gnu: python-dill: Update to 0.4.1.

* gnu/packages/python-xyz.scm (python-dill): Update to 0.4.1. [source]: Switch to git-fetch. [arguments] <test-backend, test-flags>: Use 'custom backend instead of overwriting test phase. <phases>: Use default 'check. [native-inputs]: Remove python-wheel. [home-page]: Update to URL to http://dill.rtfd.io/. Change-Id: Ifd949babdc06ed4e33cdadae6f392c224f53197a
gnu: python-asttokens: Update to 3.0.1.
2026-07-08 04:54:05 +02:00 · 2026-05-30 00:50:45 +01:00 · 2026-05-30 00:50:45 +01:00 · 2026-05-30 00:50:45 +01:00 · 2026-05-30 00:50:45 +01:00 · 2026-05-30 00:50:45 +01:00
127 changed files with 7584 additions and 5965 deletions
@@ -292,12 +292,12 @@ guix/build-system/julia\.scm                       @guix/julia
 gnu/packages/(kde)(-.+|)\.scm$                     @guix/kde
-gnu/build/linux-modules\.scm                       @guix/kernel
+gnu/build/linux-modules\.scm                       @guix/linux-libre
-gnu/packages/aux-files/linux-libre.*$              @guix/kernel
+gnu/packages/aux-files/linux-libre.*$              @guix/linux-libre
-gnu/packages/linux\.scm                            @guix/kernel
+gnu/packages/linux\.scm                            @guix/linux-libre
-gnu/tests/linux-modules\.scm                       @guix/kernel
+gnu/tests/linux-modules\.scm                       @guix/linux-libre
-guix/build/linux-module-build-system\.scm          @guix/kernel
+guix/build/linux-module-build-system\.scm          @guix/linux-libre
-guix/build-system/linux-module\.scm                @guix/kernel
+guix/build-system/linux-module\.scm                @guix/linux-libre
 gnu/packages/lisp(-.+|)\.scm$                      @guix/lisp
 guix/build/asdf-build-system\.scm                  @guix/lisp
@@ -120,6 +120,7 @@ running 'guix-daemon $extra_options'" >&2
    "@abs_top_builddir@/pre-inst-env"				\
 	"@abs_top_builddir@/guix-daemon"			\
        $extra_options						\
        --allow-aslr                                            \
 	--substitute-urls="$GUIX_BINARY_SUBSTITUTE_URL" &
    daemon_pid=$!
@@ -618,6 +618,33 @@ enhance @code{scheme-mode} and Geiser.  @xref{Introduction,,,
 emacs-guix, Emacs-Guix Reference Manual}, to make sure you don't miss
 out!
@unnumberedsubsubsec Submitting Pull Requests Following the AGit Workflow
@cindex AGit workflow, for pull requests (Emacs).
@url{https://codeberg.org/halvin/agitjo, Agitjo} is a helper to ease
 AGit workflow based patch submission (@pxref{Submitting Patches}).
 Install it with:
@example
 guix install emacs-agitjo
@end example
 Assuming your local checkout is on the branch containing the changes you
 would like to submit for inclusion in the @code{master} branch, use
@command{M-x agitjo-push} then:
@itemize
@item
 Set options like the title @option{-t} and the session identifier
@option{-s}.
@item
 Invoke one of the push commands to execute a @command{git push} operation.
@end itemize
 When creating a new pull request, a dedicated buffer will open for
 drafting a description. The force-push option @option{-f} is enabled to
 push changes to the existing pull request.
@unnumberedsubsubsec Taming Boilerplate with Templates
@cindex code snippets
@@ -152,6 +152,7 @@ Copyright @copyright{} 2026 David Elsing@*
 Copyright @copyright{} 2026 Nguyễn Gia Phong@*
 Copyright @copyright{} 2026 Yarl Baudig@*
 Copyright @copyright{} 2026 Joan Vilardaga Castro@*
 Copyright @copyright{} 2026 Nemin@*
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -305,6 +306,7 @@ Package Management
 Substitutes
 * Official Substitute Servers::  One particular source of substitutes.
 * Volunteer Run Mirrors::        Additional, regional sources of substitutes.
 * Substitute Server Authorization::  How to enable or disable substitutes.
 * Getting Substitutes from Other Servers::  Substitute diversity.
 * Substitute Authentication::   How Guix verifies substitutes.
@@ -1779,6 +1781,21 @@ user namespaces is missing (@pxref{Build Environment Setup}).  Use at
 your own risk!
@end quotation
@cindex ASLR (address space layout randomization), for builds
@cindex address space layout randomization (ASLR), for builds
@cindex Docker, running @command{guix-daemon}
@cindex @command{guix-daemon}, running under Docker
@item --allow-aslr
 Allow builds to start even if @acronym{ASLR, Address Space Layout
 Randomization} cannot be disabled on Linux systems.  This is normally
 done so as to increase reproducibility, but some environments, such as
 those affected by Docker's default seccomp policy, don't permit
 disabling ASLR.  Passing this option will allow builds to start with
 reduced reproducibility regardless.
 Note that passing this option doesn't ensure that ASLR is enabled, it
 only allows builds to start even when disabling it is blocked.
@item --isolate-host-loopback
 Prevent fixed-output chroot builds from accessing the host loopback.
 When this is used, fixed-output builds will have their own loopback
@@ -3936,6 +3953,7 @@ also result from derivation builds, can be available as substitutes.
@menu
 * Official Substitute Servers::  One particular source of substitutes.
 * Volunteer Run Mirrors::  Additional, regional sources of substitutes.
 * Substitute Server Authorization::  How to enable or disable substitutes.
 * Getting Substitutes from Other Servers::  Substitute diversity.
 * Substitute Authentication::   How Guix verifies substitutes.
@@ -3966,13 +3984,54 @@ could use the information gathered to determine, for instance, whether
 your system has unpatched security vulnerabilities.
 Substitutes from the official build farms are enabled by default when
-using Guix System (@pxref{GNU Distribution}).  However,
+using Guix System (@pxref{GNU Distribution}).  However, they are
-they are disabled by default when using Guix on a foreign distribution,
+disabled by default when using Guix on a foreign distribution, unless
-unless you have explicitly enabled them via one of the recommended
+you have explicitly enabled them via one of the recommended installation
-installation steps (@pxref{Installation}).  The following paragraphs
+steps (@pxref{Installation}).  Please @pxref{Substitute Server
-describe how to enable or disable substitutes for the official build
+Authorization} on how to enable or disable substitutes for the official
-farm; the same procedure can also be used to enable substitutes for any
+build farm; the same procedure can also be used to enable substitutes
-other substitute server.
+for any other substitute server.
@node Volunteer Run Mirrors
@subsection Volunteer Run Mirrors
@cindex substitutes
@cindex mirrors
 Beyond the two official substitute servers, there are additionally
 volunteer run mirrors.  These mirrors do not build their own
 substitutes, but rather copy them from the official build farm and
 distribute them to users.  Enabling a mirror may be beneficial in case
 the official servers are temporarily unavailable or provide inadequate
 bandwidth at the user's location.
@quotation Note
 Mirrored substitutes are signed by the original builder, not the mirror.
 This means that mirror operators @strong{cannot} add or modify binaries,
 as long as you trust only the official substitute servers,
@pxref{Substitute Server Authorization}.
@end quotation
 List of volunteer run mirrors, grouped by location (with the build farm
 they mirror in parentheses):
@table @asis
@item Germany
@itemize
@item @code{https://hydra-guix-129.guix.gnu.org} (bordeaux.guix.gnu.org)
@end itemize
@item People's Republic of China
@itemize
@item @code{https://mirrors.sjtug.sjtu.edu.cn/guix} (ci.guix.gnu.org)
@item @code{https://mirrors.sjtug.sjtu.edu.cn/guix-bordeaux} (bordeaux.guix.gnu.org)
@end itemize
@item Russia
@itemize
@item @code{https://mirror.yandex.ru/mirrors/guix/} (bordeaux.guix.gnu.org)
@end itemize
@end table
 To enable receiving substitutions from these mirrors, please @pxref{Getting
 Substitutes from Other Servers}.
@node Substitute Server Authorization
@subsection Substitute Server Authorization
@@ -36234,6 +36293,10 @@ Launch the app as this group (it must be an existing group).
 A list of sockets (as path strings) which gunicorn will be listening
 on.  This list must contain at least one socket.
@item @code{control-socket} (default: #f) (type: string)
 If set, creates a gunicorn control-socket at the given path.  Note that,
 the control socket should refer to a path listed in @code{mappings}.
@item @code{socket-user} (default: @code{user}) (type: string)
 Owner of the directory containing the socket (must be an existing user).
@@ -38069,6 +38132,21 @@ This is the type of the dnsmasq service, whose value should be a
           (servers '("192.168.1.1"))))
@end lisp
 The following example shows a slightly more complex configuration that
 defines an authoritative DNS server on a given subdomain.
@lisp
 (service dnsmasq-service-type
         (dnsmasq-configuration
           (listen-addresses '("10.1.1.1"))
           (no-resolv? #t)
           (no-hosts? #t)
           (authoritative-servers '("vpn.example.com")) ;self
           (authoritative-zones '("vpn.example.com"))
           (host-records '("some-service.vpn.example.com,10.1.1.1"))))
@end lisp
 For more examples, refer to @samp{man 8 dnsmasq.}
@code{dnsmasq-service-type} provides two actions:
@table @code
@@ -38158,12 +38236,33 @@ ie a subnet for which an interface exists on the server.
@item @code{listen-addresses} (default: @code{'()})
 Listen on the given IP addresses.
@item @code{ipv4?} (default: @code{#t})
 Whether to include A records in answers.
@item @code{ipv6?} (default: @code{#t})
 Whether to include AAAA records in answers.
@item @code{resolv-file} (default: @code{"/etc/resolv.conf"})
 The file to read the IP address of the upstream nameservers from.
@item @code{no-resolv?} (default: @code{#f})
 When true, don't read @var{resolv-file}.
@item @code{authoritative-servers} (default: @code{'()})
 A list of strings corresponding to valid @option{--auth-server} values,
 such as a domain name.  This is useful to make @command{dnsmasq}
 authoritative for a given domain name or interface.
@item @code{authoritative-zones} (default: @code{'()})
 A list of strings corresponding to valid @option{--auth-zone} values,
 such as a domain name.  This is useful to make @command{dnsmasq}
 authoritative for a given domain name.  Note that this must be used in
 conjunction with the @code{authoritative-servers} option.
@item @code{host-records} (default: @code{'()})
 A list of strings corresponding to valid @option{--host-record} values,
 for example @code{'("some-service.example.com,10.1.1.1")}.
@item @code{forward-private-reverse-lookup?} (default: @code{#t})
 When false, all reverse lookups for private IP ranges are answered with
 "no such domain" rather than being forwarded upstream.
@@ -38172,6 +38271,12 @@ When false, all reverse lookups for private IP ranges are answered with
 When true, dnsmasq queries the servers in the same order as they appear
 in @var{servers}.
@item @code{locals} (default: @code{'()})
 Specify domain name @emph{patterns} which should be treated as local,
 that is, for which there should be no delegation to upstream servers.
 Provided pattern values should be of the form
@code{'("/vpn.example.com/")}.
@item @code{servers} (default: @code{'()})
 Specify IP address of upstream servers directly.
@@ -876,8 +876,8 @@ and the maven-build-system."
        "The plasma desktop environment, and KDE Applications."
        #:scope (list (make-regexp* "^gnu/packages/(kde)(-.+|)\\.scm$"))))
-(define-team kernel
+(define-team linux-libre
-  (team 'kernel
+  (team 'linux-libre
        #:name "Linux-libre kernel team"
        #:scope (list "gnu/build/linux-modules.scm"
                      (make-regexp* "^gnu/packages/aux-files/linux-libre.*$")
@@ -1298,7 +1298,7 @@ the \"texlive\" importer."
 (define-member (person "Leo Famulari"
                       "leo@famulari.name"
                       "lfam")
-  kernel)
+  linux-libre)
 (define-member (person "Efraim Flashner"
                       "efraim@flashner.co.il"
@@ -1383,7 +1383,7 @@ the \"texlive\" importer."
 (define-member (person "Vagrant Cascadian"
                       "vagrant@debian.org"
                       "vagrantc")
-  debian embedded kernel)
+  debian embedded linux-libre)
 (define-member (person "Vagrant Cascadian"        ;XXX: duplicate
                       "vagrant@reproducible-builds.org"
@@ -1537,7 +1537,7 @@ the \"texlive\" importer."
 (define-member (person "Rodion Goritskov"
                       "rodion@goritskov.com"
                       "rodion-goritskov")
-  games java kde kernel release)
+  games java kde linux-libre release)
 (define-member (person "Jason Conroy"
                       "jconroy@tscripta.net"
@@ -1577,7 +1577,7 @@ the \"texlive\" importer."
 (define-member (person "Nguyễn Gia Phong"
                       "cnx@loang.net"
                       "cnx")
-  build-tools python qa-packages sysadmin vcs)
+  build-tools lua qa-packages sysadmin vcs)
 (define-member (person "Lilah Tascheter"
                       "lilah@lunabee.space"
@@ -1622,7 +1622,7 @@ the \"texlive\" importer."
 (define-member (person "Wilko Meyer"
                       "w@wmeyer.eu"
                       "theesm")
-  kernel perl)
+  linux-libre perl)
 (define-member (person "Untrusem"
                       "mysticmoksh@riseup.net"
@@ -173,7 +173,16 @@ SYSTEM."
 (define (core-packages system)
  "Return the 'core' package set suitable for SYSTEM, which might be a system
 type or a GNU triplet."
-  (cond ((target-linux? system) (append %core-packages %linux-packages))
+  (cond ((target-linux? system)
         (append %core-packages
                 %linux-packages
                 (cond ((target-arm32? system)
                        (list linux-libre-arm-generic))
                       ((target-aarch64? system)
                        (list linux-libre-arm64-generic))
                       ((target-riscv64? system)
                        (list linux-libre-riscv64-generic))
                       (else '()))))
        ((target-hurd? system) (append %core-packages %hurd-packages))
        ((target-mingw? system) %core-packages-for-mingw)
        (else '())))
@@ -1006,6 +1006,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/alure-dumb-2.patch			\
  %D%/packages/patches/amd-smi-newer-libdrm.patch		\
  %D%/packages/patches/amd-smi-python.patch			\
  %D%/packages/patches/angband-remove-nonfree-tile-options.patch	\
  %D%/packages/patches/ibus-anthy-fix-tests.patch		\
  %D%/packages/patches/ibus-table-paths.patch			\
  %D%/packages/patches/antiword-CVE-2014-8123.patch			\
@@ -1880,6 +1881,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/lua-5.4-pkgconfig.patch			\
  %D%/packages/patches/lua-5.4-liblua-so.patch			\
  %D%/packages/patches/lua-5.4-search-paths.patch		\
  %D%/packages/patches/lua-5.5-search-paths.patch		\
  %D%/packages/patches/lua-5.x-search-path-helpers.patch	\
  %D%/packages/patches/lua-lgi-fix-pango.patch			\
  %D%/packages/patches/lua-lgi-fix-ref.patch			\
@@ -2366,16 +2368,8 @@ dist_patch_DATA =						\
  %D%/packages/patches/renpy-fix-integer-slots.patch			\
  %D%/packages/patches/reposurgeon-add-missing-docbook-files.patch	\
  %D%/packages/patches/rdkit-unbundle-external-dependencies.patch	\
  %D%/packages/patches/r-biostrings-r4.6.0-compat.patch		\
  %D%/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch \
  %D%/packages/patches/r-httpuv-1.6.6-unvendor-libuv.patch	\
  %D%/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch \
  %D%/packages/patches/r-rsamtools-r-4.6.0-compat.patch		\
  %D%/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch \
  %D%/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch \
  %D%/packages/patches/r-sapa-lapack.patch			\
  %D%/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch \
  %D%/packages/patches/r-sparsearray-r-4.6.0-compat.patch	\
  %D%/packages/patches/ripperx-missing-file.patch		\
  %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
  %D%/packages/patches/rtosc-0.3.1-fix-invalid-comparison-operator.patch	\
@@ -2460,6 +2454,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/shared-mime-info-xdgmime-path.patch	\
  %D%/packages/patches/sharutils-CVE-2018-1000097.patch		\
  %D%/packages/patches/showtime-python-3.11-compat.patch        \
  %D%/packages/patches/simpleitk-r-4.6.0.patch			\
  %D%/packages/patches/sipwitch-fix-build-with-exosip5.patch	\
  %D%/packages/patches/slim-config.patch			\
  %D%/packages/patches/slim-gcc-14.patch			\
@@ -2494,6 +2489,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/swift-corelibs-libdispatch-5.7.3-modulemap.patch	\
  %D%/packages/patches/swift-llvm-5.7.3-linux.patch	\
  %D%/packages/patches/swig-support-gcc-12.patch		\
  %D%/packages/patches/swig-support-r-4.6.0.patch		\
  %D%/packages/patches/swish-e-search.patch			\
  %D%/packages/patches/swish-e-format-security.patch		\
  %D%/packages/patches/t1lib-CVE-2010-2642.patch		\
@@ -1084,7 +1084,7 @@ console.")
 (define-public btop
  (package
    (name "btop")
-    (version "1.4.6")
+    (version "1.4.7")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -1093,7 +1093,7 @@ console.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1nj58dbv3c0rj8fngldkyrmdmacmjnbg8ch1c07ik97kqnnzd3l7"))))
+                "0d3cr5l6gpcwhxgnrizny5b5kg6fys2hy9a58bc68w4n2hc040fy"))))
    (build-system gnu-build-system)
    (native-inputs (list lowdown))
    (arguments
@@ -137,7 +137,6 @@
  #:use-module (gnu packages music)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages onc-rpc)
  #:use-module (gnu packages oneapi)
  #:use-module (gnu packages perl)
@@ -2136,7 +2135,17 @@ envelope follower, distortion effects, tape effects and more.")
 	        (base32
                 "01hnx4hhbz3ap3bw15s42q4q1mw1mhdjwygq4550wvjfg6k4ga8w"))))
      (build-system waf-build-system)
-      (arguments (list #:tests? #false)) ;There are no tests.
+      (arguments
       (list
        #:tests? #false ;There are no tests.
        #:phases
        '(modify-phases %standard-phases
           (add-after 'unpack 'python3.12-compatibility
             (lambda _
               (substitute* "waflib/Context.py"
                 (("imp.new_module") "types.ModuleType")
                 (("import os, re, imp, sys")
                  "import os, re, types, sys")))))))
      (inputs (list lv2))
      (native-inputs (list pkg-config))
      (home-page "https://git.drobilla.net/cgit.cgi/omins.lv2.git/")
@@ -1430,33 +1430,86 @@ within this package are the 3000 bone marrow cells used for vignettes.")
      (license license:gpl3))))
 (define-public r-pizzarr
-  (let ((commit "5f4705789ba29344dcb97023f290a26a7f7abd0c")
+  (package
-        (revision "2"))
+    (name "r-pizzarr")
-    (package
+    (version "0.2.0")
-      (name "r-pizzarr")
+    (source
-      (version (git-version "0.1.0" revision commit))
+     (origin
-      (source
+       (method git-fetch)
-       (origin
+       (uri (git-reference
-         (method git-fetch)
+              (url "https://github.com/keller-mark/pizzarr")
-         (uri (git-reference
+              (commit (string-append "v" version))))
-               (url "https://github.com/keller-mark/pizzarr")
+       (file-name (git-file-name name version))
-               (commit commit)))
+       (sha256
-         (file-name (git-file-name name version))
+        (base32 "1m38c57pfliycxkhb3mwgh01cl2q76r1jhd3vnk07dbfhqdbqai6"))))
-         (sha256
+    (properties `((upstream-name . "pizzarr")))
-          (base32 "17pd6bk8kvnrvvyfqvm8q47kzghlfyfjdd9b7cwiazc5xr4vz6f0"))))
+    (build-system cargo-build-system)
-      (properties `((upstream-name . "pizzarr")))
+    (arguments
-      (build-system r-build-system)
+     (list
-      ;; Some tests require Internet access.
+      #:imported-modules
-      (arguments (list #:tests? #false))
+      (append %cargo-build-system-modules
-      (propagated-inputs (list r-jsonlite r-memoise r-qs r-r6 r-stringr))
+              %r-build-system-modules)
-      (native-inputs (list r-pbapply r-testthat r-vcr))
+      #:modules
-      (home-page "https://github.com/keller-mark/pizzarr")
+      '((guix build cargo-build-system)
-      (synopsis "Slice into Zarr arrays in R")
+        ((guix build r-build-system) #:prefix r:)
-      (description
+        (guix build utils))
-       "This package provides an implementation of chunked, compressed,
+      #:cargo-build-flags
      '(list "--target-dir=./target" "--release")
      #:phases
      #~(append (modify-phases %standard-phases
                  (add-after 'unpack 'patch-Makevars
                    (lambda _
                      ;; At this point we've already built the Rust parts.
                      (substitute* "src/Makevars.in"
                        (("^all:.*") "all:")
                        (("^\\$\\(STATLIB\\):") "NOBODYCARES:")
                        (("@PKG_LIBS_EXTRA@") "@PKG_LIBS_EXTRA@ -lzstd -lz"))))
                  (add-after 'patch-Makevars 'chdir
                    (lambda _ (chdir "src/rust")))
                  (add-after 'chdir 'patch-rust-dependency
                    (lambda _
                      (setenv "RUSTFLAGS" "--print=native-static-libs")
                      (substitute* "Cargo.toml"
                        (("extendr-api = \\{ git.* \\}") "extendr-api = \"0.8.1\""))))
                  (add-after 'package 'chdir-back
                    (lambda _ (chdir "../..")))
                  (delete 'install)
                  (delete 'check))
                (modify-phases (@ (guix build r-build-system) %standard-phases)
                  (delete 'unpack)
                  (replace 'patch-tests
                    (lambda* (#:key inputs outputs tests? #:allow-other-keys)
                      ((assoc-ref (@ (guix build r-build-system) %standard-phases)
                                  'patch-tests)
                       #:skipped-tests
                       ;; These files contain tests that require Internet access.
                       '("test-compat.R" "test-get.R"
                         ;; HttpStore requires the crul package
                         ("test-zarrs-dispatch.R" "can_use_zarrs_create returns FALSE for HttpStore")
                         ("test-zarrs-store-cache.R" "HttpStore get_store_identifier returns URL")))))
                  (replace 'check
                    (lambda* (#:key inputs outputs tests? #:allow-other-keys)
                      ((assoc-ref (@ (guix build r-build-system) %standard-phases)
                                  'check)
                       #:test-target "tests"
                       #:test-types #false
                       #:inputs inputs
                       #:outputs outputs
                       #:tests? tests?)))))))
    (propagated-inputs (list r-jsonlite r-memoise r-qs2 r-r6 r-stringr))
    (inputs
     (cons* openssl zlib `(,zstd "lib")
            (cargo-inputs 'r-pizzarr)))
    (native-inputs
     (list pkg-config
           r-minimal r-pbapply r-testthat r-vcr))
    (home-page "https://github.com/keller-mark/pizzarr")
    (synopsis "Slice into Zarr arrays in R")
    (description
     "This package provides an implementation of chunked, compressed,
 N-dimensional arrays for R, Zarr specification version 2 (2024)
 <doi:10.5281/zenodo.11320255>.")
-      (license license:expat))))
+    (license license:expat)))
 (define-public r-rhtslib12
  (let ((commit "ee186daf04876969c7f31c16a0e0fda8e7c16a30")
@@ -4572,8 +4625,11 @@ into separate processes; and more.")
     (list
      #:phases
      #~(modify-phases %standard-phases
-          (add-after 'unpack 'python3.11-compatibility
+          (add-after 'unpack 'python3.12-compatibility
            (lambda _
              ;; This was removed in Python 3.12
              (substitute* "Bio/Align/_aligners.c"
                (("case PyUnicode_WCHAR_KIND:") ""))
              ;; Py_TYPE was changed to an inline static function in Python
              ;; 3.11, so it cannot be used on the left-hand side.
              (substitute* "Bio/triemodule.c"
@@ -13990,33 +14046,20 @@ of scRNA-seq data.")
 (define-public r-misha
  (package
    (name "r-misha")
-    (version "4.1.0")
+    (version "5.6.23")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/tanaylab/misha")
-             (commit version)))
+             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "0bgivx3lzjh3173jsfrhb5kvhjsn53br0n4hmyx7i3dwy2cnnp2p"))
+         "1k973j04iq02dy4f7qgi3cmp3rcx5yinyx0m7vyag54rqanird8x"))))
       ;; Delete bundled executable.
       (snippet
        '(delete-file "exec/bigWigToWig"))))
    (build-system r-build-system)
-    (arguments
+    (propagated-inputs (list r-curl r-digest r-magrittr r-ps r-yaml))
-     `(#:phases
+    (native-inputs (list r-knitr r-testthat))
       (modify-phases %standard-phases
         (add-after 'unpack 'do-not-use-bundled-bigWigToWig
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "R/misha.R"
               (("get\\(\".GLIBDIR\"\\), \"/exec/bigWigToWig")
                (string-append "\""
                               (assoc-ref inputs "kentutils")
                               "/bin/bigWigToWig"))))))))
    (inputs
     (list kentutils))
    (home-page "https://github.com/tanaylab/misha")
    (synopsis "Toolkit for analysis of genomic data")
    (description "This package is intended to help users to efficiently
@@ -18816,26 +18859,28 @@ activity prediction from transcriptomics data, and its R implementation
      (build-system r-build-system)
      (arguments
       (list
        #:skipped-tests
        ;; These tests attempt to connect to the Internet.
        '(("test-liana_utils.R" "Test liana pipe")
          ("test-liana_tensor.R"
           ".*Test tensor wrapper.*"
           ".*Test decompose_tensor.*")
          ;; XXX: This test returns a data.frame instead of an error.
          ("test-liana_cytotalk.R" ".*Test Cytotalk Wrap.*"))
        #:phases
        '(modify-phases %standard-phases
           ;; This is needed to find ~/.config/OmnipathR/omnipathr.yml
           (add-after 'unpack 'set-HOME
             (lambda _ (setenv "HOME" "/tmp")))
-           (add-after 'unpack 'disable-bad-tests
+           (add-after 'unpack 'seurat-compatibility
             (lambda _
-               ;; These tests attempt to connect to the Internet.
+               ;; The `slot` argument of `GetAssayData()` was deprecated in
-               (substitute* "tests/testthat/test-liana_utils.R"
+               ;; SeuratObject 5.0.0.
-                 ((".*Test liana pipe.*" m)
+               (substitute* '("R/cellchat_pipe.R"
-                  (string-append m "skip('guix')\n")))
+                              "R/sca_pipe.R"
-               (substitute* "tests/testthat/test-liana_tensor.R"
+                              "R/liana_prep.R"
-                 ((".*Test tensor wrapper.*" m)
+                              "R/natmi_pipe.R")
-                  (string-append m "skip('guix')\n"))
+                 (("slot =") "layer =")))))))
                 ((".*Test decompose_tensor.*" m)
                  (string-append m "skip('guix')\n")))
               ;; XXX: This test returns a data.frame instead of an error.
               (substitute* "tests/testthat/test-liana_cytotalk.R"
                 ((".*Test Cytotalk Wrap.*" m)
                  (string-append m "skip('guix')\n"))))))))
      (propagated-inputs
       (list r-basilisk
             r-basilisk-utils
@@ -21700,70 +21745,6 @@ want to explore e.g.: the function of a set of differentially expressed
 genes.")
      (license license:gpl3))))
 (define-public r-seurat-utils
  (let ((commit "c0374cc9e25ce391ba8013fda0f8c7babbb9201d")
        (revision "1"))
    (package
      (name "r-seurat-utils")
      (version (git-version "2.5.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/vertesy/Seurat.utils")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "15l86b43q245gzz7gsr5rhs4sir74lc14d64yqxfqcb0zrb2bzzd"))))
      (properties `((upstream-name . "Seurat.utils")))
      (build-system r-build-system)
      (propagated-inputs (list r-codeandroll2
                               r-cowplot
                               r-databaselinke-r
                               r-dplyr
                               r-enhancedvolcano
                               r-foreach
                               r-ggcorrplot
                               r-ggexpress
                               r-ggplot2
                               r-ggpubr
                               r-ggrepel
                               r-hgnchelper
                               r-htmlwidgets
                               r-job
                               r-magrittr
                               r-markdownhelpers
                               r-markdownreports
                               r-matrix
                               r-matrixstats
                               r-pheatmap
                               r-plotly
                               r-princurve
                               r-qs
                               r-r-utils
                               r-readr
                               r-readwriter
                               r-reshape2
                               r-rstudioapi
                               r-scales
                               r-seurat
                               r-soupx
                               r-sparsematrixstats
                               r-stringendo
                               r-stringr
                               r-tibble
                               r-tictoc
                               r-tidyverse
                               r-vroom))
      (home-page "https://github.com/vertesy/Seurat.utils")
      (synopsis "Collection of utility functions for Seurat")
      (description
       "This is a collection of utility functions for Seurat.  These functions
 allow the automation and multiplexing of plotting, 3D plotting, visualization
 of statistics & QC, interaction with the Seurat object.  Some functionalities
 require functions from CodeAndRoll and MarkdownReports libraries.")
      (license license:gpl3))))
 (define-public r-seuratextend
  (let ((commit "5dacd7c1e1da3bc0e78ab81d60056f6d7da3d386")
        (revision "1"))
@@ -22478,38 +22459,39 @@ frames with arbitrary sets of columns.")
      (license license:expat))))
 (define-public r-imagearray
-  (let ((commit "2f90694fa33ed8320a6a2f7e0ad5c8a1796cbfc6")
+  (package
-        (revision "1"))
+    (name "r-imagearray")
-    (package
+    (version "1.0.0")
-      (name "r-imagearray")
+    (source
-      (version (git-version "0.99.6" revision commit))
+     (origin
-      (source
+       (method url-fetch)
-       (origin
+       (uri (bioconductor-uri "ImageArray" version))
-         (method git-fetch)
+       (sha256
-         (uri (git-reference
+        (base32 "07zq5fcw2dsvm4qaksaj4gy9gj5lxcgq82l497c5kgvl4wba049c"))))
-               (url "https://github.com/BIMSBbioinfo/ImageArray")
+    (properties `((upstream-name . "ImageArray")))
-               (commit commit)))
+    (build-system r-build-system)
-         (file-name (git-file-name name version))
+    (arguments
-         (sha256
+     (list
-          (base32 "1mf68b007dc5wdzdva4vkjgkavgagjk45qv05f7vahbpi24yjj4n"))))
+      #:skipped-tests
-      (properties `((upstream-name . "ImageArray")))
+      ;; RBiomFormats is not installed.
-      (build-system r-build-system)
+      '(("test-array.R" "check indexing \\(BFArray\\)"))))
-      (propagated-inputs (list r-delayedarray
+    (propagated-inputs (list r-delayedarray
-                               r-ebimage
+                             r-ebimage
-                               r-hdf5array
+                             r-hdf5array
-                               r-magick
+                             r-magick
-                               r-rarr
+                             r-rarr
-                               r-rhdf5
+                             r-rhdf5
-                               r-s4arrays
+                             r-s4arrays
-                               r-s4vectors))
+                             r-s4vectors
-      (native-inputs (list r-knitr r-testthat))
+                             r-zarrarray))
-      (home-page "https://github.com/BIMSBbioinfo/ImageArray")
+    (native-inputs (list r-ggplot2 r-knitr r-testthat))
-      (synopsis "Framework for on-disk and in-memory image arrays")
+    (home-page "https://github.com/BIMSBbioinfo/ImageArray")
-      (description
+    (synopsis "Framework for on-disk and in-memory image arrays")
-       "@code{ImageArray} provides a framework for on-disk and in-memory image
+    (description
-arrays, specifically for pyramidal images stored in either HDF5 files or Zarr
+     "@code{ImageArray} provides a framework for on-disk and in-memory image
-stores.")
+arrays, specifically for pyramidal images stored in HDF5, Zarr and life
-      (license license:expat))))
+sciences image file formats (OME Bio-Formats).")
    (license license:expat)))
 (define-public r-velocyto
  (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350")
@@ -22593,7 +22575,7 @@ dependencies of @code{VoltRon} package.")
 (define-public r-voltron
  (package
    (name "r-voltron")
-    (version "0.2.5")
+    (version "0.2.6")
    (source
     (origin
       (method git-fetch)
@@ -22602,7 +22584,7 @@ dependencies of @code{VoltRon} package.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "057n4yipkq3gnlyrb63l2ryi78nlmaas02avargm352g5ra1xl9s"))))
+        (base32 "00fl5dmyd9ad4hd0cblgi0415sf6q4q67wh04r7fws828vs5vaj1"))))
    (properties `((upstream-name . "VoltRon")))
    (build-system r-build-system)
    (arguments
@@ -22666,18 +22648,15 @@ guix_python <- \"~a\";"
                             r-irlba
                             r-magick
                             r-matrix
                             r-pizzarr
                             r-rann
                             r-rcdt
                             r-rcpp
                             r-rcppannoy
                             r-rcpparmadillo
                             r-reshape2
                             r-reticulate
                             r-rhdf5
                             r-rjson
                             r-rlang
                             r-s4arrays
                             r-s4vectors
                             r-shiny
                             r-shinyjs
                             r-sp
@@ -22730,8 +22709,8 @@ spots, cells and even molecules.")
    (license license:expat)))
 (define-public r-zarrdataframe
-  (let ((commit "84c7db2f6f5f84b4a4308f8eb72bedc131fb68bc")
+  (let ((commit "f5f671521934b2afc3c511f8c09181bc7bb789a4")
-        (revision "2"))
+        (revision "3"))
    (package
      (name "r-zarrdataframe")
      (version (git-version "0.0.0" revision commit))
@@ -22743,13 +22722,13 @@ spots, cells and even molecules.")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
-          (base32 "1idrvdlzbwyixlg830sn19vfdn3n3irmlyr4ncf7dpk72r08g3hw"))))
+          (base32 "0klp2njn6qsa8n6c01v1z2dfaa93lhbzhwhbyhl23h8gg7d28yc1"))))
      (properties
       '((upstream-name . "ZarrDataFrame")
         (updater-extra-native-inputs . ("r-testthat"))))
      (build-system r-build-system)
      (propagated-inputs (list r-biocgenerics r-delayedarray r-rarr
-                               r-s4vectors))
+                               r-s4vectors r-zarrarray))
      (native-inputs (list r-knitr r-testthat))
      (home-page "https://github.com/BIMSBbioinfo/ZarrDataFrame")
      (synopsis "Bioconductor-friendly Bindings for Zarr")
@@ -22761,39 +22740,35 @@ frames with arbitrary sets of columns.")
      (license license:expat))))
 (define-public r-zarrarray
-  (let ((commit "3cc3e6acf986074dfaece2ad23f9b56962054625")
+  (package
-        (revision "2"))
+    (name "r-zarrarray")
-    (package
+    (version "1.0.0")
-      (name "r-zarrarray")
+    (source
-      (version (git-version "1.0" revision commit))
+     (origin
-      (source
+       (method url-fetch)
-       (origin
+       (uri (bioconductor-uri "ZarrArray" version))
-         (method git-fetch)
+       (sha256
-         (uri (git-reference
+        (base32 "1ny91qg257kgb1hz2h4jvb0rna9cwyw7fqyj5axv52r3b98xn040"))))
-               (url "https://github.com/BIMSBbioinfo/ZarrArray")
+    (properties `((upstream-name . "ZarrArray")))
-               (commit commit)))
+    (build-system r-build-system)
-         (file-name (git-file-name name version))
+    (propagated-inputs (list r-biocgenerics
-         (sha256
+                             r-delayedarray
-          (base32 "1qjj92cpxpm3zh05vf60h5gmcn1qady0s38hibb0l57iwdhlhrb3"))))
+                             r-iranges
-      (properties
+                             r-rarr
-       '((upstream-name . "ZarrArray")
+                             r-s4arrays
-         (updater-extra-native-inputs . ("r-testthat"))))
+                             r-s4vectors
-      (build-system r-build-system)
+                             r-sparsearray))
-      ;; The tests seem to be outdated.
+    (native-inputs (list r-knitr r-testthat))
-      (arguments (list #:tests? #false))
+    (home-page "https://bioconductor.org/packages/ZarrArray")
-      (propagated-inputs (list r-biocgenerics
+    (synopsis "Bring Zarr datasets in R as DelayedArray objects")
-                               r-delayedarray
+    (description
-                               r-iranges
+     "The @code{ZarrArray} package leverages the Rarr package to bring Zarr
-                               r-matrix
+datasets in R as @code{DelayedArray} objects.  The main class in the package
-                               r-rarr
+is the @code{ZarrArray} class.  A @code{ZarrArray} object is an array-like
-                               r-s4arrays
+object that represents a Zarr dataset in R. @code{ZarrArray} objects are
-                               r-s4vectors
+@code{DelayedArray} derivatives and therefore support all operations (delayed
-                               r-sparsearray))
+or block-processed) supported by @code{DelayedArray} objects.")
-      (native-inputs (list r-testthat))
+    (license license:artistic2.0)))
      (home-page "https://github.com/BIMSBbioinfo/ZarrArray")
      (synopsis "Zarr backend for DelayedArray objects")
      (description "Zarr backend for @code{DelayedArray} objects.")
      (license license:expat))))
 (define-public methyldackel
  (package
@@ -24431,79 +24406,77 @@ It also handles cell type-specific differential expression.")
      (license license:gpl3))))
 (define-public r-spectre
-  (let ((commit "ff5314fd5b3f29121e52f948d91e222a19dd4d25")
+  (package
-        (revision "1"))
+    (name "r-spectre")
-    (package
+    (version "1.3.0")
-      (name "r-spectre")
+    (source
-      (version "1.2.0")
+     (origin
-      (source
+       (method git-fetch)
-       (origin
+       (uri (git-reference
-         (method git-fetch)
+              (url "https://github.com/ImmuneDynamics/Spectre")
-         (uri (git-reference
+              (commit (string-append "v" version))))
-               (url "https://github.com/ImmuneDynamics/Spectre")
+       (file-name (git-file-name name version))
-               (commit commit)))
+       (sha256
-         (file-name (git-file-name name version))
+        (base32
-         (sha256
+         "15g9w08x0pz2ia9qfalhcg3z5z2zx2085mfbr8gx9w5yxnw475ld"))))
-          (base32
+    (properties `((upstream-name . "Spectre")))
-           "0hziqlaq6mnkxi4bwp5xilxy90yh1vz1j1n117d38vmchvclx9yq"))))
+    (build-system r-build-system)
-      (properties `((upstream-name . "Spectre")))
+    (propagated-inputs
-      (build-system r-build-system)
+     (list r-biobase
-      (propagated-inputs
+           r-biocmanager
-       (list r-biobase
+           r-caret
-             r-biocmanager
+           r-class
-             r-caret
+           r-colorramps
-             r-class
+           r-data-table
-             r-colorramps
+           r-dendsort
-             r-data-table
+           r-devtools
-             r-dendsort
+           r-dplyr
-             r-devtools
+           r-exactextractr
-             r-dplyr
+           r-factoextra
-             r-exactextractr
+           r-flowcore
-             r-factoextra
+           r-flowsom
-             r-flowcore
+           r-flowviz
-             r-flowsom
+           r-fnn
-             r-flowviz
+           r-ggplot2
-             r-fnn
+           r-ggpointdensity
-             r-ggplot2
+           r-ggpubr
-             r-ggpointdensity
+           r-ggraph
-             r-ggpubr
+           r-ggthemes
-             r-ggraph
+           r-gridextra
-             r-ggthemes
+           r-gridextra
-             r-gridextra
+           r-gtools
-             r-gridextra
+           r-hdf5array
-             r-gtools
+           r-irlba
-             r-hdf5array
+           r-patchwork
-             r-irlba
+           r-pheatmap
-             r-patchwork
+           r-plyr
-             r-pheatmap
+           r-qs2
-             r-plyr
+           r-raster
-             r-qs
+           r-rcolorbrewer
-             r-raster
+           r-rhdf5
-             r-rcolorbrewer
+           r-rstudioapi
-             r-rhdf5
+           r-rsvd
-             r-rstudioapi
+           r-rtsne
-             r-rsvd
+           r-s2
-             r-rtsne
+           r-scales
-             r-s2
+           r-scattermore
-             r-scales
+           r-sf
-             r-scattermore
+           r-sp
-             r-sf
+           r-stars
-             r-sp
+           r-stringr
-             r-stars
+           r-tidygraph
-             r-stringr
+           r-tidyr
-             r-tidygraph
+           r-tidyr
-             r-tidyr
+           r-tiff
-             r-tidyr
+           r-umap
-             r-tiff
+           r-uwot))
-             r-umap
+    (home-page "https://github.com/ImmuneDynamics/Spectre")
-             r-uwot))
+    (synopsis "High-dimensional cytometry and imaging analysis")
-      (home-page "https://github.com/ImmuneDynamics/Spectre")
+    (description
-      (synopsis "High-dimensional cytometry and imaging analysis")
+     "This package provides a computational toolkit in R for the
      (description
       "This package provides a computational toolkit in R for the
 integration, exploration, and analysis of high-dimensional single-cell
 cytometry and imaging data.")
-      (license license:expat))))
+    (license license:expat)))
 (define-public r-compgenomrdata
  (let ((commit "24484cb77631e1123ead6c329b9d62c160e600c6")
@@ -48,6 +48,7 @@
  #:use-module (gnu packages base)
  #:use-module (gnu packages disk)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cdrom)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
@@ -65,7 +66,6 @@
  #:use-module (gnu packages man)
  #:use-module (gnu packages mtools)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages package-management)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
@@ -1815,63 +1815,68 @@ For more information, refer to
 (define-public os-prober
  (package
    (name "os-prober")
-    (version "1.81")
+    (version "1.84")
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "mirror://debian/pool/main/o/os-prober/os-prober_"
+       (uri (git-reference
-                           version ".tar.xz"))
+              (url "https://salsa.debian.org/installer-team/os-prober.git")
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "10w8jz6mqhp0skdcam9mpgv79vx1sv7lkpra3rqjg0jkhvn2in9g"))))
+        (base32 "1bji3w6nbqaz8zqrbmy8b1j5dph9xn7bdh1cd2z8ia1q125i6mgp"))))
    (build-system gnu-build-system)
    (arguments
-     `(#:modules ((guix build gnu-build-system)
+     (list
      #:tests? #f                       ; No tests.
