gnu: r-s4vectors: Patch for R 4.6.0.

* gnu/packages/bioconductor.scm (r-s4vectors)[arguments]: Add phase 'R-4.6.0-compatibility. Change-Id: I731250e9dcfc62cfb2cafbf88e2f1e2d6b932828
gnu: r-mlr3misc: Skip one test.
2026-04-28 06:34:05 +00:00 · 2026-04-25 13:46:02 +02:00 · 2026-04-25 10:52:24 +02:00 · 2026-04-25 09:45:00 +02:00 · 2026-04-25 09:44:59 +02:00 · 2026-04-25 09:44:55 +02:00
25 changed files with 2103 additions and 2301 deletions
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1699,6 +1699,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/libcss-check-format.patch		\
  %D%/packages/patches/libeb-gcc-14.patch			\
  %D%/packages/patches/libextractor-tidy-support.patch		\
+  %D%/packages/patches/libfossil-skip-amalgamation.patch	\
  %D%/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch	\
  %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch	\
  %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.3.0.patch	\
@@ -1713,7 +1714,6 @@ dist_patch_DATA =						\
  %D%/packages/patches/libretro-dolphin-emu-libusb-assert.patch \
  %D%/packages/patches/libretro-dolphin-emu-vulkan-headers.patch        \
  %D%/packages/patches/libretranslate-use-flasgger.patch	\
-  %D%/packages/patches/librewolf-150.0-encoding_rs-rust-fix.patch       \
  %D%/packages/patches/librewolf-add-store-to-rdd-allowlist.patch       \
  %D%/packages/patches/librewolf-compare-paths.patch		\
  %D%/packages/patches/librewolf-neuter-locale-download.patch	\
--- a/gnu/packages/bash.scm
+++ b/gnu/packages/bash.scm
@@ -37,8 +37,6 @@
  #:use-module (gnu packages elf)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages readline)
-  #:use-module (gnu packages ruby-check)
-  #:use-module (gnu packages ruby-xyz)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages libffi)
@@ -55,7 +53,6 @@
  #:use-module (guix store)
  #:use-module (guix build-system copy)
  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system ruby)
  #:use-module (guix build-system trivial)
  #:autoload   (guix gnupg) (gnupg-verify*)
  #:autoload   (guix base32) (bytevector->nix-base32-string)
@@ -516,46 +513,6 @@ function interface (FFI) directly in your shell.  In other words, it allows
 you to call routines in shared libraries from within Bash.")
    (license license:expat)))

-(define-public bashly
-  (package
-    (name "bashly")
-    (version "1.3.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (rubygems-uri "bashly" version))
-       (sha256
-        (base32 "17msjzca5ifx8biimdjps655w51yc82d5ys9hwn749bi2f3n8mcz"))))
-    (build-system ruby-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                (invoke "rspec" "-c" "spec")))))))
-    (native-inputs (list ruby-rspec))
-    (propagated-inputs (list ruby-colsole
-                             ruby-completely
-                             ruby-filewatcher
-                             ruby-gtx
-                             ruby-logger
-                             ruby-lp
-                             ruby-mister-bin
-                             ruby-ostruct
-                             ruby-requires
-                             ruby-tty-markdown))
-    (synopsis
-     "Create feature-rich Bash scrips using simple YAML configuration")
-    (description
-     "Bashly is a CLI for generating feature-rich Bash command line
-tools.  Bashly lets you focus on your specific code, without worrying about
-command line argument parsing, usage texts, error messages and other functions
-that are usually handled by a framework in other programming languages.")
-    (home-page "https://bashly.dev/")
-    (license license:expat)))
-
 (define-public blesh
  (package
    (name "blesh")
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -913,7 +913,7 @@ suite native in R.")
 (define-public r-bpcells
  (package
    (name "r-bpcells")
-    (version "0.3.0")
+    (version "0.3.1")
    (source
     (origin
       (method git-fetch)
@@ -922,7 +922,7 @@ suite native in R.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "12h1di45fg06nhsliii7v0h1z567pkpis1xm4ar1qr8ns1n8iljw"))
+        (base32 "0yqgcajq83g25mznwcngaw7pi6vcqxqdnynpgb95yci57k3wrp6j"))
       (modules '((guix build utils)))
       (snippet
        '(delete-file-recursively "r/src/vendor/highway"))))
@@ -931,13 +931,15 @@ suite native in R.")
    (arguments
     (list
      #:phases
-      '(modify-phases %standard-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")))
+         ,@(if (target-x86-32?)
+               '((add-after 'chdir 'require-sse2
+                   ;; This avoids falling back to the scalar backend in
+                   ;; highway, which fails to build.
+                   (lambda _ (setenv "CFLAGS" "-msse2"))))
+               '()))))
    (propagated-inputs
     (list r-dplyr
           r-ggplot2
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
--- a/gnu/packages/duckdb.scm
+++ b/gnu/packages/duckdb.scm
@@ -148,13 +148,13 @@ system.")
 (define-public r-duckdb
  (package
    (name "r-duckdb")
-    (version "1.5.1")
+    (version "1.5.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "duckdb" version))
       (sha256
-        (base32 "177621m08whqqk4yhj3zrr08l3d9hhlqh3gm9jzhi5cplg47cksq"))
+        (base32 "1dldlfwvc33czvlxfmwaj4p9y6sjjj5iqy98yda47a8kclrqmyam"))
       ;; 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.
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -781,54 +781,6 @@ balance windows (keeping them roughly the same size) whenever the window
 configuration changes, e.g. after splitting or deleting a window.")
      (license license:bsd-3))))

