configure-flags
+       #~(list (string-append "STRIP=" #$(strip-for-target)))
        #:phases
-       (modify-phases %standard-phases
-         (add-after 'configure 'patch-absolute-paths
-           (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* '("src/testdir/Makefile"
-                            "src/testdir/test_channel.vim"
-                            "src/testdir/test_filetype.vim"
-                            "src/testdir/test_normal.vim"
-                            "src/testdir/test_plugin_matchparen.vim"
-                            "src/testdir/test_popupwin.vim"
-                            "src/testdir/test_prompt_buffer.vim"
-                            "src/testdir/test_shell.vim"
-                            "src/testdir/test_suspend.vim"
-                            "src/testdir/test_terminal.vim"
-                            "src/testdir/test_terminal2.vim")
-               (("/bin/sh") (which "sh")))
-             (substitute* "src/testdir/test_autocmd.vim"
-               (("/bin/kill") (which "kill")))
-             (substitute* '("runtime/syntax/sh.vim"
-                            "src/if_cscope.c")
-               (("/bin/sh") (search-input-file inputs "/bin/sh")))))
-         (add-before 'check 'set-environment-variables
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; One of the tests tests timezone-dependent functions.
-             (setenv "TZDIR"
-                     (search-input-directory inputs "share/zoneinfo"))
+       #~(modify-phases %standard-phases
+           (add-after 'configure 'patch-absolute-paths
+             (lambda _
+               (with-directory-excursion "src/testdir"
+                 (substitute* '("Makefile"
+                                "test_channel.vim"
+                                "test_filetype.vim"
+                                "test_normal.vim"
+                                "test_plugin_matchparen.vim"
+                                "test_popupwin.vim"
+                                "test_prompt_buffer.vim"
+                                "test_shell.vim"
+                                "test_suspend.vim"
+                                "test_terminal.vim"
+                                "test_terminal2.vim")
+                   (("/bin/sh") (which "sh")))
+                 (substitute* "test_autocmd.vim"
+                   (("/bin/kill") (which "kill"))))
+               (substitute* '("runtime/syntax/sh.vim" "src/if_cscope.c")
+                 (("/bin/sh" all)
+                  (string-append #$(this-package-input "tcsh") all)))))
+           (add-before 'check 'skip-or-fix-failing-tests
+             (lambda _
+               ;; One of the tests tests timezone-dependent functions.
+               (setenv "TZDIR"
+                       #$(file-append (this-package-native-input "tzdata")
+                                      "/share/zoneinfo"))
 
-             ;; Make sure the TERM environment variable is set for the tests.
-             (setenv "TERM" "xterm")))
-         (add-before 'check 'skip-or-fix-failing-tests
-           (lambda _
-             ;; These tests try to download from the internet.
-             (setenv "TEST_SKIP_PAT"
-                     "Test_glvs_default")
+               ;; Make sure the TERM environment variable is set for the tests.
+               (setenv "TERM" "xterm")
 
-             ;; Ignore failure of some flaky tests.
-             (setenv "TEST_MAY_FAIL"
-                     (string-join
-                       (list "Test_write_backup_symlink"
-                             ;; These tests compare the output of commands and
-                             ;; expect to run on a FHS-compliant system.
-                             "Test_echo_verbose_system"
-                             "Test_matchparen_ignore_sh_case"
-                             "Test_popup_drag_termwin"
-                             "Test_combining_double_width"
-                             "Test_open_term_from_cmd"
-                             "Test_terminal_postponed_scrollback")
-                       ","))
+               ;; These tests try to download from the internet.
+               (setenv "TEST_SKIP_PAT" "Test_glvs_default")
 