      #:modules '((guix build gnu-build-system)
                  (guix build utils)
-                  (ice-9 regex)         ; for string-match
+                  (ice-9 regex)         ; string-match
-                  (srfi srfi-26))       ; for cut
+                  (srfi srfi-26))       ; cut
-       #:make-flags
+      #:make-flags
-       (list ,(string-append "CC=" (cc-for-target)))
+      #~(list (string-append "CC=" #$(cc-for-target)))
-       #:tests? #f                      ; no tests
+      #:phases
-       #:phases
+      #~(modify-phases %standard-phases
-       (modify-phases %standard-phases
+          (replace 'configure
-         (replace 'configure
+            (lambda _
-           (lambda* (#:key outputs #:allow-other-keys)
+              (substitute* (find-files ".")
-             (substitute* (find-files ".")
+                (("/usr") #$output))
-               (("/usr") (assoc-ref outputs "out")))
+              (substitute* (find-files "." "50mounted-tests$")
-             (substitute* (find-files "." "50mounted-tests$")
+                (("mkdir") "mkdir -p -v"))))
-               (("mkdir") "mkdir -p"))))
+          (replace 'install
-         (replace 'install
+            (lambda _
-           (lambda* (#:key outputs #:allow-other-keys)
+              (define (find-files-non-recursive directory)
-             (define (find-files-non-recursive directory)
+                (find-files directory
-               (find-files directory
+                            (lambda (file stat)
-                           (lambda (file stat)
+                              (string-match (string-append "^" directory "/[^/]*$")
-                             (string-match (string-append "^" directory "/[^/]*$")
+                                            file))
-                                           file))
+                            #:directories? #t))
                           #:directories? #t))
-             (let* ((out (assoc-ref outputs "out"))
+              (let ((bin (string-append #$output "/bin"))
-                    (bin (string-append out "/bin"))
+                     (lib (string-append #$output "/lib"))
-                    (lib (string-append out "/lib"))
+                     (share (string-append #$output "/share")))
-                    (share (string-append out "/share")))
+                (for-each (cut install-file <> bin)
-               (for-each (cut install-file <> bin)
+                          (list "linux-boot-prober" "os-prober"))
-                         (list "linux-boot-prober" "os-prober"))
+                (install-file "newns" (string-append lib "/os-prober"))
-               (install-file "newns" (string-append lib "/os-prober"))
+                (install-file "common.sh" (string-append share "/os-prober"))
-               (install-file "common.sh" (string-append share "/os-prober"))
+                (install-file "os-probes/mounted/powerpc/20macosx"
-               (install-file "os-probes/mounted/powerpc/20macosx"
+                              (string-append lib "/os-probes/mounted"))
-                             (string-append lib "/os-probes/mounted"))
+                (for-each
-               (for-each
+                 (lambda (directory)
-                (lambda (directory)
+                   (for-each
-                  (for-each
+                    (lambda (file)
-                   (lambda (file)
+                      (let ((destination (string-append lib "/" directory
-                     (let ((destination (string-append lib "/" directory
+                                                        "/" (basename file))))
-                                                       "/" (basename file))))
+                        (mkdir-p (dirname destination))
-                       (mkdir-p (dirname destination))
+                        (copy-recursively file destination)))
-                       (copy-recursively file destination)))
+                    (append (find-files-non-recursive (string-append directory "/common"))
-                   (append (find-files-non-recursive (string-append directory "/common"))
+                            (find-files-non-recursive (string-append directory "/x86")))))
-                           (find-files-non-recursive (string-append directory "/x86")))))
+                 (list "linux-boot-probes"
-                (list "os-probes" "os-probes/mounted" "os-probes/init"
+                       "linux-boot-probes/mounted"
-                      "linux-boot-probes" "linux-boot-probes/mounted"))))))))
+                       "os-probes"
-    (home-page "https://joeyh.name/code/os-prober")
+                       "os-probes/init"
                       "os-probes/mounted"))))))))
    (home-page "https://joeyh.name/code/os-prober/")
    (synopsis "Detect other operating systems")
    (description "os-prober probes disks on the system for other operating
 systems so that they can be added to the bootloader.  It also works out how to
@@ -64,7 +64,6 @@
  #:use-module (gnu packages logging)
  #:use-module (gnu packages lua)
  #:use-module (gnu packages man)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages package-management)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages perl)
@@ -77,6 +76,7 @@
  #:use-module (gnu packages python-crypto)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages re2c)
  #:use-module (gnu packages regex)
  #:use-module (gnu packages rpc)
  #:use-module (gnu packages serialization)
@@ -104,7 +104,8 @@
  #:use-module (guix packages)
  #:use-module (guix search-paths)
  #:use-module (guix utils)
-  #:use-module (ice-9 optargs))
+  #:use-module (ice-9 optargs)
  #:use-module (srfi srfi-1))
 (define-public acr
  (package
@@ -1483,3 +1484,114 @@ Features:
@item Support for languages outside C/C++ (e.g. Go, Rust, Zig).
@end itemize")
   (license license:asl2.0)))
 (define-public ninja/pinned
  (hidden-package
   (package
     (name "ninja")
     (version "1.13.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/ninja-build/ninja")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
                 "0lp9dmxbjyjwv089i8mgq3nvnhpbnsn01ifm05m9s47w7cifrl8g"))))
     (build-system gnu-build-system)
     (inputs (list python-wrapper re2c))
     (arguments
      '(; Tests now require googletest, which is a circular dependency.
        #:tests? #f
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
            (lambda _
              (substitute* "src/subprocess-posix.cc"
                (("/bin/sh") (which "sh")))
              (substitute* "src/subprocess_test.cc"
                (("/bin/echo") (which "echo")))))
          (replace 'build
            (lambda _
              (invoke "./configure.py" "--bootstrap")))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
                (invoke "./configure.py")
                (invoke "./ninja" "ninja_test")
                (invoke "./ninja_test"))))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin"))
                     (doc (string-append out "/share/doc/ninja")))
                (install-file "ninja" bin)
                (install-file "doc/manual.asciidoc" doc)))))))
     (home-page "https://ninja-build.org/")
     (synopsis "Small build system")
     (description
      "Ninja is a small build system with a focus on speed.  It differs from
 other build systems in two major respects: it is designed to have its input
 files generated by a higher-level build system, and it is designed to run
 builds as fast as possible.")
    (license license:asl2.0))))
 (define-public ninja
  (package/inherit ninja/pinned
    (properties (alist-delete 'hidden? (package-properties ninja/pinned)))))
 (define-public samurai
  (package
    (name "samurai")
    (version "1.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/michaelforney/samurai")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "04iw18hgkm72yrl83a2xh1jc47w9rilpb95kwick0j37b4q3gxj4"))))
    (build-system gnu-build-system)
    (arguments
     (list #:tests? #f                  ;no test suite
           #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
                                (string-append "PREFIX=" #$output))
           #:phases #~(modify-phases %standard-phases
                        (add-after 'unpack 'patch-/bin/sh
                          (lambda* (#:key inputs #:allow-other-keys)
                            (substitute* "build.c"
                              (("/bin/sh")
                               (search-input-file inputs "bin/sh")))))
                        (delete 'configure))))
    (inputs (list bash-minimal))
    (home-page "https://github.com/michaelforney/samurai")
    (synopsis "Ninja-compatible build tool written in C")
    (description "@code{samurai} is a ninja-compatible build tool written in
 C99 with a focus on simplicity, speed, and portability.  It is
 feature-complete and supports most of the same options as ninja.  This package
 provides the command @command{samu}.  For a @command{ninja} command
 replacement, use the @code{samu-as-ninja-wrapper} package.")
    (license (list license:asl2.0               ;for the most part
                   license:expat))))            ;htab.h, htab.c and tree.c
 (define-public samu-as-ninja-wrapper
  (package/inherit samurai
    (name "samu-as-ninja-wrapper")
    (build-system trivial-build-system)
    (arguments
     (list #:builder
           (with-imported-modules '((guix build utils))
             #~(begin
                 (use-modules (guix build utils))
                 (let ((bindir (string-append #$output "/bin"))
                       (samu (string-append #$(this-package-input "samurai")
                                            "/bin/samu")))
                   (mkdir-p bindir)
                   (symlink samu (string-append bindir "/ninja")))))))
    (inputs (list samurai))
    (description "This package provides the @command{ninja} command,
 implemented as a symbolic link to the @command{samu} command of @code{samurai}
 package.")))
@@ -302,7 +302,7 @@ will name the threaded machine type unless THREADS? is provided as #f."
    (name "chez-scheme-for-racket")
    ;; The version should match `(scheme-version #t)`.
    ;; See s/cmacros.ss c. line 360.
-    (version "10.3.0-pre-release.2") ; expect a chez-nanopass-bootstrap update
+    (version "10.4.0-pre-release.1-1") ; expect a chez-nanopass-bootstrap update
    (source #f)
    (build-system gnu-build-system)
    (inputs `(,@(if (nix-system->native-chez-machine-type)
@@ -507,7 +507,7 @@ version of Chez Scheme.")
    (name "chez-scheme")
    ;; The version should match `(scheme-version-number #t)`.
    ;; See s/cmacros.ss c. line 360.
-    (version "10.2.0") ; expect a chez-nanopass-bootstrap update
+    (version "10.4.0") ; expect a chez-nanopass-bootstrap update
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -515,7 +515,7 @@ version of Chez Scheme.")
                    (commit (string-append "v" version))))
              (sha256
               (base32
-                "14iv4kfkyvrkigr1n2prf71n2l3vs0sf0549rvh6y4x2faa2l329"))
+                "079vlkl27qdvsg1rsynmd828m42n98c2dnldkhsxf2slfsqd9kv5"))
              (file-name (git-file-name name version))
              (patches (search-patches "chez-scheme-bin-sh.patch"))
              (snippet #~(begin
@@ -840,9 +840,9 @@ User's Guix}, among other documents.")
 (define-public chez-nanopass-bootstrap
  (hidden-package
   (package
-     (name "chez-nanopass")
+     (name "chez-nanopass-bootstrap")
-     (version "1.9.2")
+     (version "1.9.4")
-     (properties `((chez-nanopass-release-date . "October 18, 2020")))
+     (properties '((chez-nanopass-release-date . "December 29, 2025")))
     (source
      (origin
        (method git-fetch)
@@ -850,7 +850,7 @@ User's Guix}, among other documents.")
              (url "https://github.com/nanopass/nanopass-framework-scheme")
              (commit (string-append "v" version))))
        (sha256
-         (base32 "16vjsik9rrzbabbhbxbaha51ppi3f9n8rk59pc6zdyffs0vziy4i"))
+         (base32 "1qq0vnbrvcialgjgnblfq3qp1ilqg94h0kg896ksd9v4g7ipj9v0"))
        (file-name (git-file-name "nanopass-framework-scheme" version))
        (snippet
         #~(begin
@@ -929,10 +929,9 @@ create compilers, making them easier to understand and maintain.")
 (define-public chez-nanopass
  (package
    (inherit chez-nanopass-bootstrap)
-    ;; This release has a significant bug fix.  Expect the next releases of
+    (name "chez-nanopass")
-    ;; chez-scheme{,-for-racket} to want this for chez-nanopass-bootstrap.
+    (version "1.9.4")
-    (version "1.9.3")
+    (properties '((chez-nanopass-release-date . "December 29, 2025")))
    (properties '((chez-nanopass-release-date . "August 24, 2025")))
    (source
     (let ((bootstrap-origin (package-source chez-nanopass-bootstrap)))
       (origin
@@ -941,7 +940,7 @@ create compilers, making them easier to understand and maintain.")
                (url (git-reference-url (origin-uri bootstrap-origin)))
                (commit (string-append "v" version))))
         (sha256
-          (base32 "0757x3a3b4kcd3jk52h4ikqzv7cc1mvphlw592f0r5pz99bkxiin"))
+          (base32 "1qq0vnbrvcialgjgnblfq3qp1ilqg94h0kg896ksd9v4g7ipj9v0"))
         (file-name (git-file-name "nanopass-framework-scheme" version)))))
    (native-inputs (list chez-scheme stex))))
@@ -53,7 +53,6 @@
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages kerberos)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages node)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages pciutils)
@@ -1475,7 +1475,7 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
 (define-public 7zip
  (package
    (name "7zip")
-    (version "26.00")
+    (version "26.01")
    (source
     (origin
       (method git-fetch)
@@ -1483,7 +1483,7 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
              (url "https://github.com/ip7z/7zip")
              (commit version)))
       (sha256
-        (base32 "1fvgl9qp2pl5c0jmvgbdx6qig3qd80mhxvml42yby8y412x65sh7"))
+        (base32 "0qwzn9pz1m6f8q20cqgmfqp1qx6s7959xnyikpr60n1v8c1mj98q"))
       (file-name (git-file-name name version))
       (modules '((guix build utils)
                  (ice-9 regex)))
@@ -127,6 +127,76 @@ formats:
 It also comes with example files generated by bincfg.")
    (license license:gpl3+)))
 (define-public bucts
  (package
    (name "bucts")
    (version %coreboot-version)
    (source %coreboot-origin)
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f ;no tests
      #:make-flags #~(list (string-append "CC=" #$(cc-for-target)))
      #:phases #~(modify-phases %standard-phases
                   (delete 'configure) ;no configure script
                   (add-after 'unpack 'enter-source
                     (lambda _
                       (chdir "util/bucts")))
                   (add-after 'enter-source 'set-version
                     (lambda _
                       (substitute* "Makefile"
                         (("^VERSION:=*")
                          #$(string-append "VERSION:=" version)))))
                   ;; no install target
                   (replace 'install
                     (lambda _
                       (let ((bin (string-append #$output "/bin"))
                             (doc (string-append #$output "/share/doc/bucts/"))
                             (licenses (string-append #$output
                                        "/share/licenses/bucts/")))
                         (install-file "bucts" bin)
                         (install-file "readme.md" doc)
                         (install-file "../../COPYING" licenses)))))))
    (inputs (list pciutils))
    (home-page "https://coreboot.org")
    (synopsis "Tool to swap the BIOS bootblock and backup bootblock on the
 Intel I945 chipsets")
    (description
     "The @command{bucts} command can flip a bit in the BUC.TS register of the
 Intel I945 chipsets and show the register status.  When the bit is set, it
 swaps the bootblock location.  Because the bootblock region is often set
 read-only by the default BIOS, this enables to bypass that restriction and is
 used as part of a procedure to replace the nonfree BIOS with free software on
 various computers (Lenovo X60, X60s, X60T, T60, probably more).")
    (license license:gpl2)))
 (define-public ectool
  (package
    (name "ectool")
    (version %coreboot-version)
    (source %coreboot-origin)
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f ; no test suite
      #:make-flags
      #~(list (string-append "CC=" #$(cc-for-target))
              "INSTALL=install"
              (string-append "PREFIX=" #$output))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'chdir
            (lambda _
              (chdir "util/ectool")))
          (delete 'configure)))) ; no configure script
    (home-page "https://doc.coreboot.org/util.html")
    (synopsis "Tool to dump and modify @acronym{EC, Embedded Controller} RAM
 on computers such as laptops")
    (description "This package provides @command{ectool}, a program to dump
 and modify the contents of @acronym{EC, Embedded Controller} RAM
 on mobile computers.")
    (license license:gpl2)))
 (define-public ifdtool
  (package
    (name "ifdtool")
@@ -5645,7 +5645,7 @@ with integrated support for finding required rows quickly.")
 (define-public apache-arrow
  (package
    (name "apache-arrow")
-    (version "23.0.1")
+    (version "24.0.0")
    (source
     (origin
       (method git-fetch)
@@ -5655,7 +5655,7 @@ with integrated support for finding required rows quickly.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "1qn7wgavi3kiz4d6w1naqj5631bg87fnj6gbhaxmpmynm5hi9wm7"))))
+         "1j3gs5ffa9gx2y2nggmi2zn5rj0bsnjnxrzfnipx6050jz6n8dx9"))))
    (build-system cmake-build-system)
    (arguments
     (list
@@ -5823,6 +5823,8 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
           pkg-config
           python-cython
           python-pytest
           python-pytest-runner
           python-scikit-build-core
           python-setuptools-scm
           python-setuptools))
    (outputs '("out"))
@@ -77,7 +77,6 @@
  #:use-module (gnu packages mail)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages pretty-print)
@@ -105,7 +105,6 @@
  #:use-module (gnu packages libbsd)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages perl-web)
@@ -105,7 +105,7 @@ prefixing to determine WebSocket endpoints versus HTTP endpoints.")
 (define-public python-channels
  (package
    (name "python-channels")
-    (version "4.2.2")
+    (version "4.3.2")
    (source
     (origin
       (method git-fetch) ; no tests in PyPI
@@ -114,8 +114,14 @@ prefixing to determine WebSocket endpoints versus HTTP endpoints.")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0x7w29qpj2acrzf8hcgymsyr5gk3aj2wkbvlwcr01ygd6as8h7hz"))))
+        (base32 "0lxq5l0729ms4xzbn1rq968qpi7ipa9aj1wjvzrpdxd3mmlg2618"))))
    (build-system pyproject-build-system)
    (arguments
     '(#:phases
       (modify-phases %standard-phases
         (add-before 'check 'delete-selenium-tests
           (lambda* _
             (delete-file "tests/sample_project/tests/test_selenium.py"))))))
    (propagated-inputs (list python-asgiref python-django))
    ;; Channels develops and maintains Daphne but any other ASGI server can be
    ;; used, so keep it in native-inputs for tests.
@@ -200,13 +206,13 @@ your project into different processes.")
 (define-public python-django
  (package
    (name "python-django")
-    (version "5.2.13")
+    (version "6.0.5")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "django" version))
       (sha256
-        (base32 "1i1vlffzhwbzp6r6y8ycvwklc45diy4c6i897z379l48a7dqj5d3"))))
+        (base32 "0saj5w1pmfl2bf6smmbx2h8v6b9n9djdsbp46v468a4ax5r6hvdw"))))
    (build-system pyproject-build-system)
    (arguments
     '(#:test-flags
@@ -374,28 +380,27 @@ and adapters that are useful for non-trivial configuration scenarios.")
 (define-public python-django-extensions
  (package
    (name "python-django-extensions")
-    (version "4.1")
+    (properties '((commit . "32ddfb0499bec7f39f9fbb44568d2781cecd1f32")
                  (revision . "0")))
    (version (git-version "4.1"
                          (assoc-ref properties 'revision)
                          (assoc-ref properties 'commit)))
    (source
     (origin
       (method git-fetch)
       ;; Fetch from the git repository, so that the tests can be run.
       (uri (git-reference
             (url "https://github.com/django-extensions/django-extensions")
-             (commit version)))
+             (commit (assoc-ref properties 'commit))))
       (file-name (string-append name "-" version))
       (sha256
-        (base32 "1qayan9za7ylvzkwp6p0l0735gavnzd1kdjsfc178smq6xnby0ss"))))
+        (base32 "09gk82rsmqgaz4pqk0xvb4mgfprls8h1wm24p74d0ykdi7li2plg"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      ;; The 5 tests in test_dumbscript.py fail (OperationalError).
      #:test-flags
-      #~(list "--ignore" "tests/test_dumpscript.py"
+      #~(list "--ignore" "tests/test_dumpscript.py")))
              "-k" (string-append
                    ;; These fail for unknown reasons.
                    "not test_do_export_emails_format_vcard_start"
                    " and not test_initialize_runserver_plus"
                    " and not test_should_highlight_python_syntax_with_name"))))
    (propagated-inputs
     (list python-django))
    (native-inputs
@@ -406,6 +411,8 @@ and adapters that are useful for non-trivial configuration scenarios.")
           python-pytest-django
           python-setuptools
           python-shortuuid
           python-vobject
           python-werkzeug
           tzdata-for-tests))
    (home-page "https://github.com/django-extensions/django-extensions")
    (synopsis "Custom management extensions for Django")
@@ -41,6 +41,7 @@
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages curl)
@@ -48,7 +49,6 @@
  #:use-module (gnu packages gdb)
  #:use-module (gnu packages libedit)
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
@@ -1425,7 +1425,7 @@ and TCP-capable recursive DNS server for finding domains on the internet.")
 (define-public openresolv
  (package
    (name "openresolv")
-    (version "3.17.4")
+    (version "3.13.2")
    (source
     (origin
       (method git-fetch)
@@ -1435,7 +1435,7 @@ and TCP-capable recursive DNS server for finding domains on the internet.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "1lawj50qhr2yj7fy3p8x4m3kqz4lbvghnjc4jlqnxp484hg83ki3"))
+         "03m8n0j0kxxm5kpl66gz4lxr1qqgrp8zlkaq9j8fz27fih0g75xf"))
       (patches
        (search-patches "openresolv-restartcmd-guix.patch"))))
    (build-system gnu-build-system)
@@ -1314,7 +1314,7 @@ package.")
       #:tests? #f)) ;no test suite
    (native-inputs (list asciidoc
                         gettext-minimal
-                         git-minimal
+                         git-minimal/pinned
                         perl
                         perl-unicode-linebreak
                         perl-yaml-tiny
@@ -2521,7 +2521,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
 (define-public nvc
  (package
    (name "nvc")
-    (version "1.20.1")
+    (version "1.21.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -2530,7 +2530,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1b38x2ch468s4p6mrq6c8s0d95vb84p6w4v8in79l4w7sfy8jnr0"))))
+                "00hnrzk9dw88srfmjxxb9xkgnd5n26pmqlcw1bff1y0bckblsr38"))))
    (build-system gnu-build-system)
    (arguments
     (list #:out-of-source? #t
@@ -15526,34 +15526,6 @@ underlying library functionality for performing various activities related to
 the game of chess.")
    (license license:gpl3+)))
 (define-public emacs-4clojure
  ;; There is no release.  Base version is extracted from Version keyword in
  ;; the main file.
  (let ((commit "4eccf8c7d4341a36c269451838114b27836699f9")
        (revision "1"))
    (package
      (name "emacs-4clojure")
      (version (git-version "0.2.1" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/emacsorphanage/4clojure")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "19x653lzc1dxil4ix257hciidbdmbhaxhs6qhlkwi9ygjrlrgvnk"))))
      (build-system emacs-build-system)
      (propagated-inputs
       (list emacs-request))
      (home-page "https://github.com/emacsorphanage/4clojure/")
      (synopsis "Open and evaluate 4clojure questions in Emacs")
      (description "Emacs 4clojure interacts with
@url{http://www.4clojure.com, 4clojure} problems.  You can open a specific
 question and move to the next or previous one.  You can also verify your
 answers.")
      (license license:gpl3+))))
 (define-public emacs-base16-theme
  (package
    (name "emacs-base16-theme")
@@ -23859,8 +23831,8 @@ actually changing the buffer's text.")
 (define-public emacs-diff-hl
  ;; No new tags or releases since 2024.
-  (let ((commit "e79aa49ad3cbbe85379cf6646db3aaacd3b04708")
+  (let ((commit "7d873b2f58908de1ea2f499da9bf993e088953d7")
-        (revision "0"))
+        (revision "1"))
    (package
      (name "emacs-diff-hl")
      (version (git-version "1.10.0" revision commit))
@@ -23872,7 +23844,7 @@ actually changing the buffer's text.")
                (commit commit)))
         (file-name (git-file-name name version))
         (sha256
-          (base32 "0fvxngcbx36vqj72fllfp5iqwihcqd1dfhmqr3m1284191q83na3"))))
+          (base32 "15a9cjlpjsfcb2hxqbb123389qhiqs06mn01pas2l0jqhc2p86v9"))))
      (build-system emacs-build-system)
      (arguments
       (list
@@ -23895,7 +23867,7 @@ actually changing the buffer's text.")
                (invoke "git" "init")
                (invoke "git" "add" ".")
                (invoke "git" "commit" "-m" "Commit all."))))))
-      (native-inputs (list git-minimal))
+      (native-inputs (list git-minimal/pinned))
      (home-page "https://github.com/dgutov/diff-hl")
      (synopsis "Highlight uncommitted changes using VC")
      (description
@@ -68,6 +68,7 @@
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cdrom)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cmake)
@@ -107,7 +108,6 @@
  #:use-module (gnu packages music)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages parallel)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages pretty-print)
@@ -129,7 +129,6 @@
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pdf)
@@ -74,6 +74,7 @@
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2026 Joan Vilardaga Castro <codeberg-hn80@joanvc.cat>
 ;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
 ;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2817,6 +2818,32 @@ family.")
 (define-deprecated-package font-adobe-source-serif-pro
  font-adobe-source-serif)
 (define-public font-medieval-sharp
  ;; No releases, use newest commit.
  (let ((commit "ee7510b6b13854fd340e7d2e44c218780f672cd1")
        (revision "1"))
    (package
      (name "font-medieval-sharp")
      ;; From FONTLOG.txt.
      (version (git-version "3.1.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
                (url "https://github.com/wmk69/Medieval-Sharp")
                (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "1r300591pra4nxpm5kppl5q3ihsp01wk2zh24f9pvv0jgf1ik87x"))))
      (build-system font-build-system)
      (home-page "https://github.com/wmk69/Medieval-Sharp")
      (synopsis "Font based on gothic letters")
      (description
       "Medieval Sharp is a font created for inscriptions on stone, based on
 gothic letters.")
      (license license:silofl1.1))))
 (define-public font-microsoft-cascadia
  (package
    (name "font-microsoft-cascadia")
@@ -4260,7 +4287,7 @@ typographical palette.")
 (define-public font-mona-sans
  (package
    (name "font-mona-sans")
-    (version "2.0.26")
+    (version "2.0.27")
    (source
     (origin
       (method git-fetch)
@@ -4270,7 +4297,7 @@ typographical palette.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "09b6apxq659y4dkkm5swy683q6hviibv1cd48ragm5rd1376hsaz"))))
+         "10xbs857d21zrfx0cpzcsyyk76j921qq68qpz5r2kl4jr3gz541z"))))
    (build-system font-build-system)
    (outputs '("out" "ttf" "woff"))
    (home-page "https://github.com/mona-sans")
@@ -47,6 +47,7 @@
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages datastructures)
@@ -69,7 +70,6 @@
  #:use-module (gnu packages linux)
  #:use-module (gnu packages man)
  #:use-module (gnu packages mc)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
@@ -98,6 +98,7 @@
 ;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2026 Nikita Alkhovik <forgoty13@gmail.com>
 ;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -200,7 +201,6 @@
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages netpbm)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages oneapi)
  #:use-module (gnu packages opencl)
@@ -3988,27 +3988,26 @@ that beneath its ruins lay buried an ancient evil.")
        (base32 "0hgzdvlh0j42w4q9kch9xvhnbvcrypac01xhpksw35gj9my887cp"))
       (modules '((guix build utils)))
       (snippet
        ;; So, some of the sounds/graphics/tilesets are under different
        ;; licenses... some of them even nonfree!  This is a console-only
        ;; version of this package so we just remove them.
        ;; In the future, if someone tries to make a graphical variant of
        ;; this package, they can deal with that mess themselves. :)
        '(begin
-           (for-each (lambda (subdir)
+           (for-each delete-file-recursively
-                       (let ((lib-subdir (string-append "lib/" subdir)))
+                     '("lib/tiles/shockbolt" ;nonfree
-                         (delete-file-recursively lib-subdir)))
+                       "src/win"))      ;contains .dlls!
-                     '("fonts" "icons" "sounds" "tiles"))
+           ;; Don't build the shockbolt directory either.
-           (substitute* "lib/Makefile"
+           (substitute* "lib/tiles/Makefile"
-             ;; And don't try to invoke makefiles in the directories we removed.
+             (("shockbolt") ""))))
-             (("gamedata customize help screens fonts tiles sounds icons user")
+       (patches (search-patches "angband-remove-nonfree-tile-options.patch"))))
              "gamedata customize help screens user"))
           ;; Remove nonfree .dll files too.
           (delete-file-recursively "src/win")))))
    (build-system gnu-build-system)
    (arguments
-     `(#:configure-flags (list (string-append "--bindir=" %output "/bin"))
+     `(#:configure-flags (list (string-append "--bindir=" %output "/bin")
                               "--disable-x11")
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'disable-graphics-and-sounds
           (lambda _
             (substitute* "lib/Makefile"
               ;; Do not build any graphics for this version.
               (("gamedata customize help screens fonts tiles sounds icons user")
                "gamedata customize help screens user"))))
         (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
@@ -4058,6 +4057,59 @@ the depths below Angband, seeking riches, fighting monsters, and preparing to
 fight Morgoth, the Lord of Darkness.")
    (license license:gpl2)))
 (define-public angband-sdl2
  (package
    (inherit angband)
    (name "angband-sdl2")
    (arguments
     (substitute-keyword-arguments
         (package-arguments angband)
       ((#:configure-flags flags)
        #~(cons* "--enable-sdl2" #$flags))
       ((#:phases phases)
        #~(modify-phases #$phases
            (delete 'disable-graphics-and-sounds)
            (add-after 'unpack 'patch-sdl-wrapper-headers
              (lambda _
                (with-directory-excursion "src"
                  (substitute* '("snd-sdl.c"
                                 "main-sdl2.c"
                                 "sdl2/pui-win.h")
                    (("\"SDL_image.h\"") "\"SDL2/SDL_image.h\"")
                    (("\"SDL_mixer.h\"") "\"SDL2/SDL_mixer.h\"")
                    (("\"SDL_ttf.h\"") "\"SDL2/SDL_ttf.h\"")))))
            (add-after 'unpack 'patch-desktop-file
              (lambda* (#:key outputs #:allow-other-keys)
                 (let ((out (assoc-ref outputs "out")))
                   (substitute* "lib/icons/angband-sdl2.desktop"
                     (("Exec=angband" _)
                      (string-append "Exec=" #$output "/bin/angband-sdl2"))))))
            (add-after 'install 'rename-binary
              (lambda _
                (with-directory-excursion #$output
                  ;; allows parallel installation with angband
                  (rename-file "bin/angband"
                               "bin/angband-sdl2"))))))))
    (inputs
     (modify-inputs inputs
       (prepend sdl2
                sdl2-image
                sdl2-mixer
                sdl2-ttf)))
    (description "Angband is a Classic dungeon exploration roguelike.  Explore
 the depths below Angband, seeking riches, fighting monsters, and preparing to
 fight Morgoth, the Lord of Darkness.
 This version includes the SDL2 frontend, providing tilesets and sounds which
 can be enabled through in-game options.")
    ;; XXX: fonts and adam bolt tileset are free but being clarified:
    ;; https://github.com/angband/angband/issues/6608
    ;; For the rest, see:
    ;; https://github.com/angband/angband/blob/master/docs/copying.rst
    (license (list license:gpl2            ;code, nomad+old tilesets
                   license:cc-by-sa3.0     ;david gervais tileset
                   license:cc-by-sa4.0)))) ;sounds
 (define-public pingus
  ;; Latest release is from 2021-12-24.
  (let ((commit "7d65221e1cd1026053c8a5a08ad911fbdd13d3ed")
@@ -80,14 +80,14 @@
 (define-public gdb-17
  (package
    (name "gdb")
-    (version "17.1")
+    (version "17.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/gdb/gdb-"
                                  version ".tar.xz"))
              (sha256
               (base32
-                "0xnqqv3j463r5rnfmblj3zwhf0l0lyy4bp1zaid8zxn9fignz68l"))))
+                "1312lccryan1jfkjwkbw9mpxgyfnmlr8dj4lbkxx3cz4f86nq0qw"))))
    (build-system gnu-build-system)
    (outputs '("out" "debug"))
    (arguments
@@ -128,7 +128,6 @@
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages pdf)
  #:use-module (gnu packages perl)
@@ -2529,7 +2529,7 @@ forgotten when the session ends.")
 (define-public evince
  (package
    (name "evince")
-    (version "48.1")
+    (version "48.4")
    (source
     (origin
       (method url-fetch)
@@ -2537,7 +2537,7 @@ forgotten when the session ends.")
                           (version-major version) "/"
                           "evince-" version ".tar.xz"))
       (sha256
-        (base32 "047s8d4qh9jijk1kp4kfzy4afwwcd0kr11a8j1dkypd0ldprm2vx"))))
+        (base32 "0s46prlb55ghnz136ra8whmrirydmz08lzjrrpa3arl8cb3cb5pj"))))
    (build-system meson-build-system)
    (arguments
     `(#:glib-or-gtk? #t
@@ -2,8 +2,9 @@
 ;;; Copyright © 2023 JOULAUD François <Francois.JOULAUD@radiofrance.com>
 ;;; Copyright © 2025 Maxim Cournoyer <maxim@guixotic.coop>
 ;;; Copyright © 2025 Tomas Volf <~@wolfsden.cz>
-;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2025-2026 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2025 jgart <jgart@dismail.de>
 ;;; Copyright © 2026 Ankit Gadiya <git@argp.in>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -48,7 +49,7 @@
 (define-public go-chroma
  (package
    (name "go-chroma")
-    (version "2.20.0")
+    (version "2.24.1")
    (source
     (origin
       (method git-fetch)
@@ -57,7 +58,7 @@
              (commit (string-append "v" version ))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "05w4hnfcxqdlsz7mkc0m3jbp1aj67wzyhq5jh8ldfgnyjnlafia3"))))
+        (base32 "0kww0yhwqzzgl8n3alislf0136rk7kh507bbvr32a30wmk5dzi81"))))
    (build-system go-build-system)
    (arguments
     (list
@@ -83,17 +84,16 @@ translators for Pygments lexers and styles.")
 (define-public go-fxlint
  (package
    (name "go-fxlint")
-    (version "0.0.0-20251227140935-d5da5b04ac90")
+    (version "1.24.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/uber-go/fx")
-              (commit (go-version->git-ref version
+              (commit (string-append "v" version ))))
                                           #:subdir "tools"))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0yw9x95v82dcxh0zf13inz8c3q7p2hmzqzgja360b1yifi01rvrc"))))
+        (base32 "0iifq4gjd873l444qh32x2zzsz2yinrvpjsdfphxsfk1h0cyk4q9"))))
    (build-system go-build-system)
    (arguments
     (list
@@ -115,7 +115,7 @@ that handle none of the event types.")
 (define-public go-jsonnet
  (package
    (name "go-jsonnet")
-    (version "0.21.0")
+    (version "0.22.0")
    (source
     (origin
       (method git-fetch)
@@ -124,7 +124,7 @@ that handle none of the event types.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0d05f16qxabfhaj0l3da3x7zl5g8jbvkcyn39bidd2a278sb3p97"))))
+        (base32 "1c7h14rvavgadvbsyfa9j4rchsgxb5j363f53rhcvghvmblzddiv"))))
    (build-system go-build-system)
    (arguments
     (list
@@ -276,19 +276,20 @@ import of a 3rd party package at runtime).")
    (name "gopls")
    ;; XXX: Starting from 0.14.0 gppls needs golang.org/x/telemetry, which
    ;; needs to be discussed if it may be included in Guix.
-    (version "0.19.1")
+    (version "0.22.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
-             (url "https://go.googlesource.com/tools")
+              (url "https://go.googlesource.com/tools")
-             (commit (go-version->git-ref version #:subdir "gopls"))))
+              (commit (go-version->git-ref version #:subdir "gopls"))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1dihdw4nzp21hlbwxf6qyhyfgavi1a55lmlyk36czd85v0jcp6a0"))))
+        (base32 "0n5ixvk6c8hww5z9lvf74dx6p4j573bq3ssvp77n6033l0fcbv94"))))
    (build-system go-build-system)
    (arguments
     (list
      #:go go-1.26
      #:install-source? #f
      #:import-path "golang.org/x/tools/gopls"
      #:unpack-path "golang.org/x/tools"
@@ -311,11 +312,13 @@ import of a 3rd party package at runtime).")
              (setenv "GODEBUG" "gotypesalias=1"))))))
    (native-inputs
     (list go-github-com-fatih-gomodifytags
           go-github-com-fsnotify-fsnotify
           go-github-com-google-go-cmp
           go-github-com-google-jsonschema-go
           go-github-com-jba-templatecheck
           go-github-com-modelcontextprotocol-go-sdk
           go-golang-org-x-mod
           go-golang-org-x-sync
           go-golang-org-x-sys
           go-golang-org-x-telemetry
           go-golang-org-x-text
           go-golang-org-x-tools
@@ -2151,6 +2151,57 @@ testing and improve the efficiency of unit test writing.")
 testing of time-sensitive code.")
    (license license:expat)))
 (define-public go-github-com-josharian-mapfs
  (package
    (name "go-github-com-josharian-mapfs")
    (version "0.0.0-20210615234106-095c008854e6")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/josharian/mapfs")
             (commit (go-version->git-ref version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "09i6shqwacx8nm6jfyhc1zvry8fcb3ddd98m96skzybv9lckq7h4"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/josharian/mapfs"))
    (home-page "https://github.com/josharian/mapfs")
    (synopsis "Fork of Go std's testing/fstest.MapFS")
    (description
     "This is a fork of the @code{MapFS} component of the Go standard
 library's testing/fstest package.")
    (license license:bsd-3)))
 (define-public go-github-com-josharian-txtarfs
  (package
    (name "go-github-com-josharian-txtarfs")
    (version "0.0.0-20240408113805-5dc76b8fe6bf")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/josharian/txtarfs")
              (commit (go-version->git-ref version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "129rf6hviw46rxcnnkc8jb1k579798rrhnh1k3nn7npi260ia44m"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/josharian/txtarfs"))
    (propagated-inputs
     (list go-github-com-josharian-mapfs
           go-golang-org-x-tools))
    (home-page "https://github.com/josharian/txtarfs")
    (synopsis "Convert a txtar to an io.FS")
    (description
     "This package turns a @url{https://pkg.go.dev/golang.org/x/tools/txtar,
 txtar} into an @url{https://pkg.go.dev/io/fs, fs.FS}.")
    (license license:expat)))
 (define-public go-github-com-joshdk-go-junit
  (package
    (name "go-github-com-joshdk-go-junit")
@@ -2662,6 +2713,56 @@ error messages, preserving the order of @code{have} (actual result) before
@code{want} (expected result) to minimize confusion.")
    (license license:asl2.0)))
 (define-public go-github-com-newmo-oss-go-caller
  (package
    (name "go-github-com-newmo-oss-go-caller")
    (version "0.1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/newmo-oss/go-caller")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1hn0wj2v6yvn83lpilbcb9xpa36fmcbv83rk6fhr2rwckp2dxy8p"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/newmo-oss/go-caller"))
    (native-inputs
     (list go-github-com-google-go-cmp))
    (home-page "https://github.com/newmo-oss/go-caller")
    (synopsis "Collect stack traces at runtime")
    (description
     "This package provides a library for collecting stack traces at runtime.")
    (license license:expat)))
 (define-public go-github-com-newmo-oss-gotestingmock
  (package
    (name "go-github-com-newmo-oss-gotestingmock")
    (version "0.2.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/newmo-oss/gotestingmock")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1flgmarj961k4vl6d7i2740snrdfjiv4aigb87v5aznvi8bwa5d3"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/newmo-oss/gotestingmock"))
    (propagated-inputs
     (list go-github-com-newmo-oss-go-caller))
    (home-page "https://github.com/newmo-oss/gotestingmock")
    (synopsis "Mocking utilities for Go")
    (description
     "This package provides mocking utilities for unit tests in Go.")
    (license license:expat)))
 (define-public go-github-com-onsi-ginkgo
  (package
    (name "go-github-com-onsi-ginkgo")
@@ -3267,6 +3368,84 @@ and CLI tool.")
 such as readers and writers that fail after N consecutive reads/writes.")
    (license license:expat)))
 (define-public go-github-com-tenntenn-golden
  (package
    (name "go-github-com-tenntenn-golden")
    (version "0.5.5")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/tenntenn/golden")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "09w3h7c4z930z91dg7bfs9m680pw9zgqyyikw88gisv1z86y3qlz"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/tenntenn/golden"))
    (native-inputs
     (list go-github-com-google-go-cmp))
    (propagated-inputs
     (list go-github-com-josharian-txtarfs
           go-golang-org-x-tools))
    (home-page "https://github.com/tenntenn/golden")
    (synopsis "Utilities for golden file tests")
    (description "This package provides utilities for golden file tests.")
    (license license:expat)))
 (define-public go-github-com-tenntenn-modver
  (package
    (name "go-github-com-tenntenn-modver")
    (version "1.0.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/tenntenn/modver")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1p4402lizz5ny0l49yxa65ryhx09wm8g13lx4pw0nw0s4r06rw3g"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/tenntenn/modver"))
    (native-inputs
     (list go-github-com-google-go-cmp))
    (propagated-inputs
     (list go-github-com-hashicorp-go-version))
    (home-page "https://github.com/tenntenn/modver")
    (synopsis "Utility for Go modules")
    (description "This package provides utilities for Go modules.")
    (license license:expat)))
 (define-public go-github-com-tenntenn-text-transform
  (package
    (name "go-github-com-tenntenn-text-transform")
    (version "0.0.0-20250402111347-ba836492e880")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/tenntenn/text")
              (commit (go-version->git-ref version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "19f302js8pxyqnl189992zp6pl169b4gpgn6wywpdir77vm56pih"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/tenntenn/text/transform"
      #:unpack-path "github.com/tenntenn/text"))
    (propagated-inputs
     (list go-golang-org-x-text))
    (home-page "https://github.com/tenntenn/text")
    (synopsis "Text transformation utilities")
    (description "This package provides text transformation utilities in Go.")
    (license license:expat)))
 (define-public go-github-com-tj-assert
  (package
    (name "go-github-com-tj-assert")
@@ -3549,6 +3728,34 @@ goroutine leaks and understanding goroutine lifecycles.")
 based on Go @code{testing} library procedures.")
    (license license:cc0)))
 (define-public go-gitlab-com-bosi-decorder
  (package
    (name "go-gitlab-com-bosi-decorder")
    (version "0.4.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://gitlab.com/bosi/decorder")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0g9x5f7mhvdzwki57902qgb4ih2gipkg255nf9hjv30flfnl2294"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "gitlab.com/bosi/decorder"
      #:test-flags #~(list "-vet=off")))
    (propagated-inputs
     (list go-golang-org-x-tools))
    (home-page "https://gitlab.com/bosi/decorder")
    (synopsis "Declaration order and number linter for golang")
    (description
     "This package provides a declaration order linter for Go.  In case of
 this tool declarations are @code{type}, @code{const}, @code{var} and
@code{func}.")