-(define-public emacs-ben
-  (package
-    (name "emacs-ben")
-    (version "0.12.11")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://codeberg.org/pastor/ben.el")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0iqrk87dl567vwpwm8rmplrpva475a04s6c34rm24xfy2m7wrwk6"))))
-    (build-system emacs-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'set-environment
-            (lambda _
-              ;; Since the testsuite uses `direnv', the build needs a home
-              ;; directory so `direnv' can allow the contents of the `.envrc`
-              ;; files generated for the different tests.
-              (setenv "HOME" "/tmp")
-              (setenv "OFFLINE" "1") ;Enable offline tests.
-              (emacs-substitute-variables "ben.el"
-                ("ben-direnv-executable"
-                 #$(file-append (this-package-input "direnv")
-                                "/bin/direnv"))))))))
-    (inputs (list direnv))
-    (propagated-inputs (list emacs-inheritenv))
-    (home-page "https://codeberg.org/pastor/ben.el")
-    (synopsis "Asynchronous buffer-local environments via @command{direnv}")
-    (description
-     "This package allows you to load environments buffer locally.  The
-package is named @command{ben}, which stands for Buffer ENvironments.
-
-The project relies on @uref{https://direnv.net, direnv} which allows setting
-per-directory environments through @file{.envrc} files.
-
-The main improvement of @command{ben} over @command{envrc} is the asynchronous
-processing of environments, which prevents Emacs from freezing.  This is
-especially useful while loading computationally heavy environments, such when
-loading @file{.envrc} files that rely on Guix.  In these cases, computations
-can take hours to complete.  This package aims to facilitate loading such
-environments in the background.")
-    (license license:gpl3+)))
-
 (define-public emacs-bookmark-plus
  (package
    (name "emacs-bookmark-plus")
@@ -39910,7 +39862,7 @@ user interfaces for various built-in modes.")
 (define-public emacs-calibredb
  (package
    (name "emacs-calibredb")
-    (version "2.14.0")
+    (version "2.13.0")
    (source
     (origin
       (method git-fetch)
@@ -39919,40 +39871,31 @@ user interfaces for various built-in modes.")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1g0jg6a6fgvxd5bsydckbqwf899d2d9732laz4k1k476mbws5dqy"))))
+        (base32 "1a4gyc3gcq18j29pw2i296d70nvx5fbzlw9fdmqwzncciqz5as6m"))))
    (build-system emacs-build-system)
    (arguments
     (list
-      #:include #~(cons "\\.py$" %default-include)
-      #:tests? #f                       ;no tests
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'patch-paths
            (lambda* (#:key inputs #:allow-other-keys)
+              (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"))
-                    (ebook-meta
-                     (search-input-file inputs "/bin/ebook-meta"))
-                    (folder-program
-                     (string-append #$output
-                                    "/share/emacs/site-lisp/calibredb-"
-                                    #$version "/calibredb-folder.py")))
+                     (search-input-file inputs "/bin/calibre-debug")))
                (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-ebook-meta-program" ebook-meta)
-                  ("calibredb-folder-program" folder-program))))))))
+                  ("calibredb-debug-program" calibre-debug))))))))
    (inputs
     (list calibre))
    (propagated-inputs
-     (list emacs-dash emacs-esxml emacs-request emacs-s))
+     (list emacs-dash emacs-esxml emacs-s))
    (home-page "https://github.com/chenyanming/calibredb.el")
    (synopsis "Yet another calibre client for Emacs")
    (description "This package integrates calibre into Emacs.
@@ -41550,65 +41493,17 @@ time.")
    (build-system emacs-build-system)
    (arguments
     (list
-      #:test-command #~(list "make" "tests")
-      #:phases
-      #~(modify-phases %standard-phases
-          ;; Move the source files to the top level, which is
-          ;; included in the EMACSLOADPATH.
-          (add-after 'unpack 'move-source-files
-            (lambda _
-              (let ((el-files (find-files "./lisp" ".*\\.el$")))
-                (for-each (lambda (f)
-                            (rename-file f
-                                         (basename f)))
-                          el-files))))
-          (add-before 'check 'fix-tests
-            (lambda _
-              (substitute* "Makefile"
-                (("cask") ""))
-              (substitute* "test/ert-helper.el"
-                (("lisp\\/") ""))))
-          (add-before 'check 'skip-failing-tests
-            (lambda _
-              (let-syntax
-                  ((disable-tests
-                    (syntax-rules ()
-                      ((_ file ())
-                       (syntax-error "test names list must not be empty"))
-                      ((_ file (test-name ...))
-                       (substitute* file
-                         (((string-append
-                            "^\\(ert-deftest " test-name ".*") all)
-                          (string-append all "(skip-unless nil)\n")) ...)))))
-                (disable-tests
-                 "test/mastodon-profile-tests.el"
-                 ("mastodon-profile--add-author-bylines"
-                  "mastodon-profile--make-author-buffer"))
-                (disable-tests
-                 "test/mastodon-auth-tests.el"
-                 ("mastodon-auth--handle-token-response--good"
-                  "mastodon-auth-plstore-token-check"))
-                (disable-tests
-                 "test/mastodon-client-tests.el"
-                 ("mastodon-client--make-user-active"
-                  "mastodon-client--store"
-                  "mastodon-client--store-access-token"))
-                (disable-tests
-                 "test/mastodon-tl-tests.el"
-                 ("mastodon-tl--byline-timestamp-has-relative-display"
-                  "mastodon-tl--next-tab-item--no-spaces-at-ends"
-                  "mastodon-tl--next-tab-item--with-spaces-at-ends"))
-                (disable-tests
-                 "test/mastodon-media-tests.el"
-                 ("mastodon-media--get-avatar-rendering"
-                  "mastodon-media--inline-images"
-                  "mastodon-media--load-image-from-url-avatar-with-imagemagic"
-                  "mastodon-media--load-image-from-url-avatar-without-imagemagic"
-                  "mastodon-media--load-image-from-url-media-link-with-imagemagic"
-                  "mastodon-media--load-image-from-url-media-link-without-imagemagic"
-                  "mastodon-media--load-image-from-url-url-fetching-fails"
-                  "mastodon-media--process-image-response"))))))))
-    (native-inputs (list emacs-el-mock))
+      #:tests? #f ; requires cask
+      #:phases #~(modify-phases %standard-phases
+                   ;; Move the source files to the top level, which is
+                   ;; included in the EMACSLOADPATH.
+                   (add-after 'unpack 'move-source-files
+                     (lambda _
+                       (let ((el-files (find-files "./lisp" ".*\\.el$")))
+                         (for-each (lambda (f)
+                                     (rename-file f
+                                                  (basename f)))
+                                   el-files)))))))
    (propagated-inputs
     (list emacs-persist emacs-tp))
    (home-page "https://codeberg.org/martianh/mastodon.el")
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -425,14 +425,29 @@ hierarchical hexagonal geospatial indexing system")
               (base32
                "00qdk9a4048pzfj2rhzkfw3lvm642znf6kr4x29i3d94494pxsnn"))))
    (build-system cmake-build-system)
-    (arguments `(#:phases
-                 (modify-phases %standard-phases
-                   (add-after
-                    'unpack 'patch-test-shebangs
-                    (lambda _
-                      (substitute* '("tests/xmltester/testrunner.sh"
-                                     "tests/xmltester/safe_to_xml.sh")
-                        (("/bin/sh") (which "sh"))))))))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ,@(if (or (target-x86-32?) (target-arm32?))
+               '((add-after 'unpack 'disable-broken-tests
+                   (lambda _
+                     ;; This test fails due to limited accuracy.
+                     (delete-file "tests/xmltester/tests/general/TestCentroid.xml")
+                     (with-directory-excursion "tests/unit"
+                       ;; These also fail due to limited accuracy.
+                       (delete-file "algorithm/MinimumAreaRectangleTest.cpp")
+                       (delete-file "capi/GEOSMinimumRotatedRectangleTest.cpp")
+                       ;; It is unclear why these fail, but I'm guessing:
+                       ;; limited accuracy.
+                       (delete-file "linearref/LengthIndexedLineTest.cpp")
+                       (delete-file "math/DDTest.cpp")))))
+               '())
+         (add-after
+             'unpack 'patch-test-shebangs
+           (lambda _
+             (substitute* '("tests/xmltester/testrunner.sh"
+                            "tests/xmltester/safe_to_xml.sh")
+               (("/bin/sh") (which "sh"))))))))
    (inputs
     (list glib))
    (home-page "https://libgeos.org/")
@@ -955,6 +970,29 @@ hydrology and waste deposition.")
        (base32
         "03r6mspfv22fs4x4jcgv25v9gsj5k6zy8incvyf94qf50g47s2bc"))))
    (build-system cmake-build-system)
+    (arguments
+     (if (target-32bit?)
+         (list
+          #:phases
+          '(modify-phases %standard-phases
+             (add-after 'unpack 'patch-tests
+               (lambda _
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/unit/test_factory.cpp"
+                   (("^TEST\\(factory, AuthorityFactory_createUnitOfMeasure_linear_us_survey_foot\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_grids.cpp"
+                   (("^TEST_F\\(GridTest, VerticalShiftGridSet_gtx\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_defmodel.cpp"
+                   (("^TEST\\(defmodel, evaluator_horizontal_unit_metre\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/CMakeLists.txt"
+                   (("proj_add_gie_test\\(\"4D-API-cs2cs-style\".+") "")
+                   (("proj_add_gie_test\\(\"Builtins\".+") "")
+                   (("proj_add_gie_test\\(\"peirce_q\".+") ""))))))
+         '()))
    (native-inputs (list googletest pkg-config))
    (propagated-inputs (list curl libtiff sqlite)) ;required by proj.pc
    (home-page "https://proj.org/")
@@ -984,7 +1022,34 @@ lets developers use the functionality of Proj in their own software.")
                           version ".tar.gz"))
       (sha256
        (base32
-         "1g0hkpiablvhsmw0kn5frwgdir3q7avc45p6lc1zhhhzkv5ikydh"))))))
+         "1g0hkpiablvhsmw0kn5frwgdir3q7avc45p6lc1zhhhzkv5ikydh"))))
+    (arguments
+     (if (target-32bit?)
+         (list
+          #:phases
+          '(modify-phases %standard-phases
+             (add-after 'unpack 'patch-tests
+               (lambda _
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/unit/test_factory.cpp"
+                   (("^TEST\\(factory, AuthorityFactory_createUnitOfMeasure_linear_us_survey_foot\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_grids.cpp"
+                   (("^TEST_F\\(GridTest, VerticalShiftGridSet_gtx\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_defmodel.cpp"
+                   (("^TEST\\(defmodel, evaluator_horizontal_unit_metre\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/CMakeLists.txt"
+                   (("proj_add_gie_test\\(\"4D-API-cs2cs-style\".+") "")
+                   (("proj_add_gie_test\\(\"Builtins\".+") "")
+                   (("proj_add_gie_test\\(\"peirce_q\".+") "")
+                   (("proj_add_gie_test\\(\"adams_ws2\".+") ""))
+                 (substitute* "test/cli/CMakeLists.txt"
+                   (("proj_add_test_script_sh\\(\"testvarious\" CS2CS_BIN\\)") ""))))))
+         '()))))
+