-             ;; These depend on full bash.
-             (with-directory-excursion "runtime/syntax/testdir/input"
-               (for-each delete-file
-                         (list "sh_10.sh"
-                               "sh_11.sh"
-                               "sh_12.sh"
-                               "sh_14.sh"
-                               "sh_15.sh"
-                               "sh_bash.bash"
-                               "sh_bash_alias.sh"
-                               "sh_sundrous.bash")))))
-         (add-before 'install 'fix-installman.sh
-           (lambda _
-             (substitute* "src/installman.sh"
-               (("/bin/sh")
-                (which "sh")))))
-         (add-after 'install 'install-guix.vim
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((vimdir (string-append (assoc-ref outputs "out") "/share/vim")))
-               (mkdir-p vimdir)
-               (copy-file (assoc-ref inputs "guix.vim")
-                          (string-append vimdir "/vimrc"))))))))
+               ;; Ignore failure of some flaky tests.
+               (setenv "TEST_MAY_FAIL"
+                       (string-join
+                         '("Test_write_backup_symlink"
+                           ;; These tests compare the output of commands and
+                           ;; expect to run on a FHS-compliant system.
+                           "Test_echo_verbose_system"
+                           "Test_matchparen_ignore_sh_case"
+                           "Test_popup_drag_termwin"
+                           "Test_combining_double_width"
+                           "Test_open_term_from_cmd"
+                           "Test_terminal_postponed_scrollback")
+                         ","))
+
+               ;; These depend on full bash.
+               (with-directory-excursion "runtime/syntax/testdir/input"
+                 (for-each delete-file
+                           '("sh_10.sh"
+                             "sh_11.sh"
+                             "sh_12.sh"
+                             "sh_14.sh"
+                             "sh_15.sh"
+                             "sh_bash.bash"
+                             "sh_bash_alias.sh"
+                             "sh_sundrous.bash")))))
+           (add-before 'install 'fix-installman.sh
+             (lambda _
+               (substitute* "src/installman.sh"
+                 (("/bin/sh") (which "sh")))))
+           (add-after 'install 'install-guix.vim
+             (lambda _
+               (let ((vimdir (string-append #$output "/share/vim")))
+                 (mkdir-p vimdir)
+                 (copy-file #$(this-package-native-input "guix.vim")
+                            (string-append vimdir "/vimrc"))))))))
     (inputs
      (list gawk ncurses perl tcsh))                 ; For runtime/tools/vim32
     (native-inputs
      `(("libtool" ,libtool)
-       ("guix.vim" ,(search-auxiliary-file "guix.vim"))
+       ("guix.vim" ,(local-file (search-auxiliary-file "guix.vim")))
 
        ;; For tests.
        ("tzdata" ,tzdata-for-tests)))
     (home-page "https://www.vim.org/")
     (synopsis "Text editor based on vi")
-    ;; The description shares language with the vim-full package. When making
-    ;; changes, check if the other description also needs to be updated.
+    ;; This description is a subset of the vim-full package description.
+    ;; When making changes, update the other description as well.
     (description
      "Vim is a highly configurable text editor built to enable efficient text
 editing.  It is an improved version of the vi editor distributed with most UNIX
@@ -214,13 +217,13 @@ configuration files.")
              (lambda _
                (chdir "src/xxd")))
            (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (install-file "xxd" bin)))))))
+             (lambda _
+               (install-file "xxd" (string-append #$output "/bin")))))))
     (inputs `())
     (native-inputs `())
     (synopsis "Hexdump utility from vim")
-    (description "This package provides the Hexdump utility xxd that comes
+    (description
+     "This package provides the Hexdump utility xxd that comes
 with the editor vim.")))
 
