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"))

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

gnu/local.mk

@@ -1699,7 +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	\
@@ -1714,6 +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	\
@@ -2349,8 +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	\
@@ -2400,6 +2408,8 @@ dist_patch_DATA =						\
   %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/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

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-0.120.0, 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-0.120.0 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)
@@ -54,14 +54,14 @@
 (define-public codex
   (package
     (name "codex")
-    (version (package-version rust-codex-0.120.0))
+    (version (package-version rust-codex-0.124.0))
     (source
      (origin
-       (inherit (package-source rust-codex-0.120.0))
+       (inherit (package-source rust-codex-0.124.0))
        (patches (search-patches
                  "codex-acp-0.11.1-disable-code-mode.patch"
-                 "rust-codex-0.117.0-remove-patch-sections.patch"
-                 "rust-codex-0.120.0-connectors-cache-test-race.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-0.120.0-test-timeout.patch"))))
@@ -69,7 +69,12 @@
     (arguments
      (list
       #:install-source? #f
-      #:cargo-install-paths '(list "cli" "exec" "exec-server"
+      ;; 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:
@@ -317,7 +322,164 @@
                                 ;; (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")
+                                "--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"
@@ -358,22 +520,31 @@
          "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-features"
+         "codex-model-provider"
          "codex-config"
+         "codex-agent-identity"
+         "codex-aws-auth"
          "codex-hooks"
-         "codex-instructions"
          "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"
@@ -425,7 +596,7 @@
               ;; Update them to match the actual package version.
               (let ((snap-files (find-files "." "\\.snap$")))
                 (substitute* snap-files
-                  (("\\(v0\\.0\\.0\\)   ") "(v0.120.0) ")))))
+                  (("\\(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
@@ -436,32 +607,55 @@
                 (("runfiles = \\{ git = [^}]+\\}")
                  "runfiles = \"0.1.0\""))
               ;; Remove workspace members that have unbuildable deps
-              ;; (libwebrtc requires git fetch, v8-poc requires V8).
+              ;; (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\",") "")
-                (("\"code-mode\",") ""))
-              ;; Disable V8 runtime in codex-code-mode: remove path
-              ;; so cargo resolves it from the vendor (where it has
-              ;; optional = true on v8) and disable default features.
+                (("\"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 = { version = \"0.120.0\", default-features = false }"))))
+                 "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 = "0.120.0" 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 = \"0.120.0\", 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 = \"0.120.0\", 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 = \"0.120.0\""))))))
+                   (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
@@ -561,10 +755,12 @@
                 ;; double quotes.
                 (substitute*
                   (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")
@@ -613,7 +809,17 @@
               ;; ~/... and 30 snapshot tests fail.
               (setenv "HOME" "/tmp/guix-home")
               (mkdir-p "/tmp/guix-home")
-              (setenv "USER" "nixbld"))))))
+              (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)

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/emacs-xyz.scm

@@ -781,6 +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"
+                 #$(file-append (this-package-input "direnv")
+                                "/bin/direnv"))))))))
+    (inputs (list direnv))
+    (propagated-inputs (list emacs-inheritenv))
+    (home-page "https://codeberg.org/pastor/ben.el")
+    (synopsis "Asynchronous buffer-local environments via @command{direnv}")
+    (description
+     "This package allows you to load environments buffer locally.  The
+package is named @command{ben}, which stands for Buffer ENvironments.
+
+The project relies on @uref{https://direnv.net, direnv} which allows setting
+per-directory environments through @file{.envrc} files.
+
+The main improvement of @command{ben} over @command{envrc} is the asynchronous
+processing of environments, which prevents Emacs from freezing.  This is
+especially useful while loading computationally heavy environments, such when
+loading @file{.envrc} files that rely on Guix.  In these cases, computations
+can take hours to complete.  This package aims to facilitate loading such
+environments in the background.")
+    (license license:gpl3+)))
+
 (define-public emacs-bookmark-plus
   (package
     (name "emacs-bookmark-plus")
@@ -39862,7 +39910,7 @@ user interfaces for various built-in modes.")
 (define-public emacs-calibredb
   (package
     (name "emacs-calibredb")
-    (version "2.13.0")
+    (version "2.14.0")
     (source
      (origin
        (method git-fetch)
@@ -39871,31 +39919,40 @@ user interfaces for various built-in modes.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1a4gyc3gcq18j29pw2i296d70nvx5fbzlw9fdmqwzncciqz5as6m"))))
+        (base32 "1g0jg6a6fgvxd5bsydckbqwf899d2d9732laz4k1k476mbws5dqy"))))
     (build-system emacs-build-system)
     (arguments
      (list
+      #:include #~(cons "\\.py$" %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.
@@ -41493,17 +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/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/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