 (define-public python-obspy
  (package
--- a/gnu/packages/gkrellm.scm
+++ b/gnu/packages/gkrellm.scm
@@ -1,4 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -16,8 +19,44 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

 (define-module (gnu packages gkrellm)
-  #:use-module (gnu packages monitoring)
-  #:use-module (guix deprecation))
+  #:use-module (guix build-system gnu)
+  #:use-module (guix download)
+  #:use-module (guix gexp)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (gnu packages gettext)
+  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages xorg))

-(define-deprecated/public-alias gkrellm
-  (@ (guix packages monitoring) gkrellm))
+(define-public gkrellm
+  (package
+    (name "gkrellm")
+    (version "2.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://gkrellm.srcbox.net/releases/gkrellm-"
+                           version ".tar.bz2"))
+       (sha256
+        (base32 "0qvy2xmwmfy5f0g09yn9lr262shnx82ba04r5il2wj4qscg3r7h8"))))
+    (build-system gnu-build-system)
+    (inputs (list gtk+-2 libsm))
+    (native-inputs (list gettext-minimal pkg-config))
+    (arguments
+     (list
+      #:tests? #f ;there is no check target
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)) ;no configure script
+      #:make-flags
+      #~(list (string-append "INSTALLROOT=" #$output)
+              (string-append "CC=" #$(cc-for-target)))))
+    (home-page "https://gkrellm.srcbox.net/")
+    (synopsis "System monitors")
+    (description
+     "GKrellM is a single process stack of system monitors which supports
+applying themes to match its appearance to your window manager, Gtk, or any
+other theme.")
+    (license license:gpl3+)))
--- a/gnu/packages/java-bootstrap.scm
+++ b/gnu/packages/java-bootstrap.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014-2019, 2021, 2026 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2021, 2026 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017, 2022 Marius Bakke <marius@gnu.org>
@@ -226,6 +226,18 @@ JNI.")
             (setenv "JAVACMD" (search-input-file inputs "/bin/jamvm"))
             (setenv "JAVAC" (search-input-file inputs "/bin/jikes"))
             (setenv "CLASSPATH" (search-input-file inputs "/lib/rt.jar"))))
+         ,@(if (target-x86-32?)
+               ;; XXX: On i686 isFile() always seems to return true.  Patching
+               ;; this here is very ugly, but the effects are limited.  None
+               ;; of these changes remain by the time we've built Icedtea and
+               ;; the other JDKs.
+               '((add-after 'unpack 'disable-isFile-checks
+                   (lambda _
+                     (substitute* "src/main/org/apache/tools/ant/util/ResourceUtils.java"
+                       (("destFile = \\(\\(FileProvider\\).*") ""))
+                     (substitute* "src/main/org/apache/tools/ant/taskdefs/Mkdir.java"
+                       (("dir.isFile\\(\\)") "false")))))
+               '())
         (replace 'build
           (lambda* (#:key inputs outputs #:allow-other-keys)
             ;; Ant complains if this file doesn't exist.
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -1285,7 +1285,13 @@ new Date();"))))
                ;; It looks like the "--disable-warnings-as-errors" option of
                ;; the 'configure' phase is not working.
                (substitute* "make/autoconf/generated-configure.sh"
-                  (("-Werror") ""))))))
+                  (("-Werror") ""))))
+            #$@(if (target-x86-32?)
+                   ;; On i686 the C2 compiler sometimes crashes when importing
+                   ;; certificates.
+                   #~((add-before 'install-keystore 'disable-C2-compiler
+                        (lambda _ (setenv "_JAVA_OPTIONS" "-XX:TieredStopAtLevel=1"))))
+                   #~())))
       ((#:disallowed-references refs '())
        (cons* (this-package-native-input "openjdk")
               (gexp-input (this-package-native-input "openjdk") "jdk")
@@ -1844,12 +1850,50 @@ blacklisted.certs.pem"
 (define-public openjdk24
  (make-openjdk
   openjdk23 "24.0.1"
-   "0h6sbzbjyqg85iml41pswdh2z3d7h2hhb0sd5yll37r1mj5lsxmx"))
+   "0h6sbzbjyqg85iml41pswdh2z3d7h2hhb0sd5yll37r1mj5lsxmx"
+   (arguments
+    (substitute-keyword-arguments (package-arguments base)
+      ((#:configure-flags flags #~(list))
+       (if (target-x86-32?)
+           #~(cons* "--enable-deprecated-ports=yes" #$flags)
+          flags))))))

 (define-public openjdk25
  (make-openjdk
   openjdk24 "25.0.2"
-   "03aa34lscr3qbdl6qz3gqyp0nzkqfj02362mzmpkiq3y2g5xdnrj"))
+   "03aa34lscr3qbdl6qz3gqyp0nzkqfj02362mzmpkiq3y2g5xdnrj"
+   (arguments
+    (substitute-keyword-arguments (package-arguments base)
+      ((#:configure-flags flags #~(list))
+       (if (target-x86-32?)
+           ;; Full builds on 32-bit x86 architectures are not supported as of
+           ;; this version.  Best we can do is to build with the "zero" variant.
+           #~(cons* "--with-jvm-variants=zero"
+                    "--disable-precompiled-headers"
+                    #$flags)
+           flags))
+      ((#:phases phases #~%standard-phases)
+       (if (target-x86-32?)
+           #~(modify-phases #$phases
+               (replace 'install
+                 (lambda _
+                   (let ((images (car (find-files "build" "-zero-release"
+                                                  #:directories? #t))))
+                     (copy-recursively (string-append images "/images/jdk")
+                                       #$output:jdk)
+                     (copy-recursively (string-append images "/images/jre")
+                                       #$output)
+                     (copy-recursively (string-append images "/images/docs")
+                                       #$output:doc))))
+               (replace 'install-libjvm
+                 (lambda _
+                   (let ((lib-out (string-append #$output "/lib"))
+                         (lib-jdk (string-append #$output:jdk "/lib")))
+                     (symlink (string-append lib-jdk "/zero/libjvm.so")
+                              (string-append lib-jdk "/libjvm.so"))
+                     (symlink (string-append lib-out "/zero/libjvm.so")
+                              (string-append lib-out "/libjvm.so"))))))
+           phases))))))

 ;;; Convenience alias to point to the latest version of OpenJDK.
 (define-public openjdk openjdk25)
--- a/gnu/packages/librewolf.scm
+++ b/gnu/packages/librewolf.scm
@@ -125,14 +125,14 @@
  ;; ex:
  ;; tar xf /gnu/store/...-firefox-123.4.source.tar.xz -O \
  ;;     firefox-123.4/browser/locales/l10n-changesets.json | grep revision
-  (let ((commit "fefe280d909d0eee8d60edd2a6db7d969df56c5b"))
+  (let ((commit "0245ffb160688061f0e0c67ea488bcdfdacbeca4"))
    (origin
      (method git-fetch)
      (uri (git-reference
            (url "https://github.com/mozilla-l10n/firefox-l10n.git")
            (commit commit)))
      (file-name (git-file-name "firefox-l10n" commit))
-      (sha256 (base32 "0z1ksvspbn4bbzxdl2w4x7bg36j4rwhaby8g37apg4393frh558i")))))
+      (sha256 (base32 "0y8xdxql04yys0wj685v4yp3kmx1ivnndg6z11vam8vszh0j7ak6")))))