 (define-public vim-full
@@ -228,71 +231,73 @@ with the editor vim.")))
     (inherit vim)
     (name "vim-full")
     (arguments
-     `(#:configure-flags
-       (list (string-append "--with-lua-prefix="
-                            (assoc-ref %build-inputs "lua"))
-             "--with-features=huge"
-             "--enable-python3interp=yes"
-             "--enable-perlinterp=yes"
-             "--enable-rubyinterp=yes"
-             "--enable-tclinterp=yes"
-             "--enable-luainterp=yes"
-             "--enable-cscope"
-             "--enable-sniff"
-             "--enable-multibyte"
-             "--enable-xim"
-             "--disable-selinux"
-             "--enable-gui")
-       ,@(substitute-keyword-arguments arguments
-           ((#:phases phases)
-            `(modify-phases ,phases
-               (add-before 'check 'skip-some-more-tests
-                 (lambda _
-                   ;; Fontconfig can't figure out its cache directory
-                   (substitute* "src/testdir/test_startup.vim"
-                     ((".*Test_progname.*" line)
-                      (string-append line "return\n")))))
-               (add-before 'check 'start-xserver
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   ;; Some tests require an X server, but does not start one.
-                   (let ((xorg-server (assoc-ref inputs "xorg-server"))
-                         (display ":1"))
-                     (setenv "DISPLAY" display)
-                     (zero? (system (string-append xorg-server "/bin/Xvfb "
-                                                    display " &")))))))))))
+     (cons*
+       #:configure-flags
+       #~(list (string-append "--with-lua-prefix="
+                              #$(this-package-input "lua"))
+               "--with-features=huge"
+               "--enable-python3interp=yes"
+               "--enable-perlinterp=yes"
+               "--enable-rubyinterp=yes"
+               "--enable-tclinterp=yes"
+               "--enable-luainterp=yes"
+               "--enable-cscope"
+               "--enable-sniff"
+               "--enable-multibyte"
+               "--enable-xim"
+               "--disable-selinux"
+               "--enable-gui")
+       (substitute-keyword-arguments arguments
+         ((#:phases phases)
+          #~(modify-phases #$phases
+              (add-before 'check 'skip-some-more-tests
+                (lambda _
+                  ;; Fontconfig can't figure out its cache directory.
+                  (substitute* "src/testdir/test_startup.vim"
+                    ((".*Test_progname.*" line)
+                     (string-append line "return\n")))))
+              ;; Some tests require an X server, but do not start one.
+              (add-before 'check 'start-xserver
+                (lambda _
+                  (setenv "DISPLAY" ":1")
+                  (zero? (system #$(file-append
+                                     (this-package-native-input
+                                       "xorg-server")
+                                     "/bin/Xvfb :1 &"))))))))))
     (native-inputs
      (modify-inputs native-inputs
        (prepend pkg-config xorg-server-for-tests)))
     (inputs
-     `(("acl" ,acl)
-       ("at-spi2-core" ,at-spi2-core)
-       ("attr" ,attr)
-       ("cairo" ,cairo)
-       ("fontconfig" ,fontconfig)
-       ("freetype" ,freetype)
-       ("gdk-pixbuf" ,gdk-pixbuf)
-       ("gettext" ,gettext-minimal)
-       ("glib" ,glib)
-       ("gpm" ,gpm)
-       ("gtk" ,gtk+-2)
-       ("harfbuzz" ,harfbuzz)
-       ("libice" ,libice)
-       ("libpng" ,libpng)
-       ("libsm" ,libsm)
-       ("libx11" ,libx11)
-       ("libxdmcp" ,libxdmcp)
-       ("libxt" ,libxt)
-       ("libxpm" ,libxpm)
-       ("lua" ,lua)
-       ("pango" ,pango)
-       ("pixman" ,pixman)
-       ("python-3" ,python)
-       ("ruby" ,ruby)
-       ("tcl" ,tcl)
-       ,@(package-inputs vim)))
-    ;; The description shares language with the vim package. When making
-    ;; changes, check if the other description also needs to be updated.
-    (description "Vim is a highly configurable text editor built to enable efficient text
+     (modify-inputs inputs
+       (append acl
+               at-spi2-core
+               attr
+               cairo
+               fontconfig
+               freetype
+               gdk-pixbuf
+               gettext-minimal
+               glib
+               gpm
+               gtk+-2
+               harfbuzz
+               libice
+               libpng
+               libsm
+               libx11
+               libxdmcp
+               libxt
+               libxpm
+               lua
+               pango
+               pixman
+               python
+               ruby
+               tcl)))
+    ;; This description shares all but the last paragraph with the vim
+    ;; package description.  When changing one, also update the other.
+    (description
+     "Vim is a highly configurable text editor built to enable efficient text
 editing.  It is an improved version of the vi editor distributed with most UNIX
 systems.
 