@@ -1600,7 +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)
@@ -1609,7 +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

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-web.scm

@@ -386,19 +386,25 @@ devices.")
             ;; - cloud.google.com/go/compute/metadata
             ;; - cloud.google.com/go/iam
             ;; - cloud.google.com/go/kms
+            ;; - cloud.google.com/go/logging
             ;; - cloud.google.com/go/longrunning
             ;; - cloud.google.com/go/monitoring
             ;; - cloud.google.com/go/security
+            ;; - cloud.google.com/go/spanner
             ;; - cloud.google.com/go/storage
+            ;; - cloud.google.com/go/trace
             (for-each delete-file-recursively
                       (list "auth"
                             "compute/metadata"
                             "iam"
                             "kms"
+                            "logging"
                             "longrunning"
                             "monitoring"
                             "security"
-                            "storage"))))))
+                            "spanner"
+                            "storage"
+                            "trace"))))))
     (build-system go-build-system)
     (arguments
      (list
@@ -440,7 +446,6 @@ devices.")
               "pubsub/v2/internal/scheduler"
               "pubsub/v2/internal/testutil"
               "rpcreplay"
-              "spanner/spansql"
               "translate")))
     (propagated-inputs
      (list ;; go-cloud-google-com-go-storage
@@ -695,6 +700,65 @@ Service (KMS) API.")
 see: @url{https://cloud.google.com/iam, IAM specification} for more details.")
     (license license:asl2.0)))
 
+(define-public go-cloud-google-com-go-logging
+  (package
+    (name "go-cloud-google-com-go-logging")
+    (version "1.16.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/googleapis/google-cloud-go")
+              (commit (go-version->git-ref version #:subdir "logging"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "14khzbcymknsz4p40ibc8v1zsy33b33yn7fcvkfp4rkzw69wv356"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "." "logging")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "cloud.google.com/go/logging"
+      #:unpack-path "cloud.google.com/go"))
+    (native-inputs
+     ;; XXX: Remove when cycle is fixed.
+     (list go-github-com-envoyproxy-go-control-plane))
+    (propagated-inputs
+     (list go-cloud-google-com-go
+           go-cloud-google-com-go-compute-metadata
+           go-cloud-google-com-go-iam
+           go-cloud-google-com-go-longrunning
+           go-cloud-google-com-go-storage
+           go-github-com-google-go-cmp
+           go-github-com-googleapis-gax-go-v2
+           go-go-opencensus-io
+           go-go-opentelemetry-io-otel-sdk
+           go-go-opentelemetry-io-otel-trace
+           go-golang-org-x-oauth2
+           go-google-golang-org-api
+           go-google-golang-org-genproto
+           go-google-golang-org-genproto-googleapis-api
+           go-google-golang-org-genproto-googleapis-rpc
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://cloud.google.com/go")
+    (synopsis "Cloud Logging API")
+    (description
+     "Package logging contains a Cloud Logging client suitable for writing
+logs.  For reading logs, and working with sinks, metrics and monitored
+resources, see package cloud.google.com/go/logging/logadmin.")
+    (license license:asl2.0)))
+
 (define-public go-cloud-google-com-go-longrunning
   (package
     (name "go-cloud-google-com-go-longrunning")
@@ -832,6 +896,78 @@ its service definition.")
      "This package provides a Go Client Library for Certificate Authority API.")
     (license license:asl2.0)))
 
