gnu: r-mscoreutils: Patch for compatibility with R 4.6.0.

* gnu/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch: New file.
* gnu/local.mk (dist_patch_DATA): Record it.
* gnu/packages/bioconductor.scm (r-mscoreutils)[source]: Register patch.

Change-Id: If288fed9c85d7a46d1938e7699e2a9bc57447a03

.guix-authorizations

@@ -16,6 +16,8 @@
   ( ;; primary: "D0C2 EAC1 3310 822D 98DE  B57C E9C5 A2D9 0898 A02F"
    "01FD 85F4 1A7B 7F82 0583  06A5 935E BE07 36DC 857E"
    (name "avp"))
+  ("5D54 CF25 57B2 38E8 8DC1  80A2 2D22 3241 0AB7 4043"
+   (name "baleine"))
   ( ;; primary: "34FF 38BC D151 25A6 E340  A0B5 3453 2F9F AFCA 8B8E"
    "A3A4 B419 0074 087C A7DE  5698 BC45 CA67 E2F8 D007"
    (name "bavier"))

CODEOWNERS

@@ -179,6 +179,7 @@ guix/scripts/import/elpa\.scm                      @guix/emacs
 tests/import/elpa\.scm                             @guix/emacs
 
 gnu/packages/bootloaders\.scm                      @guix/embedded
+gnu/packages/coreboot\.scm                         @guix/embedded
 gnu/packages/firmware\.scm                         @guix/embedded
 
 gnu/packages/emulators\.scm                        @guix/games
@@ -318,6 +319,7 @@ gnu/packages/tor-browsers\.scm                     @guix/mozilla
 
 gnu/packages/ocaml\.scm                            @guix/ocaml
 gnu/packages/coq\.scm                              @guix/ocaml
+gnu/packages/rocq\.scm                             @guix/ocaml
 guix/build/ocaml-build-system\.scm                 @guix/ocaml
 guix/build/dune-build-system\.scm                  @guix/ocaml
 guix/build-system/ocaml\.scm                       @guix/ocaml

doc/contributing.texi

@@ -1667,6 +1667,9 @@ can be turned into a version string via @code{git-version}, for example
 @code{rust-pipewire-0.8.0.fd3d8f7} and @code{rust-pubgrub-0.3.0.b70cf70}.
 @end table
 
+When contributing Rust packages, we should have all modifications to these
+two modules, in the same commit as the package we are contributing.
+
 To avoid merge conflicts with changes from multiple branches, these two modules
 are maintained by the Rust team (@pxref{Teams}).
 
@@ -1696,6 +1699,68 @@ tree.
 @xref{Packaging Rust Crates,,, guix-cookbook, GNU Guix Cookbook}, for
 packaging workflow.
 
+@subsubsection Commit messages
+
+The commit message must have a general brief mention to entry changes
+in @code{(gnu packages rust-crates)}. For changes in @code{(gnu packages
+rust-sources)}, the commit message must explicitly mention all changes to the
+packages.
+
+Here are some examples for different situations:
+
+@itemize
+
+@item
+Adding a new Rust package:
+
+@example
+gnu: Add catppuccin-whiskers.
+
+* gnu/packages/rust-apps.scm (catppuccin-whiskers): New variable.
+* gnu/packages/rust-crates.scm (lookup-cargo-inputs)
+[catppuccin-whiskers]: New entry.
+@end example
+
+@item
+Updating a simple package:
+
+@example
+gnu: watchexec: Update to 2.3.2.
+
+* gnu/packages/rust-apps.scm (watchexec): Update to 2.3.2.
+* gnu/packages/rust-crates.scm (lookup-cargo-inputs)[watchexec]:
+Update entry.
+@end example
+
+@item
+Updating a package with sources:
+
+@example
+gnu: typst: Update to 0.14.0.
+
+* gnu/packages/rust-apps.scm (typst): Update to 0.14.0.
+[arguments]<#:rust>: Use rust-1.88.
+* gnu/packages/rust-crates.scm (lookup-cargo-inputs)[typst]: Update
+entry.
+[rust-syntect-5]: Rename to rust-syntect-5.2.
+[rust-syntect-5.3]: New entry.
+* gnu/packages/rust-sources.scm (rust-hypher-0.1): Update to 0.1.6.
+(rust-syntect-5): Rename to rust-syntect-5.2.
+[inputs]: Rename cargo-inputs rust-syntect-5 to rust-syntect-5.2.
+(rust-syntect-5.3): New variable.
+@end example
+
+@end itemize
+
+@subsubsection Resolving merge conflicts in Pull Requests
+
+For Rust crates, the recommended way to solve merge conflicts is to drop all
+changes to @code{gnu/packages/rust-crates.scm}, rebase onto the desired branch
+and run the lockfile importer again, manually adding back all relevant snippets
+(if any).
+
+@xref{Common Workflow for Resolving Merge Conflicts on Existing Pull Requests,,, guix-cookbook, GNU Guix Cookbook} for
+a suggested workflow on resolving merge conflicts.
 
 @node Elm Packages
 @subsection Elm Packages
@@ -2650,6 +2715,7 @@ applications settings page}, granting read/write access to the
 
 @cindex decision making
 @cindex consensus seeking
+Every contribution to the project involves a form of decision making.
 It is expected from all contributors, and even more so from committers,
 to help build consensus and make decisions based on consensus.  By using
 consensus, we are committed to finding solutions that everyone can live
@@ -2664,6 +2730,26 @@ resolve the deadlock.  To learn what consensus decision making means and
 understand its finer details, you are encouraged to read
 @url{https://www.seedsforchange.org.uk/consensus}.
 
+Day-to-day decision making, for instance discussions about pull requests
+(@pxref{Reviewing the Work of Others}), happens informally among
+interested parties such as contributors and members of the relevant
+teams (@pxref{Teams}).
+
+@cindex GCD, Guix Consensus Documents
+@cindex Guix Consensus Documents (GCD)
+Decisions that are expected to have an impact on most contributors
+and/or on the broader user community---e.g., changes to project-wide
+policies, to core functionality, and so on---are made following the
+@acronym{GCD, Guix Consensus Document} process.  The process provides a
+framework to formalize proposals and draw attention to them, to leave
+time for interested parties to discuss them, and to collectively accept
+or withdraw them based on input from participating team members.  It is
+defined in
+@uref{https://consensus.guix.gnu.org/gcd/001-gcd-process.html,
+GCD@tie{}001}.  Past GCDs can be seen at
+@uref{https://consensus.guix.gnu.org}, and discussions take place at
+@uref{https://codeberg.org/guix/guix-consensus-documents}.
+
 @node Commit Access
 @section Commit Access
 

doc/guix-cookbook.texi

@@ -146,6 +146,8 @@ Packaging Rust Crates
 * Common Workflow for Rust Packaging::
 * Cargo Workspaces and Development Snapshots::
 * Using Rust Libraries in Other Build Systems::
+* Common Workflow for Updating Existing Rust Packages::
+* Common Workflow for Resolving Merge Conflicts on Existing Pull Requests::
 
 System Configuration
 
@@ -1647,6 +1649,8 @@ $ guix shell rust rust:cargo cargo-audit cargo-license
 * Common Workflow for Rust Packaging::
 * Cargo Workspaces and Development Snapshots::
 * Using Rust Libraries in Other Build Systems::
+* Common Workflow for Updating Existing Rust Packages::
+* Common Workflow for Resolving Merge Conflicts on Existing Pull Requests::
 @end menu
 
 @node Common Workflow for Rust Packaging
@@ -1705,6 +1709,15 @@ $ cargo audit
 $ cargo license
 @end example
 
+@quotation Note
+Before running @command{cargo generate-lockfile}, make sure you have checked
+out the correct tag for the version you are packaging. This ensures that
+@code{Cargo.toml} matches the file used in the packages's @code{source} field.
+To make sure, you can obtain the exact source with @command{./pre-inst-env guix
+build --source <package>} and only then run @command{cargo generate-lockfile} on
+that source tree.
+@end quotation
+
 @command{cargo generate-lockfile} updates dependencies to compatible versions.
 Applying it to all Rust applications helps reduce a great number of Rust
 libraries we need to check later.  Although sometimes libraries may fail to
@@ -1987,6 +2000,316 @@ method, one of the most popular choices for Traditional Chinese users.")
     (license license:lgpl2.1+)))
 @end lisp
 
+@node Common Workflow for Updating Existing Rust Packages
+@subsubsection Common Workflow for Updating Existing Rust Packages
+
+For this example, we'll update @code{niri}. The package definition looks like
+this initially:
+
+@lisp
+(define-public niri
+  (package
+   (name "niri")
+   (version "25.08")
+   (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/YaLTeR/niri")
+                   (commit (string-append "v" version))))
+             (file-name (git-file-name name version))
+             (sha256
+              (base32
+               "09nsxd211mly8r1ys2lq6ia4jxgb980h1axrbgw748r0knfbbj7n"))))
+   (build-system cargo-build-system)
+...
+@end lisp
+
+We start by running the usual @command{guix refresh -u niri}.
+
+The @command{-u} flag will update in place the version and hash for the
+@code{niri} package.
+
+The package definition will then look like this:
+
+@lisp
+(define-public niri
+  (package
+   (name "niri")
+   (version "25.11")
+   (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/YaLTeR/niri")
+                   (commit (string-append "v" version))))
+             (file-name (git-file-name name version))
+             (sha256
+              (base32
+               "0752qm245wc2gak0jhp0fnr0rdj3z54m2h97k3cxbjym9pcn658n"))))
+   (build-system cargo-build-system)
+...
+@end lisp
+
+This means the source field was updated successfully, thus we can now proceed to
+get the updated source with @command{guix build --source niri} as follows:
+
+@example shell
+$ cp -r $(./pre-inst-env guix build --source niri) /tmp
+$ cd /tmp/<hash>-niri-25.11-checkout/
+@end example
+
+@quotation Note
+In this specific example, the source is a git checkout, thus a directory. If the
+package source is a compressed archive, you would at this point extract it to a
+directory to proceed.
+@end quotation
+
+Now, given that we have access to the @code{Cargo.toml} file, we can now run
+the following inside the checkout:
+
+@example shell
+$ guix shell rust rust:cargo -- cargo generate-lockfile
+$ guix shell rust rust:cargo -- cargo audit
+$ guix shell rust rust:cargo -- cargo license
+@end example
+
+@quotation Note
+Sometimes the package will require a more up-to-date version of rust, that is
+not yet the default rust on guix. For these cases you can use:
+@example shell
+$ guix shell -e "(@ (gnu packages rust) rust-1.90)" \
+     -e '`(,(@ (gnu packages rust) rust-1.90) "cargo")'
+@end example
+@end quotation
+
+The first command will ensure that all cargo dependencies are up to date
+and semver compatible, while also providing some other benefits, as further
+explained in @ref{Common Workflow for Rust Packaging}.
+
+The following command will warn if there are any known vulnerabilities in the
+crates being imported. The last one will output the license information of all
+the dependent crates.
+
+If everything looks good, we can now replace the contents of the @code{niri}
+indentifier, located inside the @code{lookup-cargo-inputs} variable on the
+bottom of the @file{gnu/packages/rust-crates.scm} module, with the newer updated
+crates by running the importer on the lockfile as follows:
+
+@example shell
+$ guix import -i /path/to/gnu/packages/rust-crates.scm \
+     crate -f Cargo.lock niri
+@end example
+
+@quotation Note
+For the purpose of contributing a package to Guix (@pxref{Contributing,,,
+guix, GNU Guix Reference Manual}), there is no need to cleanup the leftover
+crates as a result of the package update.  This is tasked to the rust-team
+(@pxref{Teams,,, guix, GNU Guix Reference Manual}) to periodically run a
+convenient script in @code{etc/teams/rust} to cleanup unused crates from
+@file{gnu/packages/rust-crates.scm}.
+@end quotation
+
+We then need to check whether the importer has placed some TODOs for us,
+inside @file{gnu/packages/rust-crates.scm} (you can use @command{git diff --
+gnu/packages/rust-crates.scm} for this purpose).
+
+There are a few types of TODO messages that you might encounter during this
+step, each type requiring you to perform a different action.
+
+The first one we encounter in our example is:
+
+@lisp
+(define rust-libdisplay-info-sys-0.3.0
+  ;; TODO REVIEW: Check bundled sources.
+  (crate-source "libdisplay-info-sys" "0.3.0"
+                "07xmkc2aqcdn6d58321y87rd3gzdr4nx3ncm1mmrr7w1p1ahsn96"))
+@end lisp
+
+This specific TODO message tells us that there is a high probability of
+encountering bundled sources within a crate definition generated by the
+importer.
+
+We then check if there are any bundled sources within the
+@code{rust-libdisplay-info-sys-0.3.0} crate. Since there are none (in our
+example), we can simply remove the TODO line, and continue to the next TODO.
+
+If there were any bundled sources inside the crate, we would have to patch
+it with a snippet, in order to unbundle it. You can see some examples on
+how to unbundle inside @file{gnu/packages/rust-crates.scm} (search for the
+@code{#:snippet} keyword).
+
+@quotation Note
+If the unbundle is considered too difficult to be executed (e.g. the effort
+needed to unbundle is unreasonable), the @code{TODO REVIEW} line should be
+converted to a regular TODO comment explicitly stating the unbundle was not done
+(e.g. @code{TODO: Unbundle rust-libdisplay-info-sys.}).
+@end quotation
+
+Continuing, another TODO message we encounter in this example is the following:
+
+@lisp
+(define rust-smithay-0.7.0.d743e1a
+  ;; TODO REVIEW: Define standalone package if this is a workspace.
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/Smithay/smithay.git")
+                        (commit "d743e1a317fa0f01d1c4cadd96d277a1ec7b59d9")))
+    (file-name (git-file-name "rust-smithay" "0.7.0.d743e1a"))
+    (sha256 (base32 "11327mhxxf844bs0v5bw1g9bzjssnzhidsissywy6kwng16x727v"))))
+@end lisp
+
+This specific TODO message tells us that there is a high probability of the
+@code{rust-smithay-0.7.0.d743e1a} crate being a workspace.
+
+After verifying that it is indeed a workspace, we now need to make it an
+actual package in @file{gnu/packages/rust-sources.scm}, referencing it in the
+crate-source definition (see @ref{Common Workflow for Rust Packaging} for more
+details).
+
+@quotation Note
+You can verify if a crate is a workspace by cloning the crate repository (in
+this case @code{https://github.com/Smithay/smithay.git}), checking out the
+specific revision (in this case @command{git checkout d743e1a}), and looking
+for @code{[workspace]} in its main @file{Cargo.toml} file. If it does not have a
+TOML @code{[workspace]} section, then it is not a workspace.
+@end quotation
+
+After defining the separate source package for the workspace in
+@file{gnu/packages/rust-sources.scm} (see @ref{Common Workflow for Rust
+Packaging} for more details on how to do this), the crate definition for
+@code{rust-smithay-0.7.0.d743e1a} would then become the following (notice we
+also remove the TODO line):
+
+@lisp
+(define rust-smithay-0.7.0.d743e1a package:rust-smithay-0.7.0.d743e1a)
+@end lisp
+
+If @code{rust-smithay-0.7.0.d743e1a} was not a workspace, we would simply remove
+the TODO line and move on.
+
+We then try to build the package with @command{guix build niri}, and make sure
+whether it builds successfully, which it does.
+
+As a good practice, we can further check the output of the
+@code{check-for-pregenerated-files} phase to ensure there are no extraneous
+pregenerated files inside the crates. If there are any, it is important to
+snippet them out, like these:
+
+@lisp
+(define rust-winapi-x86-64-pc-windows-gnu-0.4.0
+  (crate-source "winapi-x86_64-pc-windows-gnu" "0.4.0"
+                "0gqq64czqb64kskjryj8isp62m2sgvx25yyj3kpc2myh85w24bki"
+                #:snippet '(delete-file-recursively "lib")))
+
+(define rust-flate2-1.1.4
+  (crate-source "flate2" "1.1.4"
+                "1a8a3pk2r2dxays4ikc47ygydhpd1dcxlgqdi3r9kiiq9rb4wnnw"
+                #:snippet '(for-each delete-file-recursively '("examples" "tests"))))
+
+(define rust-flo-curves-0.3.1
+  (crate-source "flo_curves" "0.3.1"
+                "16x293dp8825jh465kgms4yyvl4960j26gh37h3skflq9zxpy8hw"
+                #:snippet '(for-each delete-file '("logo-small.png" "logo.png"))))
+
+(define rust-interception-sys-0.1.3
+  (crate-source "interception-sys" "0.1.3"
+                "1lgwbml7gzq5a5rriy708w68gx6yiw9cdg7xy2c5vsrrck7pbs5b"
+                #:snippet '(for-each delete-file (find-files "." "\\.(dll|lib)$"))))
+@end lisp
+
+@node Common Workflow for Resolving Merge Conflicts on Existing Pull Requests
+@subsubsection Common Workflow for Resolving Merge Conflicts on Existing Pull Requests
+
+Whenever a Rust package change is merged into our target branch from a different
+Pull Request, we often encounter many merge conflicts in @code{(gnu packages
+rust-crates)} when rebasing the Pull Request on top of the target branch. Since
+we should avoid modifying the rust-crates file manually (e.g. using the git
+interface to solve merge conflicts), it is recommended (and often much faster)
+to drop all changes to @code{(gnu packages rust-crates)} and run the lockfile
+importer once again, manually adding back all the manual changes.
+
+This workflow describes one of many ways to do the described procedure.
+
+In this example we'll update the @code{codeberg-cli} package, which has produced
+some merge conflicts in @file{gnu/packages/rust-crates.scm} when we tried a git
+pull rebase.
+
+Before starting, make sure we're not in a rebase environment, by aborting the
+rebase we tried previously (the one which created the merge conflicts by git
+pulling):
+
+@example
+$ git rebase --abort
+@end example
+
+@cindex git rebase --interactive
+@cindex interactive rebase
+To begin, we interactively rebase our PR branch by marking as
+@code{edit} the commit we want to edit, which is the one containing the
+@file{gnu/packages/rust-crates.scm} changes:
+
+@example
+# Change 1 to the number of relevant commits
+$ git rebase -i HEAD~1
+@end example
+
+In our example, we would mark the @code{codeberg-cli} commit like so:
+
+@example
+edit 6ef4f1ad043 # gnu: codeberg-cli: Update to 0.5.4.
+@end example
+
+After that, we'll be in rebase mode, where we can restore the changes made to
+@file{gnu/packages/rust-crates.scm}:
+
+@quotation Note
+Notice that we will lose all manual changes we have previously made to
+@file{gnu/packages/rust-crates.scm} (e.g. snippets, deleting TODO comments,
+if there were any). We'll need to manually add them back after we run the guix
+lockfile importer once again, so make sure you have them saved somewhere, for
+example in your PR link under the @code{Files changed} tab.
+@end quotation
+
+@example
+$ git restore --source=HEAD~ gnu/packages/rust-crates.scm
+@end example
+
+Having restored the file, we can stage the changes, commit, finish the rebase
+and pull rebase from the target branch:
+
+@example
+$ git add gnu/packages/rust-crates.scm
+$ git commit --amend --no-edit
+$ git rebase --continue
+$ git pull <remote> <target branch>
+@end example
+
+We then proceed to run the guix lockfile importer:
+
+@quotation Note
+Remember to checkout the correct tag you're packaging in the package repository
+checkout. Don't forget to run @code{cargo generate-lockfile} before running
+the lockfile importer, see @ref{Common Workflow for Rust Packaging} for more
+detailed steps on what to do before running the guix lockfile importer.
+@end quotation
+
+@example
+$ guix import --insert=gnu/packages/rust-crates.scm \
+      crate --lockfile=/path/to/Cargo.lock codeberg-cli
+@end example
+
+Now is the time we manually add back the snippets and remove the relevant TODOs
+we have already checked (if there are any).
+
+After running the lockfile importer and checking if there are any changes to
+manually add back, we can finally:
+
+@example
+$ git add gnu/packages/rust-crates.scm
+# Our target commit is the last one:
+$ git commit --amend --no-edit
+@end example
+
+We now have a non-conflicting tree, from which we can now update our PR with.
 
 @c *********************************************************************
 @node System Configuration

doc/guix.texi

@@ -2658,12 +2658,13 @@ bootloaders.
 
 Once you are done partitioning the target hard disk drive, you have to
 create a file system on the relevant partition(s)@footnote{Currently
-Guix System supports only ext4, btrfs, bcachefs, JFS, F2FS, and XFS
-file systems.  In particular, code that reads file system UUIDs and
-labels works only for these file system types.  For bcachefs, also add
-the @code{bcachefs-linux-module} to your @code{operating-system}'s
-@code{initrd-modules}.}.  For the ESP, if you have one and assuming it is
-@file{/dev/sda1}, run:
+Guix System can mount only ext4, btrfs, JFS, F2FS, and XFS file systems
+at boot time.  In particular, code that reads file system UUIDs and
+labels works only for these file system types.  The code for bcachefs is
+in place, but support for loading out-of-tree kernel modules in the
+initrd is not.}.
+
+For the ESP, if you have one and assuming it is @file{/dev/sda1}, run:
 
 @example
 mkfs.fat -F32 /dev/sda1
@@ -8843,12 +8844,12 @@ dependencies than the original package.  For example, the default
 optional dependency, you can define a variant that removes that
 dependency like so:
 
+@findex package/inherit
 @lisp
 (use-modules (gnu packages gdb))   ;for 'gdb'
 
 (define gdb-sans-guile
-  (package
-    (inherit gdb)
+  (package/inherit gdb
     (inputs (modify-inputs inputs
               (delete "guile")))))
 @end lisp
@@ -8856,6 +8857,23 @@ dependency like so:
 In the body of the @code{inputs} field above, @code{inputs} is bound to
 the inherited value.  Thus, the @code{modify-inputs} form above removes
 the @code{"guile"} package from the @code{inputs} field of @code{gdb}.
+
+@quotation Note
+The example above uses @code{(package/inherit gdb @dots{})} instead of
+the usual @code{(package (inherit gdb) @dots{})}.  While the latter
+would work, @code{package/inherit} does extra work: if @code{gdb} has a
+@code{replacement} field (@pxref{Security Updates}),
+@code{package/inherit} propagates the @code{inputs} changes of this
+variant to the replacement.
+
+In other words, @code{package/inherit} ensures the variant gets a
+consistent @code{replacement} when the original package has one.  Thus,
+one should generally use @code{package/inherit} when creating a variant
+for the same version, but not when targeting a different version, as in
+the @code{hello} example we saw earlier, where the replacement may be
+incorrect.
+@end quotation
+
 The @code{modify-inputs} macro is a helper that can prove useful anytime
 you want to remove, add, or replace package inputs.
 
@@ -15534,7 +15552,7 @@ gnu/packages/qt.scm:452:13: qtbase would be upgraded from 5.15.8 to 5.15.10
 @end example
 
 @cindex partial version specification, guix refresh
-A per-package equivalent to --target-version is made available by
+A per-package equivalent to @option{--target-version} is made available by
 prefixing the version specification with the @samp{~} (tilde) character.
 For example:
 
@@ -16095,7 +16113,7 @@ it unchanged.
 @item git-source
 If the @code{home-page} is a Git repository (as per
 @code{git-repository-url?}), and the actual Git repository is tagged
-with @code{version} or @code{(string-append ``v'' version)}, change the
+with a version string, possibly prefixed by ``v'', change the
 package origin to the @code{git-fetch} method
 (@pxref{origin Reference}).  Consider this example:
 
@@ -16124,14 +16142,16 @@ its @code{source} field like to:
     (inherit guile-json-3)
     (name "guile-json")
     (version "4.7.3")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference (url
-                                   "https://github.com/aconchillo/guile-json")
-                                  (commit version)))
-              (file-name (git-file-name name version))
-              (sha256 (base32
-                       "0akhm8xjv8fl55fyq0w6c9c6hi5j7mifjx01w07np7qg1cjl9f06"))))))
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/aconchillo/guile-json")
+               (commit version)))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32
+            "0akhm8xjv8fl55fyq0w6c9c6hi5j7mifjx01w07np7qg1cjl9f06"))))))
 @end lisp
 
 @end table
@@ -27248,6 +27268,28 @@ Package object for GVfs.
 @end table
 @end deftp
 
+@defvar kmonad-service-type
+This is the type of the service that runs
+@uref{https://github.com/kmonad/kmonad, KMonad}.  Its value is a
+@code{kmonad-configuration} object.  This service allows spawning
+@command{kmonad} configurations to manage keyboards.
+
+@deftp {Data Type} kmonad-configuration
+Configuration record for the KMonad service.
+
+@table @asis
+@item @code{kmonad} (default: @code{kmonad})
+The KMonad package to use.
+
+@item @code{keymaps}
+A list of files with KMonad configurations. One shepherd service will be
+created to control each configuration. Each configuration should target
+a distinct input device as KMonad operates on a per-input basis.
+
+@end table
+@end deftp
+@end defvar
+
 @defvar colord-service-type
 This is the type of the service that runs @command{colord}, a system
 service with a D-Bus

etc/teams.scm

@@ -16,6 +16,7 @@ exec $pre_inst_env_maybe guix repl -- "$0" "$@"
 ;;; Copyright © 2025 Cayetano Santos <csantosb@inventati.org>
 ;;; Copyright © 2025-2026 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2025 jgart <jgart@dismail.de>
+;;; Copyright © 2026 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -690,6 +691,7 @@ ecosystem."
   (team 'embedded
         #:name "Embedded"
         #:scope (list "gnu/packages/bootloaders.scm"
+                      "gnu/packages/coreboot.scm"
                       "gnu/packages/firmware.scm")))
 
 (define-team games
@@ -943,6 +945,7 @@ importer, and the ocaml-build-system."
         #:scope
         (list "gnu/packages/ocaml.scm"
               "gnu/packages/coq.scm"
+              "gnu/packages/rocq.scm"
               "guix/build/ocaml-build-system.scm"
               "guix/build/dune-build-system.scm"
               "guix/build-system/ocaml.scm"
@@ -1246,6 +1249,11 @@ the \"texlive\" importer."
                        "jonsger")
   mozilla)
 
+(define-member (person "Denis Carikli"
+                       "GNUtoo@cyberdimension.org"
+                       "GNUtoo")
+  embedded)
+
 (define-member (person "Ludovic Courtès"
                        "ludo@gnu.org"
                        "civodul")

etc/teams/rust/audit-rust-crates

@@ -1,6 +1,6 @@
 #!/usr/bin/env -S gawk -f
 # GNU Guix --- Functional package management for GNU
-# Copyright © 2025 Efraim Flashner <efraim@flashner.co.il>
+# Copyright © 2025, 2026 Efraim Flashner <efraim@flashner.co.il>
 #
 # This file is part of GNU Guix.
 #
@@ -21,20 +21,22 @@
 # ./etc/teams/rust/audit-rust-crates ./path/to/file.scm
 # Prints the output of cargo-audit to the shell.
 
-# Make sure we have cargo-audit in our PATH
 BEGIN {
-    if (system("which cargo-audit 1> /dev/null"))
-        exit 1;
+    "which cargo-audit" | getline cargoAudit
+    close("which cargo-audit")
+    cargoAudit = cargoAudit " audit --file -"
+
     # Parse a record at a time.
     RS = "\n\n"
-    cargoAudit = "cargo-audit audit --file -"
 }
 
-# Check the crate-source origin-only inputs
+# Check the crate-source origin-only inputs, like in rust-crates.scm
 /crate-source/ {
     for(i=3; i <= NF-2; i++) {
         if($i == "(crate-source") {
-            cargoLock = cargoLock "[[package]]\nname = " $(i+1) "\nversion = " $(i+2) "\n"
+            crateName = $(i+1)
+            crateVersion = $(i+2)
+            cargoLock = cargoLock "[[package]]\nname = " crateName "\nversion = " crateVersion "\n"
             next
         }
     }
@@ -44,27 +46,64 @@ BEGIN {
 /crate-uri/ {
     for(i=3; i <= NF; i++) {
         if($i == "(version")
-           crateVersion = $(i+1)
+            crateVersion = $(i+1)
         if($i == "(crate-uri")
-           crateName = $(i+1)
+            crateName = $(i+1)
     }
     gsub(/)/, "", crateVersion)
     cargoLock = cargoLock "[[package]]\nname = " crateName "\nversion = " crateVersion "\n"
+    next
 }
 
-# The xxxx-cargo-input variables have a set style
-# TODO: Replace the last dash between the name and the version with a space!
-# This doesn't take into account swapping between "-" and "_" so we skip it.
-#( $2 ~ /-cargo-inputs/ ) {
-#    sub(/-cargo-inputs/, "", $2)
-#    gsub(/)/, "", $0)
-#    gsub(/rust-/, "", $0)
-#    #gensub(/([[:alpha:]])-([[:digit:]]+)/, "\\1 \\2", "g", $i)
-#    print "[[package]]\nname = \"" $2 "\"\nversion = \"1.0.0\"\ndependencies = ["
-#    for (i = 4; i <= NF; i++) {
-#        print "\"" $i "\","
-#    }
-#    print "]"
-#}
+# Parse the crates created from packages using 'cargo package'
+/package:rust/ {
+    pkg = $2
+    split(pkg, name_version, "-")
+    crateVersion = name_version[length(name_version)]
+    crateName = substr(pkg, 6, (length(pkg) - length(crateVersion) - 6))
+    split(crateVersion, versionDots, ".")
+    if(crateVersion && (crateVersion != "(git-version") && (length(versionDots) == 3) && crateName) {
+        cargoLock = cargoLock "[[package]]\nname = \"" crateName "\"\nversion = \"" crateVersion "\"\n"
+    } else {
+        untested++
+        #print("Unable to test " $0)
+    }
+    next
+}
 
-END { print cargoLock | cargoAudit }
+# We make an attempt to create the crate name from the package name otherwise
+/git-reference/ {
+    for(i=3; i <= NF; i++) {
+        if($i == "(version")
+            crateVersion = $(i+1)
+        if($i == "(name")
+            crateName = $(i+1)
+        if($i == "(git-file-name") {
+            crateName = $(i+1)
+            crateVersion = $(i+2)
+        }
+    }
+    gsub(/)/, "", crateVersion)
+    gsub(/)/, "", crateName)
+    sub(/rust-/, "", crateName)
+    # The crate version MUST be major.minor.patch
+    split(crateVersion, versionParts, ".")
+    if(crateVersion && (crateVersion != "(git-version") && (length(versionParts) == 3) && crateName) {
+        cargoLock = cargoLock "[[package]]\nname = " crateName "\nversion = " crateVersion "\n"
+    } else {
+        untested++
+        #print("Unable to test " $0)
+    }
+    next
+}
+
+# Note those which we were unable to parse
+/define rust/ {
+    if($3 == "#f)")
+        next
+    print("Unable to parse " $0)
+    }
+
+{ untested++ }
+
+END { print("Number of crates untested: " untested); print cargoLock | cargoAudit }

gnu/local.mk

@@ -610,6 +610,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/rocm-apps.scm			\
   %D%/packages/rocm-libs.scm			\
   %D%/packages/rocm-tools.scm			\
+  %D%/packages/rocq.scm				\
   %D%/packages/rpc.scm				\
   %D%/packages/rpm.scm				\
   %D%/packages/rrdtool.scm			\
@@ -1130,9 +1131,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/clucene-gcc-14.patch			\
   %D%/packages/patches/clucene-pkgconfig.patch			\
   %D%/packages/patches/coda-use-system-libs.patch		\
-  %D%/packages/patches/codex-acp-0.9.2-remove-patch-sections.patch \
-  %D%/packages/patches/codex-acp-0.9.2-replace-result-flatten.patch    \
+  %D%/packages/patches/codex-acp-0.11.1-disable-code-mode.patch \
+  %D%/packages/patches/codex-acp-0.11.1-remove-patch-sections.patch \
   %D%/packages/patches/codex-0.98.0-remove-patch-sections.patch    \
+  %D%/packages/patches/rust-codex-0.117.0-remove-patch-sections.patch    \
   %D%/packages/patches/cogl-fix-double-free.patch		\
   %D%/packages/patches/collada-dom-boost.patch			\
   %D%/packages/patches/collectd-5.11.0-noinstallvar.patch	\
@@ -1466,7 +1468,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/ghostscript-no-header-creationdate.patch \
   %D%/packages/patches/gimp-fix-metadata-editor.patch		\
   %D%/packages/patches/gimp-fix-tiff-load.patch			\
-  %D%/packages/patches/git-clar-path-max.patch			\
   %D%/packages/patches/git-filter-repo-generate-doc.patch	\
   %D%/packages/patches/gklib-suitesparse.patch			\
   %D%/packages/patches/glib-appinfo-watch.patch			\
@@ -1616,7 +1617,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/hurd-refcounts-assert.patch		\
   %D%/packages/patches/hurd-rumpdisk-no-hd.patch		\
   %D%/packages/patches/hurd-startup.patch			\
-  %D%/packages/patches/hwloc-1-test-btrfs.patch			\
   %D%/packages/patches/hwloc-add-with-opencl.patch		\
   %D%/packages/patches/i3lock-blur-fix-build-on-gcc-10.patch	\
   %D%/packages/patches/i7z-gcc-10.patch				\
@@ -1652,6 +1652,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/id3lib-CVE-2007-4460.patch			\
   %D%/packages/patches/id3lib-UTF16-writing-bug.patch			\
   %D%/packages/patches/ilmbase-fix-tests.patch			\
+  %D%/packages/patches/inetutils-drop-test.patch                \
   %D%/packages/patches/inferno-fix-crash.patch		\
   %D%/packages/patches/iniparser-remove-fetchcontent-usage.patch		\
   %D%/packages/patches/inkscape-libxml2.patch		\
@@ -1698,7 +1699,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/libcss-check-format.patch		\
   %D%/packages/patches/libeb-gcc-14.patch			\
   %D%/packages/patches/libextractor-tidy-support.patch		\
-  %D%/packages/patches/libfossil-skip-amalgamation.patch	\
   %D%/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch	\
   %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch	\
   %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.3.0.patch	\
@@ -1713,6 +1713,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libretro-dolphin-emu-libusb-assert.patch \
   %D%/packages/patches/libretro-dolphin-emu-vulkan-headers.patch        \
   %D%/packages/patches/libretranslate-use-flasgger.patch	\
+  %D%/packages/patches/librewolf-150.0-encoding_rs-rust-fix.patch       \
   %D%/packages/patches/librewolf-add-store-to-rdd-allowlist.patch       \
   %D%/packages/patches/librewolf-compare-paths.patch		\
   %D%/packages/patches/librewolf-neuter-locale-download.patch	\
@@ -2348,8 +2349,16 @@ 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	\
@@ -2394,6 +2403,13 @@ dist_patch_DATA =						\
   %D%/packages/patches/rust-codex-0.98.0-test-shebangs.patch	\
   %D%/packages/patches/rust-codex-0.98.0-test-timeout.patch	\
   %D%/packages/patches/rust-codex-0.98.0-windows-sandbox-protocol-version.patch	\
+  %D%/packages/patches/rust-codex-0.117.0-core-remove-self-dep.patch	\
+  %D%/packages/patches/rust-codex-0.120.0-core-remove-self-dep.patch	\
+  %D%/packages/patches/rust-codex-0.120.0-connectors-cache-test-race.patch	\
+  %D%/packages/patches/rust-codex-0.120.0-remove-libwebrtc.patch	\
+  %D%/packages/patches/rust-codex-0.120.0-test-timeout.patch	\
+  %D%/packages/patches/rust-codex-0.124.0-code-mode-stub-toolname.patch	\
+  %D%/packages/patches/rust-codex-0.124.0-remove-patch-sections.patch	\
   %D%/packages/patches/rust-ring-0.17-ring-core.patch		\
   %D%/packages/patches/rw-igraph-0.10.patch			\
   %D%/packages/patches/rxvt-unicode-fix-cursor-position.patch	\

gnu/packages/admin.scm

@@ -1158,7 +1158,7 @@ on memory usage on GNU/Linux systems.")
 (define-public htop
   (package
     (name "htop")
-    (version "3.4.1")
+    (version "3.5.0")
     (source
      (origin
        (method git-fetch)
@@ -1166,7 +1166,7 @@ on memory usage on GNU/Linux systems.")
              (url "https://github.com/htop-dev/htop")
              (commit version)))
        (sha256
-        (base32 "058y4a4mvx9m179dyr4wi8mlm6i4ybywshadaj4cvfn9fv0r0nkx"))
+        (base32 "1r07ri0dl9xz0jn1hc2g8q3l0q4clvnxs05yagpzsz0zigp4flj5"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
@@ -1309,7 +1309,8 @@ re-executing them as necessary.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "11n01vsd51r7qraaaylhhx04hq4s6vcq0896zkz0yp1wvqfbwmm1"))))
+                "11n01vsd51r7qraaaylhhx04hq4s6vcq0896zkz0yp1wvqfbwmm1"))
+              (patches (search-patches "inetutils-drop-test.patch"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -3441,7 +3442,7 @@ modules and plugins that extend Ansible.")
      (list ansible
            bash-minimal
            encfs
-           fuse-2
+           fuse
            util-linux ;; for umount
            findutils
            git
@@ -7169,6 +7170,35 @@ stored in an SQL database.")
 (connects via USB OTG).")
     (license license:expat)))
 
+(define-public yoctofetch
+  (package
+    (name "yoctofetch")
+    (version "2.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/Phosphenius/yoctofetch.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0smkaydv74p2231gafibvqbwsy469w56hya8gz8wq0gw7m2l7zh3"))))
+    ; Support for other platforms not available per upstream:
+    ; https://codeberg.org/Phosphenius/yoctofetch#supported-platforms
+    (supported-systems '("x86_64-linux" "aarch64-linux"))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f)) ; No tests available.
+    (home-page "https://codeberg.org/Phosphenius/yoctofetch")
+    (synopsis "Fast and low footprint system fetch tool for the Linux UAPI")
+    (description
+     "This package provides a system fetch tool, similar to
+@command{neofetch}, @command{fastfetch}, etc.  It is lightweight and
+has a focus on performance.  It can be used as a greeter by starting
+it from @file{~/.bashrc} for example.")
+    (license license:agpl3+)))
+
 (define-public zzz
   (package
     (name "zzz")

gnu/packages/audio.scm

@@ -6529,22 +6529,23 @@ on the ALSA software PCM plugin.")
 (define-public snd
   (package
     (name "snd")
-    (version "25.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "ftp://ccrma-ftp.stanford.edu/pub/Lisp/"
-                                  "snd-" version ".tar.gz"))
-              (sha256
-               (base32
-                "0fgxqk0byxdj6059mb9d5qic2dqjabz49j0szsrn2y3c9nz6iyq4"))))
+    (version "26.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://ccrma.stanford.edu/software/snd/snd-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1d573mjlrn9rhl9g0a3d1rkar34q60ln8mwlbibfalpn8lsz59a0"))))
     (build-system gnu-build-system)
     (arguments
      (list
-      #:tests? #f                       ; no tests
-      #:out-of-source? #f               ; for the 'install-doc' phase
+      #:tests? #f                       ; No tests.
+      #:out-of-source? #f               ; Required by 'install-doc'.
       #:configure-flags
-      #~(let ((docdir (string-append #$output "/share/doc/"
-                                     #$name "-" #$version)))
+      #~(let
+            ((docdir (string-append #$output "/share/doc/snd-" #$version)))
           (list "--with-alsa"
                 "--with-jack"
                 "--with-gmp"
@@ -6552,18 +6553,20 @@ on the ALSA software PCM plugin.")
                 (string-append "--with-doc-dir=" docdir)))
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'install 'install-s7
+          (add-after 'install 'install-s7-h
             (lambda _
-              (install-file "s7.h" (string-append #$output "/include"))))
+              (install-file "s7.h" (string-append #$output
+                                                  "/include"))))
           (add-after 'install 'install-doc
             (lambda _
-              (let ((doc (string-append #$output "/share/doc/"
-                                        #$name "-" #$version)))
+              (let
+                  ((docdir (string-append #$output "/share/doc/snd-"
+                                          #$version)))
                 (for-each
                  (lambda (f)
-                   (install-file f doc))
+                   (install-file f docdir))
                  (find-files "." "\\.html$"))
-                (copy-recursively "pix" (string-append doc "/pix"))))))))
+                (copy-recursively "pix" (string-append docdir "/pix"))))))))
     (native-inputs
      (list pkg-config))
     (inputs
@@ -6582,13 +6585,16 @@ on the ALSA software PCM plugin.")
            timidity++
            vorbis-tools
            wavpack))
+    (home-page "https://ccrma.stanford.edu/software/snd/snd/snd.html")
     (synopsis "Sound editor")
-    (home-page "https://ccrma.stanford.edu/software/snd/")
     (description
      "Snd is a sound editor modelled loosely after Emacs.  It can be
 customized and extended using either the s7 Scheme implementation (included in
 the Snd sources), Ruby, or Forth.")
-    (license (license:non-copyleft "file://COPYING"))))
+    (license
+     ;; INFO: pkgsrc classifies this as `esdl-license', a license not included
+     ;; in OSI or FSF lists, despite being similar to ISC.
+     (license:non-copyleft "file://COPYING"))))
 
