gnu: libsigsegv: Update to 2.15.

* gnu/packages/libsigsegv.scm (libsigsegv): Update to 2.15.

Change-Id: Ie0bc45e925bfc41d5fe0a9d05d854fdfcd8ae50b
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

.dir-locals.el

@@ -141,7 +141,6 @@
    (eval . (put 'substitute* 'scheme-indent-function 1))
    (eval . (put 'match-record 'scheme-indent-function 3))
    (eval . (put 'match-record-lambda 'scheme-indent-function 2))
-   (eval . (put 'with-fluids 'scheme-indent-function 2))
 
    ;; TODO: Contribute these to Emacs' scheme-mode.
    (eval . (put 'let-keywords 'scheme-indent-function 3))

.forgejo/pull_request_template.md

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

.guix-authorizations

@@ -23,8 +23,6 @@
    (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

@@ -239,7 +239,6 @@ tests/guix-home\.sh                                @guix/home
 tests/home-import\.scm                             @guix/home
 tests/home-services\.scm                           @guix/home
 
-gnu/packages/fabric-management\.scm                @guix/hpc
 gnu/packages/mpi\.scm                              @guix/hpc
 gnu/packages/oneapi\.scm                           @guix/hpc
 gnu/packages/opencl\.scm                           @guix/hpc
@@ -348,6 +347,7 @@ 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

Makefile.am

@@ -802,17 +802,17 @@ EXTRA_DIST +=						\
   etc/manifests/upgrade.scm				\
   scripts/guix.in					\
   tests/cve-sample.json					\
-  tests/keys/openpgp/civodul.pub			\
-  tests/keys/openpgp/dsa.pub				\
-  tests/keys/openpgp/ed25519-2.pub			\
-  tests/keys/openpgp/ed25519-2.sec			\
-  tests/keys/openpgp/ed25519-3.pub			\
-  tests/keys/openpgp/ed25519-3.sec			\
-  tests/keys/openpgp/ed25519.pub			\
-  tests/keys/openpgp/ed25519.sec			\
-  tests/keys/openpgp/rsa.pub				\
-  tests/keys/openpgp/signing-key.pub			\
-  tests/keys/openpgp/signing-key.sec			\
+  tests/keys/civodul.pub				\
+  tests/keys/dsa.pub					\
+  tests/keys/ed25519-2.pub				\
+  tests/keys/ed25519-2.sec				\
+  tests/keys/ed25519-3.pub				\
+  tests/keys/ed25519-3.sec				\
+  tests/keys/ed25519.pub				\
+  tests/keys/ed25519.sec				\
+  tests/keys/rsa.pub					\
+  tests/keys/signing-key.pub				\
+  tests/keys/signing-key.sec				\
   tests/test.drv					\
   $(TESTS)
 

NEWS

@@ -17,7 +17,6 @@ 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

build-aux/test-env.in

@@ -73,8 +73,8 @@ then
 	# Copy the keys so that the secret key has the right permissions (the
 	# daemon errors out when this is not the case.)
 	mkdir -p "$GUIX_CONFIGURATION_DIRECTORY"
-	cp "@abs_top_srcdir@/tests/keys/openpgp/signing-key.sec"	\
-	   "@abs_top_srcdir@/tests/keys/openpgp/signing-key.pub"	\
+	cp "@abs_top_srcdir@/tests/keys/signing-key.sec"	\
+	   "@abs_top_srcdir@/tests/keys/signing-key.pub"	\
 	   "$GUIX_CONFIGURATION_DIRECTORY"
 	chmod 400 "$GUIX_CONFIGURATION_DIRECTORY/signing-key.sec"
     fi

doc/guix-cookbook.texi

@@ -1276,7 +1276,9 @@ definition in @samp{$GUIX_CHECKOUT/guix/build/gnu-build-system.scm}:
   ;; Standard build phases, as a list of symbol/procedure pairs.
   (let-syntax ((phases (syntax-rules ()
                          ((_ p ...) `((p . ,p) ...)))))
-    (phases set-SOURCE-DATE-EPOCH set-paths install-locale unpack
+    (phases separate-from-pid1
+            set-GUIX_GCC_MANGLE_PREFIX_MAP set-SOURCE-DATE-EPOCH
+            set-paths install-locale unpack
             bootstrap
             patch-usr-bin-file
             patch-source-shebangs configure patch-generated-file-shebangs
@@ -1298,7 +1300,7 @@ Or from the REPL:
 (add-to-load-path "/path/to/guix/checkout")
 ,use (guix build gnu-build-system)
 (map car %standard-phases)
-@result{} (set-SOURCE-DATE-EPOCH set-paths install-locale unpack bootstrap patch-usr-bin-file patch-source-shebangs configure patch-generated-file-shebangs build check install patch-shebangs strip validate-runpath validate-documentation-location delete-info-dir-file patch-dot-desktop-files make-dynamic-linker-cache install-license-files reset-gzip-timestamps compress-documentation)
+@result{} (separate-from-pid1 set-GUIX_GCC_MANGLE_PREFIX_MAP set-SOURCE-DATE-EPOCH set-paths install-locale unpack bootstrap patch-usr-bin-file patch-source-shebangs configure patch-generated-file-shebangs build check install patch-shebangs strip validate-runpath validate-documentation-location delete-info-dir-file patch-dot-desktop-files make-dynamic-linker-cache install-license-files reset-gzip-timestamps compress-documentation)
 @end lisp
 
 If you want to know more about what happens during those phases, consult the

doc/guix.texi

@@ -2658,11 +2658,9 @@ 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 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
+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
 @file{/dev/sda1}, run:
 
 @example
@@ -19148,10 +19146,6 @@ swap file is encrypted because the entire device is encrypted.
 @xref{Swap Space}, or @xref{Preparing for Installation,,Disk
 Partitioning}, for an example.
 
-When using GRUB as the bootloader, the LUKS password is only requested
-once: GRUB passes the master key to the initial RAM disk automatically.
-@xref{Bootloader Configuration, Automatic LUKS Master Key Passing}, for
-details.
 
 @end defvar
 
@@ -27021,32 +27015,6 @@ 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
@@ -36593,14 +36561,13 @@ 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, which must end
-with a slash, be created manually, and be writable by php-fpm.
+be able to use @code{cache-dir} as its cache directory.
 @end deffn
 
 A simple setup for cat-avatar-generator can look like this:
@@ -44276,11 +44243,10 @@ behind a reverse proxy and serve repositories from a custom location.
 (service fossil-service-type
          (fossil-configuration
           (repository "/srv/museum")
-          (list-repositories? #t)
+          (repo-list? #t)
           (base-url "https://museum.example")
-          (compress? #f)
-          (https? #t)
-          (socket-file "/var/run/fossil.sock")))
+          (socket-file "/var/run/fossil.sock")
+          (compress? #f)))
 @end lisp
 
 @deftp {Data Type} fossil-configuration
@@ -48426,10 +48392,9 @@ A string denoting the name service (@pxref{Services in the NSS
 configuration,,, libc, The GNU C Library Reference Manual}).
 
 Note that name services listed here must be visible to nscd.  This is
-achieved by providing the list of packages implementing the needed
-services via the @code{name-services} field of the
-@code{nscd-configuration} record to be used with the @code{nscd-service-type}
-service (@pxref{Base Services, @code{nscd-configuration}}).
+achieved by passing the @code{#:name-services} argument to
+@code{nscd-service} the list of packages providing the needed name
+services (@pxref{Base Services, @code{nscd-service}}).
 
 @item reaction
 An action specified using the @code{lookup-specification} macro
@@ -48872,56 +48837,49 @@ This option in enabled by default.  In some cases involving the
 in RAM, it can be handy to disable the option by setting it to
 @code{#f}.
 
-@subsubheading Automatic LUKS Master Key Passing
-
-When booting from a LUKS-encrypted device using GRUB, the password is
-normally requested twice: once by GRUB to access @file{/boot}, and a
-second time by the initial RAM disk to mount the root file system.
-
-When GRUB's @code{cryptomount} command unlocks a LUKS device, GRUB
-retains the volume's master key in memory.  The @code{cryptodisk}
-module exposes these master keys via a GRUB-internal virtual file
-system called @dfn{procfs}, accessible as @code{(proc)/luks_script}.
-Each line of this virtual file has the form:
-
-@example
-luks_mount @var{uuid} @var{offset} @var{sector-size} @var{cipher-mode-iv} @var{hex-master-key}
-@end example
-
-@noindent
-(or @code{luks2_mount} for LUKS2 volumes).
-
-When the store resides on an encrypted device, the generated GRUB
-configuration automatically injects this virtual file into the initial
-RAM disk using GRUB's @code{newc:} initrd prefix---a documented
-mechanism for synthesizing a CPIO archive on the fly
-(@pxref{GNU/Linux,,, grub, GNU GRUB manual}).  The resulting initrd
-line is equivalent to:
-
-@example
-initrd newc:etc/luks_script:(proc)/luks_script @dots{} /boot/initrd
-@end example
-
-@noindent
-The initial RAM disk then reads @file{/etc/luks_script}, looks up the
-matching UUID, and calls @command{cryptsetup open --volume-key-file} to
-unlock the device without prompting for a password a second time.  If
-the master key is missing or does not match, the system falls back to
-an interactive password prompt, so this mechanism is transparent to the
-user.
-
-No configuration is required: GRUB's @code{procfs} and @code{luks}
-modules are loaded automatically when encrypted devices are declared
-via @code{luks-device-mapping} (@pxref{Mapped Devices}).
-
 @item @code{extra-initrd} (default: @code{#f})
 File name of an additional initrd to load during the boot.  It may or
 may not point to a file in the store, but the main use case is for
 out-of-store files containing secrets.
 
+In order to be able to provide decryption keys for LUKS devices, they
+need to be available in the initial RAM disk.  However they cannot be
+stored inside the usual initrd, since it is stored in the store and
+being world-readable (as files in the store are) is not a desired
+property for an initrd containing decryption keys.  You can therefore
+use this field to instruct GRUB to also load a manually created initrd
+not stored in the store.
+
 For any use case not involving secrets, you should use regular initrd
 (@pxref{operating-system Reference, @code{initrd}}) instead.
 
+Suitable image can be created for example like this:
+
+@example
+echo /key-file.bin | cpio -oH newc >/key-file.cpio
+chmod 0000 /key-file.cpio
+@end example
+
+After it is created, you can use it in this manner:
+
+@lisp
+;; Operating system with encrypted boot partition
+(operating-system
+  @dots{}
+  (bootloader (bootloader-configuration
+               (bootloader grub-efi-bootloader)
+               (targets '("/boot/efi"))
+               ;; Load the initrd with a key file...
+               (extra-initrd "/key-file.cpio")))
+  (mapped-devices
+   (list (mapped-device
+          (source (uuid "12345678-1234-1234-1234-123456789abc"))
+          (target "my-root")
+          (type luks-device-mapping)
+          ;; ... and use it to unlock the root device.
+          (arguments '(#:key-file "/key-file.bin"))))))
+@end lisp
+
 Be careful when using this option, since pointing to a file that is not
 readable by the grub while booting will cause the boot to fail and
 require a manual edit of the initrd line in the grub menu.

etc/news.scm

@@ -46,8 +46,7 @@
  (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")
-         (pt "Registros podem referir-se a valores herdados de campos ainda não evaluados (thunks)"))
+         (de "Vererbung in Verbundsobjekten erlaubt Verweise auf geerbte Werte verzögert ausgewerteter Felder"))
         (body
          (en "A new feature has been added to records—the facility used when
 defining packages, services, operating systems, and many other things—that,
@@ -115,42 +114,7 @@ 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.")
-         (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.")))
+@code{inputs} im obigen Beispiel – kann gleichnamige Bindungen überschatten.")))
 
  (entry (commit "b52ce9041ad58aeababd2d50d3e72bc23dffff60")
         (title

etc/teams.scm

@@ -786,8 +786,7 @@ the haskell-build-system."
   (team 'hpc
         #:name "High-performance computing team"
         #:description "High-performance computing (HPC) related packages."
-        #:scope (list "gnu/packages/fabric-management.scm"
-                      "gnu/packages/mpi.scm"
+        #:scope (list "gnu/packages/mpi.scm"
                       "gnu/packages/oneapi.scm"
                       "gnu/packages/opencl.scm"
                       "gnu/packages/parallel.scm"
@@ -992,7 +991,8 @@ 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/packages/benchmark.scm"
+        #:scope (list "gnu/ci.scm"
+                      "gnu/packages/benchmark.scm"
                       "gnu/packages/check.scm"
                       "gnu/packages/ci.scm"
                       "gnu/packages/code.scm"

etc/teams/hpc/mpi-manifest.scm

@@ -1,44 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2026 Ludovic Courtès <ludo@gnu.org>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
-
-;; This manifest lists all MPI-related packages: useful for 'guix refresh',
-;; 'guix build', etc.
-
-(use-modules (guix)
-             (gnu packages fabric-management)
-             (gnu packages linux)
-             (gnu packages mpi)
-             (gnu packages parallel))
-
-;; The packages below are what constitutes the MPI stack: helper libraries,
-;; interconnect drivers, and MPI implementations.
-(packages->manifest
- (list cassini-headers
-       cxi-driver
-       hwloc
-       libcxi
-       libfabric
-       mpich
-       openmpi-5
-       openpmix
-       opensm
-       prrte
-       psm
-       psm2
-       rdma-core
-       ucx))

gnu/bootloader/grub.scm

@@ -404,10 +404,7 @@ when booting a root file system on a Btrfs subvolume."
               (initrd (normalize-file (menu-entry-initrd entry)
                                       device-mount-point
                                       store-directory-prefix))
-              (extra-initrd (bootloader-configuration-extra-initrd config))
-              (luks-script-initrd
-               (and (pair? store-crypto-devices)
-                    "newc:etc/luks_script:(proc)/luks_script")))
+              (extra-initrd (bootloader-configuration-extra-initrd config)))
           ;; Here DEVICE is the store and DEVICE-MOUNT-POINT is its mount point.
           ;; Use the right file names for LINUX and INITRD in case
           ;; DEVICE-MOUNT-POINT is not "/", meaning that the store is on a
@@ -415,20 +412,14 @@ when booting a root file system on a Btrfs subvolume."
 
           ;; When STORE-DIRECTORY-PREFIX is defined, prepend it the linux and
           ;; initrd paths, to allow booting from a Btrfs subvolume.
-
-          ;; When the store is on an encrypted device, inject GRUB's
-          ;; (proc)/luks_script into the initrd as /etc/luks_script so the
-          ;; initrd can use the already-decrypted master key to open LUKS
-          ;; volumes without prompting for the password a second time.
           #~(format port "menuentry ~s {
   ~a
   linux ~a ~a
-  initrd ~a ~a ~a
+  initrd ~a ~a
 }~%"
                     #$label
                     #$(grub-root-search device linux)
                     #$linux (string-join (list #$@arguments))
-                    (or #$luks-script-initrd "")
                     (or #$extra-initrd "")
                     #$initrd)))
        (multiboot-kernel
@@ -473,7 +464,7 @@ menuentry ~s {
           ;; Other type of devices aren't implemented.
           #~()))
     (let ((devices (map crypto-device->cryptomount store-crypto-devices))
-          (modules #~(format port "insmod procfs~%insmod luks~%insmod luks2~%")))
+          (modules #~(format port "insmod luks~%insmod luks2~%")))
       (if (null? devices)
           devices
           (cons modules devices))))

gnu/build/file-systems.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014-2018, 2020-2022, 2026 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014-2018, 2020-2022 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>
@@ -1455,14 +1455,9 @@ 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)
-                     (string-trim-both
-                      (call-with-output-string
-                        (lambda (port)
-                          (print-exception port #f
-                                           (exception-kind c)
-                                           (exception-args c))))))
+                     (exception-message c))
              (unless (file-system-mount-may-fail? fs)
                (raise c))))
       (let* ((type    (file-system-type fs))

gnu/home/services/niri.scm

@@ -19,7 +19,6 @@
 (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)
@@ -41,15 +40,14 @@
 
 (define (home-niri-shepherd-service config)
   "Return a shepherd service that runs Niri, a scrollable tiling Wayland
-compositor.  The service starts Niri with appropriate environment variables
-set for a Wayland desktop session."
+compositor.  The service starts Niri in a DBus session 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 #$(file-append bash "/bin/bash") "-l"
-                          "-c" "exec niri --session")
+                          "-c" "exec dbus-run-session niri --session")
                     #:environment-variables
                     (append (list #$@(niri-configuration-environment-variables config))
                             '("DESKTOP_SESSION=niri"
@@ -68,8 +66,6 @@ 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

@@ -75,6 +75,7 @@
 # Copyright © 2025 Nigko Yerden <nigko.yerden@gmail.com>
 # Copyright © 2025 Cayetano Santos <csantosb@inventati.org>
 # Copyright © 2025 bdunahu <bdunahu@operationnull.com>
+# Copyright © 2025 Nikita Mitasov <me@ch4og.com>
 #
 # This file is part of GNU Guix.
 #
@@ -423,7 +424,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/kde-utils.scm			\
   %D%/packages/kerberos.scm			\
   %D%/packages/kodi.scm				\
-  %D%/packages/kubernetes.scm	        	\
   %D%/packages/language.scm			\
   %D%/packages/lc0.scm			\
   %D%/packages/lean.scm				\
@@ -1064,6 +1064,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/binutils-loongson-workaround.patch	\
   %D%/packages/patches/binutils-mingw-w64-deterministic.patch	\
   %D%/packages/patches/binutils-2.41-fix-cross.patch		\
+  %D%/packages/patches/binutils-reproducible-tar.patch		\
   %D%/packages/patches/bloomberg-bde-tools-fix-install-path.patch	\
   %D%/packages/patches/bmake-run-check-separately.patch	\
   %D%/packages/patches/boolector-find-googletest.patch	\
@@ -1170,7 +1171,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/curlftpfs-fix-memory-leak.patch		\
   %D%/packages/patches/curlftpfs-fix-no_verify_hostname.patch	\
   %D%/packages/patches/cursynth-wave-rand.patch			\
-  %D%/packages/patches/cvc5-reproducible-build.patch		\
   %D%/packages/patches/cvs-CVE-2017-12836.patch		\
   %D%/packages/patches/cyrus-sasl-fix-time-h.patch              \
   %D%/packages/patches/d-feet-drop-unused-meson-argument.patch	\
@@ -1320,6 +1320,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/flatpak-fix-fonts-icons.patch	\
   %D%/packages/patches/flatpak-fix-icon-validation.patch	\
   %D%/packages/patches/flatpak-unset-gdk-pixbuf-for-sandbox.patch	\
+  %D%/packages/patches/flex-fix-make-dependencies.patch         \
   %D%/packages/patches/fluxbox-1.3.7-no-dynamic-cursor.patch	\
   %D%/packages/patches/fluxbox-1.3.7-gcc.patch			\
   %D%/packages/patches/fmt-9-overspecified-tests.patch	\
@@ -1377,6 +1378,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gcc-fix-texi2pod.patch			\
   %D%/packages/patches/gcc-hurd-split-stack.patch 		\
   %D%/packages/patches/gcc-libstdc++-newer-gcc.patch		\
+  %D%/packages/patches/gcc-mangle-guix-store.patch		\
   %D%/packages/patches/gcc-4.8-libsanitizer-fix.patch		\
   %D%/packages/patches/gcc-4.9-inline.patch		\
   %D%/packages/patches/gcc-4.9-libsanitizer-fix.patch		\
@@ -1444,7 +1446,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/ghc-basement-fix-32-bit.patch		\
   %D%/packages/patches/ghc-testsuite-dlopen-pie.patch		\
   %D%/packages/patches/ghc-testsuite-grep-compat.patch		\
-  %D%/packages/patches/ghc-testsuite-recomp015-execstack.patch	\
   %D%/packages/patches/ghc-aeson-encodeDouble.patch		\
   %D%/packages/patches/ghc-basement-fix-32bit.patch		\
   %D%/packages/patches/ghc-bytestring-handle-ghc9.patch	\
@@ -1486,6 +1487,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/glibc-cross-objdump.patch		\
   %D%/packages/patches/glibc-dl-cache.patch			\
   %D%/packages/patches/glibc-guix-locpath.patch			\
+  %D%/packages/patches/glibc-fix-path-attribute-in-getconf.patch \
   %D%/packages/patches/glibc-hidden-visibility-ldconfig.patch	\
   %D%/packages/patches/glibc-hurd-clock_gettime_monotonic.patch	\
   %D%/packages/patches/glibc-hurd-clock_t_centiseconds.patch	\
@@ -1652,6 +1654,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/inkscape-libxml2.patch		\
   %D%/packages/patches/instead-use-games-path.patch		\
   %D%/packages/patches/intltool-perl-compatibility.patch	\
+  %D%/packages/patches/inetutils-hurd64.patch			\
   %D%/packages/patches/insight-toolkit-fix-build.patch			\
   %D%/packages/patches/irrlicht-use-system-libs.patch		\
   %D%/packages/patches/irrlicht-link-against-needed-libs.patch	\
@@ -1683,6 +1686,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/jfsutils-gcc-compat.patch		\
   %D%/packages/patches/jfsutils-include-systypes.patch		\
   %D%/packages/patches/john-the-ripper-jumbo-with-gcc-11.patch	\
+  %D%/packages/patches/json-c-0.12-CVE-2020-12762.patch		\
   %D%/packages/patches/json-c-0.13-CVE-2020-12762.patch		\
   %D%/packages/patches/jsonnet-include-cstdint-for-gcc-13-builds.patch	\
   %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch	\
@@ -1754,7 +1758,6 @@ 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			\
@@ -1808,6 +1811,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libqalculate-3.8.0-libcurl-ssl-fix.patch	\
   %D%/packages/patches/libquicktime-ffmpeg.patch 		\
   %D%/packages/patches/libsepol-versioned-docbook.patch		\
+  %D%/packages/patches/libskk-fix-invalid-escape.patch		\
   %D%/packages/patches/libsoup-auth-digest-fix-crash.patch      \
   %D%/packages/patches/libsoup-deadlock-in-add_listener_in_thread.patch \
   %D%/packages/patches/libsoup-fix-merge-of-ranges.patch        \
@@ -1824,8 +1828,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/libtiff-CVE-2022-34526.patch		\
   %D%/packages/patches/libtirpc-CVE-2021-46828.patch		\
   %D%/packages/patches/libtirpc-hurd.patch			\
-  %D%/packages/patches/libtool-grep-compat.patch		\
-  %D%/packages/patches/libtool-skip-tests2.patch		\
   %D%/packages/patches/libtree-fix-check-non-x86.patch		\
   %D%/packages/patches/libusb-0.1-disable-tests.patch		\
   %D%/packages/patches/libusb-for-axoloti.patch			\
@@ -1975,7 +1977,6 @@ 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	\
@@ -2334,6 +2335,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/rapidcheck-fix-libs.patch		\
   %D%/packages/patches/ratpoison-shell.patch			\
   %D%/packages/patches/retroarch-unbundle-spirv-cross.patch	\
+  %D%/packages/patches/rct-add-missing-headers.patch		\
   %D%/packages/patches/readline-link-ncurses.patch		\
   %D%/packages/patches/renpy-python-3.11-compat.patch			\
   %D%/packages/patches/renpy-fix-integer-slots.patch			\
@@ -2343,6 +2345,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/r-sapa-lapack.patch			\
   %D%/packages/patches/ripperx-missing-file.patch		\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
+  %D%/packages/patches/rtags-separate-rct.patch			\
   %D%/packages/patches/rtosc-0.3.1-fix-invalid-comparison-operator.patch	\
   %D%/packages/patches/racket-chez-scheme-bin-sh.patch		\
   %D%/packages/patches/racket-launcher-config-dir.patch		\
@@ -2375,6 +2378,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ruby-flores-fix-deprecations.patch	\
   %D%/packages/patches/ruby-latex-decode-fix-test.patch		\
   %D%/packages/patches/ruby-mustache-1.1.1-fix-race-condition-tests.patch \
+  %D%/packages/patches/ruby-pg-fix-connect-timeout.patch	\
   %D%/packages/patches/ruby-x25519-automatic-fallback-non-x86_64.patch \
   %D%/packages/patches/rust-1.64-fix-riscv64-bootstrap.patch	\
   %D%/packages/patches/rust-1.70-fix-rustix-build.patch	\
@@ -2465,7 +2469,6 @@ 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

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

gnu/packages/acl.scm

@@ -43,7 +43,7 @@
 (define-public acl
   (package
     (name "acl")
-    (version "2.3.1")
+    (version "2.3.2")
     (source
      (origin
       (method url-fetch)
@@ -51,7 +51,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "1bqi7hj0xkpivwg7lx5cv3yvs9ks1i6azvpgbvfpzcq1i736233n"))))
+        "0z1gi82zc2xcbchfagd7apn2s7camaagj8y6hmysl1wpcanxnasz"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)

gnu/packages/admin.scm

@@ -1302,14 +1302,14 @@ re-executing them as necessary.")
 (define-public inetutils
   (package
     (name "inetutils")
-    (version "2.7")
+    (version "2.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/inetutils/inetutils-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "11n01vsd51r7qraaaylhhx04hq4s6vcq0896zkz0yp1wvqfbwmm1"))))
+                "0q1257ci22g2jbdiqs00mharc1lqkbibdlkhj23f3si6qjxkn17s"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -1340,7 +1340,17 @@ re-executing them as necessary.")
                              "\\\""))
       ;; On some systems, 'libls.sh' may fail with an error such as:
       ;; "Failed to tell switch -a apart from -A".
-      #:parallel-tests? #f))
+      #:parallel-tests? #f
+      #:phases (if (target-hurd64?)
+                   #~(modify-phases %standard-phases
+                       (add-after 'unpack 'apply-hurd64-patch
+                         (lambda _
+                           (let ((patch
+                                  #$(local-file
+                                     (search-patch
+                                      "inetutils-hurd64.patch"))))
+                             (invoke "patch" "--force" "-p1" "-i" patch)))))
+                   #~%standard-phases)))
     (inputs
      (list coreutils
            shadow                     ;for login (used in telnetd and rlogind)
@@ -1363,7 +1373,7 @@ hostname.")
 (define-public shadow
   (package
     (name "shadow")
-    (version "4.19.0")
+    (version "4.13")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1371,7 +1381,7 @@ hostname.")
                     "download/" version "/shadow-" version ".tar.xz"))
               (sha256
                (base32
-                "0crbcfdp7ayyii33srinwd0yr27dkx9mbzglx1d0mvhr1z28xclw"))))
+                "0b6xz415b4y3y5nk3pw9xibv05kln4cjbmhybyncmrx2g5fj9zls"))))
     (build-system gnu-build-system)
     (arguments
      `(;; Assume System V `setpgrp (void)', which is the default on GNU
@@ -1380,9 +1390,7 @@ hostname.")
        '(,@(if (target-hurd?)
              '()
              '("--with-libpam"))
-         "--disable-logind" ;; no systemd
-         "--without-libbsd" ;; no libbsd
-         "shadow_cv_logdir=/var/log"
+          "shadow_cv_logdir=/var/log"
           "ac_cv_func_setpgrp_void=yes")
        #:phases
        (modify-phases %standard-phases
@@ -1418,8 +1426,15 @@ hostname.")
              ;; The top-level Makefile.am wrongfully has "SUBDIRS += man"
              ;; under "if ENABLE_REGENERATE_MAN", even though prebuilt man
              ;; pages are available.  Thus, install them manually.
-             (invoke "make" "-C" "man" "install"))))))
-    (native-inputs (list pkg-config))
+             (invoke "make" "-C" "man" "install")))
+         (add-after 'install-man-pages 'remove-groups
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Remove `groups', which is already provided by Coreutils.
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (man (string-append out "/share/man")))
+               (delete-file (string-append bin "/groups"))
+               (for-each delete-file (find-files man "^groups\\."))))))))
     (inputs
      (append (if (target-hurd?)
                  '()
@@ -3141,7 +3156,7 @@ track changes in important system configuration files.")
 (define-public libcap-ng
   (package
     (name "libcap-ng")
-    (version "0.9.3")
+    (version "0.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3150,20 +3165,12 @@ track changes in important system configuration files.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "13iy7dddcslpmmdhybgvfcgznsvpaa4r3fp9ldlpkq592lw8yyva"))))
+                "0izrrh2kmhi6dcy5iqcccmx90nwlaqcglhc60sl8n5ds8il14pi8"))))
     (build-system gnu-build-system)
     (arguments
-     (list
-      #:configure-flags
-      #~(list "--disable-static"
-              "--without-python")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'patch-configure-ac
-            (lambda _
-              (substitute* "configure.ac"
-                (("linux/sock_diag.h" all)
-                 (string-append all " \\"))))))))
+     `(#:configure-flags
+       (list "--disable-static"
+             "--without-python")))
     (inputs
      (list libbpf))
     (native-inputs
@@ -4981,16 +4988,16 @@ Python loading in HPC environments.")
   (let ((real-name "inxi"))
     (package
       (name "inxi-minimal")
-      (version "3.3.40-1")
+      (version "3.3.31-2")
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://codeberg.org/smxi/inxi")
+               (url "https://github.com/smxi/inxi")
                (commit version)))
          (file-name (git-file-name real-name version))
          (sha256
-          (base32 "0ivj0dcx7d2hmmkhyql156sb08385rzw640z9kyq4cv1n8ndz58s"))))
+          (base32 "1fca5minalpmizbxh5kmjiv8xrl7k6g91zn8d84fxmbhsk8vn3kk"))))
       (build-system trivial-build-system)
       (inputs
        (list bash-minimal
@@ -5016,8 +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)
-             (patch-shebang "inxi" (list (dirname (search-input-file
-                                                    %build-inputs "bin/perl"))))
+             (with-fluids ((%default-port-encoding #f))
+               (substitute* "inxi" (("/usr/bin/env perl") (which "perl"))))
              (let ((bin (string-append %output "/bin")))
                (install-file "inxi" bin)
                (wrap-program (string-append bin "/inxi")
@@ -5032,8 +5039,7 @@ Python loading in HPC environments.")
                                    ((member name '("util-linux"))
                                     (string-append (store-append "/bin") ":"
                                                    (store-append "/sbin")))
-                                   ((member name '("dmidecode" "iproute2" "lvm2"
-                                                   "mdadm"))
+                                   ((member name '("dmidecode" "iproute2"))
                                     (store-append "/sbin"))
                                    (else (store-append "/bin")))))))
                            %build-inputs)))
@@ -5061,7 +5067,6 @@ 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)
@@ -5087,14 +5092,11 @@ 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
@@ -5600,61 +5602,69 @@ representation to stdout.")
 (define-public hosts
   (package
     (name "hosts")
-    (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
+    (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)
     (inputs
-     (list gawk
-           bash-minimal
-           coreutils
-           diffutils
-           grep
-           ncurses ;for tput
-           sed))
+     `(("bats" ,bats) ;for test
+       ("awk" ,gawk)
+       ("bash" ,bash)
+       ("coreutils" ,coreutils)
+       ("diffutils" ,diffutils)
+       ("grep" ,grep)
+       ("ncurses" ,ncurses) ;tput
+       ("sed" ,sed)))
     (arguments
-     (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"))))))))
+     `(#: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)))
     (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

@@ -4,7 +4,6 @@
 ;;; 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.
 ;;;
@@ -22,52 +21,49 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages adns)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (gnu packages m4)
-  #:use-module (gnu packages pkg-config)
+  #:use-module (guix gexp)
+  #:use-module (guix licenses)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix utils)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
-  #:use-module (guix download)
-  #:use-module (guix git-download)
-  #:use-module (guix gexp)
-  #:use-module (guix packages)
-  #:use-module (guix utils))
+  #:use-module (gnu packages m4)
+  #:use-module (gnu packages pkg-config))
 
 (define-public adns
   (package
     (name "adns")
     (version "1.6.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "git://git.chiark.greenend.org.uk/~ianmdlvl/adns.git")
-              (commit (string-append "adns-" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "0ln3l5j7wb1xazrzl76p9xar52p6l2k1cwy7jazxw1acl71k9h5n"))))
+    (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"))))
     (build-system gnu-build-system)
     (arguments
-     (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"))))
+     ;; 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))
     (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 @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+)))
+     "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+)))
 
 (define-public c-ares
   (package
@@ -150,7 +146,7 @@ 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 (license:x11-style "https://c-ares.haxx.se/license.html"))))
+    (license (x11-style "https://c-ares.haxx.se/license.html"))))
 
 (define-public c-ares-for-node-lts
   (hidden-package c-ares))

gnu/packages/algebra.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2022, 2023, 2024, 2025 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2013, 2015, 2017, 2018, 2021 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016-2026 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2016-2025 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016, 2018, 2019, 2021, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2020-2022 Efraim Flashner <efraim@flashner.co.il>
@@ -406,7 +406,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "2.0.0-21")
+    (version "2.0.0-10")
     (source
      (origin
        (method url-fetch)
@@ -418,7 +418,7 @@ precision.")
               "https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/"
               "stable/main/source/giac_" version ".tar.gz"))
        (sha256
-        (base32 "1j6bip76hhqvycapf7xy26y0b8g5zzx4gwkfsr7bf6m2h71a2zry"))))
+        (base32 "1lzb0jjmkg5ml1qfl0m00qqng4sxgfqwrbq10gpkp4b301k2ckv1"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/android.scm

@@ -1387,7 +1387,6 @@ mounted via FUSE.")
        (uri (git-reference
              (url "https://github.com/anestisb/android-simg2img")
              (commit version)))
-       (file-name (git-file-name name version))
        (sha256
         (base32
          "0drwvqxbhajka580j93z8ldckhjlpr0i84nh20krdpxcp54xvldh"))))

gnu/packages/apl.scm

@@ -30,26 +30,20 @@
   #:use-module (guix packages)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial)
-  #:use-module (gnu packages algebra)
-  #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gettext)
-  #:use-module (gnu packages gtk)
-  #:use-module (gnu packages image)
   #:use-module (gnu packages java)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages pcre)
-  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages readline)
-  #:use-module (gnu packages sqlite)
-  #:use-module (gnu packages xorg))
+  #:use-module (gnu packages sqlite))
 
 (define-public apl
-  (let ((revision 1977))
+  (let ((revision 1550))
     (package
       (name "apl")
-      (version (string-append "2.0.1-r" (number->string revision)))
+      (version (string-append "1.8-r" (number->string revision)))
       (source
        (origin
          (method svn-fetch)
@@ -58,18 +52,12 @@
                (revision revision)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "1llm1hqpfd71jrhd4pizhmvvca5wr18v8zqfajwmvjjxcmzfkvv1"))))
+          (base32 "1bgc3a09f35zrqq2irhm1hspppnxjqas0fmcw14hkc7910br9ip3"))))
       (build-system gnu-build-system)
       (home-page "https://www.gnu.org/software/apl/")
-      (native-inputs (list gettext-minimal which pkg-config))
       (inputs
        (list gettext-minimal
-             libxcb
-             fftw
              openblas
-             gsl
-             libpng
-             gtk+
              pcre2
              readline
              sqlite))
@@ -81,11 +69,15 @@
              #~(modify-phases %standard-phases
                  (add-before 'configure 'fix-configure
                    (lambda _
-                     (substitute* "configure"
-                       ;; Manually set the SVN revision, since the directory
-                       ;; is unversioned and we know it anyway.
-                       (("\\$apl_ARCHIVE_SVNINFO")
-                        #$(number->string revision))))))))
+                     (substitute* "buildtag.sh"
+                       ;; Don't exit on failed SVN-related calls.
+                       (("^ +return 0\n") "")
+                       ;; Manually set the SVN revision, since the directory is
+                       ;; unversioned and we know it anyway.
+                       (("^SVNINFO=.*")
+                        (string-append "SVNINFO=" #$(number->string revision) "\n"))
+                       ;; Requires running ‘svn info’ on a versioned directory.
+                       (("\\\\\"\\$ARCHIVE_SVNINFO\\\\\"") "\\\"\\\"")))))))
       (synopsis "APL interpreter")
       (description
        "GNU APL is a free interpreter for the programming language APL.  It is

gnu/packages/appimage.scm

@@ -19,11 +19,9 @@
 (define-module (gnu packages appimage)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages base)
-  #:use-module (gnu packages c)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages file-systems)
   #:use-module (gnu packages linux)
-  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages)
   #:use-module (guix build-system gnu)
   #:use-module (guix gexp)
@@ -32,9 +30,9 @@
   #:use-module (guix utils))
 
 (define-public appimage-type2-runtime
-  (let ((revision "1")
+  (let ((revision "0")
         ;; No releases, just the latest commit.
-        (commit "caf24f9f712084686bfc24a70b75e50df0aefb9c"))
+        (commit "47b665594856b4e8928f8932adcf6d13061d8c30"))
     (package
       (name "appimage-type2-runtime")
       (version (git-version "continuous" revision commit))
@@ -46,16 +44,16 @@
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "17z0byws3dp375wcyq5xwy5npqy7hslqw21n677dp38z4f940nzv"))))
+          (base32 "0954crhlbapxis96g1s0vfpf78ybr64zvjalak387ksxj560g44x"))))
       (build-system gnu-build-system)
       (arguments
        (list
         #:tests? #f                     ; No tests
         #:make-flags
-        #~(list "-Csrc/runtime" "runtime"
+        #~(list "-Csrc/runtime" "runtime-fuse3"
                 (string-append "CC=" #$(cc-for-target))
                 (string-append
-                 "CFLAGS=" "-I" #$(this-package-input "fuse") "/include/fuse3/"
+                 "CFLAGS=" "-I" #$(this-package-input "fuse") "/include/fuse/"
                  " -DGIT_COMMIT='\"" "guix-" #$version "\"'"
                  " -D_FILE_OFFSET_BITS=64"
                  " -static"
@@ -66,22 +64,17 @@
           (ice-9 binary-ports))
         #:phases
         #~(modify-phases %standard-phases
-            (add-after 'unpack 'use-pkgconfig-flags
-              (lambda _
-                (substitute* "src/runtime/Makefile"
-                  (("-lmimalloc")
-                   "$(pkg-config --cflags mimalloc)"))))
             (delete 'configure)
             (replace 'install
               (lambda _
-                (install-file "src/runtime/runtime"
+                (install-file "src/runtime/runtime-fuse3"
                               (string-append #$output "/bin"))))
             ;; Must be after all elf reliant phases.  Used to identify the
             ;; executable as an AppImage as per the specification.
             (add-after 'make-dynamic-linker-cache 'set-magic-bytes
               (lambda _
                 (let ((port (open (string-append #$output
-                                                 "/bin/runtime")
+                                                 "/bin/runtime-fuse3")
                                   (logior O_WRONLY))))
                   (seek port 8 SEEK_SET)
                   (put-bytevector port #vu8(#x41 #x49 #x02))
@@ -91,12 +84,9 @@
               (this-package-input "fuse")
               (gexp-input (this-package-input "zstd") "static")
               (gexp-input (this-package-input "zlib") "static"))))
-      (native-inputs (list pkg-config))
       ;; Only needed at build time.
-      (inputs (list `(,fuse "out")
-                    `(,fuse "static")
-                    mimalloc
-                    squashfuse-for-appimage
+      (inputs (list squashfuse-for-appimage
+                    fuse-for-appimage
                     `(,zstd "static")
                     `(,zlib "static")))
       (synopsis "Runtime for executing AppImages")

gnu/packages/apr.scm

@@ -34,14 +34,14 @@
 (define-public apr
   (package
     (name "apr")
-    (version "1.7.6")
+    (version "1.7.4")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://apache/apr/apr-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "0cpbbmng9ir8rjl9nxwljkzmrkpk4b1nsj8vg4ssfpapsa90s0s9"))
+               "0xsmqgjiyw3s6va5dm86djnjzg9r0qc1zsldwz4sd8pkhglqsr7w"))
              (patches
               (search-patches "apr-skip-getservbyname-test.patch"))
              (patch-flags '("-p0"))))

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, 2025-2026 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2023 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"))
-                (patches
-                 (search-patches "tao-synth-include-string-you-use.patch"))))
+                  "1jds2l3cb96b02jxd7lmrjjl9s7mylnrvg6fpw0j8c141bk8vyg3"))))
       (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
@@ -6358,59 +6358,6 @@ 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")
@@ -8043,7 +7990,6 @@ Home Page}.")
              (commit version)
              ;; For test files.
              (recursive? #true)))
-       (file-name (git-file-name name version))
        (sha256
         (base32 "065x43hx670rjrclxi4hiqxscllb16v9s7myjvg7rd5pd3y0k7sg"))))
     (build-system pyproject-build-system)
@@ -8174,7 +8120,7 @@ and DSD streams.")
 (define-public qpwgraph
   (package
     (name "qpwgraph")
-    (version "1.0.0")
+    (version "0.9.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -8183,7 +8129,7 @@ and DSD streams.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0l3fflfpwkqy4iif8ifzzr3yy39ahzqdixx5g3rhj3zzbaysj73h"))))
+                "03001pvcbvr206k00751232gm50x1icf086z8c5hiakl2ym79gwl"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f))                ; no tests

gnu/packages/autotools.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
-;;; Copyright © 2012-2018, 2020-2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012-2018, 2020-2022, 2026 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
 ;;; Copyright © 2014 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2015, 2017, 2018 Mark H Weaver <mhw@netris.org>
@@ -157,7 +157,7 @@ know anything about Autoconf or M4.")
        (base32
         "0niz4852fgyavfh3gr4h4kzalk01nk70v6vfsja6r3ap349mr25s"))))))
 
-(define-public autoconf autoconf-2.69)
+(define-public autoconf autoconf-2.72)
 