 (define* (make-librewolf-source #:key version firefox-hash librewolf-hash l10n)
  (let* ((ff-src (firefox-source-origin
@@ -205,8 +205,7 @@
       (search-patches
        "librewolf-compare-paths.patch"
        "librewolf-use-system-wide-dir.patch"
-        "librewolf-add-store-to-rdd-allowlist.patch"
-        "librewolf-150.0-encoding_rs-rust-fix.patch"))
+        "librewolf-add-store-to-rdd-allowlist.patch"))
      ;; Slim down the tarball by removing unbundled libraries and 75 Mo (800+
      ;; Mo uncompressed) of unused tests.
      ;; TODO: Unbundle security/nss and media/libpng.
@@ -245,17 +244,17 @@
 ;; It's used for cache validation and therefore can lead to strange bugs.
 ;; ex: date '+%Y%m%d%H%M%S'
 ;; or: (format-time-string "%Y%m%d%H%M%S")
-(define %librewolf-build-id "20260421153818")
+(define %librewolf-build-id "20260409162101")

 (define-public librewolf
  (package
    (name "librewolf")
-    (version "150.0-1")
+    (version "149.0.2-2")
    (source
     (make-librewolf-source
      #:version version
-      #:firefox-hash "151rxzl80dm8jsxl6fwzgbirwq4zpms5adwwnbjcwdd1r3s3vr7v"
-      #:librewolf-hash "0iw9v3zc1fxc93yyhldqarxaypgmbndh2ylsy330kcbpb6p1gnmr"
+      #:firefox-hash "1kkhg3lgyakinn5ankxrlxbf39wi61mqbhwrj1l4q5l7y0n1m4va"
+      #:librewolf-hash "1bai8g2kc9snck2f724al29q6r57vkj3d7v58rf0mgzpqzvwnw5f"
      #:l10n firefox-l10n))
    (build-system gnu-build-system)
    (arguments
@@ -353,18 +352,18 @@
                             (cdr pref)))
                   `(("extensions.getAddons.search.browseURL"
                      ,(string-append
-                        "https://gnuzilla.gnu.org/"
+                        "https://gnuzilla.gnu.org/mozzarella/"
                        "search.php?q=%TERMS%"))
                     ("extensions.getAddons.get.url" .
-                      "https://gnuzilla.gnu.org")
+                      "https://gnuzilla.gnu.org/mozzarella")
                     ("extensions.getAddons.link.url" .
-                      "https://gnuzilla.gnu.org")
+                      "https://gnuzilla.gnu.org/mozzarella")
                     ("extensions.getAddons.discovery.api_url" .
-                      "https://gnuzilla.gnu.org")
+                      "https://gnuzilla.gnu.org/mozzarella")
                     ("extensions.getAddons.langpacks.url" .
-                      "https://gnuzilla.gnu.org")
+                      "https://gnuzilla.gnu.org/mozzarella")
                     ("lightweightThemes.getMoreURL" .
-                      "https://gnuzilla.gnu.org")))))))
+                      "https://gnuzilla.gnu.org/mozzarella")))))))
          (add-after 'patch-source-shebangs 'patch-cargo-checksums
            (lambda _
              (use-modules (guix build cargo-utils))
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2475,6 +2475,9 @@ similar to MATLAB, GNU Octave or SciPy.")
                   ;; "--enable-doxygen"
                   "--enable-dot"
                   "--enable-netcdf-4"
+                   #$@(if (or (target-x86-32?) (target-arm32?))
+                          '("CFLAGS=-Wno-error=incompatible-pointer-types")
+                          '())
                   (string-append "--with-plugin-dir=" #$output "/lib/hdf5-plugins"))
           #:phases
           #~(modify-phases %standard-phases
@@ -2486,7 +2489,15 @@ similar to MATLAB, GNU Octave or SciPy.")
                     (("testurl.sh") ""))
                   (substitute* "nczarr_test/Makefile.in"
                     (("/bin/bash")
-                      (search-input-file inputs "bin/bash")))))
+                      (search-input-file inputs "bin/bash")))
+                   ;; This test fails on 32 bit platforms.
+                   #$@(if (or (target-x86-32?) (target-arm32?))
+                          '((substitute* '("ncdump/tst_netcdf4_4.sh"
+                                           "ncdump/tst_nccopy4.sh")
+                              (("#!/bin/sh" m) (string-append m "\nexit 0\n")))
+                            (substitute* "ncdump/Makefile.in"
+                              (("tst_netcdf4_4.log") "")))
+                          '())))
               (add-before 'configure 'fix-source-date
                 (lambda _
                   ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
@@ -11458,7 +11469,7 @@ expression parsing and evaluation.")
 (define-public highs
  (package
    (name "highs")
-    (version "1.14.0")
+    (version "1.10.0")
    (source
     (origin
       (method git-fetch)
@@ -11467,14 +11478,14 @@ expression parsing and evaluation.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "16y664rzvxd8785195k0srz0842zvl0zdkf6qi103p503pj81afh"))))
+        (base32 "19q99nkk6r6k91gxp8a5rjil1399qyfgfc6jqlg2gd82vpcw8c8b"))))
    (build-system cmake-build-system)
    (home-page "https://highs.dev")
    (synopsis "High performance software for linear optimization")
    (description
     "HiGHS provides serial and parallel solvers for large-scale sparse
 linear programming (LP), mixed-integer programming (MIP), and quadratic
-programming (QP) models.")
+programming (QP) models")
    (license license:expat)))

 (define-public trilinos-zoltan
--- a/gnu/packages/monitoring.scm
+++ b/gnu/packages/monitoring.scm
@@ -1,16 +1,11 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2015 Siniša Biđin <sinisa@bidin.eu>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2021, 2021 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2021 Stefan Reichör <stefan@xsteve.at>
-;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
+;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018-2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2018, 2019, 2020 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
-;;; Copyright © 2019, 2023 Vasile Dumitrascu <va511e@yahoo.com>
 ;;; Copyright © 2020 Alex ter Weele <alex.ter.weele@gmail.com>
 ;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
 ;;; Copyright © 2021, 2022 Marius Bakke <marius@gnu.org>
@@ -24,6 +19,9 @@
 ;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;; Copyright © 2025 Giacomo Leidi <therewasa@fishinthecalculator.me>
 ;;; Copyright © 2025 Christian Birk Sørensen <chrbirks@gmail.com>
+;;; Copyright © 2015 Siniša Biđin <sinisa@bidin.eu>
+;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2019, 2023 Vasile Dumitrascu <va511e@yahoo.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -72,7 +70,6 @@
  #:use-module (gnu packages golang-check)
  #:use-module (gnu packages golang-web)
  #:use-module (gnu packages golang-xyz)
-  #:use-module (gnu packages gtk)
  #:use-module (gnu packages image)
  #:use-module (gnu packages lua)
  #:use-module (gnu packages mail)
@@ -414,37 +411,6 @@ system statistics (CPU, disk, and memory usage, etc.) and more on the
 desktop.")
    (license license:gpl3+)))