 (define-public libspecbleach
   (package

gnu/packages/bioinformatics.scm

@@ -913,7 +913,7 @@ suite native in R.")
 (define-public r-bpcells
   (package
     (name "r-bpcells")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method git-fetch)
@@ -922,7 +922,7 @@ suite native in R.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12h1di45fg06nhsliii7v0h1z567pkpis1xm4ar1qr8ns1n8iljw"))
+        (base32 "0yqgcajq83g25mznwcngaw7pi6vcqxqdnynpgb95yci57k3wrp6j"))
        (modules '((guix build utils)))
        (snippet
         '(delete-file-recursively "r/src/vendor/highway"))))
@@ -931,13 +931,15 @@ suite native in R.")
     (arguments
      (list
       #:phases
-      '(modify-phases %standard-phases
+      `(modify-phases %standard-phases
          (add-after 'unpack 'chdir
-           (lambda _
-             (substitute* "r/configure"
-               (("tools/hwy-test.cpp" m)
-                (string-append m " $HWY_LIBS $HWY_CFLAGS")))
-             (chdir "r"))))))
+           (lambda _ (chdir "r")))
+         ,@(if (target-x86-32?)
+               '((add-after 'chdir 'require-sse2
+                   ;; This avoids falling back to the scalar backend in
+                   ;; highway, which fails to build.
+                   (lambda _ (setenv "CFLAGS" "-msse2"))))
+               '()))))
     (propagated-inputs
      (list r-dplyr
            r-ggplot2
@@ -22349,37 +22351,6 @@ combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM),
 1973. (Algorithm 7.)")
     (license license:expat)))
 
-(define-public fsom
-  (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3"))
-    (package
-      (name "fsom")
-      (version (git-version "0.0.0" "1" commit))
-      (source (origin
-        (method git-fetch)
-        (uri (git-reference
-              (url "https://github.com/ekg/fsom/")
-              (commit commit)))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi"))))
-      (build-system gnu-build-system)
-      (arguments
-       `(#:tests? #f ; There are no tests to run.
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure) ; There is no configure phase.
-           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (install-file "fsom" bin)))))))
-      (native-inputs
-       (list gcc-6))
-      (home-page "https://github.com/ekg/fsom")
-      (synopsis "Manage SOM (Self-Organizing Maps) neural networks")
-      (description "A tiny C library for managing SOM (Self-Organizing Maps)
-neural networks.")
-      (license license:gpl3))))
-
 (define-public fastahack
   (package
     (name "fastahack")

gnu/packages/build-tools.scm

@@ -275,14 +275,14 @@ generate such a compilation database.")
 (define-public bmake
   (package
     (name "bmake")
-    (version "20260313")
+    (version "20260406")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "http://www.crufty.net/ftp/pub/sjg/bmake-" version ".tar.gz"))
        (sha256
-        (base32 "0xgryknmv625idw37rq89mpl5rymwdb15j5w8zxwy1gf8b6z7j3n"))
+        (base32 "09nzd9v12n2pwxmf67056kzjnvxcpk5q2x1fs5qkrsk1ssh5yvpd"))
        (patches (search-patches "bmake-run-check-separately.patch"))))
     (build-system gnu-build-system)
     (inputs

gnu/packages/c.scm

@@ -23,7 +23,7 @@
 ;;; Copyright © 2023, 2024 David Elsing <david.elsing@posteo.net>
 ;;; Copyright @ 2022, Kitzman <kitzman@disroot.org>
 ;;; Copyright @ 2025 Dariqq <dariqq@posteo.net>
-;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
+;;; Copyright © 2025, 2026 Ashish SHUKLA <ashish.is@lostca.se>
 ;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
 ;;; Copyright © 2026 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
@@ -1762,7 +1762,7 @@ string.h, but with a utf8* prefix instead of the str* prefix.")
 (define-public simdutf
   (package
     (name "simdutf")
-    (version "7.7.1")
+    (version "9.0.0")
     (source
      (origin
        (method git-fetch)
@@ -1771,7 +1771,7 @@ string.h, but with a utf8* prefix instead of the str* prefix.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0kw4j4qqcfjaii667xa745pklj50m70nqq8cj5agj714acczbk7y"))))
+        (base32 "0f5ccvqj7pfa69m9y1kxp2v1lybx6x8i9pykdqfkr7dydqbhrhx6"))))
     (build-system cmake-build-system)
     (arguments (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")))
     (synopsis "SIMD Unicode validation and transcoding")

gnu/packages/check.scm

@@ -3131,7 +3131,7 @@ time by mocking the datetime module.")
 (define-public python-flaky
   (package
     (name "python-flaky")
-    (version "3.8.1")
+    (version "3.8.1")  ; On bump, remove some skipped tests in python-cherrypy.
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "flaky" version))
@@ -3719,30 +3719,6 @@ system.  The code under test requires no modification to work with pyfakefs.")
 directories and files.")
     (license license:expat)))
 
-(define-public python-pytest-tornado5
-  (package
-    (name "python-pytest-tornado5")
-    (version "2.0.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "pytest-tornado5" version))
-              (sha256
-               (base32
-                "0qb62jw2w0xr6y942yp0qxiy755bismjfpnxaxjjm05gy2pymr8d"))))
-    (build-system pyproject-build-system)
-    (arguments
-     ;; Tests require pytest < 6
-     (list #:tests? #f))
-    (propagated-inputs (list python-pytest python-tornado))
-    (native-inputs (list python-setuptools python-wheel))
-    (home-page "https://github.com/vidartf/pytest-tornado")
-    (synopsis
-     "Fixtures and markers to simplify testing of Tornado applications")
-    (description
-     "This package provides a @code{py.test} plugin supplying fixtures and
-markers to simplify testing of asynchronous tornado applications.")
-    (license license:asl2.0)))
-
 (define-public guile-proba
   (package
     (name "guile-proba")

gnu/packages/chemistry.scm

@@ -580,7 +580,7 @@ stored with user-specified precision.")
            python-sphinx))
     (inputs
      (list fftwf
-           `(,hwloc-2 "lib")
+           `(,hwloc "lib")
            libtirpc
            lmfit
            muparser

gnu/packages/codex.scm

@@ -18,10 +18,10 @@
 
 ;;; This module is separate from (gnu packages rust-apps) to avoid a
 ;;; circular module dependency: (gnu packages rust-sources), which
-;;; defines rust-codex-0.98.0, transitively loads (gnu packages
+;;; defines rust-codex-0.124.0, transitively loads (gnu packages
 ;;; rust-apps) through its #:use-module chain.  If the codex package
 ;;; lived in rust-apps.scm, loading rust-sources would trigger loading
-;;; rust-apps before rust-codex-0.98.0 is defined, causing an unbound
+;;; rust-apps before rust-codex-0.124.0 is defined, causing an unbound
 ;;; variable error.
 
 (define-module (gnu packages codex)
@@ -36,33 +36,46 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages libunwind)
   #:use-module (gnu packages llvm)
+  #:use-module (gnu packages lsof)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages rust-sources)
   #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages textutils)
+  #:use-module (gnu packages nss)
   #:use-module (gnu packages tls)
-  #:use-module (gnu packages version-control))
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages virtualization))
 
 (define-public codex
   (package
     (name "codex")
-    (version (package-version rust-codex-0.98.0))
+    (version (package-version rust-codex-0.124.0))
     (source
      (origin
-       (inherit (package-source rust-codex-0.98.0))
+       (inherit (package-source rust-codex-0.124.0))
        (patches (search-patches
-                 "codex-0.98.0-remove-patch-sections.patch"
+                 "codex-acp-0.11.1-disable-code-mode.patch"
+                 "rust-codex-0.124.0-code-mode-stub-toolname.patch"
+                 "rust-codex-0.124.0-remove-patch-sections.patch"
+                 "rust-codex-0.120.0-remove-libwebrtc.patch"
                  "rust-codex-0.98.0-test-shebangs.patch"
-                 "rust-codex-0.98.0-test-timeout.patch"))))
+                 "rust-codex-0.120.0-test-timeout.patch"))))
     (build-system cargo-build-system)
     (arguments
      (list
       #:install-source? #f
-      #:cargo-install-paths '(list "cli" "exec" "exec-server"
-                                   "linux-sandbox" "mcp-server" "network-proxy"
+      ;; exec-server is library-only in 0.124 (no [[bin]] in
+      ;; exec-server/Cargo.toml); cargo install --path exec-server fails
+      ;; with "no packages found with binaries or examples".  Drop it
+      ;; from the install paths -- the library is consumed via the
+      ;; workspace by other binaries here, not installed standalone.
+      #:cargo-install-paths '(list "cli" "exec"
+                                   "linux-sandbox" "mcp-server"
                                    "app-server" "tui")
       ;; schema_fixtures_match_generated (upstream fixture is stale:
       ;; FileChange::Update in codex-protocol gained old_content,
@@ -71,72 +84,55 @@
       #:cargo-test-flags '(list "--workspace"
                                 "--exclude" "codex-app-server-protocol"
                                 "--"
-                                ;; These tests exercise sandbox denial and
-                                ;; escalation, which requires Landlock to
-                                ;; cleanly deny filesystem access.  Inside the
-                                ;; build container Landlock returns NotEnforced
-                                ;; and the sandbox binary panics instead.
-                                ;; Disabling Landlock would not help either,
-                                ;; since these tests need a working sandbox to
-                                ;; have anything to deny and escalate.
+                                ;;; BEGIN Landlock returns NotEnforced
+                                ;;; in the build container; the sandbox
+                                ;;; binary panics instead of cleanly
+                                ;;; denying filesystem access.
+                                ;; Sandbox denial and escalation tests.
                                 "--skip" "sandbox_denied_shell_returns_original_output"
+                                ;; Sandbox denial and escalation tests.
                                 "--skip" "shell_escalated_permissions_rejected_then_ok"
+                                ;; Sandbox denial and escalation tests.
                                 "--skip" "unified_exec_runs_under_sandbox"
-                                ;; These tests (in codex-exec) directly call
-                                ;; spawn_command_under_linux_sandbox to verify
-                                ;; that python and bash work correctly inside
-                                ;; the Landlock sandbox.  The sandbox binary
-                                ;; (codex-exec) panics with LandlockRestrict
-                                ;; (exit code 101) before the inner command
-                                ;; even starts.
+                                ;; codex-exec: spawn_command_under_linux_sandbox
+                                ;; panics with LandlockRestrict (exit 101).
                                 "--skip" "python_getpwuid_works_under_sandbox"
+                                ;; Same as above.
                                 "--skip" "python_multiprocessing_lock_works_under_sandbox"
+                                ;; Same as above.
                                 "--skip" "sandbox_distinguishes_command_and_policy_cwds"
-                                ;; These linux-sandbox tests directly invoke
-                                ;; the Landlock sandbox via
-                                ;; process_exec_tool_call; same root cause.
+                                ;; linux-sandbox: process_exec_tool_call
+                                ;; invokes Landlock; same panic.
                                 "--skip" "test_writable_root"
+                                ;; Same as above.
                                 "--skip" "test_timeout"
+                                ;; Same as above.
                                 "--skip" "test_root_read"
+                                ;; Same as above.
                                 "--skip" "test_dev_null_write"
+                                ;; Same as above.
                                 "--skip" "test_no_new_privs_is_enabled"
-                                ;; This test iterates many approval scenarios;
-                                ;; one of them
-                                ;; (danger_full_access_on_request_allows_network)
-                                ;; runs a command through the Landlock sandbox
-                                ;; binary, which panics with LandlockRestrict
-                                ;; inside the build container.  Cargo --skip
-                                ;; cannot target individual scenarios, so we
-                                ;; skip the entire matrix.
+                                ;; One scenario runs through Landlock
+                                ;; which panics; cargo --skip cannot
+                                ;; target individual scenarios.
                                 "--skip" "approval_matrix_covers_all_modes"
-                                ;; This test verifies session-level patch
-                                ;; approval caching: approve once, skip
-                                ;; future prompts for the same file.  When
-                                ;; Landlock is unavailable (as in the Guix
-                                ;; build container) the sandbox binary panics,
-                                ;; triggering the escalation-retry path, which
-                                ;; interferes with the approval cache and
-                                ;; causes a spurious re-prompt on the second
-                                ;; patch.
+                                ;; Landlock panic triggers escalation-retry
+                                ;; which interferes with the approval cache.
                                 "--skip" "approving_apply_patch_for_session_skips_future_prompts_for_same_file"
                                 ;; These tests expect to interrupt a
                                 ;; long-running 'sleep 60' and receive
-                                ;; TurnAborted.  Default test config is
-                                ;; OnRequest + ReadOnly.  What happens:
+                                ;; TurnAborted.  What happens:
                                 ;;
                                 ;; 1. ReadOnly wraps the command with
                                 ;;    codex-linux-sandbox (Landlock-based).
-                                ;; 2. Landlock is unavailable in the Guix
-                                ;;    build container, so the sandbox
-                                ;;    binary exits instantly (~1 ms).
+                                ;; 2. Landlock is unavailable, so the
+                                ;;    sandbox binary exits instantly.
                                 ;; 3. Orchestrator gets SandboxErr::Denied.
                                 ;;    wants_no_sandbox_approval(OnRequest)
-                                ;;    returns false (sandboxing.rs:222),
-                                ;;    so no escalation -- denial returned
-                                ;;    directly.
+                                ;;    returns false, so no escalation --
+                                ;;    denial returned directly.
                                 ;; 4. ToolEmitter::finish sends the error
-                                ;;    to the mock model as
-                                ;;    function_call_output.
+                                ;;    to the mock model.
                                 ;; 5. Second mock SSE response fires,
                                 ;;    turn finishes with TurnComplete.
                                 ;; 6. Op::Interrupt arrives 100 ms later,
@@ -150,74 +146,370 @@
                                 ;; has only one mock response (so the turn
                                 ;; cannot complete first).
                                 "--skip" "interrupt_persists_turn_aborted_marker_in_next_request"
+                                ;; Same causal chain as above.
                                 "--skip" "interrupt_tool_records_history_entries"
-                                ;; Upstream bug: test hardcodes "0.0.0" in the
-                                ;; expected user-agent string but the workspace
-                                ;; version is "0.98.0".
-                                "--skip" "get_user_agent_returns_current_codex_user_agent"
-                                ;; Same upstream bug: mcp-server tests
-                                ;; check the initialize response which
-                                ;; includes "version": "0.0.0" but the
-                                ;; server returns "0.98.0".
+                                ;; WorkspaceWrite sandbox policy wraps
+                                ;; commands with codex-linux-sandbox;
+                                ;; Landlock panics, command never runs,
+                                ;; exit_code is None instead of Some(0).
+                                "--skip" "request_permissions_grants_apply_to_later_exec_command_calls"
+                                ;; Same root cause.
+                                "--skip" "request_permissions_grants_apply_to_later_shell_command_calls"
+                                ;; Same root cause.
+                                "--skip" "partial_request_permissions_grants_do_not_preapprove_new_permissions"
+                                ;;; END Landlock
+                                ;;; BEGIN mcp_process.rs initialize
+                                ;;; assertion expects "version":"0.0.0"
+                                ;;; but the server returns "0.120.0".
                                 "--skip" "test_codex_tool_passes_base_instructions"
                                 "--skip" "test_shell_command_approval_triggers_elicitation"
                                 "--skip" "test_patch_approval_triggers_elicitation"
-                                ;; These codex-exec-server tests need
-                                ;; "dotslash", a Meta tool that lazily
-                                ;; downloads pre-built binaries from a
-                                ;; JSON manifest.  The test helper
-                                ;; create_transport runs
-                                ;; `dotslash -- fetch <path>` to obtain a
-                                ;; custom bash binary described in
-                                ;; exec-server/tests/suite/bash.
-                                ;; dotslash is not available in the build
-                                ;; container.
-                                "--skip" "list_tools"
-                                "--skip" "accept_elicitation_for_prompt_rule"
-                                ;;; Test isolation bug: each test in
-                                ;;; state/src/runtime.rs calls
-                                ;;; unique_temp_dir() to get its own
-                                ;;; temporary directory (and thus its
-                                ;;; own SQLite database).  That function
-                                ;;; names directories using the current
-                                ;;; nanosecond timestamp, so when tests
-                                ;;; run in parallel several can receive
-                                ;;; the same name and open the same
-                                ;;; database.  The initial SQLite
-                                ;;; migration runs CREATE TABLE threads
-                                ;;; (without IF NOT EXISTS), so any init
-                                ;;; after the first panics with "table
-                                ;;; threads already exists".  Any of
-                                ;;; these tests
-                                ;;; can be the victim.
+                                ;;; END version mismatch
+                                ;;; BEGIN Test isolation bug:
+                                ;;; unique_temp_dir() in
+                                ;;; state/src/runtime.rs names dirs
+                                ;;; using nanosecond timestamps, so
+                                ;;; parallel tests can collide.  The
+                                ;;; SQLite migration runs CREATE TABLE
+                                ;;; threads (without IF NOT EXISTS),
+                                ;;; so the second init panics with
+                                ;;; "table threads already exists".
                                 "--skip" "init_removes_legacy_state_db_files"
                                 "--skip" "upsert_and_get_thread_memory"
                                 "--skip" "get_last_n_thread_memories_for_cwd_matches_exactly"
                                 "--skip" "upsert_thread_memory_errors_for_unknown_thread"
                                 "--skip" "get_last_n_thread_memories_for_cwd_zero_returns_empty"
                                 "--skip" "get_last_n_thread_memories_for_cwd_does_not_prefix_match"
-                                "--skip" "deleting_thread_cascades_thread_memory")
+                                "--skip" "deleting_thread_cascades_thread_memory"
+                                ;;; END SQLite test isolation
+                                ;; The test spawns 'sh' after
+                                ;; env_clear() with an empty env map;
+                                ;; glibc execvp uses confstr(_CS_PATH)
+                                ;; ("/bin:/usr/bin") when PATH is
+                                ;; unset, but /bin/sh does not exist
+                                ;; in the build container.
+                                "--skip" "cancellation_expiration_keeps_process_alive_until_terminated"
+                                ;; Proxy baseline_policy returns 403
+                                ;; "not_allowed_local" for example.com;
+                                ;; test expects 200.
+                                "--skip" "managed_network_proxy_decider_survives_full_access_start"
+                                ;;; BEGIN bash_snapshot_script() uses
+                                ;;; "compgen -e" to list exports but
+                                ;;; bash-minimal lacks programmable
+                                ;;; completion; export section is empty.
+                                ;; stdout.contains("VALID_NAME") fails.
+                                "--skip" "bash_snapshot_filters_invalid_exports"
+                                ;; stdout.contains("MULTILINE_CERT") fails.
+                                "--skip" "bash_snapshot_preserves_multiline_exports"
+                                ;; snapshot.contains("PATH") fails.
+                                "--skip" "linux_bash_snapshot_includes_sections"
+                                ;;; END compgen
+                                ;; substitute* patches PAGER to store
+                                ;; path of cat; test expects bare "cat".
+                                "--skip" "unified_exec_env_injects_defaults"
+                                ;;; BEGIN V8 disabled (codex-code-mode
+                                ;;; default-features = false).
+                                "--skip" "suite::code_mode::"
+                                "--skip" "suite::js_repl::"
+                                "--skip" "suite::view_image::js_repl_"
+                                ;;; END V8 disabled
+                                ;;; BEGIN same compgen root cause:
+                                ;;; assert_posix_snapshot_sections
+                                ;;; asserts snapshot.contains("PATH").
+                                "--skip" "linux_shell_command_uses_shell_snapshot"
+                                "--skip" "linux_unified_exec_uses_shell_snapshot"
+                                "--skip" "shell_command_snapshot_still_intercepts_apply_patch"
+                                ;;; END compgen / shell snapshot
+                                ;;; BEGIN These sandbox tests set
+                                ;;; exclude_slash_tmp: true which makes
+                                ;;; bwrap exclude /tmp from its mount
+                                ;;; namespace.  Since Guix builds under
+                                ;;; /tmp, the codex-linux-sandbox binary
+                                ;;; becomes invisible to bwrap even though
+                                ;;; the test adds the helper dir as a
+                                ;;; filesystem carve-out -- the parent /tmp
+                                ;;; bind-mount is absent so the carve-out
+                                ;;; has nothing to carve out of.
+                                "--skip" "sandbox_reenables_writable_subpaths_under_unreadable_parents"
+                                "--skip" "managed_proxy_mode_routes_through_bridge_and_blocks_direct_egress"
+                                ;;; END exclude_slash_tmp
+                                ;; Expects 3 TerminalInteraction events
+                                ;; across timed poll windows; under CPU
+                                ;; contention events merge into 2.
+                                "--skip" "unified_exec_terminal_interaction_captures_delayed_output"
+                                ;;; BEGIN assert_parallel_duration
+                                ;;; requires < 1600 ms for parallel ops.
+                                ;; Two 300 ms test_sync_tool calls.
+                                "--skip" "read_file_tools_run_in_parallel"
+                                ;; Two "sleep 0.25" shell commands.
+                                "--skip" "shell_tools_run_in_parallel"
+                                ;; One test_sync_tool + one shell sleep.
+                                "--skip" "mixed_parallel_tools_run_in_parallel"
+                                ;;; END assert_parallel_duration
+                                ;; Asserts elapsed >= 4500 ms and
+                                ;; < 5800 ms for a 5 s timeout; under
+                                ;; contention elapsed drifts past 5800.
+                                "--skip" "remote_models_request_times_out_after_5s"
+                                ;; Queued inter-agent mail must be
+                                ;; injected between the reasoning/
+                                ;; commentary item and the gate release;
+                                ;; under contention the gate fires before
+                                ;; the mail is processed, so the snapshot
+                                ;; shows the stale function_call instead
+                                ;; of the expected mail message.
+                                "--skip" "queued_inter_agent_mail_triggers_follow_up_after_commentary_message_item"
+                                ;; Same root cause: snapshot mismatch at
+                                ;; pending_input.rs assert_two_responses_
+                                ;; input_snapshot; expects mail at position
+                                ;; 04 but gets function_call/shell instead.
+                                "--skip" "queued_inter_agent_mail_triggers_follow_up_after_reasoning_item"
+                                ;;; BEGIN DNS for hostnames like
+                                ;;; example.com fails in the build
+                                ;;; sandbox.  host_resolves_to_non_
+                                ;;; public_ip() in runtime.rs treats
+                                ;;; failed DNS as non-public and
+                                ;;; returns NotAllowedLocal, so tests
+                                ;;; expecting Allowed or Decider get
+                                ;;; Deny/BaselinePolicy instead.
+                                "--skip" "host_blocked_requires_allowlist_match"
+                                "--skip" "add_allowed_domain_removes_matching_deny_entry"
+                                "--skip" "host_blocked_subdomain_wildcards_exclude_apex"
+                                "--skip" "host_blocked_global_wildcard_allowlist_allows_public_hosts_except_denylist"
+                                "--skip" "evaluate_host_policy_emits_domain_event_for_decider_ask"
+                                "--skip" "evaluate_host_policy_emits_domain_event_for_decider_allow_override"
+                                "--skip" "http_connect_accept_blocks_in_limited_mode"
+                                "--skip" "http_connect_accept_allows_allowlisted_host_in_full_mode"
+                                "--skip" "mitm_policy_blocks_disallowed_method_and_records_telemetry"
+                                ;;; END DNS failure / NotAllowedLocal
+                                ;;; BEGIN Flaky: wiremock mock expects
+                                ;;; 1 POST to /codex/safety/arc but
+                                ;;; receives 0.  Passes in some builds,
+                                ;;; fails in others with identical code
+                                ;;; and env.  The identical custom_
+                                ;;; variant always passes; only the
+                                ;;; CODEX_APPS_MCP_SERVER_NAME variant
+                                ;;; flakes, suggesting a timing race
+                                ;;; in the async POST under contention.
+                                "--skip" "approve_mode_blocks_when_arc_returns_interrupt_for_model"
+                                "--skip" "approve_mode_blocks_when_arc_returns_interrupt_without_annotations"
+                                ;;; END ARC monitor flake
+                                ;;; BEGIN nss-certs sets SSL_CERT_FILE
+                                ;;; which makes build_reqwest_client load
+                                ;;; 171 CA certs via add_root_certificate.
+                                ;;; This changes the reqwest TLS backend
+                                ;;; configuration; the ARC safety POST to
+                                ;;; the localhost mock server never arrives
+                                ;;; (wiremock expects 1 request, gets 0).
+                                "--skip" "approve_mode_blocks_when_arc_returns_interrupt_for_model"
+                                "--skip" "approve_mode_blocks_when_arc_returns_interrupt_without_annotations"
+                                ;;; END nss-certs / ARC monitor
+                                ;; Upstream bug: JsonRpcConnection has
+                                ;; no websocket keepalive or read timeout.
+                                ;; When the exec-server is killed, the
+                                ;; client's reader task blocks on
+                                ;; websocket_reader.next() forever because
+                                ;; TCP doesn't detect the dead peer without
+                                ;; a write or keepalive probe.  Previously
+                                ;; masked because empty env made "sleep 10"
+                                ;; fail instantly; with PATH the process
+                                ;; lives long enough to hit the deadlock.
+                                "--skip" "remote_exec_process_reports_transport_disconnect"
+                                ;; 500 ms timeout on MCP list response
+                                ;; (mcp_server_status.rs timeout at
+                                ;; Duration::from_millis(500)).  With
+                                ;; nss-certs TLS now works, so the
+                                ;; startup plugin sync HTTP requests
+                                ;; (chatgpt.com, api.github.com) wait
+                                ;; for TCP timeout instead of failing
+                                ;; instantly at TLS, eating the budget.
+                                "--skip" "mcp_server_status_list_tools_and_auth_only_skips_slow_inventory_calls"
+                                ;;; BEGIN Stack overflow in 'current_thread'
+                                ;;; tokio runtime.  The sibling tests in
+                                ;;; tracing_tests.rs use the local helper
+                                ;;; run_current_thread_test_with_stack
+                                ;;; (4 MiB) but this one uses bare
+                                ;;; #[tokio::test] on the 2 MiB default
+                                ;;; test-thread stack, and TurnStart's
+                                ;;; future graph exceeds it.  With
+                                ;;; RUST_MIN_STACK raised the overflow is
+                                ;;; gone but the test then deterministically
+                                ;;; times out waiting for a span tagged
+                                ;;; codex.op = "user_input" on the remote
+                                ;;; trace that upstream never emits on that
+                                ;;; trace in our environment.
+                                "--skip" "turn_start_jsonrpc_span_parents_core_turn_spans"
+                                ;;; END tracing test stack/timeout
+                                ;;; BEGIN The upstream loader resolves the
+                                ;;; MCP OAuth credentials store mode by
+                                ;;; calling
+                                ;;; resolve_mcp_oauth_credentials_store_mode
+                                ;;; with env!("CARGO_PKG_VERSION") -- which
+                                ;;; in the released 0.124.0 tarball is
+                                ;;; "0.124.0".  These fixture tests
+                                ;;; construct the expected Config by
+                                ;;; passing the LOCAL_DEV_BUILD_VERSION
+                                ;;; constant ("0.0.0") to the same
+                                ;;; resolver, and the resolver only returns
+                                ;;; File for "0.0.0" -- Auto otherwise.
+                                ;;; Upstream CI builds from a checkout
+                                ;;; still carrying version = "0.0.0" so the
+                                ;;; tests pass there; they cannot pass
+                                ;;; against a released tag.
+                                "--skip" "test_precedence_fixture_with_gpt3_profile"
+                                "--skip" "test_precedence_fixture_with_gpt5_profile"
+                                "--skip" "test_precedence_fixture_with_o3_profile"
+                                "--skip" "test_precedence_fixture_with_zdr_profile"
+                                ;;; END LOCAL_DEV_BUILD_VERSION fixture mismatch
+                                ;;; BEGIN Verifies that Codex's user-shell
+                                ;;; spawn produces a child where
+                                ;;; CODEX_SANDBOX_NETWORK_DISABLED is unset
+                                ;;; (asserts stdout == "not-set").  We
+                                ;;; deliberately set that env var at the
+                                ;;; check phase to trigger upstream's
+                                ;;; skip_if_no_network! guards; the var then
+                                ;;; leaks into the spawned shell and the
+                                ;;; assertion fails.  The guix skip is a
+                                ;;; direct cost of the network-gate fix --
+                                ;;; trading one broken test for two that
+                                ;;; now skip cleanly.
+                                "--skip" "user_shell_command_does_not_set_network_sandbox_env_var"
+                                ;;; END CODEX_SANDBOX_NETWORK_DISABLED leak
+                                ;;; BEGIN The exec-server/tests/file_system
+                                ;;; integration tests invoke the real
+                                ;;; system bwrap, which tries to execvp the
+                                ;;; test binary at the cargo target path
+                                ;;; under the build dir.  Same root cause
+                                ;;; as the existing
+                                ;;; sandbox_reenables_writable_subpaths_under_unreadable_parents
+                                ;;; skip: guix builds live under /tmp but
+                                ;;; bwrap's mount namespace excludes /tmp,
+                                ;;; making the binary invisible inside the
+                                ;;; namespace.
+                                "--skip" "file_system_copy_preserves_symlink_source"
+                                "--skip" "file_system_copy_rejects_symlink_escape_destination"
+                                "--skip" "file_system_copy_rejects_symlink_escape_source"
+                                "--skip" "file_system_create_directory_rejects_symlink_escape"
+                                "--skip" "file_system_read_directory_rejects_symlink_escape"
+                                "--skip" "file_system_remove_rejects_symlink_escape"
+                                "--skip" "file_system_remove_removes_symlink_not_target"
+                                "--skip" "file_system_sandboxed_read_allows_readable_root"
+                                "--skip" "file_system_sandboxed_read_rejects_symlink_escape"
+                                "--skip" "file_system_sandboxed_read_rejects_symlink_parent_dotdot_escape"
+                                "--skip" "file_system_sandboxed_write_allows_additional_write_root"
+                                "--skip" "file_system_sandboxed_write_rejects_symlink_escape"
+                                "--skip" "file_system_sandboxed_write_rejects_unwritable_path"
+                                ;;; END bwrap-cant-see-/tmp file_system tests
+                                ;;; BEGIN Landlock is unavailable on Guix,
+                                ;;; so the sandbox cannot deny network
+                                ;;; syscalls.  These tests expect
+                                ;;; SandboxErr::Denied for the nc, ping,
+                                ;;; ssh, getent, and dev_tcp_redirection
+                                ;;; commands but those commands instead
+                                ;;; block on connect() until the test's 2s
+                                ;;; timeout fires (Timeout, exit 124).
+                                ;;; Same root cause as the Landlock skips
+                                ;;; at the top of this list; new test names
+                                ;;; in 0.124.
+                                "--skip" "sandbox_blocks_nc"
+                                "--skip" "sandbox_blocks_ping"
+                                "--skip" "sandbox_blocks_dev_tcp_redirection"
+                                "--skip" "sandbox_blocks_getent"
+                                "--skip" "sandbox_blocks_ssh"
+                                ;;; END Landlock network block
+                                ;;; BEGIN Requires github.com network access.
+                                ;;; With no "extraKnownMarketplaces" entry
+                                ;;; in settings.json,
+                                ;;; collect_marketplace_import_sources
+                                ;;; inserts a fallback entry for the
+                                ;;; "claude-plugins-official" marketplace
+                                ;;; pointing at the github shorthand
+                                ;;; "anthropics/claude-plugins-official".
+                                ;;; add_marketplace -> parse_marketplace_source
+                                ;;; expands that to a github.com/.git URL
+                                ;;; and clone_git_source runs 'git clone'.
+                                ;;; The Guix build sandbox has no network,
+                                ;;; so the clone fails and the marketplace
+                                ;;; lands in failed_marketplaces.  No mock
+                                ;;; cloner is injected via
+                                ;;; ExternalAgentConfigService::new_for_test,
+                                ;;; so there is no in-tree way to satisfy
+                                ;;; the test offline.
+                                "--skip" "import_plugins_infers_claude_official_marketplace_when_missing_from_settings"
+                                ;;; END github.com network access
+                                ;;; BEGIN Async race between the rollout
+                                ;;; writer task and a direct SQLite read.
+                                ;;; The test calls
+                                ;;; update_memory_settings_with_app_server,
+                                ;;; which routes through the in-memory
+                                ;;; thread path on the app-server's
+                                ;;; ThreadMemoryModeSet handler ->
+                                ;;; Session::set_thread_memory_mode ->
+                                ;;; persist_thread_memory_mode_update,
+                                ;;; which writes a RolloutItem::SessionMeta
+                                ;;; with the new mode to the rollout file
+                                ;;; via recorder.record_items + flush.  The
+                                ;;; rollout writer task then asynchronously
+                                ;;; calls sync_thread_state_after_write,
+                                ;;; which calls state_db::apply_rollout_items
+                                ;;; to mirror the SessionMeta into SQLite.
+                                ;;; flush() only awaits the rollout-file
+                                ;;; write, not the subsequent SQLite sync.
+                                ;;; The test opens a fresh StateRuntime and
+                                ;;; reads get_thread_memory_mode
+                                ;;; immediately, so it observes the creation
+                                ;;; default of "enabled" written by
+                                ;;; upsert_thread_with_creation_memory_mode
+                                ;;; instead of the new "disabled".  Upstream
+                                ;;; CI wins this race; we lose.
+                                "--skip" "update_memory_settings_updates_current_thread_memory_mode"
+                                ;;; END memory-mode rollout/sqlite race
+                                ;;; BEGIN The Stopwatch::new constructor in
+                                ;;; codex_shell_escalation anchors
+                                ;;; T0 = Instant::now() at construction;
+                                ;;; the spawned cancellation task fires at
+                                ;;; T0 + limit.  The test captures
+                                ;;; start = Instant::now() at T1 > T0 (after
+                                ;;; cancellation_token() returns) and
+                                ;;; asserts start.elapsed() >= limit,
+                                ;;; i.e. (T0 + limit) - T1 >= limit, which
+                                ;;; is always false by the offset T1 - T0.
+                                ;;; The test only passes when scheduler
+                                ;;; jitter on the sleep wakeup happens to
+                                ;;; exceed that offset.  Upstream wins the
+                                ;;; race; we don't always.
+                                "--skip" "cancellation_receiver_fires_after_limit"
+                                ;;; END Stopwatch construction/start offset race
+                                )
       #:cargo-package-crates
       ''(;;; Tier 0: No internal deps.
+         "codex-ansi-escape"
          "codex-async-utils"
+         "codex-backend-openapi-models"
          "codex-client"
          "codex-execpolicy"
          "codex-file-search"
-         "codex-git"
+         "codex-git-utils"
          "codex-keyring-store"
+         "codex-process-hardening"
          "codex-utils-absolute-path"
          "codex-utils-cache"
          "codex-utils-cargo-bin"
+         "codex-utils-elapsed"
+         "codex-utils-fuzzy-match"
          "codex-utils-home-dir"
          "codex-utils-json-to-toml"
+         "codex-utils-path"
+         "codex-utils-plugins"
          "codex-utils-pty"
          "codex-utils-readiness"
+         "codex-utils-rustls-provider"
+         "codex-utils-sleep-inhibitor"
+         "codex-utils-stream-parser"
          "codex-utils-string"
-         "codex-backend-openapi-models"
-         "codex-process-hardening"
-         "codex-ansi-escape"
-         ;;; Tier 1: Depends on tier 0.
+         "codex-utils-template"
+         ;;; Tier 1.
          "codex-utils-image"
+         "codex-utils-output-truncation"
          "codex-apply-patch"
          "codex-protocol"
          "codex-windows-sandbox"
@@ -226,35 +518,69 @@
          "codex-secrets"
          "codex-execpolicy-legacy"
          "codex-debug-client"
+         "codex-analytics"
+         "codex-rollout"
+         "codex-rollout-trace"
+         "codex-terminal-detection"
+         "codex-utils-approval-presets"
+         "codex-utils-cli"
+         "codex-uds"
+         "codex-install-context"
+         "codex-device-key"
          ;;; Tier 2.
          "codex-app-server-protocol"
          "codex-rmcp-client"
          "codex-otel"
+         "codex-thread-store"
          "codex-state"
-         "codex-core"
-         "codex-linux-sandbox"
+         "codex-features"
+         "codex-model-provider"
+         "codex-config"
+         "codex-agent-identity"
+         "codex-aws-auth"
+         "codex-hooks"
+         "codex-code-mode"
          "codex-feedback"
+         "codex-skills"
+         "codex-test-binary-support"
+         "codex-core"
+         "codex-core-plugins"
+         "codex-utils-sandbox-summary"
+         "codex-linux-sandbox"
+         "codex-sandboxing"
+         "codex-connectors"
+         "codex-core-skills"
          ;;; Tier 3.
          "codex-arg0"
          "codex-lmstudio"
          "codex-login"
          "codex-ollama"
-         "codex-common"
+         "codex-utils-oss"
          "codex-mcp-server"
          "codex-backend-client"
          "codex-responses-api-proxy"
+         "codex-shell-command"
+         "codex-shell-escalation"
+         "codex-plugin"
+         "codex-model-provider-info"
+         "codex-models-manager"
          ;;; Tier 4.
          "codex-cloud-requirements"
          "codex-exec"
          "codex-exec-server"
-         "codex-stdio-to-uds"
          "codex-network-proxy"
+         "codex-stdio-to-uds"
          "codex-chatgpt"
          "codex-cloud-tasks-client"
+         "codex-cloud-tasks-mock-client"
+         "codex-tools"
+         "codex-mcp"
+         "codex-collaboration-mode-templates"
          ;;; Tier 5.
          "codex-app-server"
          "codex-app-server-test-client"
          "codex-tui"
+         "codex-response-debug-context"
          ;;; Tier 6.
          "codex-cloud-tasks"
          ;; The main executable.
@@ -270,7 +596,7 @@
               ;; Update them to match the actual package version.
               (let ((snap-files (find-files "." "\\.snap$")))
                 (substitute* snap-files
-                  (("\\(v0\\.0\\.0\\) ") "(v0.98.0)")))))
+                  (("\\(v0\\.0\\.0\\)   ") "(v0.124.0) ")))))
           (add-after 'chdir-to-workspace 'patch-git-deps-to-vendor
             (lambda _
               ;; Replace git dependencies with version references so cargo
@@ -279,23 +605,57 @@
                 (("nucleo = \\{ git = [^}]+\\}")
                  "nucleo = \"0.5.0\"")
                 (("runfiles = \\{ git = [^}]+\\}")
-                 "runfiles = \"0.1.0\""))))
-          (add-after 'chdir-to-workspace 'add-version-to-workspace-deps
+                 "runfiles = \"0.1.0\""))
+              ;; Remove workspace members that have unbuildable deps
+              ;; (v8-poc requires V8).  code-mode stays a workspace member
+              ;; so its codex-protocol resolves to the same local copy as
+              ;; the rest of the build; disabling its default features
+              ;; (below) avoids pulling in V8.
+              (substitute* "Cargo.toml"
+                (("\"v8-poc\",") ""))
+              ;; Disable V8 runtime in codex-code-mode by turning off
+              ;; default features.  Keep path= so code-mode is resolved
+              ;; from the local source tree and shares codex-protocol
+              ;; (and other workspace crates) with the rest of the build;
+              ;; resolving it from the vendor instead introduces a
+              ;; duplicate codex-protocol and causes E0308 type
+              ;; mismatches in codex-tools.
+              (substitute* "Cargo.toml"
+                (("codex-code-mode = \\{ path = \"code-mode\" \\}")
+                 "codex-code-mode = { path = \"code-mode\", default-features = false }"))
+              ;; cargo build at workspace root ignores per-dep
+              ;; default-features=false and builds code-mode with its
+              ;; own default features, which include v8-runtime and
+              ;; would pull in V8.  Make the default feature empty.
+              (substitute* "code-mode/Cargo.toml"
+                (("^default = \\[\"v8-runtime\"\\]") "default = []"))))
+          (add-after 'patch-git-deps-to-vendor 'add-version-to-workspace-deps
             (lambda _
               ;; cargo package requires all dependencies to have versions.
-              ;; cargo package requires all dependencies to have versions.
-              ;; Add version = "0.98.0" to internal path dependencies.
+              ;; Add version = "0.124.0" to internal path dependencies.
               (let ((cargo-files (find-files "." "^Cargo\\.toml$")))
                 (substitute* cargo-files
                   ;; Handle inline deps: name = { path = "..." }
                   (("(codex-[a-z0-9-]+) = \\{ path = " all name)
-                   (string-append name " = { version = \"0.98.0\", path = "))
+                   (string-append name " = { version = \"0.124.0\", path = "))
                   ;; Handle inline deps with package: name = { package = "...", path = "..." }
                   (("(codex-[a-z0-9-]+) = \\{ package = " all name)
-                   (string-append name " = { version = \"0.98.0\", package = "))
+                   (string-append name " = { version = \"0.124.0\", package = "))
                   ;; Handle section deps: [dependencies.X] with path = "..."
                   (("^(path = \"\\.\\./[^\"]*\")" all path-line)
-                   (string-append path-line "\nversion = \"0.98.0\""))))))
+                   (string-append path-line "\nversion = \"0.124.0\""))))))
+          (add-after 'chdir-to-workspace 'use-gnu-store-in-sandbox
+            (lambda _
+              ;; LINUX_PLATFORM_DEFAULT_READ_ROOTS in linux-sandbox/src/
+              ;; bwrap.rs is the read-only baseline that codex's bwrap
+              ;; sandbox bind-mounts so commands can read /usr/bin/ls,
+              ;; libc, etc.  Upstream lists "/nix/store" for NixOS;
+              ;; Guix's equivalent is "/gnu/store".  Without this swap,
+              ;; the codex sandbox cannot locate any binaries on a Guix
+              ;; system because every "system" path resolves into
+              ;; /gnu/store/<hash>-pkg/bin/...
+              (substitute* "linux-sandbox/src/bwrap.rs"
+                (("\"/nix/store\"") "\"/gnu/store\""))))
           (add-after 'chdir-to-workspace 'patch-hardcoded-paths
             (lambda* (#:key inputs #:allow-other-keys)
               (let ((bash-bin (string-append
@@ -325,6 +685,14 @@
                    (string-append "\"" bash-bin "/bash "))
                   (("\"/bin/sh ")
                    (string-append "\"" bash-bin "/sh "))
+                  ;; Single-quoted paths in test assertion strings,
+                  ;; e.g. "exec '/bin/bash' -c ...".  Must match the
+                  ;; double-quoted substitutions above so both sides
+                  ;; of assert_eq!/contains use the store path.
+                  (("'/bin/bash'")
+                   (string-append "'" bash-bin "/bash'"))
+                  (("'/bin/sh'")
+                   (string-append "'" bash-bin "/sh'"))
                   ;; coreutils.
                   (("\"/bin/(cat|cp|date|echo|head|ls|rm|sleep|true|touch)\"" all cmd)
                    (string-append "\"" coreutils-bin "/" cmd "\""))
@@ -339,28 +707,132 @@
                    (string-append "\"" git-bin "/git\""))
                   (("\"/usr/bin/sed\"")
                    (string-append "\"" sed-bin "/sed\"")))
+                ;; Bare Command::new("git") and Command::new("ls")
+                ;; in codex source files that exec internally.
+                (substitute* (find-files "git-utils" "\\.rs$")
+                  (("Command::new\\(\"git\"\\)")
+                   (string-append "Command::new(\"" git-bin "/git\")")))
+                (substitute* "tui/src/get_git_diff.rs"
+                  (("Command::new\\(\"git\"\\)")
+                   (string-append "Command::new(\"" git-bin "/git\")")))
+                (substitute* "core/src/turn_diff_tracker.rs"
+                  (("Command::new\\(\"git\"\\)")
+                   (string-append "Command::new(\"" git-bin "/git\")")))
+                (substitute* "cloud-tasks/src/env_detect.rs"
+                  (("Command::new\\(\"git\"\\)")
+                   (string-append "Command::new(\"" git-bin "/git\")")))
+                (substitute* "core/src/plugins/startup_sync.rs"
+                  (("\"git\",")
+                   (string-append "\"" git-bin "/git\",")))
+                (substitute* "file-search/src/lib.rs"
+                  (("Command::new\\(\"ls\"\\)")
+                   (string-append "Command::new(\"" coreutils-bin "/ls\")")))
+                ;; Neutralize pager with absolute path to cat.
+                (substitute* "core/src/unified_exec/process_manager.rs"
+                  (("\"PAGER\", \"cat\"")
+                   (string-append "\"PAGER\", \"" coreutils-bin "/cat\""))
+                  (("\"GIT_PAGER\", \"cat\"")
+                   (string-append "\"GIT_PAGER\", \"" coreutils-bin "/cat\""))
+                  (("\"GH_PAGER\", \"cat\"")
+                   (string-append "\"GH_PAGER\", \"" coreutils-bin "/cat\"")))
+                ;; Bare /bin/sleep inside a format! string
+                ;; (no surrounding double quotes, so the main
+                ;; pattern does not match).
+                (substitute*
+                  "shell-escalation/src/unix/escalate_server.rs"
+                  (("/bin/sleep")
+                   (string-append coreutils-bin "/sleep")))
                 ;; @SHELL@ placeholder from test-shebangs patch
                 (substitute*
                   (list "rmcp-client/src/program_resolver.rs"
                         "tui/src/external_editor.rs")
                   (("@SHELL@")
                    (string-append bash-bin "/sh")))
-                ;; shebang in test-only file
+                ;; Shebangs inside raw string literals (r#"..."#)
+                ;; that are written to scripts at runtime.  The
+                ;; main "/bin/sh" patterns only match double-quoted
+                ;; occurrences; these shebangs have no surrounding
+                ;; double quotes.
                 (substitute*
-                  "core/tests/suite/user_notification.rs"
+                  (list "core/src/plugins/startup_sync_tests.rs"
+                        "core/src/tools/runtimes/shell/unix_escalation_tests.rs"
+                        "core/tests/suite/client.rs"
+                        "core/tests/suite/js_repl.rs"
+                        "core/tests/suite/skill_approval.rs"
+                        "core/tests/suite/user_notification.rs"
+                        "exec-server/tests/file_system.rs"
+                        "login/src/auth/auth_tests.rs"
+                        "models-manager/src/manager_tests.rs"
+                        "sandboxing/src/bwrap_tests.rs")
                   (("#!/bin/bash")
-                   (string-append "#!" bash-bin "/bash"))))))
+                   (string-append "#!" bash-bin "/bash"))
+                  (("#!/bin/sh")
+                   (string-append "#!" bash-bin "/sh")))
+                ;; Test helpers pass env: Default::default() to the
+                ;; spawn code which calls env_clear(), leaving
+                ;; processes with no PATH.  Inject the build-time
+                ;; PATH so tests find coreutils, bash, etc.
+                (substitute* (find-files "." "\\.rs$")
+                  (("env: Default::default\\(\\)")
+                   (string-append
+                    "env: std::env::var(\"PATH\")"
+                    ".into_iter()"
+                    ".map(|p| (\"PATH\".to_string(), p))"
+                    ".collect()")))
+                ;; Test-only absolute path; bare name works via PATH.
+                (substitute* "exec-server/tests/exec_process.rs"
+                  (("\"/usr/bin/python3\"")
+                   "\"python3\""))
+                ;; Same empty-env issue but in JSON literals
+                ;; (serde_json::json! macro).
+                (substitute* "exec-server/tests/process.rs"
+                  (("\"env\": \\{\\}")
+                   (string-append
+                    "\"env\": {\"PATH\": \""
+                    (getenv "PATH")
+                    "\"}"))))))
+          (add-before 'build 'set-bubblewrap-source
+            (lambda* (#:key inputs #:allow-other-keys)
+              (setenv "CODEX_BWRAP_SOURCE_DIR"
+                      (string-append
+                       (assoc-ref inputs "bubblewrap-source")
+                       "/"))))
+          (add-before 'build 'create-node-version-file
+            (lambda _
+              (call-with-output-file "guix-vendor/node-version.txt"
+                (lambda (port)
+                  (display "22.22.0" port)))))
           (add-before 'check 'set-home
             (lambda _
-              (setenv "HOME" "/tmp")
-              (setenv "USER" "nixbld"))))))
-    (native-inputs (list clang              ;bindgen uses libclang to parse BoringSSL's C headers
-                         cmake-minimal    ;BoringSSL is compiled from C source
-                         libunwind        ;BoringSSL tests verify stack unwinding in assembly
-                         perl python-minimal ;for tests
-                         pkg-config))
+              ;; HOME must not be a prefix of /tmp, otherwise
+              ;; the TUI's path shortener replaces /tmp/... with
+              ;; ~/... and 30 snapshot tests fail.
+              (setenv "HOME" "/tmp/guix-home")
+              (mkdir-p "/tmp/guix-home")
+              (setenv "USER" "nixbld")
+              ;; Default libtest thread stack is 2 MiB, which is not
+              ;; enough for tokio current_thread tests that drive
+              ;; codex-core's full turn pipeline.  Upstream gates such
+              ;; tests through run_current_thread_test_with_stack (4 MiB)
+              ;; in app-server/src/message_processor/tracing_tests.rs;
+              ;; raise the global default so future additions that
+              ;; forget the wrapper still pass.
+              (setenv "RUST_MIN_STACK" "8388608")
+              ;; Disable network access.
+              (setenv "CODEX_SANDBOX_NETWORK_DISABLED" "1"))))))
+    (native-inputs `(("bubblewrap" ,bubblewrap) ;tests need bwrap on PATH
+                     ("clang" ,clang)
+                     ("cmake-minimal" ,cmake-minimal)
+                     ("libunwind" ,libunwind)
+                     ("lsof" ,lsof)            ;app-server tests
+                     ("nss-certs-for-test" ,nss-certs-for-test) ;OTLP gRPC TLS
+                     ("perl" ,perl)
+                     ("procps" ,procps)         ;tests use ps
+                     ("python-minimal" ,python-minimal)
+                     ("pkg-config" ,pkg-config)
+                     ("bubblewrap-source" ,(package-source bubblewrap))))
     (inputs (cons* bash-minimal coreutils git-minimal sed
-                   openssl sqlite `(,zstd "lib")
+                   libcap oniguruma openssl sqlite zlib `(,zstd "lib")
                    (cargo-inputs 'codex)))
     (home-page "https://github.com/openai/codex")
     (synopsis "AI-assisted coding CLI and TUI")
@@ -368,13 +840,15 @@
      "Codex is an AI-powered coding assistant that runs in the terminal.
 It provides an interactive TUI for conversations with AI models, with
 support for shell command execution, file editing, and code generation.
-Configure providers via @file{~/.codex/config.toml}.")
+Configure providers via @file{~/.codex/config.toml}.
+
+codex-code-mode's V8 Javascript executor is disabled.")
     (license license:asl2.0)))
 