 (define-public autoconf-2.68
   (package (inherit autoconf)
@@ -438,14 +438,14 @@ Makefile, simplifying the entire process for the developer.")
 (define-public automake
   (package/inherit automake-1.16.5
     (name "automake")
-    (version "1.17")
+    (version "1.18.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/automake/automake-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "146rkdcwri2dkwn3pjrjs9v0wm4xyav9vvq4yw5vj4qy87yc2849"))
+                "11v8ckqx7z8hv4mq9dnhg58cwnssaa7l9136yndbhlc34xis72hn"))
               (patches
                (search-patches "automake-skip-amhello-tests.patch"))))
     (arguments
@@ -483,16 +483,14 @@ Makefile, simplifying the entire process for the developer.")
 (define-public libtool
   (package
     (name "libtool")
-    (version "2.4.7")
+    (version "2.5.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/libtool/libtool-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0pb3l4x37k6fj1lwnpzws55gi3pxl0hx56jm4bzmbrkw0mzj2zsg"))
-              (patches (search-patches "libtool-skip-tests2.patch"
-                                       "libtool-grep-compat.patch"))))
+                "0xb64rhambx6mhxwr613xgyad7ybs5hgmpmd9gccf2vbcrh5h7zq"))))
     (build-system gnu-build-system)
     (propagated-inputs (list m4))
     (native-inputs
@@ -506,43 +504,59 @@ Makefile, simplifying the entire process for the developer.")
            autoconf-wrapper))   ; others on 'autom4te'
 
     (arguments
-     `(;; Libltdl is provided as a separate package, so don't install it here.
-       #:configure-flags '("--disable-ltdl-install")
+     (list ;; Libltdl is provided as a separate package, so don't install it here.
+           #:configure-flags #~'("--disable-ltdl-install")
 
-       ;; XXX: There are test failures on mips64el-linux starting from 2.4.4:
-       ;; <http://hydra.gnu.org/build/181662>.
-       ;; Also, do not run tests when cross compiling
-       #:tests? ,(not (or (%current-target-system)
-                          (string-prefix? "mips64"
-                                          (%current-system))))
+           ;; The 'libtool' script refers to the toolchain; tolerate it.
+           #:disallowed-references '()
 
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'pre-check
-           (lambda* (#:key inputs native-inputs parallel-tests? #:allow-other-keys)
-             ;; Run the test suite in parallel, if possible.
-             (setenv "TESTSUITEFLAGS"
-                     (string-append
-                      "-j"
-                      (if parallel-tests?
-                        (number->string (parallel-job-count))
-                        "1")))
-           ;; Patch references to /bin/sh.
-           (let ((/bin/sh (search-input-file (or native-inputs inputs) "bin/sh")))
-             (substitute* "tests/testsuite"
-               (("/bin/sh") /bin/sh)))))
-         ;; These files may be copied into source trees by libtoolize,
-         ;; therefore they must not point to store file names that would be
-         ;; leaked with tarballs generated by make dist.
-         (add-after 'install 'restore-build-aux-shebang
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (dir (string-append out "/share/libtool/build-aux")))
-               (for-each (lambda (file)
-                           (format #t "restoring shebang on `~a'~%" file)
-                           (substitute* file
-                             (("^#!.*/bin/sh") "#!/bin/sh")))
-                         (find-files dir))))))))
+           ;; XXX: There are test failures on mips64el-linux starting from 2.4.4:
+           ;; <http://hydra.gnu.org/build/181662>.
+           ;; Also, do not run tests when cross compiling
+           #:tests? (not (or (%current-target-system)
+                             (string-prefix? "mips64"
+                                             (%current-system))))
+
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'skip-some-tests-on-extra-archs
+                 (lambda _
+                   (with-directory-excursion "tests"
+                     (substitute* '("demo.at" "testsuite")
+                       (("hppa\\*\\|amd64\\*\\|x86_64\\*\\|s390\\*"
+                         all)
+                        (string-append all "|arm*|mips*|riscv*"))))))
+               (add-before 'check 'pre-check
+                 (lambda* (#:key inputs native-inputs parallel-tests?
+                           #:allow-other-keys)
+                   ;; Run the test suite in parallel, if possible.
+                   (setenv "TESTSUITEFLAGS"
+                           (string-append
+                            "-j"
+                            (if parallel-tests?
+                                (number->string (parallel-job-count))
+                                "1")))
+                   ;; Patch references to /bin/sh.
+                   (let ((/bin/sh (search-input-file (or native-inputs inputs)
+                                                     "bin/sh")))
+                     (substitute* "tests/testsuite"
+                       (("/bin/sh")
+                        /bin/sh)))))
+               ;; These files may be copied into source trees by libtoolize,
+               ;; therefore they must not point to store file names that would be
+               ;; leaked with tarballs generated by make dist.
+               (add-after 'install 'restore-build-aux-shebang
+                 (lambda* (#:key outputs #:allow-other-keys)
+                   (let* ((out (assoc-ref outputs "out"))
+                          (dir (string-append out
+                                              "/share/libtool/build-aux")))
+                     (for-each (lambda (file)
+                                 (format #t "restoring shebang on `~a'~%"
+                                         file)
+                                 (substitute* file
+                                   (("^#!.*/bin/sh")
+                                    "#!/bin/sh")))
+                               (find-files dir))))))))
 
     (synopsis "Generic shared library support tools")
     (description

gnu/packages/backup.scm

@@ -547,7 +547,7 @@ remain fully idle, saving power and producing less noise.")
          "0miklk4bqblpyzh1bni4x6lqn88fa8fjn15x1k1n8bxkx60nlymd"))))
     (build-system gnu-build-system)
     (inputs
-     (list librsync))
+     (list librsync-0.9))
     (arguments
      `(#:make-flags `("CFLAGS=-fcommon"
                       ,(string-append "PREFIX=" (assoc-ref %outputs "out"))

gnu/packages/base.scm

@@ -24,6 +24,7 @@
 ;;; Copyright © 2022, 2026 John Kehayias <john@guixotic.coop>
 ;;; Copyright © 2023 Josselin Poiret <dev@jpoiret.xyz>
 ;;; Copyright © 2024, 2025 Zheng Junjie <z572@z572.online>
+;;; Copyright © 2025 Nikita Mitasov <me@ch4og.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -119,14 +120,14 @@ command-line arguments, multiple languages, and so on.")
 (define-public grep
   (package
    (name "grep")
-   (version "3.11")
+   (version "3.12")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/grep/grep-"
                                 version ".tar.xz"))
             (sha256
              (base32
-              "1avf4x8skxbqrjp5j2qr9sp5vlf8jkw2i5bdn51fl3cxx3fsxchx"))
+              "1f87i907dzw31xy1xr8xjj6z9979qq3bwmypvkm35rlh1ryb4j96"))
             (patches (search-patches "grep-timing-sensitive-test.patch"))))
    (build-system gnu-build-system)
    (native-inputs (list perl))                   ;some of the tests require it
@@ -247,47 +248,49 @@ implementation offers several extensions over the standard utility.")
    (build-system gnu-build-system)
    ;; Note: test suite requires ~1GiB of disk space.
    (arguments
-    `(,@(cond
-          ((target-hurd?)
-           '(#:make-flags
-             (list (string-append
-                     "TESTSUITEFLAGS= -k '"
-                     "!sparse"
-                     ",!renamed dirs in incrementals"
-                     ",!--exclude-tag option in incremental pass"
-                     ",!incremental dumps with -C"
-                     ",!incremental dumps of nested directories"
-                     ",!incremental restores with -C"
-                     ",!concatenated incremental archives (renames)"
-                     ",!renamed directory containing subdirectories"
-                     ",!renamed subdirectories"
-                     ",!chained renames"
-                     ",!Directory"
-                     "'"))))
-          ;; 'storing sparse files > 8G' fails on powerpc-linux, likely
-          ;; due to the small HDD and RAM present on these devices.
-          ((target-ppc32?)
-           '(#:make-flags (list (string-append "TESTSUITEFLAGS= -k "
-                                               "'!tricky time stamps"
-                                               ",!storing sparse files > 8G'"))))
-          ;; https://lists.gnu.org/archive/html/bug-tar/2021-10/msg00007.html
-          ;; tar-1.34 isn't aware of 64-bit time_t and upstream suggests
-          ;; skipping the test for this release on 32-bit systems.
-          ((target-32bit?)
-           '(#:make-flags (list "TESTSUITEFLAGS= -k '!tricky time stamps'")))
-          (else '()))
-      ;; XXX: 32-bit Hurd platforms don't support 64bit time_t
-      ,@(if (target-hurd32?)
-            (list #:configure-flags ''("--disable-year2038"))
-            '())
-      #:phases (modify-phases %standard-phases
-                 (add-before 'build 'set-shell-file-name
-                   (lambda* (#:key inputs #:allow-other-keys)
-                     ;; Do not use "/bin/sh" to run programs.
-                     (let ((bash (assoc-ref inputs "bash")))
-                       (substitute* "src/system.c"
-                         (("/bin/sh")
-                          (string-append bash "/bin/sh")))))))))
+    (append
+     (cond
+      ((target-hurd?)
+       '(#:make-flags
+         (list (string-append
+                "TESTSUITEFLAGS= -k '"
+                "!sparse"
+                ",!renamed dirs in incrementals"
+                ",!--exclude-tag option in incremental pass"
+                ",!incremental dumps with -C"
+                ",!incremental dumps of nested directories"
+                ",!incremental restores with -C"
+                ",!concatenated incremental archives (renames)"
+                ",!renamed directory containing subdirectories"
+                ",!renamed subdirectories"
+                ",!chained renames"
+                ",!Directory"
+                "'"))))
+      ;; 'storing sparse files > 8G' fails on powerpc-linux, likely
+      ;; due to the small HDD and RAM present on these devices.
+      ((target-ppc32?)
+       '(#:make-flags (list (string-append "TESTSUITEFLAGS= -k "
+                                           "'!tricky time stamps"
+                                           ",!storing sparse files > 8G'"))))
+      ;; https://lists.gnu.org/archive/html/bug-tar/2021-10/msg00007.html
+      ;; tar-1.34 isn't aware of 64-bit time_t and upstream suggests
+      ;; skipping the test for this release on 32-bit systems.
+      ((not (target-64bit?))
+       '(#:make-flags (list "TESTSUITEFLAGS= -k '!tricky time stamps'")))
+      (else '()))
+     ;; XXX: 32-bit Hurd platforms don't support 64bit time_t
+     (if (target-hurd32?)
+         (list #:configure-flags #~(list "--disable-year2038"))
+         '())
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'set-shell-file-name
+            (lambda* (#:key inputs #:allow-other-keys)
+              ;; Do not use "/bin/sh" to run programs.
+              (substitute* "src/system.c"
+                (("/bin/sh")
+                 (search-input-file inputs "bin/sh")))))))))
 
    ;; When cross-compiling, the 'set-shell-file-name' phase needs to be able
    ;; to refer to the target Bash.
@@ -306,41 +309,8 @@ standard utility.")
    (license gpl3+)
    (home-page "https://www.gnu.org/software/tar/")))
 
-;;; TODO: Replace/merge with 'patch' on core-updates.
-(define-public patch/pinned
-  (hidden-package
-   (package
-     (name "patch")
-     (version "2.7.6")
-     (source (origin
-               (method url-fetch)
-               (uri (string-append "mirror://gnu/patch/patch-"
-                                   version ".tar.xz"))
-               (sha256
-                (base32
-                 "1zfqy4rdcy279vwn2z1kbv19dcfw25d2aqy9nzvdkq5bjzd0nqdc"))
-               (patches (search-patches "patch-hurd-path-max.patch"))))
-     (build-system gnu-build-system)
-     (arguments
-      ;; Work around a cross-compilation bug whereby libpatch.a would provide
-      ;; '__mktime_internal', which conflicts with the one in libc.a.
-      (if (%current-target-system)
-          `(#:configure-flags '("gl_cv_func_working_mktime=yes"))
-          '()))
-     (native-inputs (list ed))
-     (synopsis "Apply differences to originals, with optional backups")
-     (description
-      "Patch is a program that applies changes to files based on differences
-laid out as by the program \"diff\".  The changes may be applied to one or more
-files depending on the contents of the diff file.  It accepts several
-different diff formats.  It may also be used to revert previously applied
-differences.")
-     (license gpl3+)
-     (home-page "https://savannah.gnu.org/projects/patch/"))))
-
 (define-public patch
   (package
-    (inherit patch/pinned)
     (name "patch")
     (version "2.8")
     (source (origin
@@ -350,13 +320,27 @@ differences.")
               (sha256
                (base32
                 "1qssgwgy3mfahkpgg99a35gl38vamlqb15m3c2zzrd62xrlywz7q"))))
+    (build-system gnu-build-system)
     (arguments
-     (substitute-keyword-arguments (package-arguments patch/pinned)
-       ((#:configure-flags flags #~'())
-        (if (target-hurd32?)
-            #~(cons* "--disable-year2038"
-                     #$flags)
-            flags))))
+     (list
+      #:configure-flags
+      #~(append
+         (if #$(%current-target-system)
+             (list "gl_cv_func_working_mktime=yes")
+             '())
+         (if #$(target-hurd32?)
+             (list "--disable-year2038")
+             '()))))
+    (native-inputs (list ed))
+    (synopsis "Apply differences to originals, with optional backups")
+    (description
+     "Patch is a program that applies changes to files based on differences
+laid out as by the program \"diff\".  The changes may be applied to one or more
+files depending on the contents of the diff file.  It accepts several
+different diff formats.  It may also be used to revert previously applied
+differences.")
+    (license gpl3+)
+    (home-page "https://savannah.gnu.org/projects/patch/")
     (properties '())))
 
 (define-public diffutils
@@ -632,20 +616,21 @@ standard.")
    (inputs (list guile-3.0))
    (outputs '("out" "debug"))
    (arguments
-    `(,@(if (target-hurd?)
-            '(#:configure-flags '("CFLAGS=-D__alloca=alloca"
-                                  "ac_cv_func_posix_spawn=no"))
-            '())
+    (append
+     (if (target-hurd?)
+         (list #:configure-flags '("CFLAGS=-D__alloca=alloca"
+                                   "ac_cv_func_posix_spawn=no"))
+         (list))
+     (list
       #:phases
-      (modify-phases %standard-phases
-        (add-before 'build 'set-default-shell
-          (lambda* (#:key inputs #:allow-other-keys)
-            ;; Change the default shell from /bin/sh.
-            (let ((bash (assoc-ref inputs "bash")))
+      #~(modify-phases %standard-phases
+          (add-before 'build 'set-default-shell
+            (lambda* (#:key inputs #:allow-other-keys)
+              ;; Change the default shell from /bin/sh.
               (substitute* "src/job.c"
                 (("default_shell =.*$")
-                 (format #f "default_shell = \"~a/bin/sh\";\n"
-                         bash)))))))))
+                 (format #f "default_shell = \"~a\";\n"
+                         (search-input-file inputs "/bin/sh"))))))))))
    (synopsis "Remake files automatically")
    (description
     "Make is a program that is used to control the production of
@@ -669,17 +654,17 @@ change.  GNU make offers many powerful extensions over the standard utility.")
                (base32
                 "12f5zzyq2w56g95nni65hc0g5p7154033y2f3qmjvd016szn5qnn"))))
     (arguments
-     `(#:configure-flags '("CFLAGS=-D__alloca=alloca -D__stat=stat")
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'set-default-shell
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; Change the default shell from /bin/sh.
-             (let ((bash (assoc-ref inputs "bash")))
-               (substitute* "job.c"
-                 (("default_shell =.*$")
-                  (format #f "default_shell = \"~a/bin/sh\";\n"
-                          bash)))))))))))
+     (list
+      #:configure-flags #~(list "CFLAGS=-D__alloca=alloca -D__stat=stat")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'set-default-shell
+            (lambda* (#:key inputs #:allow-other-keys)
+              ;; Change the default shell from /bin/sh.
+              (substitute* "job.c"
+                (("default_shell =.*$")
+                 (format #f "default_shell = \"~a\";\n"
+                         (search-input-file inputs "/bin/sh")))))))))))
 
 (define-public binutils
   (package
@@ -693,6 +678,7 @@ change.  GNU make offers many powerful extensions over the standard utility.")
       (sha256
        (base32 "0fnwaasfglbphqzvz5n25js9gl695p7pjbmb1z81g8gsc6k90qzn"))
       (patches (search-patches
+                "binutils-reproducible-tar.patch"
                 "binutils-2.41-fix-cross.patch"
                 "binutils-loongson-workaround.patch"))))
    (build-system gnu-build-system)
@@ -728,7 +714,8 @@ change.  GNU make offers many powerful extensions over the standard utility.")
           ;; For some reason, the build machinery insists on rebuilding .info
           ;; files, even though they're already provided by the tarball.
           #:make-flags #~'("MAKEINFO=true")))
-   (native-inputs (list bison))                   ;needed to build 'gprofng'
+   (native-inputs (list bison  ;needed to build 'gprofng'
+                        perl)) ;needed to build the man pages (pod2man)
    (synopsis "Binary utilities: bfd gas gprof ld")
    (description
     "GNU Binutils is a collection of tools for working with binary files.
@@ -908,6 +895,7 @@ the store.")
   (list "glibc-ldd-powerpc.patch"
         "glibc-2.41-ldd-x86_64.patch"
         "glibc-2.40-dl-cache.patch"
+        "glibc-fix-path-attribute-in-getconf.patch"
         "glibc-2.37-versioned-locpath.patch"
         ;; "glibc-allow-kernel-2.6.32.patch"
         "glibc-guix-locpath.patch"
@@ -957,247 +945,257 @@ the store.")
               "static"))                          ;9 MiB of .a files
 
    (arguments
-    `(#:out-of-source? #t
+    (list
+     #:out-of-source? #t
 
-      ;; The libraries have an empty RUNPATH, but some, such as the versioned
-      ;; libraries (libdl-2.24.so, etc.) have ld.so marked as NEEDED.  Since
-      ;; these libraries are always going to be found anyway, just skip
-      ;; RUNPATH checks.
-      #:validate-runpath? #f
+     ;; The libraries have an empty RUNPATH, but some, such as the versioned
+     ;; libraries (libdl-2.24.so, etc.) have ld.so marked as NEEDED.  Since
+     ;; these libraries are always going to be found anyway, just skip
+     ;; RUNPATH checks.
+     #:validate-runpath? #f
 
-      #:modules ((ice-9 ftw)
+     #:modules `((ice-9 ftw)
+                 (ice-9 match)
                  (srfi srfi-1)
                  (srfi srfi-26)
+                 (guix build gremlin)
                  (guix build utils)
                  (guix build gnu-build-system))
 
-      ;; Strip binaries but preserve the symbol table needed by Valgrind:
-      ;; <https://lists.gnu.org/archive/html/help-guix/2022-03/msg00036.html>.
-      #:strip-flags '("--strip-debug")
+     ;; Strip binaries but preserve the symbol table needed by Valgrind:
+     ;; <https://lists.gnu.org/archive/html/help-guix/2022-03/msg00036.html>.
+     #:strip-flags #~'("--strip-debug")
 
-      #:configure-flags
-      (list "--sysconfdir=/etc"
+     #:configure-flags
+     #~(list "--sysconfdir=/etc"
 
-            ;; Installing a locale archive with all the locales is to
-            ;; expensive (~100 MiB), so we rely on users to install the
-            ;; locales they really want.
-            ;;
-            ;; Set the default locale path.  In practice, $LOCPATH may be
-            ;; defined to point whatever locales users want.  However, setuid
-            ;; binaries don't honor $LOCPATH, so they'll instead look into
-            ;; $libc_cv_complocaledir; we choose /run/current-system/locale/X.Y,
-            ;; with the idea that it is going to be populated by the sysadmin.
-            ;; The "X.Y" sub-directory is because locale data formats are
-            ;; incompatible across libc versions; see
-            ;; <https://lists.gnu.org/archive/html/guix-devel/2015-08/msg00737.html>.
-            ;;
-            ;; `--localedir' is not honored, so work around it.
-            ;; See <http://sourceware.org/ml/libc-alpha/2013-03/msg00093.html>.
-            (string-append "libc_cv_complocaledir=/run/current-system/locale/"
-                           ,(version-major+minor version))
+             ;; Installing a locale archive with all the locales is to
+             ;; expensive (~100 MiB), so we rely on users to install the
+             ;; locales they really want.
+             ;;
+             ;; Set the default locale path.  In practice, $LOCPATH may be
+             ;; defined to point whatever locales users want.  However, setuid
+             ;; binaries don't honor $LOCPATH, so they'll instead look into
+             ;; $libc_cv_complocaledir; we choose /run/current-system/locale/X.Y,
+             ;; with the idea that it is going to be populated by the sysadmin.
+             ;; The "X.Y" sub-directory is because locale data formats are
+             ;; incompatible across libc versions; see
+             ;; <https://lists.gnu.org/archive/html/guix-devel/2015-08/msg00737.html>.
+             ;;
+             ;; `--localedir' is not honored, so work around it.
+             ;; See <http://sourceware.org/ml/libc-alpha/2013-03/msg00093.html>.
+             (string-append "libc_cv_complocaledir=/run/current-system/locale/"
+                            #$(version-major+minor version))
 
-            (string-append "--with-headers="
-                           (assoc-ref ,(if (%current-target-system)
-                                           '%build-target-inputs
-                                           '%build-inputs)
-                                      "kernel-headers")
-                           "/include")
+             ;; Here we need to refer to kernel headers and not glibc-mesboot
+             (string-append
+              "--with-headers="
+              (and=>
+               (find
+                (match-lambda
+                  ((label . input)
+                   (and (file-exists?
+                         (string-append input "/include/asm/ioctl.h"))
+                        ;; Ensure we're not refering to another libc.
+                        (not (file-exists?
+                              (string-append input "/include/locale.h"))))))
+                #$(if (%current-target-system)
+                      #~%build-target-inputs
+                      #~%build-inputs))
+               cdr) "/include")
 
-            ;; This is the default for most architectures as of GNU libc 2.26,
-            ;; but we specify it explicitly for clarity and consistency.  See
-            ;; "kernel-features.h" in the GNU libc for details.
-            "--enable-kernel=3.2.0"
+             ;; This is the default for most architectures as of GNU libc 2.26,
+             ;; but we specify it explicitly for clarity and consistency.  See
+             ;; "kernel-features.h" in the GNU libc for details.
+             "--enable-kernel=3.2.0"
 
-            ;; Use our Bash instead of /bin/sh.
-            (string-append "BASH_SHELL="
-                           (assoc-ref %build-inputs "bash")
-                           "/bin/bash")
+             ;; Use our Bash instead of /bin/sh.
+             (string-append "BASH_SHELL="
+                            (search-input-file %build-inputs "/bin/bash"))
 
-            ;; On GNU/Hurd we get discarded-qualifiers warnings for
-            ;; 'device_write_inband' among other things.  Ignore them.
-            ,@(if (target-hurd?)
-                  `("--disable-werror")
-                  '()))
+             ;; On GNU/Hurd we get discarded-qualifiers warnings for
+             ;; 'device_write_inband' among other things.  Ignore them.
+             #$@(if (target-hurd?)
+                    #~("--disable-werror")
+                    #~()))
 
-      #:tests? #f                                 ; XXX
-      #:phases (modify-phases %standard-phases
-                 (add-before
-                  'configure 'pre-configure
-                  (lambda* (#:key inputs native-inputs outputs
-                                  #:allow-other-keys)
-                    (let* ((out  (assoc-ref outputs "out"))
-                           (bin  (string-append out "/bin"))
-                           ;; FIXME: Normally we would look it up only in INPUTS
-                           ;; but cross-base uses it as a native input.
-                           (bash (or (assoc-ref inputs "static-bash")
-                                     (assoc-ref native-inputs "static-bash"))))
-                      ;; Install the rpc data base file under `$out/etc/rpc'.
-                      (substitute* "inet/Makefile"
-                        (("^\\$\\(inst_sysconfdir\\)/rpc(.*)$" _ suffix)
-                         (string-append out "/etc/rpc" suffix "\n"))
-                        (("^install-others =.*$")
-                         (string-append "install-others = " out "/etc/rpc\n")))
+     #:tests? #f ; XXX
+     #:phases
+     #~(modify-phases %standard-phases
+         (add-before 'configure 'pre-configure
+           (lambda* (#:key inputs native-inputs #:allow-other-keys)
+             (let* ((bin (string-append #$output "/bin"))
+                    (bash (find
+                           (match-lambda
+                             ((label . input)
+                              (let ((sh (string-append input "/bin/sh")))
+                                (and (file-exists? sh)
+                                     ;; Is it bash-static specifically? The
+                                     ;; label can't be used because of
+                                     ;; bash-mesboot during the bootstrap.
+                                     (not (file-dynamic-info sh))))))
+                           inputs))
+                    (bash (and=> bash cdr)))
+               ;; Install the rpc data base file under `$out/etc/rpc'.
+               (substitute* "inet/Makefile"
+                 (("^\\$\\(inst_sysconfdir\\)/rpc(.*)$" _ suffix)
+                  (string-append #$output "/etc/rpc" suffix "\n"))
+                 (("^install-others =.*$")
+                  (string-append "install-others = " #$output "/etc/rpc\n")))
 
-                      (substitute* "Makeconfig"
-                        ;; According to
-                        ;; <http://www.linuxfromscratch.org/lfs/view/stable/chapter05/glibc.html>,
-                        ;; linking against libgcc_s is not needed with GCC
-                        ;; 4.7.1.
-                        ((" -lgcc_s") ""))
+               (substitute* "Makeconfig"
+                 ;; According to
+                 ;; <http://www.linuxfromscratch.org/lfs/view/stable/chapter05/glibc.html>,
+                 ;; linking against libgcc_s is not needed with GCC
+                 ;; 4.7.1.
+                 ((" -lgcc_s") ""))
 
-                      ;; Tell the ld.so cache code where the store is.
-                      (substitute* "elf/dl-cache.c"
-                        (("@STORE_DIRECTORY@")
-                         (string-append "\"" (%store-directory) "\"")))
+               ;; Tell the ld.so cache code where the store is.
+               (substitute* "elf/dl-cache.c"
+                 (("@STORE_DIRECTORY@")
+                  (string-append "\"" (%store-directory) "\"")))
 
-                      ;; Have `system' use that Bash.
-                      (substitute* "sysdeps/posix/system.c"
-                        (("#define[[:blank:]]+SHELL_PATH.*$")
-                         (format #f "#define SHELL_PATH \"~a/bin/bash\"\n"
-                                 bash)))
+               ;; Have `system' use that Bash.
+               (substitute* "sysdeps/posix/system.c"
+                 (("#define[[:blank:]]+SHELL_PATH.*$")
+                  (format #f "#define SHELL_PATH \"~a/bin/bash\"\n" bash)))
 
-                      ;; Same for `popen'.
-                      (substitute* "libio/iopopen.c"
-                        (("/bin/sh")
-                         (string-append bash "/bin/sh")))
+               ;; Same for `popen'.
+               (substitute* "libio/iopopen.c"
+                 (("/bin/sh")
+                  (string-append bash "/bin/sh")))
 
-                      ;; Same for the shell used by the 'exec' functions for
-                      ;; scripts that lack a shebang.
-                      (substitute* (find-files "." "^paths\\.h$")
-                        (("#define[[:blank:]]+_PATH_BSHELL[[:blank:]].*$")
-                         (string-append "#define _PATH_BSHELL \""
-                                        bash "/bin/sh\"\n")))
+               ;; Same for the shell used by the 'exec' functions for
+               ;; scripts that lack a shebang.
+               (substitute* (find-files "." "^paths\\.h$")
+                 (("#define[[:blank:]]+_PATH_BSHELL[[:blank:]].*$")
+                  (string-append "#define _PATH_BSHELL \""
+                                 bash "/bin/sh\"\n")))
 
-                      ;; Make sure we don't retain a reference to the
-                      ;; bootstrap Perl.
-                      (substitute* "malloc/mtrace.pl"
-                        (("^#!.*")
-                         ;; The shebang can be omitted, because there's the
-                         ;; "bilingual" eval/exec magic at the top of the file.
-                         "")
-                        (("exec @PERL@")
-                         "exec perl")))))
+               ;; Make sure we don't retain a reference to the
+               ;; bootstrap Perl.
+               (substitute* "malloc/mtrace.pl"
+                 (("^#!.*")
+                  ;; The shebang can be omitted, because there's the
+                  ;; "bilingual" eval/exec magic at the top of the file.
+                  "")
+                 (("exec @PERL@")
+                  "exec perl")))))
 
-                 (add-after 'install 'move-static-libs
-                   (lambda* (#:key outputs #:allow-other-keys)
-                     ;; Move static libraries to the "static" output.
-                     ;; Note: As of GNU libc 2.34, the contents of some ".a"
-                     ;; files have been moved into "libc.so", and *both* empty
-                     ;; ".so" and ".a" files have been introduced to avoid
-                     ;; breaking existing executables and existing builds
-                     ;; respectively.  The intent of the seemingly redundant
-                     ;; empty ".a" files is to avoid newly-compiled executables
-                     ;; from having dependencies on the empty shared libraries,
-                     ;; and as such, it is useful to have these ".a" files in
-                     ;; OUT in addition to STATIC.
+         (add-after 'install 'move-static-libs
+           (lambda _
+             ;; Move static libraries to the "static" output.
+             ;; Note: As of GNU libc 2.34, the contents of some ".a"
+             ;; files have been moved into "libc.so", and *both* empty
+             ;; ".so" and ".a" files have been introduced to avoid
+             ;; breaking existing executables and existing builds
+             ;; respectively.  The intent of the seemingly redundant
+             ;; empty ".a" files is to avoid newly-compiled executables
+             ;; from having dependencies on the empty shared libraries,
+             ;; and as such, it is useful to have these ".a" files in
+             ;; OUT in addition to STATIC.
 
-                     (define (empty-static-library? file)
-                       ;; Return true if FILE is an 'ar' archive with nothing
-                       ;; beyond the header.
-                       (let ((file (string-append (assoc-ref outputs "out")
-                                                  "/lib/" file)))
-                         (and (ar-file? file)
-                              (= (stat:size (stat file)) 8))))
+             (define (empty-static-library? file)
+               ;; Return true if FILE is an 'ar' archive with nothing
+               ;; beyond the header.
+               (let ((file (string-append #$output "/lib/" file)))
+                 (and (ar-file? file)
+                      (= (stat:size (stat file)) 8))))
 
-                     (define (static-library? file)
-                       ;; Return true if FILE is a static library.  The
-                       ;; "_nonshared.a" files are referred to by libc.so,
-                       ;; libpthread.so, etc., which are in fact linker
-                       ;; scripts.
-                       (and (string-suffix? ".a" file)
-                            (not (string-contains file "_nonshared"))
-                            (not (empty-static-library? file))))
+             (define (static-library? file)
+               ;; Return true if FILE is a static library.  The
+               ;; "_nonshared.a" files are referred to by libc.so,
+               ;; libpthread.so, etc., which are in fact linker
+               ;; scripts.
+               (and (string-suffix? ".a" file)
+                    (not (string-contains file "_nonshared"))
+                    (not (empty-static-library? file))))
 
-                     (define (linker-script? file)
-                       ;; Guess whether FILE, a ".a" file, is actually a
-                       ;; linker script.
-                       (and (not (ar-file? file))
-                            (not (elf-file? file))))
+             (define (linker-script? file)
+               ;; Guess whether FILE, a ".a" file, is actually a
+               ;; linker script.
+               (and (not (ar-file? file))
+                    (not (elf-file? file))))
 
-                     (let* ((out    (assoc-ref outputs "out"))
-                            (lib    (string-append out "/lib"))
-                            (files  (scandir lib static-library?))
-                            (empty  (scandir lib empty-static-library?))
-                            (static (assoc-ref outputs "static"))
-                            (slib   (string-append static "/lib")))
-                       (mkdir-p slib)
-                       (for-each (lambda (base)
-                                   (rename-file (string-append lib "/" base)
-                                                (string-append slib "/" base)))
-                                 files)
-                       (for-each (lambda (base)
-                                   (copy-file (string-append lib "/" base)
-                                              (string-append slib "/" base)))
-                                 empty)
+             (let* ((lib (string-append #$output "/lib"))
+                    (files (scandir lib static-library?))
+                    (empty (scandir lib empty-static-library?))
+                    (slib (string-append #$output:static "/lib")))
+               (mkdir-p slib)
+               (for-each (lambda (base)
+                           (rename-file (string-append lib "/" base)
+                                        (string-append slib "/" base)))
+                         files)
+               (for-each (lambda (base)
+                           (copy-file (string-append lib "/" base)
+                                      (string-append slib "/" base)))
+                         empty)
 
-                       ;; Usually libm.a is a linker script so we need to
-                       ;; change the file names in there to refer to STATIC
-                       ;; instead of OUT.
-                       (for-each (lambda (ld-script)
-                                   (substitute* ld-script
-                                     ((out) static)))
-                                 (filter linker-script?
-                                         (map (cut string-append slib "/" <>)
-                                              files))))))
+               ;; Usually libm.a is a linker script so we need to
+               ;; change the file names in there to refer to STATIC
+               ;; instead of OUT.
+               (for-each (lambda (ld-script)
+                           (substitute* ld-script
+                             ((#$output)
+                              #$output:static)))
+                         (filter linker-script?
+                                 (map (cut string-append slib "/" <>)
+                                      files))))))
 
-                 (add-after 'install 'install-utf8-c-locale
-                   (lambda* (#:key outputs #:allow-other-keys)
-                     ;; Install the C.UTF-8 locale so there's always a UTF-8
-                     ;; locale around.
-                     (let* ((out (assoc-ref outputs "out"))
-                            (bin (string-append out "/bin"))
-                            (locale (string-append out "/lib/locale/"
-                                                   ,(package-version
-                                                     this-package))))
-                       (mkdir-p locale)
+         (add-after 'install 'install-utf8-c-locale
+           (lambda _
+             ;; Install the C.UTF-8 locale so there's always a UTF-8
+             ;; locale around.
+             (let ((bin (string-append #$output "/bin"))
+                   (locale (string-append #$output "/lib/locale/"
+                                          #$(package-version
+                                             this-package))))
+               (mkdir-p locale)
 
-                       ;; FIXME: When cross-compiling, attempt to use
-                       ;; 'localedef' from the same libc version.
-                       (invoke ,(if (%current-target-system)
-                                    "true"
-                                    '(string-append bin "/localedef"))
-                               "--no-archive" "--prefix" locale
-                               "-i" "C" "-f" "UTF-8"
-                               (string-append locale "/C.UTF-8")))))
+               ;; FIXME: When cross-compiling, attempt to use
+               ;; 'localedef' from the same libc version.
+               (invoke #$(if (%current-target-system)
+                             "true"
+                             #~(string-append bin "/localedef"))
+                       "--no-archive" "--prefix" locale
+                       "-i" "C" "-f" "UTF-8"
+                       (string-append locale "/C.UTF-8")))))
 
-                 ,@(if (target-hurd?)
-                       `((add-after 'install 'augment-libc.so
-                           (lambda* (#:key outputs #:allow-other-keys)
-                             (let ((out (assoc-ref outputs "out")))
-                               (substitute* (string-append out "/lib/libc.so")
-                                 (("/[^ ]+/lib/libc.so.0.3")
-                                  (string-append out "/lib/libc.so.0.3"
-                                                 " libmachuser.so libhurduser.so"))))))
-                         (add-after 'install 'create-machine-symlink
-                           (lambda* (#:key outputs #:allow-other-keys)
-                             (let* ((out (assoc-ref outputs "out"))
-                                    (cpu ,(match (or (%current-target-system)
-                                                     (%current-system))
-                                            ((? target-x86-32?)
-                                             "i386")
-                                            ((? target-x86-64?)
-                                             "x86_64")))
-                                    (machine (string-append
-                                              out "/include/mach/machine")))
-                               (unless (file-exists? machine)
-                                 (symlink cpu machine))))))
-                       '()))))
+         #$@(if (target-hurd?)
+                `((add-after 'install 'augment-libc.so
+                    (lambda _
+                      (substitute* (string-append #$output "/lib/libc.so")
+                        (("/[^ ]+/lib/libc.so.0.3")
+                         (string-append #$output "/lib/libc.so.0.3"
+                                        " libmachuser.so libhurduser.so")))))
+                  (add-after 'install 'create-machine-symlink
+                    (lambda _
+                      (let* ((cpu #$(match (or (%current-target-system)
+                                               (%current-system))
+                                      ((? target-x86-32?)
+                                       "i386")
+                                      ((? target-x86-64?)
+                                       "x86_64")))
+                             (machine (string-append #$output
+                                                     "/include/mach/machine")))
+                        (unless (file-exists? machine)
+                          (symlink cpu machine))))))
+                '()))))
 
-   (inputs `(("static-bash" ,static-bash)))
+   (inputs (list static-bash))
 
    ;; To build the manual, we need Texinfo and Perl.  Gettext is needed to
    ;; install the message catalogs, with 'msgfmt'.
-   (native-inputs `(("texinfo" ,texinfo)
-                    ("perl" ,perl)
-                    ("bison" ,bison)
-                    ("gettext" ,gettext-minimal)
-                    ("python" ,python-minimal)
-
-                    ,@(if (target-hurd?)
-                          `(("mig" ,mig)
-                            ("perl" ,perl))
-                          '())))
-
+   (native-inputs
+    (append
+     (list bison
+           gettext-minimal
+           perl
+           python-minimal
+           texinfo)
+     (if (target-hurd?)
+         (list mig)
+         (list))))
    (native-search-paths
     ;; Search path for packages that provide locale data.  This is useful
     ;; primarily in build environments.  Use 'GUIX_LOCPATH' rather than
@@ -1300,8 +1298,8 @@ with the Linux kernel.")
         ;; The C.UTF-8 fails to build in glibc 2.35:
         ;; <https://sourceware.org/bugzilla/show_bug.cgi?id=28861>.
         ;; It is missing altogether in versions earlier than 2.35.
-        `(modify-phases ,phases
-           (delete 'install-utf8-c-locale)))))))
+        #~(modify-phases #$phases
+            (delete 'install-utf8-c-locale)))))))
 
 (define-public glibc-2.33
   (package
@@ -1342,9 +1340,9 @@ with the Linux kernel.")
                  "libc_cv_cxx_link_ok=no"
                  #$flags))
        ((#:phases phases)
-        `(modify-phases ,phases
-           ;; This phase fails trying to create /etc/ld.so.cache
-           (delete 'install-utf8-c-locale)))))))
+        #~(modify-phases #$phases
+            ;; This phase fails trying to create /etc/ld.so.cache
+            (delete 'install-utf8-c-locale)))))))
 
 (define-public (make-gcc-libc base-gcc libc)
   "Return a GCC that targets LIBC."

gnu/packages/bash.scm

@@ -66,7 +66,7 @@
 
 (define (patch-url seqno)
   "Return the URL of Bash patch number SEQNO."
-  (format #f "mirror://gnu/bash/bash-5.2-patches/bash52-~3,'0d" seqno))
+  (format #f "mirror://gnu/bash/bash-5.3-patches/bash53-~3,'0d" seqno))
 
 (define (bash-patch seqno sha256-bv)
   "Return the origin of Bash patch SEQNO, with expected hash SHA256-BV."
@@ -79,47 +79,13 @@
   (list (bash-patch seqno (base32 hash))
         ...))
 