gnu/packages/vpn.scm

@@ -936,17 +936,16 @@ packages.")
 (define-public python-proton-vpn-api-core
   (package
     (name "python-proton-vpn-api-core")
-    (version "4.14.1")
-    (home-page "https://github.com/ProtonVPN/python-proton-vpn-api-core")
+    (version "4.18.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-              (url home-page)
+              (url "https://github.com/ProtonVPN/python-proton-vpn-api-core")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0s7qasxiwd924dps1696vlnxr7626li5c31kv2kb3c4sqk6s6867"))))
+        (base32 "0hlcgickj0ji25m3szrpb44363nvd859jr0853aqbj8yd74148vp"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -976,6 +975,7 @@ packages.")
            python-pygobject
            python-pycairo
            python-jinja2))
+    (home-page "https://github.com/ProtonVPN/python-proton-vpn-api-core")
     (synopsis "Core logic used by the other Proton VPN components")
     (description
      "This package is a core library used by other @code{python-proton-vpn-}
@@ -1105,7 +1105,7 @@ LocalAgent, server, and python-bindings for that crate.")
 (define-public proton-vpn-cli
   (package
     (name "proton-vpn-cli")
-    (version "0.1.5")
+    (version "0.1.9")
     (source
      (origin
        (method git-fetch)
@@ -1114,7 +1114,7 @@ LocalAgent, server, and python-bindings for that crate.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "076aixjwzpggwrgsrjg3z78qcv79cmqfzlpbll1c4mz94bs1gdvs"))))
+        (base32 "0fgib70x0l6hkbidb9qak0sc7158l9rqzmwmrmk0cmxqrknvvxxf"))))
     (build-system pyproject-build-system)
     (arguments
      (list

gnu/packages/web.scm

@@ -7219,29 +7219,33 @@ multicore machines.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "http://www.nocrew.org/software/httptunnel/"
+       ;; git repository has no tags, so difficult to figure out which commit
+       ;; corresponds to which version.
+       (uri (string-append "https://www.nocrew.org/software/httptunnel/"
                            name "-" version ".tar.gz"))
        (sha256
         (base32
          "0mn5s6p68n32xzadz6ds5i6bp44dyxzkq68r1yljlv470jr84bql"))
        (modules '((guix build utils)))
-       (snippet '(begin
-                   ;; Remove non-free IETF RFC documentation.
-                   (delete-file-recursively "doc")
-                   #t))))
+       ;; Remove non-free IETF RFC documentation.
+       (snippet #~(delete-file-recursively "doc"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; The default configure phase tries to pass environment variables as
-         ;; command-line arguments, which confuses the ./configure script.
-         (replace 'configure
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out")))
-               (setenv "CONFIG_SHELL" (which "bash"))
-               (invoke "./configure"
-                       (string-append "--prefix=" out))))))))
-    (home-page "http://www.nocrew.org/software/httptunnel.html")
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; The default configure phase tries to pass environment variables as
+          ;; command-line arguments, which confuses the ./configure script.
+          (replace 'configure
+            (lambda _
+                (setenv "CONFIG_SHELL" (which "bash"))
+                (setenv "CFLAGS" (string-append
+                                  "-O2 -g "
+                                  "-Wno-error=implicit-int "
+                                  "-Wno-error=implicit-function-declaration"))
+                (invoke "./configure"
+                        (string-append "--prefix=" #$output)))))))
+    (home-page "https://www.nocrew.org/software/httptunnel.html")
     (synopsis "Tunnel data connections through HTTP requests")
     (description "httptunnel creates a bidirectional virtual data connection
 tunnelled through HTTP (HyperText Transfer Protocol) requests.  This can be