 (define-public codex-acp
   (package
     (name "codex-acp")
-    (version "0.9.2")
+    (version "0.11.1")
     (source
      (origin
        (method git-fetch)
@@ -383,9 +857,8 @@ Configure providers via @file{~/.codex/config.toml}.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "190sq6s6jfz8dkj1y8305r7x6ln86qqr2j1bnfjci7f1x2wyzmsj"))
-       (patches (search-patches "codex-acp-0.9.2-remove-patch-sections.patch"
-                                "codex-acp-0.9.2-replace-result-flatten.patch"))))
+        (base32 "1rlgkbvrbdl5jhf49sjn2mifn2rq6z0vwf0gard23y1bz6sr3wmr"))
+       (patches (search-patches "codex-acp-0.11.1-remove-patch-sections.patch"))))
     (build-system cargo-build-system)
     (arguments
      (list
@@ -393,13 +866,43 @@ Configure providers via @file{~/.codex/config.toml}.")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-codex-deps
-            (lambda _
+            (lambda* (#:key inputs #:allow-other-keys)
               ;; Rewrite git dependencies to use vendored sources from rust-codex
               (substitute* "Cargo.toml"
-                (("git = \"https://github.com/zed-industries/codex\", branch = \"acp\"")
-                 "version = \"0.0.0\"")))))))
-    (native-inputs (list pkg-config))
-    (inputs (cons* openssl sqlite `(,zstd "lib") (cargo-inputs 'codex-acp)))
+                (("git = \"https://github.com/openai/codex\", tag = \"rust-v0.117.0\"")
+                 "version = \"0.117.0\""))
+              ;; Disable V8 runtime in codex-code-mode (transitive dep).
+              (let ((port (open-file "Cargo.toml" "a")))
+                (display "
+[dependencies.codex-code-mode]
+version = \"0.117.0\"
+default-features = false
+" port)
+                (close-port port))
+              ;; Point codex-linux-sandbox at system bubblewrap source.
+              (setenv "CODEX_BWRAP_SOURCE_DIR"
+                      (string-append
+                       (assoc-ref inputs "bubblewrap-source")
+                       "/"))))
+          (add-before 'check 'set-home
+            (lambda _
+              (setenv "HOME" "/tmp")
+              (setenv "USER" "nixbld")))
+          (add-before 'build 'create-node-version-file
+            (lambda _
+              ;; codex-core's js_repl uses include_str! to read
+              ;; node-version.txt four directories up from its source;
+              ;; create it where the vendored crate expects it.
+              (call-with-output-file "guix-vendor/node-version.txt"
+                (lambda (port)
+                  (display "22.22.0" port))))))))
+    (native-inputs
+     `(("cmake-minimal" ,cmake-minimal)
+       ("clang" ,clang)
+       ("pkg-config" ,pkg-config)
+       ("bubblewrap-source" ,(package-source bubblewrap))))
+    (inputs (cons* libcap openssl sqlite zlib `(,zstd "lib")
+                   (cargo-inputs 'codex-acp)))
     (home-page "https://github.com/zed-industries/codex-acp")
     (synopsis "ACP-compatible agent bridging Zed Codex with ACP clients")
     (description

gnu/packages/containers.scm

@@ -150,7 +150,7 @@ as created by Podman, CRI-O and containerd.")))
 (define-public crun
   (package
     (name "crun")
-    (version "1.25.1")
+    (version "1.26")
     (source
      (origin
        (method url-fetch)
@@ -160,7 +160,7 @@ as created by Podman, CRI-O and containerd.")))
              "/crun-" version ".tar.gz"))
        (sha256
         (base32
-         "02kksvnja234k8mpq5j7yms8npbpvh8iz3k03h21lwcqzqsb88rx"))))
+         "1hdwk5dpsz9danxiyfli07b7sqid6hr34qmhs5qjl2dcc00is89j"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/cpp.scm

@@ -44,7 +44,7 @@
 ;;; Copyright © 2024 Jakob Kirsch <jakob.kirsch@web.de>
 ;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez@gmail.com>
-;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
+;;; Copyright © 2025, 2026 Ashish SHUKLA <ashish.is@lostca.se>
 ;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;; Copyright © 2025 Romain Garbage <romain.garbage@inria.fr>
 ;;; Copyright © 2024, 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
@@ -3360,7 +3360,7 @@ which can evaluate Jsonnet files and expressions.")))
 (define-public simdjson
   (package
     (name "simdjson")
-    (version "3.13.0")
+    (version "4.6.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3369,7 +3369,7 @@ which can evaluate Jsonnet files and expressions.")))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "005yli56nrkvlyx9g9cq8dczk42r9a18l162i2s5k81lj3y7mcrp"))))
+                "0729mxnc2wjb94gr4znwlzfmgw5w2v9kd8glvn3vnjhkdnd87zry"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f                      ; tests require downloading dependencies
@@ -3608,7 +3608,7 @@ std::wstring, etc).")
 (define-public fast-float
   (package
     (name "fast-float")
-    (version "8.0.2")
+    (version "8.2.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3617,7 +3617,7 @@ std::wstring, etc).")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "19x1yklf641yrpad6lk4cq3jmird10d5ig8hicm3p9lxh92k78cl"))))
+                "1l13nsl4sgq71m7aifrmmmfyl14vp48vqdh7pb50hxqq6f8bq2b5"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -3628,12 +3628,10 @@ std::wstring, etc).")
           (add-after 'unpack 'patch-cmake-tests
             (lambda* (#:key inputs native-inputs #:allow-other-keys)
               (substitute* "tests/CMakeLists.txt"
-                (("FetchContent_GetProperties\\(supplemental_test_files.*")
-                 "")
-                (("if\\(NOT supplemental_test_files_POPULATED.*")
+                (("FetchContent_MakeAvailable\\(supplemental_test_files.*")
                  (string-append
                   "set(supplemental_test_files_BINARY_DIR "
-                  #$fast-float-test-files ")\nif(0)\n"))))))))
+                  #$fast-float-test-files ")\n"))))))))
     (native-inputs (list doctest fast-float-test-files))
     (home-page "https://github.com/fastfloat/fast_float")
     (synopsis "Floating point number parser for C++")

gnu/packages/crypto.scm

@@ -276,18 +276,17 @@ Ed448-Goldilocks and Curve448, using the Decaf encoding.")
 (define-public libsodium
   (package
     (name "libsodium")
-    (version "1.0.18")
-    (source (origin
-            (method url-fetch)
-            (uri (list (string-append
-                        "https://download.libsodium.org/libsodium/"
-                        "releases/libsodium-" version ".tar.gz")
-                       (string-append
-                        "https://download.libsodium.org/libsodium/"
-                        "releases/old/libsodium-" version ".tar.gz")))
-            (sha256
-             (base32
-              "1h9ncvj23qbbni958knzsli8dvybcswcjbx0qjjgi922nf848l3g"))))
+    (version "1.0.22")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/jedisct1/libsodium")
+              (commit (string-append version "-RELEASE"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "05lqdn6nzldsia5mv5a9xfvc5k0kybh9snwv7qsb135gva4bpjwk"))))
     (build-system gnu-build-system)
     (synopsis "Portable NaCl-based crypto library")
     (description

gnu/packages/databases.scm

@@ -70,6 +70,7 @@
 ;;; Copyright © 2025 bdunahu <bdunahu@operationnull.com>
 ;;; Copyright © 2026 Spencer King <spencer.king@wustl.edu>
 ;;; Copyright © 2026 Peter Polidoro <peter@polidoro.io>
+;;; Copyright © 2026 Josep Bigorra <jjbigorra@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -126,6 +127,7 @@
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
+  #:use-module (gnu packages guile-xyz)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages language)
@@ -198,6 +200,7 @@
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
+  #:use-module (guix build-system guile)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
@@ -5046,6 +5049,54 @@ postgresql = postgresql://nixbld@/yoyo_test~%")))
 files or Python scripts that define a list of migration steps.")
     (license license:asl2.0)))
 
+(define-public mutastructura
+  (package
+    (name "mutastructura")
+    (version "0.6.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/jjba23/mutastructura")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "08vzlc5imavqf3bdzgbh70c7z44xjhf05gr7i2g5ksl49lv39gzh"))))
+    (build-system guile-build-system)
+    (arguments
+     (list
+      #:source-directory "src"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'install-program-files
+            (lambda _
+              (let* ((bin (string-append #$output "/bin"))
+                     (share (string-append #$output "/share")))
+                (copy-recursively "resources"
+                                  (string-append share "/resources"))
+                (install-file "scripts/mutastructura" bin)
+                (install-file "scripts/log.bash"
+                              (string-append share "/scripts/"))
+                (chmod (string-append bin "/mutastructura") #o755)))))))
+    (native-inputs (list guile-3.0))
+    (propagated-inputs (list guile-dbi
+                             guile-dbd-mysql
+                             guile-dbd-sqlite3
+                             guile-dbd-postgresql
+                             guile-gcrypt))
+    (inputs (list guile-3.0 bash-minimal))
+    (home-page "https://codeberg.org/jjba23/mutastructura")
+    (synopsis "Relational database schema migrations powered by Guile Scheme")
+    (description
+     "Mutastructura provides a familiar, declarative and transactional
+approach to managing database states. It exposes a user-friendly 
+@acronym{CLI, command-line interface} and has support for PostgreSQL, MySQL, and SQLite.
+It also exposes library functions and can be imported and used directly from other Guile code.
+
+Features include executing migrations transactionally and computing SHA256
+checksums to track schema evolution in a @code{migrations_history} table.")
+    (license license:agpl3+)))
+
 (define-public python-mysqlclient
   (package
     (name "python-mysqlclient")

gnu/packages/disk.scm

@@ -31,7 +31,7 @@
 ;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2024-2025 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
-;;; Copyright © 2025 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2025, 2026 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2025 Grigory Shepelev <shegeley@gmail.com>
 ;;; Copyright © 2026 Luis Guilherme Coelho <lgcoelho@disroot.org>
 
@@ -94,6 +94,8 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-compression)
   #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages graphics)
   #:use-module (gnu packages gtk)
@@ -420,6 +422,49 @@ tables, and it understands a variety of different formats.")
 similarity.")
     (license license:gpl3+)))
 
+(define-public gdu
+  (package
+    (name "gdu")
+    (version "5.35.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dundee/gdu")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "051xf3wncdiavjwyl9djmni5vd2dqjgn6drkw2nm21c9l0rjfv6d"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:install-source? #f
+      #:import-path "github.com/dundee/gdu/v5/cmd/gdu"
+      #:unpack-path "github.com/dundee/gdu/v5"))
+    (native-inputs
+     (list go-github-com-dgraph-io-badger-v4
+           go-github-com-fatih-color
+           go-github-com-gdamore-tcell-v2
+           go-github-com-h2non-filetype
+           go-github-com-maruel-natural
+           go-github-com-mattn-go-isatty
+           go-github-com-pkg-errors
+           go-github-com-rivo-tview
+           go-github-com-sirupsen-logrus
+           go-github-com-spf13-cobra
+           go-github-com-stretchr-testify
+           go-github-com-ulikunitz-xz
+           go-golang-org-x-sys
+           go-golang-org-x-text
+           go-gopkg-in-yaml-v3
+           go-modernc-org-sqlite))
+    (home-page "https://github.com/dundee/gdu")
+    (synopsis "Disk usage analyzer")
+    (description "Gdu is a disk usage analyzer written in Go.  It is intended
+primarily for SSD disks where it can fully utilize parallel processing, but it
+also works on HDDs.")
+    (license license:expat)))
+
 (define-public gpart
   ;; The latest (0.3) release is from 2015 and is missing a crash fix.
   (let ((commit "ec03350a01ad69708b5a3e2d47b8e002b0eba6c9")

gnu/packages/duckdb.scm

@@ -148,13 +148,13 @@ system.")
 (define-public r-duckdb
   (package
     (name "r-duckdb")
-    (version "1.5.1")
+    (version "1.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "duckdb" version))
        (sha256
-        (base32 "177621m08whqqk4yhj3zrr08l3d9hhlqh3gm9jzhi5cplg47cksq"))
+        (base32 "1dldlfwvc33czvlxfmwaj4p9y6sjjj5iqy98yda47a8kclrqmyam"))
        ;; This package bundles the duckdb sources and builds a custom variant
        ;; of duckdb.  I'd be happy to link it with our duckdb library instead,
        ;; but it does not seem possible to do that.

gnu/packages/elixir-i18n.scm

@@ -290,7 +290,7 @@ based upon the Common Locale Data Repository (CLDR).")
   (package
     (inherit elixir-ex-cldr-minimal)
     (name "elixir-ex-cldr")
-    (version "2.43.2")
+    (version "2.47.2")
     (source
      (origin
        ;; The hex.pm package ships only the en locale.
@@ -300,7 +300,7 @@ based upon the Common Locale Data Repository (CLDR).")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1wgwp74ya0gkvd5pk4qv9s38p85r5yw370y4wv7jywy3hrbrj9f5"))))
+        (base32 "1rivy61aq0c9zfklm4bpvvkj7lzjgy316rwxl8qz92xqp6xa292y"))))
     (arguments
      (list
       #:phases

gnu/packages/elixir-web.scm

@@ -303,7 +303,17 @@ purposes.  Its goal is to be as close as possible to
      (list
       #:test-flags
       ;; These tests require network access to badssl.com.
-      #~(list "--exclude" "network")))
+      #~(list "--exclude" "network")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'make-reproducible
+            (lambda _
+              ;; Buffer size has been increased in OTP 28+. For more info see:
+              ;; https://github.com/erlang/otp/issues/9722#issuecomment-2808683303
+              (substitute* "test/httpoison_test.exs"
+                (("stream/20") "stream/100")
+                (("<= expected_length") "<= expected_length * 1.1")
+                ((">= max_length") ">= max_length * 0.9")))))))
     (native-inputs
      (list erlang-cowboy
            elixir-earmark

gnu/packages/emacs-xyz.scm

@@ -56,7 +56,7 @@
 ;;; Copyright © 2019 Jelle Licht <jlicht@fsfe.org>
 ;;; Copyright © 2019 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2019 Stephen Webber <montokapro@gmail.com>
-;;; Copyright © 2019, 2021 Liliana Marie Prikler <liliana.prikler@gmail.com>
+;;; Copyright © 2019, 2021—2026 Liliana Marie Prikler <liliana.prikler@gmail.com>
 ;;; Copyright © 2019 David Wilson <david@daviwil.com>
 ;;; Copyright © 2020 Paul Garlick <pgarlick@tourbillion-technology.com>
 ;;; Copyright © 2020 Robert Smith <robertsmith@posteo.net>
@@ -147,7 +147,7 @@
 ;;; Copyright © 2024 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2024, 2025 Spencer King <spencer.king@wustl.edu>
 ;;; Copyright © 2024 emma thompson <bigbookofbug@proton.me>
-;;; Copyright © 2024-2025 Liam Hupfer <liam@hpfr.net>
+;;; Copyright © 2024-2026 Liam Hupfer <liam@hpfr.net>
 ;;; Copyright © 2024-2025 Alvin Hsu <aurtzy@gmail.com>
 ;;; Copyright © 2024 Olivier Rojon <o.rojon@posteo.net>
 ;;; Copyright © 2024 Divya Ranjan Pattanaik <divya@subvertising.org>
@@ -656,6 +656,30 @@ supported algorithm is chosen to ensure interoperability with
 Emacs Lisp.")
     (license license:gpl3)))
 
+(define-public emacs-org-arbeitszeit
+  (package
+    (name "emacs-org-arbeitszeit")
+    (version "0.0.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/bkaestner/org-arbeitszeit")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0krxainwpn7bnnvbrrhivmh302i9dyfixs6l5wb7xw7qpjgwqzc8"))))
+    (build-system emacs-build-system)
+    (arguments (list #:tests? #f))      ; no tests
+    (home-page "https://github.com/bkaestner/org-arbeitszeit")
+    (synopsis "Calculate your worktime")
+    (description
+     "This package provides a new dynamic block for Org called \"arbeitszeit\"
+(German for \"working hours\").  The dynamic block collects all clocked hours and
+provides a weekly table to quickly see your accumulated overtime.  To insert a
+new block, use @samp{M-x org-dynamic-block-insert-dblock}.")
+    (license license:gpl3+)))
+
 (define-public emacs-perl-doc
   (package
     (name "emacs-perl-doc")
@@ -757,6 +781,54 @@ balance windows (keeping them roughly the same size) whenever the window
 configuration changes, e.g. after splitting or deleting a window.")
       (license license:bsd-3))))
 
+(define-public emacs-ben
+  (package
+    (name "emacs-ben")
+    (version "0.12.11")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/pastor/ben.el")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0iqrk87dl567vwpwm8rmplrpva475a04s6c34rm24xfy2m7wrwk6"))))
+    (build-system emacs-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-environment
+            (lambda _
+              ;; Since the testsuite uses `direnv', the build needs a home
+              ;; directory so `direnv' can allow the contents of the `.envrc`
+              ;; files generated for the different tests.
+              (setenv "HOME" "/tmp")
+              (setenv "OFFLINE" "1") ;Enable offline tests.
+              (emacs-substitute-variables "ben.el"
+                ("ben-direnv-executable"
+                 #$(file-append (this-package-input "direnv")
+                                "/bin/direnv"))))))))
+    (inputs (list direnv))
+    (propagated-inputs (list emacs-inheritenv))
+    (home-page "https://codeberg.org/pastor/ben.el")
+    (synopsis "Asynchronous buffer-local environments via @command{direnv}")
+    (description
+     "This package allows you to load environments buffer locally.  The
+package is named @command{ben}, which stands for Buffer ENvironments.
+
+The project relies on @uref{https://direnv.net, direnv} which allows setting
+per-directory environments through @file{.envrc} files.
+
+The main improvement of @command{ben} over @command{envrc} is the asynchronous
+processing of environments, which prevents Emacs from freezing.  This is
+especially useful while loading computationally heavy environments, such when
+loading @file{.envrc} files that rely on Guix.  In these cases, computations
+can take hours to complete.  This package aims to facilitate loading such
+environments in the background.")
+    (license license:gpl3+)))
+
 (define-public emacs-bookmark-plus
   (package
     (name "emacs-bookmark-plus")
@@ -834,7 +906,7 @@ input via a small child-frame spawned at the position of the cursor.")
 (define-public emacs-arei
   (package
     (name "emacs-arei")
-    (version "0.9.6")
+    (version "0.9.7")
     (source
      (origin
        (method git-fetch)
@@ -844,10 +916,13 @@ input via a small child-frame spawned at the position of the cursor.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1m8ic5pcshz2y2maxvbgg70n4k2kgxvj98zisqal15j7djz0hzji"))))
+         "1fp4l8rzfd7cds80p8c9jgwwlb7rsw35djh0hs50g89h937w5s02"))))
     (build-system emacs-build-system)
-    (arguments (list #:tests? #f))      ; no tests
-    (propagated-inputs (list emacs-eros emacs-sesman emacs-queue))
+    (arguments
+     (list #:lisp-directory "lisp"
+           #:tests? #f))                ; no tests
+    (propagated-inputs
+     (list emacs-consult emacs-eros emacs-sesman emacs-queue))
     (home-page "https://git.sr.ht/~abcdw/emacs-arei")
     (synopsis "Asynchronous Reliable Extensible IDE")
     (description "Sleek Guile IDE for Emacs.")
@@ -13518,8 +13593,8 @@ for compilation, debugging, documentation lookup, and so on.")
     (license (list license:gpl2+ license:public-domain))))
 
 (define-public emacs-sliver
-  (let ((commit "d08d41947bb943f25ee2de9573459a6c720e027f")
-        (revision "0"))
+  (let ((commit "b4cb9cd2a810ba59c946e2592c4a4d56060a8d22")
+        (revision "1"))
     (package
       (name "emacs-sliver")
       ;; No tagged releases. Version comes from source code.
@@ -13532,7 +13607,7 @@ for compilation, debugging, documentation lookup, and so on.")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "08qycim0mxyiqbik9hjlmzpdggl506bcsv1q1icxzd05bm73sh6n"))))
+          (base32 "1wddivmp5f4m6fdib96vfylqp4kgcw3ipdsi4b9w50dqzvrqrfjh"))))
       (build-system emacs-build-system)
       (arguments
        (list
@@ -15797,8 +15872,16 @@ versions utilizing Consult's internal API.")
     (arguments
      (list
       #:tests? #f                       ;no tests
-      #:include #~(cons "^extensions\\/consult-eglot-embark"
-                        %default-include)))
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; Move the extensions source files to the top level, which is
+          ;; included in the EMACSLOADPATH.
+          (add-after 'unpack 'move-source-files
+            (lambda _
+              (let ((el-files (find-files "./extensions" ".*\\.el$")))
+                (for-each (lambda (f)
+                            (rename-file f (basename f)))
+                          el-files)))))))
     (propagated-inputs (list emacs-consult emacs-eglot emacs-embark))
     (home-page "https://github.com/mohkale/consult-eglot")
     (synopsis "Consulting-read interface for eglot")
@@ -25071,7 +25154,7 @@ lines, and @code{gc} to comment out the target of a motion.")
 (define-public emacs-eglot
   (package
     (name "emacs-eglot")
-    (version "1.21")
+    (version "1.23")
     (source
      (origin
        (method url-fetch)
@@ -25079,7 +25162,7 @@ lines, and @code{gc} to comment out the target of a motion.")
                            ".tar"))
        (sha256
         (base32
-         "03fx22rv8ijxq0jnn7xlfqhkpk2b109ygpjbcchp41sa4q7d6nbl"))))
+         "1l83c90rdamlk576bd859jkg6406hgxi7w4c6ixlw509c66qr3s6"))))
     (build-system emacs-build-system)
     (propagated-inputs
      (list emacs-eldoc
@@ -28516,7 +28599,7 @@ unstructured, meant for quick @code{JavaScript} experiments.")
 (define-public emacs-firefox-release-notes
   (package
     (name "emacs-firefox-release-notes")
-    (version "1.7")
+    (version "1.8")
     (source
      (origin
        (method git-fetch)
@@ -28527,7 +28610,7 @@ unstructured, meant for quick @code{JavaScript} experiments.")
           (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1i9ncnn0qys0v0bqw87jwx0sa2g31n1i1gfr9zqdml3hakyz8b5f"))))
+        (base32 "13ymnx4vgiq5f3cjk3zddrq4xnv6116j5zzza67v98q7rsvzl049"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -32038,6 +32121,31 @@ leverages the Parinfer Rust Emacs library to do most of the heavy lifting.")
 bookmarks and history.")
     (license license:gpl3+)))
 