-(define %patch-series-5.2
-  ;; This is the current patches series for 5.2, generated using
+(define %patch-series-5.3
+  ;; This is the current patches series for 5.3, generated using
   ;; 'download-patches' below.
   (patch-series
-   (1 "02iibpd3jq8p1bhdzgik8ps6gi1145vr463a82gj1hivjbp2ybzl")
-   (2 "1f6p1z85qh1lavdp3xikgp0bfv0vqhvgpgwmdzlywl35hwdmxk25")
-   (3 "1zxsi869jd90hksx3nyypgyqwrxhw2ws3r6hmk76yc1lsgdhq2ba")
-   (4 "04i5liw5cg6dqkdxfgazqc2jrw40bmclx3dx45bwy259pcj7g0iq")
-   (5 "0mykflv9qnbx3jz71l4f7isadiw9knm4qimqkwsv9cv88dafpq7c")
-   (6 "13265akl8w6zyrg0l7f0x6arjgqjhllcwl6lk46rl53x4mm5dq6i")
-   (7 "146lrwkn5wgxzs6vx34wl47g69zsxdy032k40qzi626b47ya6015")
-   (8 "1s5i8hcayrv25lc8fxcr431v634yx5sii53b8fmip789s0pxjjvb")
-   (9 "1kfk25151ka9wkmk1myf12irgcmvhsd8b0nfifvhrszah9w82npr")
-   (10 "1kf1jrwm30js0v3d1r2rk4x09s1pyjp70wnd1qqhf9bmkw15ww67")
-   (11 "1x5nkvbj6hci7gx42q7qa72hg2a9wwxh85dk79gn521ypwjmy6w3")
-   (12 "0b6lcwzm7v5bzjiwaz2c8n5aj77w8ckhp2vwk4v3zsdq3z70gc9g")
-   (13 "1rkwpibd6j2ghppfhqsva2jm4kdni6b7jpdsxdps52643gc4yjq9")
-   (14 "09766vqqw4ffnmysm725v35qkhp1g9j4qgqag941xvq655pj9y9y")
-   (15 "12im449abnq5gaqjmdxr5i38kmp02fa8l8wffad3jryvd58r0wzg")
-   (16 "05arb0hzmng03cr357lf6p8af0x2a1pznsd3psll03nibfy56n0m")
-   (17 "129cvx4gfz8n23iw1lhbknbw86fyw6vh60jqj1wj3d5pr75wwj0w")
-   (18 "105am94qxjc27gga4a8asvsi01090xwjfim3s16lafwjvm4xsha6")
-   (19 "10njgv5mrc5rhsp5lvxcbm0pnzn59a8spi2nhdasifyl1a32cp1j")
-   (20 "07f0wlmqjdfarp44w3gj9gdqbqm5x20rvlhpn34ngklmxcm2bz5n")
-   (21 "1kahfqqalcwi4m73pg3ssz6lh0kcqsqax09myac7a15d2y0vhd43")
-   (22 "0w74aym0g1fh48864a3qxh89f26iaq7wsbg7244c6kjr94527dbq")
-   (23 "1lywjqbc36j5pdzfcvnz1zy30j76aqmsm190p888av0hw815b45g")
-   (24 "1hq23djqbr7s9y2324jq9mxr5bwdkmgizn3zgpchbsqp054k85cp")
-   (25 "0x9hc4silzl4d3zw4p43i5dm7w86k50j47f87lracwfgwy3z8f2i")
-   (26 "1b1fhm1dsi67r8ip17s0xvx2qq31fsxc1g9n3r931dd0k9a1zvln")
-   (27 "0fdbhvs9dkf4knncifh98a76q4gylhyvfrffq5p9q3ag5q58jap1")
-   (28 "1hdacd6sssjshmry1sscdnxxfb2r51bvdyghlfjaqgc9l85phhk0")
-   (29 "11wrlb20w6v89b96krg0gwxipwhvrda6rq1y9f972m32gsrsqp0j")
-   (30 "13v9fqgim082dmvkslsr0hs793yzhsij2s91mjswsfhj1qip7zy3")
-   (31 "15d7rddj6spwc1fy997lxx6zvzq0zbxgf2h20mhi4wgp5nzbglf2")
-   (32 "05ia6yf32hjprmyyxqawhgckxs3684ikfx8xg08zfgx9xkd7g73v")
-   (33 "1qm2aad9mf2xah6xwchga7s5pk3v308mrv9lgh50d65d236ccgh1")
-   (34 "0bi38dhkkwpm2qrzp8zpykglq6gibvv2n9f8m59gwj406cxvp7w9")
-   (35 "1r8k34y82v02yfkgws17j7i53ybb74dqnwl2jjiv0av9z93hl6l2")
-   (36 "0mwhr9hfbh2czf8klbxg6nbd2g9xl9kygvgk061vird56r4kzj8m")
-   (37 "156sbi3srzkyxajkmhb7iigq0j4nvwnpsbw88xdsxn95a4xiqb4a")))
+   (1 "0zr8wgg1gb67vxn7ws971n1znrdinczymc688ndnpy2a6qs88q0z")
+   (2 "009051z55plsy4jmmjdb3ys7li2jraynz99qg7n6a1qk025591g3")
+   (3 "1vb0gnrkmz49rcfpxjcxy0v0k5278wrlkljk9gc20nizvk3xjigj")))
 
 (define (download-patches store count)
   "Download COUNT Bash patches into store.  Return a list of
@@ -157,7 +123,7 @@ number/base32-hash tuples, directly usable in the 'patch-series' form."
                " -Wl,-rpath -Wl,"
                (assoc-ref %build-inputs "ncurses")
                "/lib")))
-         (version "5.2"))
+         (version "5.3"))
     (package
      (name "bash")
      (source (origin
@@ -166,11 +132,11 @@ number/base32-hash tuples, directly usable in the 'patch-series' form."
                     "mirror://gnu/bash/bash-" version ".tar.gz"))
               (sha256
                (base32
-                "1yrjmf0mqg2q8pqphjlark0mcmgf88b0acq7bqf4gx3zvxkc2fd1"))
+                "1fii1xaxbng9x0klxmxkm0xhmycngfz72jsgyrna4sgqcmlxhp0d"))
               (patch-flags '("-p0"))
               (patches (cons (search-patch "bash-linux-pgrp-pipe.patch")
-                             %patch-series-5.2))))
-     (version (string-append version "." (number->string (length %patch-series-5.2))))
+                             %patch-series-5.3))))
+     (version (string-append version "." (number->string (length %patch-series-5.3))))
      (build-system gnu-build-system)
 
       (outputs '("out"

gnu/packages/bioconductor.scm

@@ -3436,14 +3436,14 @@ the @code{HorvathMethylChip40} (Mammal40) array.")
 (define-public r-systempiperdata
   (package
     (name "r-systempiperdata")
-    (version "2.14.6")
+    (version "2.14.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeRdata" version
                               'experiment))
        (sha256
-        (base32 "1j7h40hcm0gyahmlilvlb83ddmwrarqn319qwpnrgwcji8fm92jd"))))
+        (base32 "1yrq1vyc0pmp3iv621cvdsavlarcca3z4bbxfzbg0ny3fyqp67pb"))))
     (properties `((upstream-name . "systemPipeRdata")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocgenerics r-biostrings r-jsonlite r-remotes))
@@ -4552,9 +4552,15 @@ these biases and construct statistically consistent estimators.")
     (build-system r-build-system)
     (arguments
      (list
-      #:skipped-tests
-      ;; This test needs Internet access.
-      '(("test-examples.R" ".*find_taxonomy\\(\\) is working.*"))))
+      #: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")))))))))
     (propagated-inputs
      (list r-ape
            r-assertthat
@@ -4605,13 +4611,13 @@ to understand their data better and discover new insights.")
 (define-public r-anndatar
   (package
     (name "r-anndatar")
-    (version "1.0.2")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anndataR" version))
        (sha256
-        (base32 "1gn1yyfs08a77zrl4cidahxim3kgcvpbsrgfxxnhhrka57xcylld"))))
+        (base32 "1vi9aqgdjy0nlbsk7628sz12jsxd9bfb79yxhh0ngijpxj9sxd4p"))))
     (properties `((upstream-name . "anndataR")))
     (build-system r-build-system)
     (arguments
@@ -4664,13 +4670,14 @@ 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
@@ -5237,13 +5244,13 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
 (define-public r-arrayqualitymetrics
   (package
     (name "r-arrayqualitymetrics")
-    (version "3.66.0")
+    (version "3.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "arrayQualityMetrics" version))
               (sha256
                (base32
-                "0y9k81vwqq74zfdrc2hvx7mg0l7572hvrsby00m20z034j7f9pmi"))))
+                "1kz2d40wx2ksy9dz1z3wylcj7y7ad9z8xphsnz39j02m4g5mbvlp"))))
     (properties
      '((upstream-name . "arrayQualityMetrics")
        ;; We don't need these.
@@ -5265,7 +5272,7 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
                              r-svglite
                              r-vsn
                              r-xml))
-    (native-inputs (list r-biocstyle r-knitr))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/arrayQualityMetrics")
     (synopsis "Quality metrics report for microarray data sets")
     (description
@@ -6103,8 +6110,10 @@ retrieval analyses, or similar technologies.")
     (build-system r-build-system)
     (arguments
      (list
-      ;; This requires internet access.
-      #:skipped-tests '("test-download.R")))
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'disable-bad-tests
+           (lambda _ (delete-file "tests/testthat/test-download.R"))))))
     (propagated-inputs (list cmake r-dir-expiry))
     (native-inputs (list r-knitr r-testthat))
     (home-page "https://github.com/LTLA/biocmake")
@@ -6412,6 +6421,17 @@ 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
@@ -7880,13 +7900,13 @@ Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
 (define-public r-isva
   (package
     (name "r-isva")
-    (version "1.10")
+    (version "1.9")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "isva" version))
               (sha256
                (base32
-                "1im1bwbf6l88m4bwwwr0z2x8bvw927s3fqbwc06s5240wc8syjpl"))))
+                "05qx9q0kg4ma23v4abhihw0vz017nq6hv2jzsiqx4d20ngh1dl4z"))))
     (properties `((upstream-name . "isva")))
     (build-system r-build-system)
     (propagated-inputs (list r-fastica r-jade r-qvalue))
@@ -8653,13 +8673,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.66.2")
+    (version "2.66.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "1awsfklcs35vrmjkc12bk5ys9w7ib0799i3d0k138y44a0837pph"))))
+                "1cmzay4z9s183dc001rxfa81ql67la9y8m0p0wsn2iwzxzx94n8g"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -10317,13 +10337,13 @@ Enrichment Analysis} (GSEA).")
 (define-public r-gsva
   (package
     (name "r-gsva")
-    (version "2.4.8")
+    (version "2.4.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GSVA" version))
               (sha256
                (base32
-                "0p9awi85dbmmyplhdfz0in4nhaavb58gpf48kqyp30rcc3v5a8h0"))))
+                "08i2s5zlm75mr7zl357cic2zxcy7aqqfv67xb0w67n48cw016ri6"))))
     (properties `((upstream-name . "GSVA")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase
@@ -10718,54 +10738,6 @@ 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")
@@ -11145,13 +11117,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-maaslin2
   (package
     (name "r-maaslin2")
-    (version "1.24.1")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Maaslin2" version))
        (sha256
-        (base32 "0z8vfx6db6xfvqdhg6n8jx3fmgwvq22facsacq6ym867kw2jafiz"))))
+        (base32 "10hdjhi1ykk513hzvs0bi6avzghqmkqns8knhz3ycv7bj3ynp70x"))))
     (properties `((upstream-name . "Maaslin2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11339,6 +11311,17 @@ 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))
@@ -11545,13 +11528,13 @@ time-series data (including a graphical user interface).")
 (define-public r-mmuphin
   (package
     (name "r-mmuphin")
-    (version "1.24.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MMUPHin" version))
        (sha256
-        (base32 "1zdk9ffa996w4acnhbs7grbji5s3plwhcl6m21yajrlck2i9y3cw"))
+        (base32 "0d8i9b6pjwz409jd46fm1n9h21hzg8zgzpvchywpyc1k896fvz4l"))
        ;; Delete generated files.
        (snippet
         '(for-each delete-file
@@ -14315,13 +14298,13 @@ level.")
 (define-public r-tcgautils
   (package
     (name "r-tcgautils")
-    (version "1.30.3")
+    (version "1.30.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "TCGAutils" version))
               (sha256
                (base32
-                "1nppp70675y3ds76jf61rhfis2lgkxqjhz48b367qa55g3q2ah61"))))
+                "1zwzx7mfp4s0v1rdjsyxj4l9w360g4qm3am8yf5lsd0biciqqh93"))))
     (properties `((upstream-name . "TCGAutils")))
     (build-system r-build-system)
     (arguments
@@ -15041,14 +15024,14 @@ unmodeled, or latent sources of noise.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "2.16.4")
+    (version "2.16.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "1zrk6ky58f30wvaxph5dc2wr418qfpwc7d8pkxpl5dhb5g7vgn8r"))))
+         "0maixi0hwqzkpiq60hf60x4q3gv3hkvmrqh3ygv0fk63g1k9f6cj"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     ;; Tests fail because genWorkenvir fails to set up the environment.
@@ -15415,13 +15398,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.")
 (define-public r-xllim
   (package
     (name "r-xllim")
-    (version "2.3.1")
+    (version "2.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xLLiM" version))
        (sha256
-        (base32 "1h2z6a3j3yi7rj5lyk7gb1iyp2vf516fgmk7wr333gfkvk522n2r"))))
+        (base32 "08v6acn6vpn8asn61ldqdryjz0xk5zyd2v63aqrc5xximpqwrp7d"))))
     (properties `((upstream-name . "xLLiM")))
     (build-system r-build-system)
     (propagated-inputs (list r-abind
@@ -16321,14 +16304,14 @@ signals directly in the Bruker format.")
 (define-public r-codedepends
   (package
     (name "r-codedepends")
-    (version "0.6.7")
+    (version "0.6.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "CodeDepends" version))
        (sha256
         (base32
-         "02sj40qxq5vywgqay9q9vpv3s6j3jjr46kc8q3v1yw2vbsmlvrz0"))))
+         "0msq5ksjqp2pjzl6f1vizw53gdf5lz520bpdr5dbjwz5mc1mp0bz"))))
     (properties `((upstream-name . "CodeDepends")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17399,14 +17382,14 @@ data.")
 (define-public r-ggtree
   (package
     (name "r-ggtree")
-    (version "4.0.5")
+    (version "4.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggtree" version))
        (sha256
         (base32
-         "0w9hqc3m35mrdqy5iwcm201pzpbl8jw6rd3wyzwp6f53wbbm2lbh"))))
+         "1qi5nispv0cirfayijybnn1nr8l6sb2adnic3y37qm3yv91w6s6z"))))
     (properties `((upstream-name . "ggtree")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18720,13 +18703,13 @@ standardization of the analyses and the development of best practices.")
 (define-public r-microbiomestat
   (package
     (name "r-microbiomestat")
-    (version "1.4")
+    (version "1.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "MicrobiomeStat" version))
               (sha256
                (base32
-                "0in28lzds3sv1xa25vs8q5mmm1ax78s2axhq7mi23njqip5xmsr1"))))
+                "02xg8l4d0z5wrdrm5dj5a0q51vsbhf3f6z2lk8294c4d85s09dhl"))))
     (properties
      '((upstream-name . "MicrobiomeStat")
        (updater-extra-inputs . ("nlopt"))
@@ -18734,21 +18717,23 @@ 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-bbotk
+    (propagated-inputs (list r-bbmisc
                              r-dplyr
                              r-foreach
                              r-ggplot2
                              r-ggrepel
+                             r-lhs
                              r-lmertest
                              r-mass
                              r-matrix
                              r-matrixstats
-                             r-mlr3
-                             r-mlr3mbo
+                             r-mlr
+                             r-mlrmbo
                              r-modeest
-                             r-paradox
+                             r-paramhelpers
                              r-rcpp
                              r-rcpparmadillo
+                             r-smoof
                              r-statmod))
     (home-page "https://cran.r-project.org/package=MicrobiomeStat")
     (synopsis "Statistical methods for microbiome compositional data")
@@ -19652,14 +19637,14 @@ correspondence between different data sources.")
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.30.5")
+    (version "1.30.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "12c6xwp29mmalvxp3asliv2hlha5vv8l37prmmcgpdi4nghfic3b"))))
+         "080q91ll8rvqf93hcmxc7kjbmmihyh0vrpxck2pqrwglbqxm4xll"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aplot
@@ -22904,14 +22889,14 @@ expression space.")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.28.3")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "016wpficnbricf4f7sgq8j53cl178f1332fh9zvlx7q560489zf1"))))
+         "1ibxynw77a8mqv9av7z828wcazjpm4sfp83hd412f2rmgkls895x"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -23543,14 +23528,14 @@ populations, splice site strength, conservation, etc.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.40.2")
+    (version "1.40.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "0k2rcgg4ll06b9j7999d4l60wpmi3vnjaqiy5ay8ppd1z0m38ygf"))))
+         "1xqy4jl8im7i4kd4iwn8hvhy172fzsadyn90kprihmvccmpd5cr3"))))
     (properties
      '((upstream-name . "variancePartition")
        (updater-extra-native-inputs . ("r-rfast"))))
@@ -23891,26 +23876,30 @@ rate} (FDR).")
 (define-public r-activedriverwgs
   (package
     (name "r-activedriverwgs")
-    (version "1.2.1")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActiveDriverWGS" version))
        (sha256
         (base32
-         "1v6lnzbaksqpc33q3bp4mwij6rrfbqhi5wk1qx32h2wr2hr4208y"))))
+         "0xnplgwxd197a4d422bsxg753q158i12ils16awd1cw30wafdxkk"))))
     (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-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat))
+     (list r-knitr r-testthat))
     (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
     (synopsis "Driver discovery tool for cancer whole genomes")
     (description
@@ -24770,13 +24759,13 @@ functionality.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.78.1")
+    (version "1.78.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1qw3xwsffdqfwpmwrpzg8rnjwv9l45lkjz8bf5272hkhgjc7b1a8"))))
+                "1dfsfj4dm9wnh4qr1sqdrwzccl3pgw58j17vr3i1bvxkrq31p1ws"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -24889,14 +24878,14 @@ db and resource files to AWS S3 buckets.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.36.2")
+    (version "1.36.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "0bhr51c58vdfvly0bh3hgr397qkq45yw8221rpr38cah7dbzvrba"))))
+         "09jwnwiq4vx7cmzq5va3rh7npjyhi1p5p344c4n0h9nr55mxzjiw"))))
     (properties
      '((upstream-name . "MultiAssayExperiment")
        (updater-extra-native-inputs
@@ -25965,13 +25954,13 @@ provided for direct creation of an in-memory tatami matrix from a HDF5 file.")
 (define-public r-beadarray
   (package
     (name "r-beadarray")
-    (version "2.60.1")
+    (version "2.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "beadarray" version))
               (sha256
                (base32
-                "1bcirbg10ai6jpa8a5ppq4450r5h2bwizb98qn0z0hmm1mm4ww9r"))))
+                "0m9hmy4xn7q2v4ra95b9h08d0qh5qmjgqmg96vabyv46gn5i7qp4"))))
     (properties `((upstream-name . "beadarray")))
     (build-system r-build-system)
     (propagated-inputs (list r-annotationdbi
@@ -26401,13 +26390,13 @@ of other packages.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.38.1")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "1p8dzjphrcqai1f8wh56jfv377dqzdfnx2sl9sn73axbsr41swa7"))))
+                "1qwygk8fg8nharrkmjs65fcl3lsdi232f2383s5j8vm1qil5gghd"))))
     (build-system r-build-system)
     (properties
      '((updater-extra-native-inputs
@@ -26512,13 +26501,13 @@ variable and significantly correlated genes.")
 (define-public r-sparsearray
   (package
     (name "r-sparsearray")
-    (version "1.10.10")
+    (version "1.10.8")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SparseArray" version))
        (sha256
-        (base32 "19c1dfa5wizq7k53a43i5dwwaqs44prclxbf1k0i3awx5wz6qlbw"))))
+        (base32 "1bjxljwfrv787ikp61xl29wx3k6624qz75gl1kzfif62vys7vgf0"))))
     (properties `((upstream-name . "SparseArray")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocgenerics
@@ -27172,14 +27161,14 @@ with your data.")
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.42.1")
+    (version "2.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "0djrd63nsqpy46acblg5k8pq6ldqccr35r6h0sf4xridpkqm78b1"))))
+         "1v5z4fmwgs3swvpa09y986sracz0nsggq8s9hp1nmwb9a9grw8px"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -27194,6 +27183,7 @@ with your data.")
            r-readr
            r-s4vectors
            r-seqinfo
+           r-snpstats
            r-tibble
            r-variantannotation))
     (native-inputs
@@ -27654,6 +27644,16 @@ 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
@@ -28409,18 +28409,28 @@ separate published packages.")
 (define-public r-biomformat
   (package
     (name "r-biomformat")
-    (version "1.38.3")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomformat" version))
        (sha256
         (base32
-         "0b0w0mfx448ph8fla3nb4i50mvpnv498kxip7rnh14xwas9rhdd7"))))
+         "1ydcgifdrgg48y7qxg0gw30h332y3yk3k3n17fajkv58mlvyx1yc"))))
     (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-rhdf5))
+     (list r-jsonlite r-matrix r-plyr r-rhdf5))
     (native-inputs (list r-knitr r-testthat))
     (home-page "https://github.com/joey711/biomformat/")
     (synopsis "Interface package for the BIOM file format")
@@ -29178,15 +29188,25 @@ reproducibility.")
 (define-public r-phyloseq
   (package
     (name "r-phyloseq")
-    (version "1.54.2")
+    (version "1.54.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "phyloseq" version))
        (sha256
-        (base32 "106zwzzwzvb5x0lz9i68wshh2nsa2rf5rmkqjqsvr4smxq6hknlj"))))
+        (base32 "1zivxag6b2bjh32k1mpn7hlvalap97rp90x3cbfynqrk6933f4bq"))))
     (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

@@ -922,10 +922,7 @@ suite native in R.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12h1di45fg06nhsliii7v0h1z567pkpis1xm4ar1qr8ns1n8iljw"))
-       (modules '((guix build utils)))
-       (snippet
-        '(delete-file-recursively "r/src/vendor/highway"))))
+        (base32 "12h1di45fg06nhsliii7v0h1z567pkpis1xm4ar1qr8ns1n8iljw"))))
     (properties `((upstream-name . "BPCells")))
     (build-system r-build-system)
     (arguments
@@ -933,11 +930,7 @@ suite native in R.")
       #:phases
       '(modify-phases %standard-phases
          (add-after 'unpack 'chdir
-           (lambda _
-             (substitute* "r/configure"
-               (("tools/hwy-test.cpp" m)
-                (string-append m " $HWY_LIBS $HWY_CFLAGS")))
-             (chdir "r"))))))
+           (lambda _ (chdir "r"))))))
     (propagated-inputs
      (list r-dplyr
            r-ggplot2
@@ -964,7 +957,7 @@ suite native in R.")
            r-igraph
            r-iranges
            r-matrixstats))
-    (inputs (list hdf5 google-highway zlib))
+    (inputs (list hdf5 zlib))
     (native-inputs (list pkg-config))
     (home-page "https://github.com/bnprks/BPCells")
     (synopsis "Single cell counts matrices to PCA")
@@ -4897,29 +4890,26 @@ relying on a complex dependency tree.")
 (define-public biosoup
   (package
     (name "biosoup")
-    (version "0.11.0")
+    (version "0.10.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/rvaser/biosoup")
-             (commit version)))
+             ;; Corresponds to version 0.10.0
+             (commit "38181f09854ff42cbd9632200a2ec9fb37a4b7b6")))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0vn1hj3h152iwahnrzghqll34qaphchi07klb3j70vgc248micbz"))))
+         "02hvyka703zagx0nvv2yx3dkc748zc8g6qbrpya7r8kfkcl7y8hw"))))
     (build-system cmake-build-system)
     (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'enable-testing
-            (lambda _
-              (substitute* "CMakeLists.txt"
-                (("target_link_libraries\\(biosoup_test")
-                 "enable_testing()
-  add_test(NAME biosoup-test COMMAND biosoup_test)
-  target_link_libraries(biosoup_test")))))))
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "./bin/biosoup_test")))))))
     (native-inputs
      (list googletest))
     (home-page "https://github.com/rvaser/biosoup")
@@ -4931,29 +4921,26 @@ used for storage and logging in bioinformatics tools.")
 (define-public bioparser
   (package
     (name "bioparser")
-    (version "3.1.0")
+    (version "3.0.13")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/rvaser/bioparser")
-             (commit version)))
+             ;; Corresponds to tag 3.0.13
+             (commit "13341e6e0855c6b358ffcea6dad216e1009e1287")))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "057zb3g8qyvbkbfzgkygrf0iphz3v4icm13pchxzrafiy7zkbmrq"))))
+         "0c5p2dl8jb12ci9f427jzrmmm9cgvc1k4fxsn2ggkfsin6r1r82i"))))
     (build-system cmake-build-system)
     (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'enable-testing
-            (lambda _
-              (substitute* "CMakeLists.txt"
-                (("target_link_libraries\\(bioparser_test")
-                 "enable_testing()
-  add_test(NAME bioparser-test COMMAND bioparser_test)
-  target_link_libraries(bioparser_test")))))))
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "./bin/bioparser_test")))))))
     (inputs
      (list biosoup))
     (propagated-inputs
@@ -4967,6 +4954,113 @@ bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib
 compressed files.")
     (license license:expat)))
 
+(define-public circtools
+  (package
+    (name "circtools")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Kevinzjy/circtools")
+             ;; Corresponds to tag v1.0.0
+             (commit "79380de59013601021ca3b1352d6f64d2fb89646")
+             (recursive? #t)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0wg1s927g32k25j967kfr8l30nmr4c0p4zvy5igvy7cs6chd60lh"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f
+       #:install-source? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-writable
+           (lambda _
+             (for-each make-file-writable (find-files "."))))
+         (add-after 'unpack 'prepare-spoa-dependencies
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "vendor/spoa/CMakeLists.txt"
+               (("find_package\\(bioparser 3.0.13 QUIET\\)")
+                "find_package(bioparser 3.0.13 CONFIG)")
+               (("find_package\\(biosoup 0.10.0 QUIET\\)")
+                "find_package(biosoup 0.10.0 CONFIG)")
+               (("GTest_FOUND") "TRUE")))))))
+    (inputs
+     (cons* bioparser biosoup (cargo-inputs 'circtools)))
+    (native-inputs
+     (list cmake-minimal pkg-config googletest))
+    (home-page "https://github.com/Kevinzjy/circtools")
+    (synopsis "Accelerating functions in CIRI toolkit")
+    (description "This package provides accelerated functions for the CIRI
+toolkit.  It also provides the @code{ccs} executable to scan for circular
+consensus sequences.")
+    (license license:expat)))
+
+(define-public ciri-long
+  (package
+    (name "ciri-long")
+    (version "1.0.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/bioinfo-biols/CIRI-long")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "10k88i1fcqchrrjv82rmylwvbwqfba0n51palhig9hsg71xs0dbi"))
+       ;; Delete bundled binary
+       (snippet '(delete-file "libs/ccs"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              (substitute* "setup.py"
+                (("'argparse[^']*',")
+                 "") ;only for python2
+                (("==")
+                 ">=")
+                ;; This package changed names.
+                (("python-Levenshtein")
+                 "levenshtein"))))
+          (add-before 'build 'build-libssw
+            (lambda _
+              (with-directory-excursion "libs/striped_smith_waterman"
+                (invoke "make" "libssw.so"))))
+          (add-before 'build 'fix-reference-to-ccs
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* "CIRI_long/pipeline.py"
+                (("'ccs -i")
+                 (string-append "'"
+                                (assoc-ref inputs "circtools") "/bin/ccs"
+                                " -i")))
+              ;; yuck!
+              (substitute* "CIRI_long/main.py"
+                (("os.chmod\\(lib_path.*")
+                 "")))))))
+    (inputs (list circtools
+                  python-biopython
+                  python-bwapy
+                  python-levenshtein
+                  python-mappy
+                  python-numpy
+                  python-pandas
+                  python-pysam
+                  python-pyspoa
+                  python-scikit-learn
+                  python-scipy))
+    (native-inputs (list python-cython python-pynose python-setuptools))
+    (home-page "https://ciri-cookbook.readthedocs.io/")
+    (synopsis "Circular RNA identification for Nanopore sequencing")
+    (description "CIRI-long is a package for circular RNA identification using
+long-read sequencing data.")
+    (license license:expat)))
+
 (define-public python-circe
   (package
     (name "python-circe")
@@ -7074,16 +7168,14 @@ CWL descriptions.")
   (package
     (name "ravanan")
     (version "0.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/arunisaac/ravanan")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "1ap9h2d92wjvnn8914baqkx6xn8zdanxmpjfg81v3qx35pn938al"))))
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/arunisaac/ravanan/releases/download/v"
+                    version "/ravanan-" version ".tar.lz"))
+              (sha256
+               (base32
+                "00ayvxsgvma3231ja1759f5fr99a4nw3j23i8qz616wfxa54745s"))))
     (arguments
      (list #:make-flags
            #~(list (string-append "prefix=" #$output)
@@ -7117,7 +7209,7 @@ CWL descriptions.")
     (inputs
      (list bash-minimal
            node
-           (lookup-package-input guix "guile")
+           guile-3.0
            guile-filesystem
            guile-gcrypt
            guile-json-4
@@ -7236,7 +7328,7 @@ genome- and pangenome-scale queries using a laptop.")
 (define-public delly
   (package
     (name "delly")
-    (version "1.7.3")
+    (version "0.8.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -7244,7 +7336,7 @@ genome- and pangenome-scale queries using a laptop.")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "1ri7m7iv3wakm7zdwqdzm5m71y0swad9n78dzrzr9gs3j7j5yxjs"))
+               (base32 "1ibnplgfzj96w8glkx17v7sld3pm402fr5ybmf3h0rlcryabxrqy"))
               (modules '((guix build utils)))
               (snippet
                '(delete-file-recursively "src/htslib"))))
@@ -13116,22 +13208,28 @@ differently labelled data.")
 (define-public r-pando
   (package
     (name "r-pando")
-    (version "1.1.1")
+    (version "1.0.5")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-              (url "https://github.com/quadbio/Pando")
-              (commit (string-append "v" version))))
+             (url "https://github.com/quadbiolab/Pando")
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1zcsg3my1ka2wprvlx8p08cdz3dqphga54d5rp418zfhcyjy4fkp"))))
+        (base32 "04kr1b28p5j7h48g32cldkg87xcmxnmd4kspygkfs7a4amihpi66"))))
     (properties `((upstream-name . "Pando")))
     (build-system r-build-system)
     (arguments
      (list
       ;; The test file data/test_seurat.rds is not included.
-      #:tests? #false))
+      #:tests? #false
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'loosen-requirements
+           (lambda _
+             (substitute* "DESCRIPTION"
+               ((" \\(==.*,") ",")))))))
     (propagated-inputs
      (list r-bayestestr
            r-foreach

gnu/packages/bison.scm

@@ -21,14 +21,15 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages bison)
-  #:use-module (guix licenses)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix utils)
-  #:use-module (guix build-system gnu)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages m4)
   #:use-module (gnu packages perl)
-  #:use-module (gnu packages flex)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix download)
+  #:use-module (guix gexp)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
   #:use-module (srfi srfi-1))
 
 (define-public bison
@@ -45,24 +46,29 @@
         "1wjvbbzrr16k1jlby3l436an3kvv492h08arbnf0gwgprha05flv"))))
     (build-system gnu-build-system)
     (arguments
-     `(;; Building in parallel on many-core systems may cause an error such as
-       ;; "mv: cannot stat 'examples/c/reccalc/scan.stamp.tmp': No such file or
-       ;; directory".  See <https://bugs.gnu.org/36238>.
-       #:parallel-build? #f
-       ;; Similarly, when building tests in parallel, Make may produce this error:
-       ;; "./examples/c/reccalc/scan.l:13:10: fatal error: parse.h: No such file
-       ;; or directory".  Full log in <https://bugs.gnu.org/36238>.
-       #:parallel-tests? #f
-       ;; On the Hurd with glibc 2.41 bison uses weak symbols from pthread
-       ;; but does not link to it.
-       ,@(if (target-hurd?)
-             (list #:configure-flags ''("LIBS=-lpthread"))
-             '())))
-    (native-inputs (list perl
-                         ;; m4 is not present in PATH when cross-building.
-                         m4))
-    (inputs (list flex))
-    (propagated-inputs (list m4))
+     (list
+      ;; Building in parallel on many-core systems may cause an error such as
+      ;; "mv: cannot stat 'examples/c/reccalc/scan.stamp.tmp': No such file or
+      ;; directory".  See <https://bugs.gnu.org/36238>.
+      #:parallel-build? #f
+      ;; Similarly, when building tests in parallel, Make may produce this error:
+      ;; "./examples/c/reccalc/scan.l:13:10: fatal error: parse.h: No such file
+      ;; or directory".  Full log in <https://bugs.gnu.org/36238>.
+      #:parallel-tests? #f
+      #:configure-flags
+      ;; On the Hurd with glibc 2.41 bison uses weak symbols from pthread
+      ;; but does not link to it.
+      (if (target-hurd?)
+          #~(list "LIBS=-lpthread")
+          #~(list))))
+    (native-inputs
+     (list perl
+           ;; m4 is not present in PATH when cross-building.
+           m4))
+    (inputs
+     (list flex))
+    (propagated-inputs
+     (list m4))
     (home-page "https://www.gnu.org/software/bison/")
     (synopsis "Yacc-compatible parser generator")
     (description
@@ -72,4 +78,4 @@ grammar.  It is versatile enough to have many applications, from parsers for
 simple tools through complex programming languages.
 
 Bison also provides an implementation of @command{yacc}, as specified by POSIX.")
-    (license gpl3+)))
+    (license license:gpl3+)))

gnu/packages/bootstrap.scm

@@ -37,7 +37,7 @@
                 #:select (raw-derivation derivation-input derivation->output-path))
   #:use-module (guix utils)
   #:use-module ((guix build utils) #:select (elf-file?))
-  #:use-module ((guix gexp) #:select (lower-object local-file))
+  #:use-module (guix gexp)
   #:use-module (guix monads)
   #:use-module (guix memoization)
   #:use-module (guix i18n)
@@ -204,10 +204,7 @@ for system '~a'")
            (uri (map (cute string-append <>
                            (bootstrap-executable-file-name system program))
                      %bootstrap-executable-base-urls))
-           ;; XXX: In the long term, migrate all boostrap executables to
-           ;; (string-append "bootstrap-" program), and drop the additional
-           ;; file-name argument.
-           (file-name file-name)
+           (file-name (string-append "bootstrap-" program))
            (hash (content-hash bv sha256))))))))
 
 (define* (bootstrap-executable program system #:optional file-name)
@@ -267,32 +264,33 @@ or false to signal an error."
     (version "0")
     (build-system trivial-build-system)
     (arguments
-     `(#:guile ,%bootstrap-guile
-       #:modules ((guix build utils))
-       #:builder
-       (begin
-         (use-modules (guix build utils))
+     (list
+      #:guile %bootstrap-guile
+      #:modules '((guix build utils))
+      #:builder
+      #~(begin
+          (use-modules (guix build utils))
 
-         (let ((out     (assoc-ref %outputs "out"))
-              (tar     (assoc-ref %build-inputs "tar"))
-              (xz      (assoc-ref %build-inputs "xz"))
-              (tarball (assoc-ref %build-inputs "tarball")))
+          (let ((tar     (assoc-ref %build-inputs "bootstrap-tar"))
+                (xz      (assoc-ref %build-inputs "bootstrap-xz"))
+                (tarball (assoc-ref %build-inputs
+                                    #$(string-append name ".tar.xz"))))
 
-          (mkdir out)
-          (copy-file tarball "binaries.tar.xz")
-          (invoke xz "-d" "binaries.tar.xz")
-          (let ((builddir (getcwd)))
-            (with-directory-excursion out
-              (invoke tar "xvf"
-                      (string-append builddir "/binaries.tar"))
-              ,@(if snippet (list snippet) '())
-              (or (not ,program-to-test)
-                  (invoke (string-append "bin/" ,program-to-test)
-                          "--version"))))))))
+            (mkdir #$output)
+            (copy-file tarball "binaries.tar.xz")
+            (invoke xz "-d" "binaries.tar.xz")
+            (let ((builddir (getcwd)))
+              (with-directory-excursion #$output
+                (invoke tar "xvf"
+                        (string-append builddir "/binaries.tar"))
+                #$@(if snippet (list snippet) '())
+                (or (not #$program-to-test)
+                    (invoke (string-append "bin/" #$program-to-test)
+                            "--version"))))))))
     (inputs
-     `(("tar" ,(bootstrap-executable "tar" (%current-system)))
-       ("xz"  ,(bootstrap-executable "xz" (%current-system)))
-       ("tarball" ,(bootstrap-origin (source (%current-system))))))
+     (list (bootstrap-executable "tar" (%current-system))
+           (bootstrap-executable "xz" (%current-system))
+           (bootstrap-origin (source (%current-system)))))
     (source #f)
     (synopsis description)
     (description description)
@@ -635,37 +633,29 @@ $out/bin/guile --version~%"
                                             (_
                                              "/20131110/static-binaries.tar.xz")))
                                      %bootstrap-base-urls))
+                           (file-name "bootstrap-binaries.tar.xz")
                            (sha256
-                            (match system
-                              ("x86_64-linux"
-                               (base32
-                                "0c533p9dhczzcsa1117gmfq3pc8w362g4mx84ik36srpr7cx2bg4"))
-                              ("i686-linux"
-                               (base32
-                                "0s5b3jb315n13m1k8095l0a5hfrsz8g0fv1b6riyc5hnxqyphlak"))
-                              ("armhf-linux"
-                               (base32
-                                "0gf0fn2kbpxkjixkmx5f4z6hv6qpmgixl69zgg74dbsfdfj8jdv5"))
-                              ("aarch64-linux"
-                               (base32
-                                "18dfiq6c6xhsdpbidigw6480wh0vdgsxqq3xindq4lpdgqlccpfh"))
-                              ("powerpc64le-linux"
-                               (base32
-                                "0afs2j9z2d1hjq42myz4iwjh0aqgzf59inifw87x6b6p1z9wv92v"))
-                              ("i586-gnu"
-                               (base32
-                                "17kllqnf3fg79gzy9ansgi801c46yh9c23h4d923plvb0nfm1cfn"))
-                              ("x86_64-gnu"
-                               (base32
-                                "0xnw5p6279m8xazbhal5ld5qxsya0249z2l6jcc7w9ndh2gnx07v"))
-                              ("powerpc-linux"
-                               (base32
-                                "0kspxy0yczan2vlih6aa9hailr2inz000fqa0gn5x9d1fxxa5y8m"))
-                              ("riscv64-linux"
-                               (base32
-                                "0x0xjlpmyh6rkr51p00gp6pscgl6zjida1rsg8vk3rinyi6rrbkg"))
-                              ("mips64el-linux"
-                               (base32
+                            (base32
+                             (match system
+                               ("x86_64-linux"
+                                "0c533p9dhczzcsa1117gmfq3pc8w362g4mx84ik36srpr7cx2bg4")
+                               ("i686-linux"
+                                "0s5b3jb315n13m1k8095l0a5hfrsz8g0fv1b6riyc5hnxqyphlak")
+                               ("armhf-linux"
+                                "0gf0fn2kbpxkjixkmx5f4z6hv6qpmgixl69zgg74dbsfdfj8jdv5")
+                               ("aarch64-linux"
+                                "18dfiq6c6xhsdpbidigw6480wh0vdgsxqq3xindq4lpdgqlccpfh")
+                               ("powerpc64le-linux"
+                                "0afs2j9z2d1hjq42myz4iwjh0aqgzf59inifw87x6b6p1z9wv92v")
+                               ("i586-gnu"
+                                "17kllqnf3fg79gzy9ansgi801c46yh9c23h4d923plvb0nfm1cfn")
+                               ("x86_64-gnu"
+                                "04zksa2457h1vcl5ry2hyzhhsg8fckvfdgadp0viba3anwms2463")
+                               ("powerpc-linux"
+                                "0kspxy0yczan2vlih6aa9hailr2inz000fqa0gn5x9d1fxxa5y8m")
+                               ("riscv64-linux"
+                                "0x0xjlpmyh6rkr51p00gp6pscgl6zjida1rsg8vk3rinyi6rrbkg")
+                               ("mips64el-linux"
                                 "072y4wyfsj1bs80r6vbybbafy8ya4vfy7qj25dklwk97m6g71753"))))))
                         "fgrep"                    ; the program to test
                         "Bootstrap binaries of Coreutils, Awk, etc."
@@ -693,6 +683,7 @@ $out/bin/guile --version~%"
                        "/i686-linux/20190815/"
                        "linux-libre-headers-stripped-4.14.67-i686-linux.tar.xz")
                  %bootstrap-base-urls))
+       (file-name "linux-libre-headers-bootstrap.tar.xz")
        (sha256
         (base32
          "0sm2z9x4wk45bh6qfs94p0w1d6hsy6dqx9sw38qsqbvxwa1qzk8s"))))
@@ -700,63 +691,56 @@ $out/bin/guile --version~%"
    "Bootstrap linux-libre-headers"))
 
 (define %bootstrap-binutils
-  (package-from-tarball "binutils-bootstrap"
-                        (lambda (system)
-                          (origin
-                           (method url-fetch)
-                           (uri (map (cut string-append <> "/" system
-                                          (match system
-                                            ("armhf-linux"
-                                             "/20150101/binutils-2.25.tar.xz")
-                                            ("aarch64-linux"
-                                             "/20170217/binutils-2.27.tar.xz")
-                                            ("powerpc64le-linux"
-                                             "/20210106/binutils-static-stripped-2.34-powerpc64le-linux-gnu.tar.xz")
-                                            ("i586-gnu"
-                                             "/20200326/binutils-static-stripped-2.34-i586-pc-gnu.tar.xz")
-                                            ("x86_64-gnu"
-                                             "/20260302/binutils-static-stripped-2.44-x86_64-pc-gnu.tar.xz")
-                                            ("powerpc-linux"
-                                             "/20200923/binutils-2.35.1.tar.xz")
-                                            ("riscv64-linux"
-                                             "/20210725/binutils-2.34.tar.xz")
-                                            (_
-                                             "/20131110/binutils-2.23.2.tar.xz")))
-                                     %bootstrap-base-urls))
-                           (sha256
-                            (match system
-                              ("x86_64-linux"
-                               (base32
-                                "1j5yivz7zkjqfsfmxzrrrffwyayjqyfxgpi89df0w4qziqs2dg20"))
-                              ("i686-linux"
-                               (base32
-                                "14jgwf9gscd7l2pnz610b1zia06dvcm2qyzvni31b8zpgmcai2v9"))
-                              ("armhf-linux"
-                               (base32
-                                "1v7dj6bzn6m36f20gw31l99xaabq4xrhrx3gwqkhhig0mdlmr69q"))
-                              ("aarch64-linux"
-                               (base32
-                                "111s7ilfiby033rczc71797xrmaa3qlv179wdvsaq132pd51xv3n"))
-                              ("powerpc64le-linux"
-                               (base32
-                                "1klxy945c61134mzhqzz2gbk8w0n8jq7arwkrvz78d22ff2q0cwz"))
-                              ("riscv64-linux"
-                               (base32
-                                "0n9qf4vbilfmh1lknhw000waakj4q6s50pnjazr5137skm976z5m"))
-                              ("i586-gnu"
-                               (base32
-                                "11kykv1kmqc5wln57rs4klaqa13hm952smkc57qcsyss21kfjprs"))
-                              ("x86_64-gnu"
-                               (base32
-                                "033bgmaa012b2lw8g76b02mjgzdnzv2yd3jvaqbhqrr5q9r3xn04"))
-                              ("powerpc-linux"
-                               (base32
-                                "0asbg1c4avkrvh057mx0942xwddd136jni382zqsxzn79ls42yq8"))
-                              ("mips64el-linux"
-                               (base32
-                                "1x8kkhcxmfyzg1ddpz2pxs6fbdl6412r7x0nzbmi5n7mj8zw2gy7"))))))
-                        "ld"                      ; the program to test
-                        "Bootstrap binaries of the GNU Binutils"))
+  (package-from-tarball
+   "binutils-bootstrap"
+   (lambda (system)
+     (origin
+       (method url-fetch)
+       (uri (map (cut string-append <> "/" system
+                      (match system
+                        ("armhf-linux"
+                         "/20150101/binutils-2.25.tar.xz")
+                        ("aarch64-linux"
+                         "/20170217/binutils-2.27.tar.xz")
+                        ("powerpc64le-linux"
+                         "/20210106/binutils-static-stripped-2.34-powerpc64le-linux-gnu.tar.xz")
+                        ("i586-gnu"
+                         "/20200326/binutils-static-stripped-2.34-i586-pc-gnu.tar.xz")
+                        ("x86_64-gnu"
+                         "/20241122/binutils-static-stripped-2.41-x86_64-pc-gnu.tar.xz")
+                        ("powerpc-linux"
+                         "/20200923/binutils-2.35.1.tar.xz")
+                        ("riscv64-linux"
+                         "/20210725/binutils-2.34.tar.xz")
+                        (_
+                         "/20131110/binutils-2.23.2.tar.xz")))
+                 %bootstrap-base-urls))
+       (file-name "binutils-bootstrap.tar.xz")
+       (sha256
+        (base32
+         (match system
+           ("x86_64-linux"
+            "1j5yivz7zkjqfsfmxzrrrffwyayjqyfxgpi89df0w4qziqs2dg20")
+           ("i686-linux"
+            "14jgwf9gscd7l2pnz610b1zia06dvcm2qyzvni31b8zpgmcai2v9")
+           ("armhf-linux"
+            "1v7dj6bzn6m36f20gw31l99xaabq4xrhrx3gwqkhhig0mdlmr69q")
+           ("aarch64-linux"
+            "111s7ilfiby033rczc71797xrmaa3qlv179wdvsaq132pd51xv3n")
+           ("powerpc64le-linux"
+            "1klxy945c61134mzhqzz2gbk8w0n8jq7arwkrvz78d22ff2q0cwz")
+           ("riscv64-linux"
+            "0n9qf4vbilfmh1lknhw000waakj4q6s50pnjazr5137skm976z5m")
+           ("i586-gnu"
+            "11kykv1kmqc5wln57rs4klaqa13hm952smkc57qcsyss21kfjprs")
+           ("x86_64-gnu"
+            "1fasv76rppnqlshjqc7dbzngic9cqswi5ydzg6w9rc075daqk8kb")
+           ("powerpc-linux"
+            "0asbg1c4avkrvh057mx0942xwddd136jni382zqsxzn79ls42yq8")
+           ("mips64el-linux"
+            "1x8kkhcxmfyzg1ddpz2pxs6fbdl6412r7x0nzbmi5n7mj8zw2gy7"))))))
+   "ld"                      ; the program to test
+   "Bootstrap binaries of the GNU Binutils"))
 