-(define-public gkrellm
-  (package
-    (name "gkrellm")
-    (version "2.5.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://gkrellm.srcbox.net/releases/gkrellm-"
-                           version ".tar.bz2"))
-       (sha256
-        (base32 "0qvy2xmwmfy5f0g09yn9lr262shnx82ba04r5il2wj4qscg3r7h8"))))
-    (build-system gnu-build-system)
-    (inputs (list gtk+-2 libsm))
-    (native-inputs (list gettext-minimal pkg-config))
-    (arguments
-     (list
-      #:tests? #f ;there is no check target
-      #:phases
-      #~(modify-phases %standard-phases
-          (delete 'configure)) ;no configure script
-      #:make-flags
-      #~(list (string-append "INSTALLROOT=" #$output)
-              (string-append "CC=" #$(cc-for-target)))))
-    (home-page "https://gkrellm.srcbox.net/")
-    (synopsis "System monitors")
-    (description
-     "GKrellM is a single process stack of system monitors which supports
-applying themes to match its appearance to your window manager, Gtk, or any
-other theme.")
-    (license license:gpl3+)))
-
 (define-public glances
  (package
    (name "glances")
--- a/gnu/packages/nss.scm
+++ b/gnu/packages/nss.scm
@@ -286,7 +286,7 @@ This package tracks the Extended Support Release (ESR) channel.")
  (package
   (inherit nss)
   (name "nss-rapid")
-   (version "3.123")
+   (version "3.121")
   (source
    (origin
      (inherit (package-source nss))
@@ -297,7 +297,7 @@ This package tracks the Extended Support Release (ESR) channel.")
              "releases/NSS_" version-with-underscores "_RTM/src/"
              "nss-" version ".tar.gz")))
      (sha256
-       (base32 "0jafdl18q9j36bwk73i462qkc24070b5llchffd7fsd2k0ri2i91"))
+       (base32 "0bk3lxmj364vlf4x2q01pf0li3mm5ixgnfnxirxqp9xyh63qyfnb"))
      (patches
       (search-patches "nss-3.56-pkgconfig.patch"
                       "nss-getcwd-nonnull.patch"
--- a/gnu/packages/patches/libfossil-skip-amalgamation.patch
+++ b/gnu/packages/patches/libfossil-skip-amalgamation.patch
@@ -0,0 +1,43 @@
+--- a/Makefile.in
+++ b/Makefile.in
+@@ -265,15 +265,11 @@
+ amal.flags     = -nc
+ amal.run       = TOPDIR="$(DIR.top)" $(SHELL.bash) $(bin.make-amal) --quiet
+ 
+ libfossil.c: $(amal.deps)
+ 	$(amal.run) $(amal.flags)
+-libfossil.h: libfossil.c
+-all: libfossil.c
+ @if ENABLE_CXX
+-libfossil.hpp: libfossil.c
+-libfossil.c++: libfossil.c
+ amal.flags += -c++
+ @endif
+ 
+ .PHONY: amal
+ amal: libfossil.c
+@@ -287,19 +283,16 @@
+ 	fossil uv sync
+ @endif
+ @endif
+ 
+ install: install-headers
+-install-headers: libfossil.h $(install-dir.include)
+-	$(INSTALL.noexec) libfossil.h $(install-dir.include)
+install-headers: include/libfossil.h $(install-dir.include)
+	$(INSTALL.noexec) $< $(install-dir.include)
+ @if ENABLE_CXX
+-libfossil++.hpp: libfossil.h
+-libfossil++.cpp: libfossil++.hpp
+-all: libfossil++.cpp
+ install-headers: install-headers++
+-install-headers++: libfossil++.hpp $(install-dir.include)
+-	$(INSTALL.noexec) libfossil++.hpp $(install-dir.include)
+install-headers++: include/libfossil.hpp $(install-dir.include)
+	$(INSTALL.noexec) $< $(install-dir.include)
+ @endif # ENABLE_CXX
+ clean: clean-amalgamation
+ clean-amalgamation:
+ 	rm -f libfossil.c libfossil.h libfossil++.cpp libfossil++.hpp
+ 	rm -f libfossil-config.h libfossil-amalgamation.zip VERSION.h
+
--- a/gnu/packages/patches/librewolf-150.0-encoding_rs-rust-fix.patch
+++ b/gnu/packages/patches/librewolf-150.0-encoding_rs-rust-fix.patch
@@ -1,260 +0,0 @@
-From d8702527f4f1f67f765330f5018bfcb182946c45 Mon Sep 17 00:00:00 2001
-From: Henri Sivonen <hsivonen@hsivonen.fi>
-Date: Tue, 21 Apr 2026 07:09:20 +0000
-Subject: [PATCH] Bug 2033279 - Make --enable-rust-simd work with Rust 1.95.
- r=firefox-build-system-reviewers,supply-chain-reviewers,ahochheiden
-
-Differential Revision: https://phabricator.services.mozilla.com/D295287
---
- .cargo/config.toml.in                         |  5 ++
- Cargo.lock                                    |  4 +-
- Cargo.toml                                    |  2 +
- supply-chain/audits.toml                      |  6 ++
- supply-chain/config.toml                      |  4 ++
- .../rust/encoding_rs/.cargo-checksum.json     |  2 +-
- .../rust/encoding_rs/.cargo_vcs_info.json     |  6 --
- third_party/rust/encoding_rs/Cargo.toml       | 60 ++++++++++---------
- third_party/rust/encoding_rs/Cargo.toml.orig  | 45 --------------
- .../rust/encoding_rs/src/x_user_defined.rs    |  2 +
- 10 files changed, 54 insertions(+), 82 deletions(-)
- delete mode 100644 third_party/rust/encoding_rs/.cargo_vcs_info.json
- delete mode 100644 third_party/rust/encoding_rs/Cargo.toml.orig
-
-diff --git a/.cargo/config.toml.in b/.cargo/config.toml.in
-index 8013ae5435dab..cabdee463415f 100644
--- a/.cargo/config.toml.in
-+++ b/.cargo/config.toml.in
-@@ -55,6 +55,11 @@ git = "https://github.com/hsivonen/any_all_workaround"
- rev = "7fb1b7034c9f172aade21ee1c8554e8d8a48af80"
- replace-with = "vendored-sources"
- 
-+[source."git+https://github.com/hsivonen/encoding_rs?rev=1236d1bc423e6ba35a06485f74a6304db2d703b5"]
-+git = "https://github.com/hsivonen/encoding_rs"
-+rev = "1236d1bc423e6ba35a06485f74a6304db2d703b5"
-+replace-with = "vendored-sources"
-+
- [source."git+https://github.com/hsivonen/rust-harfbuzz?rev=9d58a23a98772a197291d04af93f7041b7093d95"]
- git = "https://github.com/hsivonen/rust-harfbuzz"
- rev = "9d58a23a98772a197291d04af93f7041b7093d95"
-diff --git a/Cargo.lock b/Cargo.lock
-index fea2f95fbb438..63b1f818d7971 100644
--- a/Cargo.lock
-+++ b/Cargo.lock
-@@ -1914,11 +1914,11 @@ dependencies = [
- [[package]]
- name = "encoding_rs"
- version = "0.8.35"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "75030f3c4f45dafd7586dd6780965a8c7e8e285a5ecb86713e63a79c5b2766f3"
-+source = "git+https://github.com/hsivonen/encoding_rs?rev=1236d1bc423e6ba35a06485f74a6304db2d703b5#1236d1bc423e6ba35a06485f74a6304db2d703b5"
- dependencies = [
-  "any_all_workaround",
-  "cfg-if",
-+ "rustversion",
- ]
- 
- [[package]]
-diff --git a/Cargo.toml b/Cargo.toml
-index 49c695809f302..2648c32ae57e8 100644
--- a/Cargo.toml
-+++ b/Cargo.toml
-@@ -287,6 +287,8 @@ harfbuzz-sys = { git = "https://github.com/hsivonen/rust-harfbuzz", rev = "9d58a
- harfbuzz = { git = "https://github.com/hsivonen/rust-harfbuzz", rev = "9d58a23a98772a197291d04af93f7041b7093d95" }
- # Also vendor `harfbuzz-traits` to keep cargo-vendor happy.
- harfbuzz-traits = { git = "https://github.com/hsivonen/rust-harfbuzz", rev = "9d58a23a98772a197291d04af93f7041b7093d95" }
-+# Make --enable-rust-simd compatible with Rust 1.95
-+encoding_rs = { git = "https://github.com/hsivonen/encoding_rs", rev = "1236d1bc423e6ba35a06485f74a6304db2d703b5" }
- 
- # objc 0.2.7 + fa7ca43b862861dd1cd000d7ad01e6e0266cda13
- objc = { git = "https://github.com/glandium/rust-objc", rev = "4de89f5aa9851ceca4d40e7ac1e2759410c04324" }
-diff --git a/supply-chain/audits.toml b/supply-chain/audits.toml
-index 85b4037e03bdb..f4567ea6b6f94 100644
--- a/supply-chain/audits.toml
-+++ b/supply-chain/audits.toml
-@@ -2385,6 +2385,12 @@ who = "Mike Hommey <mh+mozilla@glandium.org>"
- criteria = "safe-to-deploy"
- delta = "0.8.31 -> 0.8.32"
- 
-+[[audits.encoding_rs]]
-+who = "Henri Sivonen <hsivonen@hsivonen.fi>"
-+criteria = "safe-to-deploy"
-+delta = "0.8.35 -> 0.8.35@git:1236d1bc423e6ba35a06485f74a6304db2d703b5"
-+importable = false
-+
- [[audits.enum-map]]
- who = "Kershaw Chang <kershaw@mozilla.com>"
- criteria = "safe-to-deploy"
-diff --git a/supply-chain/config.toml b/supply-chain/config.toml
-index 4cfd83dc2d608..15deefbec0574 100644
--- a/supply-chain/config.toml
-+++ b/supply-chain/config.toml
-@@ -39,6 +39,10 @@ notes = "This is the upstream code not yet released"
- audit-as-crates-io = true
- notes = "This is upstream plus a warning fix from bug 1823866."
- 
-+[policy.encoding_rs]
-+audit-as-crates-io = true
-+notes = "This is upstream plus a build fix for bug 2033279."
-+
- [policy.firefox-on-glean]
- audit-as-crates-io = false
- notes = "The crates.io version of this is just a placeholder to allow public crates to depend on firefox-on-glean."
-diff --git a/third_party/rust/encoding_rs/.cargo_vcs_info.json b/third_party/rust/encoding_rs/.cargo_vcs_info.json
-deleted file mode 100644
-index 6e5d699759e43..0000000000000
--- a/third_party/rust/encoding_rs/.cargo_vcs_info.json
-+++ /dev/null
-@@ -1,6 +0,0 @@
-{
-  "git": {
-    "sha1": "2fa58aecf537cc76ff52c0eb3d5e9f8fda466844"
-  },
-  "path_in_vcs": ""
-}
-\ No newline at end of file
-diff --git a/third_party/rust/encoding_rs/Cargo.toml b/third_party/rust/encoding_rs/Cargo.toml
-index 2adac351c2edf..0239315bab180 100644
--- a/third_party/rust/encoding_rs/Cargo.toml
-+++ b/third_party/rust/encoding_rs/Cargo.toml
-@@ -16,6 +16,7 @@ name = "encoding_rs"
- version = "0.8.35"
- authors = ["Henri Sivonen <hsivonen@hsivonen.fi>"]
- build = false
-+autolib = false
- autobins = false
- autoexamples = false
- autotests = false
-@@ -39,33 +40,6 @@ categories = [
- license = "(Apache-2.0 OR MIT) AND BSD-3-Clause"
- repository = "https://github.com/hsivonen/encoding_rs"
- 
-[profile.release]
-lto = true
-
-[lib]
-name = "encoding_rs"
-path = "src/lib.rs"
-
-[dependencies.any_all_workaround]
-version = "0.1.0"
-optional = true
-
-[dependencies.cfg-if]
-version = "1.0"
-
-[dependencies.serde]
-version = "1.0"
-optional = true
-
-[dev-dependencies.bincode]
-version = "1.0"
-
-[dev-dependencies.serde_derive]
-version = "1.0"
-
-[dev-dependencies.serde_json]
-version = "1.0"
-
- [features]
- alloc = []
- default = ["alloc"]
-@@ -84,4 +58,34 @@ fast-legacy-encode = [
- less-slow-big5-hanzi-encode = []
- less-slow-gb-hanzi-encode = []
- less-slow-kanji-encode = []
-simd-accel = ["any_all_workaround"]
-+simd-accel = [
-+    "any_all_workaround",
-+    "rustversion",
-+]
-+
-+[lib]
-+name = "encoding_rs"
-+path = "src/lib.rs"
-+
-+[dependencies]
-+cfg-if = "1.0"
-+
-+[dependencies.any_all_workaround]
-+version = "0.1.0"
-+optional = true
-+
-+[dependencies.rustversion]
-+version = "1.0.19"
-+optional = true
-+
-+[dependencies.serde]
-+version = "1.0"
-+optional = true
-+
-+[dev-dependencies]
-+bincode = "1.0"
-+serde_derive = "1.0"
-+serde_json = "1.0"
-+
-+[profile.release]
-+lto = true
-diff --git a/third_party/rust/encoding_rs/Cargo.toml.orig b/third_party/rust/encoding_rs/Cargo.toml.orig
-deleted file mode 100644
-index 0f7639d5f879b..0000000000000
--- a/third_party/rust/encoding_rs/Cargo.toml.orig
-+++ /dev/null
-@@ -1,45 +0,0 @@
-[package]
-name = "encoding_rs"
-description = "A Gecko-oriented implementation of the Encoding Standard"
-version = "0.8.35"
-edition = '2018'
-authors = ["Henri Sivonen <hsivonen@hsivonen.fi>"]
-license = "(Apache-2.0 OR MIT) AND BSD-3-Clause"
-readme = "README.md"
-documentation = "https://docs.rs/encoding_rs/"
-homepage = "https://docs.rs/encoding_rs/"
-repository = "https://github.com/hsivonen/encoding_rs"
-keywords = ["encoding", "web", "unicode", "charset"]
-categories = ["text-processing", "encoding", "web-programming", "internationalization"]
-rust-version = "1.36"
-
-[features]
-default = ["alloc"]
-alloc = []
-simd-accel = ["any_all_workaround"]
-less-slow-kanji-encode = []
-less-slow-big5-hanzi-encode = []
-less-slow-gb-hanzi-encode = []
-fast-hangul-encode = []
-fast-hanja-encode = []
-fast-kanji-encode = []
-fast-gb-hanzi-encode = []
-fast-big5-hanzi-encode = []
-fast-legacy-encode = ["fast-hangul-encode",
-                      "fast-hanja-encode",
-                      "fast-kanji-encode",
-                      "fast-gb-hanzi-encode",
-                      "fast-big5-hanzi-encode"]
-
-[dependencies]
-cfg-if = "1.0"
-serde = { version = "1.0", optional = true }
-any_all_workaround = { version = "0.1.0" , optional = true }
-
-[dev-dependencies]
-serde_derive = "1.0"
-bincode = "1.0"
-serde_json = "1.0"
-
-[profile.release]
-lto = true
-diff --git a/third_party/rust/encoding_rs/src/x_user_defined.rs b/third_party/rust/encoding_rs/src/x_user_defined.rs
-index 7af7d5e3d69da..16f1a18d7f6ce 100644
--- a/third_party/rust/encoding_rs/src/x_user_defined.rs
-+++ b/third_party/rust/encoding_rs/src/x_user_defined.rs
-@@ -16,7 +16,8 @@ cfg_if! {
-         use simd_funcs::*;
-         use core::simd::u16x8;
-         use core::simd::cmp::SimdPartialOrd;
-+        #[rustversion::since(1.95)]
-         use core::simd::Select;
- 
-         #[inline(always)]
-         fn shift_upper(unpacked: u16x8) -> u16x8 {
--- a/gnu/packages/prolog.scm
+++ b/gnu/packages/prolog.scm
@@ -237,7 +237,7 @@ it.")
 (define-public trealla
  (package
    (name "trealla")
-    (version "2.94.2")
+    (version "2.93.2")
    (source
     (origin
       (method git-fetch)
@@ -246,7 +246,7 @@ it.")
          (url "https://github.com/trealla-prolog/trealla")
          (commit (string-append "v" version))))
       (sha256
-        (base32 "15pxb1j0gwkbsp3406h0smscv9plm92splnha7gl5gz58am4109p"))
+        (base32 "0rsqka6i51ky74mzf2xlzdzss2xnldyk1wm0f5ilas6ic6pw3hir"))
       (file-name (git-file-name name version))))
    (build-system gnu-build-system)
    (inputs
--- a/gnu/packages/ruby-xyz.scm
+++ b/gnu/packages/ruby-xyz.scm
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -346,7 +346,7 @@ a focus on simplicity and productivity.")
    (home-page "https://www.ruby-lang.org")
    (license license:ruby)))