    (license license:expat)))
 (define-public go-go-abhg-dev-requiredfield
  (package
    (name "go-go-abhg-dev-requiredfield")
@@ -3657,6 +3864,60 @@ and restore them afterwards.")
 of @url{https://github.com/wadey/gocovmerge}.")
    (license license:bsd-2)))
 (define-public go-go-simpler-org-assert
  (package
    (name "go-go-simpler-org-assert")
    (version "0.9.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/go-simpler/assert")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0pg3yhicggby978n8war9n5zzigr95mvnsipnk6zgsjn6gyvjdm5"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "go-simpler.org/assert"))
    (home-page "https://go-simpler.org/assert")
    (synopsis "Assertions for the standard testing package")
    (description
     "This package implements assertions for the standard @code{testing}
 package, and is a minimalistic replacement for the @code{stretchr/testify}
 package.")
    (license license:mpl2.0)))
 (define-public go-go-simpler-org-musttag
  (package
    (name "go-go-simpler-org-musttag")
    (version "0.14.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/go-simpler/musttag")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "15kvnppc2q8ay1m8lhag0bmdx08kc68lzv78699qkyi6bcw68ajf"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "go-simpler.org/musttag"
      #:test-flags #~(list "-skip" "TestAnalyzer")))
    (native-inputs
     (list go-go-simpler-org-assert))
    (propagated-inputs
     (list go-golang-org-x-tools))
    (home-page "https://go-simpler.org/musttag")
    (synopsis "Enforce field tags in (un)marshaled structs")
    (description
     "This package checks that exported fields of a struct passed to a
@code{Marshal}-like function are annotated with the relevant tag.")
    (license license:mpl2.0)))
 (define-public go-go-simpler-org-sloglint
  (package
    (name "go-go-simpler-org-sloglint")
@@ -150,6 +150,31 @@ the @code{c2go} tool at
@url{https://github.com/andybalholm/c2go,https://github.com/andybalholm/c2go}.")
    (license license:expat)))
 (define-public go-github-com-blakesmith-ar
  (package
    (name "go-github-com-blakesmith-ar")
    (version "0.0.0-20190502131153-809d4375e1fb")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/blakesmith/ar")
              (commit (go-version->git-ref version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "00fxkc04b9cb53xxzw5gdqqpwlqv9n5kk0yn2lb5w4rgj5gm8ph1"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/blakesmith/ar"
      #:test-flags #~(list "-vet=off")))
    (home-page "https://github.com/blakesmith/ar")
    (synopsis "Golang archive file reader")
    (description
     "This package provides a Golang file reader for archive files generated
 with @code{ar}.")
    (license license:expat)))
 (define-public go-github-com-bodgit-sevenzip
  (package
    (name "go-github-com-bodgit-sevenzip")
@@ -221,6 +246,31 @@ blocks allowing it to only read the compressed blocks required.")
    (license (list license:bsd-3
                   license:expat))))
 (define-public go-github-com-cavaliergopher-cpio
  (package
    (name "go-github-com-cavaliergopher-cpio")
    (version "1.0.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/cavaliergopher/cpio")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0b1ix8z9kwfpwqi0q08ivcfcimlqk781jbzbfw7qbqavh702w3m2"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/cavaliergopher/cpio"))
    (home-page "https://github.com/cavaliergopher/cpio")
    (synopsis "Readers and writers for CPIO archives")
    (description
     "This package provides readers and writers for CPIO archives.  Currently,
 only the SVR4 (New ASCII) format is supported, both with and without
 checksums.")
    (license license:bsd-3)))
 (define-public go-github-com-containerd-stargz-snapshotter-estargz
  (package
    (name "go-github-com-containerd-stargz-snapshotter-estargz")
@@ -385,6 +435,37 @@ Implements the XFLATE format, an random-access extension to DEFLATE.
 compression format.")
    (license license:bsd-3)))
 (define-public go-github-com-google-rpmpack
  (package
    (name "go-github-com-google-rpmpack")
    (version "0.7.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/google/rpmpack")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "17h2s1g191cvbs16fnclkpb42d9mx6mdmhd04kxzv8bss7m59pr4"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/google/rpmpack"))
    (native-inputs
     (list go-github-com-google-go-cmp))
    (propagated-inputs
     (list go-github-com-cavaliergopher-cpio
           go-github-com-klauspost-compress
           go-github-com-klauspost-pgzip
           go-github-com-ulikunitz-xz))
    (home-page "https://github.com/google/rpmpack")
    (synopsis "Pack files to rpm files")
    (description
     "Package rpmpack packs files to rpm files.  It is designed to be simple
 to use and deploy, not requiring any filesystem access to create rpm files.")
    (license license:asl2.0)))
 (define-public go-github-com-hhrutter-lzw
  (package
    (name "go-github-com-hhrutter-lzw")
@@ -884,6 +965,40 @@ format's \"Extra Fields\".  The intention is to eventually support and provide
 a low-level API for the majority of PKWARE's and Info-ZIP's extra fields.")
    (license license:expat)))
 (define-public go-github-com-sassoftware-go-rpmutils
  (package
    (name "go-github-com-sassoftware-go-rpmutils")
    (version "0.4.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/sassoftware/go-rpmutils")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "06ymwjn6xvc4cpxcsh5achwgma4i075ikbzq8jm143m0pck4pmfi"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/sassoftware/go-rpmutils"))
    (native-inputs
     (list go-github-com-stretchr-testify
           go-go-uber-org-goleak))
    (propagated-inputs
     (list go-github-com-datadog-zstd
           go-github-com-klauspost-compress
           go-github-com-protonmail-go-crypto
           go-github-com-ulikunitz-xz
           go-github-com-xi2-xz
           go-golang-org-x-sys))
    (home-page "https://github.com/sassoftware/go-rpmutils")
    (synopsis "Parse RPM packages in Golang")
    (description
     "This package provides some Golang interfaces for handling RPM packages,
 such extracting RPM header and CPIO content.")
    (license license:asl2.0)))
 (define-public go-github-com-sorairolake-lzip-go
  (package
    (name "go-github-com-sorairolake-lzip-go")
@@ -607,6 +607,30 @@ Actions} locally.")
 It's a static checker for GitHub Actions workflow files.")
    (license license:expat)))
 (define-public go-gitlab-com-digitalxero-go-conventional-commit
  (package
    (name "go-gitlab-com-digitalxero-go-conventional-commit")
    (version "1.0.7")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://gitlab.com/digitalxero/go-conventional-commit.git")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1191j3k9ma5sv8w2zsw8gb1407561zll0ca8hwy0dja6s0b3z0xy"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "gitlab.com/digitalxero/go-conventional-commit"))
    (home-page "https://gitlab.com/digitalxero/go-conventional-commit")
    (synopsis "Go parser for conventional commits")
    (description
     "This package provides a Go parser for conventional-commit messages
@url{https://www.conventionalcommits.org/}.")
    (license license:expat)))
 (define-public go-github-com-xanzy-go-gitlab
  (package
    (name "go-github-com-xanzy-go-gitlab")
@@ -10796,6 +10796,33 @@ dhcpv6 and dhcpv4
@end itemize")
    (license license:bsd-3)))
 (define-public go-github-com-invopop-jsonschema
  (package
    (name "go-github-com-invopop-jsonschema")
    (version "0.14.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/invopop/jsonschema")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0y881agfaycn5l5qn2y2jmiskchi0cvn5v602hna4ljy9rv5jxw2"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/invopop/jsonschema"))
    (native-inputs
     (list go-github-com-stretchr-testify))
    (propagated-inputs
     (list go-github-com-pb33f-ordered-map-v2))
    (home-page "https://github.com/invopop/jsonschema")
    (synopsis "Go JSON Schema Reflection")
    (description
     "Package jsonschema uses reflection to generate JSON Schemas from Go types.")
    (license license:expat)))
 (define-public go-github-com-ipfs-go-cid
  (package
    (name "go-github-com-ipfs-go-cid")
@@ -16985,9 +17012,11 @@ kinds of referrer URLs (search, social, ...).")
     (list
      #:skip-build? #t
      #:import-path "github.com/sigstore/rekor"
-      ;; XXX: Remove when all inputs are packaged.
+      #:embed-files #~(list ".*\\.json")
      ;; ;; XXX: Remove when all inputs are packaged.
      #:test-subdirs
-      #~(list "pkg/events/newentry"
+      #~(list "pkg/client"
              "pkg/events/newentry"
              "pkg/indexstorage/mysql"
              "pkg/pki/minisign"
              "pkg/pki/pgp"
@@ -16995,7 +17024,10 @@ kinds of referrer URLs (search, social, ...).")
              "pkg/pki/tuf"
              "pkg/pki/x509"
              "pkg/pubsub/gcp"
-              "pkg/util")))
+              "pkg/tle"
              "pkg/types"
              "pkg/util"
              "pkg/verify")))
    (native-inputs
     (list go-github-com-asaskevich-govalidator
           go-github-com-data-dog-go-sqlmock
@@ -17023,6 +17055,7 @@ kinds of referrer URLs (search, social, ...).")
           go-github-com-go-openapi-validate
           go-github-com-go-sql-driver-mysql
           go-github-com-go-viper-mapstructure-v2
           go-github-com-google-rpmpack
           go-github-com-google-trillian
           go-github-com-grpc-ecosystem-go-grpc-middleware
           go-github-com-hashicorp-go-cleanhttp
@@ -17066,7 +17099,6 @@ kinds of referrer URLs (search, social, ...).")
           ;; go-github-com-adamkorcz-go-fuzz-headers-1
           ;; go-github-com-cavaliercoder-go-rpm
           ;; go-github-com-go-redis-redismock-v9
           ;; go-github-com-google-rpmpack
           ;; go-github-com-sassoftware-relic
           ;; go-github-com-sassoftware-relic-v7
           ;; go-go-step-sm-crypto
@@ -18549,6 +18581,31 @@ Tailscale for access control.")
 Tailscale.")
    (license license:bsd-3)))
 (define-public go-github-com-tcnksm-go-httpstat
  (package
    (name "go-github-com-tcnksm-go-httpstat")
    (version "0.2.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/tcnksm/go-httpstat")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "18jn40ra97waxx1mf23pkh6rq46y0nqd7vi3zcx9cwc39zqaf9bc"))))
    (build-system go-build-system)
    (arguments
     (list
      #:tests? #f ;Tests require network connection
      #:import-path "github.com/tcnksm/go-httpstat"))
    (home-page "https://github.com/tcnksm/go-httpstat")
    (synopsis "Trace HTTP latency information in Go")
    (description
     "Package httpstat traces HTTP latency infomation, such as DNSLookup and
 TCP Connection, on any Golang HTTP request with no big code modification.")
    (license license:expat)))
 (define-public go-github-com-tdewolff-minify-v2
  (package
    (name "go-github-com-tdewolff-minify-v2")
@@ -19080,6 +19137,30 @@ caching protocol.  It provides support to programmatically store and retrieve
 build caches, instead of relying on the standard actions/cache YAML step.")
    (license license:expat)))
 (define-public go-github-com-toqueteos-webbrowser
  (package
    (name "go-github-com-toqueteos-webbrowser")
    (version "1.2.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/toqueteos/webbrowser")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0bnn02zcfc9xkxc2qvv4q6wy5sipcwc0hwmx7hdhvv3lsw177flw"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/toqueteos/webbrowser"))
    (home-page "https://github.com/toqueteos/webbrowser")
    (synopsis "Simple API for opening web pages")
    (description
     "This package provides a simple API for opening web pages on your default
 browser.")
    (license license:expat)))
 (define-public go-github-com-transparency-dev-tessera
  (package
    (name "go-github-com-transparency-dev-tessera")
@@ -114,6 +114,7 @@
  #:use-module (gnu packages golang-compression)
  #:use-module (gnu packages golang-crypto)
  #:use-module (gnu packages golang-maths)
  #:use-module (gnu packages golang-vcs)
  #:use-module (gnu packages golang-web)
  #:use-module (gnu packages graph)
  #:use-module (gnu packages imagemagick)
@@ -1761,6 +1762,30 @@ strings for a safe use as command line arguments in the most common POSIX
 shells.")
    (license license:expat)))
 (define-public go-github-com-aleksi-pointer
  (package
    (name "go-github-com-aleksi-pointer")
    (version "1.2.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/AlekSi/pointer")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0rncmanv62wwy7ihvjhvb695mkvy4kdzhgnn90zygs9yrfzzk0wk"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/AlekSi/pointer"))
    (home-page "https://github.com/AlekSi/pointer")
    (synopsis "Helper Go library to convert between pointers and values")
    (description
     "This package provides helpers to convert between pointers and values of
 built-in and, with generics, of any types.")
    (license license:expat)))
 (define-public go-github-com-alexflint-go-filemutex
  (package
    (name "go-github-com-alexflint-go-filemutex")
@@ -4409,6 +4434,29 @@ information for Golang.")
 variables into structs.")
    (license license:expat)))
 (define-public go-github-com-caarlos0-go-version
  (package
    (name "go-github-com-caarlos0-go-version")
    (version "0.2.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/caarlos0/go-version")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0kp78am3yzffz8r70f1skq0m2vms0wk37f76hqbfg1r29hay1ban"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/caarlos0/go-version"))
    (home-page "https://github.com/caarlos0/go-version")
    (synopsis "Fetch Go module version")
    (description
     "Package goversion provides utilities to get the Go module version information.")
    (license license:expat)))
 (define-public go-github-com-calebcase-tmpfile
  (package
    (name "go-github-com-calebcase-tmpfile")
@@ -4461,6 +4509,36 @@ color palette} for Go applications.  Catppuccin is a community-driven pastel
 theme with four flavors: Latte, Frappe, Macchiato, and Mocha.")
    (license license:expat)))
 (define-public go-github-com-ccojocar-zxcvbn-go
  (package
    (name "go-github-com-ccojocar-zxcvbn-go")
    (version "1.0.4")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/ccojocar/zxcvbn-go")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0dlrd6afpfwnpj6cbbvjhwbf33ldr0nzffl8p43jrmn62mwf7cn7"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/ccojocar/zxcvbn-go"))
    (native-inputs
     (list go-github-com-stretchr-testify))
    (home-page "https://github.com/ccojocar/zxcvbn-go")
    (synopsis "Password-strength generator in Go")
    (description
     "This package provides a password strength generators written in Golang.
 It attempts to give sound password advice through pattern matching and
 conservative entropy calculations.  It finds 10k common passwords, common
 American names and surnames, common English words, and common patterns like
 dates, repeats (aaa), sequences (abcd), and QWERTY patterns. It's an active
 fork of @url{https://github.com/nbutton23/zxcvbn-go}.")
    (license license:expat)))
 (define-public go-github-com-cention-sany-utf7
  (package
    (name "go-github-com-cention-sany-utf7")
@@ -4605,7 +4683,7 @@ contexts (e.g. testing).")
 (define-public go-github-com-charlievieth-fastwalk
  (package
    (name "go-github-com-charlievieth-fastwalk")
-    (version "1.0.8")
+    (version "1.0.14")
    (source
     (origin
       (method git-fetch)
@@ -4614,7 +4692,7 @@ contexts (e.g. testing).")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "17zy17q31p8b93bf703rr0xqafp02bb0slkrgpxb8r0aaxz3zg4y"))))
+        (base32 "0ab90pdqgnd0a6ylmq35zca0imj2pp4pxz2bcmg2zx0szv3910im"))))
    (build-system go-build-system)
    (arguments
     (list
@@ -11726,6 +11804,33 @@ native Go structure.")
    (description "Package yaml implements YAML support for the Go language.")
    (license license:asl2.0)))
 (define-public go-github-com-gobuffalo-flect
  (package
    (name "go-github-com-gobuffalo-flect")
    (version "1.0.3")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/gobuffalo/flect")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0lyb1876byv9q52y6dlq17aahwl108mhp67cmxykckjpxxykb442"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/gobuffalo/flect"))
    (native-inputs
     (list go-github-com-stretchr-testify))
    (home-page "https://github.com/gobuffalo/flect")
    (synopsis "Inflection engine for Golang")
    (description
     "This package provides a new inflection engine to replace
@url{https://github.com/markbates/inflect,} designed to be more modular,
 readable, and easier to fix issues on than the original.")
    (license license:expat)))
 (define-public go-github-com-gobwas-glob
  (package
    (name "go-github-com-gobwas-glob")
@@ -12569,6 +12674,41 @@ color (24-bit, RGB)
@end itemize")
    (license license:expat)))
 (define-public go-github-com-goreleaser-chglog
  (package
    (name "go-github-com-goreleaser-chglog")
    (version "0.7.4")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/goreleaser/chglog")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "09ni4y644zhp3bf9nwy9qc9wkxrn2hla6nczg3zpn0ls8qaxjd40"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/goreleaser/chglog"))
    (native-inputs
     (list go-github-com-go-git-go-billy-v5
 	   go-github-com-google-go-cmp
           go-github-com-smartystreets-goconvey
 	   go-github-com-spf13-cobra
           go-github-com-spf13-viper))
    (propagated-inputs
     (list go-github-com-go-git-go-git-v5
           go-github-com-masterminds-semver-v3
           go-github-com-masterminds-sprig-v3
           go-gitlab-com-digitalxero-go-conventional-commit
           go-go-yaml-in-yaml-v3))
    (home-page "https://github.com/goreleaser/chglog")
    (synopsis "Changelog management Go library")
    (description
     "This package provides Go functions to manage changelogs.")
    (license license:expat)))
 (define-public go-github-com-goreleaser-fileglob
  (package
    (name "go-github-com-goreleaser-fileglob")
@@ -12599,6 +12739,66 @@ underneath and returns only matching files or directories, depending on the
 configuration.")
    (license license:expat)))
 (define-public go-github-com-goreleaser-nfpm-v2
  (package
    (name "go-github-com-goreleaser-nfpm-v2")
    (version "2.44.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/goreleaser/nfpm")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "17dmzkvy3ihjjaxi10l9xc1mcg9vmlr2v1xc4a361fa22aqigz0v"))))
    (build-system go-build-system)
    (arguments
     (list
      #:go go-1.25
      #:import-path "github.com/goreleaser/nfpm/v2"
      #:unpack-path "github.com/goreleaser/nfpm/v2"
      ;; Tests fail due to read-only filesystem when trying to manipulate mode
      ;; of the files.
      #:test-flags
      #~(list "-skip" "TestPrepareForPackager|TestDeepPathsWithGlobAndUmask")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'fix-tests
            (lambda* (#:key unpack-path #:allow-other-keys)
              (with-directory-excursion (string-append "src/" unpack-path)
                (substitute*  "rpm/rpm_test.go"
                  (("/bin/bash") (which "bash")))))))))
    (native-inputs
     (list go-github-com-caarlos0-go-version
           go-github-com-invopop-jsonschema
           go-github-com-muesli-mango-cobra
           go-github-com-muesli-roff
           go-github-com-sassoftware-go-rpmutils
           go-github-com-stretchr-testify))
    (propagated-inputs
     (list go-dario-cat-mergo
           go-github-com-aleksi-pointer
           go-github-com-blakesmith-ar
           go-github-com-google-rpmpack
           go-github-com-goreleaser-chglog
           go-github-com-goreleaser-fileglob
           go-github-com-klauspost-compress
           go-github-com-klauspost-pgzip
           go-github-com-masterminds-semver-v3
           go-github-com-protonmail-go-crypto
           go-github-com-protonmail-gopenpgp-v2
           go-github-com-spf13-cobra
           go-github-com-ulikunitz-xz
           go-gopkg-in-yaml-v3))
    (home-page "https://github.com/goreleaser/nfpm")
    (synopsis "Go library to package programs in various Linux formats")
    (description
     "nFPM is Not FPM -- provides ways to package programs in popular Linux
 packaging formats, such as @code{deb}, @code{rpm}, @code{apk}, @code{ipk} and
 Arch.")
    (license license:expat)))
 (define-public go-github-com-gorhill-cronexpr
  (package
    (name "go-github-com-gorhill-cronexpr")
@@ -20520,6 +20720,90 @@ for any given struct and a set of its potential member values.  This can be
 used to generate extensive test matrixes among other things.")
    (license license:expat)))
 (define-public go-github-com-muesli-mango
  (package
    (name "go-github-com-muesli-mango")
    (version "0.2.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/muesli/mango")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "16d0sga6cbdxzlqkibcgw0civkw11fpkcjpgv21i0q5j9mjbsjw4"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/muesli/mango"))
    (propagated-inputs
     (list go-github-com-muesli-roff))
    (home-page "https://github.com/muesli/mango")
    (synopsis "Golang man-page generator")
    (description
     "This package provides a man-page generator for the Go flag, pflag, cobra, coral,
 and kong packages.  It extracts commands, flags, and arguments from the target
 program and enables it to self-document.")
    (license license:expat)))
 (define-public go-github-com-muesli-mango-cobra
  (package
    (name "go-github-com-muesli-mango-cobra")
    (version "1.3.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/muesli/mango-cobra")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "11vvm3f2mq8yaqbfrjbzdcyvkn9f75rp4kygxyvqwc5jsw1kdwal"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/muesli/mango-cobra"))
    (propagated-inputs
     (list go-github-com-muesli-mango
           go-github-com-muesli-mango-pflag
           go-github-com-muesli-roff
           go-github-com-spf13-cobra))
    (home-page "https://github.com/muesli/mango-cobra")
    (synopsis "Cobra adapter for mango")
    (description
     "This package provides a cobra adapter for the
@url{https://github.com/muesli/mango,mango} man-page generator.")
    (license license:expat)))
 (define-public go-github-com-muesli-mango-pflag
  (package
    (name "go-github-com-muesli-mango-pflag")
    (version "0.2.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/muesli/mango-pflag")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1k4m88i9shs36a8n86k3a1vlxmdf5vwavkih2f2j3xj718hnhpw0"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/muesli/mango-pflag"))
    (propagated-inputs
     (list go-github-com-muesli-mango
           go-github-com-muesli-roff
           go-github-com-spf13-pflag))
    (home-page "https://github.com/muesli/mango-pflag")
    (synopsis "Pflag adapter for mango")
    (description
     "This package provides a pflag adapter for the
@url{https://github.com/muesli/mango, mango} man-page generator.")
    (license license:expat)))
 (define-public go-github-com-muesli-reflow
  (package
    (name "go-github-com-muesli-reflow")
@@ -20547,6 +20831,32 @@ used to generate extensive test matrixes among other things.")
 helping you to transform blocks of text.")
    (license license:expat)))
 (define-public go-github-com-muesli-roff
  (package
    (name "go-github-com-muesli-roff")
    (version "0.1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/muesli/roff")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0l263rqwq2ccr1lpamsvs48dddsr70xim8mv6rsj2x9y3prcq3yh"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/muesli/roff"
      ;; Expected title heading, got:
      ;; .TH TITLE 1 "2026-05-22" "Title" "A short description"
      #:test-flags #~(list "-skip" "TestTitleHeading")))
    (home-page "https://github.com/muesli/roff")
    (synopsis "Write roff documents in Go")
    (description "This package provides tools to write @code{roff}
 documents in Golang.")
    (license license:expat)))
 (define-public go-github-com-muesli-termenv
  (package
    (name "go-github-com-muesli-termenv")
@@ -22506,6 +22816,36 @@ expiration times, it doesn't need to serialize or transmit its contents over
 the network.")
    (license license:expat)))
 (define-public go-github-com-pb33f-ordered-map-v2
  (package
    (name "go-github-com-pb33f-ordered-map-v2")
    (version "2.3.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/pb33f/ordered-map")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1k4r1rvlziddaszm1jvgz27nkrk1jfka0zik16f4b3gmhdnmd9vc"))))
    (build-system go-build-system)
    (arguments
     (list
      #:import-path "github.com/pb33f/ordered-map/v2"))
    (native-inputs
     (list go-github-com-stretchr-testify))
    (propagated-inputs
     (list go-github-com-bahlo-generic-list-go
           go-github-com-buger-jsonparser
           go-go-yaml-in-yaml-v4))
    (home-page "https://github.com/pb33f/ordered-map")
    (synopsis "Ordered maps in Golang")
    (description
     "This package provides a Golang implementation of an ordered map, which
 is a map that also keeps track of the order in which keys were inserted.")
    (license license:asl2.0)))
 (define-public go-github-com-pbnjay-memory
  (let ((commit "7b4eea64cf580186c0eceb10dc94ba3a098af46c")
        (revision "2"))
@@ -33637,6 +33977,22 @@ library.")
 ;;; Executables:
 ;;;
 (define-public chglog
  (package/inherit go-github-com-goreleaser-chglog
    (name "chglog")
    (arguments
     (substitute-keyword-arguments arguments
       ((#:tests? _ #t) #f)
       ((#:install-source? _ #t) #f)
       ((#:import-path _) "github.com/goreleaser/chglog/cmd/chglog")
       ((#:unpack-path _ "") "github.com/goreleaser/chglog")))
    (native-inputs
     (append
      (package-native-inputs go-github-com-goreleaser-chglog)
      (package-propagated-inputs go-github-com-goreleaser-chglog)))
    (inputs '())
    (propagated-inputs '())))
 (define-public containers-storage
  (package/inherit go-github-com-containers-storage
    (name "containers-storage")
@@ -34177,6 +34533,22 @@ various modes for analyzing and transforming YAML data.")))
    (propagated-inputs '())
    (inputs '())))
 (define-public nfpm
  (package/inherit go-github-com-goreleaser-nfpm-v2
    (name "nfpm")
    (arguments
     (substitute-keyword-arguments arguments
       ((#:import-path _) "github.com/goreleaser/nfpm/v2/cmd/nfpm")
       ((#:install-source? _ #t) #f)
       ((#:tests? _ #t) #f)
       ((#:unpack-path _ "") "github.com/goreleaser/nfpm/v2")))
    (native-inputs
     (append
      (package-native-inputs go-github-com-goreleaser-nfpm-v2)
      (package-propagated-inputs go-github-com-goreleaser-nfpm-v2)))
    (inputs '())
    (propagated-inputs '())))
 (define-public oci-runtime-tool
  (package/inherit go-github-com-opencontainers-runtime-tools
    (name "oci-runtime-tool")
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017-2025 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017-2026 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018, 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2021, 2022, 2024 Efraim Flashner <efraim@flashner.co.il>
@@ -227,7 +227,7 @@ more.")
   (package
     (inherit igraph)
     (name "igraph")
-     (version "0.10.15")
+     (version "1.0.1")
     (source
      (origin
        (inherit (package-source igraph))
@@ -239,7 +239,39 @@ more.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-          "0z9jqvl65j4z6brrjlfyykba2bs10az6dx6m8g41snlfnx21a82d")))))))
+          "01mynhbl2ph0gkc0zr5klwqvczwcimfs2kdn6didwg4k8gsrcxlr"))
        (modules '((guix build utils)
                   (ice-9 ftw)
                   (srfi srfi-26)))
        ;; We need the vendored versions of qhull and cxsparse.
        (snippet '(begin
                    (delete-file-recursively "src/isomorphism/bliss")
                    (substitute* '("src/CMakeLists.txt"
                                   "etc/cmake/benchmark_helpers.cmake")
                      ;; Remove extraneous bundling related variables.
                      ((".*_IS_VENDORED.*") "")
                      ((".*add_sub.*isomorphism/bliss.*") "")
                      (("(.*TARGETS.*)bliss(.*)pcg(.*)"
                        _ part1 part2 part3)
                       (string-append part1 part2 part3))
                      ((" pcg ") " pcg_random "))))))
     (arguments
      (substitute-keyword-arguments (package-arguments igraph)
        ((#:phases phases '%standard-phases)
         #~(modify-phases #$phases
             ;; We have to use the bundled version because it has been
             ;; modified from upstream.
             (delete 'patch-suitesparse)))
        ((#:configure-flags flags)
         #~(list "-DBUILD_SHARED_LIBS=ON"
                 "-DIGRAPH_INFOMAP_SUPPORT=OFF"
                 "-DCMAKE_C_FLAGS=-Wno-error=incompatible-pointer-types"
                 ;; Use the same integer width as suitesparse-cxsparse, which
                 ;; uses int64_t in SuiteSparse v6.0.0 and later.
                 "-DIGRAPH_INTEGER_SIZE=64"))))
     (inputs
      (modify-inputs (package-inputs igraph)
        (delete "suitesparse-cxsparse"))))))
 (define-public python-igraph
  (package
@@ -111,7 +111,6 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mp3)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages opencl)
  #:use-module (gnu packages oneapi)
  #:use-module (gnu packages pciutils)
@@ -998,24 +997,17 @@ baking tools to produce normal maps.")
                   (string-append "-DLLVM_BC_GENERATOR="
                                  #$(this-package-native-input "clang")
                                  "/bin/clang++"))
-           #:phases
+           #:test-exclude (string-join
-           #~(modify-phases %standard-phases
+                           (list
-               (replace 'check
+                            "osl-imageio" ; file does not exist
-                 (lambda* (#:key tests? #:allow-other-keys)
+                            "osl-imageio.opt" ; file does not exist
-                   (when tests?
+                            "osl-imageio.opt.rs_bitcode" ; file does not exist
-                     (invoke
+                            "texture-udim"    ; file does not exist
-                      "ctest" "--exclude-regex"
+                            "texture-udim.opt" ; file does not exist
-                      (string-join
+                            "texture-udim.opt.rs_bitcode" ; file does not exist
-                       (list
+                            "example-deformer" ; could not find OSLConfig
-                        "osl-imageio" ; file does not exist
+                            "python-oslquery") ; no module oslquery
-                        "osl-imageio.opt" ; file does not exist
+                           "|")))
                        "osl-imageio.opt.rs_bitcode" ; file does not exist
                        "texture-udim"    ; file does not exist
                        "texture-udim.opt" ; file does not exist
                        "texture-udim.opt.rs_bitcode" ; file does not exist
                        "example-deformer" ; could not find OSLConfig
                        "python-oslquery") ; no module oslquery
                       "|"))))))))
    (native-inputs
     (list bison
           clang
@@ -1347,6 +1339,19 @@ basic geometries.")
       (file-name (git-file-name name version))
       (sha256
        (base32 "0gfgzwm5s50caj5s6l7irgmlifpmypd0fnm6ckzli1fdziwjgdwi"))))
    (arguments
     ;; https://gitlab.com/inkscape/lib2geom/-/work_items/82
     (if (or (target-aarch64?)
             (target-riscv64?)
             (target-ppc64le?))
         (substitute-keyword-arguments arguments
           ((#:phases phases #~%standard-phases)
            #~(modify-phases #$phases
                (add-after 'unpack 'disable-polynomial-test
                  (lambda _
                    (substitute* "tests/CMakeLists.txt"
                      (("polynomial-test") "")))))))
         arguments))
    (properties '((hidden? . #f)))))
 (define-public pstoedit
@@ -2392,6 +2397,71 @@ and engineering community.")
 (define-deprecated coin3D-4 coin3d)
 (export coin3D-4)
 (define-public skcms
  ;; No tags are available.
  (let ((commit "a7a3b15f06355692d86a3b8373c579a521598f4c")
        (revision "0"))
    (package
      (name "skcms")
      (version (git-version "0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://skia.googlesource.com/skcms")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0ylrsm7cinw59ilgbffazbgifax81kkya5cxq8q8wybnxx6z6ps6"))))
      (build-system gnu-build-system)
      (arguments
       (list
        #:phases
        #~(modify-phases %standard-phases
            (add-after 'unpack 'patch-includes
              (lambda _
                (substitute* "skcms.h"
                  (("src\\/skcms_public\\.h") "skcms/skcms_public.h"))))
            (delete 'configure)
            (replace 'build
              (lambda _
                ;; Some CPUs may not support these features.
                (let ((cflags (append '("-DSKCMS_DISABLE_HSW=1"
                                        "-DSKCMS_DISABLE_SKX=1")
                                      (if #$(target-mingw?)
                                          '("-DSKCMS_HAS_MUSTTAIL=0")
                                          '())))
                      (ldflags '("-lstdc++")))
                  (apply invoke #$(cc-for-target)
                         `("-O2" "-g" "-fPIC" ,@cflags
                           "skcms.cc"
                           "src/skcms_TransformBaseline.cc"
                           "src/skcms_TransformHsw.cc"
                           "src/skcms_TransformSkx.cc"
                           "-shared" ,@ldflags
                           "-o" "libskcms.so"))
                  (apply invoke #$(cc-for-target)
                         `(,@cflags
                           "tests.c" "test_only.c"
                           "-Wl,-rpath=." "-L." "-lskcms" ,@ldflags
                           "-o" "tests")))))
            (replace 'check
              (lambda* (#:key tests? #:allow-other-keys)
                (when tests?
                  (invoke "./tests"))))
            (replace 'install
              (lambda _
                (install-file "libskcms.so" (string-append #$output "/lib"))
                (install-file "skcms.h" (string-append #$output "/include"))
                (install-file "src/skcms_public.h"
                              (string-append #$output "/include/skcms")))))))
      (native-inputs (list ninja))
      (home-page "https://skia.org/")
      (synopsis "Color management engine")
      (description
       "skcms is the color management engine.  It is a part of @code{skia}.")
      (license license:bsd-3))))
 (define-public skia
  ;; Releases follow those of Chromium, about every 6 weeks.  The release
  ;; version can be found on this page:
@@ -341,7 +341,7 @@ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) $(srcdir)/predicates_init.c \
 (define-public xdot
  (package
    (name "xdot")
-    (version "1.4")
+    (version "1.6")
    (source
     (origin
       ;; PyPI tarball is missing some test files.
@@ -351,7 +351,7 @@ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) $(srcdir)/predicates_init.c \
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1l34ahvcz90j3j7aspp9wqvxpq10mzgq7l0sanrj142ihdnbahvy"))))
+        (base32 "0gg54k6zhdviz17aa3harc82f7bx4mpwnj292q066dzamvr87svq"))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -1173,7 +1173,8 @@ application suites.")
                     '("--no-suite=gsk-compare-gl"
                       "--no-suite=gsk-compare-cairo"
                       "--no-suite=gsk-compare-ngl"
-                       "--no-suite=gsk-compare-vulkan")
+                       "--no-suite=gsk-compare-vulkan"
                       "--no-suite=svg")
                     '()))
      #:phases
      #~(modify-phases %standard-phases
@@ -529,6 +529,17 @@ without requiring the source code to be rewritten.")
 ;;; (security or else) and this deprecation could be removed.
 (define-deprecated/public-alias guile-3.0/fixed guile-3.0/pinned)
 (define-public guile-with-gmp
  (package/inherit guile-3.0-latest
    (name "guile-with-gmp")
    (propagated-inputs
      (modify-inputs propagated-inputs
        (append gmp)))
    (arguments
     (substitute-keyword-arguments arguments
       ((#:configure-flags flags #~'())
        #~(delete "--enable-mini-gmp" #$flags))))))
 (define-public guile-3.0/pinned
  ;; A package of Guile that's rarely changed.  It is the one used in the
  ;; `base' module, and thus changing it entails a full rebuild.
@@ -36,6 +36,7 @@
  #:use-module (guix licenses)
  #:use-module (guix packages)
  #:use-module (guix gexp)
  #:use-module (guix deprecation)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix build-system cmake)
@@ -946,37 +947,42 @@ traditional Chinese output.")
 hanja dictionary and small hangul character classification.")
    (license lgpl2.1+)))
-(define-public ibus-libhangul
+(define-public ibus-hangul
  (package
-    (name "ibus-libhangul")
+    (name "ibus-hangul")
-    (version "1.5.3")
+    (version "1.5.5")
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/libhangul/ibus-hangul/"
+       (uri (git-reference
-                           "releases/download/" version
+             (url "https://github.com/libhangul/ibus-hangul")
-                           "/ibus-hangul-" version ".tar.gz"))
+             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32
+        (base32 "0wsbh6ii223wdai2qwcwy6sj5jr9zzma7511fhkfq4m2qxdhwsn7"))))
         "1400ba2p34vr9q285lqvjm73f6m677cgfdymmjpiwyrjgbbiqrjy"))))
    (build-system gnu-build-system)
    (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:make-flags
-         (add-after 'install 'wrap
+      #~'("DISABLE_GUI_TESTS=ibus-hangul")
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+      #:phases
-             (wrap-program (string-append (assoc-ref outputs "out")
+      #~(modify-phases %standard-phases
-                                          "/libexec/ibus-setup-hangul")
+          (add-after 'install 'wrap
-               `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH")))
+            (lambda* (#:key inputs #:allow-other-keys)
-               `("LD_LIBRARY_PATH" ":" prefix
+              (wrap-program (string-append #$output
-                 (,(string-append (assoc-ref inputs "libhangul") "/lib")))
+                                           "/libexec/ibus-setup-hangul")
-               `("GI_TYPELIB_PATH" ":" prefix
+                `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH")))
-                 (,(getenv "GI_TYPELIB_PATH"))))
+                `("LD_LIBRARY_PATH" ":" prefix
-             #t)))))
+                  (,(dirname (search-input-file inputs "lib/libhangul.so"))))
                `("GI_TYPELIB_PATH" ":" prefix
                  (,(getenv "GI_TYPELIB_PATH")))))))))
    (native-inputs
-     `(("pkg-config" ,pkg-config)
+     (list autoconf
-       ("gettext" ,gettext-minimal)
+           automake
-       ("glib:bin" ,glib "bin")))
+           gettext-minimal
           `(,glib "bin")
           libtool
           pkg-config))
    (inputs
     (list bash-minimal
           ibus
@@ -991,6 +997,9 @@ hanja dictionary and small hangul character classification.")
     "ibus-hangul is a Korean input method engine for IBus.")
    (license gpl2+)))
 ;; XXX: Deprecated on 2026-05-26.
 (define-deprecated-package ibus-libhangul ibus-hangul)
 (define-public ibus-table
  (package
    (name "ibus-table")
@@ -1923,7 +1923,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
 (define-public simpleitk
  (package
    (name "simpleitk")
-    (version "2.5.3")
+    (version "2.5.4")
    (source
     (origin
       (method git-fetch)
@@ -1932,7 +1932,9 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0fvacjfq0p8v7r2cmzwwh7bxb6ayavznhj0m81dah463x472qkd2"))))
+        (base32 "1bzj5naqbgv2b31iqgz7qqk9rixsvjqycjz6l7w3gm7v1aj14jpb"))
       (patches
        (search-patches "simpleitk-r-4.6.0.patch"))))
    (build-system cmake-build-system)
    (outputs '("out" "python" "r"))
    (arguments
@@ -2032,7 +2034,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
                   version "/SimpleITKData-" version ".tar.gz"))
             (sha256
              (base32
-               "0i4f87g1rh6xxisw06gwwyi8f216qqs6ih3gghi3k49vsl0h4g5d")))))
+               "0hryvi9fgqac00ng1bfhw3lm0al1dh0ka6jglba2q368nls428nx")))))
    (synopsis "Simplified interface to @acronym{ITK, Insight Toolkit}")
    (description
     "SimpleITK is an image analysis toolkit built on top of @acronym{ITK,
@@ -39,6 +39,7 @@
 ;;; Copyright © 2025 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2025 Igorj Gorjaĉev <igor@goryachev.org>
 ;;; Copyright © 2026 Daniel Littlewood <dan@danielittlewood.xyz>
 ;;; Copyright © 2026 Luis Guilherme Coelho <lgcoelho@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -94,13 +95,16 @@
  #:use-module (gnu packages gnome)
  #:use-module (gnu packages golang-build)
  #:use-module (gnu packages golang-xyz)
  #:use-module (gnu packages gstreamer)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages graphics)
  #:use-module (gnu packages haskell-xyz)
  #:use-module (gnu packages image)
  #:use-module (gnu packages image-processing)
  #:use-module (gnu packages imagemagick)
  #:use-module (gnu packages kde-frameworks)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages logging)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages pdf)
@@ -108,6 +112,7 @@
  #:use-module (gnu packages perl-check)
  #:use-module (gnu packages photo)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages pretty-print)
  #:use-module (gnu packages profiling)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
@@ -120,6 +125,8 @@
  #:use-module (gnu packages sqlite)
  #:use-module (gnu packages suckless)
  #:use-module (gnu packages stb)
  #:use-module (gnu packages tbb)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages terminals)
  #:use-module (gnu packages upnp)
  #:use-module (gnu packages version-control)
@@ -1286,6 +1293,84 @@ workspaces.
 (define-deprecated-package python-ueberzug
  ueberzug)
 (define-public ueberzugpp
  (package
    (name "ueberzugpp")
    (version "2.9.10")
    (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/jstkdng/ueberzugpp")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
         (base32 "1jac2sca4pmcxp8xcvaxhf6j15phyc85gb5n9ymajbahnd4hbcv2"))))
    (build-system cmake-build-system)
    (arguments
     (list #:tests? #f    ; no tests
           #:configure-flags
           #~(list "-DENABLE_OPENCV=ON"
                   "-DENABLE_X11=ON"
                   "-DENABLE_WAYLAND=ON")))
    (native-inputs
     (list extra-cmake-modules
           gobject-introspection
           pkg-config))
    (inputs
     (list cairo
           chafa
           cli11
           expat
           fftw
           fmt
           imagemagick
           imath
           lcms
           libexif
           libgsf
           librsvg
           libsixel
           libwebp
           libxcb
           matio
           nlohmann-json
           opencv
           openexr
           openssl
           orc
           pango
           poppler
           range-v3
           spdlog
           tbb
           vips
           wayland
           wayland-protocols
           xcb-util-image))
    (home-page "https://github.com/jstkdng/ueberzugpp")
    (synopsis "Drop in replacement for ueberzug written in C++")
    (description "Überzug++ is a command line utility written in C++ which
 allows to draw images on terminals by using X11/Wayland child windows, sixels,
 kitty and iterm2.
 Advantages over @command{w3mimgdisplay}:
@itemize
@item Support for Wayland: Sway, Hyprland, niri and Wayfire
@item No race conditions as a new window is created to display images
@item Expose events will be processed, so images will be redrawn on switch
 workspaces
@item Tmux support on X11, Sway and Hyprland
@item Terminals without the @env{WINDOWID} environment variable are supported
@item Chars are used as position - and size unit
@item No memory leak (usage of smart pointers)
@item A lot of image formats supported (through OpenCV and libvips).