 (define %bootstrap-glibc
   ;; The initial libc.
@@ -766,99 +750,91 @@ $out/bin/guile --version~%"
     (source #f)
     (build-system trivial-build-system)
     (arguments
-     `(#:guile ,%bootstrap-guile
-       #:modules ((guix build utils))
-       #:builder
-       (begin
-         (use-modules (guix build utils))
+     (list
+      #:guile %bootstrap-guile
+      #:modules '((guix build utils))
+      #:builder
+      #~(begin
+          (use-modules (guix build utils))
 
-         (let ((out     (assoc-ref %outputs "out"))
-              (tar     (assoc-ref %build-inputs "tar"))
-              (xz      (assoc-ref %build-inputs "xz"))
-              (tarball (assoc-ref %build-inputs "tarball")))
+          (let ((tar     (assoc-ref %build-inputs "bootstrap-tar"))
+                (xz      (assoc-ref %build-inputs "bootstrap-xz"))
+                (tarball (assoc-ref %build-inputs "glibc.tar.xz")))
 
-          (mkdir out)
-          (copy-file tarball "binaries.tar.xz")
-          (invoke xz "-d" "binaries.tar.xz")
-          (let ((builddir (getcwd)))
-            (with-directory-excursion out
-              (invoke tar "xvf"
-                      (string-append builddir
-                                     "/binaries.tar"))
-              (chmod "lib" #o755)
+            (mkdir #$output)
+            (copy-file tarball "binaries.tar.xz")
+            (invoke xz "-d" "binaries.tar.xz")
+            (let ((builddir (getcwd)))
+              (with-directory-excursion #$output
+                (invoke tar "xvf"
+                        (string-append builddir
+                                       "/binaries.tar"))
+                (chmod "lib" #o755)
 
-              ;; Patch linker scripts so they refer to the right file-names.
-              (substitute* ,(cond ((target-hurd64?)
-                                   ''("lib/libc.so" "lib/libm.so"))
-                                  ((and (not (target-hurd?))
-                                        (or (target-x86?)
-                                            (target-arm?)))
-                                   ''("lib/libc.so" "lib/libpthread.so"))
-                                  (else
-                                   ''("lib/libc.so")))
-                (("/[^ ]+/lib/(libc|libh|libm|libpthread|ld)" _ prefix)
-                 (string-append out "/lib/" prefix)))
-              ,@(if (target-arm32?)
-                    `((substitute* "lib/libpthread.so"
-                        (("/[^ ]+/lib/libpthread_nonshared\\.a") "")))
-                    `())))))))
+                ;; Patch linker scripts so they refer to the right file-names.
+                (substitute* #$(cond ((target-hurd64?)
+                                      ''("lib/libc.so" "lib/libm.so"))
+                                     ((and (not (target-hurd?))
+                                           (or (target-x86?)
+                                               (target-arm?)))
+                                      ''("lib/libc.so" "lib/libpthread.so"))
+                                     (else
+                                      ''("lib/libc.so")))
+                  (("/[^ ]+/lib/(libc|libh|libm|libpthread|ld)" _ prefix)
+                   (string-append #$output "/lib/" prefix)))
+                #$@(if (target-arm32?)
+                       #~((substitute* "lib/libpthread.so"
+                            (("/[^ ]+/lib/libpthread_nonshared\\.a") "")))
+                       #~())))))))
     (inputs
-     `(("tar" ,(bootstrap-executable "tar" (%current-system)))
-       ("xz"  ,(bootstrap-executable "xz" (%current-system)))
-       ("tarball" ,(bootstrap-origin
-                    (origin
-                     (method url-fetch)
-                     (uri (map (cut string-append <> "/" (%current-system)
-                                    (match (%current-system)
-                                      ("armhf-linux"
-                                       "/20150101/glibc-2.20.tar.xz")
-                                      ("aarch64-linux"
-                                       "/20170217/glibc-2.25.tar.xz")
-                                      ("powerpc64le-linux"
-                                       "/20210106/glibc-stripped-2.31-powerpc64le-linux-gnu.tar.xz")
-                                      ("i586-gnu"
-                                       "/20240816/glibc-stripped-2.39-i586-pc-gnu.tar.xz")
-                                      ("x86_64-gnu"
-                                       "/20260302/glibc-stripped-2.41-x86_64-pc-gnu.tar.xz")
-                                      ("powerpc-linux"
-                                       "/20200923/glibc-2.32.tar.xz")
-                                      ("riscv64-linux"
-                                       "/20210725/glibc-2.31.tar.xz")
-                                      (_
-                                       "/20131110/glibc-2.18.tar.xz")))
-                               %bootstrap-base-urls))
-                     (sha256
-                      (match (%current-system)
-                        ("x86_64-linux"
-                         (base32
-                          "0jlqrgavvnplj1b083s20jj9iddr4lzfvwybw5xrcis9spbfzk7v"))
-                        ("i686-linux"
-                         (base32
-                          "1hgrccw1zqdc7lvgivwa54d9l3zsim5pqm0dykxg0z522h6gr05w"))
-                        ("armhf-linux"
-                         (base32
-                          "18cmgvpllqfpn6khsmivqib7ys8ymnq0hdzi3qp24prik0ykz8gn"))
-                        ("aarch64-linux"
-                         (base32
-                          "07nx3x8598i2924rjnlrncg6rm61c9bmcczbbcpbx0fb742nvv5c"))
-                        ("powerpc64le-linux"
-                         (base32
-                          "1a1df6z8gkaq09md3jy94lixnh20599p58p0s856p10xwjaqr1iz"))
-                        ("riscv64-linux"
-                         (base32
-                          "0d9x80vm7ca1pd2whcmpm1h14zxpb58kqajlxlwffzm04xfsjnxm"))
-                        ("i586-gnu"
-                         (base32
-                          "0x2x6w611k6v9qdabacawamw2475p04hm3s0q95xcg063wjq4ig2"))
-                        ("x86_64-gnu"
-                         (base32
-                          "1lpvk0l7qqvz46cnxm64a1a40zg0gj90j3glyk67i1sh5r4znlmy"))
-                        ("powerpc-linux"
-                         (base32
-                          "0smmssyjrlk5cvx49586smmk81gkwff0i6r91n4rir4jm6ba25sb"))
-                        ("mips64el-linux"
-                         (base32
-                          "0k97a3whzx3apsi9n2cbsrr79ad6lh00klxph9hw4fqyp1abkdsg")))))))))
+     (list (bootstrap-executable "tar" (%current-system))
+           (bootstrap-executable "xz" (%current-system))
+           (bootstrap-origin
+            (origin
+              (method url-fetch)
+              (uri (map (cut string-append <> "/" (%current-system)
+                             (match (%current-system)
+                               ("armhf-linux"
+                                "/20150101/glibc-2.20.tar.xz")
+                               ("aarch64-linux"
+                                "/20170217/glibc-2.25.tar.xz")
+                               ("powerpc64le-linux"
+                                "/20210106/glibc-stripped-2.31-powerpc64le-linux-gnu.tar.xz")
+                               ("i586-gnu"
+                                "/20240816/glibc-stripped-2.39-i586-pc-gnu.tar.xz")
+                               ("x86_64-gnu"
+                                "/20241122/glibc-stripped-2.39-x86_64-pc-gnu.tar.xz")
+                               ("powerpc-linux"
+                                "/20200923/glibc-2.32.tar.xz")
+                               ("riscv64-linux"
+                                "/20210725/glibc-2.31.tar.xz")
+                               (_
+                                "/20131110/glibc-2.18.tar.xz")))
+                        %bootstrap-base-urls))
+              (file-name "glibc.tar.xz")
+              (sha256
+               (base32
+                (match (%current-system)
+                  ("x86_64-linux"
+                   "0jlqrgavvnplj1b083s20jj9iddr4lzfvwybw5xrcis9spbfzk7v")
+                  ("i686-linux"
+                   "1hgrccw1zqdc7lvgivwa54d9l3zsim5pqm0dykxg0z522h6gr05w")
+                  ("armhf-linux"
+                   "18cmgvpllqfpn6khsmivqib7ys8ymnq0hdzi3qp24prik0ykz8gn")
+                  ("aarch64-linux"
+                   "07nx3x8598i2924rjnlrncg6rm61c9bmcczbbcpbx0fb742nvv5c")
+                  ("powerpc64le-linux"
+                   "1a1df6z8gkaq09md3jy94lixnh20599p58p0s856p10xwjaqr1iz")
+                  ("riscv64-linux"
+                   "0d9x80vm7ca1pd2whcmpm1h14zxpb58kqajlxlwffzm04xfsjnxm")
+                  ("i586-gnu"
+                   "0x2x6w611k6v9qdabacawamw2475p04hm3s0q95xcg063wjq4ig2")
+                  ("x86_64-gnu"
+                   "1w4h91kxl64a62l646966i73zp2cj6w4dmyc64fh0c1hhdykxass")
+                  ("powerpc-linux"
+                   "0smmssyjrlk5cvx49586smmk81gkwff0i6r91n4rir4jm6ba25sb")
+                  ("mips64el-linux"
+                   "0k97a3whzx3apsi9n2cbsrr79ad6lh00klxph9hw4fqyp1abkdsg"))))))))
     (synopsis "Bootstrap binaries and headers of the GNU C Library")
     (description synopsis)
     (home-page #f)
@@ -873,110 +849,102 @@ $out/bin/guile --version~%"
     (source #f)
     (build-system trivial-build-system)
     (arguments
-     `(#:guile ,%bootstrap-guile
-       #:modules ((guix build utils))
-       #:builder
-       (begin
-         (use-modules (guix build utils)
-                      (ice-9 popen))
+     (list
+      #:guile %bootstrap-guile
+      #:modules '((guix build utils))
+      #:builder
+      #~(begin
+          (use-modules (guix build utils)
+                       (ice-9 popen))
 
-         (let ((out     (assoc-ref %outputs "out"))
-               (tar     (assoc-ref %build-inputs "tar"))
-               (xz      (assoc-ref %build-inputs "xz"))
-               (bash    (assoc-ref %build-inputs "bash"))
-               (libc    (assoc-ref %build-inputs "libc"))
-               (tarball (assoc-ref %build-inputs "tarball")))
+          (let ((tar     (assoc-ref %build-inputs "bootstrap-tar"))
+                (xz      (assoc-ref %build-inputs "bootstrap-xz"))
+                (bash    (assoc-ref %build-inputs "bootstrap-bash"))
+                (libc    (assoc-ref %build-inputs "glibc-bootstrap"))
+                (tarball (assoc-ref %build-inputs "gcc.tar.xz")))
 
-           (mkdir out)
-           (copy-file tarball "binaries.tar.xz") ;avoid: more than one hard link
-           (invoke xz "-d" "binaries.tar.xz")
-           (let ((builddir (getcwd))
-                 (bindir   (string-append out "/bin")))
+            (mkdir #$output)
+            (copy-file tarball "binaries.tar.xz") ;avoid: more than one hard link
+            (invoke xz "-d" "binaries.tar.xz")
+            (let ((builddir (getcwd))
+                  (bindir   (string-append #$output "/bin")))
 
-             (define (wrap-program program)
-               (let ((wrapped (format #f ".~a-wrapped" program)))
-                 (rename-file program wrapped)
-                 (call-with-output-file program
-                   (lambda (p)
-                     (format p "#!~a
+              (define (wrap-program program)
+                (let ((wrapped (format #f ".~a-wrapped" program)))
+                  (rename-file program wrapped)
+                  (call-with-output-file program
+                    (lambda (p)
+                      (format p "#!~a
 exec ~a/bin/~a -B~a/lib \
      -Wl,-rpath -Wl,~a/lib \
      -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%"
-                             bash
-                             out wrapped
-                             libc libc libc
-                             ,(glibc-dynamic-linker)))))
-               (chmod program #o555))
+                              bash
+                              #$output wrapped
+                              libc libc libc
+                              #$(glibc-dynamic-linker)))))
+                (chmod program #o555))
 
-             (with-directory-excursion out
-               (invoke tar "xvf"
-                       (string-append builddir "/binaries.tar")))
+              (with-directory-excursion #$output
+                (invoke tar "xvf"
+                        (string-append builddir "/binaries.tar")))
 
-             (with-directory-excursion bindir
-               (chmod "." #o755)
-               (for-each wrap-program
-                         ,(if (target-hurd64?)
-                              ''("gcc" "g++")
-                              ''("gcc")))))))))
+              (with-directory-excursion bindir
+                (chmod "." #o755)
+                (for-each wrap-program
+                          #$(if (target-hurd64?)
+                                ''("gcc" "g++")
+                                ''("gcc")))))))))
     (inputs
-     `(("tar" ,(bootstrap-executable "tar" (%current-system)))
-       ("xz"  ,(bootstrap-executable "xz" (%current-system)))
-       ("bash" ,(bootstrap-executable "bash" (%current-system)))
-       ("libc" ,%bootstrap-glibc)
-       ("tarball" ,(bootstrap-origin
-                    (origin
-                      (method url-fetch)
-                      (uri (map (cut string-append <> "/" (%current-system)
-                                     (match (%current-system)
-                                       ("armhf-linux"
-                                        "/20150101/gcc-4.8.4.tar.xz")
-                                       ("aarch64-linux"
-                                        "/20170217/gcc-5.4.0.tar.xz")
-                                       ("powerpc64le-linux"
-                                        "/20210106/gcc-stripped-5.5.0-powerpc64le-linux-gnu.tar.xz")
-                                       ("i586-gnu"
-                                        "/20200326/gcc-stripped-5.5.0-i586-pc-gnu.tar.xz")
-                                       ("x86_64-gnu"
-                                        "/20260302/gcc-stripped-14.3.0-x86_64-pc-gnu.tar.xz")
-                                       ("powerpc-linux"
-                                        "/20200923/gcc-5.5.0.tar.xz")
-                                       ("riscv64-linux"
-                                        "/20210725/gcc-7.5.0.tar.xz")
-                                       (_
-                                        "/20131110/gcc-4.8.2.tar.xz")))
-                                %bootstrap-base-urls))
-                      (sha256
-                       (match (%current-system)
-                         ("x86_64-linux"
-                          (base32
-                           "17ga4m6195n4fnbzdkmik834znkhs53nkypp6557pl1ps7dgqbls"))
-                         ("i686-linux"
-                          (base32
-                           "150c1arrf2k8vfy6dpxh59vcgs4p1bgiz2av5m19dynpks7rjnyw"))
-                         ("armhf-linux"
-                          (base32
-                           "0ghz825yzp43fxw53kd6afm8nkz16f7dxi9xi40bfwc8x3nbbr8v"))
-                         ("aarch64-linux"
-                          (base32
-                           "1ar3vdzyqbfm0z36kmvazvfswxhcihlacl2dzdjgiq25cqnq9ih1"))
-                         ("powerpc64le-linux"
-                          (base32
-                           "151kjsai25vz2s667bgzpisx8f281fpl3n9pxz2yrp9jlnadz3m1"))
-                         ("riscv64-linux"
-                          (base32
-                           "1k4mbnb54wj2q37fgshf5dfixixqnhn002vhzvi9pnb57xb9v14d"))
-                         ("i586-gnu"
-                          (base32
-                           "1j2zc58wzil71a34h7c70sd68dmqvcscrw3rmn2whq79vd70zvv5"))
-                         ("x86_64-gnu"
-                          (base32
-                           "1fhi7f5zld08b6qsyv1d48ha7z0vr8pxr4kf8x7aq1a3kbcv5rkz"))
-                         ("powerpc-linux"
-                          (base32
-                           "1p7df3yixhm87dw5sccc6yn1i9db1r9hnmsg87wq5xi4rfmirq7w"))
-                         ("mips64el-linux"
-                          (base32
-                           "1m5miqkyng45l745n0sfafdpjkqv9225xf44jqkygwsipj2cv9ks")))))))))
+     (list (bootstrap-executable "tar" (%current-system))
+           (bootstrap-executable "xz" (%current-system))
+           (bootstrap-executable "bash" (%current-system))
+           %bootstrap-glibc
+           (bootstrap-origin
+            (origin
+              (method url-fetch)
+              (uri (map (cut string-append <> "/" (%current-system)
+                             (match (%current-system)
+                               ("armhf-linux"
+                                "/20150101/gcc-4.8.4.tar.xz")
+                               ("aarch64-linux"
+                                "/20170217/gcc-5.4.0.tar.xz")
+                               ("powerpc64le-linux"
+                                "/20210106/gcc-stripped-5.5.0-powerpc64le-linux-gnu.tar.xz")
+                               ("i586-gnu"
+                                "/20200326/gcc-stripped-5.5.0-i586-pc-gnu.tar.xz")
+                               ("x86_64-gnu"
+                                "/20241122/gcc-stripped-14.2.0-x86_64-pc-gnu.tar.xz")
+                               ("powerpc-linux"
+                                "/20200923/gcc-5.5.0.tar.xz")
+                               ("riscv64-linux"
+                                "/20210725/gcc-7.5.0.tar.xz")
+                               (_
+                                "/20131110/gcc-4.8.2.tar.xz")))
+                        %bootstrap-base-urls))
+              (file-name "gcc.tar.xz")
+              (sha256
+               (base32
+                (match (%current-system)
+                  ("x86_64-linux"
+                   "17ga4m6195n4fnbzdkmik834znkhs53nkypp6557pl1ps7dgqbls")
+                  ("i686-linux"
+                   "150c1arrf2k8vfy6dpxh59vcgs4p1bgiz2av5m19dynpks7rjnyw")
+                  ("armhf-linux"
+                   "0ghz825yzp43fxw53kd6afm8nkz16f7dxi9xi40bfwc8x3nbbr8v")
+                  ("aarch64-linux"
+                   "1ar3vdzyqbfm0z36kmvazvfswxhcihlacl2dzdjgiq25cqnq9ih1")
+                  ("powerpc64le-linux"
+                   "151kjsai25vz2s667bgzpisx8f281fpl3n9pxz2yrp9jlnadz3m1")
+                  ("riscv64-linux"
+                   "1k4mbnb54wj2q37fgshf5dfixixqnhn002vhzvi9pnb57xb9v14d")
+                  ("i586-gnu"
+                   "1j2zc58wzil71a34h7c70sd68dmqvcscrw3rmn2whq79vd70zvv5")
+                  ("x86_64-gnu"
+                   "1cgbhc76hlccx6v2z7kk7z173lryyq3la5mmbwivl6hbl1zcqg3m")
+                  ("powerpc-linux"
+                   "1p7df3yixhm87dw5sccc6yn1i9db1r9hnmsg87wq5xi4rfmirq7w")
+                  ("mips64el-linux"
+                   "1m5miqkyng45l745n0sfafdpjkqv9225xf44jqkygwsipj2cv9ks"))))))))
     (native-search-paths
      (list (search-path-specification
             (variable "C_INCLUDE_PATH")
@@ -997,14 +965,12 @@ exec ~a/bin/~a -B~a/lib \
   ;; own packages.
   (match (%current-system)
     ((or "i686-linux" "x86_64-linux")
-     `(("linux-libre-headers" ,%bootstrap-linux-libre-headers)))
+     (list %bootstrap-linux-libre-headers))
     (_
-     `(("libc" ,%bootstrap-glibc)
-       ("gcc" ,%bootstrap-gcc)
-       ("binutils" ,%bootstrap-binutils)
-       ("coreutils&co" ,%bootstrap-coreutils&co)
-       ;; In gnu-build-system.scm, we rely on the availability of Bash.
-       ("bash" ,%bootstrap-coreutils&co)))))
+     (list %bootstrap-glibc
+           %bootstrap-gcc
+           %bootstrap-binutils
+           %bootstrap-coreutils&co))))
 
 (define %bootstrap-inputs-for-tests
   ;; These are bootstrap inputs that are cheap to produce (no compilation

gnu/packages/build-tools.scm

@@ -26,7 +26,6 @@
 ;;; 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.
 ;;;
@@ -101,7 +100,6 @@
   #: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)
@@ -141,48 +139,6 @@ 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/cinnamon.scm

@@ -253,7 +253,7 @@ as well as some desktop-wide documents.")
            pkg-config
            xorg-server-for-tests))
     (inputs
-     (list at-spi2-core
+     (list atk
            cinnamon-desktop
            exempi
            gsettings-desktop-schemas

gnu/packages/code.scm

@@ -695,6 +695,57 @@ Kcov uses DWARF debugging information for compiled programs to make it
 possible to collect coverage information without special compiler switches.")
     (license license:gpl2+)))
 
+(define-public rtags
+  (package
+    (name "rtags")
+    (version "2.18")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Andersbakken/rtags")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (patches (search-patches "rtags-separate-rct.patch"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Part of spliting rct with rtags.
+        ;; Substitute #include "rct/header.h" with #include <rct/header.h>.
+        '(with-directory-excursion "src"
+           (delete-file-recursively "rct")        ;remove bundled copy
+           (let ((files (find-files "." ".*\\.cpp|.*\\.h")))
+             (substitute* files
+               (("#include ?\"rct/(.*.h)\"" all header)
+                (string-append "#include <rct/" header ">")))
+             #t)))
+       (sha256
+        (base32
+         "0raqjbkl1ykga4ahgl9xw49cgh3cyqcf42z36z7d6fz1fw192kg0"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:build-type "RelWithDebInfo"
+       #:configure-flags
+       '("-DRTAGS_NO_ELISP_FILES=1")
+       #:tests? #f))
+    (native-inputs
+     (list pkg-config))
+    (inputs
+     (list bash-completion
+           clang
+           llvm
+           lua
+           rct
+           selene))
+    (home-page "https://github.com/Andersbakken/rtags")
+    (synopsis "Indexer for the C language family with Emacs integration")
+    (description
+     "RTags is a client/server application that indexes C/C++ code and keeps a
+persistent file-based database of references, declarations, definitions,
+symbolnames etc.  There’s also limited support for ObjC/ObjC++.  It allows you
+to find symbols by name (including nested class and namespace scope).  Most
+importantly we give you proper follow-symbol and find-references support.")
+    (license license:gpl3+)))
+
 (define-public colormake
   (package
     (name "colormake")

gnu/packages/compression.scm

@@ -406,10 +406,9 @@ file; as a result, it is often used in conjunction with \"tar\", resulting in
 
            ;; Don't attempt to run the tests when cross-compiling.
            #:tests? (not (%current-target-system))))
-    (inputs
-     `(,@(if (%current-target-system)
-             `(("bash" ,bash-minimal))
-             '())))
+    (inputs (if (%current-target-system)
+                (list bash-minimal)
+                (list)))
     (outputs '("out" "static"))
     (synopsis "High-quality data compression program")
     (description
@@ -554,7 +553,7 @@ formats, including zstd, xz, gzip, and bgzf.")
 (define-public xz
   (package
    (name "xz")
-   (version "5.4.5")
+   (version "5.8.1")
    (source (origin
             (method url-fetch)
             (uri (list (string-append "http://tukaani.org/xz/xz-" version
@@ -563,7 +562,7 @@ formats, including zstd, xz, gzip, and bgzf.")
                                       version ".tar.gz")))
             (sha256
              (base32
-              "1mmpwl4kg1vs6n653gkaldyn43dpbjh8gpk7sk0gps5f6jwr0p0k"))))
+              "0hsmg58a27jd1vq0lc6yp405978c1nfhqwndl7f10v1mk6sjay2h"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
@@ -581,7 +580,7 @@ formats, including zstd, xz, gzip, and bgzf.")
               (substitute* (string-append out "/lib/liblzma.la")
                 (("^old_library='liblzma.a'") "old_library=''"))
               #t))))))
-   (outputs '("out" "static"))
+   (outputs '("out" "static" "doc"))
    (inputs
     `(,@(if (%current-target-system)
             `(("bash" ,bash-minimal))
@@ -598,6 +597,8 @@ compression algorithm is currently LZMA2, which is used inside the .xz
 container format.  With typical files, XZ Utils create 30 % smaller output
 than gzip and 15 % smaller output than bzip2.")
    (license (list license:gpl2+ license:lgpl2.1+)) ; bits of both
+   (properties
+    `((output-synopsis "doc" "API documentation and example code")))
    (home-page "https://tukaani.org/xz/")))
 
 (define-public heatshrink

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 "0.2.0")
+    (version "0.1.1")
     (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 "1dy48qkz3ifxagijpvwg7rmq7hz3pikhdcfral6djyc9ppmz8mbm"))))
+        (base32 "1ij6rfs5pfykk8c53q029sl2qx3k572dqdfb6pn5s569l6697ci1"))))
     (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-dotenv guile-yamlpp))
+    (inputs (list guix guile-yamlpp))
     (native-search-paths
      (list $GUIX_EXTENSIONS_PATH))
     (synopsis "Guix' docker compose compatibility layer")

gnu/packages/cpp.scm

@@ -683,6 +683,38 @@ computer program to introspect and modify an object at runtime.  It is also
 the name of the library itself, which is written in C++.")
     (license license:expat)))
 
+(define-public rct
+  (let* ((commit "b3e6f41d9844ef64420e628e0c65ed98278a843a")
+         (revision "2"))
+    (package
+      (name "rct")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/Andersbakken/rct")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1m2931jacka27ghnpgf1z1plkkr64z0pga4r4zdrfpp2d7xnrdvb"))
+                (patches (search-patches "rct-add-missing-headers.patch"))
+                (file-name (git-file-name name version))))
+      (build-system cmake-build-system)
+      (arguments
+       '(#:configure-flags
+         '("-DWITH_TESTS=ON"            ; To run the test suite
+           "-DRCT_RTTI_ENABLED=ON")))
+      (native-inputs
+       (list cppunit pkg-config))
+      (inputs
+       (list openssl zlib))
+      (home-page "https://github.com/Andersbakken/rct")
+      (synopsis "C++ library providing Qt-like APIs on top of the STL")
+      (description "Rct is a set of C++ tools that provide nicer (more Qt-like)
+ APIs on top of Standard Template Library (@dfn{STL}) classes.")
+      (license (list license:expat        ; cJSON
+                     license:bsd-4)))))   ; everything else (LICENSE.txt)
+
 (define-public plutovg
   (package
     (name "plutovg")

gnu/packages/cross-base.scm

@@ -135,10 +135,20 @@
                                         (search-patches
                                          "ath9k-htc-firmware-binutils.patch")))
                  ((target-mingw? target)
-                  (package-with-extra-patches binutils
-                                              (search-patches
-                                               "binutils-cross-windres.patch"
-                                               "binutils-mingw-w64-deterministic.patch")))
+                  (package-with-extra-patches
+                   (package-with-extra-configure-variable
+                    ;; mingw binutils does not work correctly when configured
+                    ;; with `--enable-compressed-debug-sections`. An error
+                    ;; like the following will occur whenever you try to link:
+                    ;;
+                    ;;   x86_64-w64-mingw32-ld: final link failed: bad value
+                    ;;
+                    ;; TODO: This seems like a deeper problem that warrants
+                    ;; deeper investigation.
+                    binutils "--enable-compressed-debug-sections" "no")
+                   (search-patches
+                    "binutils-cross-windres.patch"
+                    "binutils-mingw-w64-deterministic.patch")))
                  (else binutils))
            target)))
 
@@ -557,16 +567,15 @@ the base compiler.  Use XBINUTILS as the associated cross-Binutils."
                         (srfi srfi-26))
              ,@(package-arguments glibc/hurd-headers))
          ((#:phases phases)
-          `(modify-phases ,phases
-             (add-after 'unpack 'set-cross-headers-path
-               (lambda* (#:key inputs #:allow-other-keys)
-                 (let* ((mach (assoc-ref inputs "gnumach-headers"))
-                        (hurd (assoc-ref inputs "hurd-headers"))
-                        (cpath (string-append mach "/include:"
-                                              hurd "/include")))
-                   (for-each (cut setenv <> cpath)
-                             ',%gcc-cross-include-paths)
-                   #t)))))
+          #~(modify-phases #$phases
+              (add-after 'unpack 'set-cross-headers-path
+                (lambda* (#:key inputs #:allow-other-keys)
+                  (let* ((mach (assoc-ref inputs "gnumach-headers"))
+                         (hurd (assoc-ref inputs "hurd-headers"))
+                         (cpath (string-append mach "/include:"
+                                               hurd "/include")))
+                    (for-each (cut setenv <> cpath)
+                              '#$%gcc-cross-include-paths))))))
          ((#:configure-flags flags)
           `(cons* ,(string-append "--build=" (%current-system))
                   ,(string-append "--host=" target)
@@ -681,80 +690,78 @@ returned."
       (name (string-append "glibc-cross-" target))
       (arguments
        (substitute-keyword-arguments
-         `(;; Disable stripping (see above.)
-           #:strip-binaries? #f
+           `(;; Disable stripping (see above.)
+             #:strip-binaries? #f
 
-           ;; This package is used as a target input, but it should not have
-           ;; the usual cross-compilation inputs since that would include
-           ;; itself.
-           #:implicit-cross-inputs? #f
+                               ;; This package is used as a target input, but it should not have
+                               ;; the usual cross-compilation inputs since that would include
+                               ;; itself.
+                               #:implicit-cross-inputs? #f
 
-           ;; We need SRFI 26.
-           #:modules ((guix build gnu-build-system)
-                      (guix build utils)
-                      (srfi srfi-26))
+                               ;; We need SRFI 26.
+                               #:modules ((guix build gnu-build-system)
+                                          (guix build utils)
+                                          (srfi srfi-26))
 
-               ,@(package-arguments libc))
-           ((#:configure-flags flags)
-            `(cons ,(string-append "--host=" target)
-                   ,(if (target-hurd? target)
-                        `(append (list "--disable-werror")
-                                 ,flags)
+                               ,@(package-arguments libc))
+         ((#:configure-flags flags)
+          #~(cons #$(string-append "--host=" target)
+                  #$(if (target-hurd? target)
+                        #~(append (list "--disable-werror")
+                                  #$flags)
                         flags)))
-           ((#:phases phases)
-            `(modify-phases ,phases
-               (add-before 'configure 'set-cross-kernel-headers-path
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   (let* ((kernel (assoc-ref inputs "kernel-headers"))
-                          (cpath (string-append kernel "/include")))
-                     (for-each (cut setenv <> cpath)
-                               ',%gcc-cross-include-paths)
-                     (setenv "CROSS_LIBRARY_PATH"
-                             (string-append kernel "/lib")) ; for Hurd's libihash
-                     #t)))
-               (add-before 'configure 'add-cross-binutils-to-PATH
-                 (lambda* (#:key native-inputs inputs #:allow-other-keys)
-                   ;; Add BINUTILS/TARGET/bin to $PATH so that 'gcc
-                   ;; -print-prog-name=objdump' returns the correct name.  See
-                   ;; <https://inbox.sourceware.org/libc-alpha/d72f5f6f-cc3a-bd89-0800-ffb068928e0f@linaro.org/t/>.
-                   (define cross-objdump
-                     (search-input-file
-                      (or native-inputs inputs)
-                      (string-append ,target "/bin/objdump")))
+         ((#:phases phases)
+          #~(modify-phases #$phases
+              (add-before 'configure 'set-cross-kernel-headers-path
+                (lambda* (#:key inputs #:allow-other-keys)
+                  (let* ((kernel (assoc-ref inputs "kernel-headers"))
+                         (cpath (string-append kernel "/include")))
+                    (for-each (cut setenv <> cpath)
+                              '#$%gcc-cross-include-paths)
+                    (setenv "CROSS_LIBRARY_PATH"
+                            (string-append kernel "/lib"))))) ; for Hurd's libihash
+              (add-before 'configure 'add-cross-binutils-to-PATH
+                (lambda* (#:key native-inputs inputs #:allow-other-keys)
+                  ;; Add BINUTILS/TARGET/bin to $PATH so that 'gcc
+                  ;; -print-prog-name=objdump' returns the correct name.  See
+                  ;; <https://inbox.sourceware.org/libc-alpha/d72f5f6f-cc3a-bd89-0800-ffb068928e0f@linaro.org/t/>.
+                  (define cross-objdump
+                    (search-input-file
+                     (or native-inputs inputs)
+                     (string-append #$target "/bin/objdump")))
 
-                   (define cross-binutils
-                     (dirname cross-objdump))
+                  (define cross-binutils
+                    (dirname cross-objdump))
 
-                   (format #t "adding '~a' to the front of 'PATH'~%"
-                           cross-binutils)
-                   (setenv "PATH" (string-append cross-binutils ":"
-                                                 (getenv "PATH")))))
+                  (format #t "adding '~a' to the front of 'PATH'~%"
+                          cross-binutils)
+                  (setenv "PATH" (string-append cross-binutils ":"
+                                                (getenv "PATH")))))
 
-               ;; This phase would require running 'localedef' built for
-               ;; TARGET, which is impossible by definition.
-               (delete 'install-utf8-c-locale)
+              ;; This phase would require running 'localedef' built for
+              ;; TARGET, which is impossible by definition.
+              (delete 'install-utf8-c-locale)
 
-               ,@(if (target-hurd? target)
-                     `((add-after 'install 'augment-libc.so
-                         (lambda* (#:key outputs #:allow-other-keys)
-                           (let ((out (assoc-ref outputs "out")))
-                             (substitute* (string-append out "/lib/libc.so")
-                               (("/[^ ]+/lib/libc.so.0.3")
-                                (string-append out "/lib/libc.so.0.3"
-                                               " libmachuser.so libhurduser.so"))))))
-                       (add-after 'install 'create-machine-symlink
-                         (lambda* (#:key outputs #:allow-other-keys)
-                           (let* ((out (assoc-ref outputs "out"))
-                                  (cpu ,(match target
-                                          ((? target-x86-32?)
-                                           "i386")
-                                          ((? target-x86-64?)
-                                           "x86_64")))
+              #$@(if (target-hurd? target)
+                     #~((add-after 'install 'augment-libc.so
+                          (lambda _
+                            (substitute* (string-append #$output "/lib/libc.so")
+                              (("/[^ ]+/lib/libc.so.0.3")
+                               (string-append #$output "/lib/libc.so.0.3"
+                                              " libmachuser.so libhurduser.so")))))
+                        (add-after 'install 'create-machine-symlink
+                          (lambda _
+                            (let ((cpu #$(match target
+                                           ((? target-x86-32?)
+                                            "i386")
+                                           ((? target-x86-64?)
+                                            "x86_64")))
                                   (machine (string-append
-                                            out "/include/mach/machine")))
-                             (unless (file-exists? machine)
-                               (symlink cpu machine))))))
-                     '())))))
+                                            #$output
+                                            "/include/mach/machine")))
+                              (unless (file-exists? machine)
+                                (symlink cpu machine))))))
+                     #~())))))
 
       ;; Shadow the native "kernel-headers" because glibc's recipe expects the
       ;; "kernel-headers" input to point to the right thing.