+(define-public emacs-shr-syntax-highlight
+  (package
+    (name "emacs-shr-syntax-highlight")
+    (version "0.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/coopi/emacs-shr-syntax-highlight")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "04ax8svpw2s0085pp93dsz5xhhbqr58ghkr1ab2g38pczlsbz18s"))))
+    (build-system emacs-build-system)
+    (home-page "https://codeberg.org/coopi/emacs-shr-syntax-highlight")
+    (synopsis "Syntax highlighting for code blocks rendered by shr")
+    (description
+     "This package adds syntax highlighting to @code{<pre>} code blocks
+rendered by @acronym{@code{shr}, Simple @acronym{HTML, HyperText Markup
+Language} Renderer}, used by @acronym{EWW, Emacs Web Wowser} and similar
+interfaces.  It reads @acronym{CSS, Cascading Style Sheets} class annotations
+such as @code{language-python} and fontifies block contents using the
+corresponding Emacs major mode.")
+    (license license:agpl3+)))
+
 (define-public emacs-stumpwm-mode
     (let ((commit "920f8fc1488f7953f205e1dda4c2ecbbbda56d6")
         (revision "3"))
@@ -39802,7 +39910,7 @@ user interfaces for various built-in modes.")
 (define-public emacs-calibredb
   (package
     (name "emacs-calibredb")
-    (version "2.13.0")
+    (version "2.14.0")
     (source
      (origin
        (method git-fetch)
@@ -39811,31 +39919,40 @@ user interfaces for various built-in modes.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1a4gyc3gcq18j29pw2i296d70nvx5fbzlw9fdmqwzncciqz5as6m"))))
+        (base32 "1g0jg6a6fgvxd5bsydckbqwf899d2d9732laz4k1k476mbws5dqy"))))
     (build-system emacs-build-system)
     (arguments
      (list
+      #:include #~(cons "\\.py$" %default-include)
+      #:tests? #f                       ;no tests
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-paths
             (lambda* (#:key inputs #:allow-other-keys)
-              (make-file-writable "calibredb-core.el")
               (let ((calibredb (search-input-file inputs "/bin/calibredb"))
                     (fetch-ebook-metadata
                      (search-input-file inputs "/bin/fetch-ebook-metadata"))
                     (ebook-convert
                      (search-input-file inputs "/bin/ebook-convert"))
                     (calibre-debug
-                     (search-input-file inputs "/bin/calibre-debug")))
+                     (search-input-file inputs "/bin/calibre-debug"))
+                    (ebook-meta
+                     (search-input-file inputs "/bin/ebook-meta"))
+                    (folder-program
+                     (string-append #$output
+                                    "/share/emacs/site-lisp/calibredb-"
+                                    #$version "/calibredb-folder.py")))
                 (emacs-substitute-variables "calibredb-core.el"
                   ("calibredb-fetch-metadata-program" fetch-ebook-metadata)
                   ("calibredb-program" calibredb)
                   ("calibredb-convert-program" ebook-convert)
-                  ("calibredb-debug-program" calibre-debug))))))))
+                  ("calibredb-debug-program" calibre-debug)
+                  ("calibredb-ebook-meta-program" ebook-meta)
+                  ("calibredb-folder-program" folder-program))))))))
     (inputs
      (list calibre))
     (propagated-inputs
-     (list emacs-dash emacs-esxml emacs-s))
+     (list emacs-dash emacs-esxml emacs-request emacs-s))
     (home-page "https://github.com/chenyanming/calibredb.el")
     (synopsis "Yet another calibre client for Emacs")
     (description "This package integrates calibre into Emacs.
@@ -41433,17 +41550,65 @@ time.")
     (build-system emacs-build-system)
     (arguments
      (list
-      #:tests? #f ; requires cask
-      #:phases #~(modify-phases %standard-phases
-                   ;; Move the source files to the top level, which is
-                   ;; included in the EMACSLOADPATH.
-                   (add-after 'unpack 'move-source-files
-                     (lambda _
-                       (let ((el-files (find-files "./lisp" ".*\\.el$")))
-                         (for-each (lambda (f)
-                                     (rename-file f
-                                                  (basename f)))
-                                   el-files)))))))
+      #:test-command #~(list "make" "tests")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; Move the source files to the top level, which is
+          ;; included in the EMACSLOADPATH.
+          (add-after 'unpack 'move-source-files
+            (lambda _
+              (let ((el-files (find-files "./lisp" ".*\\.el$")))
+                (for-each (lambda (f)
+                            (rename-file f
+                                         (basename f)))
+                          el-files))))
+          (add-before 'check 'fix-tests
+            (lambda _
+              (substitute* "Makefile"
+                (("cask") ""))
+              (substitute* "test/ert-helper.el"
+                (("lisp\\/") ""))))
+          (add-before 'check 'skip-failing-tests
+            (lambda _
+              (let-syntax
+                  ((disable-tests
+                    (syntax-rules ()
+                      ((_ file ())
+                       (syntax-error "test names list must not be empty"))
+                      ((_ file (test-name ...))
+                       (substitute* file
+                         (((string-append
+                            "^\\(ert-deftest " test-name ".*") all)
+                          (string-append all "(skip-unless nil)\n")) ...)))))
+                (disable-tests
+                 "test/mastodon-profile-tests.el"
+                 ("mastodon-profile--add-author-bylines"
+                  "mastodon-profile--make-author-buffer"))
+                (disable-tests
+                 "test/mastodon-auth-tests.el"
+                 ("mastodon-auth--handle-token-response--good"
+                  "mastodon-auth-plstore-token-check"))
+                (disable-tests
+                 "test/mastodon-client-tests.el"
+                 ("mastodon-client--make-user-active"
+                  "mastodon-client--store"
+                  "mastodon-client--store-access-token"))
+                (disable-tests
+                 "test/mastodon-tl-tests.el"
+                 ("mastodon-tl--byline-timestamp-has-relative-display"
+                  "mastodon-tl--next-tab-item--no-spaces-at-ends"
+                  "mastodon-tl--next-tab-item--with-spaces-at-ends"))
+                (disable-tests
+                 "test/mastodon-media-tests.el"
+                 ("mastodon-media--get-avatar-rendering"
+                  "mastodon-media--inline-images"
+                  "mastodon-media--load-image-from-url-avatar-with-imagemagic"
+                  "mastodon-media--load-image-from-url-avatar-without-imagemagic"
+                  "mastodon-media--load-image-from-url-media-link-with-imagemagic"
+                  "mastodon-media--load-image-from-url-media-link-without-imagemagic"
+                  "mastodon-media--load-image-from-url-url-fetching-fails"
+                  "mastodon-media--process-image-response"))))))))
+    (native-inputs (list emacs-el-mock))
     (propagated-inputs
      (list emacs-persist emacs-tp))
     (home-page "https://codeberg.org/martianh/mastodon.el")

gnu/packages/emulators.scm

@@ -3452,7 +3452,7 @@ This is a part of the TiLP project.")
 (define-public mame
   (package
     (name "mame")
-    (version "0.252")
+    (version "0.287")
     (source
      (origin
        (method git-fetch)
@@ -3461,16 +3461,16 @@ This is a part of the TiLP project.")
              (commit (apply string-append "mame" (string-split version #\.)))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "07qhcm1v47sy2wj30nx3cbhvcbgki0cl83gabr0miiw60fhgyn6j"))
+        (base32 "1p9v71gvaqiyj6sa1b0wkdksa9wnr6yr2a43ckycljjfas5s36kq"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled libraries.
         '(begin
            (with-directory-excursion "3rdparty"
              (for-each delete-file-recursively
-                       '("asio" "expat" "glm" "libflac" "libjpeg" "lua"
-                         "portaudio" "portmidi" "pugixml" "rapidjson" "SDL2"
-                         "SDL2-override" "sqlite3" "utf8proc" "zlib")))))))
+                       '("asio" "expat" "glm" "flac" "libjpeg" "lua"
+                         "portaudio" "portmidi" "pugixml" "rapidjson"
+                         "sqlite3" "utf8proc" "zlib")))))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -3604,7 +3604,9 @@ This is a part of the TiLP project.")
            libjpeg-turbo
            libxi
            libxinerama
-           lua
+           ;; MAME requires Lua compiled as C++ to work correctly.
+           ;; See https://www.mamedev.org/?p=523
+           lua-5.4-for-c++
            portaudio
            portmidi
            pugixml

gnu/packages/erlang.scm

@@ -50,7 +50,7 @@
 (define-public erlang
   (package
     (name "erlang")
-    (version "27.3.4.6")
+    (version "28.4.3")
     (source (origin
               (method git-fetch)
               ;; The tarball from http://erlang.org/download contains many
@@ -62,7 +62,7 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0dhz2c7w28ss0ypj7jh88pfs3kc8hbwiiq91in1j2miy5sn4cp3x"))
+                "1dsdmp2rccc0rhzy2w8r4amxmc6nr9hbi053j2s0bg9db30b48rc"))
               (patches (search-patches "erlang-man-path.patch"))))
     (build-system gnu-build-system)
     (native-inputs
@@ -75,7 +75,7 @@
                                "/OTP-" version "/otp_doc_man_" version ".tar.gz"))
            (sha256
             (base32
-             "1j1fcli7ma9vi4qyv67lq7yiznhpnfvcmh57bn8qxvha6ky2pngm"))))))
+             "1g17wzv8j12g9272yvv55nj4wqs09hxkv3i0vnp7d6gcs24bmphi"))))))
     (inputs
      (list ncurses openssl wxwidgets))
     (propagated-inputs

gnu/packages/fabric-management.scm

@@ -220,6 +220,7 @@ testing InfiniBand networks.")
                            "--disable-assertions"
                            "--disable-params-check"
 
+                           "--enable-mt"
                            (string-append "--with-verbs="
                                           #$(this-package-input "rdma-core"))
 

gnu/packages/finance.scm

@@ -165,7 +165,7 @@
   ;; <https://bitcoincore.org/en/lifecycle/#schedule>.
   (package
     (name "bitcoin-core")
-    (version "30.2")
+    (version "31.0")
     (source (origin
               (method url-fetch)
               (uri
@@ -173,7 +173,7 @@
                               version "/bitcoin-" version ".tar.gz"))
               (sha256
                (base32
-                "1jw4djh22v0nih0n7irdbknfbqavlc4l3b8176b5qgc88a60pl3g"))))
+                "1qxkcyq8nwq6sw4qi660z8n8356mqdsf4jvpq5ndkvrsx9gfz80b"))))
     (build-system qt-build-system)
     (arguments
      (list #:qtbase qtbase
@@ -197,9 +197,7 @@
                     "python3" "./test/functional/test_runner.py" "--timeout-factor=2"
                     (string-append "--jobs=" (number->string (parallel-job-count)))))))))
     (native-inputs
-     (list bash ; provides the sh command for system_tests
-           coreutils ; provides the cat, echo and false commands for system_tests
-           pkg-config
+     (list pkg-config
            python ; for the tests
            python-pyzmq ; for the tests
            qttools))

gnu/packages/fonts.scm

@@ -4658,46 +4658,6 @@ is a stylish type with a polished yet relaxed feel.  Its versatility makes it
 suitable for a wide range of uses.")
       (license license:silofl1.1))))
 
-(define-public font-cozette
-  (package
-    (name "font-cozette")
-    (version "1.13.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/slavfox/Cozette")
-                     (commit (string-append "v." version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "178i812n4sfsvid7jhnm683jlxqmrv4ck6qbb4nwyllhwg3gyq60"))))
-    (build-system font-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'dont-depend-on-git
-           (lambda _
-             (substitute* "build.py"
-               ;; Merely importing this module requires a git repository.
-               ;; We don't use get_changelog, so just disable the import.
-               (("from cozette_builder\\.changeloggen import get_changelog")
-                ""))))
-         (add-before 'install 'build
-           (lambda _
-             (invoke "python3" "build.py" "fonts"))))))
-    (native-inputs
-     (list fontforge
-           python
-           python-crayons
-           python-fonttools
-           python-numpy
-           python-pillow))
-    (home-page "https://github.com/slavfox/Cozette")
-    (synopsis "Bitmap programming font")
-    (description "Cozette is a 6x13px (bounding box) bitmap font based on Dina
-and heavily inspired by Creep.")
-    (license license:expat)))
-
 (define-public font-montserrat
   (package
     (name "font-montserrat")

gnu/packages/freedesktop.scm

@@ -3454,7 +3454,7 @@ interfaces.")
                            (string-append (assoc-ref outputs "out")
                                           "/share/doc/" ,name)))))))
     (native-inputs
-     (list cmake-minimal pkg-config))
+     (list cmake-minimal pkg-config scdoc))
     (inputs (list elogind
                   bash-minimal
                   grim

gnu/packages/games.scm

@@ -5534,23 +5534,13 @@ falling, themeable graphics and sounds, and replays.")
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f                  ;no test target
-           #:configure-flags #~'("-DENABLE_SYSTEM_LUA=ON")
-           #:phases
-           #~(modify-phases %standard-phases
-               (add-before 'configure 'pre-configure
-                 (lambda _
-                   ;; XXX: Our Lua doesn't have a C++ library, force C linkage.
-                   (substitute* '("src/lua/wrapper_lua.h"
-                                  "src/lua/wrapper_lualib.h"
-                                  "src/lua/wrapper_lauxlib.h")
-                     (("#include \"(lua|lualib|lauxlib)\\.h\"")
-                      "#include \"lua.hpp\"")))))))
+           #:configure-flags #~'("-DENABLE_SYSTEM_LUA=ON")))
     (inputs
      (list boost-1.83
            curl
            dbus
            libvorbis
-           lua-5.4
+           lua-5.4-for-c++
            openssl
            pango
            sdl2
@@ -5937,7 +5927,7 @@ Transport Tycoon Deluxe.")
           (add-after 'unpack 'patch-sources
             (lambda* (#:key inputs #:allow-other-keys)
               (substitute* "src/music/fluidsynth.cpp"
-                (("default_sf\\[\\] = \\{" all)
+                (("_default_soundfonts\\[\\] = \\{" all)
                  (string-append all "
 \t/* Guix hardcoded :P */
 \t\"" (search-input-file inputs "/share/soundfonts/FreePatsGM.sf2") "\",
@@ -5964,7 +5954,7 @@ Transport Tycoon Deluxe.")
   (package
     (inherit openttd)
     (name "openttd-jgrpp")
-    (version "0.70.2")
+    (version "0.71.1")
     (source
      (origin
        (method git-fetch)
@@ -5973,7 +5963,7 @@ Transport Tycoon Deluxe.")
              (commit (string-append "jgrpp-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1jzzvribf2cqvjl9cympyx9qpplljvmhqrrlw7aq4ckzl92d87z3"))))
+        (base32 "1cy1ghc1mc61hdz8lykx2ggs5nld30jdgj8y4vdli2v1ffhy7xy9"))))
     (inputs (modify-inputs inputs
               (append zstd harfbuzz)))
     (arguments

gnu/packages/geo.scm

@@ -425,14 +425,29 @@ hierarchical hexagonal geospatial indexing system")
                (base32
                 "00qdk9a4048pzfj2rhzkfw3lvm642znf6kr4x29i3d94494pxsnn"))))
     (build-system cmake-build-system)
-    (arguments `(#:phases
-                 (modify-phases %standard-phases
-                   (add-after
-                    'unpack 'patch-test-shebangs
-                    (lambda _
-                      (substitute* '("tests/xmltester/testrunner.sh"
-                                     "tests/xmltester/safe_to_xml.sh")
-                        (("/bin/sh") (which "sh"))))))))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ,@(if (or (target-x86-32?) (target-arm32?))
+               '((add-after 'unpack 'disable-broken-tests
+                   (lambda _
+                     ;; This test fails due to limited accuracy.
+                     (delete-file "tests/xmltester/tests/general/TestCentroid.xml")
+                     (with-directory-excursion "tests/unit"
+                       ;; These also fail due to limited accuracy.
+                       (delete-file "algorithm/MinimumAreaRectangleTest.cpp")
+                       (delete-file "capi/GEOSMinimumRotatedRectangleTest.cpp")
+                       ;; It is unclear why these fail, but I'm guessing:
+                       ;; limited accuracy.
+                       (delete-file "linearref/LengthIndexedLineTest.cpp")
+                       (delete-file "math/DDTest.cpp")))))
+               '())
+         (add-after
+             'unpack 'patch-test-shebangs
+           (lambda _
+             (substitute* '("tests/xmltester/testrunner.sh"
+                            "tests/xmltester/safe_to_xml.sh")
+               (("/bin/sh") (which "sh"))))))))
     (inputs
      (list glib))
     (home-page "https://libgeos.org/")
@@ -955,6 +970,29 @@ hydrology and waste deposition.")
         (base32
          "03r6mspfv22fs4x4jcgv25v9gsj5k6zy8incvyf94qf50g47s2bc"))))
     (build-system cmake-build-system)
+    (arguments
+     (if (target-32bit?)
+         (list
+          #:phases
+          '(modify-phases %standard-phases
+             (add-after 'unpack 'patch-tests
+               (lambda _
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/unit/test_factory.cpp"
+                   (("^TEST\\(factory, AuthorityFactory_createUnitOfMeasure_linear_us_survey_foot\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_grids.cpp"
+                   (("^TEST_F\\(GridTest, VerticalShiftGridSet_gtx\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_defmodel.cpp"
+                   (("^TEST\\(defmodel, evaluator_horizontal_unit_metre\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/CMakeLists.txt"
+                   (("proj_add_gie_test\\(\"4D-API-cs2cs-style\".+") "")
+                   (("proj_add_gie_test\\(\"Builtins\".+") "")
+                   (("proj_add_gie_test\\(\"peirce_q\".+") ""))))))
+         '()))
     (native-inputs (list googletest pkg-config))
     (propagated-inputs (list curl libtiff sqlite)) ;required by proj.pc
     (home-page "https://proj.org/")
@@ -984,7 +1022,34 @@ lets developers use the functionality of Proj in their own software.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1g0hkpiablvhsmw0kn5frwgdir3q7avc45p6lc1zhhhzkv5ikydh"))))))
+         "1g0hkpiablvhsmw0kn5frwgdir3q7avc45p6lc1zhhhzkv5ikydh"))))
+    (arguments
+     (if (target-32bit?)
+         (list
+          #:phases
+          '(modify-phases %standard-phases
+             (add-after 'unpack 'patch-tests
+               (lambda _
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/unit/test_factory.cpp"
+                   (("^TEST\\(factory, AuthorityFactory_createUnitOfMeasure_linear_us_survey_foot\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_grids.cpp"
+                   (("^TEST_F\\(GridTest, VerticalShiftGridSet_gtx\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_defmodel.cpp"
+                   (("^TEST\\(defmodel, evaluator_horizontal_unit_metre\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/CMakeLists.txt"
+                   (("proj_add_gie_test\\(\"4D-API-cs2cs-style\".+") "")
+                   (("proj_add_gie_test\\(\"Builtins\".+") "")
+                   (("proj_add_gie_test\\(\"peirce_q\".+") "")
+                   (("proj_add_gie_test\\(\"adams_ws2\".+") ""))
+                 (substitute* "test/cli/CMakeLists.txt"
+                   (("proj_add_test_script_sh\\(\"testvarious\" CS2CS_BIN\\)") ""))))))
+         '()))))
+
 
 (define-public python-obspy
   (package

gnu/packages/gkrellm.scm

@@ -1,7 +1,4 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -19,44 +16,8 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages gkrellm)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix utils)
-  #:use-module (gnu packages gettext)
-  #:use-module (gnu packages gtk)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages xorg))
+  #:use-module (gnu packages monitoring)
+  #:use-module (guix deprecation))
 
-(define-public gkrellm
-  (package
-    (name "gkrellm")
-    (version "2.5.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://gkrellm.srcbox.net/releases/gkrellm-"
-                           version ".tar.bz2"))
-       (sha256
-        (base32 "0qvy2xmwmfy5f0g09yn9lr262shnx82ba04r5il2wj4qscg3r7h8"))))
-    (build-system gnu-build-system)
-    (inputs (list gtk+-2 libsm))
-    (native-inputs (list gettext-minimal pkg-config))
-    (arguments
-     (list
-      #:tests? #f ;there is no check target
-      #:phases
-      #~(modify-phases %standard-phases
-          (delete 'configure)) ;no configure script
-      #:make-flags
-      #~(list (string-append "INSTALLROOT=" #$output)
-              (string-append "CC=" #$(cc-for-target)))))
-    (home-page "https://gkrellm.srcbox.net/")
-    (synopsis "System monitors")
-    (description
-     "GKrellM is a single process stack of system monitors which supports
-applying themes to match its appearance to your window manager, Gtk, or any
-other theme.")
-    (license license:gpl3+)))
+(define-deprecated/public-alias gkrellm
+  (@ (guix packages monitoring) gkrellm))

gnu/packages/gnuzilla.scm

@@ -605,9 +605,9 @@ in the case of Firefox, it is browser/locales/all-locales."
     "zh-TW"))
 
 ;;; Please keep these versions in sync with icedove.
-(define %icecat-base-version "140.9.1")
+(define %icecat-base-version "140.10.0")
 (define %icecat-version (string-append %icecat-base-version "-gnu1"))
-(define %icecat-build-id "20260414000000") ;must be of the form YYYYMMDDhhmmss
+(define %icecat-build-id "20260421000000") ;must be of the form YYYYMMDDhhmmss
 
 ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
 ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
@@ -627,9 +627,9 @@ in the case of Firefox, it is browser/locales/all-locales."
                   "firefox-" upstream-firefox-version ".source.tar.xz"))
             (sha256
              (base32
-              "1hld2kbzvrmr7pqq0r5hw639xl8kw29lm2hsbn0m4kxang1fdlj5"))))
+              "06996548nfmn4r4mfw3wvgb1mp35majc5hjyhs1krgp33ck2m1f0"))))
 
-         (gnuzilla-commit "f3595923458a5255f61a3853bd83bb5f004dc3bc")
+         (gnuzilla-commit "02125f31250c0240ee2ab1aa629ce66d4ffb9f30")
          (gnuzilla-source
           (origin
             (method git-fetch)
@@ -640,7 +640,7 @@ in the case of Firefox, it is browser/locales/all-locales."
                                       (string-take gnuzilla-commit 8)))
             (sha256
              (base32
-              "03kc08cvmdv3sxihf5hfhw2k91mg1y6f46b3x47p7q98phgk03cv"))))
+              "1hgx286gp0j46pklzzh5kvsnari1j3s0bff384m505m942k6l4hf"))))
 
          ;; 'search-patch' returns either a valid file name or #f, so wrap it
          ;; in 'assume-valid-file-name' to avoid 'local-file' warnings.
@@ -1249,6 +1249,166 @@ testing.")
        (cpe-name . "firefox_esr")
        (cpe-version . ,(first (string-split version #\-)))))))
 
+;;; TEMPORARY old version of icecat-source for use by icedove until it is updated.
+(define %icecat-140.9.1-base-version "140.9.1")
+(define %icecat-140.9.1-version (string-append %icecat-140.9.1-base-version "-gnu1"))
+(define icecat-140.9.1-source
+  (let* ((major-version (first  (string-split %icecat-140.9.1-base-version #\.)))
+         (minor-version (second (string-split %icecat-140.9.1-base-version #\.)))
+         (sub-version   (third  (string-split %icecat-140.9.1-base-version #\.)))
+
+         (upstream-firefox-version (string-append %icecat-140.9.1-base-version "esr"))
+         (upstream-firefox-source
+          (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://ftp.mozilla.org/pub/firefox/releases/"
+                  upstream-firefox-version "/source/"
+                  "firefox-" upstream-firefox-version ".source.tar.xz"))
+            (sha256
+             (base32
+              "1hld2kbzvrmr7pqq0r5hw639xl8kw29lm2hsbn0m4kxang1fdlj5"))))
+
+         (gnuzilla-commit "f3595923458a5255f61a3853bd83bb5f004dc3bc")
+         (gnuzilla-source
+          (origin
+            (method git-fetch)
+            (uri (git-reference
+                  (url "git://git.savannah.gnu.org/gnuzilla.git")
+                  (commit gnuzilla-commit)))
+            (file-name (git-file-name "gnuzilla"
+                                      (string-take gnuzilla-commit 8)))
+            (sha256
+             (base32
+              "03kc08cvmdv3sxihf5hfhw2k91mg1y6f46b3x47p7q98phgk03cv"))))
+
+         ;; 'search-patch' returns either a valid file name or #f, so wrap it
+         ;; in 'assume-valid-file-name' to avoid 'local-file' warnings.
+         (makeicecat-patch
+          (local-file (assume-valid-file-name
+                       (search-patch "icecat-makeicecat.patch")))))
+
+    (origin
+      (method computed-origin-method)
+      (file-name (string-append "icecat-" %icecat-140.9.1-version ".tar.zst"))
+      (sha256 #f)
+      (uri
+       (delay
+        (with-imported-modules '((guix build utils))
+          #~(begin
+              (use-modules (guix build utils))
+              (let ((firefox-dir
+                     (string-append "firefox-" #$%icecat-140.9.1-base-version))
+                    (icecat-dir
+                     (string-append "icecat-" #$%icecat-140.9.1-version)))
+
+                (set-path-environment-variable
+                 "PATH" '("bin")
+                 (list #+python
+                       #+(canonical-package bash)
+                       #+(canonical-package coreutils)
+                       #+(canonical-package findutils)
+                       #+(canonical-package patch)
+                       #+(canonical-package xz)
+                       #+(canonical-package zstd)
+                       #+(canonical-package sed)
+                       #+(canonical-package grep)
+                       #+(canonical-package bzip2)
+                       #+(canonical-package gzip)
+                       #+(canonical-package tar)))
+
+                (set-path-environment-variable
+                 "PYTHONPATH"
+                 (list #+(format #f "lib/python~a/site-packages"
+                                 (version-major+minor
+                                  (package-version python))))
+                 '#+(cons python-jsonschema
+                          (map second
+                               (package-transitive-propagated-inputs
+                                python-jsonschema))))
+
+                ;; We copy the gnuzilla source directory because it is
+                ;; read-only in 'gnuzilla-source', and the makeicecat script
+                ;; uses "cp -a" to copy parts of it and assumes that the
+                ;; copies will be writable.
+                (copy-recursively #+gnuzilla-source "/tmp/gnuzilla"
+                                  #:log (%make-void-port "w"))
+
+                (with-directory-excursion "/tmp/gnuzilla"
+                  (make-file-writable "makeicecat")
+                  (invoke "patch" "--force" "--no-backup-if-mismatch"
+                          "-p1" "--input" #+makeicecat-patch)
+                  (patch-shebang "makeicecat")
+                  (substitute* "makeicecat"
+                    (("^readonly FFMAJOR=(.*)" all ffmajor)
+                     (unless (string=? #$major-version
+                                       (string-trim-both ffmajor))
+                       ;; The makeicecat script cannot be expected to work
+                       ;; properly on a different version of Firefox, even if
+                       ;; no errors occur during execution.
+                       (error "makeicecat major version mismatch"))
+                     (string-append "readonly FFMAJOR=" #$major-version "\n"))
+                    (("^readonly FFMINOR=.*")
+                     (string-append "readonly FFMINOR=" #$minor-version "\n"))
+                    (("^readonly FFSUB=.*")
+                     (string-append "readonly FFSUB=" #$sub-version "\n"))
+                    (("^readonly DATADIR=.*")
+                     "readonly DATADIR=/tmp/gnuzilla/data\n")
+                    (("^readonly SOURCEDIR=.*")
+                     (string-append "readonly SOURCEDIR=" icecat-dir "\n"))
+                    (("/bin/sed")
+                     #+(file-append (canonical-package sed) "/bin/sed"))))
+
+                (format #t "Unpacking upstream firefox tarball...~%")
+                (force-output)
+                (invoke "tar" "xf" #+upstream-firefox-source)
+                (rename-file firefox-dir icecat-dir)
+
+                (with-directory-excursion icecat-dir
+                  (format #t "Populating l10n directory...~%")
+                  (force-output)
+                  (mkdir "l10n")
+                  (with-directory-excursion "l10n"
+                    (for-each
+                     (lambda (locale)
+                       (let ((locale-dir (string-append #+mozilla-l10n "/"
+                                                        locale)))
+                         (format #t "  ~a~%" locale)
+                         (force-output)
+                         (copy-recursively locale-dir locale
+                                           #:log (%make-void-port "w"))
+                         (for-each make-file-writable (find-files locale))
+                         (with-directory-excursion locale
+                           (mkdir-p "browser/chrome/browser/preferences")
+                           (call-with-output-file "browser/chrome/browser/\
+preferences/advanced-scripts.dtd"
+                             (lambda (port) #f)))))
+                     '#+%icecat-locales)
+                    (copy-recursively #+mozilla-compare-locales
+                                      "compare-locales"
+                                      #:log (%make-void-port "w"))
+                    (delete-file "compare-locales/.gitignore")))
+
+                (format #t "Running makeicecat script...~%")
+                (force-output)
+                (invoke "bash" "/tmp/gnuzilla/makeicecat")
+
+                (format #t "Packing IceCat source tarball...~%")
+                (force-output)
+                (setenv "ZSTD_NBTHREADS" (number->string (parallel-job-count)))
+                (invoke "tar" "cfa" #$output
+                        ;; Avoid non-determinism in the archive.  We set the
+                        ;; mtime of files in the archive to early 1980 because
+                        ;; the build process fails if the mtime of source
+                        ;; files is pre-1980, due to the creation of zip
+                        ;; archives.
+                        "--mtime=@315619200" ; 1980-01-02 UTC
+                        "--owner=root:0"
+                        "--group=root:0"
+                        "--sort=name"
+                        icecat-dir)))))))))
+
+
 (define %icedove-build-id "20260403000000") ;must be of the form YYYYMMDDhhmmss
 ;;; See <https://product-details.mozilla.org/1.0/thunderbird_versions.json>
 ;;; for the source of truth regarding Thunderbird releases.
@@ -1383,7 +1543,7 @@ testing.")
                ;; Extract the base Icecat tarball, renaming its top-level
                ;; directory.
                (invoke "tar" "--transform" (string-append "s,[^/]*," #$name ",")
-                       "-xf" #$icecat-source)
+                       "-xf" #$icecat-140.9.1-source)
                (chdir #$name)
 
                ;; Merge the Thunderdbird localization data.

gnu/packages/golang-check.scm

@@ -245,6 +245,55 @@ go-fuzz-headers.")
 @end itemize")
     (license license:expat)))
 
+(define-public go-github-com-alexkohler-prealloc
+  (package
+    (name "go-github-com-alexkohler-prealloc")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/alexkohler/prealloc")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "011i8yqzyjgwj17k44xvvg4bxfv8z20s0416r2d3yf4s3wqqygpq"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/alexkohler/prealloc"))
+    (home-page "https://github.com/alexkohler/prealloc")
+    (synopsis "Find slice declarations that could be preallocated")
+    (description
+     "This package is a Go static analysis tool to find slice declarations
+that could potentially be preallocated.")
+    (license license:expat)))
+
+(define-public go-github-com-alingse-asasalint
+  (package
+    (name "go-github-com-alingse-asasalint")
+    (version "0.0.11")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/alingse/asasalint")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1avz33cx3gcpps26rxijv7ic0njfmsdkbcp2mqg5yxhdcpq57s0q"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/alingse/asasalint"))
+    (propagated-inputs
+     (list go-golang-org-x-tools))
+    (home-page "https://github.com/alingse/asasalint")
+    (synopsis "Lint pass any slice as any in variadic function")
+    (description
+     "Golang linter, lint that pass any slice as any in variadic function.")
+    (license license:expat)))
+
 (define-public go-github-com-andreyvit-diff
   (package
     (name "go-github-com-andreyvit-diff")

gnu/packages/golang-crypto.scm

@@ -31,6 +31,7 @@
 ;;; Copyright © 2025 Arthur Rodrigues <arthurhdrodrigues@proton.me>
 ;;; Copyright © 2025 Patrick Norton <patrick.147.norton@gmail.com>
 ;;; Copyright © 2025 Giacomo Leidi <therewasa@fishinthecalculator.me>
+;;; Copyright © 2026 Evgeny Pisemsky <mail@pisemsky.site>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1599,7 +1600,7 @@ RSA, RSA-PSS, and ECDSA, though hooks are present for adding your own.")
 (define-public go-github-com-google-go-tpm
   (package
     (name "go-github-com-google-go-tpm")
-    (version "0.9.1")
+    (version "0.9.4")
     (source
      (origin
        (method git-fetch)
@@ -1608,7 +1609,7 @@ RSA, RSA-PSS, and ECDSA, though hooks are present for adding your own.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1c5j5cvwl45ka93nknmv454ivd7kp9n8yql19gr6z01z0s1ph7sg"))))
+        (base32 "1sp1mbr6vz36zy9w36iksirbsj5p2jslsl8zs1cdj8s4ig4lkd9d"))))
     (build-system go-build-system)
     (arguments
      (list
@@ -2873,7 +2874,7 @@ package.")
 (define-public go-github-com-refraction-networking-utls
   (package
     (name "go-github-com-refraction-networking-utls")
-    (version "1.6.0")
+    (version "1.8.2")
     (source
      (origin
        (method git-fetch)
@@ -2882,7 +2883,7 @@ package.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1iywar5vqsml4b177k2nkcxmjm8mw92g3p112yjsrpmikiwpwpyw"))))
+        (base32 "03kgwxdm2lg28fn2w5q7ql2szsiwj2xjdf477h1g3a4a9y9j6zk0"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/refraction-networking/utls"
@@ -3640,6 +3641,39 @@ algorithm described in @url{https://rfc-editor.org/rfc/rfc2898.html,RFC 2898}
 and @url{https://rfc-editor.org/rfc/rfc8018.html,RFC 8018}.")
     (license license:asl2.0)))
 
+(define-public go-github-com-xtls-reality
+  (package
+    (name "go-github-com-xtls-reality")
+    (version "0.0.0-20260322125925-9234c772ba8f")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/xtls/reality")
+              (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1wncy5aph6nmq4814xjhj6b5p1wm2fyrqn83dw0xlyxvq2z6iqfs"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/xtls/reality"))
+    (propagated-inputs
+     (list go-github-com-cloudflare-circl
+           go-github-com-juju-ratelimit
+           go-github-com-pires-go-proxyproto
+           go-github-com-refraction-networking-utls
+           go-golang-org-x-crypto
+           go-golang-org-x-sys))
+    (home-page "https://github.com/xtls/reality")
+    (synopsis "Implementation of REALITY protocol")
+    (description
+     "This package provides an implementation of REALITY protocol, which is
+intented to eliminate the detectable TLS fingerprint on the server side, while
+still maintain the secrecy.  It achieves full real TLS that is
+undistingwishable with the specified SNI to the middleman.")
+    (license (list license:bsd-3 license:mpl2.0))))
+
 (define-public go-github-com-youmark-pkcs8
   (package
     (name "go-github-com-youmark-pkcs8")

gnu/packages/golang-maths.scm

@@ -456,6 +456,29 @@ penalization.")
 FFT (Schonhage-Strassen method for multiplying integers).")
     (license license:bsd-3)))
 
+(define-public go-github-com-robinus2-golang-moving-average
+  (package
+    (name "go-github-com-robinus2-golang-moving-average")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/RobinUS2/golang-moving-average")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "02z3ad29653fz7whxkjjpq820ig9j8m68xj4kay14jyazkr5in1f"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/RobinUS2/golang-moving-average"))
+    (home-page "https://github.com/RobinUS2/golang-moving-average")
+    (synopsis "Moving average implementation for Go")
+    (description
+     "This package provides a moving average implementation for Go.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-shopspring-decimal
   (package
     (name "go-github-com-shopspring-decimal")

gnu/packages/golang-xyz.scm

@@ -75,6 +75,7 @@
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2026 Giacomo Leidi <therewasa@fishinthecalculator.me>
 ;;; Copyright © 2026 Evgeny Pisemsky <mail@pisemsky.site>
+;;; Copyright © 2026 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -524,6 +525,35 @@ file along with an index.html file.")
      "Package tcell provides a gruid Driver for making terminal apps.")
     (license license:isc)))
 
+(define-public go-codeberg-org-chavacava-garif
+  (package
+    (name "go-codeberg-org-chavacava-garif")
+    (version "0.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://codeberg.org/chavacava/garif.git")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0cz037yb9gnk9fd61pni6m0n9cbrwmlxxija5vm91mplyxlih05h"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "codeberg.org/chavacava/garif"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (home-page "https://codeberg.org/chavacava/garif")
+    (synopsis "Create and manipulate SARIF logs")
+    (description
+     "This package defines all the Go structures required to model a log file.
+
+SARIF, from Static Analysis Results Interchange Format, is a standard
+JSON-based format for the output of static analysis tools defined and promoted
+by @url{https://www.oasis-open.org/, OASIS}.")
+    (license license:expat)))
+
 (define-public go-codeberg-org-emersion-go-scfg
   (package
     (name "go-codeberg-org-emersion-go-scfg")
@@ -612,6 +642,33 @@ recursively any exported one.  It also won't merge structs inside
 maps (because they are not addressable using Go reflection).")
     (license license:bsd-3)))
 
+(define-public go-fyne-io-systray
+  (package
+    (name "go-fyne-io-systray")
+    (version "1.11.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/fyne-io/systray")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0yrd4f3n8wrqcqradmqq9w0b31hd5hali876xkynfhm3nhaz4j1i"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "fyne.io/systray"))
+    (propagated-inputs
+     (list go-github-com-godbus-dbus-v5
+           go-golang-org-x-sys))
+    (home-page "https://fyne.io/systray/")
+    (synopsis "Place an icon and menu in the notification area")
+    (description
+     "This package is a cross-platform Go library to place an icon and menu in
+the notification area.")
+    (license license:asl2.0)))
+
 (define-public go-git-sr-ht-rjarry-go-opt
   (package
     (name "go-git-sr-ht-rjarry-go-opt")
@@ -2980,6 +3037,38 @@ input from the terminal while not echoing the input back (similar to
 and is therefore compatible with cross-compiling.")
     (license license:expat)))
 
+(define-public go-github-com-bitfield-script
+  (package
+    (name "go-github-com-bitfield-script")
+    (version "0.24.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/bitfield/script")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1pzmz7n39sh9sprclzd0m0l0flf626286fh51m065yjhkqzrjw89"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/bitfield/script"
+      #:test-flags #~(list "-vet=off")))
+    (native-inputs
+     (list go-github-com-google-go-cmp))
+    (propagated-inputs
+     (list go-github-com-itchyny-gojq
+           go-github-com-rogpeppe-go-internal
+           go-mvdan-cc-sh-v3))
+    (home-page "https://github.com/bitfield/script")
+    (synopsis "Making it easy to write shell-like scripts in Go")
+    (description
+     "Package script aims to make it easy to write shell-type scripts in Go,
+for general system administration purposes: reading files, counting lines,
+matching strings, and so on.")
+    (license license:expat)))
+
 (define-public go-github-com-bitly-go-hostpool
   (package
     (name "go-github-com-bitly-go-hostpool")
@@ -4432,6 +4521,34 @@ over strings.")
 @code{https://en.wikipedia.org/wiki/WebP, WebP} images.")
     (license license:bsd-3)))
 
+(define-public go-github-com-chainguard-dev-clog
+  (package
+    (name "go-github-com-chainguard-dev-clog")
+    (version "1.8.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/chainguard-dev/clog")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0b95vw8czs2r9lscyi85vppbyqj672zm6z2n9siy1s9yv6fkys62"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/chainguard-dev/clog"))
+    (home-page "https://github.com/chainguard-dev/clog")
+    (synopsis "Context aware slog")
+    (description
+     "This package provides a context-aware Go std lib
+@url{https://pkg.go.dev/log/slog, @code{slog}}.  The context Logger can be
+used to use Loggers from the context.  This is sometimes preferred over the
+@url{https://github.com/chainguard-dev/clog#context-handler, Context Handler},
+since this can make it easier to use different loggers in different
+contexts (e.g. testing).")
+    (license license:asl2.0)))
+
 (define-public go-github-com-charlievieth-fastwalk
   (package
     (name "go-github-com-charlievieth-fastwalk")
@@ -8036,7 +8153,7 @@ supports concurrent serializable transactions.")
   (package
     (inherit go-github-com-dgraph-io-badger)
     (name "go-github-com-dgraph-io-badger-v4")
-    (version "4.5.2")
+    (version "4.9.1")
     (source
      (origin
        (method git-fetch)
@@ -8045,7 +8162,7 @@ supports concurrent serializable transactions.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0v4c69whypm3k40hrx8bw9rjrcb0swz43v056s0fadqr04j0ncwj"))))
+        (base32 "0a9lk7fw06yb89wy9rp4q50ircw5imm1cqzhyhs92d0cia5qbhh6"))))
     (arguments
      (list
       #:tests? #f ; TODO: tests hang, find out why.
@@ -8058,7 +8175,8 @@ supports concurrent serializable transactions.")
            go-github-com-klauspost-compress
            go-github-com-pkg-errors
            go-github-com-spf13-cobra
-           go-go-opencensus-io
+           go-go-opentelemetry-io-contrib-zpages
+           go-go-opentelemetry-io-otel
            go-golang-org-x-net
            go-golang-org-x-sys
            go-google-golang-org-protobuf))))
@@ -8965,6 +9083,41 @@ sub-interfaces are also provided for cases where the full Channel interface
 cannot be met (for example, @code{InChannel} for write-only channels).")
     (license license:expat)))
 
+(define-public go-github-com-eapache-go-resiliency
+  (package
+    (name "go-github-com-eapache-go-resiliency")
+    (version "1.7.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/eapache/go-resiliency")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "07a1r3c2spd37k3riy4fxz8v8ibxiprf8a3vw788whz4mlp6gm40"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:skip-build? #t
+      #:import-path "github.com/eapache/go-resiliency"))
+    (home-page "https://github.com/eapache/go-resiliency")
+    (synopsis "Resiliency patterns for golang")
+    (description
+     "Resiliency patterns for golang.  Based in part on
+@url{https://github.com/Netflix/Hystrix, Hystrix},
+@@url{https://github.com/Shopify/semian, Semian}, and others.
+
+Currently implemented patterns include:
+@itemize
+@item circuit-breaker
+@item semaphore
+@item deadline/timeout
+@item batching
+@item retriable
+@end itemize")
+    (license license:expat)))
+
 (define-public go-github-com-eapache-queue
   (package
     (name "go-github-com-eapache-queue")
@@ -17604,7 +17757,7 @@ implementing features like:
 (define-public go-github-com-maruel-natural
   (package
     (name "go-github-com-maruel-natural")
-    (version "1.1.1")
+    (version "1.3.0")
     (source
      (origin
        (method git-fetch)
@@ -17613,7 +17766,7 @@ implementing features like:
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "040aikizdd7c4zm8xindb2ps16s60i0fkf8gkll2rir7lwv6q7ks"))))
+        (base32 "1nr1ai3b7yvz4wz4k0jqvjq3978hpk9yxarn7g7i3d2sxbdc0g4q"))))
     (build-system go-build-system)
     (arguments
      (list
@@ -22786,16 +22939,16 @@ it is capable of logging at some or all levels.")
 (define-public go-github-com-rivo-tview
   (package
     (name "go-github-com-rivo-tview")
-    (version "0.0.0-20241227133733-17b7edb88c57")
+    (version "0.42.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/rivo/tview")
-             (commit (go-version->git-ref version))))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1w59vyvs8k5mzl7k39zpwcwwdgam2pbz0rnrfnnjgvkld1rh81dc"))))
+        (base32 "0jw47h92l0vp1lg6s5kng4hjv81hi8qxx9h5yilc7rzrr8l9ksd2"))))
     (build-system go-build-system)
     (arguments
      (list #:import-path "github.com/rivo/tview"))
@@ -30436,8 +30589,8 @@ The yaml package supports most of YAML 1.2, but preserves some behavior from
 ;; to build NNCP and remove vendor) dependency for Golang.  Full build depends
 ;; on Bazel <https://bazel.build/>.
 (define-public go-gvisor-dev-gvisor
-  (let ((commit "634ce95eed8d5b8e6b3e2ea30542c34cb30af148")
-        (revision "0"))
+  (let ((commit "9414b50a5633100fd7299a5a7998742575dcb669")
+        (revision "1"))
     (package
       (name "go-gvisor-dev-gvisor")
       (version (git-version "0.0.0" revision commit))
@@ -30449,7 +30602,7 @@ The yaml package supports most of YAML 1.2, but preserves some behavior from
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "1l3si6qlchwgsvaq6lxyvj8iq8n8pqxlayb1hbdf3pynxi52hfkw"))))
+          (base32 "0vqaclb2ignkcs7n463bj349m0xybdsv71i6afhzh8r05hdywzax"))))
       (build-system go-build-system)
       (arguments
        (list

gnu/packages/guile-xyz.scm

@@ -60,6 +60,7 @@
 ;;; Copyright © 2025 Andy Tai <atai@atai.org>
 ;;; Copyright © 2025 Ekaitz Zarraga <ekaitz@elenq.tech>
 ;;; Copyright © 2026 Matt Wette <matt.wette@gmail.com>
+;;; Copyright © 2026 Dzianis Jackievič <mail@miesta.by>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1167,7 +1168,7 @@ is not available for Guile 2.0.")
   (package
     (inherit guile-fibers-1.3)
     (name "guile-fibers")
-    (version "1.4.2")
+    (version "1.4.3")
     (source
      (origin (inherit (package-source guile-fibers-1.3))
              (file-name (git-file-name name version))
@@ -1176,7 +1177,7 @@ is not available for Guile 2.0.")
                     (commit (string-append "v" version))))
              (sha256
               (base32
-               "0qh0czz5qvk5mmrc8x2gmvl5psdfd22q2rhzj4jrpan6k3d55bl8"))
+               "1q0a9y0cc8rld1z7mcj61fkldhd0kn9n4yq25izxslbgg4g5h9j6"))
              (patches '())))
     (arguments
      (if (target-aarch64?)
@@ -1256,30 +1257,8 @@ is not available for Guile 2.0.")
      (modify-inputs native-inputs
        (replace "guile" guile-2.2)))))
 