@item GIF and animated WEBP support on X11, Sixel, Sway and hyprland
@item Fast image downscaling (through OpenCV and OpenCL)
@item Cache resized images for faster viewing
@end itemize")
    (license license:gpl3)))
 (define-public vv
  (package
    (name "vv")
@@ -45,6 +45,7 @@
 ;;; Copyright © 2025 Junker <dk@junkeria.club>
 ;;; Copyright © 2025 Hugo Buddelmeijer <hugo@buddelmeijer.nl>
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1104,6 +1105,53 @@ images of initially unknown height.")
    (license (list license:isc          ; pbmtools/p?m.5
                   license:gpl2+))))    ; the rest
 (define-public sjpeg
  ;; No tags available.
  (let ((commit "46da5aec5fce05faabf1facf0066e36e6b1c4dff")
        (revision "0"))
    (package
      (name "sjpeg")
      (version (git-version "0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/webmproject/sjpeg")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0r496mp2ylisspwxl4883pzbl0l8qpscd1x9l7sb5nnmknawr868"))))
      (build-system cmake-build-system)
      (arguments
       (list
        #:phases
        #~(modify-phases %standard-phases
            (add-after 'unpack 'patch-cmake
              (lambda _
                ;; Enable building shared libraries.
                (substitute* "CMakeLists.txt"
                  (("add_library\\(sjpeg " all)
                   (string-append all "SHARED ")))))
            (add-before 'check 'patch-tests
              (lambda _
                (with-directory-excursion "../source/tests"
                  (substitute* '("test_cmd.sh" "test_png_jpg.sh")
                    (("\\.\\./examples") "../../build")))))
            (replace 'check
              (lambda* (#:key tests? #:allow-other-keys)
                (when tests?
                  (with-directory-excursion "../source/tests"
                    (invoke "./test_cmd.sh")
                    (invoke "./test_png_jpg.sh"))))))))
      (inputs (list freeglut libjpeg-turbo libpng zlib))
      (home-page "https://github.com/webmproject/sjpeg")
      (synopsis "Simple JPEG encoder")
      (description
       "sjpeg is a simple encoding library for encoding baseline JPEG files.
 It is also a command-line tool that takes PNG or JPEG images as input to
 produce JPEG files.")
    (license license:asl2.0))))
 (define-public openjpeg-data
  (package
    (name "openjpeg-data")
@@ -1180,6 +1228,63 @@ JPEG 2000 Reference Software.")
    (home-page "https://github.com/uclouvain/openjpeg")
    (license license:bsd-2)))
 (define jp2k-test-codestreams
 (origin
   (method git-fetch)
   (uri (git-reference
         (url "https://github.com/aous72/jp2k_test_codestreams")
         (commit "eda0844b9f3be47d9b64194bcea5eb1ac2285e39")))
   (sha256
    (base32 "1sci4a4dvgrgmrf942zdf0hqhcx30a5lffwfy6r3hya35l3q8q8f"))))
 (define-public openjph
  (package
    (name "openjph")
    (version "0.27.3")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/aous72/OpenJPH")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1knygwn4bf6n53qr12w05yava7464x3c70rf5r20sz8adjcfccvx"))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:configure-flags
      #~(if #$(%current-target-system)
            '()
            '("-DOJPH_BUILD_TESTS=ON"))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'patch-cmake
            (lambda _
              (substitute* "tests/CMakeLists.txt"
                (("^FetchContent_MakeAvailable\\(googletest\\)")
                 #$(if (%current-target-system)
                       ""
                       "find_package(GTest REQUIRED)"))
                (("^FetchContent_MakeAvailable\\(jp2k_test_codestreams\\).*")
                 ""))))
          #$@(if (%current-target-system)
                 #~()
                 #~((add-before 'check 'unpack-jp2k-test-codestreams
                      (lambda _
                        (copy-recursively #$jp2k-test-codestreams
                                          "tests/jp2k_test_codestreams"))))))))
    (native-inputs (if (%current-target-system)
                       '()
                       (list googletest)))
    (inputs (list libtiff))
    (home-page "https://github.com/aous72/OpenJPH")
    (synopsis "JPEG2000 Part-15 (or JPH or HTJ2K) implementation")
    (description
     "OpenJPH is an implementation of @acronym{HTJ2K, High-throughput JPEG2000},
 also known as JPH, JPEG2000 Part 15, ISO/IEC 15444-15, and ITU-T T.814.")
    (license license:bsd-2)))
 (define-public openslide
  (package
    (name "openslide")
@@ -379,6 +379,15 @@ as the native format.")
                   ;; Re-instate the tests disabled in inkscape/pinned, now that
                   ;; their ImageMagick requirement is satisfied.
                   #~((replace 'check (assoc-ref gnu:%standard-phases 'check))))
            #$@(if (or (target-aarch64?)
                       (target-ppc64le?)
                       (target-riscv64?))
                   '((add-after 'unpack 'disable-geom-pathstroke-test
                       (lambda _
                         ;; https://gitlab.com/inkscape/lib2geom/-/work_items/80
                         (substitute* "testfiles/CMakeLists.txt"
                           (("    geom-pathstroke-test") "")))))
                   '())
            (replace 'wrap-program
              ;; Ensure Python is available at runtime.
              (lambda _
@@ -326,13 +326,6 @@ surveys")
 accessibility clients such as screen readers.")
    (license license:lgpl2.1+)))
 (define-public libqaccessibilityclient-qt5
  (package
    (inherit libqaccessibilityclient)
    (name "libqaccessibilityclient-qt5")
    (inputs (modify-inputs inputs
              (replace "qtbase" qtbase-5)))))
 (define-public qca
  (package
    (name "qca")
@@ -189,14 +189,14 @@ structure.  It features:
 (define-public kcachegrind
  (package
    (name "kcachegrind")
-    (version "25.12.3")
+    (version "26.04.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://kde/stable/release-service/" version
                                  "/src/kcachegrind-" version ".tar.xz"))
              (sha256
               (base32
-                "1lpgx3i2h3iq99nsssgwjpsvsn6izy4sp5l8rh7984lbd06wqsp9"))))
+                "1krd0zbssj5q9shwdpmsnzpah2p6insl0sdh3x6dbrwnlyqaydbv"))))
    (build-system cmake-build-system)
    (native-inputs
     (list extra-cmake-modules perl python qttools kdoctools))
@@ -35,6 +35,50 @@
 ;;; Libraries:
 ;;;
 (define-public go-github-com-elastic-crd-ref-docs
  (package
    (name "go-github-com-elastic-crd-ref-docs")
    (version "0.3.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/elastic/crd-ref-docs")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0vg3zjcgcq04cbqc8sk638q9v5r62w8r8x22yl7g9blbbr13sj7s"))
       (modules '((guix build utils)))
       (snippet
        #~(begin
            ;; Submodules with their own go.mod files and packaged separately:
            ;;
            ;; - github.com/elastic/crd-ref-docs/test
            (delete-file-recursively "test")))))
    (build-system go-build-system)
    (arguments
     (list
      #:skip-build? #t
      #:import-path "github.com/elastic/crd-ref-docs"))
    (native-inputs
     (list go-github-com-stretchr-testify))
    (propagated-inputs
     (list go-github-com-goccy-go-yaml
           go-github-com-masterminds-sprig-v3
           go-github-com-spf13-cobra
           go-golang-org-x-tools
           go-go-uber-org-zap
           go-k8s-io-apimachinery
           go-sigs-k8s-io-controller-runtime
           ;; go-sigs-k8s-io-gateway-api
           go-sigs-k8s-io-controller-tools))
    (home-page "https://github.com/elastic/crd-ref-docs")
    (synopsis "Kubernetes CRD reference documentation generator")
    (description
     "This package generates API reference documentation by scanning a source
 tree for exported @acronym{CustomResourceDefinition, CRD} types.")
    (license license:asl2.0)))
 (define-public go-go-etcd-io-etcd-client-v3
  (package
    (name "go-go-etcd-io-etcd-client-v3")
@@ -615,6 +659,95 @@ controllers that manipulate both Kubernetes CRDs and aggregated/built-in
 Kubernetes APIs.")
    (license license:asl2.0)))
 (define-public go-sigs-k8s-io-controller-tools
  (package
    (name "go-sigs-k8s-io-controller-tools")
    (version "0.19.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/kubernetes-sigs/controller-tools")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1n6vc681bhhk972l1ijg7m01xy3zvi5i17y6fhac1m7bs7rrgz1l"))
       (modules '((guix build utils)))
       (snippet
        #~(begin
            ;; Submodules with their own go.mod files and packaged separately:
            ;;
            ;; - github.com/google/cel-go/codelab
            (for-each delete-file-recursively
                      (list "pkg/crd/testdata"
                            "pkg/loader/testmod"
                            "pkg/webhook/testdata"
                            "pkg/deepcopy/testdata"
                            "pkg/schemapatcher/testdata"
                            "pkg/applyconfiguration/testdata/cronjob"))))))
    (build-system go-build-system)
    (arguments
     (list
      #:skip-build? #t
      #:test-flags
      #~(list "-skip" (string-join
                       ;;  Expected success, but got an error:
                       ;;   <*fs.PathError | 0xc000314a20>:
                       ;;   chdir ./testdata: no such file or directory
                       ;;   {
                       ;;       Op: "chdir",
                       ;;       Path: "./testdata",
                       ;;       Err: <syscall.Errno>0x2,
                       ;;   }
                       ;; 0 Passed | 1 Failed
                       (list "TestObjectGeneration"
                             ;; 23 Passed | 19 Failed
                             "TestCRDGeneration"
                             ;; validation_test.go:118:
                             ;; failed to create validator:
                             ;; open ./testdata/testdata.kubebuilder.io_oneofs.yaml:
                             ;; no such file or directory
                             "TestOneOfConstraints"
                             ;; 3 Passed | 8 Failed
                             "TestLoader"
                             ;; 0 Passed | 2 Failed
                             "TestInPlaceCRDSchemaGeneration"
                             ;; 0 Passed | 11 Failed
                             "TestWebhookGeneration"
                             ;; 1 Passed | 1 Failed
                             "TestVersioning")
                       "|"))
      #:import-path "sigs.k8s.io/controller-tools"
      #:embed-files
      #~(list "authoring.tmpl")))
    (native-inputs
     (list go-github-com-google-go-cmp
           go-github-com-onsi-ginkgo
           go-github-com-onsi-gomega))
    (propagated-inputs
     (list go-github-com-fatih-color
           go-github-com-gobuffalo-flect
           go-github-com-spf13-cobra
           go-github-com-spf13-pflag
           go-golang-org-x-tools
           go-golang-org-x-tools-go-packages-packagestest
           go-gopkg-in-yaml-v2
           go-gopkg-in-yaml-v3
           go-k8s-io-api
           go-k8s-io-apiextensions-apiserver
           go-k8s-io-apimachinery
           go-k8s-io-apiserver
           go-k8s-io-code-generator
           go-k8s-io-gengo-v2
           go-k8s-io-utils
           go-sigs-k8s-io-yaml))
    (home-page "https://sigs.k8s.io/controller-tools")
    (synopsis "Kubernetes controller-tools Project")
    (description
     "The Kubernetes controller-tools Project is a set of go libraries for building
 Controllers.")
    (license license:asl2.0)))
 ;;;
 ;;; Executables:
@@ -687,6 +820,45 @@ api-status.csv files
 functions
@end itemize")))
 (define-public kubernetes-controller-tools
  (package/inherit go-sigs-k8s-io-controller-tools
    (name "kubernetes-controller-tools")
    (arguments
     (substitute-keyword-arguments arguments
       ((#:import-path _) "sigs.k8s.io/controller-tools/cmd/...")
       ((#:install-source? #t #t) #f)
       ((#:skip-build? #t #t) #f)
       ((#:tests? #t #t) #f)
       ((#:unpack-path _ "") "sigs.k8s.io/controller-tools")))
    (native-inputs
     (package-propagated-inputs go-sigs-k8s-io-controller-tools))
    (propagated-inputs '())
    (inputs '())
    (description
     "This package provides helper commands to work with Kubernetes (k8s):
@itemize:
@item @command{controller-gen} - generates Kubernetes API extension resources
 and code
@item @command{helpgen} - generates marker help using @command{godoc}, based
 on the presence of a particular marker
@item @command{type-scaffold} - scaffolds out basic bits of a Kubernetes type
@end itemize
 For the Go library, refer to go-sigs-k8s-io-controller-tools package.")))
 (define-public kubernetes-crd-ref-docs
  (package/inherit go-github-com-elastic-crd-ref-docs
    (name "kubernetes-crd-ref-docs")
    (arguments
     (substitute-keyword-arguments arguments
       ((#:install-source? #t #t) #f)
       ((#:skip-build? #t #t) #f)
       ((#:tests? #t #t) #f)))
    (native-inputs
     (package-propagated-inputs go-github-com-elastic-crd-ref-docs))
    (propagated-inputs '())
    (inputs '())))
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above in alphabetic order:
@@ -15,6 +15,7 @@
 ;;; Copyright © 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2026 Nguyễn Gia Phong <cnx@loang.net>
 ;;; Copyright © 2026 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2026 Spencer King <spencer.king@wustl.edu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -37,6 +38,7 @@
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages audio)
  #:use-module (gnu packages base)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages dbm)
@@ -50,6 +52,7 @@
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages ibus)
  #:use-module (gnu packages java)
  #:use-module (gnu packages libffi)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages man)
@@ -88,7 +91,8 @@
  #:use-module (guix gexp)
  #:use-module (guix git-download)
  #:use-module (guix modules)
-  #:use-module (guix utils))
+  #:use-module (guix utils)
  #:use-module (srfi srfi-1))
 (define-public nimf
  (package
@@ -1109,6 +1113,106 @@ for longer text sequences.  As it relies on dictionaries,
 if a word is missing or mispelled, the detection will fail.")
    (license license:agpl3)))
 ;; This package provides the database files created by
 ;; The Árni Magnússon Institute for Icelandic Studies which
 ;; are needed for building certain packages.
 ;; This package is not intended to be installed directly.
 (define arnastofnun-dim
  (let ((version "May2026"))
    (origin
      (method git-fetch)
      (uri (git-reference
             (url "https://codeberg.org/spencerking/DIM-mirror")
             (commit version)))
      (file-name (git-file-name "arnastofnun-dim" version))
      (sha256
       (base32 "1ribxkdj9clafdqa572bp0qh73spv4wagyx49jqdivq8r3b631n6")))))
 (define-public python-islenska-bootstrap
  (hidden-package
   (package
     (name "python-islenska-bootstrap")
     (version "1.1.1")
     ;; Use the git source since this should not include database files.
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
               (url "https://github.com/mideind/BinPackage")
               (commit version)))
        (file-name (git-file-name "python-islenska" version))
        (sha256
         (base32 "1wgv2k41m1jmsqr1sdlj92kw5v3d5r9cg2268vfh8308pncn1fya"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:phases
       ;; Add two new phases to ensure that the database resource files
       ;; are included in the installed package. This is necessary for
       ;; running the bundled build scripts (tools/binpack.py and
       ;; tools/dawgbuilder.py) when bootstrapping.
       #~(modify-phases %standard-phases
           (add-after 'unpack 'create-manifest-in
             (lambda* (#:key inputs #:allow-other-keys)
               (with-output-to-file "MANIFEST.in"
                 (lambda ()
                   (display "graft src/islenska/resources")))))
           (add-after 'unpack 'patch-setup-py
             (lambda* (#:key inputs #:allow-other-keys)
               (substitute* "setup.py"
                 (("(.*)cffi_modules=.*" cffi indent)
                  (string-append
                   cffi
                   indent "package_data={'islenska':['src/resources/*']},\n"
                   indent "include_package_data=True,\n"))))))
       ;; Tests will fail since database files have not been bootstrapped yet.
       #:tests? #f))
     (propagated-inputs (list python-cffi python-typing-extensions))
     (native-inputs (list python-cffi python-pytest python-setuptools))
     (home-page "https://github.com/mideind/BinPackage")
     (synopsis
      "The vocabulary of modern Icelandic, encapsulated in a Python package")
     (description
      "Islenska is a Python package that embeds the vocabulary of the Database
 of Icelandic Morphology and offers various lookups and queries of the data.
 The database contains over 6.5 million entries, over 3.1 million unique word
 forms, and about 300,000 distinct lemmas.")
     (license license:expat))))
 (define-public python-islenska
  (package/inherit python-islenska-bootstrap
    (name "python-islenska")
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          ;; Delete the phases added for python-islenska-bootstrap.
          (delete 'create-manifest-in)
          (delete 'patch-setup-py)
          ;; Copy KRISTINsnid.csv to the expected directory
          ;; for the build scripts.
          (add-after 'unpack 'unpack-resources
            (lambda* (#:key inputs #:allow-other-keys)
              (install-file
               (search-input-file inputs "KRISTINsnid.csv/KRISTINsnid.csv")
               "src/islenska/resources")))
          ;; Run the build scripts
          (add-before 'build 'build-databases
            (lambda _
              (invoke "python" "tools/binpack.py")
              (invoke "python" "tools/dawgbuilder.py"))))
      #:tests? #t))
    (native-inputs (list arnastofnun-dim
                         python-cffi
                         python-islenska-bootstrap
                         python-pytest
                         python-setuptools
                         unzip))
    (license (list license:cc-by4.0     ;resource files
                   license:expat))
    (properties
     (alist-delete 'hidden? (package-properties python-islenska-bootstrap)))))
 (define-public python-sacremoses
  (package
    (name "python-sacremoses")
@@ -530,7 +530,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; The current "mainline" kernel.
-(define-public linux-libre-7.0-version "7.0.8")
+(define-public linux-libre-7.0-version "7.0.10")
 (define-public linux-libre-7.0-gnu-revision "gnu")
 (define deblob-scripts-7.0
  (linux-libre-deblob-scripts
@@ -540,7 +540,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "0a7572zw5y3k4gs4p3h5w0s9bhd63pdjxz6vxbr96sq6r8b6k02n")))
 (define-public linux-libre-7.0-pristine-source
  (let ((version linux-libre-7.0-version)
-        (hash (base32 "08nbdmgy4bbpmjzkh6n4v3shksvxpcxhy8biv5w7qkwz5jrayi8r")))
+        (hash (base32 "1p1j9s0b4qv9m0pm6vj477rqgyd1b0lsk0gy74cks3n2cbmpfj89")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-7.0)))
@@ -563,7 +563,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                            (%upstream-linux-source version hash)
                            deblob-scripts-6.19)))
-(define-public linux-libre-6.18-version "6.18.31")
+(define-public linux-libre-6.18-version "6.18.33")
 (define-public linux-libre-6.18-gnu-revision "gnu")
 (define deblob-scripts-6.18
  (linux-libre-deblob-scripts
@@ -573,7 +573,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "0qlih8w8wg4v5cwbmd34rbhb6mjgbx69i9rx3s2vxw7h42q9l0ai")))
 (define-public linux-libre-6.18-pristine-source
  (let ((version linux-libre-6.18-version)
-        (hash (base32 "1djqya5jlgg0q0ra5mvqdfcsbf13vxffhgxyqvy9qh2x91nvi850")))
+        (hash (base32 "10mp1ypsdz42jr26g1xxbw806mvpy0n35418fhsgxxlr4lqgy5kg")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-6.18)))
@@ -582,7 +582,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; Here are the support timelines:
 ;; <https://www.kernel.org/category/releases.html>
-(define-public linux-libre-6.12-version "6.12.89")
+(define-public linux-libre-6.12-version "6.12.91")
 (define-public linux-libre-6.12-gnu-revision "gnu")
 (define deblob-scripts-6.12
  (linux-libre-deblob-scripts
@@ -592,12 +592,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "1x48hpmvajz7v5wn1vdd7l5r14mq4ngzh5npz3pj81z4f1g61i0a")))
 (define-public linux-libre-6.12-pristine-source
  (let ((version linux-libre-6.12-version)
-        (hash (base32 "184r0wji02qw2n7ncx0jrf382yk20nnf79fvafim6a4x9a0gsnjq")))
+        (hash (base32 "0sbrb612b653w64g5jkpbf68y0fka2sgnwblam41k7wz2sgapwhg")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-6.12)))
-(define-public linux-libre-6.6-version "6.6.138")
+(define-public linux-libre-6.6-version "6.6.141")
 (define-public linux-libre-6.6-gnu-revision "gnu")
 (define deblob-scripts-6.6
  (linux-libre-deblob-scripts
@@ -607,12 +607,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "0xp9b2vkrb0g0rn4i33b59rhp4sgh1dbwzk28vwz7kwac6l5rcpi")))
 (define-public linux-libre-6.6-pristine-source
  (let ((version linux-libre-6.6-version)
-        (hash (base32 "03x8ald0sjzdb6kpzrw8adnc78r3mdxrx8mzbxbpwp35vdgnpl5d")))
+        (hash (base32 "1qbzxgqs7q9gyqfrf0j7p0pgjxnjj5mibamhm280mf9anqp6bhiv")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-6.6)))
-(define-public linux-libre-6.1-version "6.1.172")
+(define-public linux-libre-6.1-version "6.1.174")
 (define-public linux-libre-6.1-gnu-revision "gnu")
 (define deblob-scripts-6.1
  (linux-libre-deblob-scripts
@@ -622,12 +622,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "1w5pfws6l39dpc3lzazs1n6r4m96f6rdf6vb2scy5fhmrd933ldc")))
 (define-public linux-libre-6.1-pristine-source
  (let ((version linux-libre-6.1-version)
-        (hash (base32 "16dlfdzjcsc21m5sfbhamg8y3ay54rz8a0qqvqrmxq691mhjwrzi")))
+        (hash (base32 "0vp07x4v82qnmc1pifv3ynp2ab5mvlbfnpqvs5893bi3yrnk927d")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-6.1)))
-(define-public linux-libre-5.15-version "5.15.206")
+(define-public linux-libre-5.15-version "5.15.208")
 (define-public linux-libre-5.15-gnu-revision "gnu")
 (define deblob-scripts-5.15
  (linux-libre-deblob-scripts
@@ -637,12 +637,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "1s6km2r2mad0wpf7nqn4rqsykw1lm386l1yskmil24239fbva1f1")))
 (define-public linux-libre-5.15-pristine-source
  (let ((version linux-libre-5.15-version)
-        (hash (base32 "07z6lla7xpnn4sn3l4zw3x7m8ih8w6h54k71qrxrf5zv9i7wxijz")))
+        (hash (base32 "0wmi50q8vgblhbh77d1a4sw4snymr6srqd22bxcjg9i7wcv70gdm")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-5.15)))
-(define-public linux-libre-5.10-version "5.10.255")
+(define-public linux-libre-5.10-version "5.10.257")
 (define-public linux-libre-5.10-gnu-revision "gnu1")
 (define deblob-scripts-5.10
  (linux-libre-deblob-scripts
@@ -652,7 +652,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "1hgza8fsps7bkjf4i0f2xgvrh1r183z3i6lxrr2nr8qbi5d13qs7")))
 (define-public linux-libre-5.10-pristine-source
  (let ((version linux-libre-5.10-version)
-        (hash (base32 "19v6g2fq4nqv38irlcd9x14s6d398c56mxzpyc03q4xmpy3v6mir")))
+        (hash (base32 "1lghcrxc1fqarvym03jrcda2a3labc887ci9yjqgbmv3nphzvc88")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-5.10)))
@@ -76,6 +76,7 @@
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bdw-gc)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages crypto)
@@ -102,7 +103,6 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages notcurses)
  #:use-module (gnu packages onc-rpc)
  #:use-module (gnu packages perl)
@@ -27,7 +27,7 @@
 (define-public lout
  (package
    (name "lout")
-    (version "3.43.2")
+    (version "3.43.4")
    ;; The original version at <https://savannah.nongnu.org/projects/lout/> is
    ;; effectively abandoned, not receiving build fixes and the likes, and
@@ -41,7 +41,7 @@
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "0lvk1ffzgydgj4csaclrh3a9nwla061clgf8lda6n47masg12qzi"))))
+                "09s6mcimvhw96i3vncqa8cz04xcq9x3qir8m1nzqfny8vdwyz35n"))))
    (build-system gnu-build-system)     ; actually, just a makefile
    (outputs '("out" "doc"))
    (native-inputs
@@ -74,7 +74,6 @@
  #:use-module (gnu packages linux)
  #:use-module (gnu packages m4)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages pretty-print)
  #:use-module (gnu packages rdf)
@@ -151,6 +150,22 @@ automatic memory management with incremental garbage collection, making it ideal
 for configuration, scripting, and rapid prototyping.")
    (license license:x11)))
 (define-public lua-5.5
  (package (inherit lua)
           (version "5.5.0")
           (source (origin
                     (method url-fetch)
                     (uri (string-append "https://www.lua.org/ftp/lua-"
                                         version ".tar.gz"))
                     (sha256
                      (base32 "0gcbsr00difm2s82pflxg28zcnjka9048lncbfvwl1fhpcmw7k2p"))
                     ;; Note: Some lua-5.4 patches seem to apply without issues
                     (patches (search-patches "lua-5.4-pkgconfig.patch"
                                              "lua-5.4-liblua-so.patch"
                                              "lua-5.x-search-path-helpers.patch"
                                              "lua-5.5-search-paths.patch"))))
           (native-search-paths (lua-search-paths "5.5"))))
 (define-public lua-5.4
  (package (inherit lua)
           (version "5.4.8")
@@ -96,7 +96,6 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages monitoring)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages onc-rpc)
  #:use-module (gnu packages oneapi)
@@ -328,7 +328,7 @@ PostScript, and PDF.  Additional tools include the @command{man} viewer, and
 (define-public man-pages
  (package
    (name "man-pages")
-    (version "6.16")
+    (version "6.18")
    (source
     (origin
       (method url-fetch)
@@ -338,7 +338,7 @@ PostScript, and PDF.  Additional tools include the @command{man} viewer, and
              (string-append "mirror://kernel.org/linux/docs/man-pages/Archive/"
                             "man-pages-" version ".tar.xz")))
       (sha256
-        (base32 "18yp64vb8br49d44jmq47dc901n7p20nqs88zsf8106dfnypl94f"))))
+        (base32 "1l949fvqikf88qjxbp1wny185prd3mcgcd3s49l8qx2rigfgld69"))))
    (build-system gnu-build-system)
    (arguments
     (list
@@ -125,6 +125,7 @@
  #:use-module (gnu packages benchmark)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages calendar)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cmake)
@@ -176,7 +177,6 @@
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages netpbm)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages onc-rpc)
  #:use-module (gnu packages oneapi)
@@ -184,7 +184,7 @@ asyncio_mode = auto")))))
           python-attrs
           python-cachetools
           python-click
-           python-dbus-1.2
+           python-dbus
           python-janus
           python-keyring
           python-logbook
@@ -3857,11 +3857,15 @@ follows a traditional multi-track tape recorder control paradigm.")
     (list
      #:phases
      '(modify-phases %standard-phases
-         (add-after 'unpack 'python3.11-compatibility
+         (add-after 'unpack 'python3.12-compatibility
           (lambda _
             (substitute* '("waflib/Context.py"
                            "waflib/ConfigSet.py")
-               (("'rU'") "'r'"))))
+               (("'rU'") "'r'"))
             (substitute* "waflib/Context.py"
               (("imp.new_module") "types.ModuleType")
               (("import os, re, imp, sys")
                "import os, re, types, sys"))))
         (add-after 'unpack 'remove-sse-flags
           (lambda* (#:key system #:allow-other-keys)
             (unless (or (string-prefix? "x86_64" system)
@@ -1006,11 +1006,11 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
    (home-page "https://nng.nanomsg.org/")
    (license license:expat)))
-(define-public nng-1.10
+(define-public nng-1.11
  (package
    (inherit nng)
    (name "nng")
-    (version "1.10.1")
+    (version "1.11")
    (source
     (origin
       (method git-fetch)
@@ -1019,9 +1019,12 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "13nmz1p8qd12gyj7wm8fz1ccap47qh41sxz4jqdhj8gnd0kiy5h4"))))
+        (base32 "1l4rxwnc9knndwmy7xg53adyrm17ld7c5gxwm7vgfmgfy0my4zy8"))))
    (arguments
     (list
      ;; At least on aarch64-linux, running tests in parallel leads to ports
      ;; being unavailable in later tests, which then fail.
      #:parallel-tests? #false
      #:configure-flags
      '(list "-DNNG_ENABLE_COVERAGE=ON"
             "-DNNG_ENABLE_TLS=ON"
@@ -1035,6 +1038,7 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
               (("add_nng_test1\\(httpclient 60 NNG_SUPP_HTTP\\)") "")
               (("add_nng_test\\(tls 60\\)") ""))
             (substitute* "src/platform/CMakeLists.txt"
               ;; This test only seems to fail on aarch64-linux
               (("nng_test\\(platform_test\\)") "")
               (("nng_test\\(resolver_test\\)") ""))
             (substitute* "src/sp/transport/tcp/CMakeLists.txt"
@@ -3687,7 +3691,7 @@ can be whipped up with little effort.")
    (build-system gnu-build-system)
    (native-inputs (list pkg-config))
    (inputs
-     (list jansson libcap ncurses))
+     (list jansson ncurses))
    (arguments
     `(#:tests? #f))                    ; tests require network access
    (home-page "https://www.bitwizard.nl/mtr/")
@@ -5,6 +5,7 @@
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2025 Maxim Cournoyer <maxim@guixotic.coop>
 ;;; Copyright © 2026 Luca Kredel <luca.kredel@web.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -22,127 +23,17 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 (define-module (gnu packages ninja)
-  #:use-module ((guix licenses) #:select (asl2.0 expat))
+  #:use-module (gnu packages build-tools)
-  #:use-module (guix gexp)
+  #:use-module (guix deprecation))
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (guix git-download)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system trivial)
  #:use-module (guix utils)
  #:use-module (gnu packages)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages python)
  #:use-module (gnu packages re2c)
  #:use-module (srfi srfi-1))
-(define-public ninja/pinned
+(define-deprecated/public-alias ninja/pinned
-  (hidden-package
+  (@ (gnu packages build-tools) ninja/pinned))
   (package
     (name "ninja")
     (version "1.13.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/ninja-build/ninja")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
                 "0lp9dmxbjyjwv089i8mgq3nvnhpbnsn01ifm05m9s47w7cifrl8g"))))
     (build-system gnu-build-system)
     (inputs (list python-wrapper re2c))
     (arguments
      '(; Tests now require googletest, which is a circular dependency.
        #:tests? #f
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
            (lambda _
              (substitute* "src/subprocess-posix.cc"
                (("/bin/sh") (which "sh")))
              (substitute* "src/subprocess_test.cc"
                (("/bin/echo") (which "echo")))))
          (replace 'build
            (lambda _
              (invoke "./configure.py" "--bootstrap")))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
                (invoke "./configure.py")
                (invoke "./ninja" "ninja_test")
                (invoke "./ninja_test"))))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin"))
                     (doc (string-append out "/share/doc/ninja")))
                (install-file "ninja" bin)
                (install-file "doc/manual.asciidoc" doc)))))))
     (home-page "https://ninja-build.org/")
     (synopsis "Small build system")
     (description
      "Ninja is a small build system with a focus on speed.  It differs from
 other build systems in two major respects: it is designed to have its input
 files generated by a higher-level build system, and it is designed to run
 builds as fast as possible.")
    (license asl2.0))))
-(define-public ninja
+(define-deprecated/public-alias ninja
-  (package/inherit ninja/pinned
+  (@ (gnu packages build-tools) ninja))
    (properties (alist-delete 'hidden? (package-properties ninja/pinned)))))
-(define-public samurai
+(define-deprecated/public-alias samurai
-  (package
+  (@ (gnu packages build-tools) samurai))
    (name "samurai")
    (version "1.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/michaelforney/samurai")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "04iw18hgkm72yrl83a2xh1jc47w9rilpb95kwick0j37b4q3gxj4"))))
    (build-system gnu-build-system)
    (arguments
     (list #:tests? #f                  ;no test suite
           #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
                                (string-append "PREFIX=" #$output))
           #:phases #~(modify-phases %standard-phases
                        (add-after 'unpack 'patch-/bin/sh
                          (lambda* (#:key inputs #:allow-other-keys)
                            (substitute* "build.c"
                              (("/bin/sh")
                               (search-input-file inputs "bin/sh")))))
                        (delete 'configure))))
    (inputs (list bash-minimal))
    (home-page "https://github.com/michaelforney/samurai")
    (synopsis "Ninja-compatible build tool written in C")
    (description "@code{samurai} is a ninja-compatible build tool written in
 C99 with a focus on simplicity, speed, and portability.  It is
 feature-complete and supports most of the same options as ninja.  This package
 provides the command @command{samu}.  For a @command{ninja} command
 replacement, use the @code{samu-as-ninja-wrapper} package.")
    (license (list asl2.0               ;for the most part
                   expat))))            ;htab.h, htab.c and tree.c
-(define-public samu-as-ninja-wrapper
+(define-deprecated/public-alias samu-as-ninja-wrapper
-  (package/inherit samurai
+  (@ (gnu packages build-tools) samu-as-ninja-wrapper))
    (name "samu-as-ninja-wrapper")
    (build-system trivial-build-system)
    (arguments
     (list #:builder
           (with-imported-modules '((guix build utils))
             #~(begin
                 (use-modules (guix build utils))
                 (let ((bindir (string-append #$output "/bin"))
                       (samu (string-append #$(this-package-input "samurai")
                                            "/bin/samu")))
                   (mkdir-p bindir)
                   (symlink samu (string-append bindir "/ninja")))))))
    (inputs (list samurai))
    (description "This package provides the @command{ninja} command,
 implemented as a symbolic link to the @command{samu} command of @code{samurai}
 package.")))
@@ -109,7 +109,6 @@
  #:use-module (gnu packages markup)
  #:use-module (gnu packages nettle)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages node)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages patchutils)
@@ -304,6 +304,12 @@ human.")
                        ruby-asciidoctor/minimal))
               #~'()
               #~(list "-DWITH_XC_DOCS=NO")))
      ;; Entries have recently become sorted per the locale, and
      ;; causes testentrymodel to fail when using the C locale (see:
      ;; https://github.com/keepassxreboot/keepassxc/issues/11813).
      ;; testClip runs 'xclip', which hangs in the container,
      ;; perhaps because it lacks a TTY.
      #:test-exclude "testentrymodel|testcli"
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'record-clipboard-programs
@@ -327,17 +333,7 @@ human.")
                  "\")")))
              (substitute* "src/gui/Clipboard.cpp"
                (("\"wl-copy\"")
-                 (format #f "~s" (search-input-file inputs "bin/wl-copy"))))))
+                 (format #f "~s" (search-input-file inputs "bin/wl-copy")))))))))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
                ;; Entries have recently become sorted per the locale, and
                ;; causes testentrymodel to fail when using the C locale (see:
                ;; https://github.com/keepassxreboot/keepassxc/issues/11813).
                ;; testClip runs 'xclip', which hangs in the container,
                ;; perhaps because it lacks a TTY.
                (invoke "ctest" "--exclude-regex"
                        "testentrymodel|testcli")))))))
    (native-inputs
     (append
      (list qttools-5)
@@ -0,0 +1,26 @@
 Remove nonfree tile data.
 Note this does not remove the directories; ensure they are snippeted out separately.
 Patch by bdunahu <bdunahu@operationnull.com>.
 diff --git a/lib/tiles/list.txt b/lib/tiles/list.txt
 index 3677ba45e..eb2592c9f 100644
 --- a/lib/tiles/list.txt
 +++ b/lib/tiles/list.txt
@@ -54,15 +48,3 @@
 size:16:16:8x16.png
 pref:graf-nmd.prf
 extra:0:0:0
 -
 -name:5:Shockbolt Dark
 -directory:shockbolt
 -size:64:64:64x64.png
 -pref:graf-shb-dark.prf
 -extra:1:27:31
 -
 -name:6:Shockbolt Light
 -directory:shockbolt
 -size:64:64:64x64.png
 -pref:graf-shb-light.prf
 -extra:1:27:31
@@ -0,0 +1,50 @@
 Change Lua to use GUIX_LUA_PATH and GUIX_LUA_CPATH to construct the default
 LUA_PATH and LUA_CPATH, instead of using hard-coded paths that Guix doesn't
 populate.
 These paths don't use Lua's usual '?' path wildcard, and thus are compatible
 with Guix's search-paths mechanism.
 This patch uses functions defined in lua-5.x-search-path-helpers.patch.
 --- a/src/loadlib.c
 +++ b/src/loadlib.c
@@ -280,7 +280,9 @@
   if (path == NULL)  /* no versioned environment variable? */
     path = getenv(envname);  /* try unversioned name */
   if (path == NULL || noenv(L))  /* no environment variable? */
 -    lua_pushexternalstring(L, dft, strlen(dft), NULL, NULL);  /* use default */
 +    /* Copy our constructed default string onto the Lua stack.
 +     * Otherwise the location might be reused for another string and case us problems! */
 +    lua_pushstring(L, dft);  /* use default */
   else if ((dftmark = strstr(path, LUA_PATH_SEP LUA_PATH_SEP)) == NULL)
     lua_pushstring(L, path);  /* nothing to change */
   else {  /* path contains a ";;": insert default path in its place */
@@ -721,14 +729,25 @@
 }
 +#include "./guixpaths.c"
 +
 +
 LUAMOD_API int luaopen_package (lua_State *L) {
   luaL_getsubtable(L, LUA_REGISTRYINDEX, CLIBS);  /* create CLIBS table */
   lua_pop(L, 1);  /* will not use it now */
   luaL_newlib(L, pk_funcs);  /* create 'package' table */
   createsearcherstable(L);
 +
   /* set paths */
 +  /* Calculate default LUA_PATH and LUA_CPATH values from their
 +     corresponding GUIX_ environment variables */
 +  const char* default_path = guix_path(L); // push default_path
 +  const char* default_cpath = guix_cpath(L); // push default_cpath
 +  lua_pushvalue(L, -3); // copy the old head of the stack back to the top
 -  setpath(L, "path", LUA_PATH_VAR, LUA_PATH_DEFAULT);
 -  setpath(L, "cpath", LUA_CPATH_VAR, LUA_CPATH_DEFAULT);
 +  setpath(L, "path", LUA_PATH_VAR, default_path);
 +  setpath(L, "cpath", LUA_CPATH_VAR, default_cpath);
 +  lua_pop(L, 3); // pop our three working values back off the stack
 +
   /* store config information */
   lua_pushliteral(L, LUA_DIRSEP "\n" LUA_PATH_SEP "\n" LUA_PATH_MARK "\n"
                      LUA_EXEC_DIR "\n" LUA_IGMARK "\n");
@@ -1,513 +0,0 @@
 This patch shas been backported from the development version or Biostrings.
 From 100602242840322b5f6c267faaf8198c1a5aa2af Mon Sep 17 00:00:00 2001
 From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
 Date: Thu, 5 Mar 2026 22:36:30 -0800
 Subject: [PATCH] Biostrings 2.79.5: Get rid of never-used SparseMIndex and
 SparseList classes
 This also eliminates the non-API calls to R.
 ---
 DESCRIPTION                 |   3 +-
 NAMESPACE                   |   2 -
 R/MIndex-class.R            |  79 -------------------------
 R/SparseList-class.R        |  80 -------------------------
 man/Biostrings-internals.Rd |   9 ---
 src/Biostrings.h            |  41 -------------
 src/MIndex_class.c          |  67 ---------------------
 src/R_init_Biostrings.c     |   1 -
 src/SparseList_utils.c      | 113 ------------------------------------
 9 files changed, 1 insertion(+), 394 deletions(-)
 delete mode 100644 R/SparseList-class.R
 delete mode 100644 src/SparseList_utils.c
 diff --git a/DESCRIPTION b/DESCRIPTION
 index a5d027cc..dbc323ea 100644
 --- a/DESCRIPTION
 +++ b/DESCRIPTION
@@ -76,3 +76,3 @@ Collate: utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R GENETIC_CODE.R
         injectHardMask.R padAndClip.R strsplit-methods.R misc.R
 -        SparseList-class.R MIndex-class.R lowlevel-matching.R
 +        MIndex-class.R lowlevel-matching.R
         match-utils.R matchPattern.R maskMotif.R matchLRPatterns.R
 diff --git a/NAMESPACE b/NAMESPACE
 index ba1e3bfa..cf14db67 100644
 --- a/NAMESPACE
 +++ b/NAMESPACE
@@ -206,7 +206,6 @@ exportMethods(
 ### ==========================================================================
 ### STRING MATCHING
 ### --------------------------------------------------------------------------
 -###   SparseList-class.R
 ###   MIndex-class.R
 ###   lowlevel-matching.R
 ###   match-utils.R
@@ -220,7 +219,6 @@ exportMethods(
 ###   matchPDict.R
 exportClasses(
 -    #SparseList,
     MIndex, ByPos_MIndex,
     PreprocessedTB, Twobit, ACtree2,
     PDict3Parts,
 diff --git a/R/MIndex-class.R b/R/MIndex-class.R
 index 022f6746..f50f215e 100644
 --- a/R/MIndex-class.R
 +++ b/R/MIndex-class.R
@@ -218,82 +218,3 @@ ByPos_MIndex.combine <- function(mi_list)
     new("ByPos_MIndex", width0=ans_width0, NAMES=ans_names, ends=ans_ends)
 }
 -
 -### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 -### The "SparseMIndex" class (DISABLED FOR NOW).
 -### 
 -### Slot description:
 -###
 -###   ends_envir: a key-value list (environment) where the values are integer
 -###       vectors containing the ending positions of the pattern whose
 -###       position in the original dictionary is given by the key (the keys are
 -###       strings representing positive integers).
 -### 
 -
 -if (FALSE) {
 -
 -  setClass("SparseMIndex",
 -    contains="MIndex",
 -    representation(
 -        ends_envir="environment"
 -    )
 -  )
 -
 -  setMethod("show", "SparseMIndex",
 -    function(object)
 -    {
 -        cat("Sparse MIndex object of length ", length(object), "\n", sep="")
 -    }
 -  )
 -
 -  setMethod("[[", "SparseMIndex",
 -    function(x, i, j, ...)