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 "1.8.4")
+    (version "1.8.2")
     (source
       (origin
         (method url-fetch)
         (uri (crate-uri "b3sum" version))
         (file-name (string-append name "-" version ".tar.gz"))
         (sha256
-         (base32 "0pkra5zh680cl9q92hpzmg9flz99b06bhpg7jyhymg1nkm0anw7a"))))
+         (base32 "06qc6iv574km4j1ja4qhxyai680jkll58qzpz4mb79c0rk750dpd"))))
     (build-system cargo-build-system)
     (arguments
      (list

gnu/packages/databases.scm

@@ -1545,17 +1545,17 @@ and high-availability (HA).")
     (license license:gpl2)))                  ;'COPYING' says "version 2" only
 
 ;; Don't forget to update the other postgresql packages when upgrading this one.
-(define-public postgresql-17
+(define-public postgresql-16
   (package
     (name "postgresql")
-    (version "17.7")
+    (version "16.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "1dg9labqgph2idaypb8khdvbag29pr3h4bqv5w8k7kgc08rk97pg"))
+                "0vvd73rzj0sl294v15bh8yslakqv412bxqzlkqxyjwxa8pb6c5wp"))
               (patches (search-patches
                         "postgresql-disable-normalize_exec_path.patch"))))
     (build-system gnu-build-system)
@@ -1585,22 +1585,18 @@ and high-availability (HA).")
           (add-after 'build 'build-contrib
             (lambda _
               (invoke "make" "-C" "contrib")))
-          ;; FIXME: Install manpages too.
-          ;; The 'install-mangpages phase in postgresql-16 fails silently here.
           (add-after 'install 'install-contrib
             (lambda _
-              (invoke "make" "-C" "contrib" "install"))))))
+              (invoke "make" "-C" "contrib" "install")))
+          (add-after 'install 'install-manuals
+            (lambda _
+              (with-directory-excursion "doc/src/sgml"
+                (invoke "make" "install-man")
+                (invoke "make" "postgres.info")
+                (install-file "postgres.info"
+                              (string-append #$output "/share/info"))))))))
     (native-inputs
-     (list bison
-           docbook-xml-4.5
-           docbook-xsl
-           docbook2x
-           flex
-           libxml2
-           libxslt
-           perl
-           pkg-config
-           texinfo))
+     (list docbook-xml-4.5 docbook2x libxml2 perl pkg-config texinfo))
     (inputs
      (list icu4c readline `(,util-linux "lib") openssl zlib))
     (home-page "https://www.postgresql.org/")
@@ -1614,49 +1610,18 @@ TIMESTAMP.  It also supports storage of binary large objects, including
 pictures, sounds, or video.")
     (license (license:x11-style "file://COPYRIGHT"))))
 
-(define-public postgresql-16
-  (package
-    (inherit postgresql-17)
-    (name "postgresql")
-    (version "16.10")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://ftp.postgresql.org/pub/source/v"
-                                  version "/postgresql-" version ".tar.bz2"))
-              (sha256
-               (base32
-                "0hib575m9x3z8c71gkcv9jsyq77d3qk7q2zgzvfy6clwrvs8b16y"))
-              (patches (search-patches
-                        "postgresql-disable-normalize_exec_path.patch"))))
-    (arguments
-     (substitute-keyword-arguments (package-arguments postgresql-17)
-       ((#:phases phases #~%standard-phases)
-        #~(modify-phases #$phases
-            (add-after 'install 'install-manuals
-              (lambda _
-                (with-directory-excursion "doc/src/sgml"
-                  (invoke "make" "install-man")
-                  (invoke "make" "postgres.info")
-                  (install-file "postgres.info"
-                                (string-append #$output "/share/info")))))))))
-    (native-inputs (modify-inputs (package-native-inputs postgresql-17)
-                     (delete "bison")
-                     (delete "docbook-xsl")
-                     (delete "flex")
-                     (delete "libxslt")))))
-
 (define-public postgresql-15
   (package
     (inherit postgresql-16)
     (name "postgresql")
-    (version "15.15")
+    (version "15.8")
     (source (origin
-              (method url-fetch)
+              (inherit (package-source postgresql-16))
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "1ais46b2ij38y75i1w336as03pybyndsd2pp2q8gdjq9igmsllsp"))
+                "0snbxmlygf7m4cxjpscmz3yjn4lnqsw313y9xgpv7vk9k9gm20s4"))
               (patches (search-patches
                         "postgresql-disable-resolve_symlinks.patch"))))
     (native-inputs (modify-inputs native-inputs
@@ -1668,26 +1633,26 @@ pictures, sounds, or video.")
   (package
     (inherit postgresql-15)
     (name "postgresql")
-    (version "14.20")
+    (version "14.13")
     (source (origin
               (inherit (package-source postgresql-15))
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "0sv45dsmyplfys6dfdjdwmrczl46s82x35xdh311nxj02q7z29vm"))))))
+                "0misc5yiklflz96n7wxcdzzg0lcc4ahd0flzqsg6mcjs955krajr"))))))
 
-(define-deprecated/public postgresql-13 #f
+(define-public postgresql-13
   (package
     (inherit postgresql-14)
-    (version "13.23")
+    (version "13.16")
     (source (origin
               (inherit (package-source postgresql-14))
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "1mhz0h7b3dmc0nnxz1wp46j95jhyi3girykkr3gbg4mg4qkwihvf"))))))
+                "0rc8rpsw2lwa5af35zd8iifah02wg2rnn1i890h2h8zh55hvpjy9"))))))
 
 (define-public postgresql postgresql-14)
 
@@ -1726,7 +1691,7 @@ pictures, sounds, or video.")
 (define-public timescaledb
   (package
     (name "timescaledb")
-    (version "2.26.1")
+    (version "2.16.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1735,7 +1700,7 @@ pictures, sounds, or video.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0zfm224jyz874pk4r9qlz5c2mn1xjvairhxh6widlbh3mn62m3j8"))
+                "1v17x00a15il4r3rbr0waqjv1nwzy6rcqxgfi2hdk1x235s5dg5h"))
               (modules '((guix build utils)))
               (snippet
                ;; Remove files carrying the proprietary TIMESCALE license.
@@ -1745,7 +1710,8 @@ pictures, sounds, or video.")
                             '("scripts/c_license_header-timescale.h"
                               "scripts/license_tsl.spec"
                               "scripts/sql_license_tsl.sql"
-                              "test/t/001_replication_telemetry.pl"
+                              "test/perl/AccessNode.pm"
+                              "test/perl/DataNode.pm"
                               "test/perl/TimescaleNode.pm"))))))
     (build-system cmake-build-system)
     (arguments
@@ -1829,7 +1795,7 @@ pictures, sounds, or video.")
                  (lambda* (#:rest args)
                    (apply (assoc-ref gnu:%standard-phases 'check)
                           #:test-target "regresschecklocal" args))))))
-    (inputs (list openssl postgresql-17))
+    (inputs (list openssl postgresql))
     (home-page "https://www.timescale.com/")
     (synopsis "Time-series extension for PostgreSQL")
     (description
@@ -3078,7 +3044,7 @@ temporary directory, and destroys it when the perl script exits.")
 (define-public unixodbc
   (package
    (name "unixodbc")
-   (version "2.3.14")
+   (version "2.3.9")
    (source (origin
             (method url-fetch)
             (uri
@@ -3086,7 +3052,7 @@ temporary directory, and destroys it when the perl script exits.")
               "ftp://ftp.unixodbc.org/pub/unixODBC/unixODBC-"
               version ".tar.gz"))
             (sha256
-             (base32 "0wa7a82h5dsba23155gfhh1sp4dsbaxq6pppp6q31z017vg18a2f"))))
+             (base32 "01xj65d02i3yjy7p9z08y9jakcs5szmz4rask868n7387nn3x0sj"))))
    (build-system gnu-build-system)
    (synopsis "Data source abstraction library")
    (description "Unixodbc is a library providing an API with which to access

gnu/packages/dbm.scm

@@ -113,14 +113,7 @@
                      (for-each (lambda (x)
                                  (install-file x "aclocal"))
                                (find-files "aclocal_java"))
-                     (apply (assq-ref %standard-phases 'bootstrap) arguments)
-                     (let ((automake-files (search-input-directory
-                                            (or native-inputs inputs)
-                                            "share/automake-1.16")))
-                       (define (replace file)
-                         (symlink (string-append automake-files "/" file) file))
-                       (for-each replace '("config.sub" "config.guess"
-                                           "install-sh"))))))
+                     (apply (assq-ref %standard-phases 'bootstrap) arguments))))
                #$@(if (or (target-arm?)
                           (target-riscv64?))
                       #~((add-after 'unpack 'bdb-configure-patch
@@ -202,14 +195,7 @@ SQL, Key/Value, XML/XQuery or Java Object storage for their data model.")
                      (for-each (lambda (x)
                                  (install-file x "aclocal"))
                                (find-files "aclocal_java"))
-                     (apply (assq-ref %standard-phases 'bootstrap) arguments)
-                     (let ((automake-files (search-input-directory
-                                            (or native-inputs inputs)
-                                            "share/automake-1.16")))
-                       (define (replace file)
-                         (symlink (string-append automake-files "/" file) file))
-                       (for-each replace '("config.sub" "config.guess"
-                                           "install-sh"))))))
+                     (apply (assq-ref %standard-phases 'bootstrap) arguments))))
                (add-before 'configure 'pre-configure
                  (lambda _
                    (chdir "dist")

gnu/packages/diffoscope.scm

@@ -79,7 +79,7 @@
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "317")
+    (version "315")
     (source
      (origin
        (method git-fetch)
@@ -88,7 +88,7 @@
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "13r96c49wrpx0xa8bbkki832w58gjdgqb4khjsaawk5mb5yv4c39"))))
+        (base32 "1q2q60hw36d1capqdrg6gp2220dg87bmxgmk52m7yml4xw13zi2p"))))
     (build-system pyproject-build-system)
     (arguments
      (list

gnu/packages/disk.scm

@@ -1231,7 +1231,7 @@ passphrases.")
 (define-public ndctl
   (package
     (name "ndctl")
-    (version "84")
+    (version "78")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1240,7 +1240,7 @@ passphrases.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0jal7w4mk5l5j0qfays27kya8n1h2qwkncl0s317rfxp56bkjp6y"))))
+                "0rhmxjajxxslsikixlf9cdg5vcn42h7zzqkqj5p5pshxch368kn0"))))
     (build-system meson-build-system)
     (arguments
      ;; The test suite runs but SKIPs all tests: do not consider this tested!

gnu/packages/distributed.scm

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

gnu/packages/django.scm

@@ -549,7 +549,6 @@ when coding custom template tags.")
        (uri (git-reference
              (url "https://github.com/jazzband/django-taggit")
              (commit version)))
-       (file-name (git-file-name name version))
        (sha256
         (base32
          "1i8an3wcl7nygl5f565jcpyhyws9gabawazggxpf6m3vklxn3cj0"))))
@@ -710,13 +709,13 @@ your code.")
 (define-public python-django-filter
   (package
     (name "python-django-filter")
-    (version "25.2")
+    (version "25.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "django_filter" version))
               (sha256
                (base32
-                "08wgzqirabxzcdhh0wvv45hqr6dqxy3ifm7mjv86hi0zjd59h3kn"))))
+                "0lvi82f3dnj89ip8hry8fq8w7x632r5p84dlr451rnm8izsfxj8y"))))
     (build-system pyproject-build-system)
     (arguments
      '(#:phases

gnu/packages/dlang.scm

@@ -75,8 +75,7 @@
        (uri (string-append "https://github.com/ldc-developers/ldc/releases"
                            "/download/v" version "/ldc-" version "-src.tar.gz"))
        (sha256
-        (base32 "13pkg69wjj4ali4ikijicccpg8y6f2hghhb70z9lrqr2w3pkhqna"))
-       (patches (search-patches "ldc-i686-int128-alignment.patch"))))
+        (base32 "13pkg69wjj4ali4ikijicccpg8y6f2hghhb70z9lrqr2w3pkhqna"))))
     (build-system cmake-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -373,7 +372,6 @@ 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
@@ -478,15 +476,6 @@ 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
@@ -512,7 +501,7 @@ integration tests...\n")
                       (for-each (cut install-file <> lib-lib)
                                 (find-files "." "^libdruntime\\.so[.0-9]*$")))
                     (copy-recursively "druntime/import" out-include)
-                    (copy-recursively "generated/docs/man" out-man))
+                    (copy-recursively "compiler/docs/man" out-man))
                   (with-directory-excursion "phobos"
                     (with-directory-excursion build-sub-dir
                       (install-file "libphobos2.a" out-lib)
@@ -687,7 +676,6 @@ needed.")
                  (lambda* (#:key tests? #:allow-other-keys)
                    (when tests?
                      (invoke "bin/rdmd" "rdmd_test.d" "bin/rdmd"
-                             "-m" (if #$(target-64bit?) "64" "32")
                              "--rdmd-default-compiler" "ldmd2"))))
                (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)

gnu/packages/dns.scm

@@ -295,37 +295,35 @@ prompt the user with the option to go with insecure DNS only.")
 (define-public dnsmasq
   (package
     (name "dnsmasq")
-    (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"))))
+    (version "2.90")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://www.thekelleys.org.uk/dnsmasq/dnsmasq-"
+                    version ".tar.xz"))
+              (sha256
+               (base32
+                "1r09l537vi867hlpv6vl7nvqhscvq1kf04m896bfrgrpv2dk0l4f"))))
     (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))
-    (home-page "https://thekelleys.org.uk/dnsmasq/doc.html")
+    (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")
     (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/documentation.scm

@@ -70,7 +70,6 @@
   #:use-module (gnu packages qt)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages sphinx)
-  #:use-module (gnu packages tex)
   #:use-module (gnu packages uglifyjs)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg))
@@ -109,13 +108,10 @@
                           #$output)
                          (("\\$cfg\\{'TMPSPACE'\\} = q'[^']*'")
                           "$cfg{'TMPSPACE'} = q'/tmp'")))))))
-    (propagated-inputs (list texlive-preview texlive-xcolor texlive-dvips))
     (inputs (list perl netpbm ghostscript))
     (synopsis "LaTeX documents to HTML")
     (description "LaTeX2HTML is a utility that converts LaTeX documents to web
-pages in HTML.  Since there are many different latex packages, it is expected
-that the user has their latex installation set up correctly when invoking
-@code{latex2html}.")
+pages in HTML.")
     (home-page "https://www.latex2html.org/")
     (license license:gpl2+)))
 

gnu/packages/duckdb.scm

@@ -148,13 +148,13 @@ system.")
 (define-public r-duckdb
   (package
     (name "r-duckdb")
-    (version "1.5.1")
+    (version "1.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "duckdb" version))
        (sha256
-        (base32 "177621m08whqqk4yhj3zrr08l3d9hhlqh3gm9jzhi5cplg47cksq"))
+        (base32 "1hch36v3lsymnx30lv3cjy12gs3v3mhd44ha97l7w9mwp9wbzmxl"))
        ;; 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.
@@ -179,12 +179,10 @@ 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/education.scm

@@ -4,7 +4,7 @@
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2017-2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018-2026 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2018-2025 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Robert Smith <robertsmith@posteo.net>
 ;;; Copyright © 2020 Guy Fleury Iteriteka <gfleury@disroot.org>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
@@ -385,7 +385,7 @@ not have any other specialized device.")
 (define-public openboard
   (package
     (name "openboard")
-    (version "1.7.7")
+    (version "1.7.3")
     (source
      (origin
        (method git-fetch)
@@ -394,7 +394,7 @@ not have any other specialized device.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1i27h84p77pl1chw791fjs3vyzsjvsqc9ky2mbw7g8xpzxz1nd9j"))))
+        (base32 "1098pys5p82sx97xrhw54vlkn6jly0rhq8b09grmmx2h4mcpj2i2"))))
     (build-system qt-build-system)
     (arguments
      (list

gnu/packages/electronics.scm

@@ -240,8 +240,8 @@ are also taken from the original.")
       (license license:gpl3+))))
 
 (define-public abc
-  (let ((commit "80c8a9a1928ef8148a6b504e9590ec07c55c8bcf")
-        (revision "10"))
+  (let ((commit "c18b9a24de46d3b0209afa416511b7a1127344f9")
+        (revision "9"))
     (package
       (name "abc")
       (version (git-version "0.0" revision commit))
@@ -253,7 +253,7 @@ are also taken from the original.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1fbnwsd841z86vfv45443qfpx0l199vf08sgms8wyz19jw7m5ds6"))))
+                  "12fjhlr9r34l6kw2jyaalh53fs783r1h2zx0ldzaxxrbcslb0bxh"))))
       (build-system gnu-build-system)
       (inputs
        (list readline))
@@ -278,7 +278,7 @@ formal verification.")
   (package
     (inherit abc)
     (name "abc-yosyshq")
-    (version "0.64")
+    (version "0.63")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -287,7 +287,7 @@ formal verification.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1jk74yq7dnrnai8r9hqc10jcjmgj50jxj6hsflmvc61acm1r3f8r"))))
+                "1nwj4zhjqjgvb7fh877j51kfccwzrc591ag25qm9jirycgq1cqx6"))))
     (home-page "https://github.com/YosysHQ/abc/")
     (description "ABC is a program for sequential logic synthesis and
 formal verification.  This is the Yosyshq fork of ABC.")
@@ -296,7 +296,7 @@ formal verification.  This is the Yosyshq fork of ABC.")
 (define-public apycula
   (package
     (name "apycula")
-    (version "0.32")
+    (version "0.31")
     ;; The pypi tar.gz file includes the necessary .pickle files, not available
     ;; in the home-page repository.
     (source
@@ -304,7 +304,7 @@ formal verification.  This is the Yosyshq fork of ABC.")
        (method url-fetch)
        (uri (pypi-uri "apycula" version))
        (sha256
-        (base32 "0zz6mz1s7razbqsysaji7qwfsjj19av4mg7zclxaigz4hmq9ar0d"))))
+        (base32 "0pf43cd071kv5ann78hl5qrcj9vhndr46ds2g12sgnfjfvh6pfpg"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f ;requires Gowin EDA tools
@@ -467,7 +467,7 @@ individual low-level driver modules.")
 (define-public eqy
   (package
     (name "eqy")
-    (version "0.64")
+    (version "0.63")
     (source
      (origin
        (method git-fetch)
@@ -476,7 +476,7 @@ individual low-level driver modules.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1lsf8wm10wq67lmwz1ck30inl3byfy27ya39fj93gym5ys815ma6"))))
+        (base32 "05rk6gy0xnaksxqdkpm08i3ngh0adavfyfjyscw5l1b7d7yhfavh"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -1502,7 +1502,7 @@ an embedded event driven algorithm.")
 (define-public librelane
   (package
     (name "librelane")
-    (version "3.0.2")
+    (version "3.0.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1511,7 +1511,7 @@ an embedded event driven algorithm.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1v43adkw5c624nd06g11cb609v8pj3prfyyawbq3i4k1w1law597"))))
+                "01zi2v5qi26h09hwjafsq9k0anrc5g5fc6q5vg87k9lcwyfsi685"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2018,7 +2018,7 @@ which allows one to install the M8 firmware on any Teensy.")
 (define-public magic
   (package
     (name "magic")
-    (version "8.3.633")
+    (version "8.3.625")
     (source
      (origin
        (method git-fetch)
@@ -2027,7 +2027,7 @@ which allows one to install the M8 firmware on any Teensy.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1rwrhb0q99rpv4lbiw1sqykwzf9gj1my2wkh6mp8g36rab2vhii3"))))
+        (base32 "0ld238cdq8mzzcx7vgk67aqim0ypbfyks486z59q19yzxpr6c42s"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -2057,7 +2057,7 @@ versus schematic} tests and can assist with automatic routing.")
 (define-public mcy
   (package
     (name "mcy")
-    (version "0.64")
+    (version "0.63")
     (source
      (origin
        (method git-fetch)
@@ -2120,7 +2120,7 @@ coverage.")
 (define-public netgen
   (package
     (name "netgen")
-    (version "1.5.318")
+    (version "1.5.316")
     (source
      (origin
        (method git-fetch)
@@ -2129,7 +2129,7 @@ coverage.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "19rd8y2pspycr2296nhm60fhsgnzlyzb09wx2kgqzg6s7h6cmrr5"))))
+        (base32 "1923mynqw1wjhlcij639gdqrkifyb5lcks1x11gwpgp4gijwj3qb"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -2690,20 +2690,20 @@ formats.")
 (define-public openroad
   (package
     (name "openroad")
-    (version "26Q2")
+    (version "26Q1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
               (url "https://github.com/The-OpenROAD-Project/OpenROAD")
-              (commit version)
+              (commit "e06ca0f5f2e641cd7b138a4d9b4fdd290359eca8")
               ;; 26Q1 Uses:
-              ;; - forked, custom opensta: v2.2.0-1952-g43177bba
-              ;; - forked, custom (berkeley) abc: 20260301.0445-g17cadca08
+              ;; - forked, custom opensta: v2.2.0-1579-g9c9b5659
+              ;; - forked, custom (berkeley) abc: 20260104.1628-g4c756ffb8
               (recursive? #t)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "152j78c47wyq4sw42bwlxdhvs5g47a8jqz1qz5yzdsk9z5y4y7vl"))))
+        (base32 "13x4kqi4j489k4sz56ws4aqhp60nff1i18z6hjd6xx8y7flaik0c"))))
     (build-system qt-build-system)
     (arguments
      (list
@@ -2737,7 +2737,7 @@ formats.")
            flex
            googletest
            pkg-config
-           swig-4.4))
+           swig-4.0))
     (inputs
      (list abseil-cpp
            boost
@@ -2776,6 +2776,7 @@ clock tree synthesis, routing, parasitic extraction, and timing analysis.")
   (package
     (inherit openroad)
     (name "openroad-cli")
+    (build-system cmake-build-system)
     (arguments
      (delkw
       #:qtbase
@@ -3459,7 +3460,7 @@ form of AXI, AXI lite, and AXI stream modules.")
 (define-public python-edalize
   (package
     (name "python-edalize")
-    (version "0.6.6")
+    (version "0.6.5")
     (source
      (origin
        (method git-fetch)
@@ -3468,7 +3469,7 @@ form of AXI, AXI lite, and AXI stream modules.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "115nc15n2cx4x9irjim07zkg0287418djqd6ja7rm8jrnyldvln9"))))
+        (base32 "1drmc126a12zlynx8ps9iwghaqs058pqj2xpdysxnrj26hg3sp15"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3495,17 +3496,17 @@ form of AXI, AXI lite, and AXI stream modules.")
     (native-inputs
      (list python-pytest python-setuptools python-setuptools-scm))
     (propagated-inputs
-     (list python-importlib-metadata python-jinja2 python-pandas))
+     (list python-importlib-metadata python-jinja2))
     (home-page "https://github.com/olofk/edalize/")
     (synopsis "Python Library for interacting with EDA tools")
     (description
-     "This package can create project files for supported tools and run them in
-batch or GUI mode.  All EDA tools such as Icarus, Yosys, ModelSim, Vivado,
-Verilator, GHDL, Quartus etc get input HDL files (Verilog and VHDL) and some
-tool-specific files (constraint files,memory initialization files, IP
-description files etc).  Together with the files, perhaps a couple of Verilog
-`defines, some top-level parameters/generics or some tool-specific options are
-set.")
+     "This package implements a functionality to create project files for
+supported tools and run them in batch or GUI mode.  All EDA tools such as
+Icarus, Yosys, ModelSim, Vivado, Verilator, GHDL, Quartus etc get input HDL
+files (Verilog and VHDL) and some tool-specific files (constraint files,memory
+initialization files, IP description files etc).  Together with the files,
+perhaps a couple of Verilog `defines, some top-level parameters/generics or
+some tool-specific options are set.")
     (license license:bsd-2)))
 
 (define-public fusesoc
@@ -3999,7 +4000,7 @@ input and outputs an XML dataset.")
 (define-public qucs-s
   (package
     (name "qucs-s")
-    (version "26.1.0")                  ;update qucsator-rf accordingly
+    (version "25.2.0")                  ;update qucsator-rf accordingly
     (source
      (origin
        (method git-fetch)
@@ -4009,7 +4010,7 @@ input and outputs an XML dataset.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0aiyrcrxln4v6qm2dmigb54wl0mj499q3g18pz87m1s2lfgicpb1"))))
+         "0328irynm8vy4xjdip5286fd8nag1zdp0p6rcbhdhp4fca6wp5ak"))))
     (build-system qt-build-system)
     (arguments
      (list
@@ -4231,7 +4232,7 @@ them usable as simple logic analyzer and/or oscilloscope hardware.")
 (define-public sby
   (package
     (name "sby")
-    (version "0.64")
+    (version "0.63")
     (source
      (origin
        (method git-fetch)
@@ -4240,7 +4241,7 @@ them usable as simple logic analyzer and/or oscilloscope hardware.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0jksspdgq2grk4a80i5yfc9bazfij37wpmrlkvygpz9ys5ny1432"))))
+        (base32 "1p23w9jd95b86n7f94zpqdaz19fn2b2lyww1p8dcy9p3zrcn7750"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -4289,8 +4290,8 @@ front-end program for Yosys-based formal hardware verification flows.")
     (license license:isc)))
 
 (define-public sby-gui
-  (let ((commit "0a89301bf347c9f42932186e49ba2c0014ff3661")
-        (revision "1"))
+  (let ((commit "6c977084c17c4842c504829c6d455a07d67e119c")
+        (revision "0"))
     (package
       (name "sby-gui")
       (version (git-version "0" revision commit))
@@ -4302,13 +4303,10 @@ front-end program for Yosys-based formal hardware verification flows.")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "1zp2c7zqclsfvl5xhb8zlc1dclp2s36w2nd0x80fazsxp7ksw5gr"))))
+          (base32 "137x3s5mwbzlcv2p6671ijvbafzwhxpvszzfi9wifq0wcli6cxxg"))))
       (build-system qt-build-system)
       (arguments
-       (list
-        #:qtbase qtbase                 ;for Qt 6
-        #:tests? #f))                   ;no tests
-      (native-inputs (list python-minimal-wrapper))
+       (list #:tests? #f))               ;no tests
       (propagated-inputs (list sby))
       (home-page "https://github.com/YosysHQ/sby-gui/")
       (synopsis "Graphical user interface for code{sby}")
@@ -4663,7 +4661,7 @@ parallel computing platforms.  It also supports serial execution.")
 (define-public yosys
   (package
     (name "yosys")
-    (version "0.64")
+    (version "0.63")
     (source
      (origin
        (method git-fetch)
@@ -4671,7 +4669,7 @@ parallel computing platforms.  It also supports serial execution.")
               (url "https://github.com/YosysHQ/yosys")
               (commit (string-append "v" version))))
        (sha256
-        (base32 "13gw5msk1kv05jkb330nybvx2s0ixm6l6mdpyapnqmv3lkhby1mj"))
+        (base32 "1iaafzsc0pbd61m5hh12nzr2z4rn4n7i68l6ij9vli4m5zsxw39k"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
@@ -4784,12 +4782,12 @@ parallel computing platforms.  It also supports serial execution.")
               (git-reference
                 (url "https://github.com/povik/yosys-slang")
                 ;; No tags, nor releases.
-                (commit "4e53d772996184b07e9bfe784060f96e6cb0a267")
+                (commit "d82b0b163a725fc1a401fbb6b465cd862517ec1f")
                 (recursive? #t)))  ;requires slang and fmt
              (file-name "yosys-slang")
              (sha256
               (base32
-               "1jjr1b6xd1sr9fkyfyl4y2wkzl51m7g10bw97mnw81v2mzssrs2q")))))
+               "07h4qssphggd4mbn376vldqwzj1i16y1ix455xzr4lgx6s2q9ryg")))))
     ;; Optional dependencies increase considerably package closure.
     ;; - gtkwave: required only for vcd2fst binary, used by ‘sim’ command.
     ;; - graphviz, xdot: used by ‘show’ command to display schematics.

gnu/packages/emacs-xyz.scm

@@ -9435,40 +9435,35 @@ column by drawing a thin line down the length of the editing window.")
     (license license:gpl3+)))
 
 (define-public emacs-greader
-  (package
-    (name "emacs-greader")
-    (version "0.19.0")
-    (source
-     (origin
-       (uri (git-reference
-              (url "https://gitlab.com/michelangelo-rodriguez/greader")
-              (commit (string-append "v" version))))
-       (method git-fetch)
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "08c4i5qbr0ndbbps6y5kpp0lzfmxnwifrxssqkd9qdzj068k69k3"))))
-    (build-system emacs-build-system)
-    (arguments
-     (list #:tests? #f ;no tests
-           #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'unpack 'make-info
-                 (lambda _
-                   (invoke "makeinfo" "--no-split" "greader.texi"))))))
-    (inputs (list emacs-compat espeak-ng))
-    (native-inputs (list texinfo))
-    (home-page "https://gitlab.com/michelangelo-rodriguez/greader")
-    (synopsis
-     "Gnamù Reader, or Greader, sends buffer contents to a speech engine")
-    (description
-     "Greader is a module that sends any Emacs buffer to a @acronym{TTS,
+  (let ((commit "b25974aeae49f11b91bb78d94ab51913fdfcdc05")) ;version bump
+    (package
+      (name "emacs-greader")
+      (version "0.13.1")
+      (source
+       (origin
+         (uri (git-reference
+                (url "https://gitlab.com/michelangelo-rodriguez/greader")
+                (commit commit)))
+         (method git-fetch)
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1qkszb4yrfnzb2rqkf6vmzca53w68p78zb58frcxslxn7s5l7ih1"))))
+      (build-system emacs-build-system)
+      (arguments
+       (list #:tests? #f))              ;no tests
+      (inputs (list emacs-compat espeak-ng))
+      (home-page "https://gitlab.com/michelangelo-rodriguez/greader")
+      (synopsis
+       "Gnamù Reader, or Greader, sends buffer contents to a speech engine")
+      (description
+       "Greader is a module that sends any Emacs buffer to a @acronym{TTS,
 Text To Speech} engine, such as Espeak-NG or Speech Dispatcher.
 
 The mode supports timer reading, automatic scrolling of buffers in modes like
 Info mode, and repeating reading of regions or the whole buffer.  It also
 includes a feature to facilitate the compilation of Espeak-NG
 pronunciations.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-grep-a-lot
   (package
@@ -15158,27 +15153,6 @@ 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")
@@ -15322,33 +15296,35 @@ them easier to distinguish from other, less important buffers.")
     (license license:expat)))
 
 (define-public emacs-embark
-  (package
-    (name "emacs-embark")
-    (version "1.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/oantolin/embark")
-              (commit version)))
-       (sha256
-        (base32 "1y97kibzz36wrzcjv997qp5pliikda0dhsm9461pin3q5gv8y6kq"))
-       (file-name (git-file-name name version))))
-    (build-system emacs-build-system)
-    (arguments
-     (list
-      #:tests? #false                 ;no tests
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'install 'makeinfo
-            (lambda _ (emacs-makeinfo))))))
-    (native-inputs (list texinfo))
-    (propagated-inputs
-     (list emacs-avy emacs-consult))
-    (home-page "https://github.com/oantolin/embark")
-    (synopsis "Emacs mini-buffer actions rooted in keymaps")
-    (description
-     "This package provides a sort of right-click contextual menu for Emacs
+  (let ((commit "0bdfd38d281d6375e6e675ce6f1bd597a9e3b136")
+        (revision "1"))
+    (package
+      (name "emacs-embark")
+      (version (git-version "1.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+                (url "https://github.com/oantolin/embark")
+                (commit commit)))
+         (sha256
+          (base32 "0m9y2wraapi744fg7y6cgz6y2gx0xzaglnxqalynz44ca9z6m6y4"))
+         (file-name (git-file-name name version))))
+      (build-system emacs-build-system)
+      (arguments
+       (list
+        #:tests? #false                 ;no tests
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before 'install 'makeinfo
+              (lambda _ (emacs-makeinfo))))))
+      (native-inputs (list texinfo))
+      (propagated-inputs
+       (list emacs-avy emacs-consult))
+      (home-page "https://github.com/oantolin/embark")
+      (synopsis "Emacs mini-buffer actions rooted in keymaps")
+      (description
+       "This package provides a sort of right-click contextual menu for Emacs
 offering you relevant @emph{actions} to use on a @emph{target} determined by
 the context.
 
@@ -15362,7 +15338,7 @@ get offered actions like deleting, copying, renaming, visiting in another
 window, running a shell command on the file, etc.  For buffers the actions
 include switching to or killing the buffer.  For package names the actions
 include installing, removing or visiting the homepage.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-prescient
   (package
@@ -16999,35 +16975,6 @@ 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.
@@ -17372,11 +17319,11 @@ accessing slash commands.")
 
 (define-public emacs-claude-code-ide
   ;; Upstream does not make versioned releases.
-  (let ((commit "56db02ee386d009ddb8b1482310f1f9beeefb810")
-        (revision "2"))
+  (let ((commit "5f12e60c6d2d1802c8c1b7944bbdf935d5db1364")
+        (revision "1"))
     (package
       (name "emacs-claude-code-ide")
-      (version (git-version "0.2.7" revision commit))
+      (version (git-version "0.2.6" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -17385,7 +17332,7 @@ accessing slash commands.")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "060n6alwgnxqpqcl74c1ixjm0am1pfj2kx7v3wi4bys6dsf50zd8"))))
+          (base32 "148xcrqff6khpwf8nnadcyvz8h6mk45xz1498k0wbzy80yzd2axn"))))
       (build-system emacs-build-system)
       (arguments
        (list
@@ -17774,29 +17721,6 @@ 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")
@@ -24482,27 +24406,6 @@ key-bindings, avoiding most if not all the hassle introduced by key-binding
 conflicts.")
     (license license:gpl3+)))
 
-(define-public emacs-meow-tree-sitter
-  (package
-    (name "emacs-meow-tree-sitter")
-    (version "2.0.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://stable.melpa.org/packages/meow-tree-sitter-" version
-             ".tar"))
-       (sha256
-        (base32 "1sxa1flngzsj3hh3sp3kccwgsxq6d40wsn8vzgv0ahrxkz2s6fxg"))))
-    (build-system emacs-build-system)
-    (propagated-inputs (list emacs-meow))
-    (home-page "https://github.com/skissue/meow-tree-sitter")
-    (synopsis "Tree-sitter powered motions for Meow")
-    (description
-     "This package integrates the treesitter library in modern Emacs with
-Meow’s motions.")
-    (license (list license:gpl3+ license:mpl2.0))))
-
 (define-public emacs-xelb
   (package
     (name "emacs-xelb")
@@ -24533,9 +24436,11 @@ Meow’s motions.")
             (lambda* (#:key inputs native-inputs #:allow-other-keys)
               (substitute* "xelb-gen"
                 (("/usr/bin/env") (which "env")))
-              (invoke "make"
-                      (format #f "PROTO_PATH=~a/share/xcb"
-                              #$(this-package-native-input "xcb-proto"))))))))
+              (let ((xcb-proto #$(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))))))))
     (native-inputs (list xcb-proto))
     (propagated-inputs (list emacs-compat))
     (home-page "https://github.com/emacs-exwm/xelb")
@@ -24632,8 +24537,7 @@ of XELB.")
     (name "emacs-exwm-no-x-toolkit")
     (synopsis "Emacs X window manager (without an X toolkit)")
     (propagated-inputs
-     (modify-inputs propagated-inputs
-       (replace "emacs-xelb" emacs-xelb-no-x-toolkit)))
+     (list emacs-xelb-no-x-toolkit))
     (arguments
      (substitute-keyword-arguments arguments
        ((#:emacs emacs) `,emacs-no-x-toolkit)))))
@@ -24999,91 +24903,36 @@ with Eglot.")
 (define-public emacs-jabber
   (package
     (name "emacs-jabber")
-    (version "0.10.3")
+    (version "0.9.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://git.thanosapollo.org/emacs-jabber")
-                    (commit version)))
+                    (url "https://codeberg.org/emacs-jabber/emacs-jabber")
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1v1a09h6ndqhkwyn44cnx1b0l4p155a09mfjrfmg62li50hvw1zm"))))
+                "0ain52p79sxll0bnsb4llfp1h4pqcqx3l6im4ibia06lg2aiqhpv"))))
     (build-system emacs-build-system)
     (arguments
      (list
       #:lisp-directory "lisp"
-      #:include #~(cons "^[^/]*\\.so$"
-                        %default-include)
       #:emacs emacs                   ;requires gnutls
-      #:test-command #~(list "make" "-C" ".." "test")
+      #:test-command #~(list "ert-runner" "../tests")
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'build-native-module
+          (add-after 'unpack 'make-info
             (lambda _
-              (invoke "make" "-C" "../src")))
-          (add-before 'build-native-module 'unpack-picomemo
-            (lambda _
-              (copy-recursively
-               #$(this-package-native-input
-                  "emacs-jabber-picomemo")
-               "../src/picomemo")
-              (invoke "chmod" "--recursive" "u+w"
-                      "../src/picomemo")))
-          (add-after 'unpack 'fix-test-runner
-            (lambda _
-              ;; Replace grep -oP (Perl regex) with a
-              ;; POSIX-compatible alternative so the test
-              ;; runner counts results correctly.
-              (substitute* "../Makefile"
-                (("grep -oP '\\^Ran \\\\K\\[0-9\\]\\+'")
-                 (string-append
-                  "grep -o 'Ran [0-9]*'"
-                  " | grep -o '[0-9]*'")))))
-          (add-after 'unpack 'disable-failing-tests
-            (lambda _
-              ;; These 4 tests pass outside the build
-              ;; environment but fail inside it.
-              (define skip "\n  (skip-unless nil)")
-              (substitute*
-                  "../tests/jabber-disco-tests.el"
-                ((".*query-if-needed-cache-miss \\(\\)"
-                  all)
-                 (string-append all skip))
-                ((".*process-caps-modern.*queries \\(\\)"
-                  all)
-                 (string-append all skip)))
-              (substitute*
-                  (string-append
-                   "../tests/"
-                   "jabber-message-correct-tests.el")
-                ((".*correct-last-uses-original-id \\(\\)"
-                  all)
-                 (string-append all skip))
-                ((".*mam-syncing-skipped.*dispatch \\(\\)"
-                  all)
-                 (string-append all skip))))))))
-    (native-inputs
-     (list pkg-config
-           (origin
-             (method git-fetch)
-             (uri (git-reference
-                    (url "https://github.com/mierenhoop/picomemo")
-                    (commit "1.1.0")))
-             (file-name "emacs-jabber-picomemo")
-             (sha256
-              (base32
-               "044xd1gn9lpd5yrb3c1lmvqsc1chbkhd3vnh7800hxn23a0hxbzj")))))
-    (inputs (list mbedtls))
-    (propagated-inputs (list emacs-fsm))
-    (home-page "https://thanosapollo.org/projects/jabber/")
+              (invoke "makeinfo" "../jabber.texi"))))))
+    (native-inputs (list emacs-ert-runner texinfo))
+    (propagated-inputs (list emacs-fsm emacs-srv gnutls))
+    (home-page "https://codeberg.org/emacs-jabber/emacs-jabber")
     (synopsis "XMPP (Jabber) client for Emacs")
     (description
      "@code{jabber.el} is an XMPP client for Emacs.  XMPP (also known as
 \"Jabber\") is an instant messaging system; see @url{https://xmpp.org} for
-more information.  It supports OMEMO end-to-end encryption via picomemo.")
-    (license (list license:gpl3+    ;gpl2+ elisp, gpl3+ C
-                   license:isc))))  ;picomemo
+more information.")
+    (license license:gpl2+)))
 
 (define-public emacs-jarchive
   (package
@@ -28222,7 +28071,7 @@ match and total match information in the mode-line in various search modes.")
 (define-public emacs-pg
   (package
     (name "emacs-pg")
-    (version "0.6.4")
+    (version "0.62")
     (source (origin
               (method git-fetch)
               (uri (git-reference (url "https://github.com/emarsden/pg-el")
@@ -28230,7 +28079,7 @@ match and total match information in the mode-line in various search modes.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0w9a8y3s2dbmpqbbnxycxd38niqq2slzr26bfl4v1pfcm0w7skfz"))))
+                "0fjzrn5b4s00km71ya98vwwfyvd4rvcywxdxqzy5xfrv8crm92w6"))))
     (build-system emacs-build-system)
     (propagated-inputs (list emacs-peg))
     (home-page "https://github.com/emarsden/pg-el")
@@ -28246,7 +28095,7 @@ end users.")
 (define-public emacs-pgmacs
   (package
     (name "emacs-pgmacs")
-    (version "0.30")
+    (version "0.42")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -28255,7 +28104,7 @@ end users.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0f4mbamk2n9l7qwhi2n1kwvng6wa9yp6k2w1qn6yc07pri2mb6yc"))))
+                "0pf8y64hka1fl47dphmh4xgxiwfsd0g4q2fazq5yc48zwr9nsf02"))))
     (build-system emacs-build-system)
     (propagated-inputs
      (list emacs-pg))
@@ -28264,12 +28113,6 @@ 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")
@@ -39440,16 +39283,10 @@ user interfaces for various built-in modes.")
               (make-file-writable "calibredb-core.el")
               (let ((calibredb (search-input-file inputs "/bin/calibredb"))
                     (fetch-ebook-metadata
-                     (search-input-file inputs "/bin/fetch-ebook-metadata"))
-                    (ebook-convert
-                     (search-input-file inputs "/bin/ebook-convert"))
-                    (calibre-debug
-                     (search-input-file inputs "/bin/calibre-debug")))
+                     (search-input-file inputs "/bin/fetch-ebook-metadata")))
                 (emacs-substitute-variables "calibredb-core.el"
                   ("calibredb-fetch-metadata-program" fetch-ebook-metadata)
-                  ("calibredb-program" calibredb)
-                  ("calibredb-convert-program" ebook-convert)
-                  ("calibredb-debug-program" calibre-debug))))))))
+                  ("calibredb-program" calibredb))))))))
     (inputs
      (list calibre))
     (propagated-inputs
@@ -41149,7 +40986,7 @@ Lisp's (relatively new) EIEIO object oriented libraries.")
 (define-public emacs-fj
   (package
     (name "emacs-fj")
-    (version "0.34")
+    (version "0.33")
     (source
      (origin
        (method git-fetch)
@@ -41158,10 +40995,10 @@ Lisp's (relatively new) EIEIO object oriented libraries.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1y3k82q5iii7ddm6yj7397x2jscbcnvapd04zc5wjkqdr50cay3l"))))
+        (base32 "0cfzw9shd6jjir9zqcqbsz8vidsvs609a58aakh54dylngp52qmh"))))
     (build-system emacs-build-system)
     (arguments (list #:tests? #f))      ;depends on exemplify-ert
-    (propagated-inputs (list emacs-fedi emacs-magit emacs-tp emacs-transient))
+    (propagated-inputs (list emacs-fedi emacs-magit emacs-tp))
     (home-page "https://codeberg.org/martianh/fj.el")
     (synopsis "Client for Forgejo instances")
     (description
@@ -42222,10 +42059,10 @@ service, and connect it with Emacs via inter-process communication.")
       (license license:gpl3+))))
 
 (define-public emacs-telega
-  (let ((commit "8078beccf88c132d504ba9031062a6a2c65a1c8b"))
+  (let ((commit "805819bf81dffe2922e9e06ae02d58429d03aa1a"))
     (package
       (name "emacs-telega")
-      (version "0.8.620")               ; see telega-version in telega.el
+      (version "0.8.601")               ; see telega-version in telega.el
       (source
        (origin
          (method git-fetch)
@@ -42233,7 +42070,7 @@ service, and connect it with Emacs via inter-process communication.")
                (url "https://github.com/zevlg/telega.el")
                (commit commit)))
          (sha256
-          (base32 "1m7gs90hrmmwm7pvf5iz3y4v39psp6kbnw1d97q6v55hhgq3isxz"))
+          (base32 "0d02ymr5fw6fknzf9ikaky48swd9yfp5zn846zlwb5083p6bpmis"))
          (file-name (git-file-name "emacs-telega" version))
          (patches
           (search-patches "emacs-telega-test-env.patch"))))
@@ -46688,7 +46525,7 @@ Fennel code within Emacs.")
 (define-public emacs-org-modern
   (package
     (name "emacs-org-modern")
-    (version "1.13")
+    (version "1.12")
     (source
      (origin
        (method git-fetch)
@@ -46696,18 +46533,10 @@ Fennel code within Emacs.")
              (url "https://github.com/minad/org-modern")
              (commit version)))
        (sha256
-        (base32 "16i1nwdilhpjlphpbwi8vjfwfb721gm0mm37hjx570wx4sskvg30"))
+        (base32 "01p5k85hj677x2vk7j7a88gchp51ybiaj6iqmdhxivmcw3lb6ibi"))
        (file-name (git-file-name name version))))
     (build-system emacs-build-system)
-    (arguments
-     (list
-      #:tests? #f                       ;no tests
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'install 'makeinfo
-            (lambda _ (emacs-makeinfo))))))
     (propagated-inputs (list emacs-compat))
-    (native-inputs (list texinfo))
     (home-page "https://github.com/minad/org-modern")
     (synopsis "Modern Org style")
     (description

gnu/packages/emacs.scm

@@ -644,6 +644,32 @@ editor (console only)")
     (description "This Emacs build implements graphical UI purely in terms
 of GTK.")))
 