-(define-public guile-fibers-next
-  (let ((commit "297359f0ad655378bcc3ff0d4e96101965ef39b4")
-        (revision "0"))
-    (package
-      (inherit guile-fibers)
-      (name "guile-fibers-next")
-      (version (git-version "1.4.2"
-                            revision
-                            commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://codeberg.org/guile/fibers.git")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "0qh0czz5qvk5mmrc8x2gmvl5psdfd22q2rhzj4jrpan6k3d55bl8"))))
-      (inputs
-       (modify-inputs inputs
-         (replace "guile" guile-next)))
-      (native-inputs
-       (modify-inputs native-inputs
-         (replace "guile" guile-next))))))
+;; Deprecated on 2026-04-23
+(define-deprecated-package guile-fibers-next guile-fibers)
 
 (define-public guile-kracht
   (package
@@ -1537,7 +1516,7 @@ order to provide IDE functionality for Guile Scheme.")
 (define-public guile-ares-rs
   (package
     (name "guile-ares-rs")
-    (version "0.9.6")
+    (version "0.9.7")
     (source
      (origin
        (method git-fetch)
@@ -1547,35 +1526,42 @@ order to provide IDE functionality for Guile Scheme.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1vkww3vc0lsh5f8yh6fnh402rx3rsm0ss69rdkmplhzp4c7c4z1d"))))
+         "1xbznh5zjswfydgqg53g50ya7zm0hidin74g2glk849l9j45szw3"))))
     (build-system guile-build-system)
     (arguments
      (list
       #:source-directory "src/guile"
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'build 'install-script
+          (add-after 'build 'install-scripts
             (lambda _
-              (let* ((bin (string-append #$output "/bin"))
-                     (oldpath (string-append
-                               #$output
-                               ;; This file will be named ares-nrepl.scm for
-                               ;; the next version.
-                               "/share/guile/site/3.0/ares/scripts/ares.scm"))
-                     (newpath (string-append bin "/ares-nrepl")))
-                (mkdir bin)
-                (symlink oldpath newpath)
-                (wrap-program newpath
-                  `("GUILE_LOAD_PATH" ":" =
-                    ,(list (string-append #$output "/share/guile/site/3.0")
-                           (getenv "GUILE_LOAD_PATH")))
-                  `("GUILE_LOAD_COMPILED_PATH" ":" =
-                    ,(list (string-append #$output "/lib/guile/3.0/site-ccache")
-                           (getenv "GUILE_LOAD_COMPILED_PATH"))))
-                ;; Not needed since the wrapper followed the symlink.
-                (delete-file (string-append bin "/.ares-nrepl-real"))))))))
-    (inputs (list bash-minimal guile-3.0))
-    (propagated-inputs (list guile-fibers guile-custom-ports))
+              (define bin (string-append #$output "/bin"))
+              (define site (string-append #$output "/share/guile/site/3.0"))
+              (define ccache
+                (string-append #$output "/lib/guile/3.0/site-ccache"))
+
+              (define (install-script name)
+                (let ((oldpath
+                       (string-append site "/ares/scripts/" name ".scm"))
+                      (newpath
+                       (string-append bin "/" name)))
+                  (symlink oldpath newpath)
+                  (wrap-program newpath
+                    `("GUILE_LOAD_PATH" ":" =
+                      ,(list "$GUILE_LOAD_PATH"
+                             site
+                             (getenv "GUILE_LOAD_PATH")))
+                    `("GUILE_LOAD_COMPILED_PATH" ":" =
+                      ,(list "$GUILE_LOAD_COMPILED_PATH"
+                             ccache
+                             (getenv "GUILE_LOAD_COMPILED_PATH"))))
+                  ;; Not needed since the wrapper followed the symlink.
+                  (delete-file (string-append bin "/." name "-real"))))
+
+              (mkdir bin)
+              (for-each install-script '("ares-nrepl" "ares-suitbl")))))))
+    (inputs (list bash-minimal guile-3.0-latest))
+    (propagated-inputs (list guile-fibers))
     (home-page "https://git.sr.ht/~abcdw/guile-ares-rs")
     (synopsis "Asynchronous Reliable Extensible Sleek RPC Server for Guile")
     (description "Asynchronous Reliable Extensible Sleek RPC Server for
@@ -5707,27 +5693,32 @@ perform geometrical transforms on JPEG images.")
       (license license:gpl3+))))
 
 (define-public guile-jtd
-  (package
-    (name "guile-jtd")
-    (version "220323a")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/mwette/guile-jtd")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1l8fyqhvksarvpbr903i3ss3432jzvyvhgcqa15j922ngqh4ds6f"))))
-    (build-system guile-build-system)
-    (native-inputs (list guile-3.0))
-    (home-page "https://github.com/mwette/guile-jtd")
-    (synopsis "Python's @code{pdb.set_trace()} but for Guile")
-    (description
-     "The @code{(jtd)} module for Guile provides a procedure
+  ;; There are a few unreleased commits that include niceties such as warning
+  ;; that the debug VM must be used; use the latest commit until the next
+  ;; release comes.
+  (let ((commit "425f86ae954d6445aaedacfd4ecd50aa0022e59d")
+        (revision "0"))
+    (package
+      (name "guile-jtd")
+      (version (git-version "220323a" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/mwette/guile-jtd")
+                       (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1l8fyqhvksarvpbr903i3ss3432jzvyvhgcqa15j922ngqh4ds6f"))))
+      (build-system guile-build-system)
+      (native-inputs (list guile-3.0))
+      (home-page "https://github.com/mwette/guile-jtd")
+      (synopsis "Python's @code{pdb.set_trace()} but for Guile")
+      (description
+       "The @code{(jtd)} module for Guile provides a procedure
 @code{jump-to-debugger} for escaping to the Guile REPL for the purpose of
 debugging code.")
-    (license license:lgpl2.1+)))
+      (license license:lgpl2.1+))))
 
 (define-public guile-png
   (package
@@ -6399,6 +6390,88 @@ as signed sessions, multipart message support, etc.")
     (propagated-inputs
      (list guile2.2-irregex guile2.2-gcrypt))))
 
+(define-public guile-compose
+  (package
+    (name "guile-compose")
+    (version "0.1.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/jadzi/guile-compose.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1g68gczs96nrb0vf1hv4n07zsp2516gpiwq1wwlhcq4rzynhf12h"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:make-flags
+      #~'("GUILE_AUTO_COMPILE=0")))
+    (inputs (list guile-3.0))
+    (native-inputs (list autoconf-2.72 automake pkg-config guile-3.0 texinfo))
+    (synopsis "Procedure composition utilities for Guile Scheme")
+    (description
+     "This tiny package provides some procedures and macros to extend
+Guile Scheme procedure composition facilities.  For example, there is
+a @code{compose-top}, a reverse-order analog to native @code{compose}
+procedure.  The @code{compose-cont} is a macro, utilizing some power of
+continuations to build really flexible flows.
+
+This library is intended to stay basic and small, so it has no any
+external dependencies and can be a good base for other packages, like e.g.
+@code{guile-web-middleware}.")
+    (license (list license:lgpl3+))
+    (home-page "https://jadzi.codeberg.page/guile-compose")))
+
+(define-public guile-web-middleware
+  (package
+    (name "guile-web-middleware")
+    (version "0.11.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/jadzi/guile-web-middleware.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "01wb8v0lszphdv08ly4aqv59qm5h8yw2fgm025vkn61djspsq4j9"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:make-flags
+      #~'("GUILE_AUTO_COMPILE=0")))
+    (inputs (list guile-3.0))
+    (propagated-inputs (list guile-compose))
+    (native-inputs (list autoconf-2.72 automake pkg-config guile-3.0 texinfo))
+    (synopsis "Web application middleware composition for Guile Scheme")
+    (description
+     "This package provides means to compose a web application by
+chaining procedures, a.k.a. middlewares.  By those means, composed
+procedures form a standard request handler for any Guile's web server
+implementation.
+
+Each middleware has its own limited responsibility in request
+processing.  Also, middlewares are simple Scheme procedures, so they
+can be easily tested and shared among web applications.
+
+Out of the box, this package provides several procedures for commonly
+required tasks.  Among them:
+
+@itemize
+@item Error handling with customizable page contents.
+@item Request filtering.
+@item Request logging.
+@item Serving static files, file URL generation.
+@item Request routing, handling parameters, route URL generation.
+@item Middleware nesting, composing whole apps.
+@end itemize
+
+This package relies on @code{guile-compose} package as its only dependency.")
+    (license (list license:lgpl3+))
+    (home-page "https://jadzi.codeberg.page/guile-web-middleware")))
+
 (define-public guile-web-driver-ng
   (package
     (name "guile-web-driver-ng")
@@ -7716,13 +7789,13 @@ is an attempt to combine both into something useful.")
      (list pkg-config
            autoconf
            automake
-           guile-next
+           guile-3.0-latest
            guile-lib
-           guile-fibers-next))
+           guile-fibers))
     (inputs
-     (list guile-next))
+     (list guile-3.0-latest))
     (propagated-inputs
-     (list guile-fibers-next))
+     (list guile-fibers))
     (home-page "https://cbaines.codeberg.page/guile-knots/")
     (synopsis "Patterns and functionality to use with Guile Fibers")
     (description
@@ -8018,14 +8091,14 @@ application to open a given file or URL based on given configurations.")
 (define-public guile-goblins
   (package
     (name "guile-goblins")
-    (version "0.17.0")
+    (version "0.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://files.spritely.institute/releases"
                            "/guile-goblins/guile-goblins-" version ".tar.gz"))
        (sha256
-        (base32 "16jkmfspsnza2fdk5jr05a5pfh7x856gpg031i21s1yvy43l8mi0"))))
+        (base32 "0gj5018wmq97ln1z7x03a13z3p35xc8762id9bl9fgkxwm01df1a"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/guile.scm

@@ -653,7 +653,10 @@ GNU@tie{}Guile.  Use the @code{(ice-9 readline)} module and call its
 (define (guile-variant-package-name prefix)
   (lambda (name)
     "Return NAME with PREFIX instead of \"guile-\", when applicable."
-    (if (string-prefix? "guile-" name)
+    (if (and (string-prefix? "guile-" name)
+
+             ;; Don't rename guile-bootstrap@2.0.
+             (not (string=? "guile-bootstrap" name)))
         (string-append prefix "-"
                        (string-drop name
                                     (string-length "guile-")))
@@ -900,8 +903,8 @@ type system, elevating types to first-class status.")
 (define-public guile-git
   (package
     (name "guile-git")
-    (version "0.11.0")
-    (home-page "https://gitlab.com/guile-git/guile-git.git")
+    (version "0.11.1")
+    (home-page "https://codeberg.org/guile-git/guile-git.git")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -910,11 +913,11 @@ type system, elevating types to first-class status.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1yjyil6z4k80pjdps8v6h6lxikwxmjxvrslf2jrmq2rrfnajschz"))))
+                "0xpzchnglddphi3chv53xqaz2x6rpq3l4s023w7r4mmndb6lgz0b"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags '("GUILE_AUTO_COMPILE=0")       ; to prevent guild warnings
-       ;; https://gitlab.com/guile-git/guile-git/-/issues/20
+       ;; https://codeberg.org/guile-git/guile-git/issues/20
        ,@(if (target-ppc32?)
            `(#:phases
              (modify-phases %standard-phases
@@ -922,20 +925,7 @@ type system, elevating types to first-class status.")
                  (lambda _
                    (substitute* "Makefile.am"
                      ((".*tests/blob\\.scm.*") ""))))))
-           '())
-       ,@(if (system-hurd?)
-             (list
-              #:phases
-              #~(modify-phases %standard-phases
-                  (add-after 'unpack 'skip-tests/hurd
-                    (lambda _
-                      (substitute* "tests/proxy.scm"
-                        (("\\(test-begin.*" all)
-                         (string-append
-                          all
-                          "(when (string-ci= \"GNU\" (vector-ref (uname) 0))\n"
-                          "  (test-skip 1))\n")))))))
-             '())))
+           '())))
     (native-inputs
      (list pkg-config autoconf automake texinfo guile-3.0 guile-bytestructures))
     (inputs
@@ -1004,7 +994,7 @@ Guile's foreign function interface.")
        (file-name (string-append "guile-lzlib-" version ".tar.gz"))
        (sha256
         (base32
-         "1whgmwkr1v8m63p4aaqn8blwl9vcrswwhbfv4bm0aghl5a6rryd7"))
+         "1v1pfqp6hwl0rivs7swhqnfgznxlfnws9ldmn6avnhd10filfa3a"))
        (patches (search-patches "guile-lzlib-gcc-14.patch"
                                 "guile-lzlib-hurd64.patch"))))
     (build-system gnu-build-system)

gnu/packages/haskell-crypto.scm

@@ -914,7 +914,7 @@ regular) Diffie Hellman key exchanges, and many extensions.")
      (list #:extra-directories (list "openssl")
            #:configure-flags
            #~(list "--ghc-options=-optc=-Wno-incompatible-pointer-types")))
-    (inputs (list ghc-network openssl))
+    (inputs (list ghc-network openssl-3.0))
     (home-page "https://github.com/haskell-cryptography/HsOpenSSL")
     (synopsis "Partial OpenSSL binding for Haskell")
     (description

gnu/packages/high-availability.scm

@@ -489,11 +489,22 @@ lost.
                 "0b9d2i22ghyjarwi1c596q5mf7gj1k04k784hnmrd2d4x9hgv9ax"))))
     (build-system gnu-build-system)
     (arguments
-     (list #:configure-flags #~(list "--with-corosync" "--disable-static"
+     (list #:configure-flags #~(list "--with-corosync"
+                                     "--disable-static"
+                                     "--localstatedir=/var"
                                      (string-append "--with-initdir="
                                                     #$output "/etc/init.d")
                                      (string-append "--with-ocfdir="
-                                                    #$output "/lib"))))
+                                                    #$output "/lib"))
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-before 'configure 'pre-configure
+                 (lambda _
+                   ;; Do not attempt to install /var.
+                   (substitute* '("Makefile.am"
+                                  "daemons/schedulerd/Makefile.am")
+                     (("install-exec-local:")
+                      "install-exec-local-disabled:")))))))
     (native-inputs (list autoconf
                          automake
                          cmocka

gnu/packages/instrumentation.scm

@@ -339,30 +339,6 @@ coverage.")
     ;; that list in further version.
     (supported-systems (list "x86_64-linux"))))
 
-(define-public lttng-modules
-  (package
-    (name "lttng-modules")
-    (version "2.13.14")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://lttng.org/files/lttng-modules/"
-                                  "lttng-modules-" version ".tar.bz2"))
-              (sha256
-               (base32
-                "19jx1yz1hsbr4vwfp2nr6z52a5g50iimaak962k49diay5zryi66"))))
-    (build-system linux-module-build-system)
-    (arguments
-     `(#:tests? #f ; no tests
-       #:make-flags (list "CONFIG_LTTNG=m"
-                          "CONFIG_LTTNG_CLOCK_PLUGIN_TEST=m")))
-    (home-page "https://lttng.org/")
-    (synopsis "LTTng kernel modules for the LTTng tracer toolset")
-    (description
-     "LTTng kernel modules are Linux kernel modules which make
-LTTng kernel tracing possible.  They include essential control modules and
-many probes which instrument numerous interesting parts of Linux.")
-    (license (list license:lgpl2.1 license:gpl2 license:expat))))
-
 (define-public lttng-ust
   (package
     (name "lttng-ust")

gnu/packages/java-bootstrap.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014-2019, 2021, 2026 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2021, 2026 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017, 2022 Marius Bakke <marius@gnu.org>
@@ -226,6 +226,18 @@ JNI.")
              (setenv "JAVACMD" (search-input-file inputs "/bin/jamvm"))
              (setenv "JAVAC" (search-input-file inputs "/bin/jikes"))
              (setenv "CLASSPATH" (search-input-file inputs "/lib/rt.jar"))))
+         ,@(if (target-x86-32?)
+               ;; XXX: On i686 isFile() always seems to return true.  Patching
+               ;; this here is very ugly, but the effects are limited.  None
+               ;; of these changes remain by the time we've built Icedtea and
+               ;; the other JDKs.
+               '((add-after 'unpack 'disable-isFile-checks
+                   (lambda _
+                     (substitute* "src/main/org/apache/tools/ant/util/ResourceUtils.java"
+                       (("destFile = \\(\\(FileProvider\\).*") ""))
+                     (substitute* "src/main/org/apache/tools/ant/taskdefs/Mkdir.java"
+                       (("dir.isFile\\(\\)") "false")))))
+               '())
          (replace 'build
            (lambda* (#:key inputs outputs #:allow-other-keys)
              ;; Ant complains if this file doesn't exist.

gnu/packages/java-compression.scm

@@ -55,13 +55,12 @@
        (modify-phases %standard-phases
          (add-after 'unpack 'make-git-checkout-writable
            (lambda _
-             (for-each make-file-writable (find-files "."))
-             #t))
+             (for-each make-file-writable (find-files "."))))
          (add-before 'build 'remove-binaries
            (lambda _
              (delete-file "lib/org/xerial/snappy/OSInfo.class")
-             (delete-file-recursively "src/main/resources/org/xerial/snappy/native")
-             #t))
+             (delete-file-recursively
+              "src/main/resources/org/xerial/snappy/native")))
          (add-before 'build 'build-jni
            (lambda _
              ;; Rebuild one of the binaries we removed earlier
@@ -98,36 +97,33 @@
          (add-after 'build-jni 'copy-jni
            (lambda _
              (copy-recursively "src/main/resources/org/xerial/snappy/native"
-                               "build/classes/org/xerial/snappy/native")
-             #t))
+                               "build/classes/org/xerial/snappy/native")))
          (add-before 'build 'set-test-memory-size
            (lambda _
              (substitute* "build.xml"
-               (("<junit printsummary=") "<junit maxmemory=\"2G\" printsummary="))
-             #t))
+               (("<junit printsummary=")
+                "<junit maxmemory=\"2G\" printsummary="))))
          (add-before 'check 'fix-failing
            (lambda _
              (with-directory-excursion "src/test/java/org/xerial/snappy"
-               ;; This package assumes maven build, which puts results in "target".
-               ;; We put them in "build" instead, so fix that.
+               ;; This package assumes maven build, which puts results in
+               ;; "target". We put them in "build" instead, so fix that.
                (substitute* "SnappyLoaderTest.java"
                  (("target/classes") "build/classes"))
                ;; This requires Hadoop, which is not in Guix yet.
-               (delete-file "SnappyHadoopCompatibleOutputStreamTest.java"))
-             #t)))))
+               (delete-file "SnappyHadoopCompatibleOutputStreamTest.java")))))))
     (inputs
-     `(("osgi-framework" ,java-osgi-framework)))
+     (list java-osgi-framework))
     (propagated-inputs
-     `(("bitshuffle" ,bitshuffle-for-snappy)
-       ("snappy" ,snappy)))
+     (list bitshuffle-for-snappy snappy))
     (native-inputs
-     `(("junit" ,java-junit)
-       ("hamcrest" ,java-hamcrest-core)
-       ("xerial-core" ,java-xerial-core)
-       ("classworlds" ,java-plexus-classworlds)
-       ("commons-lang" ,java-commons-lang)
-       ("commons-io" ,java-commons-io)
-       ("perl" ,perl)))
+     (list java-junit
+           java-hamcrest-core
+           java-xerial-core
+           java-plexus-classworlds
+           java-commons-lang
+           java-commons-io
+           perl))
     (home-page "https://github.com/xerial/snappy-java")
     (synopsis "Compression/decompression algorithm in Java")
     (description "Snappy-java is a Java port of snappy, a fast C++
@@ -156,13 +152,13 @@ compressor/decompressor.")
          (add-before 'build 'remove-binaries
            (lambda _
              (delete-file "lib/org/xerial/snappy/OSInfo.class")
-             (delete-file-recursively "src/main/resources/org/xerial/snappy/native")
-             #t))
+             (delete-file-recursively
+              "src/main/resources/org/xerial/snappy/native")))
          (add-before 'build 'build-jni
            (lambda _
              ;; Rebuild one of the binaries we removed earlier
              (invoke "javac" "src/main/java/org/xerial/snappy/OSInfo.java"
-                      "-d" "lib")
+                     "-d" "lib")
              ;; Link to the dynamic snappy, not the static ones
              (substitute* "Makefile.common"
                (("-shared") "-shared -lsnappy"))
@@ -184,16 +180,14 @@ compressor/decompressor.")
          (add-after 'build-jni 'copy-jni
            (lambda _
              (copy-recursively "src/main/resources/org/xerial/snappy/native"
-                               "build/classes/org/xerial/snappy/native")
-             #t))
+                               "build/classes/org/xerial/snappy/native")))
          (add-before 'check 'fix-tests
            (lambda _
              (mkdir-p "src/test/resources/org/xerial/snappy/")
              (copy-recursively "src/test/java/org/xerial/snappy/testdata"
                                "src/test/resources/org/xerial/snappy/testdata")
              (install-file "src/test/java/org/xerial/snappy/alice29.txt"
-                           "src/test/resources/org/xerial/snappy/")
-             #t)))))))
+                           "src/test/resources/org/xerial/snappy/"))))))))
 
 (define-public java-iq80-snappy
   (package

gnu/packages/java.scm

@@ -1285,7 +1285,13 @@ new Date();"))))
                 ;; It looks like the "--disable-warnings-as-errors" option of
                 ;; the 'configure' phase is not working.
                 (substitute* "make/autoconf/generated-configure.sh"
-                  (("-Werror") ""))))))
+                  (("-Werror") ""))))
+            #$@(if (target-x86-32?)
+                   ;; On i686 the C2 compiler sometimes crashes when importing
+                   ;; certificates.
+                   #~((add-before 'install-keystore 'disable-C2-compiler
+                        (lambda _ (setenv "_JAVA_OPTIONS" "-XX:TieredStopAtLevel=1"))))
+                   #~())))
        ((#:disallowed-references refs '())
         (cons* (this-package-native-input "openjdk")
                (gexp-input (this-package-native-input "openjdk") "jdk")
@@ -1844,12 +1850,50 @@ blacklisted.certs.pem"
 (define-public openjdk24
   (make-openjdk
    openjdk23 "24.0.1"
-   "0h6sbzbjyqg85iml41pswdh2z3d7h2hhb0sd5yll37r1mj5lsxmx"))
+   "0h6sbzbjyqg85iml41pswdh2z3d7h2hhb0sd5yll37r1mj5lsxmx"
+   (arguments
+    (substitute-keyword-arguments (package-arguments base)
+      ((#:configure-flags flags #~(list))
+       (if (target-x86-32?)
+           #~(cons* "--enable-deprecated-ports=yes" #$flags)
+          flags))))))
 
 (define-public openjdk25
   (make-openjdk
    openjdk24 "25.0.2"
-   "03aa34lscr3qbdl6qz3gqyp0nzkqfj02362mzmpkiq3y2g5xdnrj"))
+   "03aa34lscr3qbdl6qz3gqyp0nzkqfj02362mzmpkiq3y2g5xdnrj"
+   (arguments
+    (substitute-keyword-arguments (package-arguments base)
+      ((#:configure-flags flags #~(list))
+       (if (target-x86-32?)
+           ;; Full builds on 32-bit x86 architectures are not supported as of
+           ;; this version.  Best we can do is to build with the "zero" variant.
+           #~(cons* "--with-jvm-variants=zero"
+                    "--disable-precompiled-headers"
+                    #$flags)
+           flags))
+      ((#:phases phases #~%standard-phases)
+       (if (target-x86-32?)
+           #~(modify-phases #$phases
+               (replace 'install
+                 (lambda _
+                   (let ((images (car (find-files "build" "-zero-release"
+                                                  #:directories? #t))))
+                     (copy-recursively (string-append images "/images/jdk")
+                                       #$output:jdk)
+                     (copy-recursively (string-append images "/images/jre")
+                                       #$output)
+                     (copy-recursively (string-append images "/images/docs")
+                                       #$output:doc))))
+               (replace 'install-libjvm
+                 (lambda _
+                   (let ((lib-out (string-append #$output "/lib"))
+                         (lib-jdk (string-append #$output:jdk "/lib")))
+                     (symlink (string-append lib-jdk "/zero/libjvm.so")
+                              (string-append lib-jdk "/libjvm.so"))
+                     (symlink (string-append lib-out "/zero/libjvm.so")
+                              (string-append lib-out "/libjvm.so"))))))
+           phases))))))
 
 ;;; Convenience alias to point to the latest version of OpenJDK.
 (define-public openjdk openjdk25)

gnu/packages/jupyter.scm

@@ -22,6 +22,7 @@
 ;;; Copyright © 2024, 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;; Copyright © 2024-2025 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2025 Ghislain Vaillant <ghislain.vaillant@inria.fr>
+;;; Copyright © 2026 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -52,7 +53,9 @@
   #:use-module (gnu packages bash)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cpp)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages docker)
+  #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages monitoring)
   #:use-module (gnu packages networking)
@@ -1710,13 +1713,13 @@ analyzing Jupyter Notebooks.")
 (define-public python-qtconsole
   (package
     (name "python-qtconsole")
-    (version "5.7.0")
+    (version "5.7.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "qtconsole" version))
        (sha256
-        (base32 "0w9i0s70dm39cxgn3vh4wcaxdywzp9j0ac7f49q4qmggx4f3fcqd"))))
+        (base32 "088m56fav6xlcw55srxz96yf7rj2ndmycy4f3m69498r2swqbd17"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1764,6 +1767,67 @@ analyzing Jupyter Notebooks.")
 rich media output.")
     (license license:bsd-3)))
 
+(define-public python-spyder-kernels
+  (package
+    (name "python-spyder-kernels")
+    (version "3.1.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/spyder-ide/spyder-kernels")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0yhrifh148g93qkwx9ggsh2kr9789apzlw91ais4dyas5yf1xj8w"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-k" (string-append
+                    ;; Avoid pulling Django for a single test.
+                    "not test_django_settings"
+                    ;; AssertionError.
+                    " and not test_umr_reload_modules"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'redirect-HOME
+            (lambda _
+              (setenv "HOME" "/tmp"))))))
+    (propagated-inputs (list python-cloudpickle
+                             python-ipykernel
+                             python-ipython
+                             python-jupyter-client
+                             python-packaging
+                             python-pyxdg
+                             python-pyzmq
+                             python-traitlets
+                             python-wurlitzer))
+    (native-inputs (list python-anyio
+                         python-cython
+                         python-dask
+                         python-h5py
+                         python-matplotlib
+                         python-numpy
+                         python-pandas
+                         python-pillow
+                         python-polars
+                         python-pyarrow
+                         python-pydicom
+                         python-pytest
+                         python-scipy
+                         python-setuptools
+                         python-xarray))
+    (home-page "https://github.com/spyder-ide/spyder-kernels")
+    (synopsis "Jupyter kernels for Spyder's console")
+    (description "This package provides Jupyter kernels for use with the
+consoles of Spyder, the Scientific Python Development Environment.
+
+These kernels can be launched either through Spyder itself or in an
+independent Python session, and allow for interactive or file-based execution
+of Python code inside Spyder.")
+    (license license:expat)))
+
 (define-public python-voila
   (package
     (name "python-voila")

gnu/packages/kde-multimedia.scm

@@ -1191,37 +1191,42 @@ CDs.")
 (define-public plasmatube
   (package
     (name "plasmatube")
-    (version "25.12.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://kde/stable/release-service/" version
-                                  "/src/plasmatube-" version ".tar.xz"))
-              (sha256
-               (base32
-                "1jc6iqcxz0zyai26vx80nyfr818r4cj8lpw0b1pbvb1vya12v8zy"))))
+    (version "26.04.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://kde/stable/release-service/" version
+                           "/src/plasmatube-" version ".tar.xz"))
+       (sha256
+        (base32 "0dby9wypbrhg6g03kvl8fc40zpnri03hf3kk3vi1z16pwc7sn093"))))
     (build-system qt-build-system)
     (native-inputs (list extra-cmake-modules pkg-config python-minimal))
     (inputs
      (list kconfig
            kcoreaddons
            kdbusaddons
+           kdeclarative ; for org.kde.kquickcontrolsaddons
+           ki18n
            kirigami
            kirigami-addons
-           ki18n
+           kitemmodels
            kwindowsystem
            mpvqt
            purpose
+           qqc2-desktop-style ; for org.kde.desktop
            qtdeclarative
+           qtkeychain-qt6
            qtmultimedia
            qtsvg
-           qtkeychain-qt6
            qtwayland
+           sonnet
            yt-dlp))
     (arguments (list #:qtbase qtbase))
     (home-page "https://apps.kde.org/plasmatube/")
-    (synopsis "Kirigami YouTube video player")
-    (description "This package provides YouTube video player based
-on QtMultimedia and @command{yt-dlp}.")
+    (synopsis "YouTube and PeerTube video player")
+    (description
+     "Plasmatube is a YouTube video player that uses Invidious and Piped
+APIs.  It can also play videos from PeerTube sources.")
     (license license:gpl3+)))
 
 (define-public rattlesnake

gnu/packages/librewolf.scm

@@ -125,14 +125,14 @@
   ;; ex:
   ;; tar xf /gnu/store/...-firefox-123.4.source.tar.xz -O \
   ;;     firefox-123.4/browser/locales/l10n-changesets.json | grep revision
-  (let ((commit "0245ffb160688061f0e0c67ea488bcdfdacbeca4"))
+  (let ((commit "fefe280d909d0eee8d60edd2a6db7d969df56c5b"))
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/mozilla-l10n/firefox-l10n.git")
             (commit commit)))
       (file-name (git-file-name "firefox-l10n" commit))
-      (sha256 (base32 "0y8xdxql04yys0wj685v4yp3kmx1ivnndg6z11vam8vszh0j7ak6")))))
+      (sha256 (base32 "0z1ksvspbn4bbzxdl2w4x7bg36j4rwhaby8g37apg4393frh558i")))))
 
 (define* (make-librewolf-source #:key version firefox-hash librewolf-hash l10n)
   (let* ((ff-src (firefox-source-origin
@@ -205,7 +205,8 @@
        (search-patches
         "librewolf-compare-paths.patch"
         "librewolf-use-system-wide-dir.patch"
-        "librewolf-add-store-to-rdd-allowlist.patch"))
+        "librewolf-add-store-to-rdd-allowlist.patch"
+        "librewolf-150.0-encoding_rs-rust-fix.patch"))
       ;; Slim down the tarball by removing unbundled libraries and 75 Mo (800+
       ;; Mo uncompressed) of unused tests.
       ;; TODO: Unbundle security/nss and media/libpng.
@@ -244,17 +245,17 @@
 ;; It's used for cache validation and therefore can lead to strange bugs.
 ;; ex: date '+%Y%m%d%H%M%S'
 ;; or: (format-time-string "%Y%m%d%H%M%S")
-(define %librewolf-build-id "20260409162101")
+(define %librewolf-build-id "20260421153818")
 
 (define-public librewolf
   (package
     (name "librewolf")
-    (version "149.0.2-2")
+    (version "150.0-1")
     (source
      (make-librewolf-source
       #:version version
-      #:firefox-hash "1kkhg3lgyakinn5ankxrlxbf39wi61mqbhwrj1l4q5l7y0n1m4va"
-      #:librewolf-hash "1bai8g2kc9snck2f724al29q6r57vkj3d7v58rf0mgzpqzvwnw5f"
+      #:firefox-hash "151rxzl80dm8jsxl6fwzgbirwq4zpms5adwwnbjcwdd1r3s3vr7v"
+      #:librewolf-hash "0iw9v3zc1fxc93yyhldqarxaypgmbndh2ylsy330kcbpb6p1gnmr"
       #:l10n firefox-l10n))
     (build-system gnu-build-system)
     (arguments
@@ -352,18 +353,18 @@
                              (cdr pref)))
                    `(("extensions.getAddons.search.browseURL"
                       ,(string-append
-                        "https://gnuzilla.gnu.org/mozzarella/"
+                        "https://gnuzilla.gnu.org/"
                         "search.php?q=%TERMS%"))
                      ("extensions.getAddons.get.url" .
-                      "https://gnuzilla.gnu.org/mozzarella")
+                      "https://gnuzilla.gnu.org")
                      ("extensions.getAddons.link.url" .
-                      "https://gnuzilla.gnu.org/mozzarella")
+                      "https://gnuzilla.gnu.org")
                      ("extensions.getAddons.discovery.api_url" .
-                      "https://gnuzilla.gnu.org/mozzarella")
+                      "https://gnuzilla.gnu.org")
                      ("extensions.getAddons.langpacks.url" .
-                      "https://gnuzilla.gnu.org/mozzarella")
+                      "https://gnuzilla.gnu.org")
                      ("lightweightThemes.getMoreURL" .
-                      "https://gnuzilla.gnu.org/mozzarella")))))))
+                      "https://gnuzilla.gnu.org")))))))
           (add-after 'patch-source-shebangs 'patch-cargo-checksums
             (lambda _
               (use-modules (guix build cargo-utils))

gnu/packages/linux.scm

@@ -2767,32 +2767,6 @@ This package provides the @command{corefreqd} data collection daemon, the
     (supported-systems (list "x86_64-linux"))
     (license license:gpl2)))
 
-(define-public librem-ec-acpi-linux-module
-  (package
-    (name "librem-ec-acpi-linux-module")
-    (version "0.9.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://source.puri.sm/nicole.faerber/librem-ec-acpi-dkms")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0m8hamf0550083jnk5q4hv20l8lfiardnkxbib4hhvqghpzzbxl0"))))
-    (build-system linux-module-build-system)
-    (arguments
-     (list #:tests? #f))                ; no test suite
-    (home-page "https://source.puri.sm/nicole.faerber/librem-ec-acpi-dkms")
-    (synopsis "Linux kernel module to control the Librem Embedded Controller")
-    (description
-     "This is the Linux kernel @acronym{ACPI, Advanced Configuration and Power
-Interface} platform driver for the @acronym{EC, Embedded Controller} firmware
-on Purism Librem laptop computers.  It allows user-space control over the
-battery charging thresholds, keyboard backlight, fans and thermal monitors,
-and the notification, WiFi, and Bluetooth LED.")
-    (license license:gpl2)))
-
 (define-public tuxedo-keyboard
   (package
     (name "tuxedo-keyboard")
@@ -2823,70 +2797,6 @@ kernel modules to control the keyboard on most Tuxedo computers. The @code{tuxed
 module is also needed for the @code{tuxedo-control-center} (short tcc) package.")
     (license license:gpl2+)))
 
-(define-public evdi
-  (package
-    (name "evdi")
-    (version "1.14.8")                  ;inherited by libevdi
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/DisplayLink/evdi")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "18n8kk4gbbj252a2dqb7mbpscfb437x42flh1fsl4g5c8brczc77"))))
-    (build-system linux-module-build-system)
-    (arguments
-     (list #:tests? #f                  ;no test suite
-           #:phases #~(modify-phases %standard-phases
-                        (add-after 'unpack 'chdir
-                          (lambda _
-                            (chdir "module"))))))
-    (home-page "https://github.com/DisplayLink/evdi")
-    (synopsis
-     "@acronym{EVDI, Extensible Virtual Display Interface} Linux kernel module")
-    (description
-     "The @acronym{EVDI, Extensible Virtual Display Interface} is a Linux kernel
-module that enables management of multiple screens, allowing user-space programs
-to take control over what happens with the image.  It is essentially a virtual
-display for which applications using the @code{libevdi} library can add, remove,
-and receive screen updates.
-
-The EVDI driver uses the standard Linux @acronym{DRM, Direct Rendering Manager}.
-Its displays can be controlled by standard tools such as @command{xrandr} and
-display settings applets in graphical environments")
-    (license license:gpl2)))
-
-(define-public libevdi
-  (package
-    (inherit evdi)
-    (name "libevdi")
-    (build-system gnu-build-system)
-    (arguments
-     (list #:tests? #f                  ;no test suite
-           #:make-flags
-           #~(list (string-append "CC=" #$(cc-for-target)))
-           #:phases #~(modify-phases %standard-phases
-                        (delete 'configure)
-                        (add-after 'unpack 'chdir
-                          (lambda _
-                            (chdir "library")))
-                        (replace 'install
-                          (lambda* _
-                            (let* ((lib (string-append #$output "/lib")))
-                              (mkdir-p lib)
-                              (install-file "libevdi.so" lib)))))))
-    (inputs (list libdrm))
-    (native-inputs (list pkg-config))
-    (synopsis
-     "@acronym{EVDI, Extensible Virtual Display Interface} user-space library")
-    (description
-     "Libevdi is a library that gives applications easy access to
-@acronym{EVDI, Extensible Virtual Display Interface} devices provided by the
-@code{evdi} driver package.")
-    (license license:lgpl2.1)))
-
 (define-public ec
   (package
     (name "ec")
@@ -2912,62 +2822,6 @@ registers of the @acronym{EC, Embedded Controller} supported by the
 @code{ec_sys} Linux driver.")
     (license license:gpl2)))
 