gnu/packages/wm.scm

@@ -518,7 +518,7 @@ loginctl commands (lock/unlock/before-sleep) and inhibit.")
 (define-public hyprland
   (package
     (name "hyprland")
-    (version "0.54.2")
+    (version "0.54.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/hyprwm/Hyprland"
@@ -535,7 +535,7 @@ loginctl commands (lock/unlock/before-sleep) and inhibit.")
                               "subprojects"))))
               (sha256
                (base32
-                "06zxx8i92n5pyyl472s3kbb6m7czg72klh6cs80jz6yhdbw9qgbj"))))
+                "1vk39k04x210zdlrszs465cwkbf6j3b3ddldk9gzffpjls8s281w"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f                  ;No tests.
@@ -2754,6 +2754,7 @@ XDG-Output for wlclock to work.")
            wayland
            wayland-protocols
            xcb-util-errors
+           xcb-util-renderutil
            xcb-util-wm
            xorg-server-xwayland))
     (native-inputs
@@ -4491,7 +4492,7 @@ Well-tested and fuzzed.
 (define-public libucl
   (package
     (name "libucl")
-    (version "0.8.2")
+    (version "0.9.4")
     (source
      (origin
        (method git-fetch)
@@ -4500,12 +4501,10 @@ Well-tested and fuzzed.
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1j8npymjhcnzbwhx1wggr88148cga921438flf1sn7mw1b9dr55f"))))
+        (base32 "149iapbqa8xwcwx27q4ydi71bjdwvbnxmkwkxs9sz6saafs539cv"))))
     (native-inputs
-     (list autoconf automake pkg-config libtool))
+     (list autoconf-2.72 automake pkg-config libtool))
     (build-system gnu-build-system)
-    (arguments
-     `(#:tests? #f)) ;; no tests
     (home-page "https://github.com/vstakhov/libucl")
     (synopsis "Universal configuration language (UCL) parser")
      (description "libucl implements a configuration language that is easy to

gnu/packages/xdisorg.scm

@@ -74,6 +74,7 @@
 ;;; Copyright © 2025 iamawacko <iamawacko@protonmail.com>
 ;;; Copyright © 2025 dan <i@dan.games>
 ;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
+;;; Copyright © 2025 Untrusem <mysticmoksh@riseup.net>
 ;;; Copyright © 2026 VnPower <vnpower@loang.net>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -145,6 +146,7 @@
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
+  #:use-module (gnu packages image-processing)
   #:use-module (gnu packages kde-frameworks)
   #:use-module (gnu packages kde-utils)
   #:use-module (gnu packages libbsd)
@@ -3308,6 +3310,36 @@ Wayland.")
 helper scripts for @code{xclip} and @code{xsel} to assist with the transition.")
     (license license:gpl3+)))
 
+(define-public wl-kbptr
+  (package
+    (name "wl-kbptr")
+    (version "0.4.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/moverest/wl-kbptr")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0fqgv4fbr7asf9chjk4wwbmqjgr6i8diac08vag122h934ph4hb7"))))
+    (build-system meson-build-system)
+    (arguments (list #:configure-flags #~'("-Dopencv=enabled")))
+    (native-inputs (list pkg-config))
+    (inputs (list gtk
+                  libxkbcommon
+                  opencv
+                  pixman
+                  wayland
+                  wayland-protocols))
+    (home-page "https://github.com/moverest/wl-kbptr")
+    (synopsis "Control the mouse pointer with the keyboard on Wayland")
+    (description
+     "This package provides a utility called @code{wl-kbptr} short for
+Wayland Keyboard Pointer, to help move the mouse pointer with the
+keyboard on Wayland.")
+    (license license:gpl3+)))
+
 (define-public autocutsel
   (package
     (name "autocutsel")

gnu/packages/zwave.scm

@@ -116,7 +116,7 @@ knowledge of the Z-Wave protocol.")
            (lambda _
              (substitute* "binding.gyp"
                (("std=c\\+\\+11")
-                "std=c++17"))))
+                "std=c++20"))))
          (replace 'build
            ;; For some reason, `npm install` doesn't build
            ;; the addon automatically, so we do it explicitly here.

gnu/services/admin.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
-;;; Copyright © 2016-2025 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016-2026 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2023 Giacomo Leidi <therewasa@fishinthecalculator.me>
 ;;; Copyright © 2024 Gabriel Wicki <gabriel@erlikon.ch>
@@ -380,6 +380,31 @@ terms of CPU and input/output.")
             "G-exp denoting the channels to use when updating the database
 (@pxref{Channels})."))
 