+(define-public emacs-xwidgets
+  (package/inherit emacs
+    (name "emacs-xwidgets")
+    (synopsis "The extensible, customizable, self-documenting text
+editor (with xwidgets support)")
+    (arguments
+     (substitute-keyword-arguments arguments
+       ((#:configure-flags flags #~'())
+        #~(cons "--with-xwidgets" #$flags))))
+    (inputs
+     (modify-inputs inputs
+       (prepend webkitgtk-with-libsoup2 libxcomposite)))))
+
+(define-public emacs-pgtk-xwidgets
+  (package
+    (inherit emacs-pgtk)
+    (name "emacs-pgtk-xwidgets")
+    (synopsis "Emacs text editor with @code{xwidgets} and @code{pgtk} support")
+    (arguments
+     (substitute-keyword-arguments arguments
+       ((#:configure-flags flags #~'())
+        #~(cons "--with-xwidgets" #$flags))))
+    (inputs
+     (modify-inputs inputs
+       (prepend gsettings-desktop-schemas webkitgtk-with-libsoup2)))))
+
 (define-public emacs-lucid
   (package/inherit emacs-no-x
     (name "emacs-lucid")
@@ -748,6 +774,7 @@ editor (with wide ints)" )
 
 (define-public emacs-next (emacs->emacs-next emacs))
 (define-public emacs-next-pgtk (emacs->emacs-next emacs-pgtk))
+(define-public emacs-next-pgtk-xwidgets (emacs->emacs-next emacs-pgtk-xwidgets))
 (define-deprecated-package emacs-next-tree-sitter
   emacs-next)
 

gnu/packages/embedded.scm

@@ -65,7 +65,6 @@
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages libftdi)
   #:use-module (gnu packages libusb)
-  #:use-module (gnu packages linux)
   #:use-module (gnu packages messaging)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
@@ -1506,8 +1505,7 @@ hardware.  The utility support USB and UART as serial link.")
                  (apply (assoc-ref cargo:%standard-phases phase)
                         #:cargo-target #$(cargo-triplet)
                         args))
-               '(prepare-rust-crates
-                 unpack-rust-crates
+               '(unpack-rust-crates
                  configure
                  check-for-pregenerated-files
                  patch-cargo-checksums)))))))
@@ -2068,27 +2066,26 @@ operations.")
     (license license:asl2.0)))
 
 (define-public ts4900-utils
-  (package
-    (name "ts4900-utils")
-    (version "3.0.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/embeddedTS/ts4900-utils")
-                     (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "08x40ii56v4cmnz9hk6rvjrc500k1bij5ns52360vczznc8lx8bx"))))
-    (build-system gnu-build-system)
-    (native-inputs
-     (list autoconf
-           automake
-           libgpiod
-           pkg-config))
-    (home-page "https://github.com/embeddedTS/ts4900-utils")
-    (synopsis "Utilities for the TS-4900 board family")
-    (description "This package contains utilities useful for boards of the
+  ;; There are no proper release nor tag; use the latest commit.
+  (let ((revision "0")
+        (commit "e10a12f8050d1d1229e711c7cfab8a0d5d93ee58"))
+    (package
+      (name "ts4900-utils")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/embeddedTS/ts4900-utils")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1vr8i425qijbwgbc10av3wr35p3x11wy6y442w0ja0yny7si8wp8"))))
+      (build-system gnu-build-system)
+      (native-inputs (list autoconf automake))
+      (home-page "https://github.com/embeddedTS/ts4900-utils")
+      (synopsis "Utilities for the TS-4900 board family")
+      (description "This package contains utilities useful for boards of the
 TS-4900 family.  The included commands are:
 @itemize @code
 @item adc8390
@@ -2101,7 +2098,7 @@ TS-4900 family.  The included commands are:
 @item tsmicroupdate
 @item tssilomon
 @end itemize")
-    (license license:bsd-2)))
+      (license license:bsd-2))))
 
 (define-public cc-tool
   (package

gnu/packages/emulators.scm

@@ -6,7 +6,7 @@
 ;;; Copyright © 2015, 2018, 2023 David Thompson <dthompson2@worcester.edu>
 ;;; Copyright © 2016 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2016, 2017, 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017-2024, 2026 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2017-2024 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2017, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017, 2018, 2019 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
@@ -3247,14 +3247,14 @@ that compiles to WebAssembly.")
 (define-public scummvm
   (package
     (name "scummvm")
-    (version "2026.2.0")
+    (version "2.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://downloads.scummvm.org/frs/scummvm/" version
                            "/scummvm-" version ".tar.xz"))
        (sha256
-        (base32 "1wv0z9c4dnjywgla9zhbkgnzahj829ybvcx9jw67hdmagnbys42f"))))
+        (base32 "1qspqawdazsxisxm1lxzgi0i4gx54qd10xyk3nmmirwxz9mg70ka"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/enchant.scm

@@ -48,7 +48,7 @@
 (define-public nuspell
   (package
     (name "nuspell")
-    (version "5.1.4")
+    (version "5.1.7")
     (source
      (origin
        (method git-fetch)
@@ -58,12 +58,14 @@
          (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "05j1hmczy6v9dyxp77vxhgyl7y5hff3v45vlp86gyh7m9lgqpmra"))))
+        (base32 "1xvy8qrpw1282akr873xzja61afnr27f1gab6jc4cgy8pkfqq308"))))
     (build-system cmake-build-system)
     (arguments
-     (if (%current-target-system)
-         (list #:configure-flags #~(list "-DBUILD_TESTING=OFF"))
-         '()))
+     (list #:configure-flags
+           #~(list "-DBUILD_DOCS=OFF"   ;do not pull Pandoc
+                   #$@(if (%current-target-system)
+                          '("-DBUILD_TESTING=OFF")
+                          '()))))
     (native-inputs (list catch2-3 pkg-config))
     (propagated-inputs (list icu4c))
     (native-search-paths (list (search-path-specification

gnu/packages/engineering.scm

@@ -50,7 +50,6 @@
 ;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
 ;;; Copyright © 2026 Daniel Khodabakhsh <d@niel.khodabakh.sh>
 ;;; Copyright © 2026 Spencer King <spencer.king@wustl.edu>
-;;; Copyright © 2026 Brent Wedderburn <mb@bean.za.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -254,21 +253,13 @@ their devices.")
           (replace 'build (assoc-ref gnu:%standard-phases 'build))
           (replace 'check (assoc-ref gnu:%standard-phases 'check))
           (replace 'install
-            (lambda _
-              (let* ((bin (string-append #$output "/bin"))
-                     (share (string-append #$output "/share"))
-                     (apps (string-append share "/applications"))
-                     (icons (string-append share "/icons/hicolor/128x128/apps")))
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((bin   (string-append #$output "/bin"))
+                    (share (string-append #$output "/share/librecad")))
                 (mkdir-p bin)
                 (install-file "unix/librecad" bin)
                 (mkdir-p share)
-                (copy-recursively "unix/resources"
-                                  (string-append share "/librecad"))
-                (mkdir-p apps)
-                (install-file "desktop/librecad.desktop" apps)
-                (mkdir-p icons)
-                (copy-file "librecad/res/main/librecad.png"
-                           (string-append icons "/librecad.png"))))))))
+                (copy-recursively "unix/resources" share)))))))
     (inputs
      (list bash-minimal boost muparser freetype qtbase-5 qtsvg-5))
     (native-inputs
@@ -2825,7 +2816,7 @@ dynamics is used by FreeCAD 1.0.0 for its new Assembly workbench.")
            qtwayland
            sqlite
            onetbb                       ;same version as opencascade-occt
-           vtk-9.5
+           vtk
            xerces-c
            yaml-cpp
            zlib))

gnu/packages/fabric-management.scm

@@ -186,7 +186,7 @@ testing InfiniBand networks.")
 (define-public ucx
   (package
     (name "ucx")
-    (version "1.20.0")
+    (version "1.19.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -196,7 +196,7 @@ testing InfiniBand networks.")
               (patches (search-patches "ucx-tcp-iface-ioctl.patch"))
               (sha256
                (base32
-                "12w1mxacml1w8zvl1hpn786cs77y056b9hxv7q1kq482bgc2si0v"))
+                "12j9200iyg6d0yr84r25hcpq8qqzfaa08klbhvgrqpflpfcljz4z"))
               (snippet
                ;; As seen in commit b0a275a5492125a13020cd095fe9934e0b5e7c6a.
                #~(begin (use-modules (guix build utils))

gnu/packages/fcitx5.scm

@@ -34,7 +34,6 @@
   #:use-module (gnu packages anthy)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages cpp)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages dictionaries)
@@ -96,7 +95,7 @@ client.")
 (define-public fcitx5
   (package
     (name "fcitx5")
-    (version "5.1.19")
+    (version "5.1.16")
     (source
      (origin
        (method url-fetch)
@@ -104,14 +103,9 @@ client.")
              "https://download.fcitx-im.org/fcitx5/fcitx5/fcitx5-"
              version "_dict.tar.zst"))
        (sha256
-        (base32 "1ngsadqdrwy99w63dmk493gg56j7r991v6pq1nwkx6apib9ykpc0"))
-       (snippet
-        #~(begin
-            (use-modules (guix build utils))
-            (delete-file-recursively "third_party")))))
+        (base32 "0lwp90wjrkiws121rqn9kzdz6p1ncsk18dkmbv0zi37yqx2mv180"))))
     (arguments
-     (list #:configure-flags #~(list "-DUSE_SYSTEMD=OFF"
-                                     "-DUSE_SYSTEM_YOGA=ON")))
+     (list #:configure-flags #~(list "-DUSE_SYSTEMD=OFF")))
     (build-system cmake-build-system)
     (inputs
      (list cairo
@@ -124,12 +118,12 @@ client.")
            gettext-minimal
            glib
            iso-codes/pinned
+           json-c
            libevent
            libuv
            libxcb
            libxkbcommon
            libxkbfile
-           nlohmann-json
            pango
            `(,util-linux "lib")         ;For libuuid.
            wayland
@@ -138,8 +132,7 @@ client.")
            xcb-util
            xcb-util-keysyms
            xcb-util-wm
-           xkeyboard-config
-           yoga))
+           xkeyboard-config))
     (native-inputs
      (list extra-cmake-modules
            zstd
@@ -161,7 +154,7 @@ client.")
 (define-public fcitx5-lua
   (package
     (name "fcitx5-lua")
-    (version "5.0.16")
+    (version "5.0.15")
     (source
      (origin
        (method url-fetch)
@@ -169,7 +162,7 @@ client.")
              "https://download.fcitx-im.org/fcitx5/fcitx5-lua/fcitx5-lua-"
              version ".tar.zst"))
        (sha256
-        (base32 "1zjiyadhqq8hijjv09khyj2shaw3ri4jgmb1ql67w9366wd0ykj2"))))
+        (base32 "1yp5z97m8n7fwvxps1gn8pflg69j3yawgabz36bpd4wl43zkgchg"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -178,7 +171,7 @@ client.")
     (inputs
      (list fcitx5 lua gettext-minimal))
     (native-inputs
-     (list extra-cmake-modules pkg-config))
+     (list extra-cmake-modules))
     (home-page "https://github.com/fcitx/fcitx5-lua")
     (synopsis "Lua support for Fcitx 5")
     (description "Fcitx5-lua allows writing Fcitx5 extension in Lua.")
@@ -187,14 +180,14 @@ client.")
 (define-public libime
   (package
     (name "libime")
-    (version "1.1.14")
+    (version "1.1.12")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://download.fcitx-im.org/fcitx5/libime/libime-"
                            version "_dict.tar.zst"))
        (sha256
-        (base32 "17r54fd6whvcxn389k4ah9mj1fc61zgama5nhiv1ilx40n1hnnpv"))))
+        (base32 "02n6xbbxfckzx5sqrclnh4cvqlnj9c5rpys07kd8r8m51paqzigq"))))
     (build-system cmake-build-system)
     (inputs
      (list fcitx5 boost (list zstd "lib")))
@@ -209,7 +202,7 @@ editors.")
 (define-public fcitx5-gtk
   (package
     (name "fcitx5-gtk")
-    (version "5.1.6")
+    (version "5.1.4")
     (source
      (origin
        (method url-fetch)
@@ -217,7 +210,7 @@ editors.")
                            "/fcitx5-gtk/fcitx5-gtk-"
                            version ".tar.zst"))
        (sha256
-        (base32 "0qj5gjdnrxcyz6a455b4379iwnzazw5a6c6dyk6wz0d2bgainc75"))))
+        (base32 "0lwl17mbfm3pxpd3y7h4sxf77npr16hyzygrc7a6v26bx6ycbkqx"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -331,7 +324,7 @@ IM module for GTK+3 applications.
 (define-public fcitx5-qt
   (package
     (name "fcitx5-qt")
-    (version "5.1.13")
+    (version "5.1.11")
     (source
      (origin
        (method url-fetch)
@@ -339,7 +332,7 @@ IM module for GTK+3 applications.
                            "/fcitx5-qt/fcitx5-qt-"
                            version ".tar.zst"))
        (sha256
-        (base32 "1yawhwnycrqp1flik3hc2vskvsyjfm6rkcdhsqnawix22r2n1wl0"))))
+        (base32 "0mc396zfafs34jraj9fdk0wyzvdzg4xi605rhrd492xcpf25b59v"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags
@@ -370,7 +363,7 @@ for Qt based application.")
 (define-public fcitx5-anthy
   (package
     (name "fcitx5-anthy")
-    (version "5.1.10")
+    (version "5.1.8")
     (source
      (origin
        (method url-fetch)
@@ -378,7 +371,7 @@ for Qt based application.")
                            "/fcitx5-anthy/fcitx5-anthy-"
                            version ".tar.zst"))
        (sha256
-        (base32 "11h7b687xj2k1hp7dqj6wh5y6i55cm8m5pqbi5vbflgg0cy5v1mp"))))
+        (base32 "1kv930nxz6q8ijb319fnnkzdyigbi36f2cwijnv4sy3rd0nykxrv"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f)) ;; no tests
@@ -394,7 +387,7 @@ the Anthy input method.")
 (define-public fcitx5-skk
   (package
     (name "fcitx5-skk")
-    (version "5.1.10")
+    (version "5.1.8")
     (source
      (origin
        (method git-fetch)
@@ -403,14 +396,14 @@ the Anthy input method.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1fjiyx6dyiqxlypr1k4024lnc077xsnx4qwrwx9hj3yjdni5f2p0"))))
+        (base32 "11h6y7rv6yppp7iy8csy7r2pi2mlnjgl8h4h8ghfwab1gm7v32fn"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f      ; no tests
            #:configure-flags
-           #~(list (string-append "-DSKK_PATH="
+           #~(list (string-append "-DSKK_DEFAULT_PATH="
                                   #$(this-package-input "skk-jisyo")
-                                  "/share/skk"))))
+                                  "/share/skk/SKK-JISYO.L"))))
     (native-inputs
      (list extra-cmake-modules gobject-introspection
            pkg-config gettext-minimal))
@@ -430,14 +423,14 @@ backend.")
 (define-public fcitx5-unikey
   (package
     (name "fcitx5-unikey")
-    (version "5.1.10")
+    (version "5.1.8")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/fcitx/fcitx5-unikey")
                     (commit version)))
               (sha256
-               (base32 "1ddg5648r8jbdr8khawfhl26020snvrlgjwppw5rlh4iw3a4m143"))
+               (base32 "1nai5v6r367iwj8yxg4flv41my57l88l9vy0id9wr3hvrvls9v31"))
               (file-name (git-file-name name version))))
     (build-system qt-build-system)
     (arguments
@@ -457,14 +450,14 @@ backend.")
 (define-public fcitx5-chewing
   (package
     (name "fcitx5-chewing")
-    (version "5.1.11")
+    (version "5.1.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/fcitx/fcitx5-chewing")
                     (commit version)))
               (sha256
-               (base32 "1x4a4vcb7vg9dx0f2bjrb2v6dcr8cwxnm8gdd47fkxqn890rgrnc"))
+               (base32 "1mgpxvmxfbqy8gymdsdmspgknh0pc751dm5rsrvdvfbd5lsa6pn6"))
               (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (arguments
@@ -486,7 +479,7 @@ backend.")
 (define-public fcitx5-chinese-addons
   (package
     (name "fcitx5-chinese-addons")
-    (version "5.1.12")
+    (version "5.1.10")
     (source
      (origin
        (method url-fetch)
@@ -494,7 +487,7 @@ backend.")
                            "/fcitx5-chinese-addons/fcitx5-chinese-addons-"
                            version "_dict.tar.zst"))
        (sha256
-        (base32 "09kk8r6pcxjhivwv4z5cdv2pqy0ry8ngnfbrcmwagzyq2jq9p2cr"))))
+        (base32 "11gnywigqys3gndb175nxk10k1ld3xvwd6kggqnxs95imc2004dd"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags
@@ -547,7 +540,7 @@ including input methods previous bundled inside Fcitx 4:
 (define-public fcitx5-configtool
   (package
     (name "fcitx5-configtool")
-    (version "5.1.13")
+    (version "5.1.11")
     (source
      (origin
        (method url-fetch)
@@ -555,7 +548,7 @@ including input methods previous bundled inside Fcitx 4:
              "https://download.fcitx-im.org/fcitx5"
              "/fcitx5-configtool/fcitx5-configtool-" version ".tar.zst"))
        (sha256
-        (base32 "1sr8ri68qbkgvnj9pr5yw680zq506h26ymfmyz7ihw5ri14a6klr"))))
+        (base32 "1c5pw6p33z7lyk16jr1w72snazdc4q83ywn0gsk68qgmmfql5qr1"))))
     (build-system qt-build-system)
     (arguments
      (list #:qtbase qtbase
@@ -668,7 +661,7 @@ for Fcitx 5 with following color variants:
 (define-public fcitx5-rime
   (package
     (name "fcitx5-rime")
-    (version "5.1.13")
+    (version "5.1.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.fcitx-im.org/fcitx5"
@@ -676,7 +669,7 @@ for Fcitx 5 with following color variants:
                                   ".tar.zst"))
               (sha256
                (base32
-                "03wcdgdhkvw5341vjv3idyksykm65y0873vkcrsi16dsp8w0h7i8"))))
+                "1blqfk8zpzd5v2r7gwjy12jbnsh26pcvad8q4mmhlg5j10yppg03"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ;no tests
@@ -707,7 +700,7 @@ output.")
 (define-public fcitx5-hangul
   (package
     (name "fcitx5-hangul")
-    (version "5.1.9")
+    (version "5.1.7")
     (source
      (origin
        (method git-fetch)
@@ -716,7 +709,7 @@ output.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0ja5faara4xz8waccpa5gbi3prh02hh3gpf915czhbkihffby6ng"))))
+        (base32 "02lkbwg25jr4hazjyxcy69midfsmxc0ksbdrfwbmqcfa3kz5d9gb"))))
     (build-system cmake-build-system)
     (native-inputs (list extra-cmake-modules pkg-config gettext-minimal))
     (inputs (list fcitx5 libhangul))

gnu/packages/file-systems.scm

@@ -88,7 +88,6 @@
   #: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)
@@ -762,7 +761,7 @@ from a mounted file system.")
   ;; completions by running a native bcachefs binary at build time.
   (package
     (name "bcachefs-tools-minimal")
-    (version "1.37.4")
+    (version "1.35.1")
     (source
      (origin
        (method git-fetch)
@@ -771,7 +770,7 @@ from a mounted file system.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "17041jphzbg0ppxlc1acr3d73zyn02spjvi5my30wak8xh9n6nan"))))
+        (base32 "1jn7fqlvhr0iazfx31wamvmf3qmgrzlf9ghvz8qazk8b6ipv77fn"))))
     (build-system cargo-build-system)
     (arguments
      (list
@@ -969,13 +968,20 @@ minimal bcachefs-tools package.  It is meant to be used in initrds.")
 (define-public bcachefs-linux-module
   (package
     (name "bcachefs-linux-module")
-    (version (package-version bcachefs-tools-minimal))
-    (source (package-source bcachefs-tools-minimal))
+    (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"))))
     (build-system linux-module-build-system)
     (arguments
      (list
-      #:make-flags #~(list "BCACHEFS_DKMS=1")
-      #:tests? #f                       ;no 'check' target
+      #:tests? #f ;no 'check' target
       #:source-directory "build/src/fs/bcachefs"
       #:phases
       #~(modify-phases %standard-phases
@@ -984,14 +990,18 @@ minimal bcachefs-tools package.  It is meant to be used in initrds.")
               (with-output-to-file ".version"
                 (lambda ()
                   (display #$version)))))
-          (add-before 'configure 'prepare-build-directory
-            (lambda* (#:key make-flags #:allow-other-keys)
-              (apply invoke "make" "install_dkms"
-                     (string-append "DESTDIR="
-                                    (getcwd) "/")
-                     "DKMSDIR=build/"
-                     make-flags))))))
-    (home-page (package-home-page bcachefs-tools-minimal))
+          (add-after 'unpack 'patch-source
+            (lambda _
+              (substitute* "Makefile"
+                ;; Remove unnecessary dependencies
+                (("^.*PKG_CONFIG.*$")
+                 ""))))
+          (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))
     (synopsis "Bcachefs Linux kernel module")
     (description
      "This package provides the Linux kernel module for Bcachefs.
@@ -2130,79 +2140,10 @@ 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")
-    (version "0.6.1")
+    (version "0.1.105")
     (source
      (origin
        (method git-fetch)
@@ -2211,7 +2152,7 @@ while working with large number of files.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "16ds2xlk6hb5cggi6di8s0aalir3mrx7rk24rw5daad1xw4dbq0y"))))
+        (base32 "03aw8pw8694jyrzpnbry05rk9718sqw66kiyq878bbb679gl7224"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -2249,8 +2190,7 @@ memory-efficient.")
                  (install-file "fuseprivate.h"
                                (string-append #$output
                                               "/include/squashfuse/")))))))))
-    (inputs (list `(,fuse "out")
-                  `(,fuse "static")
+    (inputs (list fuse-for-appimage
                   `(,zstd "lib")
                   `(,zstd "static")
                   `(,zlib "out")

gnu/packages/finance.scm

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

gnu/packages/flex.scm

@@ -26,6 +26,7 @@
   #:use-module (guix gexp)
   #:use-module (guix utils)
   #:use-module (gnu packages)
+  #:use-module (gnu packages bootstrap)
   #:use-module (gnu packages m4)
   #:use-module (gnu packages man)
   #:use-module (gnu packages bison)
@@ -43,18 +44,9 @@
                     "flex-" version ".tar.gz"))
               (sha256
                (base32
-                "15g9bv236nzi665p9ggqjlfn4dwck5835vf0bbw2cz7h5c1swyp8"))))
+                "15g9bv236nzi665p9ggqjlfn4dwck5835vf0bbw2cz7h5c1swyp8"))
+              (patches (search-patches "flex-fix-make-dependencies.patch"))))
     (build-system gnu-build-system)
-    (inputs
-     (let ((bison-for-tests
-            (package
-              (inherit bison)
-              (arguments
-               ;; Disable tests, since they require flex.
-               (substitute-keyword-arguments arguments
-                 ((#:tests? _ #f) #f)))
-              (inputs (alist-delete "flex" (package-inputs bison))))))
-       `(("bison" ,bison-for-tests))))
     (arguments
      (if (%current-target-system)
          (list #:configure-flags
@@ -63,21 +55,29 @@
          '()))
     ;; m4 is not present in PATH when cross-building
     (native-inputs
-     (list help2man m4))
+     (let ((bison-for-tests
+            (package
+             (inherit bison)
+             (arguments
+              ;; Disable tests, since they require flex.
+              (substitute-keyword-arguments arguments
+                ((#:tests? _ #f) #f)))
+             (inputs (modify-inputs inputs
+                       (delete "flex"))))))
+       (list bison-for-tests help2man m4)))
     (propagated-inputs (list m4))
     (home-page "https://github.com/westes/flex")
     (synopsis "Fast lexical analyser generator")
     (description
-     "Flex is a tool for generating scanners.  A scanner, sometimes
-called a tokenizer, is a program which recognizes lexical patterns in
-text.  The flex program reads user-specified input files, or its standard
-input if no file names are given, for a description of a scanner to
-generate.  The description is in the form of pairs of regular expressions
-and C code, called rules.  Flex generates a C source file named,
-\"lex.yy.c\", which defines the function yylex().  The file \"lex.yy.c\"
-can be compiled and linked to produce an executable.  When the executable
-is run, it analyzes its input for occurrences of text matching the
-regular expressions for each rule.  Whenever it finds a match, it
-executes the corresponding C code.")
+     "Flex is a tool for generating scanners.  A scanner, sometimes called a
+tokenizer, is a program which recognizes lexical patterns in text.  The flex
+program reads user-specified input files, or its standard input if no file
+names are given, for a description of a scanner to generate.  The description
+is in the form of pairs of regular expressions and C code, called rules.  Flex
+generates a C source file named @file{lex.yy.c}, which defines the function
+@code{yylex()}.  The @file{lex.yy.c} can be compiled and linked to produce an
+executable.  When the executable is run, it analyzes its input for occurrences
+of text matching the regular expressions for each rule.  Whenever it finds a
+match, it executes the corresponding C code.")
     (license (non-copyleft "file://COPYING"
                            "See COPYING in the distribution."))))

gnu/packages/fltk.scm

@@ -52,7 +52,6 @@
       (uri (git-reference
               (url "https://github.com/fltk/fltk")
               (commit (string-append "release-" version))))
-      (file-name (git-file-name name version))
       (sha256
        (base32 "0pnifyhhvcqfjd6iaa4m14kvfyqhjjdw0aqbcizcdhhqrl6q4pjg"))))
    (build-system gnu-build-system)

gnu/packages/fortran-xyz.scm

@@ -28,8 +28,7 @@
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages python)
-  #:use-module (gnu packages python-build))
+  #:use-module (gnu packages python))
 
 ;;; Please: Try to add new module packages in alphabetic order.
 ;;;
@@ -145,7 +144,7 @@ a.s.o.
 (define-public fortran-mctc-lib
   (package
     (name "fortran-mctc-lib")
-    (version "0.5.1")
+    (version "0.3.2")
     (source
      (origin
        (method git-fetch)
@@ -155,7 +154,7 @@ a.s.o.
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1wp8apv0psl2hkhlrd5pgnhbxk8zpxa0ijkhcnb09klbxcsi8p5f"))))
+         "1gabdxllx2pcw1mbv4gw9zpn6817ikz9ql8xs9w86wswd6f0m5kl"))))
     (build-system meson-build-system)
     (arguments
      (list
@@ -244,7 +243,7 @@ calculate partial charges used in the DFT-D4 model.")
 (define-public fortran-simple-dftd3
   (package
     (name "fortran-simple-dftd3")
-    (version "1.3.0")
+    (version "1.2.1")
     (source
      (origin
        (method git-fetch)
@@ -253,7 +252,7 @@ calculate partial charges used in the DFT-D4 model.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1602pwmxa8qjllgj7k9hq2bm4s838f6qzr7mpc0rbh28gm00c1fw"))))
+        (base32 "0aygmnax3vwz2x3ad7syksfjca4zc85nyslsibs0wg8wqfsmr33k"))))
     (build-system meson-build-system)
     (arguments
      (list
@@ -266,8 +265,7 @@ calculate partial charges used in the DFT-D4 model.")
      (list gfortran
            pkg-config
            python-minimal
-           python-cffi
-           python-setuptools))
+           python-cffi))
     (inputs
      (list fortran-mctc-lib
            fortran-mstore

gnu/packages/freedesktop.scm

@@ -1150,60 +1150,6 @@ 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")
@@ -2916,7 +2862,7 @@ to the C library @code{uchardet} to increase performance.")
 (define-public udiskie
   (package
     (name "udiskie")
-    (version "2.6.2")
+    (version "2.6.1")
     (source
      (origin
        (method git-fetch)
@@ -2925,7 +2871,7 @@ to the C library @code{uchardet} to increase performance.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0zc23yf2sw1m21xkfbpfjzbp7xykqjwq56fr2nxzlc02n7g6iqgk"))))
+        (base32 "0ngr8sdzd32mxamzfh82ar8m40z52lx91339b7dq3in0cr5r1ynp"))))
     (build-system pyproject-build-system)
     (arguments
      (list

gnu/packages/games.scm

@@ -30,7 +30,7 @@
 ;;; Copyright © 2017, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2017-2026 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2017-2025 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 okapi <okapi@firemail.cc>
 ;;; Copyright © 2018 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
 ;;; Copyright © 2018 Madalin Ionel-Patrascu <madalinionel.patrascu@mdc-berlin.de>
@@ -3964,7 +3964,7 @@ that beneath its ruins lay buried an ancient evil.")
 (define-public angband
   (package
     (name "angband")
-    (version "4.2.6")
+    (version "4.2.5")
     (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 "0hgzdvlh0j42w4q9kch9xvhnbvcrypac01xhpksw35gj9my887cp"))
+        (base32 "0kg6npbfy42mhggsqvs04khc8198i980z52xm59pws29698qazaw"))
        (modules '((guix build utils)))
        (snippet
         ;; So, some of the sounds/graphics/tilesets are under different
@@ -3989,55 +3989,12 @@ 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"))
-           ;; Remove nonfree .dll files too.
-           (delete-file-recursively "src/win")))))
+              "gamedata customize help screens user"))))))
     (build-system gnu-build-system)
     (arguments
-     `(#: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
+     `(#:tests? #f                      ; no check target
+       #:configure-flags (list (string-append "--bindir=" %output "/bin"))))
+    (native-inputs (list autoconf automake))
     (inputs (list ncurses))
     (home-page "https://rephial.org/")
     (synopsis "Dungeon exploration roguelike")
@@ -4948,7 +4905,7 @@ Protocol).")
 (define-public extremetuxracer
   (package
     (name "extremetuxracer")
-    (version "0.8.4")
+    (version "0.8.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4956,7 +4913,7 @@ Protocol).")
                     version "/etr-" version ".tar.xz"))
               (sha256
                (base32
-                "1rbk8zqfzzk90znf3f5lqqa12j0n6pm2qgwzabzmlnkm1k68acps"))))
+                "0knd22lzhzqih1w92y6m7yxha376c6ydl22wy4xm6jg2x5jlk1qw"))))
     (build-system gnu-build-system)
     (native-inputs
      (list pkg-config))
@@ -8191,7 +8148,7 @@ fish.  The whole game is accompanied by quiet, comforting music.")
 (define-public crawl
   (package
     (name "crawl")
-    (version "0.34.1")
+    (version "0.34.0")
     (source
      (origin
        (method git-fetch)
@@ -8200,7 +8157,7 @@ fish.  The whole game is accompanied by quiet, comforting music.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "09x4n4w3rw8sldwprb03yg1igwh4m09iw00g2iq30466jryys6bv"))
+        (base32 "16fsvrzcndrplw8zcn6nh8459x8zl5xdnf9r9hzh4ll2a4w9dkcr"))
        (patches (search-patches "crawl-upgrade-saves.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -11355,33 +11312,46 @@ to remap axis and buttons and a way to calibrate joysticks.")
 (define-public jumpnbump
   (package
     (name "jumpnbump")
-    (version "1.70")
+    (version "1.61")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                     (url "https://gitlab.com/LibreGames/jumpnbump.git")
-                     (commit version)))
+                    (url "https://gitlab.com/LibreGames/jumpnbump.git")
+                    (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1irpssijxrfrjm023v642dl3aw4ldlv95fh073jlpdpl1mwqz71a"))))
+                "12lwl5sl5n009nb83r8l4lakb9286csqdf1ynpmwwydy17giqsdp"))))
     (build-system gnu-build-system)
     (arguments
-     (list
-      #:make-flags
-      #~(list (string-append "CC=" #$(cc-for-target))
-              (string-append "PREFIX=" #$output)
-              "SYSINSTALL=1")
-      #:tests? #f                       ;no test
-      #:phases
-      #~(modify-phases %standard-phases
-          (delete 'configure))))        ;no configure script
+     `(#:make-flags
+       (list "CC=gcc"
+             (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:tests? #f                      ;no test
+       #:phases
+       (modify-phases %standard-phases
+         ;; There is no configure script
+         (replace 'configure
+           (lambda _
+             (substitute* "Makefile"
+               (("-funroll-loops")
+                "-funroll-loops -fcommon")
+               (("SDL_CFLAGS =")
+                "SDL_CFLAGS = -fcommon"))))
+         (add-after 'unpack 'fix-sdl-path
+           ;; XXX: For some reason, `sdl2-config' reports stand-alone SDL
+           ;; directory, not SDL-union provided as an input to the package.
+           ;; We force the latter with "--prefix=" option.
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("sdl2-config" command)
+                (string-append command " --prefix=" (assoc-ref inputs "sdl")))))))))
     (inputs
-     (list bzip2
-           (sdl-union (list sdl2 sdl2-mixer sdl2-net))
-           zlib))
+     `(("bzip2" ,bzip2)
+       ("sdl" ,(sdl-union (list sdl2 sdl2-mixer sdl2-net)))
+       ("zlib" ,zlib)))
     (native-inputs
-     (list gettext-minimal))            ;for msgfmt
+     `(("gettext" ,gettext-minimal)))   ;for msgfmt
     (home-page "https://gitlab.com/LibreGames/jumpnbump")
     (synopsis "Multiplayer platform game with bunnies")
     (description "You, as a bunny, have to jump on your opponents to make them
@@ -11517,7 +11487,7 @@ player adaptability for character progression.")
 (define-public li-ri
   (package
     (name "li-ri")
-    (version "3.1.6")
+    (version "3.1.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -11526,7 +11496,7 @@ player adaptability for character progression.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "09r6l0sbxp3q750kpbrx513yrafmg7a2769j4wgx812lsk92n3hg"))))
+                "1fd5hl9qhgvyix51la8sl34jzk4mcin8sai05gidy2r2grb1dy4s"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #false              ;no tests

gnu/packages/gawk.scm

@@ -41,13 +41,13 @@
 (define-public gawk
   (package
    (name "gawk")
-   (version "5.3.0")
+   (version "5.3.2")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/gawk/gawk-" version
                                 ".tar.xz"))
             (sha256
-             (base32 "02x97iyl9v84as4rkdrrkfk2j4vy4r3hpp3rkp3gh3qxs79id76a"))))
+             (base32 "1k699kfajwzw4dyw1m9h9kld1gdv00nfy04b2f952w6y15jlihzq"))))
    (build-system gnu-build-system)
    (arguments
     (list #:phases
@@ -56,7 +56,7 @@
                 (lambda* (#:key inputs #:allow-other-keys)
                   ;; Refer to the right shell.
                   (let ((/bin/sh (search-input-file inputs "bin/sh")))
-                    (substitute* "io.c"
+                    (substitute* '("io.c" "builtin.c")
                       (("/bin/sh") /bin/sh))
 
                     ;; When cross-compiling, remove dependencies on the
@@ -73,7 +73,7 @@
                   ;; Remove dependency on 'more' (from util-linux), which
                   ;; would needlessly complicate bootstrapping.
                   (substitute* "test/Makefile"
-                    (("\\| more") ""))
+                    (("\\| \\$\\$\\{PAGER:-more\\}") ""))
 
                   ;; Adjust the shebang in that file since it is then diff'd
                   ;; against the actual test output.

gnu/packages/gcc.scm

@@ -80,16 +80,16 @@ where the OS part is overloaded to denote a specific ABI---into GCC
   (cond ((string-match "^mips64el.*gnuabin?64$" target)
          ;; Triplets recognized by glibc as denoting the N64 ABI; see
          ;; ports/sysdeps/mips/preconfigure.
-         '("--with-abi=64"))
+         #~(list "--with-abi=64"))
 
         ((string-match "^arm.*-gnueabihf$" target)
-         '("--with-arch=armv7-a"
-           "--with-float=hard"
-           "--with-mode=thumb"
-           "--with-fpu=neon"))
+         #~(list "--with-arch=armv7-a"
+                 "--with-float=hard"
+                 "--with-mode=thumb"
+                 "--with-fpu=neon"))
 
         ((string-match "x86_64-linux-gnux32" target)
-         '("--with-abi=mx32"))
+         #~(list "--with-abi=mx32"))
 
         ((and (string-suffix? "-gnu" target)
               (not (string-contains target "-linux")))
@@ -97,36 +97,24 @@ where the OS part is overloaded to denote a specific ABI---into GCC
          ;; with:
          ;;   libcilkrts/runtime/os-unix.c:388:2: error: #error "Unknown architecture"
          ;; Cilk has been removed from GCC 8 anyway.
-         '("--disable-libcilkrts"))
+         #~(list "--disable-libcilkrts"))
 
         ;; glibc needs the 128-bit long double type on these architectures.
         ((or (string-prefix? "powerpc64le-" target)
              (string-prefix? "powerpc-" target))
-         '("--with-long-double-128"))
+         #~(list "--with-long-double-128"))
 
         ;; GCC 11.3.0's <libgcov.h> includes <sys/mman.h>, which MinGW lacks:
         ;; <https://bugs.gentoo.org/show_bug.cgi?id=843989>.
         ((target-mingw? target)
-         '("--disable-gcov"))
+         #~(list "--disable-gcov"))
 
         (else
          ;; TODO: Add `arm.*-gnueabi', etc.
-         '())))
+         #~(list))))
 
 (define-public gcc-base
   (let* ((stripped? #t)      ;whether to strip the compiler, not the libraries
-         (maybe-target-tools
-          (lambda ()
-            ;; Return the `_FOR_TARGET' variables that are needed when
-            ;; cross-compiling GCC.
-            (let ((target (%current-target-system)))
-              (if target
-                  (map (lambda (var tool)
-                         (string-append (string-append var "_FOR_TARGET")
-                                        "=" target "-" tool))
-                       '("CC"  "CXX" "LD" "AR" "NM" "OBJDUMP" "RANLIB" "STRIP")
-                       '("gcc" "g++" "ld" "ar" "nm" "objdump" "ranlib" "strip"))
-                  '()))))
          (libdir
           (let ((base '(or (assoc-ref outputs "lib")
                            (assoc-ref outputs "out"))))
@@ -134,45 +122,7 @@ where the OS part is overloaded to denote a specific ABI---into GCC
               ;; Return the directory that contains lib/libgcc_s.so et al.
               (if (%current-target-system)
                   `(string-append ,base "/" ,(%current-target-system))
-                  base))))
-         (configure-flags
-          (lambda ()
-            ;; This is terrible.  Since we have two levels of quasiquotation,
-            ;; we have to do this convoluted thing just so we can insert the
-            ;; contents of (maybe-target-tools).
-            (list 'quasiquote
-                  (append
-                   '("--enable-plugin"
-                     "--enable-languages=c,c++,objc,obj-c++"
-                     "--disable-multilib"
-                     "--with-system-zlib"
-
-                     ;; No pre-compiled libstdc++ headers, to save space.
-                     "--disable-libstdcxx-pch"
-
-                     "--with-local-prefix=/no-gcc-local-prefix"
-
-                     ;; With a separate "lib" output, the build system
-                     ;; incorrectly guesses GPLUSPLUS_INCLUDE_DIR, so force
-                     ;; it.  (Don't use a versioned sub-directory, that's
-                     ;; unnecessary.)
-                     ,(string-append "--with-gxx-include-dir="
-                                     (assoc-ref %outputs "out")
-                                     "/include/c++")
-
-                     ,(let ((libc (assoc-ref %build-inputs "libc")))
-                        (if libc
-                            (string-append "--with-native-system-header-dir=" libc
-                                           "/include")
-                            "--without-headers")))
-
-                   ;; Pass the right options for the target triplet.
-                   (let ((triplet
-                          (or (%current-target-system)
-                              (nix-system->gnu-triplet (%current-system)))))
-                     (gcc-configure-flags-for-triplet triplet))
-
-                   (maybe-target-tools))))))
+                  base)))))
     (hidden-package
      (package
        (name "gcc")
@@ -202,201 +152,239 @@ where the OS part is overloaded to denote a specific ABI---into GCC
                             texinfo-5))
 
        (arguments
-        `(#:out-of-source? #t
-          #:configure-flags ,(configure-flags)
+        (list
+         #:out-of-source? #t
+         #:configure-flags
+         #~(append
+            (list "--enable-plugin"
+                  "--enable-languages=c,c++,objc,obj-c++"
+                  "--disable-multilib"
+                  "--with-system-zlib"
 
-          #:make-flags
-          ;; None of the flags below are needed when doing a Canadian cross.
-          ;; TODO: Simplify this.
-          ,(if (%current-target-system)
-               (if stripped?
-                   ''("CFLAGS=-g0 -O2")
-                   ''())
-               `(let* ((libc        (assoc-ref %build-inputs "libc"))
-                       (libc-native (or (assoc-ref %build-inputs "libc-native")
-                                        libc)))
-                  `(,@(if libc
-                          (list (string-append "LDFLAGS_FOR_TARGET="
-                                               "-B" libc "/lib "
-                                               "-Wl,-dynamic-linker "
-                                               "-Wl," libc
-                                               ,(glibc-dynamic-linker)))
-                          '())
+                  ;; No pre-compiled libstdc++ headers, to save space.
+                  "--disable-libstdcxx-pch"
 
-                    ;; Native programs like 'genhooks' also need that right.
-                    ,(string-append "LDFLAGS="
-                                    "-Wl,-rpath=" libc-native "/lib "
-                                    "-Wl,-dynamic-linker "
-                                    "-Wl," libc-native ,(glibc-dynamic-linker))
-                    ,(string-append "BOOT_CFLAGS=-O2 "
-                                    ,(if stripped? "-g0" "-g")))))
+                  "--with-local-prefix=/no-gcc-local-prefix"
 
-          #:tests? #f
+                  ;; With a separate "lib" output, the build system
+                  ;; incorrectly guesses GPLUSPLUS_INCLUDE_DIR, so force
+                  ;; it.  (Don't use a versioned sub-directory, that's
+                  ;; unnecessary.)
+                  (string-append "--with-gxx-include-dir="
+                                 #$output "/include/c++")
 
-          #:phases
-          (modify-phases %standard-phases
-            (add-before 'configure 'relax-gcc-14s-strictness
-              (lambda* (#:key inputs #:allow-other-keys)
-                (let ((bash (assoc-ref inputs "bash"))
-                      (wrapper (string-append (getcwd) "/gcc.sh"))
-                      (stage-wrapper (string-append (getcwd) "/stage-gcc.sh")))
-                  (with-output-to-file wrapper
-                    (lambda _
-                      (format #t "#! ~a/bin/bash
+                  (let ((libc (assoc-ref %build-inputs "libc")))
+                    (if libc
+                        (string-append "--with-native-system-header-dir=" libc
+                                       "/include")
+                        "--without-headers")))
+
+            ;; Pass the right options for the target triplet.
+            #$(gcc-configure-flags-for-triplet
+               (or (%current-target-system)
+                   (nix-system->gnu-triplet (%current-system))))
+
+            ;; Return the `_FOR_TARGET' variables that are needed when
+            ;; cross-compiling GCC.
+            #$(let ((target (%current-target-system)))
+                (if target
+                    #~(map (lambda (var tool)
+                             (string-append (string-append var "_FOR_TARGET")
+                                            "=" #$target "-" tool))
+                           '("CC"  "CXX" "LD" "AR" "NM" "OBJDUMP" "RANLIB" "STRIP")
+                           '("gcc" "g++" "ld" "ar" "nm" "objdump" "ranlib" "strip"))
+                    #~(list))))
+         #:make-flags
+         (cond
+          ((and (%current-target-system) stripped?)
+           #~(list "CFLAGS=-g0 -O2"))
+          ((%current-target-system)
+           #~(list)) ;None of the flags are needed when doing a Canadian cross.
+          (else
+           #~(let* ((libc (assoc-ref %build-inputs "libc"))
+                    (libc-native (or (assoc-ref %build-inputs "libc-native")
+                                     libc))
+                    (loader #$(glibc-dynamic-linker)))
+               (cons*
+                ;; Native programs like 'genhooks' need that right.
+                (string-append "LDFLAGS="
+                               "-Wl,-rpath=" libc-native "/lib "
+                               "-Wl,-dynamic-linker "
+                               "-Wl," libc-native loader)
+                (string-append "BOOT_CFLAGS=-O2 "
+                               (if #$stripped? "-g0" "-g"))
+                (if libc
+                    (list (string-append "LDFLAGS_FOR_TARGET="
+                                         "-B" libc "/lib "
+                                         "-Wl,-dynamic-linker "
+                                         "-Wl," libc loader))
+                    (list))))))
+         #:tests? #f
+
+         #:phases
+         #~(modify-phases %standard-phases
+             (add-before 'configure 'relax-gcc-14s-strictness
+               (lambda* (#:key inputs #:allow-other-keys)
+                 (let ((bash (search-input-file inputs "/bin/bash"))
+                       (wrapper (string-append (getcwd) "/gcc.sh"))
+                       (stage-wrapper (string-append (getcwd) "/stage-gcc.sh")))
+                   (with-output-to-file wrapper
+                     (lambda _
+                       (format #t "#! ~a
 exec gcc \"$@\" \
     -Wno-error=implicit-function-declaration"
-                              bash)))
-                  (chmod wrapper #o555)
-                  (with-output-to-file stage-wrapper
-                    (lambda _
-                      (format #t "#! ~a/bin/bash
+                               bash)))
+                   (chmod wrapper #o555)
+                   (with-output-to-file stage-wrapper
+                     (lambda _
+                       (format #t "#! ~a
 exec \"$@\" \
     -Wno-error=implicit-function-declaration"
-                              bash)))
-                  (chmod stage-wrapper #o555)
-                  ;; Rather than adding CC to #:configure-flags and
-                  ;; STAGE_CC_WRAPPER to #:make-flags, we add them to the
-                  ;; environment in this easily removable stage.
-                  (cond (,(%current-target-system) ;cross-build?
-                         (setenv "CC_FOR_BUILD" wrapper))
-                        (else
-                         (setenv "CC" wrapper)
-                         (setenv "STAGE_CC_WRAPPER" stage-wrapper))))))
-            (add-before 'configure 'pre-configure
-              (lambda* (#:key inputs outputs #:allow-other-keys)
-                (let ((libdir ,(libdir))
-                      (libc   (assoc-ref inputs "libc")))
-                  (when libc
-                    ;; The following is not performed for `--without-headers'
-                    ;; cross-compiler builds.
+                               bash)))
+                   (chmod stage-wrapper #o555)
+                   ;; Rather than adding CC to #:configure-flags and
+                   ;; STAGE_CC_WRAPPER to #:make-flags, we add them to the
+                   ;; environment in this easily removable stage.
+                   (cond (#$(%current-target-system) ;cross-build?
+                          (setenv "CC_FOR_BUILD" wrapper))
+                         (else
+                          (setenv "CC" wrapper)
+                          (setenv "STAGE_CC_WRAPPER" stage-wrapper))))))
+             (add-before 'configure 'pre-configure
+               (lambda* (#:key inputs outputs #:allow-other-keys)
+                 (let ((libdir #$(libdir))
+                       (libc   (assoc-ref inputs "libc")))
+                   (when libc
+                     ;; The following is not performed for `--without-headers'
+                     ;; cross-compiler builds.
 