-(define-public lkrg
-  (package
-    (name "lkrg")
-    (version "0.9.7")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/lkrg-org/lkrg")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0k0z9caj48nqjwk3bapgfcdzi1lkizxcjj4r1dvkvwsk38mbk1c4"))))
-    (build-system linux-module-build-system)
-    (arguments
-     (list #:linux linux-libre
-           #:tests? #f
-           #:make-flags #~(list (string-append "CC="
-                                               #$(cc-for-target))
-                                (string-append "SYSSRC="
-                                               (assoc-ref %build-inputs
-                                                "linux-module-builder")
-                                               "/lib/modules/build"))))
-    (inputs (list bash-minimal))
-    (home-page "https://lkrg.org/")
-    (synopsis "Linux Kernel Runtime Guard")
-    (description
-     "This package performs runtime integrity checking of the Linux kernel and
-detection of security vulnerability exploits against the kernel.")
-    (license license:gpl2)))
-
-(define-public vhba-module
-  (package
-    (name "vhba-module")
-    (version "20211218")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "http://downloads.sourceforge.net/cdemu/vhba-module/vhba-module-"
-             version ".tar.xz"))
-       (sha256
-        (base32 "1dkprnnya0i8121p7ip4g8cww99drk7fzbwcxx65x02jqk0siibj"))))
-    (build-system linux-module-build-system)
-    (arguments
-     (list #:tests? #f))                ; no test suite
-    (home-page "https://cdemu.sourceforge.io/")
-    (synopsis "Linux kernel module that emulates SCSI devices")
-    (description
-     "The @acronym{VHBA, Virtual SCSI Host Bus Adapter} module is the link
-between the CDemu user-space daemon and the kernel Linux.  It acts as a
-low-level SCSI driver that emulates a virtual SCSI adapter which can have
-multiple virtual devices attached to it.  Its typical use with CDEmu is to
-emulate optical devices such as DVD and CD-ROM drives.")
-    (license license:gpl2+)))
-
 (define-public bbswitch-module
   ;; Use "develop" branch since stable release does not build on Linux >= 5.6.
   ;; See https://github.com/Bumblebee-Project/bbswitch/issues/205.
@@ -3164,36 +3018,6 @@ Linux kernel module, it also contains a modprobe configuration and udev rules,
 which need to be installed separately.")
     (license license:gpl3+)))
 
-(define-public vendor-reset-linux-module
-  (let ((commit "4b466e92a2d9f76ce1082cde982c7be0be91e248")
-        (revision "0"))
-    (package
-      (name "vendor-reset-linux-module")
-      (version (git-version "0.1.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/gnif/vendor-reset")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "1gaf4j20grng689c9fylcqri3j9ycnhr2bsva2z6qcdqvzl6yxbi"))))
-      (build-system linux-module-build-system)
-      (arguments
-       (list #:tests? #f)) ;no test suite
-      (home-page "https://github.com/gnif/vendor-reset")
-      (synopsis
-       "Kernel module that resets GPUs that are affected by the reset bug")
-      (description
-       "This package provides a kernel module that is capable of
-resetting hardware devices into a state where they can be
-re-initialized or passed through into a virtual machine (VFIO).
-While it would be great to have these in the kernel as PCI quirks,
-some of the reset procedures are very complex and would never be
-accepted as a quirk (ie AMD Vega 10).")
-      (license license:gpl2))))
-
 
 ;;;
 ;;; Pluggable authentication modules (PAM).
@@ -12094,7 +11918,7 @@ provides user-space tools for creating EROFS file systems.")
 (define-public rasdaemon
   (package
     (name "rasdaemon")
-    (version "0.8.3")
+    (version "0.8.4")
     (source
      (origin
        (method git-fetch)
@@ -12103,9 +11927,17 @@ provides user-space tools for creating EROFS file systems.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0vfw4vf75fnpbxnfsmpdwdzhplnccz24j23bg6nsb3b4wa8hv4sa"))))
+        (base32 "1930g35igfdw5bzcd6diy59rm1q4yirpjgqznfqfsichnmk04kmf"))))
     (native-inputs (list autoconf automake libtool pkg-config))
-    (inputs (list bash-minimal libtraceevent perl perl-dbd-sqlite sqlite dmidecode kmod))
+    (inputs
+     (list bash-minimal
+           dmidecode
+           kmod
+           libtraceevent
+           pciutils
+           perl
+           perl-dbd-sqlite
+           sqlite))
     (arguments
      (list
       #:configure-flags

gnu/packages/lua.scm

@@ -89,6 +89,7 @@
   #:use-module (gnu packages wget)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
+  #:use-module (ice-9 match)
   #:use-module ((srfi srfi-1) #:hide (zip)))
 
 (define (lua-search-paths version)
@@ -170,6 +171,22 @@ for configuration, scripting, and rapid prototyping.")
                                               "lua-5.4-search-paths.patch"))))
            (native-search-paths (lua-search-paths "5.4"))))
 
+
+(define-public lua-5.4-for-c++
+  (let ((lua-pkg lua-5.4))
+    (hidden-package
+     (package/inherit lua-pkg
+       (name (string-append (package-name lua-pkg) "-for-c++"))
+       (arguments
+        (substitute-keyword-arguments (package-arguments lua-pkg)
+          ((#:make-flags old-flags)
+           (map
+            (match-lambda
+              ((string-append "CC=" _)
+               `(string-append "CC=" ,(cxx-for-target)))
+              (else else))
+            old-flags))))))))
+
 (define-public lua-5.2
   (package (inherit lua)
            (version "5.2.4")

gnu/packages/luanti.scm

@@ -488,7 +488,7 @@ with different rules and mechanics.")
 (define-public luanti-mineclonia
   (package
     (name "luanti-mineclonia")
-    (version "0.120.1")
+    (version "0.121.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -497,7 +497,7 @@ with different rules and mechanics.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "135xllkvdravry25y1f94wqn7nxb0pnrpn7xiagh2b5vjbajhdg4"))))
+                "1c3x59iq04vfc0fa09z6g8davrr2vhdywppdbgyw64n7vk4f6br9"))))
     (build-system copy-build-system)
     (arguments
      `(#:install-plan

gnu/packages/maths.scm

@@ -2475,6 +2475,9 @@ similar to MATLAB, GNU Octave or SciPy.")
                    ;; "--enable-doxygen"
                    "--enable-dot"
                    "--enable-netcdf-4"
+                   #$@(if (or (target-x86-32?) (target-arm32?))
+                          '("CFLAGS=-Wno-error=incompatible-pointer-types")
+                          '())
                    (string-append "--with-plugin-dir=" #$output "/lib/hdf5-plugins"))
            #:phases
            #~(modify-phases %standard-phases
@@ -2486,7 +2489,15 @@ similar to MATLAB, GNU Octave or SciPy.")
                      (("testurl.sh") ""))
                    (substitute* "nczarr_test/Makefile.in"
                      (("/bin/bash")
-                      (search-input-file inputs "bin/bash")))))
+                      (search-input-file inputs "bin/bash")))
+                   ;; This test fails on 32 bit platforms.
+                   #$@(if (or (target-x86-32?) (target-arm32?))
+                          '((substitute* '("ncdump/tst_netcdf4_4.sh"
+                                           "ncdump/tst_nccopy4.sh")
+                              (("#!/bin/sh" m) (string-append m "\nexit 0\n")))
+                            (substitute* "ncdump/Makefile.in"
+                              (("tst_netcdf4_4.log") "")))
+                          '())))
                (add-before 'configure 'fix-source-date
                  (lambda _
                    ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
@@ -9647,7 +9658,7 @@ researchers and developers alike to get started on SAT.")
 (define-public kissat
   (package
     (name "kissat")
-    (version "4.0.1")
+    (version "4.0.4")
     (source
      (origin
        (method git-fetch)
@@ -9657,7 +9668,7 @@ researchers and developers alike to get started on SAT.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0acg61cfcjg13if2i375cyl4xvwmabhfhi9z8pnw971046am6bzv"))))
+         "1snimig4cp97p570nin2i38my72zvwypldyhr125i1z6cd9pa046"))))
     (build-system gnu-build-system)
     (inputs (list xz gzip lzip bzip2 p7zip))
     (arguments
@@ -9668,6 +9679,10 @@ researchers and developers alike to get started on SAT.")
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-source
             (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* "test/testfile.c"
+                ;; Don't check if /etc/passwd isn't writable.
+                ;; When building in a container/chroot, this fails spuriously.
+                ((".*/etc/passwd.*") ""))
               (substitute* "scripts/generate-build-header.sh"
                 ;; by default BUILD includes the build date which
                 ;; makes the build not reproducible.
@@ -11454,7 +11469,7 @@ expression parsing and evaluation.")
 (define-public highs
   (package
     (name "highs")
-    (version "1.10.0")
+    (version "1.14.0")
     (source
      (origin
        (method git-fetch)
@@ -11463,14 +11478,14 @@ expression parsing and evaluation.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "19q99nkk6r6k91gxp8a5rjil1399qyfgfc6jqlg2gd82vpcw8c8b"))))
+        (base32 "16y664rzvxd8785195k0srz0842zvl0zdkf6qi103p503pj81afh"))))
     (build-system cmake-build-system)
     (home-page "https://highs.dev")
     (synopsis "High performance software for linear optimization")
     (description
      "HiGHS provides serial and parallel solvers for large-scale sparse
 linear programming (LP), mixed-integer programming (MIP), and quadratic
-programming (QP) models")
+programming (QP) models.")
     (license license:expat)))
 
 (define-public trilinos-zoltan

gnu/packages/messaging.scm

@@ -1151,7 +1151,7 @@ simultaneously and therefore appear under the same nickname on IRC.")
 (define-public python-nbxmpp
   (package
     (name "python-nbxmpp")
-    (version "7.1.0")
+    (version "7.2.0")
     (source
      (origin
        (method git-fetch)
@@ -1160,7 +1160,7 @@ simultaneously and therefore appear under the same nickname on IRC.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1n7b6yv2k89hsmhmx9pi7m8l3aq97xppaz3hm7mvqgvxnlw0c1kr"))))
+        (base32 "1dyf4jh76ffbl45x4cpk6rsn1r4wck54b3d8wfd2swxaqq4p7lis"))))
     (build-system pyproject-build-system)
     (arguments (list #:test-backend #~'unittest))
     (propagated-inputs
@@ -1184,7 +1184,7 @@ of xmpppy.")
 (define-public gajim
   (package
     (name "gajim")
-    (version "2.4.5")
+    (version "2.4.6")
     (source
      (origin
        (method url-fetch)
@@ -1192,7 +1192,7 @@ of xmpppy.")
                            (version-major+minor version)
                            "/gajim-" version ".tar.gz"))
        (sha256
-         (base32 "1rkxzf1pfd29rip5bw4730fl7b2xk12zpiwnfkyzxlkmbh4j3kp2"))
+         (base32 "0ilpgkzw45scjlnag94p8v6np629v7w0ihci5a2w5d742gpqvq6c"))
        (patches
          (search-patches "gajim-honour-GAJIM_PLUGIN_PATH.patch"))))
     (build-system pyproject-build-system)
@@ -1278,7 +1278,6 @@ of xmpppy.")
            glib
            glib-networking
            gsettings-desktop-schemas
-           gsound
            libspelling
            libadwaita
            gstreamer
@@ -1293,6 +1292,7 @@ of xmpppy.")
            libsoup
            libxscrnsaver
            network-manager
+           python-cryptography
            python-css-parser
            python-dbus-1.2
            python-emoji
@@ -2839,7 +2839,7 @@ implementation of an MQTT version client class.")
 (define-public psi-plus
   (package
     (name "psi-plus")
-    (version "1.5.1484")
+    (version "1.5.2115")
     (source
      (origin
        (method git-fetch)
@@ -2853,7 +2853,7 @@ implementation of an MQTT version client class.")
         `(begin
            (delete-file-recursively "3rdparty")))
        (sha256
-        (base32 "1jsm39nzzbqkp3zc0xqx7jid6p4q1ra28xad38wjr2l1jb8qjn24"))))
+        (base32 "14za9rh7nszv5px5a2w43ysi9977zws8a5mxsh7wc8ksr693faz2"))))
     (build-system qt-build-system)
     (arguments
      `(#:tests? #f                      ; No target
@@ -2910,19 +2910,13 @@ implementation of an MQTT version client class.")
                 "qite/qiteaudio.h")
                (("qiteaudiorecorder.h")
                 "qite/qiteaudiorecorder.h"))))
-         (add-after 'install 'wrap-env
+         (add-after 'install 'wrap-executable
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))
-               (for-each
-                (lambda (name)
-                  (let ((file (string-append out "/bin/" name))
-                        (gst-plugin-path (getenv "GST_PLUGIN_SYSTEM_PATH"))
-                        (gi-typelib-path (getenv "GI_TYPELIB_PATH")))
-                    (wrap-program file
-                      `("GST_PLUGIN_SYSTEM_PATH" ":" prefix (,gst-plugin-path))
-                      `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path)))))
-                '("psi-plus")))))
-         (add-after 'wrap-env 'glib-or-gtk-compile-schemas
+               (wrap-program (string-append out "/bin/psi-plus")
+                 `("GST_PLUGIN_SYSTEM_PATH" ":" prefix (,(getenv "GST_PLUGIN_SYSTEM_PATH")))
+                 `("GI_TYPELIB_PATH" ":" prefix (,(getenv "GI_TYPELIB_PATH")))))))
+         (add-after 'wrap-executable 'glib-or-gtk-compile-schemas
            (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-compile-schemas))
          (add-after 'glib-or-gtk-compile-schemas 'glib-or-gtk-wrap
            (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
@@ -2945,6 +2939,7 @@ implementation of an MQTT version client class.")
            libgcrypt
            libgpg-error
            libidn
+           libomemo-c
            libotr
            libsignal-protocol-c
            tidy-html
@@ -2964,11 +2959,11 @@ implementation of an MQTT version client class.")
            libxcb
            libxscrnsaver
            zlib))
-    (home-page "https://psi-plus.com/")
+    (home-page "https://psi-im.com/")
     (synopsis "Qt-based XMPP Client")
     (description
-     "Psi+ is a spin-off of Psi XMPP client.  It is a powerful XMPP client
-designed for experienced users.")
+     "Psi+ is a powerful XMPP client designed for experienced users.
+It's a spin-off of the Psi XMPP client.")
     (license license:gpl2+)))
 
 (define-deprecated-package psi

gnu/packages/monitoring.scm

@@ -1,11 +1,16 @@
 ;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2015 Siniša Biđin <sinisa@bidin.eu>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2021, 2021 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2021 Stefan Reichör <stefan@xsteve.at>
-;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
 ;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
 ;;; Copyright © 2018-2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2018, 2019, 2020 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2019, 2023 Vasile Dumitrascu <va511e@yahoo.com>
 ;;; Copyright © 2020 Alex ter Weele <alex.ter.weele@gmail.com>
 ;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
 ;;; Copyright © 2021, 2022 Marius Bakke <marius@gnu.org>
@@ -19,9 +24,6 @@
 ;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;; Copyright © 2025 Giacomo Leidi <therewasa@fishinthecalculator.me>
 ;;; Copyright © 2025 Christian Birk Sørensen <chrbirks@gmail.com>
-;;; Copyright © 2015 Siniša Biđin <sinisa@bidin.eu>
-;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
-;;; Copyright © 2019, 2023 Vasile Dumitrascu <va511e@yahoo.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -70,6 +72,7 @@
   #:use-module (gnu packages golang-check)
   #:use-module (gnu packages golang-web)
   #:use-module (gnu packages golang-xyz)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages image)
   #:use-module (gnu packages lua)
   #:use-module (gnu packages mail)
@@ -411,6 +414,37 @@ system statistics (CPU, disk, and memory usage, etc.) and more on the
 desktop.")
     (license license:gpl3+)))
 
+(define-public gkrellm
+  (package
+    (name "gkrellm")
+    (version "2.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://gkrellm.srcbox.net/releases/gkrellm-"
+                           version ".tar.bz2"))
+       (sha256
+        (base32 "0qvy2xmwmfy5f0g09yn9lr262shnx82ba04r5il2wj4qscg3r7h8"))))
+    (build-system gnu-build-system)
+    (inputs (list gtk+-2 libsm))
+    (native-inputs (list gettext-minimal pkg-config))
+    (arguments
+     (list
+      #:tests? #f ;there is no check target
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)) ;no configure script
+      #:make-flags
+      #~(list (string-append "INSTALLROOT=" #$output)
+              (string-append "CC=" #$(cc-for-target)))))
+    (home-page "https://gkrellm.srcbox.net/")
+    (synopsis "System monitors")
+    (description
+     "GKrellM is a single process stack of system monitors which supports
+applying themes to match its appearance to your window manager, Gtk, or any
+other theme.")
+    (license license:gpl3+)))
+
 (define-public glances
   (package
     (name "glances")

gnu/packages/mpi.scm

@@ -76,95 +76,7 @@
   #:use-module (srfi srfi-1)
   #:use-module (ice-9 match))
 
-(define-public hwloc-1
-  (package
-    (name "hwloc")
-    (version "1.11.13")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://www.open-mpi.org/software/hwloc/v"
-                                  (version-major+minor version)
-                                  "/downloads/hwloc-" version ".tar.bz2"))
-              (sha256
-               (base32
-                "1j69p8a1pjpbpwn4w7l4dfxmaxxqikchjzqw1ncw05zmcmvlnjd4"))
-              (patches (search-patches "hwloc-1-test-btrfs.patch"))))
-
-    (properties
-     ;; Tell the 'generic-html' updater to monitor this URL for updates.
-     `((release-monitoring-url
-        . "https://www-lb.open-mpi.org/software/hwloc/current")))
-
-    (build-system gnu-build-system)
-    (outputs '("out"           ;'lstopo' & co., depends on Cairo, libx11, etc.
-               "lib"           ;small closure
-               "doc"           ;400+ section 3 man pages
-               "debug"))
-    (inputs
-     (append (if (%current-target-system)
-                 '()                  ;fewer dependencies when cross-compiling
-                 (list libx11 cairo ncurses expat))
-             (if (target-arm32?) '() (list numactl))))
-    (propagated-inputs
-     ;; hwloc.pc lists it in 'Requires.private'.
-     (list libpciaccess))
-    (native-inputs
-     (list pkg-config))
-    (arguments
-     (list #:configure-flags
-           #~(list "--localstatedir=/var")
-           #:phases
-           #~(modify-phases %standard-phases
-               (add-before 'check 'skip-linux-libnuma-test
-                 (lambda _
-                   ;; Arrange to skip 'tests/linux-libnuma', which fails on some
-                   ;; machines: <https://github.com/open-mpi/hwloc/issues/213>.
-                   (substitute* "tests/linux-libnuma.c"
-                     (("numa_available\\(\\)")
-                      "-1"))))
-               (add-after 'install 'refine-libnuma
-                 ;; Give -L arguments for libraries to avoid propagation
-                 (lambda* (#:key inputs outputs #:allow-other-keys)
-                   (let ((out  (assoc-ref outputs "lib"))
-                         (numa (assoc-ref inputs "numactl")))
-                     (substitute* (map (lambda (f) (string-append out "/" f))
-                                       '("lib/pkgconfig/hwloc.pc" "lib/libhwloc.la"))
-                       (("-lnuma" lib)
-                        (string-append "-L" numa "/lib " lib))))))
-               (add-after 'install 'avoid-circular-references
-                 (lambda* (#:key outputs #:allow-other-keys)
-                   (let ((lib (assoc-ref outputs "lib")))
-                     ;; Suppress the 'prefix=' and 'exec_prefix=' lines so that the
-                     ;; "lib" output doesn't refer to "out".
-                     (substitute* (string-append lib "/lib/pkgconfig/hwloc.pc")
-                       (("^.*prefix=.*$")
-                        "")))))
-               (add-after 'install 'move-man3-pages
-                 (lambda* (#:key outputs #:allow-other-keys)
-                   ;; Move section 3 man pages to the "doc" output.
-                   (let ((out (assoc-ref outputs "out"))
-                         (doc (assoc-ref outputs "doc")))
-                     (copy-recursively (string-append out "/share/man/man3")
-                                       (string-append doc "/share/man/man3"))
-                     (delete-file-recursively
-                      (string-append out "/share/man/man3"))))))))
-    (home-page "https://www.open-mpi.org/projects/hwloc/")
-    (synopsis "Abstraction of hardware architectures")
-    (description
-     "hwloc provides a portable abstraction (across OS,
-versions, architectures, ...) of the hierarchical topology of modern
-architectures, including NUMA memory nodes, sockets, shared caches, cores and
-simultaneous multithreading.  It also gathers various attributes such as cache
-and memory information.  It primarily aims at helping high-performance
-computing applications with gathering information about the hardware so as to
-exploit it accordingly and efficiently.
-
-hwloc may display the topology in multiple convenient formats.  It also offers
-a powerful programming interface to gather information about the hardware,
-bind processes, and much more.")
-    (license license:bsd-3)))
-
-(define-public hwloc-2
+(define-public hwloc
   (package
     (name "hwloc")
     (version "2.13.0")
@@ -274,10 +186,6 @@ a powerful programming interface to gather information about the hardware,
 bind processes, and much more.")
     (license license:bsd-3)))
 
-(define-public hwloc
-  ;; The latest stable series of hwloc.
-  hwloc-2)
-
 (define-public openmpi-4
   (package
     (name "openmpi")
@@ -306,7 +214,7 @@ bind processes, and much more.")
                                (package-supported-systems package)))
                   (list package)
                   '()))))
-       (append (list `(,hwloc-2 "lib")
+       (append (list `(,hwloc "lib")
                      gfortran
                      libfabric-1                  ;fails to build with 2.3
                      libevent
@@ -699,7 +607,7 @@ arrays) that expose a buffer interface.")
     (build-system gnu-build-system)
     (inputs
      `(,zlib
-       (,hwloc-2 "lib")
+       (,hwloc "lib")
        ,slurm
        ,@(if (and (not (%current-target-system))
                   (member (%current-system) (package-supported-systems ucx)))

gnu/packages/node.scm

@@ -966,7 +966,7 @@ fi"
            icu4c-76
            libuv-for-node-lts
            `(,nghttp2 "lib")
-           openssl
+           openssl-3.0
            zlib
            ; ngtcp2? nghttp3?
            ;; Regular build-time dependencies.
@@ -986,7 +986,7 @@ fi"
            ngtcp2
            nghttp3
            `(,nghttp2 "lib")
-           openssl
+           openssl-3.0
            zlib))
     (supported-systems
       (cons "riscv64-linux" (package-supported-systems node-bootstrap)))

gnu/packages/nss.scm

@@ -286,7 +286,7 @@ This package tracks the Extended Support Release (ESR) channel.")
   (package
    (inherit nss)
    (name "nss-rapid")
-   (version "3.121")
+   (version "3.123")
    (source
     (origin
       (inherit (package-source nss))
@@ -297,7 +297,7 @@ This package tracks the Extended Support Release (ESR) channel.")
               "releases/NSS_" version-with-underscores "_RTM/src/"
               "nss-" version ".tar.gz")))
       (sha256
-       (base32 "0bk3lxmj364vlf4x2q01pf0li3mm5ixgnfnxirxqp9xyh63qyfnb"))
+       (base32 "0jafdl18q9j36bwk73i462qkc24070b5llchffd7fsd2k0ri2i91"))
       (patches
        (search-patches "nss-3.56-pkgconfig.patch"
                        "nss-getcwd-nonnull.patch"

gnu/packages/ntp.scm

@@ -173,7 +173,7 @@ time-stamping or reference clock, sub-microsecond accuracy is possible.")
     (native-inputs (list which pkg-config))
     (inputs (cons* guile-3.0    ; for wrap-script
                    libevent
-                   openssl
+                   openssl-3.0
                    perl
                    perl-http-tiny
                    perl-io-socket-ssl

gnu/packages/nutrition.scm

@@ -81,72 +81,3 @@
     (description "This tool extracts cooking recipe from HTML structured data
 in the @url{https://schema.org/Recipe} format.")
     (license asl2.0)))
-
-(define-public gourmet
-  ;; Use the latest commit to gain Python 3 support.
-  (let ((revision "0")
-        (commit "8af29c8ded24528030e5ae2ea3461f61c1e5a575"))
-    (package
-      (name "gourmet")
-      (version (git-version "0.17.4" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-                (url "https://github.com/thinkle/gourmet")
-                (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "08fbw6zp32ws6w9czwy2sqc9c9izlkglsskshj2114d0l79z4gj8"))
-         (patches (search-patches "gourmet-sqlalchemy-compat.patch"))))
-      (build-system pyproject-build-system)
-      (arguments
-       (list
-        #:test-flags
-        ;; XXX: Some tests in deeper directories or otherwise discovered by
-        ;; Pytest are broken.
-        #~(list "--ignore-glob=gourmet/tests/**/*.py")
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-before 'build 'set-environemnt
-              (lambda _
-                (setenv "HOME" "/tmp")
-                (system "Xvfb &")
-                (setenv "DISPLAY" ":0")))
-            (add-after 'install 'install-dekstop-file-and-icons
-              (lambda _
-                (define share (string-append #$output "/share"))
-                (install-file ".flatpak/io.github.thinkle.Gourmet.desktop"
-                              (string-append share "/applications"))
-                (install-file ".flatpak/io.github.thinkle.Gourmet.svg"
-                              (string-append share "/icons/Gourmet")))))))
-      (native-inputs
-       (list python-dogtail
-             python-pytest
-             python-selenium
-             python-setuptools
-             xorg-server-for-tests))
-      (inputs
-       (list gtk+
-             python-argcomplete
-             python-beautifulsoup4
-             python-gst
-             python-keyring
-             python-lxml
-             python-pillow
-             python-pycairo
-             python-pyenchant
-             python-pygobject
-             python-requests
-             python-scrape-schema-recipe
-             python-sqlalchemy
-             python-toml))
-      (home-page "https://thinkle.github.io/gourmet/")
-      (synopsis "Recipe organizer")
-      (description
-       "Gourmet Recipe Manager is a recipe organizer that allows you to collect,
-search, organize, and browse your recipes.  Gourmet can also generate shopping
-lists and calculate nutritional information.  It imports Mealmaster,
-MasterCook and KRecipe files and exports PDFs, webpages, and other formats.")
-      (license gpl2+))))

gnu/packages/nvi.scm

@@ -1,8 +1,4 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014 Marek Benc <merkur32@gmail.com>
-;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2024 Herman Rimm <herman@rimm.ee>
-;;; Copyright © 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -20,98 +16,8 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages nvi)
-  #:use-module (gnu packages)
-  #:use-module (gnu packages autotools)
-  #:use-module (gnu packages dbm)
-  #:use-module (gnu packages ncurses)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix gexp)
-  #:use-module (guix licenses)
-  #:use-module (guix utils))
+  #:use-module (gnu packages text-editors)
+  #:use-module (guix deprecation))
 
-(define-public nvi
-  (package
-    (name "nvi")
-    (version "1.81.6")
-    (source
-      (origin
-        (method url-fetch)
-        (uri          ;; sites.google.coma/bostic.com/keithbostic/vi is stale.
-          (string-append "http://harrier.slackbuilds.org/misc/nvi-" version
-                         ".tar.bz2"))
-        (sha256
-          (base32 "0nbbs1inyrqds0ywn3ln5slv54v5zraq7lszkg8nsavv4kivhh9l"))
-        (patches (search-patches "nvi-assume-preserve-path.patch"
-                                 "nvi-dbpagesize-binpower.patch"
-                                 "nvi-add-function-prototypes.patch"
-                                 "nvi-db4.patch"))
-        (modules '((guix build utils)))
-        (snippet
-          ;; Create a wrapper for the configure script, make it executable.
-          '(let ((conf-wrap (open-output-file "configure")))
-             (display "#!/bin/sh" conf-wrap)
-             (newline conf-wrap)
-             (display
-               "../nvi-1.81.6/dist/configure --srcdir=../nvi-1.81.6/dist $@"
-               conf-wrap)
-             (newline conf-wrap)
-             (close-output-port conf-wrap)
-             (chmod "configure" #o0755)
-
-             ;; Glibc 2.30 removed the deprecated <sys/stropts.h>, so fall back
-             ;; to the internal PTY allocation logic.
-             (substitute* "ex/ex_script.c"
-               (("#ifdef HAVE_SYS5_PTY")
-                "#if defined(HAVE_SYS5_PTY) && !defined(__GLIBC__)"))
-             #t))))
-
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:out-of-source? #t
-      #:configure-flags
-      #~'("--enable-widechar"
-          #$@(if (%current-target-system)
-                 '("vi_cv_sprintf_count=yes")
-                 '()))
-      #:make-flags
-      #~(list
-         ;; Add CFLAGS to relax gcc-14's strictness.
-         ;; nvi's configure chokes on passing CFLAGS and ignores
-         ;; CFLAGS set in the environment.
-         (string-append "CFLAGS=-g -O2"
-                        " -Wno-error=incompatible-pointer-types"))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'configure 'fix-configure
-            (lambda* (#:key inputs native-inputs #:allow-other-keys)
-              ;; Replace outdated config.sub and config.guess:
-              (with-directory-excursion "dist"
-                (for-each
-                 (lambda (file)
-                   (chmod file #o755)
-                   (install-file
-                    (format #f "~a/share/automake-~a/~a"
-                            (assoc-ref (or native-inputs inputs)
-                                       "automake")
-                            #$(version-major+minor
-                               (package-version automake))
-                            file)
-                    "."))
-                 '("config.sub" "config.guess"))))))))
-    (inputs
-      (list bdb ncurses))
-    (native-inputs
-     (list automake)) ;Up to date 'config.guess' and 'config.sub'.
-    (synopsis "The Berkeley Vi Editor")
-    (description
-      "Vi is the original screen based text editor for Unix systems.  It is
-considered the standard text editor, and is available on almost all Unix
-systems.  Nvi is intended as a \"bug-for-bug compatible\" clone of the
-original BSD vi editor.  As such, it doesn't have a lot of snazzy features as
-do some of the other vi clones such as elvis and vim.  However, if all you
-want is vi, this is the one to get.")
-    (home-page "https://sites.google.com/a/bostic.com/keithbostic/vi")
-    (license bsd-3)))
+(define-deprecated/public-alias nvi
+  (@ (gnu packages text-editors) nvi))

gnu/packages/ocaml.scm

@@ -91,6 +91,7 @@
   #:use-module (gnu packages tls)
   #:use-module (gnu packages unicode)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages vim)
   #:use-module (gnu packages virtualization)
   #:use-module (gnu packages web)
   #:use-module (gnu packages web-browsers)
@@ -797,30 +798,29 @@ describing upgrade scenarios in package-based software distributions.")
 (define-public ocaml-mccs
   (package
     (name "ocaml-mccs")
-    (version "1.1+14")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/AltGr/ocaml-mccs")
-                     (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "17bvm0jhhs8h3p5sbb65asj53a8sxl634cc0kvcivpams74837zq"))))
+    (version "1.1+19")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/AltGr/ocaml-mccs")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1x1y5rhj4f0xakbgfn9f90a9xy09v99p8mc42pbnam5kghyjmxy6"))))
     (build-system dune-build-system)
     (propagated-inputs (list ocaml-cudf))
     (home-page "https://www.i3s.unice.fr/~cpjm/misc/")
     (synopsis "Upgrade path problem solver")
-    (description "Mccs (Multi Criteria CUDF Solver) is a CUDF problem solver.
+    (description
+     "Mccs (Multi Criteria CUDF Solver) is a CUDF problem solver.
 Mccs take as input a CUDF problem and computes the best solution according to
 a set of criteria.  It relies on a Integer Programming solver or a
 Pseudo Boolean solver to achieve its task.  Mccs can use a wide set of
 underlying solvers like Cplex, Gurobi, Lpsolver, Glpk, CbC, SCIP or WBO.")
-    (license (list
-               license:bsd-3
-               license:gpl3+
-               ;; With static-linking exception
-               license:lgpl2.1+))))
+    (license (list license:bsd-3 license:gpl3+
+                   ;; With static-linking exception
+                   license:lgpl2.1+))))
 
 (define-public ocaml-dose3
   (package
@@ -945,47 +945,156 @@ the opam file format.")
     ;; With static-linking exception
     (license license:lgpl2.1+)))
 
+(define-public ocaml-swhid-core
+  (package
+    (name "ocaml-swhid-core")
+    (version "0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/OCamlPro/swhid_core")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0h3zndyk94lf2lakc3cb8b7a00jqh0y1m8xk6mg61gj2kdpdbfdq"))))
+    (build-system dune-build-system)
+    (properties `((upstream-name . "swhid_core")))
+    (home-page "https://github.com/ocamlpro/swhid_core")
+    (synopsis "OCaml library to work with swhids")
+    (description
+     "swhid_core is an OCaml library to work with Software Heritage persistent
+identifiers (swhids).  This is the core library, for most use cases you should
+use the swhid library instead.")
+    (license license:isc)))
+
+(define-public ocaml-spdx-licenses
+  (package
+    (name "ocaml-spdx-licenses")
+    (version "1.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/kit-ty-kate/spdx_licenses")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "08vh9mfkq34f0l5ka94hhklc43kvz09wd04x1gkxkawn4786rf9z"))))
+    (build-system dune-build-system)
+    (native-inputs (list ocaml-alcotest))
+    (properties `((upstream-name . "spdx_licenses")))
+    (home-page "https://github.com/kit-ty-kate/spdx_licenses")
+    (synopsis "Strict SPDX License Expression parser")
+    (description
+     "This package provides an up-to-date and strict SPDX License Expression
+parser.  It implements the format described in:
+https://spdx.github.io/spdx-spec/v2.3/SPDX-license-expressions/
+See https://spdx.org/licenses/ for more details.")
+    (license license:expat)))
+
+(define-public ocaml-0install-solver
+  (package
+    (name "ocaml-0install-solver")
+    (version "2.18")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/0install/0install")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1hm72k355qwgh16hngmnd77bgawf20ipnqxfncdzl10rqrc0640b"))))
+    (build-system dune-build-system)
+    (arguments
+     `(#:package "0install-solver"))
+    (native-inputs (list ocaml-ounit2))
+    (home-page "https://docs.0install.net/developers/solver/")
+    (synopsis "Package dependency solver")
+    (description
+     "This package provides a package dependency resolver based on a SAT solver.
+This was originally written for the 0install package manager, but is now
+generic and is also used as a solver backend for opam.  The SAT solver is
+based on @code{MiniSat} (http://minisat.se/Papers.html) and the application to
+package management is based on OPIUM (Optimal Package Install/Uninstall
+Manager).  0install-solver uses a (novel?) strategy to find the optimal
+solution extremely quickly (even for a SAT-based solver).")
+    (license license:lgpl2.1+)))
+
+(define-public ocaml-opam-0install-cudf
+  (package
+    (name "ocaml-opam-0install-cudf")
+    (version "0.5.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ocaml-opam/opam-0install-cudf")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "12v1bgnxcxdylgxbsjlcr90rzwcp39rjlv191cy8g2s33nyxyi2c"))))
+    (build-system dune-build-system)
+    (propagated-inputs (list ocaml-cudf ocaml-0install-solver))
+    (native-inputs (list ocaml-alcotest))
+    (home-page "https://opam.ocaml.org")
+    (synopsis "Opam solver using 0install backend using the CUDF interface")
+    (description
+     "Opam's default solver is designed to maintain a set of packages over time,
+minimising disruption when installing new programs and finding a compromise
+solution across all packages.  In many situations (e.g. CI, local roots or
+duniverse builds) this is not necessary, and we can get a solution much faster
+by using a different algorithm.  This package provides a generic solver library
+which uses 0install's solver library.  The library uses the CUDF library in
+order to interface with opam as it is the format common used to talk to all the
+supported solvers.")
+    (license license:isc)))
+
 (define ocaml-opam-core
   (package
     (name "ocaml-opam-core")
-    (version "2.1.5")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/ocaml/opam")
-                     (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0ckd87rcmcz11iyhhm5qnmy27jbdffx6n1fr06hvrqqrzi00jljh"))))
+    (version "2.5.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ocaml/opam")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "10diw6wdl6v89kbvb8x22dbfacw1ikhl63hybyp2s7560450hygc"))))
     (build-system dune-build-system)
-    (arguments `(#:package "opam-core"
-                 ;; tests are run with the opam package
-                 #:tests? #f
-                 #:phases
-                 (modify-phases %standard-phases
-                   (add-before 'build 'pre-build
-                     (lambda* (#:key inputs make-flags #:allow-other-keys)
-                       (let ((bash (assoc-ref inputs "bash"))
-                             (bwrap (search-input-file inputs "/bin/bwrap")))
-                         (substitute* "src/core/opamSystem.ml"
-                           (("\"/bin/sh\"")
-                            (string-append "\"" bash "/bin/sh\""))
-                           (("getconf")
-                            (which "getconf")))))))))
-    (propagated-inputs
-     (list ocaml-graph
-           ocaml-re
-           ocaml-cppo))
+    (arguments
+     `(#:package "opam-core"
+       ;; tests are run with the opam package
+       #:tests? #f
+       #:phases (modify-phases %standard-phases
+                  (add-before 'build 'pre-build
+                    (lambda* (#:key inputs make-flags #:allow-other-keys)
+                      (let ((bash (assoc-ref inputs "bash"))
+                            (bwrap (search-input-file inputs "/bin/bwrap")))
+                        (substitute* "src/core/opamSystem.ml"
+                          (("\"/bin/sh\"")
+                           (string-append "\"" bash "/bin/sh\""))
+                          (("getconf")
+                           (which "getconf")))))))))
+    (propagated-inputs (list ocaml-graph
+                             ocaml-re
+                             ocaml-patch
+                             ocaml-uutf
+                             ocaml-swhid-core
+                             ocaml-jsonm
+                             ocaml-sha))
     (inputs (list bubblewrap))
-    (home-page "https://opam.ocamlpro.com/")
+    (home-page "https://opam.ocaml.org")
     (synopsis "Package manager for OCaml")
     (description
      "OPAM is a tool to manage OCaml packages.  It supports multiple
 simultaneous compiler installations, flexible package constraints, and a
 Git-friendly development workflow.")
-    ;; The 'LICENSE' file waives some requirements compared to LGPLv3.
-    (license license:lgpl3)))
+    ;; The 'LICENSE' file waives some requirements compared to LGPLv2.1.
+    (license license:lgpl2.1)))
 
 (define ocaml-opam-format
   (package
@@ -1002,24 +1111,56 @@ Git-friendly development workflow.")
 