-(define-public ruby ruby-3.4)
+(define-public ruby ruby-3.3)

 (define-public mruby
  (package
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -384,15 +384,15 @@ comparison and diagnostics.")
 (define r-with-tests
  (package
    (name "r-with-tests")
-    (version "4.5.3")
+    (version "4.6.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://cran/src/base/R-"
                                  (version-major version) "/R-"
-                                  version ".tar.gz"))
+                                  version ".tar.xz"))
              (sha256
               (base32
-                "1wmqnm813lb58c0vwhjymnkfih3a6mq4cr9xa6n72wiw57a1wp5a"))))
+                "09sszy5fykpl2lyzxw5rgiabb3f5l62bqamnm7g2q9d57xlv7wli"))))
    (build-system gnu-build-system)
    (arguments
     (list
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -10,7 +10,6 @@
 ;;; Copyright © 2024 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
 ;;; Copyright © 2025 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2026 Nguyễn Gia Phong <cnx@loang.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,7 +29,6 @@
 (define-module (gnu packages syndication)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix download)
-  #:use-module (guix fossil-download)
  #:use-module (guix git-download)
  #:use-module (guix packages)
  #:use-module (guix utils)
@@ -77,33 +75,6 @@
  #:use-module (gnu packages xorg)
  #:use-module (srfi srfi-1))