 -    {
 -        i <- normalizeDoubleBracketSubscript(i, x)
 -        ans_end <- x@ends_envir[[formatC(i, width=10, format="d", flag="0")]]
 -        if (is.null(ans_end))
 -            ans_end <- integer(0)
 -        ans_width <- rep.int(x@width0[i], length(ans_end))
 -        ans_start <- ans_end - x@width0[i] + 1L
 -        new2("IRanges", start=ans_start, width=ans_width, check=FALSE)
 -    }
 -  )
 -
 -  ### An example of a SparseMIndex object of length 5 where only the
 -  ### 2nd pattern has matches:
 -  ###   > width0 <- c(9L, 10L, 8L, 4L, 10L)
 -  ###   > ends_envir <- new.env(hash=TRUE, parent=emptyenv())
 -  ###   > ends_envir[['0000000002']] <- c(199L, 402L)
 -  ###   > mindex <- new("SparseMIndex", width0=width0, NAMES=letters[1:5], ends_envir=ends_envir)
 -  ###   > mindex[[1]]
 -  ###   > mindex[[2]]
 -  ###   > mindex[[6]] # Error in mindex[[6]] : subscript out of bounds
 -  ###   > names(mindex)
 -  ###   > mindex[["a"]]
 -  ###   > mindex[["b"]]
 -  ###   > mindex[["aa"]] # Error in mindex[["aa"]] : pattern name ‘aa’ not found
 -  ###   > startIndex(mindex)
 -  ###   > endIndex(mindex)
 -  ###   > elementNROWS(mindex)
 -  ###
 -  setMethod("startIndex", "SparseMIndex",
 -    function(x)
 -    {
 -        all.names <- TRUE
 -        .Call2("SparseMIndex_endIndex",
 -              x@ends_envir, x@width0, x@NAMES, all.names,
 -              PACKAGE="Biostrings")
 -    }
 -  )
 -  setMethod("endIndex", "SparseMIndex",
 -    function(x)
 -    {
 -        all.names <- TRUE
 -        .Call2("SparseMIndex_endIndex",
 -              x@ends_envir, NULL, x@NAMES, all.names,
 -              PACKAGE="Biostrings")
 -    }
 -  )
 -
 -}
 -
 diff --git a/R/SparseList-class.R b/R/SparseList-class.R
 deleted file mode 100644
 index 8295fd0f..00000000
 --- a/R/SparseList-class.R
 +++ /dev/null
@@ -1,80 +0,0 @@
 -### =========================================================================
 -### SparseList objects
 -### -------------------------------------------------------------------------
 -###
 -
 -setClass("SparseList",
 -    representation(
 -        length="integer",
 -        env="environment"
 -    )
 -)
 -
 -### Typical use:
 -###   env <- new.env(hash=TRUE, parent=emptyenv())
 -###   key <- formatC(98L, width=10, format="d", flag="0")
 -###   value <- 3:-2
 -###   assign(key, value, envir=env)
 -###   x <- new("SparseList", length=100L, env=env)
 -###   length(x)
 -###   ls(x)
 -###   ls(x, all.names=TRUE)
 -###   as.list(x)
 -###   as.list(x, all.names=TRUE)
 -###   x[[1]]
 -###   x[[98]
 -###   x[[101]]]
 -###
 -
 -setMethod("length", "SparseList", function(x) x@length)
 -
 -### 'pos', 'envir' and 'pattern' args are ignored
 -setMethod("ls", signature(name="SparseList"),
 -    function(name, pos, envir, all.names=FALSE, pattern)
 -    {
 -        if (!all.names)
 -            return(ls(name@env, all.names=TRUE))
 -        seq_len(length(name))
 -    }
 -)
 -
 -setMethod("as.list", "SparseList",
 -    function(x, all.names=FALSE, ...)
 -    {
 -        if (!all.names)
 -            return(as.list(x@env, all.names=TRUE))
 -        ans <- vector(mode="list", length=length(x))
 -        symbols <- ls(x)
 -        for (symb in symbols)
 -            ans[[as.integer(symb)]] <- get(symb, envir=x@env)
 -        ans
 -    }
 -)
 -
 -### Supported 'i' types: character or numeric vector of length 1.
 -setMethod("[[", "SparseList",
 -    function(x, i, j, ...)
 -    {
 -        if (!missing(j) || length(list(...)) > 0)
 -            stop("invalid subsetting")
 -        if (missing(i))
 -            stop("subscript is missing")
 -        if (!is.character(i) && !is.numeric(i))
 -            stop("invalid subscript type")
 -        if (length(i) < 1L)
 -            stop("attempt to select less than one element")
 -        if (length(i) > 1L)
 -            stop("attempt to select more than one element")
 -        if (is.na(i))
 -            stop("subscript cannot be NA")
 -        if (is.character(i))
 -            return(get(i, envir=x@env))
 -        if (!is.integer(i))
 -            i <- as.integer(i)
 -        if (i < 1L || i > length(x))
 -            stop("subscript out of bounds")
 -        i <- formatC(i, width=10, format="d", flag="0")
 -        get(i, envir=x@env)
 -    }
 -)
 -
 diff --git a/man/Biostrings-internals.Rd b/man/Biostrings-internals.Rd
 index 791b0870..609b7694 100644
 --- a/man/Biostrings-internals.Rd
 +++ b/man/Biostrings-internals.Rd
@@ -26,15 +26,6 @@
 \alias{make_XStringSet_from_strings}
 \alias{make_XStringSet_from_strings,XStringSet-method}
 -% SparseList class and methods:
 -\alias{class:SparseList}
 -\alias{SparseList-class}
 -\alias{SparseList}
 -
 -\alias{length,SparseList-method}
 -%\alias{ls,SparseList-method}
 -\alias{as.list,SparseList-method}
 -\alias{[[,SparseList-method}
 \title{Biostrings internals}
 diff --git a/src/Biostrings.h b/src/Biostrings.h
 index 6e725bd5..e86d0ff2 100644
 --- a/src/Biostrings.h
 +++ b/src/Biostrings.h
@@ -446,40 +446,6 @@ SEXP XStringSetList_unstrsplit(
 );
 -/* SparseList_utils.c */
 -
 -SEXP _SparseList_int2symb(int symb_as_int);
 -
 -int _SparseList_symb2int(SEXP symbol);
 -
 -SEXP _get_val_from_env(
 -	SEXP symbol,
 -	SEXP env,
 -	int error_on_unbound_value
 -);
 -
 -SEXP _get_val_from_SparseList(
 -	int symb_as_int,
 -	SEXP env,
 -	int error_on_unbound_value
 -);
 -
 -int _get_int_from_SparseList(
 -	int symb_as_int,
 -	SEXP env
 -);
 -
 -void _set_env_from_IntAE(
 -	SEXP env,
 -	const IntAE *int_ae
 -);
 -
 -void _set_env_from_IntAEAE(
 -	SEXP env,
 -	const IntAEAE *int_aeae
 -);
 -
 -
 /* match_reporting.c */
 int _get_match_storing_code(const char *ms_mode);
@@ -558,13 +524,6 @@ SEXP ByPos_MIndex_endIndex(
 	SEXP x_width0
 );
 -SEXP SparseMIndex_endIndex(
 -	SEXP x_ends_envir,
 -	SEXP x_width0,
 -	SEXP x_names,
 -	SEXP all_names
 -);
 -
 SEXP ByPos_MIndex_combine(SEXP ends_listlist);
 diff --git a/src/MIndex_class.c b/src/MIndex_class.c
 index 00212fe9..dd6ad546 100644
 --- a/src/MIndex_class.c
 +++ b/src/MIndex_class.c
@@ -157,73 +157,6 @@ SEXP ByPos_MIndex_endIndex(SEXP x_high2low, SEXP x_ends, SEXP x_width0)
 	return ans;
 }
 -/*
 - * --- .Call ENTRY POINT ---
 - * All the keys in 'x_ends_envir' must be representing integers left-padded with 0s
 - * so they have the same length. This works properly:
 -     library(Biostrings)
 -     ends_envir <- new.env(parent=emptyenv())
 -     ends_envir[['0000000010']] <- -2:1
 -     ends_envir[['0000000004']] <- 9:6
 -     .Call("SparseMIndex_endIndex",
 -           ends_envir, NULL, letters[1:10], TRUE,
 -           PACKAGE="Biostrings")
 -     .Call("SparseMIndex_endIndex",
 -           ends_envir, NULL, letters[1:10], FALSE,
 -           PACKAGE="Biostrings")
 - * but this doesn't:
 -     ends_envir[['3']] <- 33L
 -     .Call("SparseMIndex_endIndex",
 -           ends_envir, NULL, letters[1:10], FALSE,
 -           PACKAGE="Biostrings")
 - */
 -SEXP SparseMIndex_endIndex(SEXP x_ends_envir, SEXP x_width0, SEXP x_names, SEXP all_names)
 -{
 -	SEXP ans, ans_elt, ans_names, symbols, end;
 -	int nelt, i, j;
 -	IntAE *poffsets, *poffsets_order;
 -
 -	PROTECT(symbols = R_lsInternal(x_ends_envir, 1));
 -	poffsets = new_IntAE_from_CHARACTER(symbols, -1);
 -	nelt = IntAE_get_nelt(poffsets);
 -	if (LOGICAL(all_names)[0]) {
 -		PROTECT(ans = NEW_LIST(LENGTH(x_names)));
 -		for (i = 0; i < nelt; i++) {
 -			j = poffsets->elts[i];
 -			end = _get_val_from_env(STRING_ELT(symbols, i), x_ends_envir, 1);
 -			PROTECT(ans_elt = duplicate(end));
 -			if (x_width0 != R_NilValue)
 -				add_val_to_INTEGER(ans_elt, 1 - INTEGER(x_width0)[j]);
 -			SET_ELEMENT(ans, j, ans_elt);
 -			UNPROTECT(1);
 -		}
 -		SET_NAMES(ans, duplicate(x_names));
 -		UNPROTECT(1);
 -	} else {
 -		//poffsets_order = new_IntAE(nelt, 0, 0);
 -		//get_order_of_int_array(poffsets->elts, nelt, 0, 0,
 -		//		       poffsets_order->elts, 0);
 -		//IntAE_set_nelt(poffsets_order) = nelt; /* = poffsets_order->_buflength */
 -		PROTECT(ans = NEW_LIST(nelt));
 -		PROTECT(ans_names = NEW_CHARACTER(nelt));
 -		for (i = 0; i < nelt; i++) {
 -			//j = poffsets_order->elts[i];
 -			j = i;
 -			end = _get_val_from_env(STRING_ELT(symbols, j), x_ends_envir, 1);
 -			PROTECT(ans_elt = duplicate(end));
 -			if (x_width0 != R_NilValue)
 -				add_val_to_INTEGER(ans_elt, 1 - INTEGER(x_width0)[i]);
 -			SET_ELEMENT(ans, i, ans_elt);
 -			UNPROTECT(1);
 -			SET_STRING_ELT(ans_names, i, duplicate(STRING_ELT(x_names, poffsets->elts[j])));
 -		}
 -		SET_NAMES(ans, ans_names);
 -		UNPROTECT(2);
 -	}
 -	UNPROTECT(1);
 -	return ans;
 -}
 -
 /*
  * --- .Call ENTRY POINT ---
  */
 diff --git a/src/R_init_Biostrings.c b/src/R_init_Biostrings.c
 index 4d2943f8..c1410dbd 100644
 --- a/src/R_init_Biostrings.c
 +++ b/src/R_init_Biostrings.c
@@ -88,7 +88,6 @@ static const R_CallMethodDef callMethods[] = {
 /* MIndex_class.c */
 	CALLMETHOD_DEF(ByPos_MIndex_endIndex, 3),
 -	CALLMETHOD_DEF(SparseMIndex_endIndex, 4),
 	CALLMETHOD_DEF(ByPos_MIndex_combine, 1),
 /* lowlevel_matching.c */
 diff --git a/src/SparseList_utils.c b/src/SparseList_utils.c
 deleted file mode 100644
 index 18597b55..00000000
 --- a/src/SparseList_utils.c
 +++ /dev/null
@@ -1,113 +0,0 @@
 -/****************************************************************************
 - *                        Fast SparseList utilities                         *
 - *                            Author: H. Pag\`es                            *
 - ****************************************************************************/
 -#include "Biostrings.h"
 -#include "S4Vectors_interface.h"
 -
 -
 -SEXP _SparseList_int2symb(int symb_as_int)
 -{
 -	char symbbuf[11];
 -
 -	snprintf(symbbuf, sizeof(symbbuf), "%010d", symb_as_int);
 -	return mkChar(symbbuf); /* UNPROTECTED! */
 -}
 -
 -int _SparseList_symb2int(SEXP symbol)
 -{
 -	int symb_as_int;
 -
 -	sscanf(CHAR(symbol), "%d", &symb_as_int);
 -	return symb_as_int;
 -}
 -
 -/* 'symbol' must be a CHARSXP */
 -SEXP _get_val_from_env(SEXP symbol, SEXP env, int error_on_unbound_value)
 -{
 -	SEXP ans;
 -
 -	/* The following code was inspired by R's do_get() code.
 -	 * Note that do_get() doesn't use PROTECT at all and so do we...
 -	 */
 -	ans = findVar(install(translateChar(symbol)), env);
 -	if (ans == R_UnboundValue) {
 -		if (error_on_unbound_value)
 -			error("Biostrings internal error in _get_val_from_env(): "
 -			      "unbound value");
 -		return R_UnboundValue;
 -	}
 -	if (TYPEOF(ans) == PROMSXP)
 -		ans = eval(ans, env);
 -	if (ans != R_NilValue && NAMED(ans) == 0)
 -		SET_NAMED(ans, 1);
 -	return ans;
 -}
 -
 -SEXP _get_val_from_SparseList(int symb_as_int, SEXP env, int error_on_unbound_value)
 -{
 -	SEXP symbol, ans;
 -
 -	PROTECT(symbol = _SparseList_int2symb(symb_as_int));
 -	ans = _get_val_from_env(symbol, env, error_on_unbound_value);
 -	UNPROTECT(1);
 -	return ans;
 -}
 -
 -int _get_int_from_SparseList(int symb_as_int, SEXP env)
 -{
 -	SEXP value;
 -	int val;
 -
 -	value = _get_val_from_SparseList(symb_as_int, env, 0);
 -	if (value == R_UnboundValue)
 -		return NA_INTEGER;
 -	if (LENGTH(value) != 1)
 -		error("Biostrings internal error in _get_int_from_SparseList(): "
 -		      "value is not a single integer");
 -	val = INTEGER(value)[0];
 -	if (val == NA_INTEGER)
 -		error("Biostrings internal error in _get_int_from_SparseList(): "
 -		      "value is NA");
 -	return val;
 -}
 -
 -void _set_env_from_IntAE(SEXP env, const IntAE *int_ae)
 -{
 -	int nelt, symb_as_int, elt;
 -	SEXP symbol, value;
 -
 -	nelt = IntAE_get_nelt(int_ae);
 -	for (symb_as_int = 1; symb_as_int <= nelt; symb_as_int++)
 -	{
 -		elt = int_ae->elts[symb_as_int - 1];
 -		if (elt == NA_INTEGER)
 -			continue;
 -		PROTECT(symbol = _SparseList_int2symb(symb_as_int));
 -		PROTECT(value = ScalarInteger(elt));
 -		defineVar(install(translateChar(symbol)), value, env);
 -		UNPROTECT(2);
 -	}
 -	return;
 -}
 -
 -void _set_env_from_IntAEAE(SEXP env, const IntAEAE *int_aeae)
 -{
 -	int nelt, symb_as_int;
 -	IntAE *ae;
 -	SEXP symbol, value;
 -
 -	nelt = IntAEAE_get_nelt(int_aeae);
 -	for (symb_as_int = 1; symb_as_int <= nelt; symb_as_int++)
 -	{
 -		ae = int_aeae->elts[symb_as_int - 1];
 -		if (IntAE_get_nelt(ae) == 0)
 -			continue;
 -		PROTECT(symbol = _SparseList_int2symb(symb_as_int));
 -		PROTECT(value = new_INTEGER_from_IntAE(ae));
 -		defineVar(install(translateChar(symbol)), value, env);
 -		UNPROTECT(2);
 -	}
 -	return;
 -}
 -
@@ -1,142 +0,0 @@
 From 7fe34542bff0183c3a6a35a62df9035a71698eb2 Mon Sep 17 00:00:00 2001
 From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
 Date: Fri, 6 Mar 2026 15:54:23 -0800
 Subject: [PATCH] h5mread 1.3.2: Get rid of non-API calls to R
 ---
 DESCRIPTION                |  2 +-
 R/H5File-class.R           | 27 ++++++++++++++++-----------
 src/h5mread_index.c        |  5 +++--
 src/h5mread_startscounts.c |  3 ++-
 4 files changed, 22 insertions(+), 15 deletions(-)
 diff --git a/R/H5File-class.R b/R/H5File-class.R
 index 2735166..6aeb80f 100644
 --- a/R/H5File-class.R
 +++ b/R/H5File-class.R
@@ -73,19 +73,23 @@
     }
 }
 -.h5openfile <- function(filepath, s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
 +.h5openfile <- function(filepath, readonly=TRUE,
 +                        s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
 {
     if (!isSingleString(filepath))
         stop(wmsg("'filepath' must be a single string specifying ",
                   "the path or URL to an HDF5 file"))
 +    if (!isTRUEorFALSE(readonly))
 +        stop(wmsg("'readonly' must be TRUE or FALSE"))
     if (!isTRUEorFALSE(s3))
         stop(wmsg("'s3' must be TRUE or FALSE"))
 -
 +    if (s3 && !readonly)
 +        stop(wmsg("'readonly' must be set to TRUE when 's3' is TRUE"))
     if (s3) {
         ID <- .h5openS3file(filepath, s3credentials=s3credentials,
                                       use.rhdf5=use.rhdf5)
     } else {
 -        ID <- .h5openlocalfile(filepath, readonly=TRUE, use.rhdf5=use.rhdf5)
 +        ID <- .h5openlocalfile(filepath, readonly=readonly, use.rhdf5=use.rhdf5)
     }
     ID
 }
@@ -136,16 +140,16 @@
 .ID_is_closed <- function(ID) { is.null(ID) || is.na(ID) }
 -.open_H5FileID_xp <- function(xp, filepath, s3=FALSE, s3credentials=NULL,
 -                                            use.rhdf5=FALSE)
 +.open_H5FileID_xp <- function(xp, filepath, readonly=TRUE,
 +                              s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
 {
     ID <- .get_H5FileID_xp_ID(xp)
     if (!.ID_is_closed(ID)) {
         ## H5FileID object is already open.
         return(FALSE)
     }
 -    ID <- .h5openfile(filepath, s3=s3, s3credentials=s3credentials,
 -                                use.rhdf5=use.rhdf5)
 +    ID <- .h5openfile(filepath, readonly=readonly,
 +                      s3=s3, s3credentials=s3credentials, use.rhdf5=use.rhdf5)
     .set_H5FileID_xp_ID(xp, ID)
     TRUE
 }
@@ -183,10 +187,11 @@ close.H5FileID <- function(con, ...)
     .close_H5FileID_xp(con@xp, ..., use.rhdf5=con@from_rhdf5)
 }
 -H5FileID <- function(filepath, s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
 +H5FileID <- function(filepath, readonly=TRUE,
 +                     s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
 {
 -    ID <- .h5openfile(filepath, s3=s3, s3credentials=s3credentials,
 -                                use.rhdf5=use.rhdf5)
 +    ID <- .h5openfile(filepath, readonly=readonly,
 +                      s3=s3, s3credentials=s3credentials, use.rhdf5=use.rhdf5)
     xp <- .new_H5FileID_xp(ID)
     reg.finalizer(xp,
                   function(e) .close_H5FileID_xp(e, use.rhdf5=use.rhdf5),
@@ -272,7 +277,7 @@ H5File <- function(filepath, s3=FALSE, s3credentials=NULL, .no_rhdf5_h5id=FALSE)
         rhdf5_h5id <- new("H5FileID")
     } else {
         rhdf5_h5id <- H5FileID(filepath, s3=s3, s3credentials=s3credentials,
 -                                         use.rhdf5=TRUE)
 +                               use.rhdf5=TRUE)
     }
     if (!s3)
         filepath <- file_path_as_absolute(filepath)
 diff --git a/src/h5mread_index.c b/src/h5mread_index.c
 index 7284815..ec93c25 100644
 --- a/src/h5mread_index.c
 +++ b/src/h5mread_index.c
@@ -9,6 +9,7 @@
 #include "h5mread_helpers.h"
 #include "TouchedChunks.h"
 +#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
 #include <stdlib.h>  /* for malloc, free */
 #include <string.h>  /* for memcmp */
 //#include <time.h>
@@ -444,7 +445,7 @@ static int read_chunk_data_4_5(const H5DSetDescriptor *h5dset,
 		const size_t *Rarray_dim, SEXP Rarray,
 		int method, int use_H5Dread_chunk)
 {
 -	void *out = DATAPTR(Rarray);
 +	void *out = DATAPTR_RW(Rarray);
 	if (out == NULL)
 		return -1;
@@ -874,7 +875,7 @@ static int read_data_6(const AllTChunks *all_tchunks,
 	size_t *inner_nchip_buf = R_alloc0_size_t_array(ndim);
 	LLongAEAE *inner_breakpoint_bufs = new_LLongAEAE(ndim, ndim);
 -	void *out = DATAPTR(Rarray);
 +	void *out = DATAPTR_RW(Rarray);
 	if (out == NULL) {
 		_destroy_TChunkIterator(&tchunk_iter);
 		return -1;
 diff --git a/src/h5mread_startscounts.c b/src/h5mread_startscounts.c
 index de57fd5..959014f 100644
 --- a/src/h5mread_startscounts.c
 +++ b/src/h5mread_startscounts.c
@@ -8,6 +8,7 @@
 #include "uaselection.h"
 #include "h5mread_helpers.h"
 +#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
 #include <stdlib.h>  /* for malloc, free */
 //#include <time.h>
@@ -402,7 +403,7 @@ SEXP _h5mread_startscounts(const H5DSetDescriptor *h5dset,
 	SEXP ans = PROTECT(allocVector(h5dset->h5type->Rtype, ans_len));
 	if (ans_len != 0) {
 -		void *mem = DATAPTR(ans);
 +		void *mem = DATAPTR_RW(ans);
 		if (mem == NULL)
 			goto on_error;
 -- 
 2.52.0
@@ -1,67 +0,0 @@
 From a827c9fdeb77edefe6cca81bdb9e0344bc8d3742 Mon Sep 17 00:00:00 2001
 From: Sebastian Gibb <mail@sebastiangibb.de>
 Date: Sat, 13 Dec 2025 23:06:12 +0100
 Subject: [PATCH] fix: non-API call to R: SETLENGTH by using lengthgets
 ---
 DESCRIPTION  |  2 +-
 NEWS.md      |  6 ++++++
 src/join.c   | 12 ++++--------
 src/reduce.c |  6 ++----
 4 files changed, 13 insertions(+), 13 deletions(-)
 diff --git a/src/join.c b/src/join.c
 index f13a703..3849fdf 100644
 --- a/src/join.c
 +++ b/src/join.c
@@ -111,12 +111,10 @@ SEXP C_join_inner(SEXP x, SEXP y, SEXP tolerance, SEXP nomatch) {
             ++j;
         }
     }
 -    SETLENGTH(rx, j);
 -    SETLENGTH(ry, j);
     SEXP out = PROTECT(allocVector(VECSXP, 2));
     SEXP nms = PROTECT(allocVector(STRSXP, 2));
 -    SET_VECTOR_ELT(out, 0, rx);
 -    SET_VECTOR_ELT(out, 1, ry);
 +    SET_VECTOR_ELT(out, 0, lengthgets(rx, j));
 +    SET_VECTOR_ELT(out, 1, lengthgets(ry, j));
     SET_STRING_ELT(nms, 0, mkChar("x"));
     SET_STRING_ELT(nms, 1, mkChar("y"));
     setAttrib(out, R_NamesSymbol, nms);
@@ -201,12 +199,10 @@ SEXP C_join_outer(SEXP x, SEXP y, SEXP tolerance, SEXP nomatch) {
         ++i;
     }
 -    SETLENGTH(rx, i);
 -    SETLENGTH(ry, i);
     SEXP out = PROTECT(allocVector(VECSXP, 2));
     SEXP nms = PROTECT(allocVector(STRSXP, 2));
 -    SET_VECTOR_ELT(out, 0, rx);
 -    SET_VECTOR_ELT(out, 1, ry);
 +    SET_VECTOR_ELT(out, 0, lengthgets(rx, i));
 +    SET_VECTOR_ELT(out, 1, lengthgets(ry, i));
     SET_STRING_ELT(nms, 0, mkChar("x"));
     SET_STRING_ELT(nms, 1, mkChar("y"));
     setAttrib(out, R_NamesSymbol, nms);
 diff --git a/src/reduce.c b/src/reduce.c
 index 5f87966..8e48058 100644
 --- a/src/reduce.c
 +++ b/src/reduce.c
@@ -66,11 +66,9 @@ SEXP C_reduce(SEXP start, SEXP end, SEXP check) {
         }
     }
 -    SETLENGTH(rs, pos + 1);
 -    SETLENGTH(re, pos + 1);
     SEXP out = PROTECT(allocVector(VECSXP, 2));
 -    SET_VECTOR_ELT(out, 0, rs);
 -    SET_VECTOR_ELT(out, 1, re);
 +    SET_VECTOR_ELT(out, 0, lengthgets(rs, pos + 1));
 +    SET_VECTOR_ELT(out, 1, lengthgets(re, pos + 1));
     UNPROTECT(4);
 -- 
 2.52.0
@@ -1,114 +0,0 @@
 From 57dc6579d8b53af9e633016705fa9a1cbe58c8c8 Mon Sep 17 00:00:00 2001
 From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
 Date: Fri, 6 Mar 2026 16:48:20 -0800
 Subject: [PATCH] Rsamtools 2.27.1: Get rid of non-API calls to R
 ---
 DESCRIPTION     | 2 +-
 src/utilities.h | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)
 diff --git a/src/utilities.h b/src/utilities.h
 index bffb98f7..f9d5e09f 100644
 --- a/src/utilities.h
 +++ b/src/utilities.h
@@ -51,8 +51,7 @@ SEXP find_mate_within_groups(SEXP group_sizes,
 /* call-building macros */
 #define NEW_CALL(S, T, NAME, ENV, N)            \
 -    PROTECT(S = T = allocList(N));              \
 -    SET_TYPEOF(T, LANGSXP);                     \
 +    PROTECT(S = T = LCONS(R_NilValue, allocList(N-1))); \
     SETCAR(T, findFun(install(NAME), ENV));     \
     T = CDR(T)
 #define CSET_CDR(T, NAME, VALUE)                \
 From 8cdec143023e8348a4f8bdc310acd609d14fe493 Mon Sep 17 00:00:00 2001
 From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
 Date: Fri, 6 Mar 2026 16:59:42 -0800
 Subject: [PATCH] oops, forgot to also get rid of non-API call to FORMALS()
 ---
 src/pileupbam.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 diff --git a/src/pileupbam.c b/src/pileupbam.c
 index f3256ba..7725628 100644
 --- a/src/pileupbam.c
 +++ b/src/pileupbam.c
@@ -655,7 +655,7 @@ SEXP apply_pileups(SEXP files, SEXP names, SEXP regions, SEXP param,
     if (R_NilValue == regions)
         Rf_error("'NULL' regions not (yet) supported");
     _checkparams(regions, R_NilValue, R_NilValue);
 -    if (!Rf_isFunction(callback) || 1L != Rf_length(FORMALS(callback)))
 +    if (!Rf_isFunction(callback) || 1L != Rf_length(R_ClosureFormals(callback)))
         Rf_error("'callback' must be a function of 1 argument");
     call = PROTECT(Rf_lang2(callback, R_NilValue));
 From ee01a1f13f3b012b0717247d1f21580225b6f3a0 Mon Sep 17 00:00:00 2001
 From: vjcitn <stvjc@channing.harvard.edu>
 Date: Wed, 8 Apr 2026 14:04:26 -0400
 Subject: [PATCH] API solutions
 ---
 DESCRIPTION     |  2 +-
 src/tabixfile.c |  4 ++++
 src/utilities.c | 13 ++++++++++---
 3 files changed, 15 insertions(+), 4 deletions(-)
 diff --git a/src/tabixfile.c b/src/tabixfile.c
 index 230a381..6f96568 100644
 --- a/src/tabixfile.c
 +++ b/src/tabixfile.c
@@ -187,8 +187,12 @@ SEXP index_tabix(SEXP filename, SEXP format, SEXP seq, SEXP begin, SEXP end,
         LOGICAL(zeroBased)[0] == TRUE)
         conf.preset |= TBX_UCSC;
 +/* following is deprecated in HTSLIB with no precise replacement proposed */
 +/* seems unimportant */
 +/*
     if (bgzf_is_bgzf(fn) != 1)
         Rf_error("file does not appear to be bgzip'd");
 +*/
     if (tbx_index_build(fn, 0, &conf) == -1)
         Rf_error("index build failed");
 diff --git a/src/utilities.c b/src/utilities.c
 index e224f91..d15c1d1 100644
 --- a/src/utilities.c
 +++ b/src/utilities.c
@@ -5,6 +5,13 @@
 #include "XVector_interface.h"
 #include <htslib/khash.h>
 +#include <Rversion.h>
 +
 +#if R_VERSION < R_Version(4, 6, 0)
 +# define R_getVar(x,y,z) findVar(x,y)
 +#endif
 +
 +
 void *_Rs_Realloc_impl(void *p, size_t n, size_t t)
 {
     /* R_Realloc(p, 0, *) fails inappropriately */
@@ -30,7 +37,7 @@ SEXP _get_namespace(const char *pkg)
 void _as_strand(SEXP vec)
 {
     SEXP nmspc = PROTECT(_get_namespace("Rsamtools"));
 -    SEXP lvls = PROTECT(eval(findVar(install(".STRAND_LEVELS"), nmspc), nmspc));
 +    SEXP lvls = PROTECT(eval(R_getVar(install(".STRAND_LEVELS"), nmspc, TRUE), nmspc));
     _as_factor_SEXP(vec, lvls);
     UNPROTECT(2);
 }
@@ -38,8 +45,8 @@ void _as_strand(SEXP vec)
 void _as_nucleotide(SEXP vec)
 {
     SEXP nmspc = PROTECT(_get_namespace("Rsamtools"));
 -    SEXP lvls = PROTECT(eval(findVar(install(".PILEUP_NUCLEOTIDE_LEVELS"),
 -                                     nmspc), nmspc));
 +    SEXP lvls = PROTECT(eval(R_getVar(install(".PILEUP_NUCLEOTIDE_LEVELS"),
 +                                     nmspc, TRUE), nmspc));
     _as_factor_SEXP(vec, lvls);
     UNPROTECT(2);
 }
@@ -1,103 +0,0 @@
 From e39852a54312bbc6ba435848890cc2a7f612357c Mon Sep 17 00:00:00 2001
 From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
 Date: Fri, 6 Mar 2026 17:04:19 -0800
 Subject: [PATCH] ShortRead 1.69.3: Get rid of non-API calls to R
 ---
 DESCRIPTION |  2 +-
 src/call.h  |  3 +--
 src/io.c    | 10 +++++-----
 3 files changed, 7 insertions(+), 8 deletions(-)
 diff --git a/src/call.h b/src/call.h
 index e15bb5e..e72bbd6 100644
 --- a/src/call.h
 +++ b/src/call.h
@@ -6,8 +6,7 @@ extern "C" {
 #endif
 #define NEW_CALL(S, T, NAME, ENV, N)				\
 -    PROTECT((S) = (T) = allocList((N)));			\
 -    SET_TYPEOF((T), LANGSXP);                                   \
 +    PROTECT((S) = (T) = LCONS(R_NilValue, allocList((N)-1)));	\
     SETCAR((T), findFun(install((NAME)), (ENV)));               \
     (T) = CDR((T))
 #define CSET_CDR(T, NAME, VALUE)				\
 diff --git a/src/io.c b/src/io.c
 index 25a0111..9cf4bf8 100644
 --- a/src/io.c
 +++ b/src/io.c
@@ -46,9 +46,9 @@ SEXP write_fastq(SEXP id, SEXP sread, SEXP quality,
                  SEXP fname, SEXP fmode, SEXP full, SEXP compress,
                  SEXP max_width)
 {
 -    if (!(IS_S4_OBJECT(id) && strcmp(get_classname(id), "BStringSet") == 0))
 +    if (!(Rf_isS4(id) && strcmp(get_classname(id), "BStringSet") == 0))
         Rf_error("'%s' must be '%s'", "id", "BStringSet");
 -    if (!(IS_S4_OBJECT(sread) &&
 +    if (!(Rf_isS4(sread) &&
           strcmp(get_classname(sread), "DNAStringSet") == 0))
         Rf_error("'%s' must be '%s'", "sread", "DNAStringSet");
     /* check in R -- C-level R_check_super... is not adequate */
@@ -693,14 +693,14 @@ int _solexa_export_make_id(SEXP result)
         *x = INTEGER(VECTOR_ELT(result, SLX_X)),
         *y = INTEGER(VECTOR_ELT(result, SLX_Y)), *pairedReadNumber = NULL;
     const SEXP
 -        * run = STRING_PTR(VECTOR_ELT(result, SLX_RUN)),
 +        * run = STRING_PTR_RO(VECTOR_ELT(result, SLX_RUN)),
         *multiplexIndex = NULL,
 -        *machine = STRING_PTR(VECTOR_ELT(result, SLX_MACHINE));
 +        *machine = STRING_PTR_RO(VECTOR_ELT(result, SLX_MACHINE));
     const Rboolean
         withMultiplexIndex = R_NilValue != VECTOR_ELT(result, SLX_MULTIPLEX),
         withPairedReadNumber = R_NilValue != VECTOR_ELT(result, SLX_PAIRID);
     if (withMultiplexIndex)
 -        multiplexIndex = STRING_PTR(VECTOR_ELT(result, SLX_MULTIPLEX));
 +        multiplexIndex = STRING_PTR_RO(VECTOR_ELT(result, SLX_MULTIPLEX));
     if (withPairedReadNumber)
         pairedReadNumber = INTEGER(VECTOR_ELT(result, SLX_PAIRID));
 -- 
 2.52.0
 From 2e3368a35e3955a0a92b7f3e2c8dface6709d135 Mon Sep 17 00:00:00 2001
 From: vjcitn <stvjc@channing.harvard.edu>
 Date: Thu, 16 Apr 2026 16:54:15 +0000
 Subject: [PATCH] fixapi
 ---
 src/util.c | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)
 diff --git a/src/util.c b/src/util.c
 index 4a10a90..59c089b 100644
 --- a/src/util.c
 +++ b/src/util.c
@@ -6,6 +6,14 @@ unsigned char _bDecode(char);
 unsigned char _dnaDecode(char);
 unsigned char _rnaDecode(char);
 +
 +#include <Rversion.h>
 +
 +#if R_VERSION < R_Version(4, 6, 0)
 +# define R_getVar(x,y,z) findVar(x,y)
 +#endif
 +
 +
 /*
  * Encode / decode XString wrappers
  */
@@ -80,7 +88,7 @@ SEXP _get_namespace(const char *pkg)
 SEXP _get_strand_levels()
 {
     SEXP nmspc = PROTECT(_get_namespace("ShortRead"));
 -    SEXP ans = eval(findVar(install(".STRAND_LEVELS"), nmspc), nmspc);
 +    SEXP ans = eval(R_getVar(install(".STRAND_LEVELS"), nmspc, TRUE), nmspc);
     UNPROTECT(1);
     return ans;
 }
 -- 
 2.52.0
@@ -1,412 +0,0 @@
 From 803cda41994a22890e0a6e379e6588084d4bc91b Mon Sep 17 00:00:00 2001
 From: vjcitn <stvjc@channing.harvard.edu>
 Date: Fri, 13 Mar 2026 04:04:59 -0400
 Subject: [PATCH 1/2] fixed non-API except for IS_S4_OBJECT
 ---
 src/bind.c             |  8 ++++----
 src/glm_test_R.c       | 20 ++++++++++----------
 src/imputation.c       |  8 ++++----
 src/input.c            |  2 +-
 src/plink.c            |  2 +-
 src/read_uncertain.c   |  4 ++--
 src/readped.c          |  2 +-
 src/single_snp_tests.c |  8 ++++----
 src/snp_summary.c      |  8 ++++----
 src/snpmpy.c           |  8 ++++----
 src/structure.c        |  4 ++--
 src/subset.c           |  2 +-
 src/switch.c           |  2 +-
 src/tdt.c              |  8 ++++----
 src/testBig.c          |  2 +-
 15 files changed, 44 insertions(+), 44 deletions(-)
 diff --git a/src/bind.c b/src/bind.c
 index 44b1536..fa87e7c 100644
 --- a/src/bind.c
 +++ b/src/bind.c
@@ -19,7 +19,7 @@ SEXP snp_rbind(SEXP args) {
     const SEXP This = CAR(args);
     Class = getAttrib(This, R_ClassSymbol);
     if (TYPEOF(Class) != STRSXP) {
 -      Class = R_data_class(This, FALSE);
 +      Class = R_class(This);
     }
     const char *cli = CHAR(STRING_ELT(Class, 0));
     if(!IS_S4_OBJECT(This)) {
@@ -66,7 +66,7 @@ SEXP snp_rbind(SEXP args) {
   SEXP Result, Rnames, Dnames, Diploid = R_NilValue;
   PROTECT(Result = allocMatrix(RAWSXP, nr, nc));
   classgets(Result, duplicate(Class));
 -  SET_S4_OBJECT(Result);
 +  Rf_asS4(Result, TRUE, 0);
   PROTECT(Rnames = allocVector(STRSXP, nr));
   PROTECT(Dnames = allocVector(VECSXP, 2));
   SET_VECTOR_ELT(Dnames, 0, Rnames);
@@ -148,7 +148,7 @@ SEXP snp_cbind(SEXP args) {
     SEXP This = CAR(args);
     Class = getAttrib(This, R_ClassSymbol);
     if (TYPEOF(Class) != STRSXP) {
 -      Class = R_data_class(This, FALSE);
 +      Class = R_class(This);
     }
     const char *cli = CHAR(STRING_ELT(Class, 0));
     if(!IS_S4_OBJECT(This)) {
@@ -205,7 +205,7 @@ SEXP snp_cbind(SEXP args) {
   SEXP Result, Cnames, Dnames;
   PROTECT(Result = allocMatrix(RAWSXP, nr, nc));
   classgets(Result, duplicate(Class));
 -  SET_S4_OBJECT(Result);
 +  Rf_asS4(Result, TRUE, 0);
   PROTECT(Dnames = allocVector(VECSXP, 2));
   setAttrib(Result, R_DimNamesSymbol, Dnames);
   PROTECT(Cnames = allocVector(STRSXP, nc));
 diff --git a/src/glm_test_R.c b/src/glm_test_R.c
 index d865182..dc8ebef 100644
 --- a/src/glm_test_R.c
 +++ b/src/glm_test_R.c
@@ -19,8 +19,8 @@ SEXP snp_lhs_score(const SEXP Y, const SEXP X, const SEXP Stratum,
   /* Y should be a SnpMatrix or an XSnpMatrix */
   const char *classY = NULL;
 -  if (TYPEOF(R_data_class(Y, FALSE)) == STRSXP) {
 -    classY = CHAR(STRING_ELT(R_data_class(Y, FALSE), 0));
 +  if (TYPEOF(R_class(Y)) == STRSXP) {
 +    classY = CHAR(STRING_ELT(R_class(Y), 0));
   } else {
     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
   }
@@ -431,8 +431,8 @@ SEXP snp_rhs_score(SEXP Y, SEXP family, SEXP link,
   /* Z should be a SnpMatrix or an XSnpMatrix */
   const char *classZ = NULL;
 -  if (TYPEOF(R_data_class(Z, FALSE)) == STRSXP) {
 -    classZ = CHAR(STRING_ELT(R_data_class(Z, FALSE), 0));
 +  if (TYPEOF(R_class(Z)) == STRSXP) {
 +    classZ = CHAR(STRING_ELT(R_class(Z), 0));
   } else {
     classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
   }
@@ -1003,8 +1003,8 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
   /* Y should be a SnpMatrix or an XSnpMatrix */
   const char *classY = NULL;
 -  if (TYPEOF(R_data_class(Y, FALSE)) == STRSXP) {
 -    classY = CHAR(STRING_ELT(R_data_class(Y, FALSE), 0));
 +  if (TYPEOF(R_class(Y)) == STRSXP) {
 +    classY = CHAR(STRING_ELT(R_class(Y), 0));
   } else {
     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
   }
@@ -1286,7 +1286,7 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
   LOGICAL(Lhs)[0] = 1;
   setAttrib(Estimates, install("snpLHS"), Lhs);
   UNPROTECT(6);
 -  SET_S4_OBJECT(Estimates);
 +  Rf_asS4(Estimates, TRUE, 0);
   return(Estimates);
 }
@@ -1360,8 +1360,8 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
 /* Z should be a SnpMatrix or an XSnpMatrix */
   const char *classZ = NULL;
 -  if (TYPEOF(R_data_class(Z, FALSE)) == STRSXP) {
 -    classZ = CHAR(STRING_ELT(R_data_class(Z, FALSE), 0));
 +  if (TYPEOF(R_class(Z)) == STRSXP) {
 +    classZ = CHAR(STRING_ELT(R_class(Z), 0));
   } else {
     classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
   }
@@ -1724,7 +1724,7 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
   UNPROTECT(gen_names? 7: 6);
 -  SET_S4_OBJECT(Estimates);
 +  Rf_asS4(Estimates, TRUE, 0);
   return(Estimates);
 }
 diff --git a/src/imputation.c b/src/imputation.c
 index ff9403b..d796c1b 100644
 --- a/src/imputation.c
 +++ b/src/imputation.c
@@ -77,7 +77,7 @@ SEXP snp_impute(const SEXP X, const SEXP Y, const SEXP Xord, const SEXP Yord,
   int *diploid = NULL;
   SEXP cl = GET_CLASS(X);
   if (TYPEOF(cl) != STRSXP) {
 -    cl = R_data_class(X, FALSE); /* S4 way of getting class attribute */
 +    cl = R_class(X); /* S4 way of getting class attribute */
   }
   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
     SEXP Diploid = R_do_slot(X, mkString("diploid"));
@@ -395,7 +395,7 @@ SEXP snp_impute(const SEXP X, const SEXP Y, const SEXP Xord, const SEXP Yord,
   PROTECT(Maxpred = allocVector(INTSXP, 1));
   INTEGER(Maxpred)[0] = maxpred;
   setAttrib(Result, install("Max.predictors"), Maxpred);
 -  SET_S4_OBJECT(Result);
 +  Rf_asS4(Result, TRUE, 0);
   /* Tidy up */
@@ -701,7 +701,7 @@ SEXP impute_snps(const SEXP Rules, const SEXP Snps, const SEXP Subset,
   int *diploid_in=NULL, *diploid=NULL;
   SEXP cl = GET_CLASS(Snps);
   if (TYPEOF(cl) != STRSXP) {
 -    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
 +    cl = R_class(Snps); /* S4 way of getting class attribute */
   }
   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
     SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
@@ -753,7 +753,7 @@ SEXP impute_snps(const SEXP Rules, const SEXP Snps, const SEXP Subset,
     SET_STRING_ELT(Package, 0, mkChar("snpStats"));
     setAttrib(Class, install("package"), Package);
     classgets(Result, Class);
 -    SET_S4_OBJECT(Result);
 +    Rf_asS4(Result, TRUE, 0);
   }
   PROTECT(Dimnames = allocVector(VECSXP, 2));
   SET_VECTOR_ELT(Dimnames, 0, VECTOR_ELT(names, 0));