 (define-public opam-installer
   (package
-    (inherit ocaml-opam-core)
     (name "opam-installer")
-    (native-inputs (list ocaml-opam-format
-                         ocaml-cmdliner))
-    (inputs '())
-    (propagated-inputs '())
-    (arguments `(#:package "opam-installer"
-                 ;; requires all of opam
-                 #:tests? #f))
+    (version "2.5.1")
+    ;; opam has some library dependencies that in turn depend on
+    ;; opam-installer (https://codeberg.org/guix/guix/issues/3588).  To break
+    ;; the cycle, we build opam-installer from a version of the release that
+    ;; vendors all dependencies. Then the remaining opam packages can be built
+    ;; in the usual way from git sources.
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/ocaml/opam/releases/download/"
+                           version "/opam-full-" version ".tar.gz"))
+       (sha256
+        (base32 "1v9k00az5lkdrlb64xb9h8xasnsz73kms0j0bz64hh2wbypvzia8"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      ;; Tests depend on the full opam package.
+      #:tests? #f
+      #:configure-flags
+      #~'("--with-vendored-deps")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-shell-path
+            (lambda _
+              (let ((sh (which "sh")))
+                (substitute* "configure"
+                  (("/bin/sh") sh)))))
+          ;; The Makefile builds both opam and opam-installer, but we
+          ;; only want the latter.
+          (replace 'install
+            (lambda _
+              (define (install source dest-dir)
+                (install-file source
+                              (string-append #$output "/" dest-dir)))
+              (install "opam-installer" "bin")
+              (install "_build/default/doc/man/opam-installer.1"
+                       "share/man/man1"))))))
+    (native-inputs (list ocaml))
+    (home-page "https://opam.ocaml.org")
     (synopsis "Tool for installing OCaml packages")
-    (description "@var{opam-installer} is a tool for installing OCaml packages
+    (description
+     "@var{opam-installer} is a tool for installing OCaml packages
 based on @code{.install} files defined by the OPAM package manager.  It is
 useful for installing OCaml packages without requiring the entirety of
 OPAM.")
-    (properties
-     ;; opam-installer is used as a tool and not as a library, we can use the
-     ;; OCaml 4.14 compiled opam until opam is compatible with OCaml 5.0.
-     `((ocaml5.0-variant . ,(delay opam-installer))))))
+    (properties `((ocaml5.0-variant unquote
+                                    (delay opam-installer))))
+    ;; The 'LICENSE' file waives some requirements compared to LGPLv2.1.
+    (license license:lgpl2.1)))
 
 (define ocaml-opam-repository
   (package
@@ -1056,7 +1197,7 @@ OPAM.")
                             (string-append "add_sys_mounts "
                                            (%store-directory)
                                            " /run/current-system /usr")))))))))
-    (inputs (list bubblewrap))
+    (inputs (list bubblewrap ocaml-spdx-licenses))
     (propagated-inputs (list ocaml-opam-repository))))
 
 (define ocaml-opam-solver
@@ -1066,7 +1207,8 @@ OPAM.")
     (inputs '())
     (propagated-inputs (list ocaml-opam-format
                              ocaml-mccs
-                             ocaml-dose3))
+                             ocaml-dose3
+                             ocaml-opam-0install-cudf))
     (arguments `(#:package "opam-solver"
                  ;; tests are run with the opam package
                  #:tests? #f
@@ -1093,7 +1235,7 @@ OPAM.")
            ocaml-opam-repository
            ocaml-base64
            ocaml-re
-           ocaml-cmdliner))))
+           ocaml-spdx-licenses))))
 
 (define-public opam
   (package
@@ -1102,120 +1244,171 @@ OPAM.")
     (build-system dune-build-system)
     (arguments
      `(#:package "opam"
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'prepare-checks
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; Opam tests need to run an isolated environment from a writable
-             ;; home directory.
-             (mkdir-p "test-home")
-             (setenv "HOME" (string-append (getcwd) "/test-home"))
-             (with-output-to-file (string-append (getcwd) "/test-home/.gitconfig")
-               (lambda _
-                 (display "[user]
+       #:phases (modify-phases %standard-phases
+                  (add-before 'check 'prepare-checks
+                    (lambda* (#:key inputs #:allow-other-keys)
+                      ;; Opam tests need to run an isolated environment from a writable
+                      ;; home directory.
+                      (mkdir-p "test-home")
+                      (setenv "HOME"
+                              (string-append (getcwd) "/test-home"))
+                      (with-output-to-file (string-append (getcwd)
+                                            "/test-home/.gitconfig")
+                        (lambda _
+                          (display "[user]
 email = guix@localhost.none
-name = Guix Builder")
-                 (newline)))
+name = Guix Builder
 
-             ;; Opam tests require data from opam-repository. Instead of
-             ;; downloading them with wget from the guix environment, copy the
-             ;; content to the expected directory.
-             (substitute* "tests/reftests/dune.inc"
-               (("tar -C.*opam-archive-([0-9a-f]*)[^)]*" _ commit)
-                (string-append "rmdir %{targets}) (run cp -r "
-                               (assoc-ref inputs (string-append "opam-repo-" commit))
-                               "/ %{targets}) (run chmod +w -R %{targets}"))
-               (("wget[^)]*") "touch %{targets}")
-               ;; Disable a failing test because it tries to clone a git
-               ;; repository from inside bwrap
-               (("diff upgrade-format.test upgrade-format.out") "run true")
-               ;; Disable a failing test because it tries to figure out which
-               ;; distro this is, and it doesn't know Guix
-               (("diff pin.unix.test pin.unix.out") "run true")
-               ;; Disable a failing test because of a failed expansion
-               (("diff opamroot-versions.test opamroot-versions.out") "run true")
-               ;; Disable a failing test, probably because the repository we
-               ;; replaced is not as expected
-               (("diff opamrt-big-upgrade.test opamrt-big-upgrade.out") "run true")
-               ;; Disable a failing test because of missing sandboxing
-               ;; functionality
-               (("diff init.test init.out") "run true"))
-             (substitute* "tests/reftests/dune"
-               ;; Because of our changes to the previous file, we cannot check
-               ;; it can be regenerated
-               (("diff dune.inc dune.inc.gen") "run true"))
-             ;; Ensure we can run the generated build.sh (no /bin/sh)
-             (substitute* '("tests/reftests/legacy-local.test"
-                            "tests/reftests/legacy-git.test")
-               (("#! ?/bin/sh")
-                (string-append "#!"
-                               (search-input-file inputs "/bin/sh"))))
-             (substitute* "tests/reftests/testing-env"
-               (("OPAMSTRICT=1")
-                (string-append "OPAMSTRICT=1\nLIBRARY_PATH="
-                               (assoc-ref inputs "libc") "/lib"))))))))
-    (native-inputs
-      (let ((opam-repo (lambda (commit hash)
-                         (origin
-                           (method git-fetch)
-                           (uri (git-reference
-                                  (url "https://github.com/ocaml/opam-repository")
-                                  (commit commit)))
-                           (file-name (git-file-name "opam-repo" commit))
-                           (sha256 (base32 hash))))))
-       `(("dune" ,dune)
-         ("ocaml-cppo" ,ocaml-cppo)
+[protocol \"file\"]
+allow = always")
+                          (newline)))
 
-         ;; For tests.
-         ("git" ,git-minimal/pinned)
-         ("openssl" ,openssl)
-         ("python" ,python-wrapper)
-         ("rsync" ,rsync)
-         ("unzip" ,unzip)
-         ("which" ,which)
+                      ;; Opam tests require data from opam-repository. Instead
+                      ;; of downloading them with wget from the guix
+                      ;; environment, copy the content to the expected
+                      ;; directory.
+                      (substitute* "tests/reftests/dune.inc"
+                        (("tar -C.*opam-archive-([0-9a-f]*)[^)]*" _ commit)
+                         (string-append "rmdir %{targets}) (run cp -r "
+                          (begin
+                            ;; When updating opam, uncomment the following
+                            ;; call.  It will list "opam-repo" commit-ish
+                            ;; required to run tests (see native-inputs
+                            ;; below).  Remove versions that are no longer
+                            ;; required, and add new ones if necessary.
+                            ;;
+                            ;; (pk commit)
+                            (assoc-ref inputs
+                                       (string-append "opam-repo-" commit)))
+                          "/ %{targets}) (run chmod +w -R %{targets}"))
+                        (("wget[^)]*")
+                         "touch %{targets}")
 
-         ;; Data for tests
-         ("opam-repo-0070613707"
-          ,(opam-repo "00706137074d536d2019d2d222fbe1bea929deda"
-                      "1gv1vvmfscj7wirfv6qncp8pf81wygnpzjwd0lyqcxm7g8r8lb4w"))
-         ("opam-repo-009e00fa"
-          ,(opam-repo "009e00fa86300d11c311309a2544e5c6c3eb8de2"
-                      "1wwy0rwrsjf4q10j1rh1dazk32fbzhzy6f7zl6qmndidx9b1bq7w"))
-         ("opam-repo-7090735c"
-          ,(opam-repo "7090735c9d1dd2dc481c4128c5ef4d3667238f15"
-                      "1bccsgjhlp64lmvfjfn6viywf3x73ji75myg9ssf1ij1fkmabn0z"))
-         ("opam-repo-a5d7cdc0"
-          ,(opam-repo "a5d7cdc0c91452b0aef4fa71c331ee5237f6dddd"
-                      "0z7kawqisy07088p5xjxwpvmvzlbj1d9cgdipsj90yx7nc5qh369"))
-         ("opam-repo-ad4dd344"
-          ,(opam-repo "ad4dd344fe5cd1cab49ced49d6758a9844549fb4"
-                      "1a1qj47kj8xjdnc4zc50ijrix1kym1n7k20n3viki80a7518baw8"))
-         ("opam-repo-c1842d168d"
-          ,(opam-repo "c1842d168de956caf06d7ac8588e65020d7594d8"
-                      "142y1ac7sprygyh91shcp0zcyfxjjkshi9g44qgg4rx60rbsbhai"))
-         ("opam-repo-c1d23f0e"
-          ,(opam-repo "c1d23f0e17ec83a036ebfbad1c78311b898a2ca0"
-                      "0j9abisx3ifzm66ci3p45mngmz4f0fx7yd9jjxrz3f8w5jffc9ii"))
-         ("opam-repo-f372039d"
-          ,(opam-repo "f372039db86a970ef3e662adbfe0d4f5cd980701"
-                      "0ld7fcry6ss6fmrpswvr6bikgx299w97h0gwrjjh7kd7rydsjdws"))
-         ("opam-repo-11ea1cb"
-          ,(opam-repo "11ea1cb6f2418b1f8a6679e4422771a04c9c3655"
-                      "1s4p0wfn3bx97yvm8xvj3yhzv2pz0jwml68g2ybv37hj9mpbrsq0"))
-         ("opam-repo-297366c"
-          ,(opam-repo "297366cd01c3aaf29b967bf0b34ccc7989d4d5b3"
-                      "1ysg69gys37nc2cxivs2ikh6xp0gj85if4rcrr874mqb9z12dm0j"))
-         ("opam-repo-3235916"
-          ,(opam-repo "3235916a162a59d7c82dac3fe24214975d48f1aa"
-                      "1yf73rv2n740a4s9g7a9k4j91b4k7al88nwnw9cdw0k2ncbmr486"))
-         ("opam-repo-de897adf36c4230dfea812f40c98223b31c4521a"
-          ,(opam-repo "de897adf36c4230dfea812f40c98223b31c4521a"
-                      "1m18x9gcwnbar8yv9sbfz8a3qpw412fp9cf4d6fb7syn0p0h96jw")))))
-    (inputs (list ocaml-opam-client))
-    (properties
-     ;; OPAM is used as a tool and not as a library, we can use the OCaml 4.14
-     ;; compiled opam until opam is compatible with OCaml 5.0.
-     `((ocaml5.0-variant . ,(delay opam))))))
+                        ;; Selectively disable a fraction of opam's "reftests"
+                        ;; (CRAM-style regression tests). Most of these tests
+                        ;; make assumptions about the build environment that
+                        ;; don't hold for Guix.
+
+                        ;; Test tries to clone a git repository from inside
+                        ;; bwrap
+                        (("diff upgrade-format.test upgrade-format.out")
+                         "run true")
+                        ;; Test tries to figure out which distro this is, and
+                        ;; it doesn't know Guix
+                        (("diff pin.unix.test pin.unix.out")
+                         "run true")
+                        ;; A variable expansion fails.
+                        (("diff opamroot-versions.test opamroot-versions.out")
+                         "run true")
+                        ;; The repository we replaced is probably not as
+                        ;; expected
+                        (("diff opamrt-big-upgrade.test opamrt-big-upgrade.out")
+                         "run true")
+                        ;; Disable a failing test because of missing sandboxing
+                        ;; functionality
+                        (("diff init.test init.out")
+                         "run true")
+                        ;; These tests try to normalize output to exclude
+                        ;; version strings, but this seems to break some
+                        ;; output assertions if $BASEDIR happens to include
+                        ;; the version.
+                        (("diff cli-versioning.test cli-versioning.out")
+                         "run true")
+                        (("diff hooks-variables.test hooks-variables.out")
+                         "run true")
+                        ;; Fails on noisy git output.
+                        (("diff action-disk.test action-disk.out")
+                         "run true")
+                        ;; Requires network access.
+                        (("diff download.test download.out")
+                         "run true")
+                        (("diff swhid.unix.test swhid.unix.out")
+                         "run true")
+                        ;; Depends on 3rd-party git repos.
+                        (("diff lock.test lock.out")
+                         "run true"))
+
+                      (substitute* "tests/reftests/dune"
+                        ;; Because of our changes to the previous file, we
+                        ;; cannot check it can be regenerated
+                        (("diff dune.inc dune.inc.gen")
+                         "run true"))
+                      ;; Ensure we can run the generated build.sh (no /bin/sh)
+                      (substitute* '("tests/reftests/legacy-local.test"
+                                     "tests/reftests/legacy-git.test")
+                        (("#! ?/bin/sh")
+                         (string-append "#!"
+                                        (search-input-file inputs "/bin/sh"))))
+                      (substitute* "tests/reftests/testing-env"
+                        (("OPAMSTRICT=1")
+                         (string-append "OPAMSTRICT=1\nLIBRARY_PATH="
+                                        (assoc-ref inputs "libc") "/lib"))))))))
+
+    (native-inputs (let ((opam-repo (lambda (commit hash)
+                                      (origin
+                                        (method git-fetch)
+                                        (uri (git-reference
+                                              (url
+                                               "https://github.com/ocaml/opam-repository")
+                                              (commit commit)))
+                                        (file-name (git-file-name "opam-repo"
+                                                                  commit))
+                                        (sha256 (base32 hash))))))
+                     `(("dune" ,dune)
+
+                       ;; For tests.
+                       ("git" ,git-minimal/pinned)
+                       ("openssl" ,openssl)
+                       ("python" ,python-wrapper)
+                       ("rsync" ,rsync)
+                       ("unzip" ,unzip)
+                       ("which" ,which)
+                       ("xxd" ,xxd)
+
+                       ;; Data for tests
+                       ("opam-repo-0070613707" ,(opam-repo
+                                                 "00706137074d536d2019d2d222fbe1bea929deda"
+                                                 "1gv1vvmfscj7wirfv6qncp8pf81wygnpzjwd0lyqcxm7g8r8lb4w"))
+                       ("opam-repo-009e00fa" ,(opam-repo
+                                               "009e00fa86300d11c311309a2544e5c6c3eb8de2"
+                                               "1wwy0rwrsjf4q10j1rh1dazk32fbzhzy6f7zl6qmndidx9b1bq7w"))
+                       ("opam-repo-11ea1cb" ,(opam-repo
+                                              "11ea1cb6f2418b1f8a6679e4422771a04c9c3655"
+                                              "1s4p0wfn3bx97yvm8xvj3yhzv2pz0jwml68g2ybv37hj9mpbrsq0"))
+                       ("opam-repo-143dd2a2f59f5befbf3cb90bb2667f911737fbf8" ,
+                        (opam-repo "143dd2a2f59f5befbf3cb90bb2667f911737fbf8"
+                         "1kliiy9n2j8myxhbz1brq6yingfy0si1bmv15j1hbnbpyi3bavr9"))
+                       ("opam-repo-297366c" ,(opam-repo
+                                              "297366cd01c3aaf29b967bf0b34ccc7989d4d5b3"
+                                              "1ysg69gys37nc2cxivs2ikh6xp0gj85if4rcrr874mqb9z12dm0j"))
+                       ("opam-repo-3235916" ,(opam-repo
+                                              "3235916a162a59d7c82dac3fe24214975d48f1aa"
+                                              "1yf73rv2n740a4s9g7a9k4j91b4k7al88nwnw9cdw0k2ncbmr486"))
+                       ("opam-repo-7090735c" ,(opam-repo
+                                               "7090735c9d1dd2dc481c4128c5ef4d3667238f15"
+                                               "1bccsgjhlp64lmvfjfn6viywf3x73ji75myg9ssf1ij1fkmabn0z"))
+                       ("opam-repo-7371c1d9" ,(opam-repo
+                                               "7371c1d9c53000840fb9a6d8ec13d87ffaa98401"
+                                               "0lmy3rmp5liyp2dsx4s90rjdwc012947ig2fz6y97s3pmwsbf9g8"))
+                       ("opam-repo-a5d7cdc0" ,(opam-repo
+                                               "a5d7cdc0c91452b0aef4fa71c331ee5237f6dddd"
+                                               "0z7kawqisy07088p5xjxwpvmvzlbj1d9cgdipsj90yx7nc5qh369"))
+                       ("opam-repo-ad4dd344" ,(opam-repo
+                                               "ad4dd344fe5cd1cab49ced49d6758a9844549fb4"
+                                               "1a1qj47kj8xjdnc4zc50ijrix1kym1n7k20n3viki80a7518baw8"))
+                       ("opam-repo-c1842d168d" ,(opam-repo
+                                                 "c1842d168de956caf06d7ac8588e65020d7594d8"
+                                                 "142y1ac7sprygyh91shcp0zcyfxjjkshi9g44qgg4rx60rbsbhai"))
+                       ("opam-repo-c1ba97dafe95c865d37ad4d88f6e57c9ffbe7f0a" ,
+                        (opam-repo "c1ba97dafe95c865d37ad4d88f6e57c9ffbe7f0a"
+                         "0sllm110dvs3w1k7qhias5y8v6ikkk2knw97v1fk9lnw4lq45gv6"))
+                       ("opam-repo-de897adf36c4230dfea812f40c98223b31c4521a" ,
+                        (opam-repo "de897adf36c4230dfea812f40c98223b31c4521a"
+                         "1m18x9gcwnbar8yv9sbfz8a3qpw412fp9cf4d6fb7syn0p0h96jw"))
+                       ("opam-repo-f372039d" ,(opam-repo
+                                               "f372039db86a970ef3e662adbfe0d4f5cd980701"
+                                               "0ld7fcry6ss6fmrpswvr6bikgx299w97h0gwrjjh7kd7rydsjdws")))))
+    (inputs (list ocaml-opam-client))))
 
 (define-public ocaml-opam-monorepo
   (package
@@ -4124,6 +4317,32 @@ and command-line tool.")
 length of domain names are preserved throughout the module.")
     (license license:isc)))
 
+(define-public ocaml-patch
+  (package
+    (name "ocaml-patch")
+    (version "3.1.0")
+    (build-system dune-build-system)
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/hannesm/patch")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1zg35f427ixd3jhkiwk91sil45pmf6ns7yfcgyi6gf2r0y241xn3"))))
+    (native-inputs (list ocaml-alcotest))
+    (home-page "https://github.com/hannesm/patch")
+    (synopsis "Applies unified diffs in pure OCaml")
+    (description
+     "This package applies unified diffs in pure OCaml.
+
+The loosely specified diff file format is widely used for transmitting
+differences of line-based information.  The motivating example is opam, which
+is able to validate updates being cryptographically signed (e.g. conex) by
+providing a unified diff.")
+    (license license:isc)))
+
 (define-public ocaml-macaddr
   (package
     (name "ocaml-macaddr")

gnu/packages/package-management.scm

@@ -817,7 +817,33 @@ high-performance computing} clusters.")
      (list
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'register-guix-extension
+          (add-after 'unpack 'set-load-paths-in-entry-point
+            (lambda _
+              (define load-path
+                (cons (string-append #$output
+                                     "/share/guile/site/"
+                                     (target-guile-effective-version))
+                      (parse-path (getenv "GUILE_LOAD_PATH"))))
+              (define load-compiled-path
+                (cons (string-append #$output
+                                     "/lib/guile/"
+                                     (target-guile-effective-version)
+                                     "/site-ccache")
+                      (parse-path (getenv "GUILE_LOAD_COMPILED_PATH"))))
+              (define search-paths-header
+                `(begin
+                   (set! %load-path
+                         (append (list ,@load-path) %load-path))
+                   (set! %load-compiled-path
+                         (append (list ,@load-compiled-path)
+                                 %load-compiled-path))))
+              (substitute* "guix/extensions/toys.scm"
+                (("^\\(define-module \\(guix extensions toys\\)")
+                 (string-append
+                  (with-output-to-string
+                    (lambda () (write search-paths-header)))
+                  "\n(define-module (guix extensions toys)")))))
+          (add-after 'set-load-paths-in-entry-point 'register-guix-extension
             (lambda* (#:key outputs #:allow-other-keys)
               (let ((ext-path (string-append #$output "/share/guix/extensions")))
                 (mkdir-p ext-path)
@@ -1199,13 +1225,13 @@ transactions from C or Python.")
              automake
 
              ;; Guile libraries are needed here for cross-compilation.
-             guile-next
+             guile-3.0-latest
              guile-gnutls
              guile-json-4
              guix
              guix-data-service
              guix-build-coordinator
-             guile-fibers-next
+             guile-fibers
              guile-knots
              guile-pfds
              guile-prometheus
@@ -1216,7 +1242,7 @@ transactions from C or Python.")
              guix
              guix-data-service
              guix-build-coordinator
-             guile-fibers-next
+             guile-fibers
              guile-knots
              guile-pfds
              guile-prometheus
@@ -2185,7 +2211,7 @@ environments.")
                                           "guile-gnutls"
                                           #$@(if (target-hurd?)
                                                  '()
-                                                 '("guile-fibers-next"
+                                                 '("guile-fibers"
                                                    "guile-knots")))))
                        (wrap-program file
                          `("PATH" ":" prefix
@@ -2229,12 +2255,12 @@ environments.")
              guile-gcrypt
              guix
              guile-prometheus
-             guile-fibers-next
+             guile-fibers
              guile-knots
              guile-lib
-             guile-next))
+             guile-3.0-latest))
       (inputs
-       (list guile-next
+       (list guile-3.0-latest
              sqlite-next
              bash-minimal
              (libc-utf8-locales-for-target)
@@ -2249,7 +2275,7 @@ environments.")
              guile-sqlite3
              guix
              guile-gnutls
-             guile-fibers-next
+             guile-fibers
              guile-knots))
       (home-page "https://git.cbaines.net/guix/build-coordinator/")
       (synopsis "Tool to help build derivations")
@@ -2285,9 +2311,9 @@ outputs of those builds.")
            guix
            guile-prometheus
            guile-lib
-           guile-next))
+           guile-3.0-latest))
     (inputs
-     (list guile-next
+     (list guile-3.0-latest
            guix
            guile-prometheus
            guile-gcrypt
@@ -2438,7 +2464,7 @@ in an isolated environment, in separate namespaces.")
                                           "guile-prometheus"
                                           "guile-sqlite3"
                                           "guile-gnutls"
-                                          "guile-fibers-next"
+                                          "guile-fibers"
                                           "guile-knots")))
                        (wrap-program file
                          `("GUILE_LOAD_PATH" ":" prefix
@@ -2468,11 +2494,12 @@ in an isolated environment, in separate namespaces.")
 
              ;; Guile libraries are needed here for cross-compilation.
              guile-next
+             guile-3.0-latest
              guile-aws
              guile-json-4
              guile-gcrypt
              guix
-             guile-fibers-next
+             guile-fibers
              guile-knots
              guile-prometheus
              guile-lib
@@ -2481,13 +2508,13 @@ in an isolated environment, in separate namespaces.")
              guile-sqlite3))
       (inputs
        (list bash-minimal
-             guile-next))
+             guile-3.0-latest))
       (propagated-inputs
        (list guile-aws
              guile-json-4
              guile-gcrypt
              guix
-             guile-fibers-next
+             guile-fibers
              guile-knots
              guile-prometheus
              guile-lib

gnu/packages/parallel.scm

@@ -254,7 +254,7 @@ when jobs finish.")
     (inputs
      (append
        (list freeipmi
-             `(,hwloc-2 "lib")
+             `(,hwloc "lib")
              json-c
              linux-pam)
        (if (supported-package? openpmix-4)

gnu/packages/pascal.scm

@@ -39,6 +39,7 @@
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages qt)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
   #:use-module (ice-9 match))
@@ -323,7 +324,7 @@ Pascal programs.")
 (define-public lazarus
   (package
     (name "lazarus")
-    (version "2.2.6")
+    (version "4.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -336,48 +337,95 @@ Pascal programs.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0hpk6fxmy1h1q0df41jg1vnp8g8vynrg5v5ad43lv229nizfs3wj"))))
+                "1mkimvd5hiwlsxpjwqnhd7lwb0x2icnf9ks09wza7j5xaq7xjswy"))))
     (build-system gnu-build-system)
     (arguments
      (list #:tests? #f ;No tests exist
            #:make-flags #~(list (string-append "INSTALL_PREFIX="
-                                               #$output))
-           #:phases #~(modify-phases %standard-phases
-                        (delete 'configure)
-                        (replace 'build
-                          (lambda* (#:key inputs outputs #:allow-other-keys)
-                            (let* ((libdirs (map (lambda (x)
-                                                   (assoc-ref inputs x))
-                                                 '("glib" "gdk-pixbuf"
-                                                   "gtk+"
-                                                   "libx11"
-                                                   "libx11"
-                                                   "pango"
-                                                   "cairo"
-                                                   "at-spi2-core")))
-                                   (libs (append (map (lambda (name)
-                                                        (string-append "-Fl"
-                                                                       name
-                                                                       "/lib"))
-                                                      libdirs)
-                                                 (map (lambda (name)
-                                                        (string-append
-                                                         "-k-rpath=" name
-                                                         "/lib")) libdirs))))
-                              (setenv "LAZARUS_LIBPATHS"
-                                      (string-join libs " "))
-                              (setenv "MAKEFLAGS"
-                                      (string-append "LHELP_OPT="
-                                                     (string-join libs "\\ "))))
-                            (invoke "make" "bigide"))))))
-    (native-inputs (list fpc pkg-config))
-    (inputs (list glib
-                  gdk-pixbuf
-                  gtk+-2
-                  libx11
-                  pango
-                  cairo
-                  at-spi2-core))
+                                               #$output)
+                                "LCL_PLATFORM=qt6")
+           #:phases
+           #~(modify-phases %standard-phases
+               (delete 'configure)
+               ;; lcl/interfaces/qt6/cbindings/ ships the C++ source of
+               ;; libQt6Pas -- the Qt6 C-ABI bridge that LCL's qt6
+               ;; widgetset calls into.  Build it with qmake6 and stage
+               ;; the library so the IDE finds it at runtime.
+               (add-before 'build 'build-qt6pas
+                 (lambda _
+                   (with-directory-excursion "lcl/interfaces/qt6/cbindings"
+                     (invoke "qmake6" "Qt6Pas.pro"
+                             (string-append "PREFIX=" #$output))
+                     (invoke "make" "-j"
+                             (number->string (parallel-job-count))))))
+               (replace 'build
+                 (lambda* (#:key inputs make-flags #:allow-other-keys)
+                   (let* ((qt6pas-build
+                           (string-append (getcwd)
+                                          "/lcl/interfaces/qt6/cbindings"))
+                          (qt6pas-runtime
+                           (string-append #$output "/lib"))
+                          (input-libs
+                           (map (lambda (x)
+                                  (string-append (assoc-ref inputs x) "/lib"))
+                                '("qtbase" "libx11")))
+                          ;; Link against the build tree so the linker
+                          ;; resolves libQt6Pas now; bake the final
+                          ;; $out/lib into RUNPATH so the installed
+                          ;; binary finds it at runtime.
+                          (fpc-args
+                           (append (map (lambda (d)
+                                          (string-append "-Fl" d))
+                                        (cons qt6pas-build input-libs))
+                                   (map (lambda (d)
+                                          (string-append "-k-rpath=" d))
+                                        (cons qt6pas-runtime input-libs)))))
+                     (setenv "LAZARUS_LIBPATHS"
+                             (string-join fpc-args " "))
+                     (setenv "MAKEFLAGS"
+                             (string-append "LHELP_OPT="
+                                            (string-join fpc-args "\\ "))))
+                   (apply invoke "make" "bigide" make-flags)))
+               (add-after 'install 'wrap-qt
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   ;; Qt6 apps load their platform plugins
+                   ;; (libqxcb.so, libqwayland.so, ...) from
+                   ;; QT_PLUGIN_PATH; each qt input has its plugins
+                   ;; under lib/qt6/plugins/.  Wrap lazarus-ide so the
+                   ;; wayland/xcb platform plugins are found at runtime.
+                   (let ((plugin-path
+                          (string-join
+                           (map (lambda (i)
+                                  (string-append (assoc-ref inputs i)
+                                                 "/lib/qt6/plugins"))
+                                '("qtbase" "qtsvg" "qtwayland"))
+                           ":")))
+                     (for-each
+                      (lambda (prog)
+                        (wrap-program (string-append #$output "/bin/" prog)
+                          `("QT_PLUGIN_PATH" ":" prefix (,plugin-path))))
+                      '("lazarus-ide" "startlazarus")))))
+               (add-after 'install 'install-qt6pas
+                 (lambda _
+                   ;; qmake's `make install' tries to copy libQt6Pas.so
+                   ;; into Qt's install prefix (read-only store path);
+                   ;; place it under $out/lib/ instead.
+                   (let ((src "lcl/interfaces/qt6/cbindings")
+                         (dst (string-append #$output "/lib")))
+                     (mkdir-p dst)
+                     (for-each
+                      (lambda (f)
+                        (let ((sf (string-append src "/" f))
+                              (df (string-append dst "/" f)))
+                          (if (eq? 'symlink (stat:type (lstat sf)))
+                              (symlink (readlink sf) df)
+                              (copy-file sf df))))
+                      '("libQt6Pas.so"
+                        "libQt6Pas.so.6"
+                        "libQt6Pas.so.6.2"
+                        "libQt6Pas.so.6.2.10"))))))))
+    (native-inputs (list fpc pkg-config qtbase qttools))
+    (inputs (list qtbase qtsvg qtwayland libx11))
     (synopsis "Integrated development environment for Pascal")
     (description "This package provides an integrated development environment
 for Pascal.")

gnu/packages/patches/codex-acp-0.11.1-disable-code-mode.patch

@@ -0,0 +1,128 @@
+Author: Danny Milosavljevic <dannym@friendly-machines.com>
+Date: 2026-04-13
+License: ASL2.0
+
+Make V8 an optional dependency in codex-code-mode.
+
+The V8 engine is only needed for actually executing JavaScript in the
+code-mode sandbox.  The description helpers, tool name constants, and
+data types do not require V8.  Gate the runtime and service modules
+behind a "v8-runtime" feature so that consumers like codex-acp that
+never use code-mode can avoid the V8 build dependency.
+
+--- a/codex-rs/code-mode/Cargo.toml	2026-04-13 16:14:49.459504037 +0000
++++ codex-rs/code-mode/Cargo.toml	2026-04-13 16:14:49.466438318 +0000
+@@ -12,6 +12,10 @@
+ [lints]
+ workspace = true
+
++[features]
++default = ["v8-runtime"]
++v8-runtime = ["dep:v8"]
++
+ [dependencies]
+ async-trait = { workspace = true }
+ serde = { workspace = true, features = ["derive"] }
+@@ -19,7 +23,7 @@
+ tokio = { workspace = true, features = ["macros", "rt", "sync", "time"] }
+ tokio-util = { workspace = true, features = ["rt"] }
+ tracing = { workspace = true }
+-v8 = { workspace = true }
++v8 = { workspace = true, optional = true }
+
+ [dev-dependencies]
+ pretty_assertions = { workspace = true }
+--- a/codex-rs/code-mode/src/lib.rs	2026-04-13 16:14:49.461337956 +0000
++++ codex-rs/code-mode/src/lib.rs	2026-04-13 16:14:49.470869556 +0000
+@@ -1,6 +1,8 @@
+ mod description;
+ mod response;
++#[cfg(feature = "v8-runtime")]
+ mod runtime;
++#[cfg(feature = "v8-runtime")]
+ mod service;
+
+ pub use description::CODE_MODE_PRAGMA_PREFIX;
+@@ -16,15 +18,82 @@
+ pub use description::render_json_schema_to_typescript;
+ pub use response::FunctionCallOutputContentItem;
+ pub use response::ImageDetail;
++
++#[cfg(feature = "v8-runtime")]
+ pub use runtime::DEFAULT_EXEC_YIELD_TIME_MS;
++#[cfg(feature = "v8-runtime")]
+ pub use runtime::DEFAULT_MAX_OUTPUT_TOKENS_PER_EXEC_CALL;
++#[cfg(feature = "v8-runtime")]
+ pub use runtime::DEFAULT_WAIT_YIELD_TIME_MS;
++#[cfg(feature = "v8-runtime")]
+ pub use runtime::ExecuteRequest;
++#[cfg(feature = "v8-runtime")]
+ pub use runtime::RuntimeResponse;
++#[cfg(feature = "v8-runtime")]
+ pub use runtime::WaitRequest;
++#[cfg(feature = "v8-runtime")]
+ pub use service::CodeModeService;
++#[cfg(feature = "v8-runtime")]
+ pub use service::CodeModeTurnHost;
++#[cfg(feature = "v8-runtime")]
+ pub use service::CodeModeTurnWorker;
+
++// Stub types when V8 is not available.
++#[cfg(not(feature = "v8-runtime"))]
++pub const DEFAULT_EXEC_YIELD_TIME_MS: u64 = 10_000;
++#[cfg(not(feature = "v8-runtime"))]
++pub const DEFAULT_MAX_OUTPUT_TOKENS_PER_EXEC_CALL: usize = 10_000;
++#[cfg(not(feature = "v8-runtime"))]
++pub const DEFAULT_WAIT_YIELD_TIME_MS: u64 = 10_000;
++
++#[cfg(not(feature = "v8-runtime"))]
++pub struct ExecuteRequest {
++    pub tool_call_id: String,
++    pub enabled_tools: Vec<ToolDefinition>,
++    pub source: String,
++    pub stored_values: std::collections::HashMap<String, serde_json::Value>,
++    pub yield_time_ms: Option<u64>,
++    pub max_output_tokens: Option<usize>,
++}
++
++#[cfg(not(feature = "v8-runtime"))]
++#[derive(Clone, Debug)]
++pub struct WaitRequest {
++    pub cell_id: String,
++    pub yield_time_ms: u64,
++    pub terminate: bool,
++}
++
++#[cfg(not(feature = "v8-runtime"))]
++#[derive(Debug, PartialEq)]
++pub enum RuntimeResponse {
++    Yielded { cell_id: String, content_items: Vec<FunctionCallOutputContentItem> },
++    Terminated { cell_id: String, content_items: Vec<FunctionCallOutputContentItem> },
++    Result { cell_id: String, content_items: Vec<FunctionCallOutputContentItem>, stored_values: std::collections::HashMap<String, serde_json::Value>, error_text: Option<String> },
++}
++
++#[cfg(not(feature = "v8-runtime"))]
++#[async_trait::async_trait]
++pub trait CodeModeTurnHost: Send + Sync {
++    async fn invoke_tool(&self, tool_name: String, input: Option<serde_json::Value>, cancellation_token: tokio_util::sync::CancellationToken) -> Result<serde_json::Value, String>;
++    async fn notify(&self, call_id: String, cell_id: String, text: String) -> Result<(), String>;
++}
++
++#[cfg(not(feature = "v8-runtime"))]
++pub struct CodeModeService;
++
++#[cfg(not(feature = "v8-runtime"))]
++impl CodeModeService {
++    pub fn new() -> Self { Self }
++    pub async fn stored_values(&self) -> std::collections::HashMap<String, serde_json::Value> { Default::default() }
++    pub async fn replace_stored_values(&self, _values: std::collections::HashMap<String, serde_json::Value>) {}
++    pub async fn execute(&self, _request: ExecuteRequest) -> Result<RuntimeResponse, String> { Err("code-mode requires v8-runtime feature".into()) }
++    pub async fn wait(&self, _request: WaitRequest) -> Result<RuntimeResponse, String> { Err("code-mode requires v8-runtime feature".into()) }
++    pub fn start_turn_worker(&self, _host: std::sync::Arc<dyn CodeModeTurnHost>) -> CodeModeTurnWorker { CodeModeTurnWorker }
++}
++
++#[cfg(not(feature = "v8-runtime"))]
++pub struct CodeModeTurnWorker;
++
+ pub const PUBLIC_TOOL_NAME: &str = "exec";
+ pub const WAIT_TOOL_NAME: &str = "wait";

gnu/packages/patches/codex-acp-0.11.1-remove-patch-sections.patch

@@ -0,0 +1,20 @@
+Author: Danny Milosavljevic <dannym@friendly-machines.com>
+Date: 2026-02-08
+License: ASL2.0
+
+Remove [patch.crates-io] section.
+
+This section points to git repositories which are unavailable in an
+offline build.  The vendored tokio-tungstenite and tungstenite forks
+are provided as cargo-inputs instead.
+
+--- a/Cargo.toml
++++ b/Cargo.toml
+@@ -52,7 +52,3 @@
+ let-underscore = "warn"
+ rust-2018-idioms = "warn"
+ unused = "warn"
+-
+-[patch.crates-io]
+-tokio-tungstenite = { git = "https://github.com/openai-oss-forks/tokio-tungstenite", rev = "132f5b39c862e3a970f731d709608b3e6276d5f6" }
+-tungstenite = { git = "https://github.com/openai-oss-forks/tungstenite-rs", rev = "9200079d3b54a1ff51072e24d81fd354f085156f" }

gnu/packages/patches/codex-acp-0.9.2-remove-patch-sections.patch

@@ -1,21 +0,0 @@
-Author: Danny Milosavljevic <dannym@friendly-machines.com>
-Date: 2026-02-08
-License: ASL2.0
-
-Remove [patch.crates-io] and [patch.'ssh://...'] sections.
-
-These sections point to git repositories which are unavailable in an
-offline build.  The vendored tokio-tungstenite and tungstenite forks
-are provided as cargo-inputs instead.
-
-diff -u a/Cargo.toml b/Cargo.toml
---- a/Cargo.toml
-+++ b/Cargo.toml
-@@ -47,8 +47,2 @@
- unused = "warn"
--
--[patch.crates-io]
--tokio-tungstenite = { git = "https://github.com/JakkuSakura/tokio-tungstenite", branch = "proxy-support" }
--
--[patch.'ssh://git@github.com/JakkuSakura/tungstenite-rs.git']
--tungstenite = { git = "https://github.com/JakkuSakura/tungstenite-rs", branch = "proxy-support" }

gnu/packages/patches/codex-acp-0.9.2-replace-result-flatten.patch

@@ -1,52 +0,0 @@
-Author: Danny Milosavljevic <dannym@friendly-machines.com>
-Date: 2026-02-08
-License: ASL2.0
-
-Replace Result::flatten() with and_then(|x| x).
-
-Result::flatten() was stabilized in Rust 1.89.0 but the build
-toolchain only provides Rust 1.88.0.  Use the equivalent
-.and_then(|x| x) form which works on all stable Rust versions.
-
-diff -u a/src/local_spawner.rs b/src/local_spawner.rs
---- a/src/local_spawner.rs
-+++ b/src/local_spawner.rs
-@@ -156,7 +156,7 @@
-         });
-         rx.recv()
-             .map_err(|e| std::io::Error::other(e.to_string()))
--            .flatten()
-+            .and_then(|x| x)
-     }
-
-     fn write(&self, path: &std::path::Path, contents: &[u8]) -> std::io::Result<()> {
-@@ -174,7 +174,7 @@
-         });
-         rx.recv()
-             .map_err(|e| std::io::Error::other(e.to_string()))
--            .flatten()
-+            .and_then(|x| x)
-     }
- }
-
-@@ -207,7 +207,7 @@
-             let file = rx
-                 .await
-                 .map_err(|e| std::io::Error::other(e.to_string()))
--                .flatten()?;
-+                .and_then(|x| x)?;
-
-             Ok(Box::new(tokio::io::BufReader::new(Cursor::new(file.into_bytes()))) as _)
-         })
-diff -u a/src/thread.rs b/src/thread.rs
---- a/src/thread.rs
-+++ b/src/thread.rs
-@@ -1817,7 +1817,7 @@
-                     let mut new_custom_prompts = load_custom_prompts
-                         .await
-                         .map_err(|_| Error::internal_error())
--                        .flatten()
-+                        .and_then(|x| x)
-                         .inspect_err(|e| error!("Failed to load custom prompts {e:?}"))
-                         .unwrap_or_default();
-

gnu/packages/patches/git-clar-path-max.patch

@@ -1,16 +0,0 @@
-On GNU/Hurd, 'PATH_MAX' is undefined.  Provide a reasonable default value.
-Adapted from <https://github.com/libgit2/libgit2/pull/7100>.
-
-diff --git a/tests/clar/clar.h b/tests/clar/clar.h
-index ca72292ae91..98e2b14e880 100644
---- a/t/unit-tests/clar/clar.h
-+++ b/t/unit-tests/clar/clar.h
-@@ -14,6 +14,8 @@
- # define CLAR_MAX_PATH 4096
- #elif defined(_WIN32)
- # define CLAR_MAX_PATH MAX_PATH
-+#elif !defined(PATH_MAX)			  /* GNU/Hurd */
-+# define CLAR_MAX_PATH 4096
- #else
- # define CLAR_MAX_PATH PATH_MAX
- #endif