+(define-public go-cloud-google-com-go-spanner
+  (package
+    (name "go-cloud-google-com-go-spanner")
+    (version "1.91.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/googleapis/google-cloud-go")
+              (commit (go-version->git-ref version #:subdir "spanner"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "05jgalbqb9n1whlpdkj40rvyk8lg39q5w4l463ycsj2301pmr90h"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "." "spanner")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "cloud.google.com/go/spanner"
+      #:unpack-path "cloud.google.com/go"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-benchmarks
+            (lambda* (#:key import-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" import-path)
+                (delete-file-recursively "benchmarks")))))))
+    (native-inputs
+     (list go-github-com-google-go-cmp
+           ;; XXX: Remove when cycle is fixed.
+           go-github-com-envoyproxy-go-control-plane))
+    (propagated-inputs
+     (list go-cloud-google-com-go
+           go-cloud-google-com-go-iam
+           go-cloud-google-com-go-longrunning
+           go-cloud-google-com-go-monitoring
+           go-github-com-google-uuid
+           go-github-com-googleapis-gax-go-v2
+           go-github-com-googlecloudplatform-grpc-gcp-go-grpcgcp
+           go-go-opencensus-io
+           go-go-opentelemetry-io-contrib-detectors-gcp
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-metric
+           go-go-opentelemetry-io-otel-sdk
+           go-go-opentelemetry-io-otel-sdk-metric
+           go-go-opentelemetry-io-otel-trace
+           go-golang-org-x-oauth2
+           go-golang-org-x-sync
+           go-google-golang-org-api
+           go-google-golang-org-genproto
+           go-google-golang-org-genproto-googleapis-api
+           go-google-golang-org-genproto-googleapis-rpc
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://cloud.google.com/go")
+    (synopsis "Cloud Spanner databases Go client")
+    (description
+     "Package spanner provides a client for reading and writing to Cloud
+Spanner databases.  See
+@url{https://cloud.google.com/spanner/docs/getting-started/go/} for an
+introduction to Cloud Spanner and additional help on using this API.")
+    (license license:asl2.0)))
+
 (define-public go-cloud-google-com-go-storage
   (package
     (name "go-cloud-google-com-go-storage")
@@ -897,6 +1033,59 @@ Google Cloud Storage stores data in named objects, which are grouped into
 buckets.")
     (license license:asl2.0)))
 
+(define-public go-cloud-google-com-go-trace
+  (package
+    (name "go-cloud-google-com-go-trace")
+    (version "1.14.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/googleapis/google-cloud-go")
+              (commit (go-version->git-ref version #:subdir "trace"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "14khzbcymknsz4p40ibc8v1zsy33b33yn7fcvkfp4rkzw69wv356"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "." "trace")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:skip-build? #t
+      #:import-path "cloud.google.com/go/trace"
+      #:unpack-path "cloud.google.com/go"))
+    (propagated-inputs
+     (list go-github-com-googleapis-gax-go-v2
+           go-google-golang-org-api
+           go-google-golang-org-genproto
+           go-google-golang-org-genproto-googleapis-api
+           go-google-golang-org-genproto-googleapis-rpc
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://cloud.google.com/go")
+    (synopsis "Go Client Library for Cloud Trace API")
+    (description
+     "This package implements the @url{https://cloud.google.com/stackdriver,
+Stackdriver} Trace API in Golang.  Stackdriver Trace is a distributed tracing
+system that collects latency data from your applications and displays it in
+the Google Cloud Platform Console.
+
+It sends application trace data to Stackdriver Trace for viewing.  Trace data
+is collected for all App Engine applications by default.  Trace data from
+other applications can be provided using this API.  This library is used to
+interact with the Trace API directly.")
+    (license license:asl2.0)))
+
 (define-public go-code-gitea-io-sdk-gitea
   (package
     (name "go-code-gitea-io-sdk-gitea")
@@ -1406,6 +1595,39 @@ AWS Lambda and API Gateway or ALB without changing the existing HTTP
 handlers.")
     (license license:asl2.0)))
 
+(define-public go-github-com-akutz-memconn
+  (package
+    (name "go-github-com-akutz-memconn")
+    (version "0.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/akutz/memconn")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1mhghzcx2zxr4bpyf4wx3j7ph9srw38wxg78svwbjh930r2kzssq"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/akutz/memconn"
+      #:test-flags
+      #~(list "-skip" (string-join
+                       ;; Tests fail with insecure algorithm
+                       (list "TestTLS_Memu"
+                             "TestTLS_Memb"
+                             "TestTLS_TCP"
+                             "TestTLS_UNIX"
+                             "TestTLS_HTTP_Memu"
+                             "TestTLS_HTTP_Memb")
+                       "|"))))
+    (home-page "https://github.com/akutz/memconn")
+    (synopsis "In-memory network stack for Go")
+    (description
+     "This package provides named, in-memory network connections for Go.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-alexliesenfeld-health
   (package
     (name "go-github-com-alexliesenfeld-health")
@@ -3595,6 +3817,33 @@ differentiate between installs of Mozilla software in @code{installs.ini} and
                              "TestStructToDateTime")
                        "|"))))))
 