-(define-public fead
-  (package
-    (name "fead")
-    (version "1.0.1")
-    (source
-     (origin
-       (method fossil-fetch)
-       (uri (fossil-reference
-             (uri "https://chim.loan/fead")
-             (check-in version)))
-       (sha256
-        (base32 "0fzxabmxpyd04v5ym20xhjcnh0vqdwc6z1xjrq676d2k0hr2rzz2"))))
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:tests? #f                       ;no test
-      #:make-flags #~(list (string-append "PREFIX=" #$output))
-      #:phases #~(modify-phases %standard-phases
-                   (delete 'configure))))
-    (inputs (list python))
-    (native-inputs (list help2man))
-    (home-page "https://chim.loan/fead")
-    (synopsis "Advert generator from web feeds")
-    (description "Fead a tool for advertising other blogs you like on your own
-by embedding the summary of their latest posts extracted from their web feed.")
-    (license license:agpl3+)))
-
 (define-public giara
  (package
    (name "giara")
--- a/gnu/packages/text-editors.scm
+++ b/gnu/packages/text-editors.scm
@@ -875,29 +875,30 @@ compiled, requires few libraries, and starts up quickly.")
 (define-public e3
  (package
    (name "e3")
-    (version "2.82.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://codeberg.org/museoa/e3editor")
-              (commit version)))
-       (sha256
-        (base32
-         "1l57rxin3kv6iiw91rhjzl3bpk0gkfp3nrx7wmqikk1nycmkfbhm"))))
+    (version "2.82")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://sites.google.com/site/e3editor/Home/"
+                                  "e3-" version ".tgz"))
+              (sha256
+               (base32
+                "0919kadkas020maqq37852isnzp053q2fnws2zh3mz81d1jiviak"))
+              (modules '((guix build utils)))
+
+              ;; Remove pre-built binaries.
+              (snippet '(begin
+                          (delete-file-recursively "bin")
+                          #t))))
    (build-system gnu-build-system)
    (arguments
-     (list
-      #:tests? #f
-      #:make-flags
-      #~(list (string-append "PREFIX=" #$output))
-      #:phases
-      #~(modify-phases %standard-phases
-          (delete 'configure))))
+     `(#:tests? #f
+       #:make-flags (list (string-append "PREFIX="
+                                         (assoc-ref %outputs "out")))
+       #:phases (modify-phases %standard-phases
+                  (delete 'configure))))
    (native-inputs
     (list nasm))
-    (supported-systems '("x86_64-linux" "i686-linux"))
-    (home-page "https://codeberg.org/museoa/e3editor")
+    (home-page "https://sites.google.com/site/e3editor/")
    (synopsis "Tiny text editor written in assembly")
    (description
     "e3 is a micro text editor with an executable code size between 3800 and
@@ -906,6 +907,7 @@ of the basic functions one expects plus built in arithmetic calculations.
 UTF-8 coding of unicode characters is supported as well.  e3 can use
 Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings.  e3 can be used on
 16, 32, and 64-bit CPUs.")
+    (supported-systems '("x86_64-linux" "i686-linux"))
    (license license:gpl2+)))

 (define-public mg
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -3522,113 +3522,106 @@ modification time.")
    (license license:bsd-2)))

 (define-public libfossil
-  (package
-    (name "libfossil")
-    (version "0.6.0")
-    (source
-     (origin
-       (method fossil-fetch)
-       (uri (fossil-reference
-             (uri "https://fossil.wanderinghorse.net/r/libfossil")
-             (check-in version)))
-       (file-name (fossil-file-name name version))
-       (sha256
-        (base32 "0haaczpjnjpkiikf0q70nfabm2csdk6dl9rh80j0sh90wfvkyqwm"))
-       (modules '((guix build utils)
-                  (ice-9 ftw)
-                  (srfi srfi-26)))
-       (snippet
-        #~(begin
-            (define (delete-all-but directory . preserve)
-              (with-directory-excursion directory
-                (let* ((pred (negate (cut member <>
-                                          (cons* "." ".." preserve))))
-                       (items (scandir "." pred)))
-                  (for-each (cut delete-file-recursively <>) items))))
-            (delete-all-but "autosetup" "proj.tcl" "wh-common.tcl")
-            (delete-file-recursively "extsrc")
-            ;; Re-create Fossil check-out manifests,
-            ;; whose content does not affect in semantics.
-            (for-each
-              (lambda (file)
-                (call-with-output-file file (const #t)))
-              '("manifest" "manifest.uuid"))))))
-    (build-system gnu-build-system)
-    (arguments
-     (list #:configure-flags
-           #~(list "--no-debug" "--no-fnc" ;TODO: C++ and Tcl binding?
-                   (string-append "--with-sqlite="
-                                  #$(this-package-input "sqlite"))
-                   (string-append "--soname=libfossil.so"))
-           #:phases
-           #~(modify-phases %standard-phases
-               (replace 'configure
-                 (lambda* (#:key configure-flags #:allow-other-keys)
-                   (apply invoke "autosetup"
-                          (string-append "--prefix=" #$output)
-                          configure-flags)))
-               (replace 'check
-                 (lambda* (#:key tests? #:allow-other-keys)
-                   (when tests?
-                     (substitute* "sanity-checks.sh"
-                       ;; FIXME: these tests requires a Fossil checkout.
-                       (("\\./f-sanity.*") "")
-                       (("\\./f-parseparty.*") ""))
-                     (setenv "LD_LIBRARY_PATH" (getcwd))
-                     (invoke "./sanity-checks.sh")))))))
-    (native-inputs (list autosetup))
-    (inputs (list sqlite-next zlib))
-    (home-page "https://fossil.wanderinghorse.net/r/libfossil")
-    (synopsis "Unofficial Fossil SCM Library API")
-    (description
-     "@code{libfossil} is an alternative interface into Fossil repositories,
-as opposed to a replacement for the core fossil application,
-intended for new ways to access and manipulate fossil repositories.")
-    (license license:bsd-2)))
-
-(define-public fnc
-  (let ((check-in
-         "c158d7ac2175078b4b783157be92de38aa627dc1a237febab9ec92093420cedb")
+  (let ((ci "914ed6dcaff13bf7209c9f27ccfb77c2d8fdf36b8d2133aa1590258b0708f035")
        (revision "0"))
    (package
-      (name "fnc")
-      (version (fossil-version "0.19" revision check-in))
+      (name "libfossil")
+      (version (fossil-version "0.6.0" revision ci))
      (source
       (origin
         (method fossil-fetch)
         (uri (fossil-reference
-               (uri "https://fnc.sh")
-               (check-in check-in)))
+               (uri "https://fossil.wanderinghorse.net/r/libfossil")
+               (check-in ci)))
         (file-name (fossil-file-name name version))
         (sha256
-          (base32 "09m0bgzy0yjglsgrqq03sdq4p2rwi3y8m84979j066z1c5b444iz"))
-         (modules '((guix build utils)))
-         (snippet #~(begin
-                      (delete-file-recursively "lib")
-                      (substitute* (find-files "." "\\.c$")
-                        (("^#include \"libfossil.h\"")
-                         "#include <fossil-scm/libfossil.h>"))
-                      (substitute* "fnc.bld.mk"
-                        ((" \\$\\{SQLITE_OBJS\\} \\$\\{FOSSIL_OBJS\\}") "")
-                        (("-lm -lutil -lz ") "")
-                        ;; Fix cross-compiling.
-                        (("install -s") "install"))))))
+          (base32 "0a0ycnnba2izmiqjj8hgvjgjdwhpn0x36lhy3vmw4j7bhny0df52"))
+         (patches (search-patches "libfossil-skip-amalgamation.patch"))
+         (modules '((guix build utils)
+                    (ice-9 ftw)
+                    (srfi srfi-26)))
+         (snippet
+          #~(begin
+              (define (delete-all-but directory . preserve)
+                (with-directory-excursion directory
+                  (let* ((pred (negate (cut member <>
+                                            (cons* "." ".." preserve))))
+                         (items (scandir "." pred)))
+                    (for-each (cut delete-file-recursively <>) items))))
+              (delete-all-but "autosetup" "proj.tcl" "wh-common.tcl")
+              (delete-file-recursively "extsrc")
+              ;; Re-create Fossil check-out manifests,
+              ;; whose content does not affect in semantics.
+              (for-each
+                (lambda (file)
+                  (call-with-output-file file (const #t)))
+                '("manifest" "manifest.uuid"))))))
      (build-system gnu-build-system)
      (arguments
-       (list
-        #:phases #~(modify-phases %standard-phases
-                     (delete 'configure))
-        #:tests? #f                     ;no tests
-        #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
-                             "LDFLAGS=-lfossil -lsqlite3"
-                             (string-append "PREFIX=" #$output))))
-      (inputs (list libfossil ncurses sqlite-next))
-      (home-page "https://fnc.sh")
-      (synopsis "Interactive text-based user interface for Fossil")
-      (description "fnc uses ncurses and libfossil to create a fossil user
+       (list #:configure-flags
+             #~(list "--no-debug" "--no-fnc" ;TODO: C++ and Tcl binding?
+                     (string-append "--with-sqlite="
+                                    #$(this-package-input "sqlite"))
+                     (string-append "--soname=libfossil.so"))
+             #:phases
+             #~(modify-phases %standard-phases
+                 (replace 'configure
+                   (lambda* (#:key configure-flags #:allow-other-keys)
+                     (apply invoke "autosetup"
+                            (string-append "--prefix=" #$output)
+                            configure-flags)))
+                 (replace 'check
+                   (lambda* (#:key tests? #:allow-other-keys)
+                     (when tests?
+                       (substitute* "sanity-checks.sh"
+                         ;; FIXME: these tests requires a Fossil checkout.
+                         (("\\./f-sanity.*") "")
+                         (("\\./f-parseparty.*") ""))
+                       (setenv "LD_LIBRARY_PATH" (getcwd))
+                       (invoke "./sanity-checks.sh")))))))
+      (native-inputs (list autosetup))
+      (inputs (list sqlite-next zlib))
+      (home-page "https://fossil.wanderinghorse.net/r/libfossil")
+      (synopsis "Unofficial Fossil SCM Library API")
+      (description
+       "@code{libfossil} is an alternative interface into Fossil repositories,
+as opposed to a replacement for the core fossil application,
+intended for new ways to access and manipulate fossil repositories.")
+      (license license:bsd-2))))
+
+(define-public fnc
+  (package
+    (name "fnc")
+    (version "0.18")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append "https://fnc.bsdbox.org/uv/dl/fnc-"
+                              version ".tar.gz"))
+              (sha256
+               (base32
+                "1067rr4nqngld1nqa8c7imp9n3w5fp7rpc7khh6l84q2w1klrya9"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (delete 'configure)
+                   ;; fix cross-compiling.
+                   (add-after 'unpack 'don-t-use-install-s
+                     (lambda _
+                       (substitute* "fnc.bld.mk"
+                         (("install -s")
+                          "install")))))
+      #:tests? #f                       ; no tests
+      #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
+                           (string-append "PREFIX=" #$output))))
+    (inputs (list ncurses zlib sqlite-next))
+    (home-page "https://fnc.bsdbox.org")
+    (synopsis "Interactive text-based user interface for Fossil")
+    (description "fnc uses ncurses and libfossil to create a fossil user
 interface in the terminal.  It can view local changes at the hunk level to
 prepare atomic commits.")
-      (license license:isc))))
+    (license license:isc)))