-                    ;; Join multi-line definitions of GLIBC_DYNAMIC_LINKER* into a
-                    ;; single line, to allow the next step to work properly.
-                    (for-each
-                     (lambda (x)
-                       (substitute* (find-files "gcc/config"
-                                                "^(linux|gnu|sysv4)(64|-elf|-eabi)?\\.h$")
-                         (("(#define (GLIBC|GNU_USER)_DYNAMIC_LINKER.*)\\\\\n$" _ line)
-                          line)))
-                     '(1 2 3))
+                     ;; Join multi-line definitions of GLIBC_DYNAMIC_LINKER* into a
+                     ;; single line, to allow the next step to work properly.
+                     (for-each
+                      (lambda (x)
+                        (substitute* (find-files "gcc/config"
+                                                 "^(linux|gnu|sysv4)(64|-elf|-eabi)?\\.h$")
+                          (("(#define (GLIBC|GNU_USER)_DYNAMIC_LINKER.*)\\\\\n$" _ line)
+                           line)))
+                      '(1 2 3))
 
-                    ;; Fix the dynamic linker's file name.
-                    (substitute* (find-files "gcc/config"
-                                             "^(linux|gnu|sysv4)(64|-elf|-eabi)?\\.h$")
-                      (("#define (GLIBC|GNU_USER)_DYNAMIC_LINKER([^ \t]*).*$"
-                        _ gnu-user suffix)
-                       (format #f "#define ~a_DYNAMIC_LINKER~a \"~a\"~%"
-                               gnu-user suffix
-                               (string-append libc ,(glibc-dynamic-linker)))))
+                     ;; Fix the dynamic linker's file name.
+                     (substitute* (find-files "gcc/config"
+                                              "^(linux|gnu|sysv4)(64|-elf|-eabi)?\\.h$")
+                       (("#define (GLIBC|GNU_USER)_DYNAMIC_LINKER([^ \t]*).*$"
+                         _ gnu-user suffix)
+                        (format #f "#define ~a_DYNAMIC_LINKER~a \"~a\"~%"
+                                gnu-user suffix
+                                (string-append libc #$(glibc-dynamic-linker)))))
 
-                    ;; Tell where to find libstdc++, libc, and `?crt*.o', except
-                    ;; `crt{begin,end}.o', which come with GCC.
-                    (substitute* (find-files "gcc/config"
-                                             "^gnu-user.*\\.h$")
-                      (("#define GNU_USER_TARGET_LIB_SPEC (.*)$" _ suffix)
-                       ;; Help libgcc_s.so be found (see also below.)  Always use
-                       ;; '-lgcc_s' so that libgcc_s.so is always found by those
-                       ;; programs that use 'pthread_cancel' (glibc dlopens
-                       ;; libgcc_s.so when pthread_cancel support is needed, but
-                       ;; having it in the application's RUNPATH isn't enough; see
-                       ;; <http://sourceware.org/ml/libc-help/2013-11/msg00023.html>.)
-                       ;;
-                       ;; NOTE: The '-lgcc_s' added below needs to be removed in a
-                       ;; later phase of %gcc-static.  If you change the string
-                       ;; below, make sure to update the relevant code in
-                       ;; %gcc-static package as needed.
-                       (format #f "#define GNU_USER_TARGET_LIB_SPEC \
+                     ;; Tell where to find libstdc++, libc, and `?crt*.o', except
+                     ;; `crt{begin,end}.o', which come with GCC.
+                     (substitute* (find-files "gcc/config"
+                                              "^gnu-user.*\\.h$")
+                       (("#define GNU_USER_TARGET_LIB_SPEC (.*)$" _ suffix)
+                        ;; Help libgcc_s.so be found (see also below.)  Always use
+                        ;; '-lgcc_s' so that libgcc_s.so is always found by those
+                        ;; programs that use 'pthread_cancel' (glibc dlopens
+                        ;; libgcc_s.so when pthread_cancel support is needed, but
+                        ;; having it in the application's RUNPATH isn't enough; see
+                        ;; <http://sourceware.org/ml/libc-help/2013-11/msg00023.html>.)
+                        ;;
+                        ;; NOTE: The '-lgcc_s' added below needs to be removed in a
+                        ;; later phase of %gcc-static.  If you change the string
+                        ;; below, make sure to update the relevant code in
+                        ;; %gcc-static package as needed.
+                        (format #f "#define GNU_USER_TARGET_LIB_SPEC \
 \"-L~a/lib %{!static:-rpath=~a/lib %{!static-libgcc:-rpath=~a/lib -lgcc_s}} \" ~a"
-                               libc libc libdir suffix))
-                      (("#define GNU_USER_TARGET_STARTFILE_SPEC.*$" line)
-                       (format #f "#define STANDARD_STARTFILE_PREFIX_1 \"~a/lib/\"
+                                libc libc libdir suffix))
+                       (("#define GNU_USER_TARGET_STARTFILE_SPEC.*$" line)
+                        (format #f "#define STANDARD_STARTFILE_PREFIX_1 \"~a/lib/\"
 #define STANDARD_STARTFILE_PREFIX_2 \"\"
 ~a"
-                               libc line)))
+                                libc line)))
 
-                    ;; The rs6000 (a.k.a. powerpc) config in GCC does not use
-                    ;; GNU_USER_* defines.  Do the above for this case.
-                    (substitute*
-                        "gcc/config/rs6000/sysv4.h"
-                      (("#define LIB_LINUX_SPEC (.*)$" _ suffix)
-                       (format #f "#define LIB_LINUX_SPEC \
+                     ;; The rs6000 (a.k.a. powerpc) config in GCC does not use
+                     ;; GNU_USER_* defines.  Do the above for this case.
+                     (substitute*
+                         "gcc/config/rs6000/sysv4.h"
+                       (("#define LIB_LINUX_SPEC (.*)$" _ suffix)
+                        (format #f "#define LIB_LINUX_SPEC \
 \"-L~a/lib %{!static:-rpath=~a/lib %{!static-libgcc:-rpath=~a/lib -lgcc_s}} \" ~a"
-                               libc libc libdir suffix))
-                      (("#define	STARTFILE_LINUX_SPEC.*$" line)
-                       (format #f "#define STANDARD_STARTFILE_PREFIX_1 \"~a/lib/\"
+                                libc libc libdir suffix))
+                       (("#define	STARTFILE_LINUX_SPEC.*$" line)
+                        (format #f "#define STANDARD_STARTFILE_PREFIX_1 \"~a/lib/\"
 #define STANDARD_STARTFILE_PREFIX_2 \"\"
 ~a"
-                               libc line))))
+                                libc line))))
 
-                  (when (file-exists? "gcc/config/rs6000")
-                    ;; Force powerpc libdir to be /lib and not /lib64
-                    (substitute* (find-files "gcc/config/rs6000")
-                      (("/lib64") "/lib")))
+                   (when (file-exists? "gcc/config/rs6000")
+                     ;; Force powerpc libdir to be /lib and not /lib64
+                     (substitute* (find-files "gcc/config/rs6000")
+                       (("/lib64") "/lib")))
 
-                  ;; Don't retain a dependency on the build-time sed.
-                  (substitute* "fixincludes/fixincl.x"
-                    (("static char const sed_cmd_z\\[\\] =.*;")
-                     "static char const sed_cmd_z[] = \"sed\";"))
+                   ;; Don't retain a dependency on the build-time sed.
+                   (substitute* "fixincludes/fixincl.x"
+                     (("static char const sed_cmd_z\\[\\] =.*;")
+                      "static char const sed_cmd_z[] = \"sed\";"))
 
-                  ;; Aarch64 support didn't land in GCC until the 4.8 series.
-                  (when (file-exists? "gcc/config/aarch64")
-                    ;; Force Aarch64 libdir to be /lib and not /lib64
-                    (substitute* "gcc/config/aarch64/t-aarch64-linux"
-                      (("lib64") "lib")))
+                   ;; Aarch64 support didn't land in GCC until the 4.8 series.
+                   (when (file-exists? "gcc/config/aarch64")
+                     ;; Force Aarch64 libdir to be /lib and not /lib64
+                     (substitute* "gcc/config/aarch64/t-aarch64-linux"
+                       (("lib64") "lib")))
 
-                  ;; The STARTFILE_PREFIX_SPEC prevents gcc from finding the
-                  ;; gcc:lib output, which causes ld to not find -lgcc_s.
-                  (when (file-exists? "gcc/config/riscv")
-                    (substitute* '("gcc/config/riscv/linux.h"
-                                   "gcc/config/riscv/riscv.h")  ; GCC < 10
-                      (("define STARTFILE_PREFIX_SPEC")
-                      "define __STARTFILE_PREFIX_SPEC")))
+                   ;; The STARTFILE_PREFIX_SPEC prevents gcc from finding the
+                   ;; gcc:lib output, which causes ld to not find -lgcc_s.
+                   (when (file-exists? "gcc/config/riscv")
+                     (substitute* '("gcc/config/riscv/linux.h"
+                                    "gcc/config/riscv/riscv.h")  ; GCC < 10
+                       (("define STARTFILE_PREFIX_SPEC")
+                        "define __STARTFILE_PREFIX_SPEC")))
 
-                  (when (file-exists? "libbacktrace")
-                    ;; GCC 4.8+ comes with libbacktrace.  By default it builds
-                    ;; with -Werror, which fails with a -Wcast-qual error in glibc
-                    ;; 2.21's stdlib-bsearch.h.  Remove -Werror.
-                    (substitute* "libbacktrace/configure"
-                      (("WARN_FLAGS=(.*)-Werror" _ flags)
-                       (string-append "WARN_FLAGS=" flags)))
+                   (when (file-exists? "libbacktrace")
+                     ;; GCC 4.8+ comes with libbacktrace.  By default it builds
+                     ;; with -Werror, which fails with a -Wcast-qual error in glibc
+                     ;; 2.21's stdlib-bsearch.h.  Remove -Werror.
+                     (substitute* "libbacktrace/configure"
+                       (("WARN_FLAGS=(.*)-Werror" _ flags)
+                        (string-append "WARN_FLAGS=" flags)))
 
-                    (when (file-exists? "libsanitizer/libbacktrace")
-                      ;; Same in libsanitizer's bundled copy (!) found in 4.9+.
-                      (substitute* "libsanitizer/libbacktrace/Makefile.in"
-                        (("-Werror")
-                         ""))))
+                     (when (file-exists? "libsanitizer/libbacktrace")
+                       ;; Same in libsanitizer's bundled copy (!) found in 4.9+.
+                       (substitute* "libsanitizer/libbacktrace/Makefile.in"
+                         (("-Werror")
+                          ""))))
 
-                  ;; Add a RUNPATH to libstdc++.so so that it finds libgcc_s.
-                  ;; See <https://gcc.gnu.org/bugzilla/show_bug.cgi?id=32354>
-                  ;; and <http://bugs.gnu.org/20358>.
-                  (substitute* "libstdc++-v3/src/Makefile.in"
-                    (("^OPT_LDFLAGS = ")
-                     "OPT_LDFLAGS = -Wl,-rpath=$(libdir) "))
+                   ;; Add a RUNPATH to libstdc++.so so that it finds libgcc_s.
+                   ;; See <https://gcc.gnu.org/bugzilla/show_bug.cgi?id=32354>
+                   ;; and <http://bugs.gnu.org/20358>.
+                   (substitute* "libstdc++-v3/src/Makefile.in"
+                     (("^OPT_LDFLAGS = ")
+                      "OPT_LDFLAGS = -Wl,-rpath=$(libdir) "))
 
-                  ;; Move libstdc++*-gdb.py to the "lib" output to avoid a
-                  ;; circularity between "out" and "lib".  (Note:
-                  ;; --with-python-dir is useless because it imposes $(prefix) as
-                  ;; the parent directory.)
-                  (substitute* "libstdc++-v3/python/Makefile.in"
-                    (("pythondir = .*$")
-                     (string-append "pythondir = " libdir "/share"
-                                    "/gcc-$(gcc_version)/python\n")))
+                   ;; Move libstdc++*-gdb.py to the "lib" output to avoid a
+                   ;; circularity between "out" and "lib".  (Note:
+                   ;; --with-python-dir is useless because it imposes $(prefix) as
+                   ;; the parent directory.)
+                   (substitute* "libstdc++-v3/python/Makefile.in"
+                     (("pythondir = .*$")
+                      (string-append "pythondir = " libdir "/share"
+                                     "/gcc-$(gcc_version)/python\n")))
 
-                  ;; Avoid another circularity between the outputs: this #define
-                  ;; ends up in auto-host.h in the "lib" output, referring to
-                  ;; "out".  (This variable is used to augment cpp's search path,
-                  ;; but there's nothing useful to look for here.)
-                  (substitute* "gcc/config.in"
-                    (("PREFIX_INCLUDE_DIR")
-                     "PREFIX_INCLUDE_DIR_isnt_necessary_here")))))
+                   ;; Avoid another circularity between the outputs: this #define
+                   ;; ends up in auto-host.h in the "lib" output, referring to
+                   ;; "out".  (This variable is used to augment cpp's search path,
+                   ;; but there's nothing useful to look for here.)
+                   (substitute* "gcc/config.in"
+                     (("PREFIX_INCLUDE_DIR")
+                      "PREFIX_INCLUDE_DIR_isnt_necessary_here")))))
 
-            (add-after 'configure 'post-configure
-              (lambda _
-                ;; Don't store configure flags, to avoid retaining references to
-                ;; build-time dependencies---e.g., `--with-ppl=/gnu/store/xxx'.
-                (substitute* "Makefile"
-                  (("^TOPLEVEL_CONFIGURE_ARGUMENTS=(.*)$" _ rest)
-                   "TOPLEVEL_CONFIGURE_ARGUMENTS=\n")))))))
+             (add-after 'configure 'post-configure
+               (lambda _
+                 ;; Don't store configure flags, to avoid retaining references to
+                 ;; build-time dependencies---e.g., `--with-ppl=/gnu/store/xxx'.
+                 (substitute* "Makefile"
+                   (("^TOPLEVEL_CONFIGURE_ARGUMENTS=(.*)$" _ rest)
+                    "TOPLEVEL_CONFIGURE_ARGUMENTS=\n")))))))
        (native-search-paths %gcc-search-paths)
        (properties `((gcc-libc . ,(assoc-ref inputs "libc"))))
        (synopsis "GNU Compiler Collection")
@@ -440,21 +428,21 @@ Go.  It also includes runtime support libraries for these languages.")
             `((srfi srfi-1)
               ,@modules))
            ((#:phases phases)
-            `(modify-phases ,phases
-               (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   (let ((libc (assoc-ref inputs "libc"))
-                         (gcc (assoc-ref inputs  "gcc")))
-                     (setenv "CPLUS_INCLUDE_PATH"
-                             (string-join (fold delete
-                                                (string-split (getenv "CPLUS_INCLUDE_PATH")
-                                                              #\:)
-                                                (list (string-append libc "/include")
-                                                      (string-append gcc "/include/c++")))
-                                          ":"))
-                     (format #t
-                             "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
-                             (getenv "CPLUS_INCLUDE_PATH"))))))))))
+            #~(modify-phases #$phases
+                (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+                  (lambda* (#:key inputs #:allow-other-keys)
+                    (let ((libc (assoc-ref inputs "libc"))
+                          (gcc (assoc-ref inputs  "gcc")))
+                      (setenv "CPLUS_INCLUDE_PATH"
+                              (string-join (fold delete
+                                                 (string-split (getenv "CPLUS_INCLUDE_PATH")
+                                                               #\:)
+                                                 (list (string-append libc "/include")
+                                                       (string-append gcc "/include/c++")))
+                                           ":"))
+                      (format #t
+                              "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+                              (getenv "CPLUS_INCLUDE_PATH"))))))))))
     (supported-systems (fold delete %supported-systems
                              '("aarch64-linux" "riscv64-linux"
                                "powerpc64le-linux" "x86_64-gnu")))))
@@ -498,21 +486,21 @@ Go.  It also includes runtime support libraries for these languages.")
            ;; For native builds of some GCC versions the C++ include path needs to
            ;; be adjusted so it does not interfere with GCC's own build processes.
            ((#:phases phases)
-            `(modify-phases ,phases
-               (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   (let ((libc (assoc-ref inputs "libc"))
-                         (gcc (assoc-ref inputs  "gcc")))
-                     (setenv "CPLUS_INCLUDE_PATH"
-                             (string-join (fold delete
-                                                (string-split (getenv "CPLUS_INCLUDE_PATH")
-                                                              #\:)
-                                                (list (string-append libc "/include")
-                                                      (string-append gcc "/include/c++")))
-                                          ":"))
-                     (format #t
-                             "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
-                             (getenv "CPLUS_INCLUDE_PATH"))))))))))
+            #~(modify-phases #$phases
+                (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+                  (lambda* (#:key inputs #:allow-other-keys)
+                    (let ((libc (assoc-ref inputs "libc"))
+                          (gcc (assoc-ref inputs  "gcc")))
+                      (setenv "CPLUS_INCLUDE_PATH"
+                              (string-join (fold delete
+                                                 (string-split (getenv "CPLUS_INCLUDE_PATH")
+                                                               #\:)
+                                                 (list (string-append libc "/include")
+                                                       (string-append gcc "/include/c++")))
+                                           ":"))
+                      (format #t
+                              "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+                              (getenv "CPLUS_INCLUDE_PATH"))))))))))
     (supported-systems (fold delete %supported-systems
                              '("riscv64-linux" "x86_64-gnu")))
     (inputs
@@ -981,7 +969,8 @@ It also includes runtime support libraries for these languages.")
               (patches (search-patches "gcc-12-strmov-store-file-names.patch"
                                        "gcc-5.0-libvtv-runpath.patch"
                                        "gcc-13-libsanitizer-no-crypt.patch"
-                                       "gcc-libstdc++-newer-gcc.patch"))
+                                       "gcc-libstdc++-newer-gcc.patch"
+                                       "gcc-mangle-guix-store.patch"))
               (modules '((guix build utils)))
               (snippet gcc-canadian-cross-objdump-snippet)))
     (arguments
@@ -1012,7 +1001,8 @@ It also includes runtime support libraries for these languages.")
                (base32
                 "0fna78ly417g69fdm4i5f3ms96g8xzzjza8gwp41lqr5fqlpgp70"))
               (patches (search-patches "gcc-12-strmov-store-file-names.patch"
-                                       "gcc-5.0-libvtv-runpath.patch"))
+                                       "gcc-5.0-libvtv-runpath.patch"
+                                       "gcc-mangle-guix-store.patch"))
               (modules '((guix build utils)))
               (snippet gcc-canadian-cross-objdump-snippet)))
     (arguments (substitute-keyword-arguments arguments
@@ -1045,7 +1035,8 @@ It also includes runtime support libraries for these languages.")
                 "0knj4ph6y7r7yhnp1v4339af7mki5nkh7ni9b948433bhabdk3s3"))
               (patches (search-patches "gcc-12-strmov-store-file-names.patch"
                                        "gcc-5.0-libvtv-runpath.patch"
-                                       "gcc-hurd-split-stack.patch"))
+                                       "gcc-hurd-split-stack.patch"
+                                       "gcc-mangle-guix-store.patch"))
               (modules '((guix build utils)))
               (snippet gcc-canadian-cross-objdump-snippet)))
     (arguments

gnu/packages/gettext.scm

@@ -13,6 +13,7 @@
 ;;; Copyright © 2020 EuAndreh <eu@euandre.org>
 ;;; Copyright © 2022, 2024, 2025 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023 Maxim Cournoyer maxim@guixotic.coop>
+;;; Copyright © 2026 Robin Templeton <robin@guixotic.coop>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -57,24 +58,21 @@
 (define-public gettext-minimal
   (package
     (name "gettext-minimal")
-    (version "0.23.1")
+    (version "1.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/gettext/gettext-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0j8fijicvg8jkrisgsqbpnbmfb2mz3gx2p6pcwip82731yb7i9aj"))))
+                "06jgjxnm5xhw0d0zwl9birlwfxfgfqhk9q029j3h9941r5wrpnc5"))))
     (build-system gnu-build-system)
     (outputs '("out"
                "doc"))                            ;9 MiB of HTML
     (inputs
      (list libunistring
            libxml2
-           ;; TODO: ncurses is only needed for the 'libtextstyle' library.
-           ;; The next version of gettext can use a separate libtextstyle,
-           ;; but for now we include it here in 'gettext-minimal'.
-           ncurses))
+           libtextstyle))
     (arguments
      (list #:configure-flags #~'("--with-included-libunistring=no"
                                  "--with-included-libxml=no")
@@ -93,11 +91,11 @@
                      (("/bin/pwd") "pwd"))))
                (add-before 'check 'patch-tests
                  (lambda* (#:key inputs #:allow-other-keys)
-                   ;;libgettextlib-0.23.so => not found
+                   ;;libgettextlib-1.0.so => not found
                    (substitute* "gettext-tools/gnulib-tests/test-execute.sh"
                      (("^#!.*" all)
                       (string-append all "exit 77;\n")))
-                   (let* ((bash (which "sh")))
+                   (let* ((bash (search-input-file inputs "bin/sh")))
                      ;; Some of the files we're patching are
                      ;; ISO-8859-1-encoded, so choose it as the default
                      ;; encoding so the byte encoding is preserved.
@@ -106,7 +104,7 @@
                            (find-files "gettext-tools/tests"
                                        "^(lang-sh|msg(exec|filter)-[0-9])")
                          (("#![[:blank:]]/bin/sh")
-                          (format #f "#!~a" bash)))
+                          (string-append "#!" bash)))
 
                        (substitute* (cons "gettext-tools/src/msginit.c"
                                           (find-files "gettext-tools/gnulib-tests"
@@ -124,6 +122,14 @@
                                    ;; See 'coreutils' for the rationale.
                                    ((" test-tls\\$\\(EXEEXT\\) ") " ")))
                               '())))))
+               (add-after 'install 'patch-gettext.sh
+                 (lambda _
+                   ;; This matches only the relevant command invocations, but
+                   ;; is sensitive to the formatting of gettext.sh.  (The
+                   ;; string "gettext" appears in program output.)
+                   (substitute* (string-append #$output "/bin/gettext.sh")
+                     (("(^  |`|; )(gettext|ngettext|envsubst)" _ prefix program)
+                      (string-append prefix #$output "/bin/" program)))))
           #$@(if (%current-target-system)
                  #~((add-after 'install 'patch-cross-shebangs
                       (lambda _
@@ -151,30 +157,31 @@ translated messages from the catalogs.  Nearly all GNU packages use Gettext.")
                   (cpe-name . "gettext")))
     (license gpl3+)))                             ;some files are under GPLv2+
 
-(define-public gettext-minimal-0.21
+;; Starting with gettext 0.24 some gnulib files are no longer public.
+;; keep this here to easily fix autoreconf
+(define-public gettext-minimal-0.23
   (package/inherit gettext-minimal
-    (version "0.21")
+    (version "0.23.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/gettext/gettext-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "04kbg1sx0ncfrsbr85ggjslqkzzb243fcw9nyh3rrv1a22ihszf7"))
-              (patches (search-patches "gettext-libunicode-update.patch"))))
+                "0j8fijicvg8jkrisgsqbpnbmfb2mz3gx2p6pcwip82731yb7i9aj"))))
     (arguments
      (substitute-keyword-arguments arguments
-       ((#:phases phases)
-        #~(modify-phases #$phases
-            (add-after 'unpack 'touch-test
-              (lambda _
-                (with-output-to-file "gettext-tools/gnulib-tests/test-execute.sh"
-                  (lambda _ (display "")))))
-            (add-before 'check 'patch-test
-              (lambda _
-                ;; This test fails with ggc-14.
-                (substitute* "gettext-tools/tests/xgettext-javascript-6"
-                  (("^#!.*" all) (string-append all "exit 77;\n")))))))))))
+       ((#:make-flags flags)
+        ;; these gnulib tests fail with newer libunistring
+        #~(cons (string-append "XFAIL_TESTS="
+                               "test-uc_tolower "
+                               "test-ctype_alnum "
+                               "test-ctype_alpha "
+                               "test-ctype_graph "
+                               "test-ctype_lower "
+                               "test-ctype_print "
+                               "test-ctype_punct "
+                               "test-ctype_upper") #$flags))))))
 
 ;; Use that name to avoid clashes with Guile's 'gettext' procedure.
 ;;
@@ -203,22 +210,17 @@ translated messages from the catalogs.  Nearly all GNU packages use Gettext.")
 (define-public libtextstyle
   (package
     (name "libtextstyle")
-    (version "0.21")
-    (source (origin
-              (inherit (package-source gnu-gettext))
-              (uri (string-append "mirror://gnu/gettext/gettext-"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "04kbg1sx0ncfrsbr85ggjslqkzzb243fcw9nyh3rrv1a22ihszf7"))))
+    (version (package-version gnu-gettext))
+    (source (package-source gnu-gettext))
     (build-system gnu-build-system)
     (arguments
-     '(#:configure-flags '("--disable-static")
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'chdir
-                    (lambda _
-                      (chdir "libtextstyle")
-                      #t)))))
+     (list
+      #:configure-flags #~(list "--disable-static")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'chdir
+            (lambda _
+              (chdir "libtextstyle"))))))
     ;; libtextstyle bundles libxml2, glib (a small subset thereof), and
     ;; libcroco, but it purposefully prevents users from using an external
     ;; copy, to reduce the startup time of programs using libtextstyle.

gnu/packages/gimp.scm

@@ -398,8 +398,7 @@ 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")
-                           ,(string-append #$output "/lib/girepository-1.0")))
+                          (,(getenv "GI_TYPELIB_PATH")))
                         `("GUIX_PYTHONPATH" prefix
                           (,(getenv "GUIX_PYTHONPATH")))
                         `("GDK_PIXBUF_MODULE_FILE" =

gnu/packages/gnome-circle.scm

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

gnu/packages/gnome.scm

@@ -564,7 +564,6 @@ It is written in C using GObject and libsoup.")
     (arguments
      `(#:configure-flags
        (list
-        "CFLAGS=-g -O2 -Wno-error=incompatible-pointer-types"
         "--disable-static"
         "--enable-gtk-doc"
         (string-append "--with-html-dir="

gnu/packages/gnupg.scm

@@ -92,7 +92,6 @@
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system qt)
   #:use-module (ice-9 match)
   #:use-module (guix build-system meson)
   #:use-module (srfi srfi-1))
@@ -935,22 +934,7 @@ software.")))
     (inherit pinentry-tty)
     (name "pinentry-qt")
     (arguments
-     (list #:configure-flags
-           #~(list "--enable-fallback-curses")
-           #:imported-modules
-           (append %default-gnu-imported-modules
-                   %qt-build-system-modules)
-           #:modules
-           '((guix build utils)
-             (guix build gnu-build-system)
-             ((guix build qt-build-system) #:prefix qt:))
-           #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'install 'qt-wrap
-                 (lambda args
-                   (apply (assoc-ref qt:%standard-phases 'qt-wrap)
-                          #:qtbase #$(this-package-input "qtbase")
-                          args))))))
+     `(#:configure-flags '("--enable-fallback-curses")))
     (inputs
      (modify-inputs inputs
        (prepend qtbase qtwayland)))

gnu/packages/gnustep.scm

@@ -117,7 +117,7 @@ GCC runtime.
 (define-public windowmaker
   (package
     (name "windowmaker")
-    (version "0.96.0")
+    (version "0.95.9")
     (synopsis "NeXTSTEP-like window manager")
     (source (origin
               (method url-fetch)
@@ -126,58 +126,60 @@ GCC runtime.
                     "wmaker-" version "/WindowMaker-" version ".tar.gz"))
               (sha256
                (base32
-                "0vbgjbqnv2gcpimnrh2fc383gxcdfhgz1j3f2lfa4jng4fx31qag"))))
+                "055pqvlkhipyjn7m6bb3fs4zz9rd1ynzl0mmwbhp05ihc3zmh8zj"))))
     (build-system gnu-build-system)
     (arguments
-     (list
-      #:modules '((guix build gnu-build-system)
+     `(#:modules ((guix build gnu-build-system)
                   (guix build utils)
                   (ice-9 match))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'configure 'pre-configure
-            (lambda _
-              ;; 'wmaker' wants to invoke 'wmaker.inst' the first time,
-              ;; and the 'wmsetbg', so make sure it uses the right ones.
-              ;; We can't use a wrapper here because that would pollute
-              ;; $PATH in the whole session.
-              (let* ((bin (string-append #$output "/bin")))
-                (substitute* "src/main.c"
-                  (("\"wmaker\\.inst")
-                   (string-append "\"" bin "/wmaker.inst")))
-                (substitute* '("src/defaults.c" "WPrefs.app/Menu.c")
-                  (("\"wmsetbg")
-                   (string-append "\"" bin "/wmsetbg")))
-                ;; Add enough cells to the command character array to
-                ;; allow passing our large path to the wmsetbg binary.
-                ;; The path to wmsetbg in Guix requires 67 extra characters.
-                (substitute* "src/defaults.c"
-                  (("len = strlen\\(text\\) \\+ 40;")
-                   (string-append "len = strlen(text) + 107;"))))))
-          (add-after 'install 'install-xsession
-            (lambda _
-              (let* ((xsessions (string-append #$output "/share/xsessions")))
-                (mkdir-p xsessions)
-                (call-with-output-file
-                    (string-append xsessions "/windowmaker.desktop")
-                  (lambda (port)
-                    (format port "~
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'pre-configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; 'wmaker' wants to invoke 'wmaker.inst' the first time,
+             ;; and the 'wmsetbg', so make sure it uses the right ones.
+             ;; We can't use a wrapper here because that would pollute
+             ;; $PATH in the whole session.
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (substitute* "src/main.c"
+                 (("\"wmaker\\.inst")
+                  (string-append "\"" bin "/wmaker.inst")))
+               (substitute* '("src/defaults.c" "WPrefs.app/Menu.c")
+                 (("\"wmsetbg")
+                  (string-append "\"" bin "/wmsetbg")))
+               ;; Add enough cells to the command character array to
+               ;; allow passing our large path to the wmsetbg binary.
+               ;; The path to wmsetbg in Guix requires 67 extra characters.
+               (substitute* "src/defaults.c"
+                 (("len = strlen\\(text\\) \\+ 40;")
+                  (string-append "len = strlen(text) + 107;"))))))
+         (add-after 'install 'install-xsession
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (xsessions (string-append out "/share/xsessions")))
+               (mkdir-p xsessions)
+               (call-with-output-file
+                   (string-append xsessions "/windowmaker.desktop")
+                 (lambda (port)
+                   (format port "~
                     [Desktop Entry]~@
                     Name=Window Maker~@
                     Comment=~a~@
                     Exec=~a/bin/wmaker~@
                     Type=Application~%"
-                            (string-map (match-lambda
-                                          (#\newline #\space)
-                                          (chr chr))
-                                        #$synopsis) #$output))))))
-          (add-after 'install-xsession 'wrap
-            (lambda _
-              (let* ((bin (string-append #$output "/bin")))
-                ;; In turn, 'wmaker.inst' wants to invoke 'wmmenugen'
-                ;; etc., so make sure everything is in $PATH.
-                (wrap-program (string-append bin "/wmaker.inst")
-                  `("PATH" ":" prefix (,bin)))))))))
+                           (string-map (match-lambda
+                                         (#\newline #\space)
+                                         (chr chr))
+                                       ,synopsis) out))))))
+         (add-after 'install-xsession 'wrap
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               ;; In turn, 'wmaker.inst' wants to invoke 'wmmenugen'
+               ;; etc., so make sure everything is in $PATH.
+               (wrap-program (string-append bin "/wmaker.inst")
+                 `("PATH" ":" prefix (,bin)))))))))
     (inputs
      (list bash-minimal                 ;for wrap-program
            fontconfig

gnu/packages/gnuzilla.scm

@@ -604,7 +604,6 @@ 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
@@ -1249,29 +1248,24 @@ testing.")
        (cpe-name . "firefox_esr")
        (cpe-version . ,(first (string-split version #\-)))))))
 
-(define %icedove-build-id "20260324000000") ;must be of the form YYYYMMDDhhmmss
+(define %icedove-build-id "20260224000000") ;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.
-;;; 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")
+(define %icedove-version "140.8.0")
 
 ;; 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 "8be9f2d3072c225a1e5f153745a18984c2babf8f")))
+          (changeset "aa377fbf351e6b10b053e6afa421755c82d5fcf7")))
     (file-name (string-append "thunderbird-" %icedove-version "-checkout"))
     (sha256
      (base32
-      "04j35957x03m5x7mhh8zxa86mwjy0is2vb614sr4inkvvz4rs2hg"))
+      "0595jg1qbwclzi9qssljqkisrm2dn99rzxzaz2mcfi7b1kvbfaki"))
     (patches (search-patches "icedove-observer-fix.patch"))))
 
 ;;; To regenerate, see the `format-locales' helper defined above.
@@ -1348,8 +1342,7 @@ 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>)
-  ;; where the hash in the URL is the changeset from thunderbird-comm-source.
-  (let* ((commit "7c86eab97e77f00ca7ed8f224d38338a3ed46693")
+  (let* ((commit "b6fd3d6c75ba35d91fe131a654df76ca86f35ac5")
          (revision "0")
          (version (git-version %icedove-version revision commit)))
     (origin
@@ -1360,7 +1353,7 @@ testing.")
       (file-name (git-file-name "thunderbird-l10n" version))
       (sha256
        (base32
-        "1navma2gwcgbbiwcwrc5lrx2jk3qmrnrc6i8pvhb8156pz4cg5nd")))))
+        "0n4df6kv70a6mxxsqwc83nhj8vl7acv9bcbf07nkcsjjxh3szvqc")))))
 
 (define icedove-source
   (let ((name (string-append "icedove-" %icedove-version)))

gnu/packages/golang-build.scm

@@ -181,7 +181,7 @@ collections like from @code{container/tree}.
      "This package provides a library for calling C functions from Go without
 Cgo.
 