 diff --git a/src/input.c b/src/input.c
 index 1d2a95b..60cdad8 100644
 --- a/src/input.c
 +++ b/src/input.c
@@ -330,7 +330,7 @@ SEXP insnp_new(const SEXP Filenames, const SEXP Sample_id, const SEXP Snp_id,
   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
   setAttrib(Class, install("package"), Package);
   classgets(Result, Class);
 -  SET_S4_OBJECT(Result);
 +  Rf_asS4(Result, TRUE, 0);
   unsigned char *result = RAW(Result);
   memset(result, 0x00, Nsample*Nsnp);
 diff --git a/src/plink.c b/src/plink.c
 index a413440..9095c2d 100644
 --- a/src/plink.c
 +++ b/src/plink.c
@@ -59,7 +59,7 @@ SEXP readbed(SEXP Bed, SEXP Id, SEXP Snps, SEXP Rsel, SEXP Csel) {
   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
   setAttrib(Class, install("package"), Package);
   classgets(Result, Class);
 -  SET_S4_OBJECT(Result);
 +  Rf_asS4(Result, TRUE, 0);
   unsigned char *result = RAW(Result); 
   R_xlen_t ncell = (R_xlen_t)nrow*(R_xlen_t)ncol;
 diff --git a/src/read_uncertain.c b/src/read_uncertain.c
 index 2e3b901..fd82617 100644
 --- a/src/read_uncertain.c
 +++ b/src/read_uncertain.c
@@ -137,7 +137,7 @@ SEXP read_mach(const SEXP Filename, const SEXP Colnames, const SEXP Nsubject) {
   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
   setAttrib(Class, install("package"), Package);
   classgets(Result, Class);
 -  SET_S4_OBJECT(Result);
 +  Rf_asS4(Result, TRUE, 0);
   UNPROTECT(2);
   /* Read in data */
@@ -278,7 +278,7 @@ SEXP read_impute(const SEXP Filename, const SEXP Rownames, const SEXP Nsnp,
   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
   setAttrib(Class, install("package"), Package);
   classgets(Result, Class);
 -  SET_S4_OBJECT(Result);
 +  Rf_asS4(Result, TRUE, 0);
   UNPROTECT(2);
   char buffer[BUFFERSIZE];
 diff --git a/src/readped.c b/src/readped.c
 index 4e8563e..020d05f 100644
 --- a/src/readped.c
 +++ b/src/readped.c
@@ -327,7 +327,7 @@ SEXP readped(SEXP filename, SEXP snp_names, SEXP missing, SEXP X, SEXP sep) {
   else
     SET_STRING_ELT(SMClass, 0, mkChar("SnpMatrix"));
   classgets(Smat, SMClass);
 -  SET_S4_OBJECT(Smat);
 +  Rf_asS4(Smat, TRUE, 0);
   PROTECT(DimNames = allocVector(VECSXP, 2));
   SET_VECTOR_ELT(DimNames, 0, duplicate(Rnames));
   protected += 2;
 diff --git a/src/single_snp_tests.c b/src/single_snp_tests.c
 index a242e17..08bd098 100644
 --- a/src/single_snp_tests.c
 +++ b/src/single_snp_tests.c
@@ -53,8 +53,8 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
   /* SNPs ---- should be a SnpMatrix or an XSnpMatrix */
   const char *classS = NULL;
 -  if (TYPEOF(R_data_class(Snps, FALSE)) == STRSXP) {
 -    classS = CHAR(STRING_ELT(R_data_class(Snps, FALSE), 0));
 +  if (TYPEOF(R_class(Snps)) == STRSXP) {
 +    classS = CHAR(STRING_ELT(R_class(Snps), 0));
   } else {
     classS = CHAR(STRING_ELT(getAttrib(Snps, R_ClassSymbol), 0));
   }
@@ -108,8 +108,8 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
   index_db name_index;
   if (!isNull(Rules)) {
     const char *classR = NULL;
 -    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
 -      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
 +    if (TYPEOF(R_class(Rules)) == STRSXP) {
 +      classR = CHAR(STRING_ELT(R_class(Rules), 0));
     } else {
       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
     }
 diff --git a/src/snp_summary.c b/src/snp_summary.c
 index 9b53693..6f181c9 100644
 --- a/src/snp_summary.c
 +++ b/src/snp_summary.c
@@ -47,8 +47,8 @@ SEXP X_snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
   SEXP ruleNames = R_NilValue;
   if (!isNull(Rules)) {
     const char *classR = NULL;
 -    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
 -      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
 +    if (TYPEOF(R_class(Rules)) == STRSXP) {
 +      classR = CHAR(STRING_ELT(R_class(Rules), 0));
     } else {
       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
     }
@@ -321,8 +321,8 @@ SEXP snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
   SEXP ruleNames = R_NilValue;
   if (!isNull(Rules)) {
     const char *classR = NULL;
 -    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
 -      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
 +    if (TYPEOF(R_class(Rules)) == STRSXP) {
 +      classR = CHAR(STRING_ELT(R_class(Rules), 0));
     } else {
       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
     }
 diff --git a/src/snpmpy.c b/src/snpmpy.c
 index 2447048..56b84d9 100644
 --- a/src/snpmpy.c
 +++ b/src/snpmpy.c
@@ -34,7 +34,7 @@ SEXP snp_pre(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
   int *ifdiploid = NULL;
   SEXP cl = GET_CLASS(Snps);
   if (TYPEOF(cl) != STRSXP) {
 -    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
 +    cl = R_class(Snps); /* S4 way of getting class attribute */
   }
   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
     SEXP diploid = R_do_slot(Snps, mkString("diploid"));
@@ -55,7 +55,7 @@ SEXP snp_pre(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
   cl = GET_CLASS(Mat);
   if (TYPEOF(cl) != STRSXP) {
 -    cl = R_data_class(Mat, FALSE); /* S4 way of getting class attribute */
 +    cl = R_class(Mat); /* S4 way of getting class attribute */
   }
   if (strcmp(CHAR(STRING_ELT(cl, 0)), "matrix"))
     error("Argument error - Mat wrong type");
@@ -161,7 +161,7 @@ SEXP snp_post(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
   int *ifdiploid = NULL;
   SEXP cl = GET_CLASS(Snps);
   if (TYPEOF(cl) != STRSXP) {
 -    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
 +    cl = R_class(Snps); /* S4 way of getting class attribute */
   }
   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
     SEXP diploid = R_do_slot(Snps, mkString("diploid"));
@@ -182,7 +182,7 @@ SEXP snp_post(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
   cl = GET_CLASS(Mat);
   if (TYPEOF(cl) != STRSXP) {
 -    cl = R_data_class(Mat, FALSE); /* S4 way of getting class attribute */
 +    cl = R_class(Mat); /* S4 way of getting class attribute */
   }
   if (strcmp(CHAR(STRING_ELT(cl, 0)), "matrix"))
     error("Argument error - Mat wrong type");
 diff --git a/src/structure.c b/src/structure.c
 index 2a05635..1f9b62e 100644
 --- a/src/structure.c
 +++ b/src/structure.c
@@ -66,7 +66,7 @@ SEXP xxt(const SEXP Snps, const SEXP Strata, const SEXP Correct_for_missing,
   int *ifDiploid = NULL;
   SEXP cl = GET_CLASS(Snps);
   if (TYPEOF(cl) != STRSXP) {
 -    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
 +    cl = R_class(Snps); /* S4 way of getting class attribute */
   }
   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
     SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
@@ -409,7 +409,7 @@ SEXP ibs_count(const SEXP Snps, const SEXP Uncertain) {
   int *ifDiploid = NULL;
   SEXP cl = GET_CLASS(Snps);
   if (TYPEOF(cl) != STRSXP) {
 -    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
 +    cl = R_class(Snps); /* S4 way of getting class attribute */
   }
   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
     SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
 diff --git a/src/subset.c b/src/subset.c
 index cc7992d..4c2e2c4 100644
 --- a/src/subset.c
 +++ b/src/subset.c
@@ -55,7 +55,7 @@ SEXP subset(SEXP X, SEXP Rows, SEXP Cols) {
   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
   setAttrib(Rclass, install("package"), Package);
   setAttrib(Result, R_ClassSymbol, Rclass);
 -  SET_S4_OBJECT(Result);
 +  Rf_asS4(Result, TRUE, 0);
   PROTECT(Rdim = allocVector(INTSXP, 2));
   int *rdim = INTEGER(Rdim);
   rdim[0] = nrows;
 diff --git a/src/switch.c b/src/switch.c
 index 60f7e6c..e2a3287 100644
 --- a/src/switch.c
 +++ b/src/switch.c
@@ -16,7 +16,7 @@ SEXP test_switch(const SEXP Snps, const SEXP Snps2, const SEXP Split,
   int *female = NULL;
   SEXP cl = GET_CLASS(Snps);
   if (TYPEOF(cl) != STRSXP) {
 -    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
 +    cl = R_class(Snps); /* S4 way of getting class attribute */
   }
   SEXP diploid = NULL;
   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
 diff --git a/src/tdt.c b/src/tdt.c
 index cece0d9..000d1c7 100644
 --- a/src/tdt.c
 +++ b/src/tdt.c
@@ -43,8 +43,8 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
   /* SNPs ---- should be a SnpMatrix or an XSnpMatrix */
   const char *classS = NULL;
 -  if (TYPEOF(R_data_class(Snps, FALSE)) == STRSXP) {
 -    classS = CHAR(STRING_ELT(R_data_class(Snps, FALSE), 0));
 +  if (TYPEOF(R_class(Snps)) == STRSXP) {
 +    classS = CHAR(STRING_ELT(R_class(Snps), 0));
   } else {
     classS = CHAR(STRING_ELT(getAttrib(Snps, R_ClassSymbol), 0));
   }
@@ -84,8 +84,8 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
   GTYPE **gt2ht = NULL;
   if (!isNull(Rules)) {
     const char *classR = NULL;
 -    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
 -      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
 +    if (TYPEOF(R_class(Rules)) == STRSXP) {
 +      classR = CHAR(STRING_ELT(R_class(Rules), 0));
     } else {
       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
     }
 diff --git a/src/testBig.c b/src/testBig.c
 index a6eb76f..3dca1da 100644
 --- a/src/testBig.c
 +++ b/src/testBig.c
@@ -18,7 +18,7 @@ SEXP snp_big(SEXP nrow, SEXP ncol) {
   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
   setAttrib(Class, install("package"), Package);
   classgets(Result, Class);
 -  SET_S4_OBJECT(Result);
 +  Rf_asS4(Result, TRUE, 0);
   PROTECT(Dnames = allocVector(VECSXP, 2));
   setAttrib(Result, R_DimNamesSymbol, Dnames);
 -- 
 2.52.0
@@ -1,149 +0,0 @@
 From a505297e347aa72510ecfc83e7009668693e1260 Mon Sep 17 00:00:00 2001
 From: vjcitn <stvjc@channing.harvard.edu>
 Date: Fri, 13 Mar 2026 04:06:37 -0400
 Subject: [PATCH 2/2] fixed IS_S4_OBJECT
 ---
 src/bind.c             | 4 ++--
 src/fst.c              | 2 +-
 src/glm_test_R.c       | 8 ++++----
 src/single_snp_tests.c | 2 +-
 src/snp_summary.c      | 6 +++---
 src/tdt.c              | 2 +-
 6 files changed, 12 insertions(+), 12 deletions(-)
 diff --git a/src/bind.c b/src/bind.c
 index fa87e7c..b3ef928 100644
 --- a/src/bind.c
 +++ b/src/bind.c
@@ -22,7 +22,7 @@ SEXP snp_rbind(SEXP args) {
       Class = R_class(This);
     }
     const char *cli = CHAR(STRING_ELT(Class, 0));
 -    if(!IS_S4_OBJECT(This)) {
 +    if(!Rf_isS4(This)) {
       warning("rbinding SnpMatrix object without S4 object bit");
     }
     int nci = ncols(This);
@@ -151,7 +151,7 @@ SEXP snp_cbind(SEXP args) {
       Class = R_class(This);
     }
     const char *cli = CHAR(STRING_ELT(Class, 0));
 -    if(!IS_S4_OBJECT(This)) {
 +    if(!Rf_isS4(This)) {
       warning("cbinding SnpMatrix object without S4 object bit");
     }
     SEXP Di = R_NilValue;
 diff --git a/src/fst.c b/src/fst.c
 index bbc39c0..5451a51 100644
 --- a/src/fst.c
 +++ b/src/fst.c
@@ -23,7 +23,7 @@ SEXP Fst(SEXP Snps, SEXP Group, SEXP HapMap) {
     ifX = 0; /* to avoid warning message */
     error("Argument error - class(Snps)");
   }
 -  if(!IS_S4_OBJECT(Snps)) {
 +  if(!Rf_isS4(Snps)) {
     error("Argument error - Snps is not S4 object");
   }
 diff --git a/src/glm_test_R.c b/src/glm_test_R.c
 index dc8ebef..fe9d9c8 100644
 --- a/src/glm_test_R.c
 +++ b/src/glm_test_R.c
@@ -24,7 +24,7 @@ SEXP snp_lhs_score(const SEXP Y, const SEXP X, const SEXP Stratum,
   } else {
     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
   }
 -  if(!IS_S4_OBJECT(Y)) {
 +  if(!Rf_isS4(Y)) {
     error("Y in snp_lhs_score is missing S4 Object bit");
   }
   int ifX = 0;
@@ -443,7 +443,7 @@ SEXP snp_rhs_score(SEXP Y, SEXP family, SEXP link,
     ifX = 1;
   else 
     error("Argument error - class(Z)");
 -  if (!IS_S4_OBJECT(Z)) {
 +  if (!Rf_isS4(Z)) {
     error("Z in snp_rhs_score is missing S4 Object bit");
   }
@@ -1008,7 +1008,7 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
   } else {
     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
   }
 -  if(!IS_S4_OBJECT(Y)) {
 +  if(!Rf_isS4(Y)) {
     error("Y in snp_lhs_score is missing S4 Object bit");
   }
   int ifX = 0;
@@ -1365,7 +1365,7 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
   } else {
     classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
   }
 -  if(!IS_S4_OBJECT(Z)) {
 +  if(!Rf_isS4(Z)) {
     error("Z in snp_rhs_score is missing S4 Object bit");
   }
   int ifX = 0;
 diff --git a/src/single_snp_tests.c b/src/single_snp_tests.c
 index 08bd098..b577300 100644
 --- a/src/single_snp_tests.c
 +++ b/src/single_snp_tests.c
@@ -67,7 +67,7 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
     ifX = 0; /* to avoid warning message */
     error("Argument error - class(Snps)");
   }
 -  if(!IS_S4_OBJECT(Snps)) {
 +  if(!Rf_isS4(Snps)) {
     error("Argument error - Snps is not S4 object");
   }
 diff --git a/src/snp_summary.c b/src/snp_summary.c
 index 6f181c9..c2f1c73 100644
 --- a/src/snp_summary.c
 +++ b/src/snp_summary.c
@@ -24,7 +24,7 @@ SEXP X_snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
   if (Snps == R_NilValue) {
     error("Argument error - Snps = NULL");
   }
 -  if(!IS_S4_OBJECT(Snps)) {
 +  if(!Rf_isS4(Snps)) {
     error("Argument error - Snps is not S4 object");
   }
   const unsigned char *snps = RAW(Snps);
@@ -298,7 +298,7 @@ SEXP snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
   if (Snps == R_NilValue) {
     error("Argument error - Snps = NULL");
   }
 -  if(!IS_S4_OBJECT(Snps)) {
 +  if(!Rf_isS4(Snps)) {
     error("Argument error - Snps is not S4 object");
   }
   const unsigned char *snps = RAW(Snps);
@@ -538,7 +538,7 @@ SEXP row_summary(const SEXP Snps) {
   if (Snps == R_NilValue) {
     error("Argument error - Snps = NULL");
   }
 -  if(!IS_S4_OBJECT(Snps)) {
 +  if(!Rf_isS4(Snps)) {
     error("Argument error - Snps is not S4 object");
   }
   const unsigned char *snps = RAW(Snps);
 diff --git a/src/tdt.c b/src/tdt.c
 index 000d1c7..634e1b3 100644
 --- a/src/tdt.c
 +++ b/src/tdt.c
@@ -57,7 +57,7 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
     ifX = 0; /* to avoid warning message */
     error("Argument error - class(Snps)");
   }
 -  if(!IS_S4_OBJECT(Snps)) {
 +  if(!Rf_isS4(Snps)) {
     error("Argument error - Snps is not S4 object");
   }
 -- 
 2.52.0
@@ -1,259 +0,0 @@
 From 633aa6e3f671e9b58b3508b3944ff0dd45f34f8a Mon Sep 17 00:00:00 2001
 From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
 Date: Thu, 5 Mar 2026 14:58:23 -0800
 Subject: [PATCH] SparseArray 1.11.11: Get rid of non-API calls to R
 From 65383c02f986832b1416c6ad39da800d8ced05df Mon Sep 17 00:00:00 2001
 From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
 Date: Tue, 31 Mar 2026 11:38:20 -0700
 Subject: [PATCH] SparseArray 1.11.13: Use R_getVar() instead of findVar() when
 R >= 4.6.0
 ---
 DESCRIPTION                     |  2 +-
 src/Makevars                    |  1 +
 src/Rvector_utils.c             | 15 ++++++++-------
 src/SparseArray_aperm.c         |  2 +-
 src/SparseArray_matrixStats.c   |  5 +++--
 src/SparseArray_subassignment.c |  6 +++---
 src/SparseVec.h                 |  3 ++-
 src/leaf_utils.c                |  5 +++--
 src/test.c                      |  3 +++
 9 files changed, 25 insertions(+), 17 deletions(-)
 diff --git a/src/Makevars b/src/Makevars
 index 0ee3615..1c5b86e 100644
 --- a/src/Makevars
 +++ b/src/Makevars
@@ -1,2 +1,3 @@
 +## See https://cran.r-project.org/doc/manuals/r-release/R-exts.html#OpenMP-support
 PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
 diff --git a/src/Rvector_utils.c b/src/Rvector_utils.c
 index ad80168..7e61ac1 100644
 --- a/src/Rvector_utils.c
 +++ b/src/Rvector_utils.c
@@ -4,6 +4,7 @@
  ****************************************************************************/
 #include "Rvector_utils.h"
 +#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
 #include <string.h>  /* for memset() and memcpy() */
@@ -242,7 +243,7 @@ void _fill_Rvector_block_with_val(SEXP Rvector,
 				     (const SEXP) val);
 		return;
 	}
 -	_set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector),
 +	_set_elts_to_val(TYPEOF(Rvector), DATAPTR_RW(Rvector),
 			 block_offset, block_len, val);
 }
@@ -260,7 +261,7 @@ void _fill_Rvector_block_with_zeros(SEXP Rvector,
 				     R_NilValue);
 		return;
 	}
 -	_set_elts_to_zero(Rtype, DATAPTR(Rvector), block_offset, block_len);
 +	_set_elts_to_zero(Rtype, DATAPTR_RW(Rvector), block_offset, block_len);
 	return;
 }
@@ -268,7 +269,7 @@ void _fill_Rvector_block_with_zeros(SEXP Rvector,
 void _fill_Rvector_block_with_ones(SEXP Rvector,
 		R_xlen_t block_offset, R_xlen_t block_len)
 {
 -	_set_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
 +	_set_elts_to_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
 			 block_offset, block_len);
 	return;
 }
@@ -277,7 +278,7 @@ void _fill_Rvector_block_with_ones(SEXP Rvector,
 void _fill_Rvector_block_with_minus_one(SEXP Rvector,
 		R_xlen_t block_offset, R_xlen_t block_len)
 {
 -	_set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR(Rvector),
 +	_set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
 			 block_offset, block_len);
 	return;
 }
@@ -293,7 +294,7 @@ void _fill_Rvector_block_with_NA(SEXP Rvector,
 					  NA_STRING);
 		return;
 	}
 -	_set_elts_to_NA(Rtype, DATAPTR(Rvector), block_offset, block_len);
 +	_set_elts_to_NA(Rtype, DATAPTR_RW(Rvector), block_offset, block_len);
 	return;
 }
@@ -460,7 +461,7 @@ void _fill_Rvector_subset_with_zeros(SEXP Rvector,
 				R_NilValue);
 		return;
 	}
 -	_set_selected_elts_to_zero(Rtype, DATAPTR(Rvector),
 +	_set_selected_elts_to_zero(Rtype, DATAPTR_RW(Rvector),
 				selection, selection_len, selection_offset);
 	return;
 }
@@ -470,7 +471,7 @@ void _fill_Rvector_subset_with_ones(SEXP Rvector,
 		const int *selection, int selection_len,
 		R_xlen_t selection_offset)
 {
 -	_set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
 +	_set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
 				  selection, selection_len, selection_offset);
 	return;
 }
 diff --git a/src/SparseArray_aperm.c b/src/SparseArray_aperm.c
 index 0bd092e..bbeaf2c 100644
 --- a/src/SparseArray_aperm.c
 +++ b/src/SparseArray_aperm.c
@@ -721,7 +721,7 @@ static SEXP REC_grow_output_tree(const int *dim, int ndim,
 	const type *nzvals_p = NULL;  /* -Wmaybe-uninitialized */	\
 	type v;								\
 	if (nzvals != R_NilValue) {  /* standard leaf */		\
 -		nzvals_p = (const type *) DATAPTR(nzvals);		\
 +		nzvals_p = DATAPTR_RO(nzvals);				\
 	} else {  /* lacunar leaf */					\
 		v = type ## 1;						\
 	}								\
 diff --git a/src/SparseArray_matrixStats.c b/src/SparseArray_matrixStats.c
 index b626553..debacf6 100644
 --- a/src/SparseArray_matrixStats.c
 +++ b/src/SparseArray_matrixStats.c
@@ -16,6 +16,7 @@
 #include "leaf_utils.h"
 #include "SparseArray_summarization.h"
 +#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
 #include <string.h>  /* for memcpy() and memset() */
@@ -272,7 +273,7 @@ SEXP C_colStats_SVT(SEXP x_dim, SEXP x_dimnames, SEXP x_type,
 	int warn = 0;
 	REC_colStats_SVT(x_SVT, x_bg_is_na, INTEGER(x_dim), LENGTH(x_dim),
 			 &summarize_op,
 -			 DATAPTR(ans), ans_Rtype,
 +			 DATAPTR_RW(ans), ans_Rtype,
 			 out_incs, ans_ndim, pardim,
 			 &warn);
 	if (warn)
@@ -1175,7 +1176,7 @@ SEXP C_rowStats_SVT(SEXP x_dim, SEXP x_dimnames, SEXP x_type,
 		SVT_rowMinsMaxs(x_SVT, x_Rtype, x_bg_is_na,
 			INTEGER(x_dim), LENGTH(x_dim),
 			opcode, narm,
 -			DATAPTR(ans), LENGTH(ans), ans_Rtype,
 +			DATAPTR_RW(ans), LENGTH(ans), ans_Rtype,
 			out_incs, ans_ndim, nstrata);
 		break;
 	    case SUM_OPCODE:
 diff --git a/src/SparseArray_subassignment.c b/src/SparseArray_subassignment.c
 index 4cf1c3d..c3b2d5e 100644
 --- a/src/SparseArray_subassignment.c
 +++ b/src/SparseArray_subassignment.c
@@ -966,13 +966,13 @@ static inline int next_coords0(NindexIterator *Nindex_iter)
 		midx_p++;
 		coords0_p++;
 	}
 -	printf("coords0: ");
 +	//printf("coords0: ");
 	coords0_p = Nindex_iter->coords0_buf;
 	for (along = Nindex_iter->margin; along < Nindex_iter->ndim; along++) {
 -		printf(" %3d", *coords0_p);
 +		//printf(" %3d", *coords0_p);
 		coords0_p++;
 	}
 -	printf("\n");
 +	//printf("\n");
 	return 1;
 }
 diff --git a/src/SparseVec.h b/src/SparseVec.h
 index 894709b..73cd841 100644
 --- a/src/SparseVec.h
 +++ b/src/SparseVec.h
@@ -5,6 +5,7 @@
 #include "Rvector_utils.h"
 +#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
 #include <limits.h>  /* for INT_MAX */
@@ -122,7 +123,7 @@ static inline SparseVec toSparseVec(SEXP nzvals, SEXP nzoffs,
 		if (IS_STRSXP_OR_VECSXP(Rtype)) {
 			sv.nzvals = nzvals;
 		} else {
 -			sv.nzvals = DATAPTR(nzvals);
 +			sv.nzvals = DATAPTR_RW(nzvals);
 		}
 	}
 	sv.nzoffs = INTEGER(nzoffs);
 diff --git a/src/leaf_utils.c b/src/leaf_utils.c
 index e8066c3..c5ff3aa 100644
 --- a/src/leaf_utils.c
 +++ b/src/leaf_utils.c
@@ -10,6 +10,7 @@
 #include "SparseVec_subsetting.h"
 #include "SparseVec_subassignment.h"
 +#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
 #include <string.h>  /* for memcpy() */
@@ -129,7 +130,7 @@ SEXP _make_leaf_from_two_arrays(SEXPTYPE Rtype,
 			return ans;
 		}
 		ans_nzvals = PROTECT(allocVector(Rtype, nzcount));
 -		memcpy(DATAPTR(ans_nzvals), nzvals_p, Rtype_size * nzcount);
 +		memcpy(DATAPTR_RW(ans_nzvals), nzvals_p, Rtype_size * nzcount);
 	}
 	SEXP ans = zip_leaf(ans_nzvals, ans_nzoffs, 0);
 	UNPROTECT(2);
@@ -156,7 +157,7 @@ static SEXP make_leaf_from_Rvector_subset(SEXP Rvector,
 	if (avoid_copy_if_all_selected &&
 	    selection_offset == 0 && selection_len == XLENGTH(Rvector) &&
 -	    ATTRIB(Rvector) == R_NilValue)
 +	    !ANY_ATTRIB(Rvector))
 	{
 		/* The full 'Rvector' is selected so can be reused as-is
 		   with no need to copy the selected elements to a new SEXP. */
 diff --git a/src/test.c b/src/test.c
 index 493538f..2205fa2 100644
 --- a/src/test.c
 +++ b/src/test.c
@@ -111,6 +111,9 @@ SEXP C_simple_omp_parallel_for_loop(SEXP nloop)
 	for (int i = 0; i < INTEGER(nloop)[0]; i++) {
 #ifdef _OPENMP
 		int thread_num = omp_get_thread_num();
 +		/* Can't use Rprintf() here because it's not thread-safe (it
 +		   can trigger R's garbage collector which itself is not
 +		   thread-safe). */
 		printf("thread_num = %d\n", thread_num);
 #endif
 	}
 diff --git a/src/readSparseCSV.c b/src/readSparseCSV.c
 index a3d8da0..de1cb95 100644
 --- a/src/readSparseCSV.c
 +++ b/src/readSparseCSV.c
@@ -11,6 +11,7 @@
 #include "ExtendableJaggedArray.h"
 #include <R_ext/Connections.h>
 +#include <Rversion.h>
 #include <string.h>  /* for memcpy() */
@@ -111,7 +112,11 @@ static SEXP dump_env_as_list_or_R_NilValue(SEXP env, int ans_len)
 	is_empty = 1;
 	for (i = 0; i < ans_len; i++) {
 		key = PROTECT(idx0_to_key(i));
 +#if R_VERSION < R_Version(4, 6, 0)
 		ans_elt = findVar(install(translateChar(key)), env);
 +#else
 +		ans_elt = R_getVar(install(translateChar(key)), env, FALSE);
 +#endif
 		UNPROTECT(1);
 		if (ans_elt == R_UnboundValue)
 			continue;
@@ -0,0 +1,46 @@
 From 1654599ea228efdd7b378ff44ed4e19d547641e0 Mon Sep 17 00:00:00 2001
 From: Bradley Lowekamp <blowekamp@mail.nih.gov>
 Date: Wed, 29 Apr 2026 16:22:49 +0000
 Subject: [PATCH 1/8] BUG: Replace removed CLOENV with R_ClosureEnv for R 4.6.0
 compatibility
 R 4.6.0 removed the non-API macro CLOENV from its public headers.
 The replacement R_ClosureEnv() was added in R 4.5.0. Add a version-
 guarded backport so that builds against older R versions (< 4.5.0)
 continue to work.
 Fixes #2574
 ---
 Wrapping/R/sitkRCommand.cxx | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)
 diff --git a/Wrapping/R/sitkRCommand.cxx b/Wrapping/R/sitkRCommand.cxx
 index 216a9327b8..c3a62bead9 100644
 --- a/Wrapping/R/sitkRCommand.cxx
 +++ b/Wrapping/R/sitkRCommand.cxx
@@ -19,10 +19,15 @@
 // The python header defines _POSIX_C_SOURCE without a preceding #undef
 #include <iostream>
 #include <Rinternals.h>
 +#include <Rversion.h>
 #include "sitkRCommand.h"
 #include "sitkExceptionObject.h"
 +// R_ClosureEnv was added in R 4.5.0, CLOENV was removed in R 4.6.0
 +#if R_VERSION < R_Version(4, 5, 0)
 +#  define R_ClosureEnv(x) CLOENV(x)
 +#endif
 namespace itk
 {
@@ -86,7 +91,7 @@ RCommand::SetFunctionClosure(SEXP FN)
     // element
     R_fcall = PROTECT(Rf_lang1(this->m_FunctionClosure));
     this->SetCallbackRCallable(R_fcall);
 -    this->SetCallbackREnviron(CLOENV(this->m_FunctionClosure));
 +    this->SetCallbackREnviron(R_ClosureEnv(this->m_FunctionClosure));
     UNPROTECT(1);
   }
 }
@@ -0,0 +1,171 @@
 From 494259f19b3ca4ad0b11c858bc3ba9b587fa2ed5 Mon Sep 17 00:00:00 2001
 From: Bradley Lowekamp <blowekamp@mail.nih.gov>
 Date: Thu, 30 Apr 2026 16:09:54 +0000
 Subject: [PATCH 1/2] [R] Fix compilation with R 4.6.0 which removed non-API
 macros #3407
 R 4.6.0 (April 2025) removed the non-API macro SET_S4_OBJECT and made
 CHARACTER_POINTER return a const pointer, breaking compilation of SWIG
 generated R code.
 Replace with proper R API equivalents:
 - SET_S4_OBJECT(x) -> x = Rf_asS4(x, TRUE, 0)  (3 sites in rrun.swg)
 - CHARACTER_POINTER(v)[i] = ... -> SET_STRING_ELT(v, i, ...)  (2 sites in std_vector.i)
 - CHARACTER_POINTER() via pstr -> STRING_ELT(, i) directly  (argcargv.i)
 All replacement APIs have been available since R 2.x so no version
 guards are required.
 ---
 CHANGES.current    | 6 ++++++
 Lib/r/argcargv.i   | 4 +---
 Lib/r/rrun.swg     | 6 +++---
 Lib/r/std_vector.i | 4 ++--
 4 files changed, 12 insertions(+), 8 deletions(-)
 diff --git a/Lib/r/argcargv.i b/Lib/r/argcargv.i
 index 73380f4e2c9..af7aa14d66c 100644
 --- a/Lib/r/argcargv.i
 +++ b/Lib/r/argcargv.i
@@ -14,7 +14,6 @@
 %}
 %typemap(in) (int ARGC, char **ARGV) {
   $1_ltype i;
 -  SEXP *pstr;
   if ($input == R_NilValue) {
     /* Empty array */
     $1 = 0;
@@ -22,14 +21,13 @@
     SWIG_exception_fail(SWIG_RuntimeError, "Wrong array type.");
   } else {
     $1 = Rf_length($input);
 -    pstr = CHARACTER_POINTER($input);
   }
   $2 = ($2_ltype) malloc(($1+1)*sizeof($*2_ltype));
   if ($2 == NULL) {
     SWIG_exception_fail(SWIG_MemoryError, "Memory allocation failed.");
   }
   for (i = 0; i < $1; i++) {
 -    $2[i] = ($*2_ltype)STRING_VALUE(pstr[i]);
 +    $2[i] = ($*2_ltype)STRING_VALUE(STRING_ELT($input, i));
   }
   $2[i] = NULL;
 }
 diff --git a/Lib/r/rrun.swg b/Lib/r/rrun.swg
 index 4c03d5884d7..5dee391f32f 100644
 --- a/Lib/r/rrun.swg
 +++ b/Lib/r/rrun.swg
@@ -267,7 +267,7 @@ SWIG_MakePtr(void *ptr, const char *typeName, int flags)
     R_RegisterCFinalizer(external, R_SWIG_ReferenceFinalizer);
   r_obj = SET_SLOT(r_obj, Rf_mkString((char *) "ref"), external);
 -  SET_S4_OBJECT(r_obj);
 +  r_obj = Rf_asS4(r_obj, TRUE, 0);
   Rf_unprotect(2);
   return(r_obj);
@@ -285,7 +285,7 @@ R_SWIG_create_SWIG_R_Array(const char *typeName, SEXP ref, int len)
    Rf_protect(arr = R_do_slot_assign(arr, Rf_mkString("dims"), Rf_ScalarInteger(len)));
    Rf_unprotect(3); 			   
 -   SET_S4_OBJECT(arr);	
 +   arr = Rf_asS4(arr, TRUE, 0);
    return arr;
 }
@@ -308,7 +308,7 @@ SWIG_R_NewPointerObj(void *ptr, swig_type_info *type, int flags) {
   }
   rptr = R_MakeExternalPtr(ptr, 
   R_MakeExternalPtr(type, R_NilValue, R_NilValue), R_NilValue); 
 -  SET_S4_OBJECT(rptr);
 +  rptr = Rf_asS4(rptr, TRUE, 0);
   return rptr;
 }
 diff --git a/Lib/r/std_vector.i b/Lib/r/std_vector.i
 index 6b32c9f6fc2..7db6d3814ac 100644
 --- a/Lib/r/std_vector.i
 +++ b/Lib/r/std_vector.i
@@ -203,7 +203,7 @@
          PROTECT(result = Rf_allocVector(STRSXP, val->size()));
          for (unsigned pos = 0; pos < val->size(); pos++)
            {
 -             CHARACTER_POINTER(result)[pos] = Rf_mkChar(((*val)[pos]).c_str());
 +             SET_STRING_ELT(result, pos, Rf_mkChar(((*val)[pos]).c_str()));
            }
         UNPROTECT(1);
         return(result);
@@ -669,7 +669,7 @@
             // Fill the R vector
             for (unsigned vpos = 0; vpos < val->at(pos).size(); ++vpos)
               {
 -                CHARACTER_POINTER(VECTOR_ELT(result, pos))[vpos] = Rf_mkChar(val->at(pos).at(vpos).c_str());
 +                SET_STRING_ELT(VECTOR_ELT(result, pos), vpos, Rf_mkChar(val->at(pos).at(vpos).c_str()));
               }
           }
         UNPROTECT(1);
 From 77d8826b46a967af158e982d56008aea2c8f6cb1 Mon Sep 17 00:00:00 2001
 From: Erez Geva <ErezGeva2@gmail.com>
 Date: Fri, 1 May 2026 18:47:42 +0200
 Subject: [PATCH 2/2] Add versioned `R` testing
 Signed-off-by: Erez Geva <ErezGeva2@gmail.com>
 ---
 .github/workflows/linux.yml |  7 +++++++
 Tools/CI-linux-install.sh   | 20 +++++++++++++++++++-
 configure.ac                | 11 +++++++++++
 3 files changed, 37 insertions(+), 1 deletion(-)
 diff --git a/Tools/CI-linux-install.sh b/Tools/CI-linux-install.sh
 index ad74ad3f21f..8f459899906 100644
 --- a/Tools/CI-linux-install.sh
 +++ b/Tools/CI-linux-install.sh
@@ -181,7 +181,25 @@ case "$SWIGLANG" in
 		fi
 		;;
 	"r")
 -		$RETRY sudo apt-get -qq install r-base
 +		if [[ -n "$VER" ]]; then
 +			# Should helps with old version, but do not work
 +			#$RETRY sudo apt-get -qq remove r-base r-base-core r-base-dev r-base-html r-doc-html r-recommended
 +			sudo sed -i 's%^# deb-src %deb-src %' /etc/apt/sources.list
 +			sudo sed -i 's%^Types: deb$%Types: deb deb-src%' /etc/apt/sources.list.d/*
 +			$RETRY sudo apt-get -qq update
 +			$RETRY sudo apt-get -qq build-dep r-base
 +			r_build=`mktemp -d`
 +			r_tarball=R-$VER.tar.gz
 +			URL=https://cran.r-project.org/src/base/R-${VER:0:1}
 +			$RETRY wget $URL/$r_tarball
 +			tar -xf "$r_tarball" --strip-components=1 -C "$r_build"
 +			cd "$r_build"
 +			./configure
 +			make
 +			sudo make install
 +		else
 +			$RETRY sudo apt-get -qq install r-base
 +		fi
 		;;
 	"ruby")
 		if [[ "$VER" ]]; then
 diff --git a/configure.ac b/configure.ac
 index e113f4b877c..e309b36ff45 100644
 --- a/configure.ac
 +++ b/configure.ac
@@ -2292,6 +2292,17 @@ else
 if test "x$RBIN" = xyes; then
    AC_PATH_PROG(RBIN, R)
 fi
 +if test -n "$RBIN" && test -x "$RBIN"; then
 +   r_min_version=2.4.0
 +   AC_MSG_CHECKING([for R version])
 +   r_version=`R --version | grep 'R version' | sed 's%^R version %%;s% (.*%%'`
 +   AS_VERSION_COMPARE(["$r_version"], ["$r_min_version"],
 +                  [AC_MSG_RESULT([older then $r_min_version])
 +                   AS_UNSET([RBIN])],        dnl bellow r_min_version
 +                  [AC_MSG_RESULT([$r_version])],   dnl equal r_min_version
 +                  [AC_MSG_RESULT([$r_version])])   dnl above r_min_version
 +fi
 +
 fi
 AC_SUBST(RBIN)
@@ -98,7 +98,6 @@
  #:use-module (gnu packages lua)
  #:use-module (gnu packages man)
  #:use-module (gnu packages markup)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages ocr)
@@ -47,7 +47,6 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages noweb)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
@@ -55,7 +55,6 @@
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages protobuf)
  #:use-module (gnu packages pkg-config)
@@ -237,7 +237,7 @@ it.")
 (define-public trealla
  (package
    (name "trealla")
-    (version "2.100.6")
+    (version "2.100.24")
    (source
     (origin
       (method git-fetch)
@@ -246,7 +246,7 @@ it.")
          (url "https://github.com/trealla-prolog/trealla")
          (commit (string-append "v" version))))
       (sha256
-        (base32 "0iy8477l9sf8p2jks8dlk5irssh1m4yyj7rflwvirbv19maaaghg"))
+        (base32 "09jm5hs2lv481yzf76p646jx6467zx98bbbsg24xh3glk1f9gaaq"))
       (file-name (git-file-name name version))))
    (build-system gnu-build-system)
    (inputs
@@ -41,7 +41,7 @@
 ;;; Copyright © 2025 Matthew Elwin <elwin@northwestern.edu>
 ;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez@gmail.com>
-;;; Copyright © 2025 Zheng Junjie <z572@z572.online> 
+;;; Copyright © 2025 Zheng Junjie <z572@z572.online>
 ;;; Copyright © 2026 Nguyễn Gia Phong <cnx@loang.net>
 ;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
 ;;;
@@ -66,6 +66,7 @@
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages check)
@@ -77,7 +78,6 @@
  #:use-module (gnu packages jupyter)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages openstack)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
@@ -2246,18 +2246,21 @@ attachments).
 (define-public python-pyflakes
  (package
    (name "python-pyflakes")
-    (version "3.2.0")
+    (version "3.4.0")
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "pyflakes" version))
+       (uri (git-reference
              (url "https://github.com/PyCQA/pyflakes")
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0gxgz0kg008pgmjk1dn8z3g00dfa9pc3f80pm6r1yqjly4zn0q8w"))))
+        (base32 "0ag6j4flayslbxcqipmfy5njawzy66py71p63mpjsys4gy70jhg1"))))
    (build-system pyproject-build-system)
    (arguments
     (list #:test-backend #~'unittest))
    (native-inputs
-     (list python-pytest
+     (list python-setuptools))
           python-setuptools
           python-wheel))
    (home-page "https://github.com/PyCQA/pyflakes")
    (synopsis "Passive checker of Python programs")
    (description
@@ -40,13 +40,13 @@
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system pyproject)
  #:use-module (gnu packages)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages libffi)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages check)
  #:use-module (gnu packages machine-learning)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
@@ -40,6 +40,7 @@
 ;;; Copyright © 2025 Ghislain Vaillant <ghislain.vaillant@inria.fr>
 ;;; Copyright © 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2026 Reza Housseini <reza@housseini.me>
 ;;; Copyright © 2026 Spencer King <spencer.king@wustl.edu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -87,7 +88,6 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages perl)
@@ -535,6 +535,42 @@ setting up, manipulating, running, visualizing and analyzing atomistic
 simulations.")