 (define-public myrepos
  (package
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -3749,31 +3749,6 @@ productive, customizable lisp based systems.")
 control module for StumpWM.")
      (license license:gpl3))))

-(define-public sbcl-stumpwm-acpi-backlight
-  (package
-    (name "sbcl-stumpwm-acpi-backlight")
-    (version "0.1.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/Junker/stumpwm-acpi-backlight")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1dih6fzy77f3r60fwhsk0dw3qksadzj991k1i28z0da64fpshm0a"))))
-    (arguments
-     (list
-      #:asd-systems ''("acpi-backlight")
-      #:tests? #f)) ; There are no tests.
-    (build-system asdf-build-system/sbcl)
-    (inputs (list stumpwm))
-    (home-page "https://github.com/Junker/stumpwm-acpi-backlight")
-    (synopsis "ACPI backlight control module for StumpWM")
-    (description
-     "ACPI backlight control module for StumpWM.")
-    (license license:gpl3)))
-
 (define-public sbcl-stumpwm-binwarp
  (package
    (inherit stumpwm-contrib)
@@ -3791,40 +3766,6 @@ control module for StumpWM.")
 mouse control mode for StumpWM.")
    (license (list license:gpl2+ license:gpl3+ license:bsd-2))))

-(define-public sbcl-stumpwm-bluetooth
-  (package
-    (name "sbcl-stumpwm-bluetooth")
-    (version "0.1.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/Junker/stumpwm-bluetooth")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "08a028r83kd66a3smiyzi9hadk3w89qdhha7hsd9ffh3gdk5s99a"))))
-    (arguments
-     (list
-      #:asd-systems ''("bluetooth")
-      #:tests? #f ; There are no tests.
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'fix-bin-path
-            (lambda* (#:key inputs #:allow-other-keys)
-              (substitute* "bluetooth.lisp"
-                (("/usr/bin/bluetoothctl")
-                 (search-input-file inputs "bin/bluetoothctl"))))))))
-    (build-system asdf-build-system/sbcl)
-    (inputs (list stumpwm
-                  bluez
-                  sbcl-bordeaux-threads))
-    (home-page "https://github.com/Junker/stumpwm-bluetooth")
-    (synopsis "StumpWM module for controlling Bluetooth devices")
-    (description
-     "StumpWM module for controlling Bluetooth devices via bluetoothctl.")
-    (license license:gpl3)))
-
 (define-public sbcl-stumpwm-stump-nm
  (package
    (inherit stumpwm-contrib)
@@ -3851,7 +3792,7 @@ not a replacement for nmtui and/or nmcli.")
 (define-public sbcl-stumpwm-tomato
  (package
    (name "sbcl-stumpwm-tomato")
-    (version "0.2.0")
+    (version "0.1.0")
    (source
     (origin
       (method git-fetch)
@@ -3860,7 +3801,7 @@ not a replacement for nmtui and/or nmcli.")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0r00f8qi5kzf1sxx19fxr2lvc32bw3xlz75qrnxl5vgwsl8qafr5"))))
+        (base32 "0qq11spvhrcq74gh0dw0p4859ai2mqzbxa45gjbf599kmcybp1pa"))))
    (build-system asdf-build-system/sbcl)
    (inputs (list stumpwm))
    (arguments
@@ -4138,41 +4079,6 @@ layouts in StumpWM.")
 one in Emacs.")
    (license license:gpl3+)))

-(define-public sbcl-stumpwm-wpctl
-  (package
-    (name "sbcl-stumpwm-wpctl")
-    (version "0.2.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/Junker/stumpwm-wpctl")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1c3i5z1cmhd96xnlsb40ykgk60cyignl1m4f61i9k9vq05n83pdj"))))
-    (arguments
-     (list #:asd-systems ''("wpctl")
-           #:tests? #f ; There are no tests.
-           #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'unpack 'fix-wpctl-path
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   (substitute* "wpctl.lisp"
-                     (("/usr/bin/wpctl")
-                      (search-input-file inputs "bin/wpctl"))))))))
-    (build-system asdf-build-system/sbcl)
-    (inputs
-     (list stumpwm
-           wireplumber-minimal
-           sbcl-parse-float
-           sbcl-bordeaux-threads))
-    (home-page "https://github.com/Junker/stumpwm-wpctl")
-    (synopsis "StumpWM PipeWire module")
-    (description
-     "PipeWire (WirePlumber) volume and microphone control module for StumpWM.")
-    (license license:gpl3)))
-
 (define-public sbcl-stumpwm-screenshot
  (package
    (inherit stumpwm-contrib)