+(define %package-database-file
+  ;; System-wide package database used by 'guix locate'.
+  ;; See 'system-database-file' in (guix scripts locate).
+  "/var/cache/guix/locate/db.sqlite")
+
+(define %package-database-accounts
+  (list (user-account
+          (name "guix-locate")
+          (group "guix-locate")
+          (system? #t)
+          (comment "Account running 'guix locate'")
+          (home-directory "/var/run/guix-locate"))
+        (user-group
+          (name "guix-locate")
+          (system? #t))))
+
+(define %package-database-activation
+  ;; Create the package database directory at activation time.  Make it
+  ;; writable by 'guix-locate' and world-readable.
+  #~(begin
+      (use-modules (guix build utils))
+      (let ((directory #$(dirname %package-database-file))
+            (owner (getpwnam "guix-locate")))
+        (mkdir-p/perms directory owner #o755))))
+
 (define (package-database-shepherd-services configuration)
   (match-record configuration <package-database-configuration>
     (package schedule method channels)
@@ -388,8 +413,6 @@ terms of CPU and input/output.")
              (provision '(package-database-update))
              (requirement '(user-processes guix-daemon))
              (modules '((shepherd service timer)))
-             ;; XXX: The whole thing's running as "root" just because it needs
-             ;; write access to /var/cache/guix/locate.
              (start #~(make-timer-constructor
                        #$(if (string? schedule)
                              #~(cron-string->calendar-event #$schedule)
@@ -397,8 +420,13 @@ terms of CPU and input/output.")
                        (command '(#$(file-append package "/bin/guix")
                                   "time-machine" "-C" #$channels
                                   "--" "locate" "--update"
+                                  #$(string-append "--database="
+                                                   %package-database-file)
                                   #$(string-append
-                                     "--method=" (symbol->string method))))
+                                     "--method=" (symbol->string method)))
+                                #:user "guix-locate"
+                                #:group "guix-locate")
+                       #:log-file "/var/log/guix-locate.log"
                        #:wait-for-termination? #t))
              (stop #~(make-timer-destructor))
              (documentation
@@ -410,7 +438,11 @@ be queried by the 'guix locate' command.")
   (service-type
    (name 'package-database)
    (extensions (list (service-extension shepherd-root-service-type
-                                        package-database-shepherd-services)))
+                                        package-database-shepherd-services)
+                     (service-extension activation-service-type
+                                        (const %package-database-activation))
+                     (service-extension account-service-type
+                                        (const %package-database-accounts))))
    (description
     "Periodically update the package database used by the @code{guix locate} command,
 which lets you search for packages that provide a given file.")

gnu/services/desktop.scm

@@ -22,6 +22,7 @@
 ;;; Copyright © 2025 Jonathan Brielmaier <jonathan.brielmaier@web.de>
 ;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez@gmail.com>
 ;;; Copyright © 2025 dan <i@dan.games>
+;;; Copyright © 2026 Noé Lopez <noelopez@free.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -143,6 +144,9 @@
             elogind-service  ; deprecated
             elogind-service-type
 
+            gardenhostd-configuration
+            gardenhostd-service-type
+
             %gdm-file-system
             gdm-file-system-service
 
@@ -1641,6 +1645,33 @@ types (graphical, console, remote, etc.).  It can also clean up after users
 when they log out."
   (service elogind-service-type config))
 
+
+;;;
+;;; Gardenhostd.
+;;;
+
+(define-configuration/no-serialization gardenhostd-configuration
+  (gardenhostd
+   (package gardenhostd)
+   "The gardenhostd package to use."))
+
+(define (gardenhostd-profile config)
+  (list (gardenhostd-configuration-gardenhostd config)))
+
+(define gardenhostd-service-type
+  (service-type
+   (name 'gardenhostd)
+   (extensions
+    (list
+     (service-extension dbus-root-service-type gardenhostd-profile)
+     (service-extension polkit-service-type gardenhostd-profile)))
+   (default-value (gardenhostd-configuration))
+   (description "This service provides gardenhostd, a partial
+implementation of the systemd-hostnamed daemon.  It provides the
+org.freedesktop.hostname1 D-Bus interface, which helps applications
+like gnome-control-center retrieve and modify the system’s hostname,
+as well as set a pretty hostname for display.")))
+
 
 ;;;
 ;;; Fontconfig and other desktop file-systems.

gnu/services/vpn.scm

@@ -92,6 +92,8 @@
             wireguard-configuration-table
             wireguard-configuration-auto-start?
 
+            wireguard-configuration-file
+
             wireguard-service-type))
 
 ;;;

gnu/services/web.scm

@@ -1501,7 +1501,7 @@ a webserver.")
 