+(define-public go-github-com-brunoscheufler-aws-ecs-metadata-go
+  (package
+    (name "go-github-com-brunoscheufler-aws-ecs-metadata-go")
+    (version "0.0.0-20221221133751-67e37ae746cd")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/BrunoScheufler/aws-ecs-metadata-go")
+              (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1x9kn49sl6793zqq4nrbsyfhqh7i3xr25syck2ybpcqkd3mmb8k6"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/brunoscheufler/aws-ecs-metadata-go"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (home-page "https://github.com/brunoscheufler/aws-ecs-metadata-go")
+    (synopsis "Retrieve AWS ECS Task metadata")
+    (description
+     "This package provides a minimal wrapper library to fetch
+@acronym{Elastic Container Service, ECS} Task metadata from any Go service
+running in container provisioned by AWS Fargate.")
+    (license license:expat)))
+
 (define-public go-github-com-buger-jsonparser
   (package
     (name "go-github-com-buger-jsonparser")
@@ -6166,7 +6415,7 @@ application's http.Handlers.")
 (define-public go-github-com-files-com-files-sdk-go-v3
   (package
     (name "go-github-com-files-com-files-sdk-go-v3")
-    (version "3.3.7")
+    (version "3.3.95")
     (source
      (origin
        (method git-fetch)
@@ -6175,7 +6424,7 @@ application's http.Handlers.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1syx75vbamwrx5x5glf4542ml8myj9kqqkig8hmy97lhzq4d4n7a"))))
+        (base32 "19mxsybv9lyq57nf5xvll41g7f6z90lq9hrdx1p4w20mj0f51wyj"))))
     (build-system go-build-system)
     (arguments
      (list
@@ -6191,7 +6440,6 @@ application's http.Handlers.")
            go-github-com-stretchr-testify))
     (propagated-inputs
      (list go-github-com-appscode-go-querystring
-           go-github-com-bradfitz-iter
            go-github-com-chilts-sid
            go-github-com-dustin-go-humanize
            go-github-com-hashicorp-go-retryablehttp
@@ -6201,6 +6449,7 @@ application's http.Handlers.")
            go-github-com-sabhiram-go-gitignore
            go-github-com-samber-lo
            go-github-com-winfsp-cgofuse
+           go-golang-org-x-sync
            go-golang-org-x-sys
            go-golang-org-x-text
            go-moul-io-http2curl-v2))
@@ -8245,6 +8494,51 @@ Terraform by using the enterprise certificates feature.")
 for clients and servers based on @code{gRPC} and Google API conventions.")
     (license license:bsd-3)))
 
+(define-public go-github-com-googlecloudplatform-grpc-gcp-go-grpcgcp
+  (package
+    (name "go-github-com-googlecloudplatform-grpc-gcp-go-grpcgcp")
+    (version "1.6.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/GoogleCloudPlatform/grpc-gcp-go")
+              (commit (go-version->git-ref version #:subdir "grpcgcp"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0p7zwbi6gg99mzi7albscf7jn63qxs714h6vars735an13bbvl12"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:go go-1.25
+      #:import-path "github.com/GoogleCloudPlatform/grpc-gcp-go/grpcgcp"
+      #:unpack-path "github.com/GoogleCloudPlatform/grpc-gcp-go"
+      ;; gcp_multiendpoint_test.go:441: endpoint wanted "localhost:50051", got
+      ;; "127.0.0.3:50051"
+      #:test-flags #~(list "-skip" "TestGCPMultiEndpoint")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'pre-check
+            (lambda _
+              ;; See: <https://go.dev/blog/synctest>.
+              (setenv "GOEXPERIMENT" "synctest")
+              (setenv "GODEBUG" "asynctimerchan=0"))))))
+    (native-inputs
+     (list go-github-com-golang-mock
+           go-github-com-google-go-cmp))
+    (propagated-inputs
+     (list go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-metric
+           go-go-opentelemetry-io-otel-sdk-metric
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://github.com/GoogleCloudPlatform/grpc-gcp-go")
+    (synopsis "Grpc supports for Google Cloud APIs")
+    (description
+     "Package grpcgcp provides gRPC supports for Google Cloud APIs.  For now
+it provides connection management with affinity support.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-googlecloudplatform-opentelemetry-operations-go-detectors-gcp
   (package
     (name
@@ -8334,6 +8628,110 @@ testing of the detection functions in real GCP environments.")
 send collected metrics to Google Cloud.")
     (license license:asl2.0)))
 