    (license license:lgpl2.1+)))
 (define-public python-autoray
  (package
    (name "python-autoray")
    (version "0.8.10")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/jcmgray/autoray")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1gqfkpdng09l804xm9r1r098w10gr1bc5ax2xmhrpz9niybv71f5"))))
    (build-system pyproject-build-system)
    ;; tests: 1758 passed, 1483 skipped, 96 xfailed, 4 warnings
    (native-inputs
     (list python-hatch-vcs
           python-hatchling
           python-pytest))
    (propagated-inputs
     (list python-dask
           python-matplotlib
           python-networkx
           python-numpy
           python-opt-einsum
           python-scipy
           python-sparse))
    (home-page "https://github.com/jcmgray/autoray")
    (synopsis "Library for abstracting tensor operations")
    (description
     "This package provides a lightweight Python library for
 abstracting tensor operations.  It provides an automatic dispatch mechanism
 that means you can write backend agnostic code that works for any library
 that provides a @code{numpy} compatible API.")
    (license license:asl2.0)))
 (define-public python-baycomp
  (package
    (name "python-baycomp")
@@ -1115,6 +1151,93 @@ computing in Python.  It extends both the @code{concurrent.futures} and
@code{dask} APIs to moderate sized clusters.")
    (license license:bsd-3)))
 (define-public python-dvc-data
  (package
    (name "python-dvc-data")
    (version "3.16.12")
    (home-page "https://github.com/iterative/dvc-data")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "dvc_data" version))
              (sha256
               (base32
                "156iwdn7v5jhwbpwz92n28qiasgcbmcqv9vxg8xbvdfxzlzw0b7r"))))
    (build-system pyproject-build-system)
    (propagated-inputs
     (list python-attrs
           python-dictdiffer
           python-diskcache
           python-dvc-objects
           python-fsspec
           python-funcy-1.14
           python-orjson
           python-pygtrie
           python-sqltrie
           python-tqdm))
    (native-inputs
     (list python-click
           python-pytest
           python-pytest-benchmark
           python-pytest-mock
           ;; python-pytest-servers is not packaged in Guix yet
           python-setuptools
           python-setuptools-scm
           python-typer
           python-wheel))
    (arguments
     (list
      #:test-flags
      ;; TODO: package python-pytest-server with its transitive dependencies
      #~(list "--ignore=tests/hashfile/test_db.py"
              "--ignore=tests/hashfile/test_db_index.py"
              "--ignore=tests/hashfile/test_obj.py"
              "--ignore=tests/index/test_build.py"
              "--ignore=tests/index/test_checkout.py"
              "--ignore=tests/index/test_fs.py"
              "--ignore=tests/index/test_index.py"
              "--ignore=tests/index/test_storage.py")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'patch-pyproject
            (lambda _
              ;; setuptools cannot handle both license and license-files
              (substitute* "pyproject.toml"
                (("^license = .*") "license = {text = \"Apache-2.0\"}\n")
                (("^license-files = .*") "")))))))
    (synopsis "DVC's data management subsystem")
    (description "Dvc data is DVC's data management subsystem.")
    (license license:asl2.0)))
 (define-public python-dvc-objects
  (package
    (name "python-dvc-objects")
    (version "5.1.1")
    (home-page "https://github.com/iterative/dvc-objects")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "dvc_objects" version))
       (sha256
        (base32 "1amx5z8k2v2hbsajg0dcd5dxmmlv9bnbchpas95s8sj86cm8yc4y"))))
    (build-system pyproject-build-system)
    (propagated-inputs (list python-fsspec
                             python-funcy-1.14))
    (native-inputs
     (list python-mypy
           python-pytest
           python-pytest-asyncio
           python-pytest-benchmark
           python-pytest-mock
           python-pytest-sugar
           python-reflink
           python-setuptools
           python-setuptools-scm
           python-wheel))
    (synopsis "Filesystem and object-db level abstractions for DVC")
    (description "Dvc objects provides a filesystem and object-db level
 abstractions to use in dvc and dvc-data.")
    (license license:asl2.0)))
 (define-public python-ecos
  (package
    (name "python-ecos")
@@ -1161,6 +1284,47 @@ numerical software for solving convex second-order cone programs (SOCPs).")
 which uncovers hidden structures in categorical data")
    (license license:expat)))
 (define-public python-einops
  (package
    (name "python-einops")
    (version "0.8.1")
    (source
     (origin
       (method git-fetch) ;PyPI misses .ipynb files required for tests
       (uri (git-reference
             (url "https://github.com/arogozhnikov/einops")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "07xd5a4sya3mr003f17hxykcbq3zf3mnr51qagv7fy55qcnbkn97"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      ;; Skip optional dependency on Jupyter during tests.
      #~(list "--ignore=scripts/test_notebooks.py")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'set-backend
            (lambda _
              ;; Einops supports different backends, but we test
              ;; only NumPy for availability and simplicity.
              (setenv "EINOPS_TEST_BACKENDS" "numpy"))))))
    (native-inputs
     (list python-hatchling
           python-nbconvert
           python-nbformat
           python-parameterized
           python-pytest))
    (propagated-inputs
     (list python-numpy))
    (home-page "https://einops.rocks/")
    (synopsis "Tensor operations for different backends")
    (description
     "Einops provides a set of tensor operations for NumPy and multiple deep
 learning frameworks.")
    (license license:expat)))
 (define-public python-fast-histogram
  (package
    (name "python-fast-histogram")
@@ -1233,6 +1397,35 @@ clustering schemes efficiently.  The package is made with two interfaces to
 standard software: R and Python.")
    (license license:bsd-2)))
 ;; XXX: Not maintained since 2019. The project was archived by the owner on
 ;; Nov 2, 2020. It is now read-only.
 (define-public python-fbpca
  (package
    (name "python-fbpca")
    (version "1.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "fbpca" version))
              (sha256
               (base32
                "1lbjqhqsdmqk86lb86q3ywf7561zmdny1dfvgwqkyrkr4ij7f1hm"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      ;; TypeError: 'dia_matrix' object is not subscriptable
      #~(list "--deselect=fbpca.py::TestPCA::test_sparse"
              "fbpca.py")))
    (native-inputs (list python-pytest python-setuptools))
    (propagated-inputs
     (list python-numpy python-scipy))
    (home-page "https://fbpca.readthedocs.io/")
    (synopsis "Functions for principal component analysis and accuracy checks")
    (description
     "This package provides fast computations for @dfn{principal component
 analysis} (PCA), SVD, and eigendecompositions via randomized methods")
    (license license:bsd-3)))
 (define-public python-fgivenx
  (package
    (name "python-fgivenx")
@@ -4627,76 +4820,6 @@ changed, it made sense to abstract away the nuisance of having to re-learn
 them.")
  (license license:bsd-3)))
 ;; XXX: Not maintained since 2019. The project was archived by the owner on
 ;; Nov 2, 2020. It is now read-only.
 (define-public python-fbpca
  (package
    (name "python-fbpca")
    (version "1.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "fbpca" version))
              (sha256
               (base32
                "1lbjqhqsdmqk86lb86q3ywf7561zmdny1dfvgwqkyrkr4ij7f1hm"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      ;; TypeError: 'dia_matrix' object is not subscriptable
      #~(list "--deselect=fbpca.py::TestPCA::test_sparse"
              "fbpca.py")))
    (native-inputs (list python-pytest python-setuptools))
    (propagated-inputs
     (list python-numpy python-scipy))
    (home-page "https://fbpca.readthedocs.io/")
    (synopsis "Functions for principal component analysis and accuracy checks")
    (description
     "This package provides fast computations for @dfn{principal component
 analysis} (PCA), SVD, and eigendecompositions via randomized methods")
    (license license:bsd-3)))
 (define-public python-einops
  (package
    (name "python-einops")
    (version "0.8.1")
    (source
     (origin
       (method git-fetch) ;PyPI misses .ipynb files required for tests
       (uri (git-reference
             (url "https://github.com/arogozhnikov/einops")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "07xd5a4sya3mr003f17hxykcbq3zf3mnr51qagv7fy55qcnbkn97"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      ;; Skip optional dependency on Jupyter during tests.
      #~(list "--ignore=scripts/test_notebooks.py")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'set-backend
            (lambda _
              ;; Einops supports different backends, but we test
              ;; only NumPy for availability and simplicity.
              (setenv "EINOPS_TEST_BACKENDS" "numpy"))))))
    (native-inputs
     (list python-hatchling
           python-nbconvert
           python-nbformat
           python-parameterized
           python-pytest))
    (propagated-inputs
     (list python-numpy))
    (home-page "https://einops.rocks/")
    (synopsis "Tensor operations for different backends")
    (description
     "Einops provides a set of tensor operations for NumPy and multiple deep
 learning frameworks.")
    (license license:expat)))
 (define-public python-uhi
  (package
    (name "python-uhi")
@@ -6267,93 +6390,6 @@ well as key metadata and SIRENE database containing data on all French
 compagnies.")
    (license license:expat)))
 (define-public python-dvc-objects
  (package
    (name "python-dvc-objects")
    (version "5.1.1")
    (home-page "https://github.com/iterative/dvc-objects")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "dvc_objects" version))
       (sha256
        (base32 "1amx5z8k2v2hbsajg0dcd5dxmmlv9bnbchpas95s8sj86cm8yc4y"))))
    (build-system pyproject-build-system)
    (propagated-inputs (list python-fsspec
                             python-funcy-1.14))
    (native-inputs
     (list python-mypy
           python-pytest
           python-pytest-asyncio
           python-pytest-benchmark
           python-pytest-mock
           python-pytest-sugar
           python-reflink
           python-setuptools
           python-setuptools-scm
           python-wheel))
    (synopsis "Filesystem and object-db level abstractions for DVC")
    (description "Dvc objects provides a filesystem and object-db level
 abstractions to use in dvc and dvc-data.")
    (license license:asl2.0)))
 (define-public python-dvc-data
  (package
    (name "python-dvc-data")
    (version "3.16.12")
    (home-page "https://github.com/iterative/dvc-data")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "dvc_data" version))
              (sha256
               (base32
                "156iwdn7v5jhwbpwz92n28qiasgcbmcqv9vxg8xbvdfxzlzw0b7r"))))
    (build-system pyproject-build-system)
    (propagated-inputs
     (list python-attrs
           python-dictdiffer
           python-diskcache
           python-dvc-objects
           python-fsspec
           python-funcy-1.14
           python-orjson
           python-pygtrie
           python-sqltrie
           python-tqdm))
    (native-inputs
     (list python-click
           python-pytest
           python-pytest-benchmark
           python-pytest-mock
           ;; python-pytest-servers is not packaged in Guix yet
           python-setuptools
           python-setuptools-scm
           python-typer
           python-wheel))
    (arguments
     (list
      #:test-flags
      ;; TODO: package python-pytest-server with its transitive dependencies
      #~(list "--ignore=tests/hashfile/test_db.py"
              "--ignore=tests/hashfile/test_db_index.py"
              "--ignore=tests/hashfile/test_obj.py"
              "--ignore=tests/index/test_build.py"
              "--ignore=tests/index/test_checkout.py"
              "--ignore=tests/index/test_fs.py"
              "--ignore=tests/index/test_index.py"
              "--ignore=tests/index/test_storage.py")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'patch-pyproject
            (lambda _
              ;; setuptools cannot handle both license and license-files
              (substitute* "pyproject.toml"
                (("^license = .*") "license = {text = \"Apache-2.0\"}\n")
                (("^license-files = .*") "")))))))
    (synopsis "DVC's data management subsystem")
    (description "Dvc data is DVC's data management subsystem.")
    (license license:asl2.0)))
 (define-public python-pyqtgraph
  (package
    (name "python-pyqtgraph")
@@ -2378,7 +2378,7 @@ for adding, removing and dropping callbacks.")
    (build-system pyproject-build-system)
    (arguments
     (list
-      ;; tests: 3045 passed, 32 skipped, 29 xfailed, 2 subtests passed
+      ;; tests: 3046 passed, 31 skipped, 29 xfailed, 2 subtests passed
      #:test-flags
      '(list
        "-o" "addopts=''"               ; Avoid -p pytest_cov.
@@ -2449,7 +2449,6 @@ for adding, removing and dropping callbacks.")
     (list gunicorn-bootstrap
           python-cython
           python-freezegun
           python-isal
           python-pytest
           python-pytest-mock
           python-pytest-xdist
@@ -2761,12 +2760,12 @@ stream is an enhanced asynchronous iterable.")
 (define-public python-asgiref
  (package
    (name "python-asgiref")
-    (version "3.8.1")
+    (version "3.11.1")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "asgiref" version))
              (sha256
-               (base32 "146mhkn3zp2bqf7j6r3chdlvfzgs5x1lrnqahsllgjdyl20bshy3"))))
+               (base32 "1km4xlaa21z2h0gz8x84gfgrq8k2mhg48rc0hkz3wxky7g24s62z"))))
    (build-system pyproject-build-system)
    (native-inputs
     (list python-pytest
@@ -268,7 +268,6 @@
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages node)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages openstack)
@@ -3733,23 +3732,31 @@ libraries to make them compatible with the Array API standard")
 (define-public python-array-api-strict
  (package
    (name "python-array-api-strict")
-    (version "2.4.1")
+    (version "2.5")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "array_api_strict" version))
       (sha256
-        (base32 "0k1v3h54y1yny8mhgwjk6p51zf87farfk1xn9842g5lcrfhxqxvc"))))
+        (base32 "1ig116ld5k8wx82ahld4l7qcb0d4s5s4f4a0nrflrh3hzabyarvp"))))
    (build-system pyproject-build-system)
    (arguments
     (list
-      ;; tests: 584 passed, 1 skipped, 2 deselected
+      ;; tests: 585 passed, 2 deselected
      #:test-flags
-      ;; ModuleNotFoundError: No module named 'numpy', not sure why?
+      ;; hypothesis.errors.InvalidArgument:
-      #~(list "-k" (string-append "not test_disabled_extensions"
+      ;; xp.__array_api_version__='2025.12', but it must be a valid version
      ;; string ('2021.12', '2022.12', '2023.12', '2024.12'). If the standard
      ;; version you want is not available, please ensure you're using the
      ;; latest version of Hypothesis, then open an issue if one doesn't
      ;; already exist.
      #~(list "--ignore=array_api_strict/tests/test_set_functions.py"
              ;; ModuleNotFoundError: No module named 'numpy', not sure why?
              "-k" (string-append "not test_disabled_extensions"
                                  " and not test_environment_variables"))))
    (native-inputs
-     (list python-pytest
+     (list python-hypothesis
           python-pytest
           python-setuptools
           python-setuptools-scm))
    (propagated-inputs
@@ -8945,16 +8952,20 @@ and convert DDL to BigQuery JSON schema.")
 (define-public python-jsonschema
  (package
    (name "python-jsonschema")
-    (version "4.23.0")
+    (version "4.26.0")
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "jsonschema" version))
+       (uri (git-reference
              (url "https://github.com/Julian/jsonschema")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1i3b4sckkc3v8vckqa11xbrj695qzrzsfzrkclra6lb3ybz9f56p"))))
+        (base32 "0p89jy7s1agi2zqrsdm56p843k847n9cixjsc12hnzscll37kysk"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      ;; tests: 7744 passed, 71 skipped
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'check 'pre-check
@@ -8964,21 +8975,20 @@ and convert DDL to BigQuery JSON schema.")
     (list python-hatchling
           python-hatch-fancy-pypi-readme
           python-hatch-vcs
-           ;; For <tests/test_cli.py::TestCLIIntegration::test_license>.
+           python-jsonpath-ng
           python-pip
           python-pytest))
    (propagated-inputs
     (list python-attrs
           python-fqdn
           python-idna
           python-importlib-resources
           python-isoduration
           python-jsonpointer
           python-jsonschema-specifications
           python-rfc3339-validator
           python-rfc3986-validator
           python-referencing-bootstrap
           python-rpds-py
           ;; [optional]
           python-fqdn
           python-idna
           python-isoduration
           python-jsonpointer
           python-rfc3339-validator
           python-rfc3986-validator
           python-uri-template
           python-webcolors))
    (home-page "https://github.com/Julian/jsonschema")
@@ -9316,7 +9326,8 @@ JavaScript-like message boxes.  Types of dialog boxes include:
           ;; See <https://github.com/pympler/pympler/issues/134>.
           "--deselect=test/muppy/test_summary.py::SummaryTest::test_repr_function"
           ;; This test times out.
-           "--deselect=test/gui/test_web.py::WebGuiTest::test_traceback")))
+           "--deselect=test/gui/test_web.py::WebGuiTest::test_traceback"
           "--deselect=test/muppy/test_tracker.py::TrackerTest::test_otracker_diff")))
      (native-inputs
       (list python-pytest python-setuptools))
      (home-page "https://pythonhosted.org/Pympler/")
@@ -10045,13 +10056,13 @@ Google and Numpydoc format.")
 (define-public python-docutils
  (package
    (name "python-docutils")
-    (version "0.21.2")
+    (version "0.22.4")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "docutils" version))
       (sha256
-        (base32 "0vwqzbmzdvwx23myx4cg8s8mdkrqnfxpa9yi7jm2s66z5rrihsrs"))))
+        (base32 "0s4ryafs954ivgb7bifzpbv98vb2mcr0s8wi9nvwpglsvqgkpdad"))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -11483,13 +11494,16 @@ For some datatypes the overhead can be reduced by using khash by factor 4-8.")
  ;; TODO: Move to python-build.
  (package
    (name "python-cython")
-    (version "3.1.7")
+    (version "3.2.5")
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "cython" version))
+       (uri (git-reference
              (url "https://github.com/cython/cython")
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0gaslzb3virk4v6yh5a7dp6ka1lm267v994g8r25lck1702vjy3g"))))
+        (base32 "07n0x4z0ifkhl8hi47amqhqfjc6jlh5dra9r54nlsnwnai83psy1"))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -11497,17 +11511,16 @@ For some datatypes the overhead can be reduced by using khash by factor 4-8.")
      #:test-flags
      #~(list "runtests.py"
              "-vv"
-              "-j" (number->string (parallel-job-count))
+              ;; Some tests fail when number of cores are 24, keep on save
              ;; minimal count.
              "-j" (number->string (min 8 (parallel-job-count)))
              "-x" (string-join
                    (list "annotate_html"
                          "Debugger"
                          ;; It introduces cycle.
                          "numpy_test"
                          ;; It fails with AssertionError: Failed doctest test
                          ;; for complex_numbers_cpp.double_abs.
                          ;; See: <https://github.com/cython/cython/issues/6528>.
                          "complex_numbers_cpp"
                          ;; This test fails when running on 24 cores.
                          "cpp_stl_conversion"
                          #$@(if (target-32bit?)
                                 ;; XXX: On 32-bit architectures, running the
                                 ;; parallel tests fails on many-core systems.
@@ -11534,8 +11547,7 @@ For some datatypes the overhead can be reduced by using khash by factor 4-8.")
              (setenv "HOME" "/tmp"))))))
    (native-inputs
     (list libxcrypt
-           python-setuptools
+           python-setuptools))
           python-wheel))
    ;; we need the full python package and not just the python-wrapper
    ;; because we need libpython3.3m.so
    (inputs
@@ -11610,16 +11622,8 @@ def load_dynamic(name, path):
              ;; time of the test suite.
              (setenv "CFLAGS" "-O0"))))))))
-(define-public python-cython-next
+;; XXX: Deprecated on <2026-05-28>.
-  (package
+(define-public python-cython-next python-cython)
    (inherit python-cython)
    (version "3.2.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "cython" version))
       (sha256
        (base32 "0d0n0yyicr7icd4f5kn1wwbjqyad6j4m640xlqlk3ixchgad7bf3"))))))
 ;; NOTE: when upgrading numpy please make sure that python-numba,
 ;; python-pandas and python-scipy still build, as these three packages are
@@ -11627,49 +11631,41 @@ def load_dynamic(name, path):
 (define-public python-numpy
  (package
    (name "python-numpy")
-    (version "2.3.1")
+    (version "2.4.6")
    (source
     (origin
       ;; XXX: When switching to Git it fails to find Numpy's fork of Meson
       ;; git submodule -- <https://github.com/numpy/meson>.
       (method url-fetch)
       (uri (string-append
             "https://github.com/numpy/numpy/releases/download/v"
             version "/numpy-" version ".tar.gz"))
       (sha256
-        (base32 "0aqx8hsw54wfp7iv0h0ljlpsygvmrmi3rjic6rsa6v92lhhaxj8y"))))
+        (base32 "1nkx73blw298dzdk6blhrsann60cgdy7q6n3q9m785ia9865g8zk"))))
    (build-system pyproject-build-system)
    (arguments
     (list
-      ;; tests: 47513 passed, 1740 skipped, 33 xfailed, 5 xpassed, 341 warnings
+      ;; tests: 47255 passed, 1079 skipped, 32 xfailed, 2 xpassed, 318 warnings
      #:modules '((guix build utils)
                  (guix build pyproject-build-system)
                  (ice-9 format))
      #:test-flags
      #~(list "-m" "not slow"
-              "--numprocesses" (number->string (min 8 (parallel-job-count)))
+              "--numprocesses" (number->string (min 8 (parallel-job-count))))
              ;; See: <https://github.com/numpy/numpy/issues/27531>,
              ;;      <https://github.com/numpy/numpy/issues/17685>,
              ;;      <https://github.com/numpy/numpy/issues/17635>.
              "-k" "not test_api_importable")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'fix-executable-paths
-            (lambda _
+            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "numpy/distutils/exec_command.py"
                (("'/bin/sh'")
                 (format #f "~s" (which "bash"))))
              (substitute* "numpy/meson.build"
                ;; Relay on python from the PATH instead of full reference
                ;; stored in built wheel.
-                (("'py.full_path\\(\\)'") "'python'"))))
+                (("'py.full_path\\(\\)'") "'python'"))
-          ;; This isn't architecture specific.
+              (substitute* "numpy/_core/tests/test_cpu_features.py"
-          ;; TODO: Remove this conditional and apply for all builds.
+                (("/bin/true")
-          #$@(if (target-ppc64le?)
+                 (search-input-file inputs "bin/true")))))
                 #~((add-after 'unpack 'patch-bin-true
                      (lambda* (#:key inputs #:allow-other-keys)
                        (substitute* "numpy/_core/tests/test_cpu_features.py"
                          (("/bin/true")
                           (search-input-file inputs "bin/true"))))))
                 #~())
          (add-before 'build 'parallelize-build
            (lambda _
              (setenv "OMP_NUM_THREAD"
@@ -11689,7 +11685,7 @@ def load_dynamic(name, path):
                                 (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
                         ":")))))
          (add-before 'build 'configure-blas
-            (lambda* (#:key inputs #:allow-other-keys)
+            (lambda _
              (call-with-output-file "site.cfg"
                (lambda (port)
                  (format port
@@ -11701,7 +11697,11 @@ include_dirs = ~:*~a/include~%" #$(this-package-input "openblas"))))))
            (lambda* (#:key tests? test-flags #:allow-other-keys)
              (when tests?
                (with-directory-excursion #$output
-                  (apply invoke "pytest" test-flags)))))
+                  (apply invoke "pytest" test-flags)
                  (let ((pytest-cache (string-append #$output
                                                     "/.pytest_cache")))
                    (when (access? pytest-cache X_OK)
                      (delete-file-recursively pytest-cache)))))))
          ;; The executables provided by this package ('f2py' and 'numpy-config')
          ;; only depend on Python.  By customizing the wrap phase we can ensure
          ;; that we don't add all Python packages listed in native-inputs to
@@ -11718,12 +11718,14 @@ include_dirs = ~:*~a/include~%" #$(this-package-input "openblas"))))))
                       (find-files (in-vicinity #$output "/bin"))))))))
    (native-inputs
     (list gfortran
           python-cython
           python-hypothesis
           python-meson
           python-pytest
-           python-pytest-xdist
+           python-pytest-xdist))
-           python-setuptools
+    (inputs
-           python-typing-extensions))
+     (list bash
           openblas))
    (home-page "https://numpy.org")
    (synopsis "Fundamental package for scientific computing with Python")
    (description "NumPy is the fundamental package for scientific computing
@@ -13494,7 +13496,7 @@ Python list with elements of type @code{PIL.Image} (from the
 (define-public python-pillow
  (package
    (name "python-pillow")
-    (version "12.1.1")
+    (version "12.2.0")
    (source
     (origin
       (method git-fetch)
@@ -13503,7 +13505,7 @@ Python list with elements of type @code{PIL.Image} (from the
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1g374rklljx0941j6d1gib9pgcq3scmqw9psqaj2c7m8pilqsn9n"))))
+        (base32 "140ynzxpazq6gq041bhkzx314z4kkzv3wlmvph68a0nkj9nqa3pg"))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -13544,7 +13546,7 @@ stored in a few basic pixel formats.  It should provide a solid foundation for
 a general image processing tool.")
    (properties `((cpe-name . "pillow")))
    (license (license:x11-style
-              "https://github.com/python-pillow/Pillow/blob/12.1.1/LICENSE"
+              "https://github.com/python-pillow/Pillow/blob/12.2.0/LICENSE"
              "MIT-CMU License"))))
 (define-public python-pillow-avif-plugin
@@ -15532,20 +15534,21 @@ to Python code.")
 (define-public python-asttokens
  (package
    (name "python-asttokens")
-    (version "3.0.0")
+    (version "3.0.1")
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "asttokens" version))
+       (uri (git-reference
-       (sha256
+             (url "https://github.com/gristlabs/asttokens")
-        (base32 "1ixv6n8cg08n9h6rwyhd3lkzyjiwpbfv56dk338w3c32inm8pk8d"))))
+             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256 (base32 "1qqi7dygcv58czrsafc4gf41prfb6shd0crx33kd9wypk0v29afn"))))
    (build-system pyproject-build-system)
    (native-inputs
     (list python-astroid
           python-pytest
           python-setuptools
-           python-setuptools-scm
+           python-setuptools-scm))
           python-wheel))
    (home-page "https://github.com/gristlabs/asttokens")
    (synopsis "Python library to annotate abstract syntax trees")
    (description "The @code{asttokens} module annotates Python abstract syntax
@@ -17627,6 +17630,14 @@ should be stored on various operating systems.")
       (sha256
        (base32 "0vm1r1jlaiagj0l9yf7j6zn9w3733dr2169911c0svgrr3gwiwn9"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'fix-tests
           (lambda _
             (substitute* "pasta/augment/inline_test.py"
               (("assertRaisesRegexp") "assertRaisesRegex")))))))
    (propagated-inputs (list python-six))
    (native-inputs (list python-pytest python-setuptools))
    (home-page "https://github.com/google/pasta")
@@ -18115,14 +18126,16 @@ primary use case is APIs defined before keyword-only parameters existed.")
 (define-public python-pyasn1
  (package
    (name "python-pyasn1")
-    (version "0.6.1")
+    (version "0.6.3")
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "pyasn1" version))
+       (uri (git-reference
              (url "https://github.com/pyasn1/pyasn1")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32
+        (base32 "0b22m94j163nikfkl031hgrfasb6wgqp3374b8dbr84jalkl0ykw"))))
         "0d5h500ig8sp72pabd1wcyglc4951xalbkqahf056dl4vlmhsn3g"))))
    (build-system pyproject-build-system)
    (arguments
     (list #:test-backend #~'unittest
@@ -18304,9 +18317,21 @@ is binding LibSass.")
       (sha256
        (base32 "1fj4zkcnx3mk7kbnf4d6pjgv331n17wzpphpwdnmr498ghbsph9k"))))
    (build-system pyproject-build-system)
-    (arguments (list #:tests? #f))  ;circular dependency with python-aiohttp
+    (arguments
     (list
      #:tests? #f  ;circular dependency with python-aiohttp
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'python3.12-compatibility
           (lambda _
             (substitute* '("idna_ssl.py"
                            "tests/test_base.py")
               (("import ssl")
                "import ssl\nimport urllib3")
               (("ssl.match_hostname")
                "urllib3.util.ssl_match_hostname")))))))
    (native-inputs (list python-setuptools))
-    (propagated-inputs (list python-idna))
+    (propagated-inputs (list python-idna python-urllib3))
    (home-page "https://github.com/aio-libs/idna-ssl")
    (synopsis "Support Unicode(idna) domains for Python's @code{ssl} module")
    (description
@@ -22728,20 +22753,22 @@ times.
 (define-public python-lazy-object-proxy
  (package
    (name "python-lazy-object-proxy")
-    (version "1.11.0")
+    (version "1.12.0")
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "lazy_object_proxy" version))
+       (uri (git-reference
              (url "https://github.com/ionelmc/python-lazy-object-proxy")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "174fswfrsqr7yj72f8fyry34qxgagbfw37vzljxbp7schq8l91qq"))))
+        (base32 "1qig879igkjmj4mir26b0n40w3vn5jqn293172s6npxnb4k90kzk"))))
    (build-system pyproject-build-system)
    (native-inputs
     (list python-pytest
           python-pytest-benchmark
           python-setuptools
-           python-setuptools-scm
+           python-setuptools-scm))
           python-wheel))
    (home-page "https://github.com/ionelmc/python-lazy-object-proxy")
    (synopsis "Lazy object proxy for Python")
    (description
@@ -24769,7 +24796,7 @@ instead of servers and network commands.")
 (define-public python-astroid
  (package
    (name "python-astroid")
-    (version "3.3.11")
+    (version "4.1.2")
    (source
     (origin
       (method git-fetch)
@@ -24778,24 +24805,12 @@ instead of servers and network commands.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1x5903kmi47pc87r949lym2cwl0xg885xyy730adxv0g6r083zwn"))))
+        (base32 "04x82slqxyyv0pikz680sw5aj2vbid1s7zdnzgqj7dlbz68c0ch0"))))
    (build-system pyproject-build-system)
    (arguments
     ;; UserWarning: pkg_resources is deprecated as an API. See
     ;; https://setuptools.pypa.io/en/latest/pkg_resources.html. The
     ;; pkg_resources package is slated for removal as early as
     ;; 2025-11-30. Refrain from using this package or pin to Setuptools<81.
     (list #:test-flags
           #~(list "-k" "not test_identify_old_namespace_package_protocol")))
    (native-inputs
     (list python-mypy-minimal
           python-pytest
-           python-setuptools
+           python-setuptools))
           python-wheel))
    (propagated-inputs
     (list python-lazy-object-proxy
           python-typing-extensions
           python-wrapt))
    (home-page "https://github.com/PyCQA/astroid")
    (synopsis "Python source code base representation")
    (description "@code{python-astroid} provides a common base representation
@@ -27911,26 +27926,23 @@ codecs for use in data storage and communication applications.")
 (define-public python-dill
  (package
    (name "python-dill")
-    (version "0.4.0")
+    (version "0.4.1")
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "dill" version))
+       (uri (git-reference
              (url "https://github.com/uqfoundation/dill")
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1w5w5hlijw7ahqji45ssyvdip5pv074h4nw97bsj8ws7vz9g2cq6"))))
+        (base32 "09ig6820sd68cjixl5vkwkwvvgdii8qhaikc1rxhabhwxfymc7v2"))))
    (build-system pyproject-build-system)
    (arguments
-     (list
+     (list #:test-backend #~'custom
-      #:phases #~(modify-phases %standard-phases
+           #:test-flags #~(list "dill/tests/__main__.py")))
                   (replace 'check
                     (lambda* (#:key tests? #:allow-other-keys)
                       (if tests?
                           ;; Extracted from tox.ini
                           (invoke "python" "dill/tests/__main__.py")
                           (format #t "test suite not run~%")))))))
    (native-inputs
-     (list python-setuptools python-wheel))
+     (list python-setuptools))
-    (home-page "https://pypi.org/project/dill/")
+    (home-page "http://dill.rtfd.io/")
    (synopsis "Serialize all of Python")
    (description "Dill extends Python's @code{pickle} module for serializing
 and de-serializing Python objects to the majority of the built-in Python
@@ -30892,14 +30904,20 @@ positioning, and keyboard input.")
 (define-public python-readme-renderer
  (package
    (name "python-readme-renderer")
-    (version "44.0")
+    (properties '((commit . "e603eb17fcabd6bd20706d278fc24a7e9a663190")
                  (revision . "0")))
    (version (git-version "44.0"
                          (assoc-ref properties 'revision)
                          (assoc-ref properties 'commit)))
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "readme_renderer" version))
+       (uri (git-reference
              (url "https://github.com/pypa/readme_renderer")
              (commit (assoc-ref properties 'commit))))
       (file-name (git-file-name name version))
       (sha256
-        (base32
+        (base32 "15w3lzgg8gcq22saqy2cpnv3hvkrixhyn57fcg1p1bm2njh1hr61"))))
         "1qfiqm3w1ydpbipns5nifa7h4wraxd72nh7imif819mzmd7064l7"))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -33495,18 +33513,22 @@ systems in Python.")
 (define-public python-dotenv
  (package
    (name "python-dotenv")
-    (version "1.1.1")
+    (version "1.2.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "python_dotenv" version))
       (sha256
-        (base32 "1aw9c5gw2gfjf7n3s7k6lb6ybz090hh60wq0daz4azr52sbkk9m8"))))
+        (base32 "1wwwg7gasqmnv5y2hb3w1155c8nai6zzih8x5hn0ifnpzf8ildrc"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      ;; .dotenv-real instead of dotenv
      #~(list "-k not test_run_with_dotenv_and_command_flags")))
    (native-inputs
     (list python-pytest
-           python-setuptools
+           python-setuptools))
           python-sh))
    (propagated-inputs
     (list python-click))
    (home-page "https://saurabh-kumar.com/python-dotenv/")
@@ -34595,19 +34617,22 @@ for styling strings in the terminal.")
 (define-public python-multipart
  (package
    (name "python-multipart")
-    (version "0.0.20")
+    (version "0.0.29")
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              (uri (pypi-uri "python_multipart" version))
+       (method git-fetch)
-              (sha256
+       (uri (git-reference
-               (base32
+              (url "https://github.com/Kludex/python-multipart")
-                "04wxzakk3hs4z4xf3ldhym3gm46hjicn4iwiw150c8wfbfscml4d"))))
+              (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "06rxa2xymdqri8zydy7xw2cnpsnzlv2jzdy9g86m5fpfca0pp9fm"))))
    (build-system pyproject-build-system)
    (native-inputs
     (list python-hatchling
           python-pytest
           python-pyyaml))
-    (home-page "https://github.com/andrew-d/python-multipart")
+    (home-page "https://github.com/Kludex/python-multipart")
    (synopsis "Streaming multipart parser for Python")
    (description
     "This package provides a streaming multipart parser for Python.")
@@ -35868,13 +35893,13 @@ line by line or column by column or a combination of both.")
 (define-public python-rpds-py
  (package
    (name "python-rpds-py")
-    (version "0.10.6")
+    (version "0.30.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "rpds_py" version))
              (sha256
               (base32
-                "0l5slkvhq2vf64mapimmj6ginsv01mc4niyj90vvz3assq4agrac"))))
+                "110y8k62b9xb3slny7gf89943xpbji3s7vl7yz0g0jh1j37zg3yx"))))
    (build-system cargo-build-system)
    (arguments
     (list
@@ -38374,18 +38399,32 @@ and @code{tokens_to_src} to roundtrip.")
 (define-public python-tomlkit
  (package
    (name "python-tomlkit")
-    (version "0.13.3")
+    (version "0.15.0")
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "tomlkit" version))
+       (uri (git-reference
              (url "https://github.com/sdispater/tomlkit")
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "18fjmmhiv5jkkg1dwidmxd0sjqnkf675igizxsa2ppspxr3z4323"))))
+        (base32 "00sv5x8j78zkirzh9rl89lkpwfwhkhrq4mql2p4rqws1j37zx88g"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          ;; toml-test is submodule to
          ;; <https://github.com/toml-lang/toml-test>.
          (add-after 'unpack 'copy-toml-test-source
            (lambda _
              (copy-recursively
               #$(package-source (this-package-native-input "toml-test"))
               "tests/toml-test"))))))
    (native-inputs
     (list python-poetry-core
           python-pytest
-           python-pyyaml))
+           toml-test))
    (home-page "https://github.com/sdispater/tomlkit")
    (synopsis "Style-preserving TOML library")
    (description
@@ -39748,6 +39787,31 @@ progress, among other things.")
 for linkify-it-py projects.")
    (license license:expat)))
 (define-public python-udapi
  (package
    (name "python-udapi")
    (version "0.5.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/udapi/udapi-python")
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1z9nyj0jmd2yk58c5kag4fkfb7y478di859xi56xc7fhvmyjf7nj"))))
    (build-system pyproject-build-system)
    (native-inputs
     (list python-pytest python-setuptools))
    (propagated-inputs
     (list python-colorama python-termcolor))
    (home-page "http://udapi.readthedocs.io")
    (synopsis "Framework for processing Universal Dependencies data")
    (description
     "This package is a Python library providing an API for processing
 Universal Dependencies data.")
    (license license:gpl3+)))
 (define-public python-ujson
  (package
    (name "python-ujson")
@@ -1255,7 +1255,7 @@ base, via the @file{pythoncapi_compat.h} header file.")
 (define-public micropython
  (package
    (name "micropython")
-    (version "1.26.1")
+    (version "1.28.0")
    (source
      (origin
        (method url-fetch)
@@ -1263,7 +1263,7 @@ base, via the @file{pythoncapi_compat.h} header file.")
                            "releases/download/v" version
                            "/micropython-" version ".tar.xz"))
        (sha256
-         (base32 "165c8g60f5zf82gw2d94snyjmcgn999jn4i8ngyc0wk2vwa6bghj"))
+         (base32 "05d2gd3g8v3paxf4fin4cv5scgnc4yl0jdahpjs37nmqaybcahsf"))
      (modules '((guix build utils)))
      (snippet
       '(begin
@@ -74,6 +74,7 @@
  #:use-module (gnu packages bash)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages crypto)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cmake)
@@ -112,7 +113,6 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages markup)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages node)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages pciutils)
@@ -179,9 +179,9 @@ official project.")
    (home-page "https://github.com/oclero/qtappinstancemanager")
    (license license:expat)))
-(define-public qcoro-qt5
+(define-public qcoro-qt6
  (package
-    (name "qcoro-qt5")
+    (name "qcoro-qt6")
    (version "0.11.0")
    (source
     (origin
@@ -194,31 +194,18 @@ official project.")
        (base32 "0g9laaw1mkp5ynpp3c7aingndcmgncbacslq3p6bzwjisdd6xr5m"))))
    (build-system qt-build-system)
    (arguments
-     (list #:configure-flags
+     (list #:qtbase qtbase
           #:configure-flags
           #~(list "-DCMAKE_CXX_FLAGS=-fPIC"
-                   (string-append "-DUSE_QT_VERSION="
+                   "-DUSE_QT_VERSION=6")))
                                  #$(version-major
                                     (package-version
                                      (this-package-input "qtbase")))))))
    (native-inputs (list dbus))         ;for tests
-    (inputs (list qtbase-5 qtdeclarative-5 qtwebsockets-5))
+    (inputs (list qtdeclarative qtwebsockets libxkbcommon))
    (home-page "https://qcoro.dvratil.cz/")
-    (synopsis "C++ Coroutine Library for Qt5")
+    (synopsis "C++ Coroutine Library for Qt6")
    (description "QCoro is a C++ library that provide set of tools to make use
 of C++20 coroutines in connection with certain asynchronous Qt actions.")
    (license license:expat)))
 (define-public qcoro-qt6
  (package
    (inherit qcoro-qt5)
    (name "qcoro-qt6")
    (synopsis "C++ Coroutine Library for Qt6")
    (inputs (modify-inputs inputs
              (replace "qtbase" qtbase)
              (replace "qtdeclarative" qtdeclarative)
              (replace "qtwebsockets" qtwebsockets)
              (append libxkbcommon)))))
 (define-public qlementine
  (package
    (name "qlementine")
@@ -1674,13 +1661,6 @@ from within Qt 5.")))
 XLSX document format.")
     (license license:expat)))
 (define-public qxlsx-qt5
  (package/inherit qxlsx
    (name "qxlsx-qt5")
    (inputs
     (list qtbase-5))
    (synopsis "Qt5 build for the qxlsx library")))
 (define-public qtxmlpatterns-5
  (package (inherit qtsvg-5)
    (name "qtxmlpatterns")
@@ -6465,9 +6445,9 @@ handles the authentication process of an account and securely stores the
 credentials and service-specific settings.")
    (license license:lgpl2.1+)))
-(define-public packagekit-qt5
+(define-public packagekit-qt6
  (package
-    (name "packagekit-qt5")
+    (name "packagekit-qt6")
    (version "1.1.2")
    (source (origin
              (method git-fetch)
@@ -6479,29 +6459,17 @@ credentials and service-specific settings.")
               (base32
                "1nx8xfhz9v4pc0mz1ir0pq47skpc3w3yj8wqa4m5yky87ib5xcxc"))))
    (build-system cmake-build-system)
-    (arguments '(#:tests? #f))          ;no test suite
+    (arguments
-    (native-inputs (list pkg-config))
+      (list
-    (inputs (list packagekit qtbase-5))
+        #:tests? #f          ;no test suite
        #:configure-flags #~(list "-DBUILD_WITH_QT6=ON")))
    (inputs (list packagekit qtbase))
    (home-page "https://www.freedesktop.org/software/PackageKit/pk-intro.html")
    (synopsis "Qt5 bindings for PackageKit")
    (description "Provides Qt5 bindings to PackageKit which is a DBUS
 abstraction layer that allows the session user to manage packages in
 a secure way.")
    (license license:lgpl2.1+)))
 (define-public packagekit-qt6
  (package
    (inherit packagekit-qt5)
    (name "packagekit-qt6")
    (arguments (substitute-keyword-arguments arguments
                 ((#:configure-flags flags #~'())
                  #~(cons "-DBUILD_WITH_QT6=ON" #$flags))))
    (inputs (modify-inputs inputs
              (replace "qtbase" qtbase)))
    (synopsis "Qt6 bindings for PackageKit")
    (description "Provides Qt6 bindings to PackageKit which is a DBUS
 abstraction layer that allows the session user to manage packages in
-a secure way.")))
+a secure way.")