gnu/packages/patches/hwloc-1-test-btrfs.patch

@@ -1,54 +0,0 @@
-From 093316a897a2eb4972a7a3a5888f40975d03f6bf Mon Sep 17 00:00:00 2001
-From: Brice Goglin <Brice.Goglin@inria.fr>
-Date: Tue, 5 Apr 2022 17:39:50 +0200
-Subject: [PATCH] linux: (partial) fix the discovery of hugepages on btrfs
- fsroot
-
-btrfs always returns 1 in directory stat.st_nlink.
-It breaks make check in tests/linux/ because the hugepages discovery
-uses st_nlink to allocate the memory page_types array.
-
-Always allocate at least 3 page_types slots
-(enough for all known cases, 1 for normal, 2 for huge pages)
-
-(partially cherry-picked from commit 7f351cec9bfe54a031f35ad16c9cfb99784d76dc)
-
-We don't reallocate later if needed as in 2.x commit 7f351cec9bfe54a031f35ad16c9cfb99784d76dc
-because v1.11 doesn't deserve a complete fix. Just commit the minimal change
-so that tests/linux/2i386-2t-hugepagesizecount with HWLOC_PAGESIZE_DEBUG=4096
-doesn't crash in btrfs anymore (test-topology.sh fails during make check if /tmp is in btrfs).
-
-Thanks to Philippe Swartvagher for the report.
-
-Signed-off-by: Brice Goglin <Brice.Goglin@inria.fr>
----
- src/topology-linux.c | 11 +++++++++--
- 1 file changed, 9 insertions(+), 2 deletions(-)
-
-diff --git a/src/topology-linux.c b/src/topology-linux.c
-index 58c275fea..269eca7f5 100644
---- a/src/topology-linux.c
-+++ b/src/topology-linux.c
-@@ -1,6 +1,6 @@
- /*
-  * Copyright © 2009 CNRS
-- * Copyright © 2009-2019 Inria.  All rights reserved.
-+ * Copyright © 2009-2022 Inria.  All rights reserved.
-  * Copyright © 2009-2013, 2015 Université Bordeaux
-  * Copyright © 2009-2014 Cisco Systems, Inc.  All rights reserved.
-  * Copyright © 2015 Intel, Inc.  All rights reserved.
-@@ -2329,7 +2329,14 @@ hwloc_get_procfs_meminfo_info(struct hwloc_topology *topology,
- 
-   err = hwloc_stat("/sys/kernel/mm/hugepages", &st, data->root_fd);
-   if (!err) {
--    types = 1 + st.st_nlink-2;
-+    types = 1 /* normal non-huge size */ + st.st_nlink - 2 /* ignore . and .. */;
-+    if (types < 3)
-+      /* some buggy filesystems (e.g. btrfs when reading from fsroot)
-+       * return wrong st_nlink for directories (always 1 for btrfs).
-+       * use 3 as a sane default (default page + 2 huge sizes).
-+       * hwloc_parse_hugepages_info() will extend it if needed.
-+       */
-+      types = 3;
-     has_sysfs_hugepages = 1;
-   }

gnu/packages/patches/inetutils-drop-test.patch

@@ -0,0 +1,26 @@
+To be remove when updating inetutils.
+See
+https://cgit.git.savannah.gnu.org/cgit/inetutils.git/commit/?id=556621adc3dcb62dbb28c54905cef15837947115
+https://codeberg.org/guix/guix/issues/7995
+
+diff --git a/tests/libls.sh b/tests/libls.sh
+index 827020f2..9fdef8be 100755
+--- a/tests/libls.sh
++++ b/tests/libls.sh
+@@ -91,7 +91,6 @@ REPLY_a1=`$LS -a1 $LSDIR`
+ REPLY_A1=`$LS -A1 $LSDIR`
+
+ REPLY_C=`$LS -C $LSDIR`
+-REPLY_Cf=`$LS -Cf $LSDIR`
+ REPLY_Cr=`$LS -Cr $LSDIR`
+ REPLY_Ct=`$LS -Ct $LSDIR`
+ REPLY_x=`$LS -x $LSDIR`
+@@ -130,9 +129,6 @@ test `echo "$diff" | $GREP -c -v '^[.]\{1,2\}$'` -eq 0 ||
+     fi
+   }
+
+-test x"$REPLY_C" != x"$REPLY_Cf" ||
+-  { errno=1; echo >&2 'Failed to disable sorting with "-f".'; }
+-
+ test x"$REPLY_C" != x"$REPLY_Cr" ||
+   { errno=1; echo >&2 'Failed to reverse sorting with "-r".'; }

gnu/packages/patches/libfossil-skip-amalgamation.patch

@@ -1,43 +0,0 @@
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -265,15 +265,11 @@
- amal.flags     = -nc
- amal.run       = TOPDIR="$(DIR.top)" $(SHELL.bash) $(bin.make-amal) --quiet
- 
- libfossil.c: $(amal.deps)
- 	$(amal.run) $(amal.flags)
--libfossil.h: libfossil.c
--all: libfossil.c
- @if ENABLE_CXX
--libfossil.hpp: libfossil.c
--libfossil.c++: libfossil.c
- amal.flags += -c++
- @endif
- 
- .PHONY: amal
- amal: libfossil.c
-@@ -287,19 +283,16 @@
- 	fossil uv sync
- @endif
- @endif
- 
- install: install-headers
--install-headers: libfossil.h $(install-dir.include)
--	$(INSTALL.noexec) libfossil.h $(install-dir.include)
-+install-headers: include/libfossil.h $(install-dir.include)
-+	$(INSTALL.noexec) $< $(install-dir.include)
- @if ENABLE_CXX
--libfossil++.hpp: libfossil.h
--libfossil++.cpp: libfossil++.hpp
--all: libfossil++.cpp
- install-headers: install-headers++
--install-headers++: libfossil++.hpp $(install-dir.include)
--	$(INSTALL.noexec) libfossil++.hpp $(install-dir.include)
-+install-headers++: include/libfossil.hpp $(install-dir.include)
-+	$(INSTALL.noexec) $< $(install-dir.include)
- @endif # ENABLE_CXX
- clean: clean-amalgamation
- clean-amalgamation:
- 	rm -f libfossil.c libfossil.h libfossil++.cpp libfossil++.hpp
- 	rm -f libfossil-config.h libfossil-amalgamation.zip VERSION.h
-

gnu/packages/patches/librewolf-150.0-encoding_rs-rust-fix.patch

@@ -0,0 +1,260 @@
+From d8702527f4f1f67f765330f5018bfcb182946c45 Mon Sep 17 00:00:00 2001
+From: Henri Sivonen <hsivonen@hsivonen.fi>
+Date: Tue, 21 Apr 2026 07:09:20 +0000
+Subject: [PATCH] Bug 2033279 - Make --enable-rust-simd work with Rust 1.95.
+ r=firefox-build-system-reviewers,supply-chain-reviewers,ahochheiden
+
+Differential Revision: https://phabricator.services.mozilla.com/D295287
+---
+ .cargo/config.toml.in                         |  5 ++
+ Cargo.lock                                    |  4 +-
+ Cargo.toml                                    |  2 +
+ supply-chain/audits.toml                      |  6 ++
+ supply-chain/config.toml                      |  4 ++
+ .../rust/encoding_rs/.cargo-checksum.json     |  2 +-
+ .../rust/encoding_rs/.cargo_vcs_info.json     |  6 --
+ third_party/rust/encoding_rs/Cargo.toml       | 60 ++++++++++---------
+ third_party/rust/encoding_rs/Cargo.toml.orig  | 45 --------------
+ .../rust/encoding_rs/src/x_user_defined.rs    |  2 +
+ 10 files changed, 54 insertions(+), 82 deletions(-)
+ delete mode 100644 third_party/rust/encoding_rs/.cargo_vcs_info.json
+ delete mode 100644 third_party/rust/encoding_rs/Cargo.toml.orig
+
+diff --git a/.cargo/config.toml.in b/.cargo/config.toml.in
+index 8013ae5435dab..cabdee463415f 100644
+--- a/.cargo/config.toml.in
++++ b/.cargo/config.toml.in
+@@ -55,6 +55,11 @@ git = "https://github.com/hsivonen/any_all_workaround"
+ rev = "7fb1b7034c9f172aade21ee1c8554e8d8a48af80"
+ replace-with = "vendored-sources"
+ 
++[source."git+https://github.com/hsivonen/encoding_rs?rev=1236d1bc423e6ba35a06485f74a6304db2d703b5"]
++git = "https://github.com/hsivonen/encoding_rs"
++rev = "1236d1bc423e6ba35a06485f74a6304db2d703b5"
++replace-with = "vendored-sources"
++
+ [source."git+https://github.com/hsivonen/rust-harfbuzz?rev=9d58a23a98772a197291d04af93f7041b7093d95"]
+ git = "https://github.com/hsivonen/rust-harfbuzz"
+ rev = "9d58a23a98772a197291d04af93f7041b7093d95"
+diff --git a/Cargo.lock b/Cargo.lock
+index fea2f95fbb438..63b1f818d7971 100644
+--- a/Cargo.lock
++++ b/Cargo.lock
+@@ -1914,11 +1914,11 @@ dependencies = [
+ [[package]]
+ name = "encoding_rs"
+ version = "0.8.35"
+-source = "registry+https://github.com/rust-lang/crates.io-index"
+-checksum = "75030f3c4f45dafd7586dd6780965a8c7e8e285a5ecb86713e63a79c5b2766f3"
++source = "git+https://github.com/hsivonen/encoding_rs?rev=1236d1bc423e6ba35a06485f74a6304db2d703b5#1236d1bc423e6ba35a06485f74a6304db2d703b5"
+ dependencies = [
+  "any_all_workaround",
+  "cfg-if",
++ "rustversion",
+ ]
+ 
+ [[package]]
+diff --git a/Cargo.toml b/Cargo.toml
+index 49c695809f302..2648c32ae57e8 100644
+--- a/Cargo.toml
++++ b/Cargo.toml
+@@ -287,6 +287,8 @@ harfbuzz-sys = { git = "https://github.com/hsivonen/rust-harfbuzz", rev = "9d58a
+ harfbuzz = { git = "https://github.com/hsivonen/rust-harfbuzz", rev = "9d58a23a98772a197291d04af93f7041b7093d95" }
+ # Also vendor `harfbuzz-traits` to keep cargo-vendor happy.
+ harfbuzz-traits = { git = "https://github.com/hsivonen/rust-harfbuzz", rev = "9d58a23a98772a197291d04af93f7041b7093d95" }
++# Make --enable-rust-simd compatible with Rust 1.95
++encoding_rs = { git = "https://github.com/hsivonen/encoding_rs", rev = "1236d1bc423e6ba35a06485f74a6304db2d703b5" }
+ 
+ # objc 0.2.7 + fa7ca43b862861dd1cd000d7ad01e6e0266cda13
+ objc = { git = "https://github.com/glandium/rust-objc", rev = "4de89f5aa9851ceca4d40e7ac1e2759410c04324" }
+diff --git a/supply-chain/audits.toml b/supply-chain/audits.toml
+index 85b4037e03bdb..f4567ea6b6f94 100644
+--- a/supply-chain/audits.toml
++++ b/supply-chain/audits.toml
+@@ -2385,6 +2385,12 @@ who = "Mike Hommey <mh+mozilla@glandium.org>"
+ criteria = "safe-to-deploy"
+ delta = "0.8.31 -> 0.8.32"
+ 
++[[audits.encoding_rs]]
++who = "Henri Sivonen <hsivonen@hsivonen.fi>"
++criteria = "safe-to-deploy"
++delta = "0.8.35 -> 0.8.35@git:1236d1bc423e6ba35a06485f74a6304db2d703b5"
++importable = false
++
+ [[audits.enum-map]]
+ who = "Kershaw Chang <kershaw@mozilla.com>"
+ criteria = "safe-to-deploy"
+diff --git a/supply-chain/config.toml b/supply-chain/config.toml
+index 4cfd83dc2d608..15deefbec0574 100644
+--- a/supply-chain/config.toml
++++ b/supply-chain/config.toml
+@@ -39,6 +39,10 @@ notes = "This is the upstream code not yet released"
+ audit-as-crates-io = true
+ notes = "This is upstream plus a warning fix from bug 1823866."
+ 
++[policy.encoding_rs]
++audit-as-crates-io = true
++notes = "This is upstream plus a build fix for bug 2033279."
++
+ [policy.firefox-on-glean]
+ audit-as-crates-io = false
+ notes = "The crates.io version of this is just a placeholder to allow public crates to depend on firefox-on-glean."
+diff --git a/third_party/rust/encoding_rs/.cargo_vcs_info.json b/third_party/rust/encoding_rs/.cargo_vcs_info.json
+deleted file mode 100644
+index 6e5d699759e43..0000000000000
+--- a/third_party/rust/encoding_rs/.cargo_vcs_info.json
++++ /dev/null
+@@ -1,6 +0,0 @@
+-{
+-  "git": {
+-    "sha1": "2fa58aecf537cc76ff52c0eb3d5e9f8fda466844"
+-  },
+-  "path_in_vcs": ""
+-}
+\ No newline at end of file
+diff --git a/third_party/rust/encoding_rs/Cargo.toml b/third_party/rust/encoding_rs/Cargo.toml
+index 2adac351c2edf..0239315bab180 100644
+--- a/third_party/rust/encoding_rs/Cargo.toml
++++ b/third_party/rust/encoding_rs/Cargo.toml
+@@ -16,6 +16,7 @@ name = "encoding_rs"
+ version = "0.8.35"
+ authors = ["Henri Sivonen <hsivonen@hsivonen.fi>"]
+ build = false
++autolib = false
+ autobins = false
+ autoexamples = false
+ autotests = false
+@@ -39,33 +40,6 @@ categories = [
+ license = "(Apache-2.0 OR MIT) AND BSD-3-Clause"
+ repository = "https://github.com/hsivonen/encoding_rs"
+ 
+-[profile.release]
+-lto = true
+-
+-[lib]
+-name = "encoding_rs"
+-path = "src/lib.rs"
+-
+-[dependencies.any_all_workaround]
+-version = "0.1.0"
+-optional = true
+-
+-[dependencies.cfg-if]
+-version = "1.0"
+-
+-[dependencies.serde]
+-version = "1.0"
+-optional = true
+-
+-[dev-dependencies.bincode]
+-version = "1.0"
+-
+-[dev-dependencies.serde_derive]
+-version = "1.0"
+-
+-[dev-dependencies.serde_json]
+-version = "1.0"
+-
+ [features]
+ alloc = []
+ default = ["alloc"]
+@@ -84,4 +58,34 @@ fast-legacy-encode = [
+ less-slow-big5-hanzi-encode = []
+ less-slow-gb-hanzi-encode = []
+ less-slow-kanji-encode = []
+-simd-accel = ["any_all_workaround"]
++simd-accel = [
++    "any_all_workaround",
++    "rustversion",
++]
++
++[lib]
++name = "encoding_rs"
++path = "src/lib.rs"
++
++[dependencies]
++cfg-if = "1.0"
++
++[dependencies.any_all_workaround]
++version = "0.1.0"
++optional = true
++
++[dependencies.rustversion]
++version = "1.0.19"
++optional = true
++
++[dependencies.serde]
++version = "1.0"
++optional = true
++
++[dev-dependencies]
++bincode = "1.0"
++serde_derive = "1.0"
++serde_json = "1.0"
++
++[profile.release]
++lto = true
+diff --git a/third_party/rust/encoding_rs/Cargo.toml.orig b/third_party/rust/encoding_rs/Cargo.toml.orig
+deleted file mode 100644
+index 0f7639d5f879b..0000000000000
+--- a/third_party/rust/encoding_rs/Cargo.toml.orig
++++ /dev/null
+@@ -1,45 +0,0 @@
+-[package]
+-name = "encoding_rs"
+-description = "A Gecko-oriented implementation of the Encoding Standard"
+-version = "0.8.35"
+-edition = '2018'
+-authors = ["Henri Sivonen <hsivonen@hsivonen.fi>"]
+-license = "(Apache-2.0 OR MIT) AND BSD-3-Clause"
+-readme = "README.md"
+-documentation = "https://docs.rs/encoding_rs/"
+-homepage = "https://docs.rs/encoding_rs/"
+-repository = "https://github.com/hsivonen/encoding_rs"
+-keywords = ["encoding", "web", "unicode", "charset"]
+-categories = ["text-processing", "encoding", "web-programming", "internationalization"]
+-rust-version = "1.36"
+-
+-[features]
+-default = ["alloc"]
+-alloc = []
+-simd-accel = ["any_all_workaround"]
+-less-slow-kanji-encode = []
+-less-slow-big5-hanzi-encode = []
+-less-slow-gb-hanzi-encode = []
+-fast-hangul-encode = []
+-fast-hanja-encode = []
+-fast-kanji-encode = []
+-fast-gb-hanzi-encode = []
+-fast-big5-hanzi-encode = []
+-fast-legacy-encode = ["fast-hangul-encode",
+-                      "fast-hanja-encode",
+-                      "fast-kanji-encode",
+-                      "fast-gb-hanzi-encode",
+-                      "fast-big5-hanzi-encode"]
+-
+-[dependencies]
+-cfg-if = "1.0"
+-serde = { version = "1.0", optional = true }
+-any_all_workaround = { version = "0.1.0" , optional = true }
+-
+-[dev-dependencies]
+-serde_derive = "1.0"
+-bincode = "1.0"
+-serde_json = "1.0"
+-
+-[profile.release]
+-lto = true
+diff --git a/third_party/rust/encoding_rs/src/x_user_defined.rs b/third_party/rust/encoding_rs/src/x_user_defined.rs
+index 7af7d5e3d69da..16f1a18d7f6ce 100644
+--- a/third_party/rust/encoding_rs/src/x_user_defined.rs
++++ b/third_party/rust/encoding_rs/src/x_user_defined.rs
+@@ -16,7 +16,8 @@ cfg_if! {
+         use simd_funcs::*;
+         use core::simd::u16x8;
+         use core::simd::cmp::SimdPartialOrd;
++        #[rustversion::since(1.95)]
+         use core::simd::Select;
+ 
+         #[inline(always)]
+         fn shift_upper(unpacked: u16x8) -> u16x8 {

gnu/packages/patches/r-biostrings-r4.6.0-compat.patch

@@ -0,0 +1,513 @@
+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;
+-}
+-

gnu/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch

@@ -0,0 +1,142 @@
+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
+

gnu/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch

@@ -0,0 +1,67 @@
+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
+

gnu/packages/patches/r-rsamtools-r-4.6.0-compat.patch

@@ -0,0 +1,114 @@
+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);
+ }

gnu/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch

@@ -0,0 +1,103 @@
+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
+

gnu/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch

@@ -0,0 +1,412 @@
+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
+

gnu/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch

@@ -0,0 +1,149 @@
+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
+

gnu/packages/patches/r-sparsearray-r-4.6.0-compat.patch

@@ -0,0 +1,259 @@
+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;

gnu/packages/patches/rust-codex-0.117.0-core-remove-self-dep.patch

@@ -0,0 +1,20 @@
+Author: Danny Milosavljevic <dannym@friendly-machines.com>
+Date: 2026-02-08
+License: ASL2.0
+Subject: Remove codex-core circular dev-dependencies.
+
+codex-core has a dev-dependency on codex-arg0 which in turn depends on
+codex-core.  This causes cargo package to fail when resolving from the
+vendor directory because codex-arg0 is not yet available at the time
+codex-core is packaged.
+
+--- a/codex-rs/core/Cargo.toml
++++ b/codex-rs/core/Cargo.toml
+@@ -144,7 +144,6 @@
+ [dev-dependencies]
+ assert_cmd = { workspace = true }
+ assert_matches = { workspace = true }
+-codex-arg0 = { workspace = true }
+ codex-otel = { workspace = true, features = [
+     "disable-default-metrics-exporter",
+ ] }

gnu/packages/patches/rust-codex-0.117.0-remove-patch-sections.patch

@@ -0,0 +1,30 @@
+Author: Danny Milosavljevic <dannym@friendly-machines.com>
+Date: 2026-02-08
+License: ASL2.0
+Subject: Remove [patch.crates-io] and [patch.'ssh://...'] sections.
+
+The [patch] sections point to git repositories which are unavailable
+in an offline build.  The vendored crossterm, ratatui,
+tokio-tungstenite and tungstenite forks are provided as cargo-inputs
+instead.
+
+--- a/codex-rs/Cargo.toml
++++ b/codex-rs/Cargo.toml
+@@ -423,17 +423,3 @@
+ debug = 1         # Reduce debug symbol size
+ inherits = "test"
+ opt-level = 0
+-
+-[patch.crates-io]
+-# Uncomment to debug local changes.
+-# ratatui = { path = "../../ratatui" }
+-crossterm = { git = "https://github.com/nornagon/crossterm", branch = "nornagon/color-query" }
+-ratatui = { git = "https://github.com/nornagon/ratatui", branch = "nornagon-v0.29.0-patch" }
+-tokio-tungstenite = { git = "https://github.com/openai-oss-forks/tokio-tungstenite", rev = "132f5b39c862e3a970f731d709608b3e6276d5f6" }
+-tungstenite = { git = "https://github.com/openai-oss-forks/tungstenite-rs", rev = "9200079d3b54a1ff51072e24d81fd354f085156f" }
+-
+-# Uncomment to debug local changes.
+-# rmcp = { path = "../../rust-sdk/crates/rmcp" }
+-
+-[patch."ssh://git@github.com/openai-oss-forks/tungstenite-rs.git"]
+-tungstenite = { git = "https://github.com/openai-oss-forks/tungstenite-rs", rev = "9200079d3b54a1ff51072e24d81fd354f085156f" }

gnu/packages/patches/rust-codex-0.120.0-connectors-cache-test-race.patch

@@ -0,0 +1,26 @@
+Author: Danny Milosavljevic <dannym@friendly-machines.com>
+Date: 2026-04-14
+License: ASL2.0
+Subject: Fix race condition in codex-connectors cache test.
+
+ALL_CONNECTORS_CACHE is a single global Option, not a map.  When Rust's
+test runner executes tests in parallel, the
+list_all_connectors_merges_and_normalizes_directory_apps test can
+overwrite the cache entry between the two calls in
+list_all_connectors_uses_shared_cache, causing a key mismatch and a
+spurious "cache should have been used" failure.
+
+Fix by clearing the cache at the start of the cache test so it does not
+depend on execution order relative to other tests.
+
+--- a/codex-rs/connectors/src/lib.rs
++++ b/codex-rs/connectors/src/lib.rs
+@@ -441,6 +441,9 @@
+     #[tokio::test]
+     async fn list_all_connectors_uses_shared_cache() -> anyhow::Result<()> {
++        // Clear any stale cache entry left by a concurrently running test.
++        *ALL_CONNECTORS_CACHE.lock().unwrap() = None;
++
+         let calls = Arc::new(AtomicUsize::new(0));
+         let call_counter = Arc::clone(&calls);
+         let key = cache_key("shared");

gnu/packages/patches/rust-codex-0.120.0-core-remove-self-dep.patch

@@ -0,0 +1,20 @@
+Author: Danny Milosavljevic <dannym@friendly-machines.com>
+Date: 2026-02-08
+License: ASL2.0
+Subject: Remove codex-core circular dev-dependencies.
+
+codex-core has a dev-dependency on codex-arg0 which in turn depends on
+codex-core.  This causes cargo package to fail when resolving from the
+vendor directory because codex-arg0 is not yet available at the time
+codex-core is packaged.
+
+--- a/codex-rs/core/Cargo.toml
++++ b/codex-rs/core/Cargo.toml
+@@ -134,7 +134,6 @@
+ [dev-dependencies]
+ assert_cmd = { workspace = true }
+ assert_matches = { workspace = true }
+-codex-arg0 = { workspace = true }
+ codex-otel = { workspace = true }
+ codex-utils-cargo-bin = { workspace = true }
+ core_test_support = { workspace = true }

gnu/packages/patches/rust-codex-0.120.0-remove-libwebrtc.patch

@@ -0,0 +1,16 @@
+Author: Danny Milosavljevic <dannym@friendly-machines.com>
+Date: 2026-04-14
+License: ASL2.0
+Subject: Remove macOS-only libwebrtc git dependency.
+
+--- a/codex-rs/realtime-webrtc/Cargo.toml
++++ b/codex-rs/realtime-webrtc/Cargo.toml
+@@ -12,8 +12,5 @@
+ thiserror = { workspace = true }
+ tokio = { workspace = true, features = ["rt-multi-thread"] }
+
+-[target.'cfg(target_os = "macos")'.dependencies]
+-libwebrtc = { version = "0.3.26", git = "https://github.com/juberti-oai/rust-sdks.git", rev = "e2d1d1d230c6fc9df171ccb181423f957bb3c1f0" }
+-
+ [lints]
+ workspace = true

gnu/packages/patches/rust-codex-0.120.0-test-timeout.patch

@@ -0,0 +1,20 @@
+Author: Danny Milosavljevic <dannym@friendly-machines.com>
+Date: 2026-03-05
+License: ASL2.0
+Subject: Increase per-event test timeout from 10 to 30 seconds.
+
+In resource-constrained build environments, image processing (resize,
+base64-encode, JSON serialization) can exceed 10 seconds under CPU
+contention, causing intermittent test failures.
+
+--- a/codex-rs/core/tests/common/lib.rs
++++ b/codex-rs/core/tests/common/lib.rs
+@@ -283,7 +283,7 @@
+     use tokio::time::timeout;
+     loop {
+         // Allow a bit more time to accommodate async startup work (e.g. config IO, tool discovery)
+-        let ev = timeout(wait_time.max(Duration::from_secs(10)), codex.next_event())
++        let ev = timeout(wait_time.max(Duration::from_secs(30)), codex.next_event())
+             .await
+             .expect("timeout waiting for event")
+             .expect("stream ended unexpectedly");

gnu/packages/patches/rust-codex-0.124.0-code-mode-stub-toolname.patch

@@ -0,0 +1,25 @@
+Author: Danny Milosavljevic <dannym@friendly-machines.com>
+Date: 2026-04-26
+License: ASL2.0
+Subject: Stub CodeModeTurnHost::invoke_tool signature uses ToolName.
+
+In codex 0.117 the upstream trait took `tool_name: String`, so the
+disable-code-mode patch's `cfg(not(feature = "v8-runtime"))` stub used
+String to match.  In codex 0.124 the upstream trait takes
+`codex_protocol::ToolName`, and core/src/tools/code_mode/mod.rs's impl
+of CodeModeTurnHost passes `ToolName`, so the stub must match the new
+signature here too.  This patch is applied only to codex 0.124+ on top
+of the shared disable-code-mode patch; codex-acp (which still pins
+rust-v0.117.0 where code-mode has no codex-protocol dep) keeps the
+String-based stub.
+
+--- a/codex-rs/code-mode/src/lib.rs
++++ b/codex-rs/code-mode/src/lib.rs
+@@ -77,7 +77,7 @@
+ #[cfg(not(feature = "v8-runtime"))]
+ #[async_trait::async_trait]
+ pub trait CodeModeTurnHost: Send + Sync {
+-    async fn invoke_tool(&self, tool_name: String, input: Option<serde_json::Value>, cancellation_token: tokio_util::sync::CancellationToken) -> Result<serde_json::Value, String>;
++    async fn invoke_tool(&self, tool_name: codex_protocol::ToolName, input: Option<serde_json::Value>, cancellation_token: tokio_util::sync::CancellationToken) -> Result<serde_json::Value, String>;
+     async fn notify(&self, call_id: String, cell_id: String, text: String) -> Result<(), String>;
+ }

gnu/packages/patches/rust-codex-0.124.0-remove-patch-sections.patch

@@ -0,0 +1,29 @@
+Author: Danny Milosavljevic <dannym@friendly-machines.com>
+Date: 2026-04-23
+License: ASL2.0
+Subject: Remove [patch.crates-io] and [patch.'ssh://...'] sections.
+
+The [patch] sections point to git repositories which are unavailable
+in an offline build.  The vendored crossterm, ratatui,
+tokio-tungstenite and tungstenite forks are provided as cargo-inputs
+instead.
+
+--- a/codex-rs/Cargo.toml	2026-04-23 22:49:56.599115735 +0000
++++ b/codex-rs/Cargo.toml	2026-04-23 22:49:56.601899894 +0000
+@@ -470,16 +470,3 @@
+ inherits = "test"
+ opt-level = 0
+ 
+-[patch.crates-io]
+-# Uncomment to debug local changes.
+-# ratatui = { path = "../../ratatui" }
+-crossterm = { git = "https://github.com/nornagon/crossterm", rev = "87db8bfa6dc99427fd3b071681b07fc31c6ce995" }
+-ratatui = { git = "https://github.com/nornagon/ratatui", rev = "9b2ad1298408c45918ee9f8241a6f95498cdbed2" }
+-tokio-tungstenite = { git = "https://github.com/openai-oss-forks/tokio-tungstenite", rev = "132f5b39c862e3a970f731d709608b3e6276d5f6" }
+-tungstenite = { git = "https://github.com/openai-oss-forks/tungstenite-rs", rev = "9200079d3b54a1ff51072e24d81fd354f085156f" }
+-
+-# Uncomment to debug local changes.
+-# rmcp = { path = "../../rust-sdk/crates/rmcp" }
+-
+-[patch."ssh://git@github.com/openai-oss-forks/tungstenite-rs.git"]
+-tungstenite = { git = "https://github.com/openai-oss-forks/tungstenite-rs", rev = "9200079d3b54a1ff51072e24d81fd354f085156f" }

gnu/packages/photo.scm

@@ -359,7 +359,7 @@ MTP, and much more.")
 (define-public perl-image-exiftool
   (package
     (name "perl-image-exiftool")
-    (version "12.70")
+    (version "13.55")
     (source
      (origin
        (method url-fetch)
@@ -371,7 +371,7 @@ MTP, and much more.")
                             "Image-ExifTool-" version ".tar.gz")))
        (sha256
         (base32
-         "1zmg5jsdqmr9mnmxg614brdgr9ddmspcc11rs4xkygnc8lj55cjc"))))
+         "0rv6hiqd44npnjzcn5ig5d0rnpgbzkdp5bbi526561nl9b9q2k2z"))))
     (build-system perl-build-system)
     (arguments
      (list #:phases

gnu/packages/plan9.scm

@@ -143,8 +143,8 @@ reconstruct a Plan 9 terminal-like experience from a non-Plan 9 system.")
 
 (define-public plan9port
   ;; no releases
-  (let ((commit "f8681acb374fa0d5ed1568dbedb00a4abe1ca6f1")
-        (revision "1"))
+  (let ((commit "b379c7cc9dd9a810a9873d444e9742fcad3f5997")
+        (revision "2"))
     (package
       (name "plan9port")
       (version (git-version "0.1.0" revision commit))
@@ -156,7 +156,7 @@ reconstruct a Plan 9 terminal-like experience from a non-Plan 9 system.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "01343jvn8kr63i78h8xlgscn6wihdsr44xzh1cylvhigjbqw8n2x"))
+                  "0mvchnbk9kywm9fsw0cb621g435kav4sd1facb71v0jy7xwzw1fz"))
                 (modules '((guix build utils)))
                 (snippet #~(for-each delete-file-recursively
                                      '("font/luc" ;nonfree
@@ -171,8 +171,8 @@ reconstruct a Plan 9 terminal-like experience from a non-Plan 9 system.")
                    (lambda _
                      (let ((dest (string-append #$output "/plan9")))
                        (substitute* "INSTALL"
-                         ;; Install fontsrv, which is enabled in LOCAL.config.
-                         (("rm -f bin/fontsrv") ""))
+                         ;; Pass the check for freetype to install fontsrv.
+                         (("\\[ -f a\\.out ]") "true"))
                        (delete-file "src/cmd/mk/mk.pdf")
                        ;; TODO: substitute font in src/cmd/venti/srv/graph.c
                        (substitute* "src/cmd/acme/acme.c"
@@ -201,8 +201,8 @@ reconstruct a Plan 9 terminal-like experience from a non-Plan 9 system.")
                          (("luc/unicode.6.font")
                            "fixed/unicode.6x9.font"))
                        (substitute* "bin/9c"
-                         (("which")
-                          (which "which")))
+                         (("[$][(]which uniq[)]")
+                          "uniq"))
                        (substitute* "src/cmd/fontsrv/freetyperules.sh"
                          (("'\\$i'/freetype2")
                           (string-append "-I"
@@ -210,8 +210,7 @@ reconstruct a Plan 9 terminal-like experience from a non-Plan 9 system.")
                                          "/include/freetype2")))
                        (with-output-to-file "LOCAL.config"
                          (lambda _
-                           (format #t "CC9=~a~%" #$(cc-for-target))
-                           (format #t "FONTSRV=fontsrv~%")))
+                           (format #t "CC9=~a~%" #$(cc-for-target))))
                        (setenv "X11" #$libx11)
                        (setenv "PLAN9" (getcwd))
                        (setenv "PLAN9_TARGET" dest))))
@@ -241,6 +240,7 @@ reconstruct a Plan 9 terminal-like experience from a non-Plan 9 system.")
                                    "troff"
                                    "postscript"))
                        (install-file "rcmain" dest)
+                       (install-file "config" dest)
                        (mkdir-p (string-append #$output "/bin"))
                        (symlink (string-append dest "/bin/9")
                                 (string-append #$output "/bin/9")))))

gnu/packages/prolog.scm

@@ -237,7 +237,7 @@ it.")
 (define-public trealla
   (package
     (name "trealla")
-    (version "2.92.38")
+    (version "2.94.4")
     (source
      (origin
        (method git-fetch)
@@ -246,7 +246,7 @@ it.")
           (url "https://github.com/trealla-prolog/trealla")
           (commit (string-append "v" version))))
        (sha256
-        (base32 "12nv54j7rgh784lszgynw50k9h3la8b0d2si2bskfvydmpyk45pm"))
+        (base32 "050x9m79j1bi17mj7zzbhlnn7ia26k51qrhp5z43wsx0rpp0hfqb"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (inputs
@@ -302,13 +302,13 @@ interpreter with ISO Prolog aspirations.")
 (define-public logtalk
   (package
     (name "logtalk")
-    (version "3.80.0")
+    (version "3.99.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://logtalk.org/files/logtalk-"
                            version ".tar.bz2"))
-       (sha256 (base32 "0g4cc0qv921234548k3rkv1sdayicaa6zzh15vgn82ri9apwm3nh"))))
+       (sha256 (base32 "04namz3lj2j1j741bb41qy5c172b9zawp1li148i7pd2s0jiwjjr"))))
     (build-system gnu-build-system)
     (arguments
      (list #:tests? #f                  ;no tests

gnu/packages/python-check.scm

@@ -13,7 +13,7 @@
 ;;; Copyright © 2020, 2022 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2020 Matthew James Kraai <kraai@ftbfs.org>
 ;;; Copyright © 2020 Edouard Klein <edk@beaver-labs.com>
-;;; Copyright © 2020, 2021, 2025 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021, 2025, 2026 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020 Tanguy Le Carrour <tanguy@bioneland.org>
 ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr>
 ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
@@ -1663,6 +1663,49 @@ cProfile or profile modules, depending on what is available.  It's a
 successor of @url{https://github.com/rkern/line_profiler}.")
     (license license:bsd-3)))
 
+(define-public python-lsp-ruff
+  (package
+    (name "python-lsp-ruff")
+    (version "2.3.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/python-lsp/python-lsp-ruff")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1xjvqyn3qn54cq63ay9n1rr1wkzx04bf99cki68n46gm8nwjvn6m"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags #~(list (string-append
+                            ;; Tests below do a diff check on the ruff store
+                            ;; path against the python store path.
+                            "-k" "not test_ruff_settings"
+                            " and not test_ruff_config_param"))
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'use-system-ruff
+                     ;; This package requests Ruff from PyPI.  Make it use
+                     ;; the guix package instead.
+                     (lambda _
+                       (substitute* "pyproject.toml"
+                         (("\"ruff.*\",") "")))))))
+    (propagated-inputs (list python-cattrs
+                             python-lsprotocol
+                             python-lsp-server
+                             python-tomli
+                             ;; Ruff is detected by shutil.which.
+                             ruff))
+    (native-inputs (list python-pytest python-setuptools))
+    (home-page "https://github.com/python-lsp/python-lsp-ruff")
+    (synopsis "Ruff linting plugin for @code{pylsp}")
+    (description
+     "@code{python-lsp-ruff} is a plugin for @code{python-lsp-server} that
+adds linting, code actions and formatting capabilities that are provided by
+Ruff.")
+    (license license:expat)))
+
 (define-public python-mamba
   (package
     (name "python-mamba")
@@ -2246,6 +2289,32 @@ wrapper above tools such as Pyflakes, pydocstyle, pycodestyle and McCabe,
 among others.")
     (license license:lgpl3+)))
 
+(define-public python-pylint-venv
+  (package
+    (name "python-pylint-venv")
+    (version "3.0.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/jgosmann/pylint-venv/")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "06va7vy3bg331aab589wcr3nmafxlya0ac1as39qqyvkbdz9b5bl"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; Test is a simple shell script that activates a virtual environment
+     ;; and runs pylint inside of it.  There are no checks.
+     (list #:tests? #f))
+    (native-inputs (list python-poetry-core))
+    (home-page "https://github.com/jgosmann/pylint-venv/")
+    (synopsis
+     "Pylint init-hook to share a Pylint installation across virtualenvs")
+    (description "@code{pylint-venv} provides a Pylint init-hook to use the
+same Pylint installation with different virtual environments.")
+    (license license:expat)))
+
 (define-public python-pynose
   (package
     (name "python-pynose")

gnu/packages/python-crypto.scm

@@ -1142,20 +1142,23 @@ provides drop-in compatibility with PyCrypto.")))
 (define-public python-m2crypto
   (package
     (name "python-m2crypto")
-    (version "0.38.0")
+    (version "0.47.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "M2Crypto" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/m2crypto/m2crypto")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1jyynaybncgjp8rndrwjpj5gnbrislngimf6ind9874h6052dwlr"))))
+        (base32 "090dvgnjmqidh0c318kipysiy24cn1rwbmxl4vybnqd57n65xsn8"))))
     (build-system pyproject-build-system)
     (arguments
      `(;; FIXME: Tests start failing with time due to date checks in TLS
        ;; certificates.
        #:tests? #f))
     (inputs (list openssl))
-    (native-inputs (list swig-4.0 python-setuptools python-wheel))
+    (native-inputs (list swig python-setuptools))
     (home-page "https://gitlab.com/m2crypto/m2crypto")
     (synopsis "Python crypto and TLS toolkit")
     (description "@code{M2Crypto} is a complete Python wrapper for OpenSSL

gnu/packages/python-graphics.scm

@@ -809,7 +809,7 @@ wrappers for common SDL2 functionality.")
 (define-public python-qtawesome
   (package
     (name "python-qtawesome")
-    (version "1.4.0")
+    (version "1.4.2")
     (source
      (origin
        (method git-fetch)
@@ -818,7 +818,7 @@ wrappers for common SDL2 functionality.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "109anjlnin5cafx579clj1x21ggig3qkcm2g1wlx0lshxqzjadan"))))
+        (base32 "16vjnngg5hjmmbp0c2ikgc88g8q0l44n1w3wa04ga5zfhd1yhyn2"))))
     (build-system pyproject-build-system)
     (arguments
      (list