 (define* (cat-avatar-generator-service
           #:key
-          (cache-dir "/var/cache/cat-avatar-generator")
+          (cache-dir "/var/cache/cat-avatar-generator/")
           (package cat-avatar-generator)
           (configuration (nginx-server-configuration)))
   (simple-service

gnu/system/linux-initrd.scm

@@ -154,7 +154,11 @@ MODULES and taken from LINUX."
                  '())))
 
             (define modules-to-lookup
-              (lset-difference string=? '#$modules builtin-modules))
+              (remove (lambda (module)
+                        (member (normalize-module-name module)
+                                ;; Normalized by `file-name->module-name'.
+                                builtin-modules))
+                      '#$modules))
 
             (define modules
               (let* ((lookup  (cut find-module-file module-dir <>))

guix/build-system/node.scm

@@ -30,10 +30,16 @@
   #:use-module (guix search-paths)
   #:use-module (guix build-system)
   #:use-module (guix build-system gnu)
-  #:export (%node-build-system-modules
+  #:export (%default-lockfiles
+            %node-build-system-modules
             node-build
             node-build-system))
 
+(define %default-lockfiles
+  (list "package-lock.json"
+        "yarn.lock"
+        "npm-shrinkwrap.json"))
+
 (define %node-build-system-modules
   ;; Build-side modules imported by default.
   `((guix build node-build-system)
@@ -47,6 +53,10 @@
   "Return the default Node package, resolved lazily."
   (@* (gnu packages node) node-lts))
 
+(define (default-guile-json)
+  "Return the default guile-json package, resolved lazily."
+  (@* (gnu packages guile) guile-json-4))
+
 (define* (lower name
                 #:key source inputs native-inputs outputs system target
                 (node (default-node))
@@ -78,17 +88,12 @@
          (build node-build)
          (arguments (strip-keyword-arguments private-keywords arguments)))))
 
-(define (default-guile-json)
-  "Return the default guile-json package."
-  ;; Lazily resolve the binding to avoid a circular dependency.
-  (let ((mod (resolve-interface '(gnu packages guile))))
-    (module-ref mod 'guile-json-4)))
-
 (define* (node-build name inputs
                      #:key
                      source
                      (npm-flags ''())
                      (test-target "test")
+                     (lockfiles %default-lockfiles)
                      (tests? #t)
                      (phases '%standard-phases)
                      (outputs '("out"))
@@ -110,6 +115,7 @@
                         #:system #$system
                         #:npm-flags #$npm-flags
                         #:test-target #$test-target
+                        #:lockfiles '#$lockfiles
                         #:tests? #$tests?
                         #:phases #$phases
                         #:outputs #$(outputs->gexp outputs)

guix/build-system/r.scm

@@ -110,7 +110,7 @@ release corresponding to NAME and VERSION."
                   (tests? #t)
                   (test-target "tests")
                   (test-types #f)
-                  test-directory
+                  (test-directory "tests/testthat")
                   skipped-tests
                   (configure-flags ''())
                   (phases '%standard-phases)

guix/build-system/tree-sitter.scm

@@ -105,6 +105,7 @@
                             source
                             (phases '%standard-phases)
                             (grammar-directories '("."))
+                            (lockfiles %default-lockfiles)
                             (tests? #t)
                             (outputs '("out" "js"))
                             (search-paths '())
@@ -123,6 +124,7 @@
                                #:source #+source
                                #:system #$system
                                #:phases #$phases
+                               #:lockfiles '#$lockfiles
                                #:tests? #$tests?
                                #:grammar-directories '#$grammar-directories
                                #:outputs #$(outputs->gexp outputs)
@@ -145,6 +147,7 @@
                                   guile source
                                   (phases '%standard-phases)
                                   (grammar-directories '("."))
+                                  (lockfiles %default-lockfiles)
                                   (tests? #t)
                                   (outputs '("out" "js"))
                                   (search-paths '())
@@ -179,6 +182,7 @@
                                #:build #$build
                                #:target #$target
                                #:phases #$phases
+                               #:lockfiles '#$lockfiles
                                #:tests? #$tests?
                                #:grammar-directories '#$grammar-directories
                                #:outputs #$(outputs->gexp outputs)