    (license license:lgpl2.1+)))
 ;; fork for support qt6
 (define-public signond-qt6
@@ -202,7 +202,7 @@
 ;;
 ;; CODE:
-(define %racket-version "8.18") ; Remember to update chez-scheme-for-racket!
+(define %racket-version "9.1") ; Remember to update chez-scheme-for-racket!
 (define %racket-commit
  (string-append "v" %racket-version))
 (define %racket-origin
@@ -212,7 +212,7 @@
          (url "https://github.com/racket/racket")
          (commit %racket-commit)))
    (sha256
-     (base32 "0m38im7a3b3w7sdl15vpsrx7dxw5iz22f1zzffy1bkbbqz45pm87"))
+     (base32 "1yc6lkydg32998ajnqws83zakksmbp3hb21spq0sfaq4v7wg2ng6"))
    (file-name (git-file-name "racket" %racket-version))
    (patches (search-patches "racket-chez-scheme-bin-sh.patch"
                             "racket-launcher-config-dir.patch"
@@ -695,6 +695,7 @@ DrRacket IDE, are not included.")
         ("net-lib" "pkgs/net-lib")
         ("racket-doc" "pkgs/racket-doc")
         ("racket-index" "pkgs/racket-index")
         ("racket-index-exe" "pkgs/racket-index-exe")
         ("scheme-doc" "pkgs/scheme-doc")
         ("sandbox-lib" "pkgs/sandbox-lib")
         ("sequence-tools-lib" "pkgs/sequence-tools-lib")
@@ -706,10 +707,10 @@ DrRacket IDE, are not included.")
       "class-iop" (base32 "08z57q83cr7wnh6g8ah3hdhmsmf9zp1jfs7yvxv188l3hzvygy5l")
       '("class-iop-lib"))
      (simple-racket-origin
-       "compatibility" (base32 "1d1py9wizi4jnzak7b6d0p9filxv1x9mlx5gsp3yhcjajigq182p")
+       "compatibility" (base32 "0q5k4p44sf2y4gl69js11qvicyzqwy16ry74bvj1vrn8i8xws55b")
       '("compatibility" "compatibility-doc" "compatibility-lib"))
      (simple-racket-origin
-       "contract-profile" (base32 "1xm2z8g0dpv5d9h2sg680vx1a8ix9gbsdpxxb8qv1w7akp73paj3")
+       "contract-profile" (base32 "068z8flwcznqg0bjk227i2qapqbciyrckgqf8mvk57gxmr6zh3d3")
       '(("contract-profile" ".")))
      (simple-racket-origin
       "data" (base32 "11ai6c9h0brbblc6xn045ajj4gyrvbjpk1pqcqm1m0dy9q2rzd4a")
@@ -718,7 +719,7 @@ DrRacket IDE, are not included.")
       "datalog" (base32 "0nf6cy4djpyhfvgpa6yn72apbz9s83gp0qg95pzjd0az4v6qwq1s")
       '(("datalog" ".")))
      (simple-racket-origin
-       "db" (base32 "0qwl8gyd71sm56kcs021g99cpw5bibaycvk1x7ng69jhkylg6q6f")
+       "db" (base32 "09f2wysqmgs46nbzmwrhbn6jqnkpj6bsabm6s6kw8qmp6azca9q2")
       '("db" "db-doc" "db-lib"))
      (simple-racket-origin
       "deinprogramm" (base32 "1zkasf94gzp97q0fhrd065d56zv10h0j0ncmaghzglkmjj8c3vvx")
@@ -731,10 +732,10 @@ DrRacket IDE, are not included.")
       "distributed-places" (base32 "1dajpkj9balqcpv6cdk9hwjz592h1vq8rrx5vncariiac4vbdpa0")
       '("distributed-places" "distributed-places-doc" "distributed-places-lib"))
      (simple-racket-origin
-       "draw" (base32 "1nny22h0hnd40qs3ndkhfrgg793y6f4gl9jpdz1g2k0cpr3818rg")
+       "draw" (base32 "157r861rx2avbjpqhrrxwdqxwf5ksvw38km3pw7rxiwvwh9nys8k")
       '("draw" "draw-doc" "draw-lib"))
      (simple-racket-origin
-       "drracket" (base32 "07qh9dzgd2xhd0375z78vcsf32za08cacj4s2mcrhilcvcgw9s0j")
+       "drracket" (base32 "17sszhx5nd549w7kj6pd3c3cyjps2swbp7rmg36yaxm71pli5gs5")
       '("drracket"
         "drracket-core"
         "drracket-core-lib"
@@ -753,7 +754,7 @@ DrRacket IDE, are not included.")
       "eopl" (base32 "0qihajdpwf2q7hbs6fsw6mmmzy57kgzgry3vyp9z8w7ay8df3w15")
       '(("eopl" ".")))
      (simple-racket-origin
-       "errortrace" (base32 "0l9k2rx6z4jkid7kxhbs763s66pxbzvfrgxajykbrmqkv77lhb3w")
+       "errortrace" (base32 "02z80khr4kqhcpq1k3djz7jgkwa31vnacid4qx8naab9dkbcp5x8")
       '("errortrace" "errortrace-doc" "errortrace-lib"))
      (simple-racket-origin
       "expeditor" (base32 "1nk88jq0blzcw45fr8nwp024cysplayi3paaay4z824lkn1smzaa")
@@ -770,13 +771,13 @@ DrRacket IDE, are not included.")
       "games" (base32 "13z7fnbr48s98lmfxc0nbfhbqkd4hphymy2r63hqm783xzn6ylzi")
       '(("games" ".")))
      (simple-racket-origin
-       "gui" (base32 "0qkxa8cq0cblriamd7x502g918kjvq4348l6c8qmqdpn9cw9mg2h")
+       "gui" (base32 "1c47622y5cf1p7nnbycaf53m8vakf55lqzv8byqzj7zcvcsh8s16")
       '("gui" "gui-doc" "gui-lib" "tex-table"))
      (simple-racket-origin
-       "gui-pkg-manager" (base32 "024880k3wmvkqhjc954prrkavwv3bgafcw00ajz7h2llygh0aqpl")
+       "gui-pkg-manager" (base32 "1f0ssg37kdk3xn9js616ns345565q39j9h51wzd99753iqd45m92")
       '("gui-pkg-manager-lib"))
      (simple-racket-origin
-       "htdp" (base32 "14bdv86zxs87rvvvbwvq3x0sqpg1hj16whjcv20r96c26b1xxj36")
+       "htdp" (base32 "02a5zny1njys40jfsi2spw82ar0kkbfddpk10al822ajs1manhak")
       '("htdp" "htdp-doc" "htdp-lib"))
      (simple-racket-origin
       "html" (base32 "18n1jnjgzfknc8nv8dppi85nb8q08gqdwkg6hfjk08x0p00anx2x")
@@ -791,16 +792,16 @@ DrRacket IDE, are not included.")
       "lazy" (base32 "0rn8kd0ih7aw6fj1g7jdvi5978a6q4hyd6gbh89nb6j5ijvlgn43")
       '(("lazy" ".")))
      (simple-racket-origin
-       "macro-debugger" (base32 "133b74pxavbafcsmp34kgvwmx1l6xx4bykzvgwwjg3kg2fa5bg1g")
+       "macro-debugger" (base32 "08qmkrvm3qvac4829izmlwl9qrlsc1f6y8yqiradibhm05k7rwg7")
       '("macro-debugger" "macro-debugger-text-lib"))
      (simple-racket-origin
-       "main-distribution" (base32 "0m2n9s32s8a4a2gn4ywrm9l8jycdm5ayi5w9kh5wchhrrw7qzq7y")
+       "main-distribution" (base32 "0gk7wrwy0r1yllk827h8awfswngl1lhlq765d6s42y841v33jn0i")
       '(("main-distribution" ".")))
      (simple-racket-origin
       "make" (base32 "10852fj30bz5r46c3d99s37fkgy5yh44gb01j29sf3kxnhi0g2sa")
       '(("make" ".")))
      (simple-racket-origin
-       "math" (base32 "1399mynmcrybipjsy2ikzs600jjxda0lah653w3vx2lfspsn31if")
+       "math" (base32 "1mgqxx9lbwhd8if3mxz7ji2wryvihjmq5imn2316skkvr16yy8mx")
       '("math" "math-doc" "math-lib"))
      (simple-racket-origin
       "mysterx" (base32 "11p9jzrafw0hizhl0cs4sxx7rv281185q8hryic2rpk0kzjdyr48")
@@ -809,7 +810,7 @@ DrRacket IDE, are not included.")
       "mzcom" (base32 "0rc9pfj7gwm5azghqvcibz6si1x5s2v8mr2yngk7ssq9gzfbi6a4")
       '(("mzcom" ".")))
      (simple-racket-origin
-       "mzscheme" (base32 "04kyrhznq46mklacf7pms4fv47zsimqqk3948r3w2ym9n04fhjsx")
+       "mzscheme" (base32 "0p7bp8rmzw7k12sjxdqlxf31d8ama4wv9qz6ryvnmjn2qyhrr3d1")
       '("mzscheme" "mzscheme-doc" "mzscheme-lib"))
      (racket-packages-origin
       "net-cookies" (origin
@@ -818,7 +819,7 @@ DrRacket IDE, are not included.")
                             (url "https://github.com/RenaissanceBug/racket-cookies")
                             (commit %racket-commit)))
                       (sha256 (base32
-                                "1fbl717w5801bydx3nzwxddd1rh1cc0gxwpjc7ka9zh5ak09sb0w"))
+                                "0v6lbpv8ly4jwpjr3rk0q6izpsnfp45ysgrhngpw7jshkjc5wgyd"))
                       (file-name
                        (git-file-name "RenaissanceBug-racket-cookies" %racket-version)))
       '("net-cookies" "net-cookies-doc" "net-cookies-lib"))
@@ -838,16 +839,16 @@ DrRacket IDE, are not included.")
       "option-contract" (base32 "1914dcxy6qzpg3cpnzdm9lj0kwyw8xdb85mwiamqfkbg0xlyyhpa")
       '("option-contract" "option-contract-doc" "option-contract-lib"))
      (simple-racket-origin
-       "parser-tools" (base32 "0i822p7ik6q03l7mrlf0qb63xdxvx06yl5lg1g1qri5wmi5xj0pb")
+       "parser-tools" (base32 "0dp99d1a47kqyg2iqdijm5781qnd571iwvg85dvrjc76ab4pccgd")
       '("parser-tools" "parser-tools-doc" "parser-tools-lib"))
      (simple-racket-origin
       "pconvert" (base32 "0xw9f9692v2qp16fwmwmwmrb118kpz259vmx8cq6s9vsw0112zpq")
       '("pconvert-lib" "pconvert-doc"))
      (simple-racket-origin
-       "pict" (base32 "17pldgiifmwi968dwlk23c1wnrlks0x7aj5jdmdfsf9xgq31wkb5")
+       "pict" (base32 "1xs1k98nr052p5v30abn7kl8pm1rdwj8xqvrghw8b62bvhhb072a")
       '("pict" "pict-doc" "pict-lib"))
      (simple-racket-origin
-       "pict-snip" (base32 "081nwiy4a0n4f7xws16hqbhf0j3kz5alizndi3nnyr3chm4kng6x")
+       "pict-snip" (base32 "1qrqbigw6arhccqgqzblfqqcpsdy15dwb0y22axwxgpw1ax0ki6f")
       '("pict-snip" "pict-snip-doc" "pict-snip-lib"))
      (simple-racket-origin
       "picturing-programs" (base32 "1a3d6nw9n827b4711nvgrnw7w47k4fxvk8c2a8br6a1l748kxkwy")
@@ -865,7 +866,7 @@ DrRacket IDE, are not included.")
       "preprocessor" (base32 "1p5aid58ifnjy4xl0ysh85cq39k25661v975jrpk182z3k5621mg")
       '(("preprocessor" ".")))
      (simple-racket-origin
-       "profile" (base32 "10lv3iz58hqk043llnbqrkmjnm1pbvr4j1j188g85zg798rqyjzs")
+       "profile" (base32 "1n6jlhkq0zs2sd132k92nvw08qscadjz3d6p2r5pjlcdawkmkik0")
       '("profile" "profile-doc" "profile-lib"))
      (racket-packages-origin
       "quickscript" (origin
@@ -895,7 +896,7 @@ DrRacket IDE, are not included.")
                         (git-file-name "jeapostrophe-racket-cheat" %racket-version)))
       '(("racket-cheat" ".")))
      (simple-racket-origin
-       "racklog" (base32 "0fr8xij0sssfnmwn6dfdi4jj3l62f2yj3jrjljv13kaycrfls032")
+       "racklog" (base32 "0i2jnghb5vqmk2f0cppgggyp73zy1q0dlhpvxrzdxw39skmhmgkc")
       '(("racklog" ".")))
      (simple-racket-origin
       "rackunit" (base32 "191x4lgxg1bbkimdndg6j562zyxq48l0g21f9j2ln2hmh9s1v065")
@@ -914,7 +915,7 @@ DrRacket IDE, are not included.")
       "realm" (base32 "0rlvwyd6rpyl0zda4a5p8dp346fvqzc8555dgfnrhliymkxb6x4g")
       '(("realm" ".")))
      (simple-racket-origin
-       "redex" (base32 "1h60mhaaiiwqcnmskqfrl6jhg4d97xjdcxnhw9krm4aysa9b9bwf")
+       "redex" (base32 "1gg36wpd5kw01dwz353j5xvd2c673aws5l3jn2h2rzqlslk49dw7")
       '("redex"
         "redex-benchmark"
         "redex-doc"
@@ -929,7 +930,7 @@ DrRacket IDE, are not included.")
       "scheme-lib" (base32 "0pcf0y8rp4qyjhaz5ww5sr5diq0wpcdfrrnask7zapyklzx1jx8x")
       '(("scheme-lib" ".")))
      (simple-racket-origin
-       "scribble" (base32 "0pg8brgyyziw3y8fp6ls6ii7i02cmm5168i4zmqfxjzywswljf17")
+       "scribble" (base32 "1h6rkkbvxa6fwcpv6y5n14y984z4bxlhn04hhv8r7398a6jsldg6")
       '("scribble"
         "scribble-doc"
         "scribble-html-lib"
@@ -955,13 +956,13 @@ DrRacket IDE, are not included.")
       "slatex" (base32 "0pkm2isbbdk63slrbsxcql7rr0wdrw5kapw1xq4ps5k8dhlzv8x0")
       '(("slatex" ".")))
      (simple-racket-origin
-       "slideshow" (base32 "0dyg20qs40s2d6ha28zb9h5x4v7phkddinqm446b4jishyrg7dqc")
+       "slideshow" (base32 "1aprcapyj0362lfh2pbcyxf4r2k01zmp6yy9ppag0xbz0jw437im")
       '("slideshow" "slideshow-doc" "slideshow-exe" "slideshow-lib" "slideshow-plugin"))
      (simple-racket-origin
-       "snip" (base32 "1jpy5728w9bszgsjczlzrjjxsvqlcn4ah6gd3rp0plp8zzk9mq0s")
+       "snip" (base32 "10727bi2ybn2ahlkpikdknwfzfsppaw5wkvjmzd380jp1fw91q67")
       '("snip" "snip-lib"))
      (simple-racket-origin
-       "typed-racket" (base32 "00d5pb5h34066q4prb9v5s5m9ggbby31f3anshd9vfsrzhd38p4n")
+       "typed-racket" (base32 "1cmp3065fp9lm6rsfml7x5bvnilh1fs9k0511l11qdismz2sndpy")
       '("source-syntax"
         "typed-racket"
         "typed-racket-compatibility"
@@ -972,7 +973,7 @@ DrRacket IDE, are not included.")
       "srfi" (base32 "07q7wdgnf88z1rq0bfpn4b41abhfswa38c0s2hkn325blk53k4a6")
       '("srfi" "srfi-doc" "srfi-lib" "srfi-lite-lib"))
      (simple-racket-origin
-       "string-constants" (base32 "0llalgdncn18ix5xnx82yyms221g47xh7s3w6inch53ip3yc6ksr")
+       "string-constants" (base32 "085anm6s5ghg5bfggavknpr52py1a72qwjihvp0rnxpkf181sn8c")
       '("string-constants" "string-constants-doc" "string-constants-lib"))
      (simple-racket-origin
       "swindle" (base32 "1q8vdxpzczzwdw2mys2caab45yvadmqkixsr29k8pl03n8dsg8j9")
@@ -984,16 +985,16 @@ DrRacket IDE, are not included.")
       "trace" (base32 "1zx0kfbacidg5rllbvx842x949ra22n004irs3vm1hqmwmixy3is")
       '(("trace" ".")))
      (simple-racket-origin
-       "unix-socket" (base32 "02dfwas5ynbpyz74w9kwb4wgb37y5wys7svrlmir8k0n9ph9vq0y")
+       "unix-socket" (base32 "039r2aqc6xc4b3x95ggjg4ab1pfiff6pavi4d40662zgwbi61pwk")
       '("unix-socket" "unix-socket-doc" "unix-socket-lib"))
      (simple-racket-origin
-       "web-server" (base32 "0ry5vwjd06ml9hmspgrwci8c99syx7zhp9sgldmhwwfvf5m1g29d")
+       "web-server" (base32 "0v66z9dklf02lc0g357h4rnfq5pnk87d1qz59sfrlzz24phxg9g6")
       '("web-server" "web-server-doc" "web-server-lib"))
      (simple-racket-origin
       "wxme" (base32 "1qp5gr9gqsakiq3alw6m4yyv5vw4i3hp4y4nhq8vl2nkjmirvn0b")
       '("wxme" "wxme-lib"))
      (simple-racket-origin
-       "xrepl" (base32 "0sw531zvd8xqckmrh5da4fiq0sfjyg1nj5d508l7bl3azn35khil")
+       "xrepl" (base32 "1kkcm68qyck2d6mp56h1j5fnfbx938a15dnyn1cf5yqpj9cc637m")
       '("xrepl" "xrepl-doc" "xrepl-lib"))))
    (build-system gnu-build-system)
    (arguments
@@ -31,7 +31,7 @@
 ;;; Copyright © 2022-2025 Remco van 't Veer <remco@remworks.net>
 ;;; Copyright © 2022 Taiju HIGASHI <higashi@taiju.info>
 ;;; Copyright © 2023 Yovan Naumovski <yovan@gorski.stream>
-;;; Copyright © 2023, 2024, 2025 gemmaro <gemmaro.dev@gmail.com>
+;;; Copyright © 2023, 2024, 2025, 2026 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023, 2024 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2023, 2024 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2023-2025 Hartmut Goebel <h.goebel@crazy-compilers.com>
@@ -8201,19 +8201,27 @@ differences (added or removed nodes) between two XML/HTML documents.")
 (define-public ruby-racc
  (package
    (name "ruby-racc")
-    (version "1.5.2")
+    (version "1.8.1")
    (source
     (origin
-       (method url-fetch)
+       (method git-fetch) ;for tests
-       (uri (rubygems-uri "racc" version))
+       (uri (git-reference
             (url "https://github.com/ruby/racc")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "178k7r0xn689spviqzhvazzvxfq6fyjldxb3ywjbgipbfi4s8j1g"))))
+         "1sg2mqp6yxdxrn9kbbsxkd6930fxvm4yjl8knsc0wq6fkipnhm8q"))))
    (build-system ruby-build-system)
    (arguments
-     `(#:tests? #f))            ; Fails while parsing test instructions.
+     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'build 'compile
            (lambda _
              (invoke "rake" "compile"))))))
    (native-inputs
-     (list ruby-hoe ruby-rake-compiler))
+     (list ruby-rake-compiler ruby-test-unit-ruby-core))
    (synopsis "LALR(1) parser generator for Ruby")
    (description
     "Racc is a LALR(1) parser generator.  It is written in Ruby itself, and
@@ -116,7 +116,6 @@
  #:use-module (gnu packages lua)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages shells)
  #:use-module (gnu packages ssh)
  #:use-module (gnu packages pcre)
@@ -4212,14 +4211,14 @@ background agent taking care of maintaining the necessary state.")
 (define-public rust-cargo-c
  (package
    (name "rust-cargo-c")
-    (version "0.10.22+cargo-0.96.0")
+    (version "0.10.20+cargo-0.94.0")
    (source
      (origin
        (method url-fetch)
        (uri (crate-uri "cargo-c" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-         (base32 "1j5122hla12v6xjpvsvzv10gzvm80dbf65b2cy6669kcpjvlk1v0"))))
+         (base32 "0q1198xlkcd50nxx722s18lpm6hacnvzqqacb0xdld8ll9z3m5ay"))))
    (build-system cargo-build-system)
    (arguments (list #:install-source? #f))
    (native-inputs
@@ -37,6 +37,8 @@
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages rust)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages virtualization))
@@ -246,6 +248,48 @@ transliterating them.  It supports Emoji and Chinese.")
       ;; checkout and does not need a cargo input.
       (inputs (cargo-inputs 'rust-deunicode-1.6.2.cfb8552))))))
 ;; Workspace dependency of r-pizzarr.
 (define-public rust-extendr-0.8.1.93d7244
  (let ((commit "93d7244e3145d94186bc2f35258ad0ef25a28908")
        (revision "1"))
    (hidden-package
     (package
       (name "rust-extendr")
       (version (git-version "0.8.1" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
                        (url "https://github.com/extendr/extendr")
                        (commit commit)))
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "03d16y7f1r0y1s8gwzw7wzn5yhcqr1wn0vga9dvdjxpbga372vx7"))))
       (build-system cargo-build-system)
       (arguments
        (list
         #:cargo-package-crates
         ;; Note that the order matters!
         '(list "extendr-ffi"
                "extendr-macros"
                "extendr-api"
                "extendr-engine")
         #:phases
         #~(modify-phases %standard-phases
             (add-after 'unpack 'set-R_HOME
               (lambda _
                 (delete-file-recursively ".cargo")
                 (setenv "R_HOME"
                         (string-append
                          #$(this-package-input "r-minimal")
                          "/lib/R")))))))
       (inputs (cons r-minimal (cargo-inputs 'extendr)))
       (home-page "https://extendr.rs/")
       (synopsis "R extension library for Rust")
       (description "This library allows you to extend R with Rust.  It can be
 used to write R packages that link with Rust libraries.")
       (license license:expat)))))
 ;; Workspace dependency of zed.
 ;;
 ;; Cargo side: Cargo unifies dependency versions across zed's
@@ -576,40 +620,6 @@ for Rust.")
 UTF-32 support.")
     (license (list license:expat license:unlicense)))))
 (define-public rust-pipewire-0.8.0.fd3d8f7
  (let ((commit "fd3d8f7861a29c2eeaa4c393402e013578bb36d9")
        (revision "0"))
    (hidden-package
     (package
       (name "rust-pipewire")
       (version (git-version "0.8.0" revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://gitlab.freedesktop.org/pipewire/pipewire-rs.git")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
           (base32 "1hzyhz7xg0mz8a5y9j6yil513p1m610q3j9pzf6q55vdh5mcn79v"))))
       (build-system cargo-build-system)
       (arguments
        (list #:skip-build? #t
              #:cargo-package-crates
              ''("libspa-sys" "libspa" "pipewire-sys" "pipewire")
              #:phases
              #~(modify-phases %standard-phases
                  ;; Avoid circular dependency.
                  (add-after 'unpack 'remove-dev-dependencies
                    (lambda _
                      (substitute* "libspa/Cargo.toml"
                        (("^pipewire.*") "")))))))
       (inputs (cargo-inputs 'rust-pipewire-0.8.0.fd3d8f7))
       (home-page "https://pipewire.org/")
       (synopsis "Rust bindings for PipeWire")
       (description "This package provides Rust bindings for PipeWire.")
       (license license:expat)))))
 ;; Workspace dependency of zed.
 ;;
 ;; Cargo side: Cargo unifies dependency versions across zed's
@@ -127,15 +127,11 @@
    (arguments
     (substitute-keyword-arguments (package-arguments base-rust)
       ((#:disallowed-references _ '())
-        (list (this-package-native-input "rust")
+        (list (this-package-native-input "rustc-bootstrap")))))
              ;; Refer to cargo as #$rustc:cargo.
              (gexp-input (this-package-native-input "rust") "cargo")))))
    (native-inputs
-     (list pkg-config
+     (modify-inputs native-inputs
-           python-minimal-wrapper
+       (replace "rustc-bootstrap" base-rust)
-           python-setuptools-bootstrap
+       (replace "cargo-bootstrap" (list base-rust "cargo"))))))
           base-rust
           `(,base-rust "cargo")))))
 ;;; Note: mrustc's only purpose is to be able to bootstrap Rust; it's designed
 ;;; to be used in source form.
@@ -604,33 +600,40 @@ safety and thread safety guarantees.")
             (setenv "PATH" (string-append "/tmp/bin:" (getenv "PATH")))))
         (replace 'configure
           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (call-with-output-file "config.toml"
+             (let* ((out (assoc-ref outputs "out"))
-               (lambda (port)
+                    (gcc (assoc-ref inputs "gcc"))
-                 (display (string-append "
+                    (python (assoc-ref inputs "python"))
                    (binutils (assoc-ref inputs "binutils"))
                    (rustc (assoc-ref inputs "rustc-bootstrap"))
                    (cargo (assoc-ref inputs "cargo-bootstrap"))
                    (llvm (assoc-ref inputs "llvm")))
               (call-with-output-file "config.toml"
                 (lambda (port)
                   (display (string-append "
 [llvm]
 [build]
-cargo = \"" (search-input-file inputs "bin/cargo") "\"
+cargo = \"" cargo "/bin/cargo" "\"
-rustc = \"" (search-input-file inputs "bin/rustc") "\"
+rustc = \"" rustc "/bin/rustc" "\"
 docs = false
-python = \"" (search-input-file inputs "bin/python") "\"
+python = \"" python "/bin/python" "\"
 vendor = true
 submodules = false
 [install]
-prefix = \"" (assoc-ref outputs "out") "\"
+prefix = \"" out "\"
 sysconfdir = \"etc\"
 [rust]
 debug=false
 jemalloc=false
-default-linker = \"" (search-input-file inputs "bin/gcc") "\"
+default-linker = \"" gcc "/bin/gcc" "\"
 channel = \"stable\"
 rpath = true
 [target." ,(platform-rust-target (lookup-platform-by-system (%current-system))) "]
-llvm-config = \"" (search-input-file inputs "bin/llvm-config") "\"
+llvm-config = \"" llvm "/bin/llvm-config" "\"
-cc = \"" (search-input-file inputs "bin/gcc") "\"
+cc = \"" gcc "/bin/gcc" "\"
-cxx = \"" (search-input-file inputs "bin/g++") "\"
+cxx = \"" gcc "/bin/g++" "\"
-ar = \"" (search-input-file inputs "bin/ar") "\"
+ar = \"" binutils "/bin/ar" "\"
 [dist]
-") port)))))
+") port))))))
         (replace 'build
           ;; The standard library source location moved in this release.
           (lambda* (#:key parallel-build? #:allow-other-keys)
@@ -691,15 +694,15 @@ ar = \"" (search-input-file inputs "bin/ar") "\"
                 `("LIBRARY_PATH" ":"
                   suffix (,(string-append libc "/lib"))))))))))
    (native-inputs
-     (list pkg-config
+     `(("pkg-config" ,pkg-config)
-           python-minimal-wrapper
+       ("python" ,python-minimal-wrapper)
-           python-setuptools-bootstrap
+       ("python-setuptools" ,python-setuptools-bootstrap)
-           rust-bootstrap-1.54
+       ("rustc-bootstrap" ,rust-bootstrap-1.54)
-           `(,rust-bootstrap-1.54 "cargo")))
+       ("cargo-bootstrap" ,rust-bootstrap-1.54 "cargo")))
    (inputs
-     (list bash-minimal
+     `(("bash" ,bash-minimal)
-           llvm-13
+       ("llvm" ,llvm-13)
-           openssl))
+       ("openssl" ,openssl)))
    ;; rustc invokes gcc, so we need to set its search paths accordingly.
    (native-search-paths
     %gcc-search-paths)
@@ -1152,11 +1155,9 @@ safety and thread safety guarantees.")
           (package-arguments base-rust)))
      (native-inputs
       (if (supported-package? rust-bootstrap-1.74)
-           (list pkg-config
+           (modify-inputs native-inputs
-                 python-minimal-wrapper
+             (replace "cargo-bootstrap" (list rust-bootstrap-1.74 "cargo"))
-                 python-setuptools-bootstrap
+             (replace "rustc-bootstrap" rust-bootstrap-1.74))
                 rust-bootstrap-1.74
                 (list rust-bootstrap-1.74 "cargo"))
           (package-native-inputs base-rust)))
      (inputs (modify-inputs inputs
                (replace "llvm" llvm-17))))))
@@ -1173,8 +1174,8 @@ safety and thread safety guarantees.")
             (delete 'add-cc-shim-to-path))))))))
 (define-public rust-1.77
-  (let ((base-rust (rust-bootstrapped-package rust-1.76 "1.77.2"
+  (let ((base-rust (rust-bootstrapped-package rust-1.76 "1.77.1"
-                    "1hrq2r9brhwl77qv18qk4pqrzfgnn9w6fwf7vgykhrjrizpmf566")))
+                    "18d4ncdzp0nfimmw029xdf7vv1hgh82v30mjnnixnllzar66w47f")))
    (package
      (inherit base-rust)
      (arguments
@@ -1621,8 +1622,8 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
 (define-public rust-1.91
  (let ((base-rust
         (rust-bootstrapped-package
-          rust-1.90 "1.91.1"
+          rust-1.90 "1.91.0"
-          "08sp8idsymyrqj70sxhfjz5zx7nfl4vl4i7hc495fqczsc2y5p1q")))
+          "12iysk87bmhlcdcbr939y8cdfcx0an4z9ixjlbq16c3ma60m4zrj")))
    (package
      (inherit base-rust)
      (source
@@ -1771,8 +1772,8 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
 (define-public rust-1.93
  (let ((base-rust
         (rust-bootstrapped-package
-          rust-1.92 "1.93.1"
+          rust-1.92 "1.93.0"
-          "07z02gq7x54sdbisbzcigk95h01qz0ckg52hz77g7jfrnd20l8sc")))
+          "01d7a1mvyvqmq9khyw5cbnwyngzgb4pxpdwhqgzl669j7kc2n4b9")))
    (package
      (inherit base-rust)
      (source
@@ -1915,67 +1916,6 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
                     (copy-recursively "stage2/lib"
                                       (string-append out "/lib")))))))))))))
 (define-public rust-1.95
  (let ((base-rust
         (rust-bootstrapped-package
          rust-1.94 "1.95.0"
          "05d53hj717ildhvm3rln7821r08nzbbfk72nqcvpb5j67sl856za")))
    (package
      (inherit base-rust)
      (source
       (origin
         (inherit (package-source base-rust))
         (snippet
          '(begin
             (for-each delete-file-recursively
                       '("src/llvm-project"
                         "vendor/curl-sys-0.4.79+curl-8.12.0/curl"
                         "vendor/curl-sys-0.4.83+curl-8.15.0/curl"
                         "vendor/curl-sys-0.4.84+curl-8.17.0/curl"
                         "vendor/jemalloc-sys-0.5.3+5.3.0-patched/jemalloc"
                         "vendor/jemalloc-sys-0.5.4+5.3.0-patched/jemalloc"
                         "vendor/libffi-sys-4.1.0/libffi"
                         "vendor/libmimalloc-sys-0.1.44/c_src/mimalloc"
                         "vendor/libz-sys-1.1.21/src/zlib"
                         "vendor/libz-sys-1.1.23/src/zlib"
                         "vendor/openssl-src-111.28.2+1.1.1w/openssl"
                         "vendor/openssl-src-300.5.0+3.5.0/openssl"
                         "vendor/openssl-src-300.5.4+3.5.4/openssl"
                         "vendor/tikv-jemalloc-sys-0.5.4+5.3.0-patched/jemalloc"
                         "vendor/tikv-jemalloc-sys-0.6.1+5.3.0-1-\
 ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
             ;; Remove vendored dynamically linked libraries.
             ;; find . -not -type d -executable -exec file {} \+ | grep ELF
             ;; Also remove the bundled (mostly Windows) libraries.
             (for-each delete-file
                       (find-files "vendor" "\\.(a|dll|exe|lib)$"))
             ;; Use the packaged nghttp2.
             (for-each
              (lambda (ver)
                (let ((vendored-dir
                       (format #f "vendor/libnghttp2-sys-~a/nghttp2" ver))
                      (build-rs
                       (format #f "vendor/libnghttp2-sys-~a/build.rs" ver)))
                  (delete-file-recursively vendored-dir)
                  (delete-file build-rs)
                  (call-with-output-file build-rs
                    (lambda (port)
                      (format port "fn main() {~@
                         println!(\"cargo:rustc-link-lib=nghttp2\");~@
                         }~%")))))
              '("0.1.11+1.64.0"))
             ;; Adjust vendored dependency to explicitly use rustix with libc
             ;; backend.
             (substitute* '("vendor/tempfile-3.14.0/Cargo.toml"
                            "vendor/tempfile-3.16.0/Cargo.toml"
                            "vendor/tempfile-3.19.1/Cargo.toml"
                            "vendor/tempfile-3.20.0/Cargo.toml"
                            "vendor/tempfile-3.21.0/Cargo.toml"
                            "vendor/tempfile-3.23.0/Cargo.toml"
                            "vendor/tempfile-3.24.0/Cargo.toml")
               (("features = \\[\"fs\"" all)
                (string-append all ", \"use-libc\""))))))))))
 (define (make-ignore-test-list strs)
  "Function to make creating a list to ignore tests a bit easier."
  (map (lambda (str)
@@ -1990,7 +1930,7 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
 ;;; Here we take the latest included Rust, make it public, and re-enable tests
 ;;; and extra components such as rustfmt.
 (define-public rust
-  (let ((base-rust rust-1.95))
+  (let ((base-rust rust-1.93))
    (package
      (inherit base-rust)
      (properties (append
@@ -2002,21 +1942,15 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
       (substitute-keyword-arguments
         (strip-keyword-arguments '(#:tests?)
                                  (package-arguments base-rust))
         ((#:disallowed-references _ '())
          (list (this-package-native-input "rustc-bootstrap")
                ;; Refer to cargo-bootstrap as #$rustc-bootstrap:cargo.
                (gexp-input (this-package-native-input "rustc-bootstrap")
                            "cargo")))
         ((#:modules modules)
          (cons '(srfi srfi-26) modules))
         ((#:phases phases)
          `(modify-phases ,phases
             (add-after 'unpack 'patch-shebangs-in-tests
               (lambda* (#:key inputs #:allow-other-keys)
                 (with-directory-excursion
                   "src/tools/rust-analyzer/crates/parser/test_data"
                   (substitute* '("lexer/ok/shebang_frontmatter.rast"
                                  "parser/inline/ok/frontmatter.rast")
                     (("/usr/bin/env cargo")
                      (search-input-file inputs "bin/cargo")))
                   (substitute* "lexer/ok/single_line_comments.rast"
                     (("/usr/bin/env bash")
                      (search-input-file inputs "bin/bash"))))))
             (add-after 'unpack 'disable-tests-requiring-git
               (lambda _
                 (substitute* "src/tools/cargo/tests/testsuite/publish_lockfile.rs"
@@ -2108,13 +2042,15 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
               (lambda* (#:key inputs #:allow-other-keys)
                 (mkdir-p "src/llvm-project/compiler-rt")
                 (copy-recursively
-                  (search-input-directory inputs "/compiler-rt")
+                  (string-append (assoc-ref inputs "clang-source")
                                 "/compiler-rt")
                  "src/llvm-project/compiler-rt")))
             (add-after 'unpack 'unpack-libunwind
               (lambda* (#:key inputs #:allow-other-keys)
                 (mkdir-p "src/llvm-project/libunwind")
                 (copy-recursively
-                  (search-input-directory inputs "/libunwind")
+                  (string-append (assoc-ref inputs "clang-source")
                                 "/libunwind")
                  "src/llvm-project/libunwind")))
             (replace 'patch-cargo-checksums
               (lambda _
@@ -2156,7 +2092,6 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
                           "library/std" ;rustc
                           "src/tools/cargo"
                           "src/tools/clippy"
                           "src/tools/llvm-bitcode-linker"
                           "src/tools/rust-analyzer"
                           "src/tools/rustfmt"))))
             (replace 'check
@@ -2176,10 +2111,7 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
             (replace 'install
               ;; Phase overridden to also install more tools.
               (lambda* (#:key outputs #:allow-other-keys)
-                 ;; Install rustc, std, and llvm-bitcode-linker.
+                 (invoke "./x.py" "install")
                 ;; rust-src is handled separately in 'install-rust-src'.
                 (invoke "./x.py" "install" "compiler/rustc" "library/std"
                         "llvm-bitcode-linker")
                 (substitute* "config.toml"
                   ;; Adjust the prefix to the 'cargo' output.
                   (("prefix = \"[^\"]*\"")
@@ -2227,7 +2159,7 @@ ge13ca993e8ccb9ba9847cc330696e02839f328f7/jemalloc"))
                 (with-directory-excursion
                   (string-append (assoc-ref outputs "rust-src")
                                  "/lib/rustlib/src/rust/src/tools/")
-                   (substitute* (find-files "." "\\.(rs|rast)$")
+                   (substitute* (find-files "." "\\.rs$")
                     (("#!.*/bin/cargo")
                      (string-append "#!" (assoc-ref outputs "cargo")
                                     "/bin/cargo"))))))
@@ -2246,15 +2178,14 @@ exec -a \"$0\" \"~a\" \"$@\""
                                              "/lib/rustlib/src/rust/library")
                               (string-append bin "/.rust-analyzer-real"))))
                   (chmod (string-append bin "/rust-analyzer") #o755))))))))
-      (native-inputs
+      (native-inputs (cons*
-       (modify-inputs (package-native-inputs base-rust)
+                      ;; Keep in sync with the llvm used to build rust.
-        (prepend
+                      `("clang-source" ,(package-source clang-runtime-21))
-          ;; Keep in sync with the llvm used to build rust.
+                      ;; Add test inputs.
-          (package-source clang-runtime-21)
+                      `("gdb" ,gdb/pinned)
-          ;; Add test inputs.
+                      `("git-minimal" ,git-minimal/pinned)
-          gdb/pinned
+                      `("procps" ,procps)
-          git-minimal/pinned
+                      (package-native-inputs base-rust)))
          procps)))
      (native-search-paths
       (cons*
         ;; For HTTPS access, Cargo reads from a single-file certificate
@@ -244,26 +244,21 @@ This Guix package is built to use the nettle cryptographic library.")
 (define-public sequoia-wot-tools
  (package
    (name "sequoia-wot-tools")
-    (version "0.15.0")
+    (version "0.15.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
-              (url "https://gitlab.com/sequoia-pgp/sequoia-wot")
+              (url "https://gitlab.com/sequoia-pgp/sequoia-wot.git/")
-              (commit (string-append "v" version))))
+              (commit (string-append "sequoia-wot/v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "03wa4l582hx0qq28pkhrf0pagckyx6df01pb4chyngadk49q1xn7"))))
+        (base32 "18v713n36sq5pvd1pbs34v7dly1bi614kwra09qxpsxk0ffp225z"))))
    (build-system cargo-build-system)
    (arguments
     (list
       #:features '(list "sequoia-openpgp/crypto-nettle")
       #:cargo-package-crates ''("tools")
       #:cargo-test-flags
       '(list "--"
              "--skip=gpg_trust_roots"
              "--skip=backward_propagation::tests::cliques"
              "--skip=tests::cliques")
       #:install-source? #f
       #:cargo-install-paths ''("tools")
       #:phases
@@ -276,11 +271,12 @@ This Guix package is built to use the nettle cryptographic library.")
                 (for-each (lambda (file)
                             (install-file file man1))
                           (find-files "target/release" "\\.1$"))
-                 (mkdir-p (string-append out "/etc/bash_completion.d"))
+                 (mkdir-p (string-append out "/share/bash-completion/completions"))
                 (mkdir-p (string-append share "/fish/vendor_completions.d"))
                 (mkdir-p (string-append share "/elvish/lib"))
                 (copy-file (car (find-files "target/release" "sq-wot.bash"))
-                            (string-append out "/etc/bash_completion.d/sq-wot"))
+                            (string-append
                              out "/share/bash-completion/completions/sq-wot"))
                 (copy-file (car (find-files "target/release" "sq-wot.fish"))
                            (string-append
                              share "/fish/vendor_completions.d/sq-wot.fish"))
@@ -292,7 +288,7 @@ This Guix package is built to use the nettle cryptographic library.")
    (inputs
     (cons* nettle openssl sqlite (cargo-inputs 'sequoia-wot-tools)))
    (native-inputs
-     (list clang pkg-config))
+     (list clang gnupg pkg-config))
    (home-page "https://sequoia-pgp.org/")
    (synopsis "Implementation of OpenPGP's web of trust")
    (description
@@ -924,7 +924,7 @@ and aims to be maximally portable across operating systems and C compilers.")
 (define-public loksh
  (package
    (name "loksh")
-    (version "7.8")
+    (version "7.9")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -936,7 +936,7 @@ and aims to be maximally portable across operating systems and C compilers.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1x5kg01r0k7g825ia71f8an6585azba8x5khwdvq4dmnib11vakm"))))
+                "0nwssdxcqs3fypfg884cwcmp21kmwsqrr5rvm1cck1qx5240hyjb"))))
    (build-system meson-build-system)
    (inputs (list ncurses))
    (native-inputs (list pkg-config))
@@ -25,6 +25,7 @@
  #:use-module (guix build-system cmake)
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages compression)
@@ -34,7 +35,6 @@
  #:use-module (gnu packages libffi)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
@@ -88,7 +88,9 @@ you tailor the wrapping process to suit your application.")
                                 name "-" version ".tar.gz"))
              (sha256
               (base32
-                "1kqz533599d00rrz0g2ryf8w2ynb25ayylpx10nmkxsndiq2l5j0"))))
+                "1kqz533599d00rrz0g2ryf8w2ynb25ayylpx10nmkxsndiq2l5j0"))
              (patches
               (search-patches "swig-support-r-4.6.0.patch"))))
    (native-inputs (list boost
                         pcre2 ; for pcre2-config
                         ;; The following are for tests and examples:
--- a/Show More
+++ b/Show More