-Features:
+Featues:
 @itemize
 @item build for other platforms easily without a C compiler
 @item efficiently cache entirely Go builds
@@ -1042,7 +1042,7 @@ compile does not support generics.")
      (list
       #:skip-build? #t
       #:import-path "golang.org/x/mod"
-      ;; Test tries to access:
+      ;; Test tries to acces:
       ;; "http://ct.googleapis.com/logs/argon2020/ct/v1/get-sth": dial tcp:
       ;; lookup ct.googleapis.com
       #:test-flags #~(list "-skip" "TestCertificateTransparency")))
@@ -1712,7 +1712,7 @@ values.")
     (license license:bsd-3)))
 
 (define-public go-google-golang-org-genproto-googleapis-rpc
-  ;; No release or version tags, use the latest commit.
+  ;; No release or verion tags, use the latest commit.
   (let ((commit "49b9836ed3ff1e1dd329d17e442987447e931c7d")
         (revision "1"))
     (package

gnu/packages/golang-check.scm

@@ -127,7 +127,7 @@ value and call @code{t.Fatal()} if the assertion fails.")
     (description
      "Correct is a collection of assertion libraries for Golang, intended to be
 used together.  It tries not to strictly enforce that, though - most of
-correct should be customizable either by changing some options or by using
+correct should be customizeable either by changing some options or by using
 only some sub-packages of correct.")
     (license license:mpl2.0)))
 
@@ -1195,7 +1195,7 @@ when comparing complex types like structures and maps.")
     (home-page "https://github.com/go-testfixtures/testfixtures")
     (synopsis "Ruby on Rails like test fixtures for Go")
     (description
-     "This package mimics the
+     "Ths package mimics the
 @url{http://guides.rubyonrails.org/testing.html#the-test-database, Ruby on
 Rails' way} of writing tests for database applications, where sample data is
 kept in fixtures files.  Before the execution of every test, the test database
@@ -1462,7 +1462,7 @@ Node @code{nock} library, it has features like:
 @item Supports map and filters to handle mocks easily
 @item Wide compatible HTTP interceptor using @code{http.RoundTripper} interface
 @item Works with any @code{net/http} compatible client, such as @code{gentleman}
-@item Network timeout/cancellation delay simulation
+@item Network timeout/cancelation delay simulation
 @item Extensible and hackable API
 @end itemize")
     (license license:expat)))
@@ -1871,7 +1871,7 @@ differently.")
               (with-directory-excursion (string-append "src/" import-path)
                 (delete-file-recursively "example"))))
           (add-after 'unpack 'preserve-PATH-from-environment
-            ;; Unlike FHS systems, Guix needs to look for its commands in PATH.
+            ;; Unlike FHS systems, Guix needs to look its commands fom PATH.
             ;; Expose it by default in the test environments.
             (lambda* (#:key tests? import-path #:allow-other-keys)
               (with-directory-excursion (string-append "src/" import-path)
@@ -2254,45 +2254,6 @@ can be used in test code as a mock of the interface.")
 Perl's @url{https://metacpan.org/pod/Test::Deep, Test::Deep perl}.")
     (license license:bsd-2)))
 
-(define-public go-github-com-maxbrunsfeld-counterfeiter-v6
-  (package
-    (name "go-github-com-maxbrunsfeld-counterfeiter")
-    (version "6.12.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/maxbrunsfeld/counterfeiter")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0c4a8gcm3l992vydldcfsvb2jk4spnmxsk2i4klqh4fpagbpa069"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/maxbrunsfeld/counterfeiter/v6"
-      #:test-flags
-      #~(list "-skip" "TestIntegration")
-      #:test-subdirs
-      #~(list "." "arguments" "command" "generator" "integration")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'build 'go-generate
-            (lambda* (#:key import-path #:allow-other-keys)
-              (with-directory-excursion (string-append "src/" import-path)
-                (invoke "go" "generate" "-v" "-n" "./...")))))))
-    (native-inputs
-     (list go-github-com-onsi-gomega
-           go-github-com-sclevine-spec
-           go-golang-org-x-text
-           go-golang-org-x-tools))
-    (home-page "https://github.com/maxbrunsfeld/counterfeiter")
-    (synopsis "Generate self-contained, type-safe test doubles in Go")
-    (description
-     "This package provides fake implementations of the object's
-collaborators.")
-    (license license:expat)))
-
 (define-public go-github-com-mfridman-tparse
   (package
     (name "go-github-com-mfridman-tparse")
@@ -2372,7 +2333,7 @@ output.")
     (home-page "https://github.com/modocache/gover")
     (synopsis "Integration with coveralls.io for *.coverprofile files")
     (description
-     "This package implements a functionality to collect all
+     "This package inplements a functionality to collect all
 @code{.coverprofile} files rooted in the project and concatenante them into a
 single file ready for https://coveralls.io/.")
     (license license:asl2.0)))
@@ -2742,31 +2703,6 @@ GIT_TRACE mechanism.")
      "This package provides tools for detecting deadlocks at run-time in Go.")
     (license license:asl2.0)))
 
-(define-public go-github-com-sclevine-spec
-  (package
-    (name "go-github-com-sclevine-spec")
-    (version "1.4.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/sclevine/spec")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0y3rqb7dd51qnw5ns7w5sy93879ybnlg6gwslbv5mkfnrk0gl7na"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/sclevine/spec"))
-    (home-page "https://github.com/sclevine/spec")
-    (synopsis "BDD-style test organizer for Go")
-    (description
-     "Spec is a simple BDD test organizer for Go.  It minimally extends the
-standard library @code{testing} package by facilitating easy organization of
-Go 1.7+ @url{https://blog.golang.org/subtests, subtests}.")
-    (license license:asl2.0)))
-
 (define-public go-github-com-shabbyrobe-gocovmerge
   (package
     (name "go-github-com-shabbyrobe-gocovmerge")
@@ -3406,33 +3342,6 @@ 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")
@@ -3643,13 +3552,6 @@ the source code, it only prints out style mistakes.")
     (propagated-inputs
      (list go-go-yaml-in-yaml-v4))))
 
-(define-public go-gopkg-in-h2non-gock-v1
-  (package/inherit go-github-com-h2non-gock
-    (name "go-gopkg-in-h2non-gock-v1")
-    (arguments
-     (substitute-keyword-arguments arguments
-       ((#:import-path _) "gopkg.in/h2non/gock.v1")))))
-
 (define-public go-gopkg-in-go-playground-assert-v1
   (package
     (inherit go-github-com-go-playground-assert-v2)

gnu/packages/golang-crypto.scm

@@ -1229,36 +1229,6 @@ MetroHash}, a high quality, high performance hash algorithm.")
      "This package provides a hashing function.")
     (license license:expat)))
 
-(define-public go-github-com-digitorus-pkcs7
-  (package
-    (name "go-github-com-digitorus-pkcs7")
-    (version "0.0.0-20250730155240-ffadbf3f398c")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/digitorus/pkcs7")
-              (commit (go-version->git-ref version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0snamp6fbg5vir0lsw5wzvyagrdd832lw6k7cnvcahcgp8l084zc"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/digitorus/pkcs7"))
-    (native-inputs
-     (list openssl))
-    (home-page "https://github.com/digitorus/pkcs7")
-    (synopsis "PKCS#7 implementation for Go")
-    (description
-     "This package implements parsing and generation of some
-PKCS#7/Cryptographic Message
-Syntax (@url{https://www.rfc-editor.org/rfc/rfc2315},
-@url{https://www.rfc-editor.org/rfc/rfc5652, RFC 2315}, RFC 5652) structures
-for Go applications.  It's an alternative fork of deprecated
-@url{https://github.com/mozilla-services/pkcs7}.")
-    (license license:expat)))
-
 (define-public go-github-com-dvsekhvalnov-jose2go
   (package
     (name "go-github-com-dvsekhvalnov-jose2go")
@@ -1444,43 +1414,6 @@ providing bidirectional mapping values to their names, plus enum convenience
 for values.")
     (license license:bsd-3)))
 
-(define-public go-github-com-getsops-gopgagent
-  (package
-    (name "go-github-com-getsops-gopgagent")
-    (version "0.0.0-20241224165529-7044f28e491e")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/getsops/gopgagent")
-              (commit (go-version->git-ref version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1n1r7jkb48y06jw2dhkaqs33j6qgwf9fvbisd1zsr6v2k7wgfvf3"))
-       (modules '((guix build utils)))
-       (snippet
-        #~(begin
-            (for-each
-             (lambda (f)
-               ;; XXX: Without this snippet the build fails with
-               ;; code in directory github.com/getsops/gopgagent
-               ;; expects import "go.mozilla.org/gopgagent"
-               (substitute* f
-                 (("import \"go\\.mozilla\\.org/gopgagent\"") "")))
-             '("gpgagent.go" "gpgagent_test.go"))
-            #t))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/getsops/gopgagent"
-      #:test-flags #~(list "-vet=off")))
-    (home-page "https://github.com/getsops/gopgagent")
-    (synopsis "GPG Agent helpers for Go")
-    (description
-     "This package provides an API to interact with the local GPG Agent from
-Golang.")
-    (license license:asl2.0)))
-
 (define-public go-github-com-gliderlabs-ssh
   (package
     (name "go-github-com-gliderlabs-ssh")
@@ -1748,35 +1681,6 @@ See http://keccak.noekeon.org.")
 MurmurHash} revision (aka MurmurHash3).")
     (license license:bsd-3)))
 
-(define-public go-github-com-hiddeco-sshsig
-  (package
-    (name "go-github-com-hiddeco-sshsig")
-    (version "0.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/hiddeco/sshsig")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1raq5j1hr693lcj7nrj3wnsyfp30w96apjxyjmlvxb7ihnkhikv1"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/hiddeco/sshsig"))
-    (native-inputs
-     (list go-github-com-stretchr-testify))
-    (propagated-inputs
-     (list go-golang-org-x-crypto))
-    (home-page "https://github.com/hiddeco/sshsig")
-    (synopsis "Messages signing and verification using SSH in Golang")
-    (description
-     "Package sshsig provides an API to sign and verify messages using SSH
-keys.  It is an implementation of the SSH Signature format as described in
-@url{https://github.com/openssh/openssh-portable/blob/V_9_3_P1/PROTOCOL.sshsig}.")
-    (license license:asl2.0)))
-
 (define-public go-github-com-jcmturner-aescts-v2
   (package
     (name "go-github-com-jcmturner-aescts-v2")
@@ -2017,7 +1921,7 @@ hash.")
     (description
      "Package ssh wraps the @code{crypto/ssh} package with a higher-level API
 for building SSH servers.  The goal of the API was to make it as simple as
-using net/http, so the API is very similar.  It's alternative fork of
+using net/http, so the API is very similar.  It's alternaive fork of
 @url{https://github.com/gliderlabs/ssh}.")
     (license license:bsd-3)))
 
@@ -3816,123 +3720,6 @@ is an extremely fast non-cryptographic hash algorithm.")
 @url{https://en.wikipedia.org/wiki/RC2, RC2} Cipher in Golang.")
     (license license:asl2.0)))
 
-(define-public go-github-com-zmap-zcertificate
-  (package
-    (name "go-github-com-zmap-zcertificate")
-    (version "0.0.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/zmap/zcertificate")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1lxayyxb0gvls1l05jglqdf8b7zxz3gw94kwbgxvshs7lc0s6hnw"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      ;; XXX: Source only, to break cycle with
-      ;; go-github-com-zmap-zcrypto. Addintional inputs requaired only to
-      ;; build CLI:
-      ;; 
-      ;; -  github.com/sirupsen/logrus
-      ;; -  github.com/zmap/zcrypto
-      ;; -  github.com/zmap/zlint/v3
-      #:skip-build? #t
-      #:tests? #f
-      #:import-path "github.com/zmap/zcertificate"))
-    (home-page "https://github.com/zmap/zcertificate")
-    (synopsis "ZCertificate")
-    (description "ZCertificate parses X.509 certificates and runs
-@@url{https://github.com/zmap/zlint,ZLint}.")
-    (license license:asl2.0)))
-
-(define-public go-github-com-zmap-zcrypto
-  (package
-    (name "go-github-com-zmap-zcrypto")
-    (version "0.0.0-20260309174858-0e3c42de5a13")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/zmap/zcrypto")
-              (commit (go-version->git-ref version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0vbgpr2jms9la1nrzxwcfn6ngi3c2pzglh3a3yfkm0ahxvh4wpca"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/zmap/zcrypto"
-      #:test-flags
-      ;; Network access is required.
-      #~(list "-skip" (string-join
-                       (list "TestFetchRemote"
-                             "TestVerifyHostname"
-                             "TestTLSVersions"
-                             "TestCipherSuitesBadSSL")
-                       "|"))))
-    (native-inputs
-     (list go-github-com-stretchr-testify
-           go-gopkg-in-check-v1))
-    (propagated-inputs
-     (list go-github-com-mreiferson-go-httpclient
-           go-github-com-op-go-logging
-           go-github-com-sirupsen-logrus
-           go-github-com-weppos-publicsuffix-go
-           go-github-com-zmap-zcertificate
-           go-golang-org-x-crypto
-           go-golang-org-x-net))
-    (home-page "https://github.com/zmap/zcrypto")
-    (synopsis "Liberal Go TLS + X.509 Library for Research")
-    (description
-     "ZCrypto is a research and data collection cryptography library, designed
-to be used for measuring and analyzing cryptographic deployments on the
-Internet.  It is largely centered around the @code{WebPKI}.")
-    ;; See LICENSE file for more details.
-    (license (list license:asl2.0 license:expat license:isc))))
-
-(define-public go-github-com-zmap-zlint-v3
-  (package
-    (name "go-github-com-zmap-zlint-v3")
-    (version "3.6.8")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/zmap/zlint")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "054ddx6xdzhdjd214kp3kby0q5w4z1d4n61fav5vz73afm4z4bij"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/zmap/zlint/v3"
-      #:unpack-path "github.com/zmap/zlint"
-      #:build-flags
-      #~(list (string-append "-ldflags=-X main.version=" #$version))
-      #:test-flags
-      ;; gen_test.go:236: exec: "git": executable file not found in $PATH
-      #~(list "-skip" "TestGetTestData|TestSaveCert")))
-    (propagated-inputs
-     (list go-github-com-pelletier-go-toml
-           go-github-com-sirupsen-logrus
-           go-github-com-zmap-zcrypto
-           go-golang-org-x-crypto
-           go-golang-org-x-net
-           go-golang-org-x-text))
-    (home-page "https://github.com/zmap/zlint")
-    (synopsis "X.509 Certificate Linter")
-    (description
-     "ZLint is a X.509 certificate linter that checks for consistency with
-standards (e.g. @url{https://www.ietf.org/rfc/rfc5280.txt, RFC 5280}) and
-other relevant PKI requirements (e.g.
-@url{https://cabforum.org/wp-content/uploads/CA-Browser-Forum-BR-1.4.8.pdf,
-CA/Browser Forum Baseline Requirements}).")
-    (license license:asl2.0)))
-
 (define-public go-gitlab-com-nyarla-go-crypt
   (package
     (name "go-gitlab-com-nyarla-go-crypt")
@@ -4412,19 +4199,6 @@ traffic.")))
 +utility to convert SSH RSA keys to GPG keys.")
     (license license:expat)))
 
-(define-public zlint
-  (package/inherit go-github-com-zmap-zlint-v3
-    (name "zlint")
-    (arguments
-     (substitute-keyword-arguments arguments
-       ((#:tests? _ #t) #f)
-       ((#:skip-build? _ #t) #f)
-       ((#:install-source? _ #t) #f)
-       ((#:import-path _) "github.com/zmap/zlint/v3/cmd/zlint")))
-    (native-inputs (package-propagated-inputs go-github-com-zmap-zlint-v3))
-    (propagated-inputs '())
-    (inputs '())))
-
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above by existing packages with similar

gnu/packages/golang-vcs.scm

@@ -295,115 +295,6 @@ using the Git pkt-line format used in various Git operations.")
          (replace "go-github-com-go-git-gcfg"
            go-github-com-go-git-gcfg-v2))))))
 
-(define-public go-github-com-cli-go-gh-v2
-  (package
-    (name "go-github-com-cli-go-gh-v2")
-    (version "2.13.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/cli/go-gh")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1a918ll60h65abs14mpnclk1w3468mi7khasixif04ihxd0rcsns"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:skip-build? #t
-      #:import-path "github.com/cli/go-gh/v2"
-      #:embed-files #~(list ".*\\.xml")
-      ;; Network access or git configuration are required.
-      #:test-flags #~(list "-skip" "TestRemotes|TestNewHTTPClient")))
-    (native-inputs
-     (list go-github-com-alecthomas-chroma-v2
-           go-github-com-leaanthony-go-ansi-parser
-           go-github-com-stretchr-testify
-           go-gopkg-in-h2non-gock-v1))
-    (propagated-inputs
-     (list go-github-com-alecaivazis-survey-v2
-           go-github-com-charmbracelet-glamour
-           go-github-com-charmbracelet-lipgloss
-           go-github-com-cli-browser
-           go-github-com-cli-safeexec
-           go-github-com-cli-shurcool-graphql
-           go-github-com-google-shlex
-           go-github-com-henvic-httpretty
-           go-github-com-itchyny-gojq
-           go-github-com-makenowjust-heredoc
-           go-github-com-masterminds-sprig-v3
-           go-github-com-mgutz-ansi
-           go-github-com-muesli-reflow
-           go-github-com-muesli-termenv
-           go-github-com-thlib-go-timezone-local
-           go-golang-org-x-term
-           go-golang-org-x-text
-           go-gopkg-in-yaml-v3))
-    (home-page "https://github.com/cli/go-gh")
-    (synopsis "Go library for the GitHub CLI")
-    (description
-     "Package gh is a library for CLI Go applications to help interface with
-the gh CLI tool, and the @code{GitHub} API.")
-    (license license:expat)))
-
-(define-public go-github-com-cli-go-internal
-  (package
-    (name "go-github-com-cli-go-internal")
-    (version "0.0.0-20241025142207-6c48bcd5ce24")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/cli/go-internal")
-              (commit (go-version->git-ref version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1s2rnmsdj22hg8hz9xv2fj1vs1k9xfz8rvz9bm1cg3ddq33hl4a5"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:skip-build? #t
-      #:import-path "github.com/cli/go-internal"
-      #:test-flags
-      ;; TestSimple/cover requires network access to proxy.golang.org.
-      #~(list "-skip" "TestSimple/cover")))
-    (propagated-inputs
-     (list go-golang-org-x-mod
-           go-golang-org-x-sys
-           go-golang-org-x-tools))
-    (home-page "https://github.com/cli/go-internal")
-    (synopsis "Internal utilities for GitHub CLI")
-    (description
-     "This package provides internal utilities for the GitHub CLI.  It is a
-hard fork of @code{testscript} to allow the @code{gh} maintainers to explore
-its use while providing flexibility for modifications and extensions.")
-    (license license:bsd-3)))
-
-(define-public go-github-com-cli-shurcool-graphql
-  (package
-    (name "go-github-com-cli-shurcool-graphql")
-    (version "0.0.4")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/cli/shurcooL-graphql")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0w5ixfr4ia35n8adadr2rsca3f04bq36fxkgh27fw7rd0mxf199l"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/cli/shurcooL-graphql"))
-    (home-page "https://github.com/cli/shurcooL-graphql")
-    (synopsis "GraphQL client implementation for GitHub CLI")
-    (description
-     "This package provides a GraphQL client implementation forked from
-@code{shurcooL/graphql}, customized for use in the GitHub CLI.")
-    (license license:expat)))
-
 (define-public go-github-com-jiangxin-goconfig
   (package
     (name "go-github-com-jiangxin-goconfig")

gnu/packages/gtk.scm

@@ -2183,9 +2183,11 @@ and routines to assist in editing internationalized text.")
     (license license:lgpl2.1+)))
 
 (define-public girara
+  ;; TODO: Move propagated inputs to inputs after core-updates is merged (as
+  ;; of 2024-03)
   (package
     (name "girara")
-    (version "2026.02.04")
+    (version "0.4.5")
     (source
      (origin
        (method git-fetch)
@@ -2194,10 +2196,35 @@ and routines to assist in editing internationalized text.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "04adir5a8g2hqgv4vzpg52i2524abpcrqf3fcffrbwp8syan0df1"))))
+        (base32 "04igidbihgq5k7fh0jd5n26w00qlb47riky6q7qlp5k314d6cd2y"))))
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'start-xserver
+            ;; Tests require a running X server.
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((xorg-server (assoc-ref inputs "xorg-server"))
+                    (display ":1"))
+                (setenv "DISPLAY" display)
+
+                ;; On busy machines, tests may take longer than
+                ;; the default of four seconds.
+                (setenv "CK_DEFAULT_TIMEOUT" "20")
+
+                ;; Don't fail due to missing '/etc/machine-id'.
+                (setenv "DBUS_FATAL_WARNINGS" "0")
+                (zero? (system (string-append xorg-server "/bin/Xvfb "
+                                              display " &")))))))))
+    (native-inputs
+     (list pkg-config
+           check
+           gettext-minimal
+           `(,glib "bin")
+           xorg-server-for-tests))
+    ;; Listed in 'Requires.private' of 'girara.pc'.
+    (propagated-inputs (list gtk+ json-glib))
     (build-system meson-build-system)
-    (native-inputs (list pkg-config))
-    (inputs (list glib))
     (home-page "https://pwmt.org/projects/girara/")
     (synopsis "Library for minimalistic gtk+3 user interfaces")
     (description "Girara is a library that implements a user interface that

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 "0.3.1")
+   (version "0.2.1")
     (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 "0j2m9nnjp7096gdy2b038p7wrx93hgw6i6rfy4gh9hkvk4q43b1m"))))
+        (base32 "1zgc9xwpz6w64rbndvl8c73lsx935byin921209acyw54j52g706"))))
    (build-system gnu-build-system)
    (arguments
     (list
@@ -948,6 +948,7 @@ 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
@@ -989,7 +990,8 @@ variables from them.")
                                              (assoc-ref inputs input)
                                              path))
                                           (list "guile-config"
-                                                "guile-dotenv"))))))
+                                                "guile-dotenv"
+                                                "nyacc"))))))
                       (bin (string-append (ungexp output) "/bin/")))
                  (wrap-program (string-append bin "dotenv")
                    (dep-path "GUILE_LOAD_PATH" site)
@@ -3939,7 +3941,7 @@ $(libdir)/guile/@GUILE_EFFECTIVE_VERSION@/site-ccache\n")))))))
      (list autoconf
            automake
            texinfo
-           gettext-minimal
+           gettext-minimal-0.23              ;for 'AC_LIB_LINKFLAGS_FROM_LIBS'
            guile-3.0
            pkg-config))
     (inputs
@@ -7590,7 +7592,7 @@ with a FSM is being built (for example, from a Makefile.)")
 (define-public guile-ini
   (package
     (name "guile-ini")
-    (version "1.0.0")
+    (version "0.5.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -7599,7 +7601,7 @@ with a FSM is being built (for example, from a Makefile.)")
               (file-name (string-append name "-" version))
               (sha256
                (base32
-                "12mfch7dznx67r5zw88pp4ma3pw6akif7kdr0kak1gvawgfy277y"))))
+                "0mz7mpcf6q1z9j9ydz1ngr4hglci3ghmharv1isx9wgby3l2dcf5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags '("GUILE_AUTO_COMPILE=0") ;to prevent guild warnings
@@ -7654,8 +7656,8 @@ is an attempt to combine both into something useful.")
       (license license:asl2.0))))
 
 (define-public guile-knots
-  (let ((commit "d79284b4715efc347b22d510c3e3134a0c584b17")
-        (revision "32"))
+  (let ((commit "cb5ec50b341f603e9d129152b45e47cf008ea126")
+        (revision "31"))
     (package
     (name "guile-knots")
     (version (git-version "0" revision commit))
@@ -7666,7 +7668,7 @@ is an attempt to combine both into something useful.")
                     (commit commit)))
               (sha256
                (base32
-                "0i87jc3dznw6pdib0yy49d8066c1jvwp2m01xi92amx45dkl8ixc"))
+                "08gcbyw7kvhk568a30kimhn37m9mygpxhswb294n1141ddmhjchh"))
               (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments

gnu/packages/guile.scm

@@ -4,7 +4,7 @@
 ;;; Copyright © 2014, 2016, 2018 David Thompson <davet@gnu.org>
 ;;; Copyright © 2014, 2017, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2017 Christine Lemmer-Webber <cwebber@dustycloud.org>
-;;; Copyright © 2016, 2023, 2024, 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2016, 2023-2025 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
@@ -212,6 +212,10 @@ without requiring the source code to be rewritten.")
       ;; <https://bugs.gnu.org/20272>, which affects 2.0, 2.2, and 3.0 so far.
       #:parallel-build? #f
 
+      #:modules ((guix build gnu-build-system)
+                 (guix build utils)
+                 (ice-9 regex))
+
       #:phases
       (modify-phases %standard-phases
         ,@(if (system-hurd?)
@@ -236,22 +240,9 @@ without requiring the source code to be rewritten.")
         (add-before 'configure 'pre-configure
           (lambda* (#:key inputs #:allow-other-keys)
             ;; Tell (ice-9 popen) the file name of Bash.
-
-            ;; TODO: On the next rebuild cycle, unconditionally use
-            ;; 'search-input-file' instead of 'assoc-ref'.
-            (let ((bash (assoc-ref inputs "bash")))
-              (substitute* "module/ice-9/popen.scm"
-                ;; If bash is #f allow fallback for user to provide
-                ;; "bash" in PATH.  This happens when cross-building to
-                ;; MinGW for which we do not have Bash yet.
-                (("/bin/sh")
-                 ,(cond ((target-mingw?)
-                         "bash")
-                        ((%current-target-system)
-                         '(search-input-file inputs "/bin/bash"))
-                        (else
-                         '(string-append bash "/bin/bash")))))
-              #t)))
+            (substitute* "module/ice-9/popen.scm"
+              (("/bin/sh")
+               (search-input-file inputs "/bin/bash")))))
         (add-after 'install 'add-libxcrypt-reference-pkgconfig
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (define out (assoc-ref outputs "out"))
@@ -263,8 +254,26 @@ without requiring the source code to be rewritten.")
                   (find-files (string-append out "/lib/pkgconfig")
                               ".*\\.pc")
                 (("-lcrypt")
-                 (string-append "-L" libxcrypt " -lcrypt")))))))))
-
+                  (string-append "-L" libxcrypt " -lcrypt"))))))
+        ,@(if (target-mingw?)
+              '()
+              '((add-after 'install 'install-major.minor-symlinks
+                  (lambda* (#:key outputs #:allow-other-keys)
+                    (let* ((out (assoc-ref outputs "out"))
+                           (bin (in-vicinity out "bin"))
+                           (m (string-match
+                               ".*-([0-9]+[.][0-9]+)[.][0-9]+$" out))
+                           (effective-version (match:substring m 1)))
+                      (define (symlink-version name)
+                        (let ((name-version
+                               (string-append name "-" effective-version)))
+                          (symlink name (in-vicinity bin name-version))))
+                      (for-each symlink-version
+                                '("guild"
+                                  "guile"
+                                  "guile-config"
+                                  "guile-snarf"
+                                  "guile-tools"))))))))))
    (native-search-paths
     (list (search-path-specification
            (variable "GUILE_LOAD_PATH")
@@ -856,17 +865,17 @@ Guile's foreign function interface.")
 (define-public guile-bytestructures
   (package
     (name "guile-bytestructures")
-    (version "2.0.2")
+    (version "1.0.10")
     (home-page "https://github.com/TaylanUB/scheme-bytestructures")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url home-page)
-                    (commit (string-append "v" version))))
+                    (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1dyhf39s16q3fvps0mfb65xrlcb8rk8m5kc82ngkwhzmf1svalpc"))))
+                "14k50jln32kkxv41hvsdgjkkfj6xlv06vc1caz01qkgk1fzh72nk"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags '("GUILE_AUTO_COMPILE=0")     ;to prevent guild warnings
@@ -900,7 +909,7 @@ type system, elevating types to first-class status.")
 (define-public guile-git
   (package
     (name "guile-git")
-    (version "0.11.0")
+    (version "0.10.0")
     (home-page "https://gitlab.com/guile-git/guile-git.git")
     (source (origin
               (method git-fetch)
@@ -910,7 +919,7 @@ type system, elevating types to first-class status.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1yjyil6z4k80pjdps8v6h6lxikwxmjxvrslf2jrmq2rrfnajschz"))))
+                "01scznpg7356ygdlgn1f2892bwg6fsvp37hbmsk4gsg0g49aj4la"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags '("GUILE_AUTO_COMPILE=0")       ; to prevent guild warnings

gnu/packages/hardware.scm

@@ -112,7 +112,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
-  #:use-module (guix build-system go)
   #:use-module (guix build-system guile)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
@@ -311,38 +310,6 @@ sharing.")
 (define-deprecated-package barrier
   deskflow)
 
-(define-public hd-idle
-  (package
-    (name "hd-idle")
-    (version "1.22")
-    (source
-     (origin
-       (method git-fetch)
-       (uri
-        (git-reference
-          (url "https://github.com/adelolmo/hd-idle")
-          (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "12nckzp00b3y91igp8jzlf6as353la6ar8gp6b646kn9gi2hrla3"))
-       (snippet
-        #~(begin
-            (use-modules (guix build utils))
-            (delete-file-recursively "vendor")))))
-    (build-system go-build-system)
-    (arguments
-     (list #:import-path "github.com/adelolmo/hd-idle"
-           #:install-source? #f))
-    (inputs
-     (list go-github-com-benmcclelland-sgio))
-    (home-page "https://github.com/adelolmo/hd-idle")
-    (synopsis "Spin down idle hard disks")
-    (description "@command{hd-idle} is a utility program for spinning down
-external disks after a period of idle time.  Since most USB hard drives do not
-support setting the idle timer via @command{hdparm}, hd-idle can be used as a
-workaround.")
-    (license license:gpl3+)))
-
 (define-public hw-probe
   (package
     (name "hw-probe")

gnu/packages/haskell.scm

@@ -1186,8 +1186,7 @@ interactive environment for the functional language Haskell.")
                  "https://www.haskell.org/ghc/dist/"
                  version "/" name "-" version "-testsuite.tar.xz"))
            (patches (search-patches "ghc-testsuite-dlopen-pie.patch"
-                                    "ghc-testsuite-grep-compat.patch"
-                                    "ghc-testsuite-recomp015-execstack.patch"))
+                                    "ghc-testsuite-grep-compat.patch"))
            (sha256
             (base32
              "0pw9r91g2np3i806g2f4f8z4jfdd7mx226cmdizk4swa7av1qf91"))
@@ -1241,7 +1240,14 @@ interactive environment for the functional language Haskell.")
                (substitute* "libraries/unix/tests/all.T"
                  (("^test\\('T8108'") "# guix skipped: test('T8108'"))
                (substitute* "libraries/unix/tests/libposix/all.T"
-                 (("^test\\('posix010'") "# guix skipped: test('posix010'"))))))))
+                 (("^test\\('posix010'") "# guix skipped: test('posix010'"))))
+           ;; binutils@2.39 warns for execstack deprecation by default, causing
+           ;; some tests to fail ; explicitely disable during linking instead.
+           (add-after 'unpack-testsuite 'fix-tests-with-binutils@2.39
+             (lambda _
+               (substitute* "testsuite/mk/test.mk"
+                 (("^TEST_HC_OPTS = ")
+                  "TEST_HC_OPTS = -optl -Wl,-z,noexecstack "))))))))
     (native-search-paths (list (search-path-specification
                                 (variable "GHC_PACKAGE_PATH")
                                 (files (list
@@ -1269,8 +1275,7 @@ interactive environment for the functional language Haskell.")
                  "https://www.haskell.org/ghc/dist/"
                  version "/ghc-" version "-testsuite.tar.xz"))
            (patches (search-patches "ghc-testsuite-dlopen-pie.patch"
-                                    "ghc-testsuite-grep-compat.patch"
-                                    "ghc-testsuite-recomp015-execstack.patch"))
+                                    "ghc-testsuite-grep-compat.patch"))
            (sha256
             (base32
              "0c55pj2820q26rikhpf636sn4mjgqsxjrl94vsywrh79dxp3k14z"))
@@ -1329,8 +1334,7 @@ interactive environment for the functional language Haskell.")
                  "https://www.haskell.org/ghc/dist/"
                  version "/ghc-" version "-testsuite.tar.xz"))
            (patches (search-patches "ghc-testsuite-dlopen-pie.patch"
-                                    "ghc-testsuite-grep-compat.patch"
-                                    "ghc-testsuite-recomp015-execstack.patch"))
+                                    "ghc-testsuite-grep-compat.patch"))
            (sha256
             (base32
              "1zl25gg6bpx5601k8h3cqnns1xfc0nqgwnh8jvn2s65ra3f2g1nz"))
@@ -1525,8 +1529,7 @@ interactive environment for the functional language Haskell.")
            (sha256
             (base32
              "1m5fzhr4gjn9ni8gxx7ag3fkbw1rspjzgv39mnfb0nkm5mw70v3s"))
-           (patches (search-patches "ghc-9.2-grep-warnings.patch"
-                                    "ghc-testsuite-recomp015-execstack.patch"))
+           (patches (search-patches "ghc-9.2-grep-warnings.patch"))
            (modules '((guix build utils)))
            (snippet
             ;; collections.Iterable was moved to collections.abc in Python 3.10.
@@ -1612,8 +1615,7 @@ SRC_HC_OPTS += -optc-mno-outline-atomics
              (sha256
               (base32
                "0cmmwhcwv9fjzvmgjj85d354858qqbmqfzaz5160xqj4yl9zk225"))
-             (patches (search-patches "ghc-9.2-grep-warnings.patch"
-                                      "ghc-testsuite-recomp015-execstack.patch"))))
+             (patches (search-patches "ghc-9.2-grep-warnings.patch"))))
          ,@(filter (match-lambda
                      (("ghc-bootstrap" . _) #f)
                      (("ghc-testsuite" . _) #f)

gnu/packages/ibus.scm

@@ -518,8 +518,6 @@ Japanese language input in most graphical applications.")
     (arguments
      (list
       #:tests? #f ;no tests
-      #:configure-flags
-      #~(list "CFLAGS=-Wno-error=incompatible-pointer-types")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-skk-jisyo
@@ -1135,7 +1133,6 @@ IBus-Table on IBus framework:
                                (string-append out "/libexec/ibus-setup-stt")))))))))
     (inputs
      (list bash-minimal
-           gst-plugins-good ; for pulsesrc
            gst-vosk
            gstreamer
            gtk

gnu/packages/image-viewers.scm

@@ -96,7 +96,6 @@
   #: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)
@@ -117,7 +116,6 @@
   #: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)
@@ -1053,67 +1051,6 @@ 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

@@ -74,7 +74,6 @@
   #: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)
@@ -107,7 +106,6 @@
   #: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)
@@ -247,29 +245,6 @@ 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")
@@ -1134,41 +1109,6 @@ 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")
@@ -2028,34 +1968,6 @@ 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/instrumentation.scm

@@ -75,26 +75,33 @@
 (define-public babeltrace
   (package
     (name "babeltrace")
-    (version "2.1.2")
+    (version "2.0.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.efficios.com/files/babeltrace/babeltrace2-"
                                   version ".tar.bz2"))
               (sha256
-               (base32 "171cn0y6qbixqggbw7minf4ggfa1j5yc0a1bsj5rnrxd6k93z0qj"))))
+               (base32 "1d7jxljbfb4y8jmxm7744ndhh9k9rw8qhmnljb19wz7flzr9x3vv"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f  ; FIXME - When Python's bindings are enabled, tests do not
                     ; pass.
        #:make-flags
        ,#~(list
-           (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib"))
+           (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib")
+           "DISTSETUPOPTS=--single-version-externally-managed") ;no .egg files
        #:configure-flags
        '("--enable-debug-info"
          "--enable-man-pages"
          "--enable-python-bindings"
          "--enable-python-plugins")
-       ))
+       #:phases
+       (modify-phases %standard-phases
+         ;; These are recommended in the project's README for a development
+         ;; build configuration.
+         (add-after 'unpack 'reconfigure
+           (lambda _
+             (delete-file "configure"))))))
     (inputs
      (list glib))
     ;; NOTE - elfutils is used for the LTTng debug information filter
@@ -103,15 +110,30 @@
     ;; `#:configure-flags`.
     (propagated-inputs
      (list elfutils))
+    ;; NOTE - python-3 is set here for generating the bindings.  Users need to
+    ;; install python-3 in their profile in order to use these bindings.
+    ;;
+    ;; NOTE - Babeltrace 2.0.4 is distributed with a aclocal.m4 that does not
+    ;; support Python3.10.  We can either disable Python's bindings or we can
+    ;; reconfigure the project with our autoconf.  This is because the
+    ;; distribution tarballs are generated on Ubuntu LTS 18.04.
+    ;;
+    ;; `paredit-raise-sexp' on the first list of native inputs and remove the
+    ;; 'autoreconf invocation whenever we bump to the next version that is
+    ;; goind to be generated on Ubuntu LTS 22.04.
     (native-inputs
-     (list asciidoc
-           bison
-           flex
-           pkg-config
-           python-3
-           python-sphinx
-           swig-4.0
-           xmltoman))
+     (append
+      (list asciidoc
+            bison
+            flex
+            pkg-config
+            python-3
+            python-sphinx
+            swig-4.0
+            xmltoman)
+      (list autoconf
+            automake
+            libtool)))
     (home-page "https://babeltrace.org/")
     (synopsis "Trace manipulation toolkit")
     (description "Babeltrace 2 is a framework for viewing, converting,
@@ -366,14 +388,14 @@ many probes which instrument numerous interesting parts of Linux.")
 (define-public lttng-ust
   (package
     (name "lttng-ust")
-    (version "2.15.0")
+    (version "2.13.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://lttng.org/files/lttng-ust/"
                                   "lttng-ust-" version ".tar.bz2"))
               (sha256
                (base32
-                "0a1yk6cci5yqkdy3fvjdky0lc1sbpcxhpm43vb3h1pahg8y75jbb"))))
+                "0dyr4j8f8y6fmfpxb3ajkc1ndwpl1baxzbyc4ksx8ym3p7d9ivyl"))))
     (build-system gnu-build-system)
     (inputs
      (list numactl))
@@ -392,19 +414,23 @@ to ring buffers shared with a consumer daemon.")
 (define-public lttng-tools
   (package
     (name "lttng-tools")
-    (version "2.15.0")
+    (version "2.13.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://lttng.org/files/lttng-tools/"
                                   "lttng-tools-" version ".tar.bz2"))
               (sha256
                (base32
-                "12pjxdfqg9ri4wng143x9dvwcrx9q2kg1isv4xc1v9vdalb92wsd"))))
+                "1jxdwm0a3z70jrx6yg57x5cswi7ycgyazng41rkgxnq7mp2gggak"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--enable-python-bindings")
-       ;; FIXME - Tests are disabled for now.
+       ;; FIXME - Tests are disabled for now because one test hangs
+       ;; indefinetely.  Also, parallel testing is not possible because of how
+       ;; the lttng-daemon handles sessions.  Thus, keep parallel testing
+       ;; disabled even after tests are enabled!
        #:tests? #f
+       #:parallel-tests? #f
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'set-environment-variables
@@ -414,8 +440,11 @@ to ring buffers shared with a consumer daemon.")
          ;; We don't put (which "man") here because LTTng uses execlp.
          (add-after 'unpack 'patch-default-man-path
            (lambda _
-             (substitute* "src/common/defaults.hpp"
-               (("/usr/bin/man") "man")))))))
+             (substitute* "src/common/defaults.h"
+               (("/usr/bin/man") "man"))))
+         (add-before 'configure 'autoreconf
+           (lambda _
+             (invoke "autoreconf" "-vfi"))))))
     ;; NOTE - Users have to install python-3 in their profile to use the
     ;; bindings.  We don't put it in the inputs, because the rest of the tools
     ;; can work without it.
@@ -423,22 +452,31 @@ to ring buffers shared with a consumer daemon.")
      (list liburcu popt numactl))
     (propagated-inputs
      (list kmod module-init-tools))
+    ;; NOTE - LTTng 2.13.9 is distributed with a aclocal.m4 that does not
+    ;; support Python3.10.  We can either disable Python's bindings or we can
+    ;; reconfigure the project with our autoconf.  This is because the
+    ;; distribution tarballs are generated on Ubuntu LTS 18.04.
+    ;;
+    ;; `paredit-raise-sexp' on the first list of native inputs and remove the
+    ;; 'autoreconf build step whenever we bump to the next version that is
+    ;; goind to be generated on Ubuntu LTS 22.04.
     (native-inputs
-     (list
-      asciidoc
-      babeltrace
-      bison
-      flex
-      libpfm4
-      libxml2
-      lttng-ust
-      perl
-      procps
-      python-3
-      swig-4.0
-      which
-      pkg-config
-      ))
+     (append
+      (list pkg-config
+            perl
+            libpfm4
+            python-3
+            swig-4.0
+            procps
+            which
+            flex
+            bison
+            asciidoc
+            libxml2
+            lttng-ust)
+      (list autoconf
+            automake
+            libtool)))
     (home-page "https://lttng.org/")
     (synopsis "LTTng userspace tracer libraries")
     (description "The lttng-tools project provides a session

gnu/packages/ipfs.scm

@@ -298,8 +298,8 @@ Verification specification
     (home-page "https://github.com/ipfs/go-bitfield")
     (synopsis "Allocated up-front Bitfield for Golang")
     (description
-     "This package implements bitfields to the standard library's @code{big.Int}
-with some optimizations for use in IPFS.")
+     "This package implements a functionality similar to standard
+@code{big.Int} with some optimizations to use in IPFS.")
     (license (list license:expat license:asl2.0))))
 
 (define-public go-github-com-ipfs-go-block-format
@@ -1191,9 +1191,11 @@ IPLD graph as detailed below.  Objects are demonstrated here using both
            go-github-com-libp2p-go-libp2p))
     (home-page "https://github.com/ipfs/go-peertaskqueue")
     (synopsis "Prioritized queue of abstract tasks distributed among peers")
+    ;; Project has nothing in README, see
+    ;; <https://github.com/ipfs/go-peertaskqueue/issues/1>.
     (description
-     "This package implements a prioritized list of tasks to be executed on
-peers.")
+     "This package implements a functionality to prioritize queue of abstract
+tasks distributed among peers.")
     (license (list license:asl2.0 license:expat))))
 
 (define-public go-github-com-ipfs-go-test

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 © 2024-2026 Ashish SHUKLA <ashish.is@lostca.se>
+;;; Copyright © 2024, 2025 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 "4.9.0")
+    (version "4.8.2")
     (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
-                "1pwayhpnyd6nq1sph4hqi43xwqgq6vj6fr8q0xqn0jx5zzjlyx8c"))))
+                "06lmbd27fdj7z7v6m096csswp73354516z64apfyz8lr5kh140wq"))))
     (build-system cmake-build-system)
     (outputs '("out" "doc"))
     (native-inputs
@@ -393,13 +393,12 @@ Conferencing} and @acronym{ICB, Internet Citizen's Band}.")
            #~(modify-phases %standard-phases
                #$@(if (target-x86?)
                       #~((add-after 'install 'move-doc
-                           (lambda _
-                             (let ((from (string-append #$output
-                                                        "/share/doc/weechat"))
-                                   (to (string-append #$output:doc
-                                                      "/share/doc/weechat")))
-                               (mkdir-p (string-append #$output:doc
-                                                       "/share/doc"))
+                           (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"))
                                (rename-file from to)))))
                       #~()))))
     (synopsis "Extensible chat client")
@@ -1039,7 +1038,6 @@ but can also be used independently as a logging bot.")
        (uri (git-reference
               (url "https://git.causal.agency/scooper")
               (commit version)))
-       (file-name (git-file-name name version))
        (sha256
         (base32 "0sqb8hg402il38pjhwa3lfyrskf1yr6yjd5fswqvk3d15v1jq4m8"))))
     (build-system gnu-build-system)

gnu/packages/java.scm

@@ -1177,7 +1177,6 @@ new Date();"))))
            fontconfig
            freetype
            giflib
-           gtk+
            lcms
            elfutils
            libjpeg-turbo
@@ -1499,7 +1498,7 @@ new Date();"))))
                               (for-each reset-file-timestamp
                                         (find-files dir #:directories? #t)))
                             (with-directory-excursion dir
-                              (let ((files (find-files ".")))
+                              (let ((files (find-files "." #:directories? #t)))
                                 (apply invoke "zip" "-0" "-X" archive files)))))))
                 (for-each repack-archive
                           (find-files #$output:doc "\\.zip$"))
@@ -1548,7 +1547,6 @@ new Date();"))))
            fontconfig
            freetype
            giflib
-           gtk+
            lcms
            libjpeg-turbo
            libpng

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 © 2023-2026 Sughosha <sughosha@disroot.org>
+;;; Copyright © 2023-2025 Sughosha <sughosha@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -70,7 +70,6 @@
   #: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))
@@ -2105,83 +2104,6 @@ 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")