+(define-public go-github-com-googlecloudplatform-opentelemetry-operations-go-exporter-trace
+  (package
+    (name "go-github-com-googlecloudplatform-opentelemetry-operations-go-exporter-trace")
+    (version "1.32.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/GoogleCloudPlatform/opentelemetry-operations-go")
+              (commit (go-version->git-ref version #:subdir "exporter/trace"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nizaaydcvvi718g5v4pgx8in6d546mmkrf7h3sxhz2yyyygvms3"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "exporter" "trace")
+            (delete-all-but "." "exporter")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path
+      (string-append "github.com/GoogleCloudPlatform/"
+                     "opentelemetry-operations-go/exporter/trace")
+      #:unpack-path
+      "github.com/GoogleCloudPlatform/opentelemetry-operations-go"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (propagated-inputs
+     (list go-cloud-google-com-go-trace
+           go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-cloudmock
+           go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-resourcemapping
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-sdk
+           go-go-opentelemetry-io-otel-trace
+           go-golang-org-x-oauth2
+           go-google-golang-org-api
+           go-google-golang-org-genproto-googleapis-rpc
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://github.com/GoogleCloudPlatform/opentelemetry-operations-go")
+    (synopsis "OpenTelemetry Google Cloud Trace Exporter")
+    (description
+     "@code{OpenTelemetry} Google Cloud Trace Exporter allows the user to send
+collected traces and spans to Google Cloud.")
+    (license license:asl2.0)))
+
+(define-public go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-cloudmock
+  (package
+    (name "go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-cloudmock")
+    (version "0.56.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/GoogleCloudPlatform/opentelemetry-operations-go")
+              (commit (go-version->git-ref version
+                                           #:subdir "internal/cloudmock"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nizaaydcvvi718g5v4pgx8in6d546mmkrf7h3sxhz2yyyygvms3"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "internal" "cloudmock")
+            (delete-all-but "." "internal")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path
+      (string-append "github.com/GoogleCloudPlatform/"
+                     "opentelemetry-operations-go/internal/cloudmock")
+      #:unpack-path
+      "github.com/GoogleCloudPlatform/opentelemetry-operations-go"))
+    (propagated-inputs
+     (list go-cloud-google-com-go-logging
+           go-cloud-google-com-go-monitoring
+           go-cloud-google-com-go-trace
+           go-google-golang-org-genproto-googleapis-api
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://github.com/GoogleCloudPlatform/opentelemetry-operations-go")
+    (synopsis "OpenTelemetry Google Cloud mock library")
+    ;; XXX: There is not any documentation for this package upstrream.
+    (description
+     "This package provides OpenTelemetry Google Cloud mock Go library.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-resourcemapping
   (package
     (name "go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-resourcemapping")
@@ -9803,6 +10201,55 @@ protocol) - used to discover UPnP services on a network
  by the IBM Cloud @code{OpenAPI} SDK Generator (openapi-sdkgen).")
     (license license:asl2.0)))
 
+(define-public go-github-com-ibm-sarama
+  (package
+    (name "go-github-com-ibm-sarama")
+    (version "1.48.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/IBM/sarama")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0ak07aqb9hznvhbnkw34vak30pzbwvh2aff22lww8gcba4c9qdn7"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/IBM/sarama"
+      #:unpack-path "github.com/IBM/sarama"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-examples
+            (lambda* (#:key tests? unpack-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" unpack-path)
+                (delete-file-recursively "examples")))))))
+    (native-inputs
+     (list go-github-com-stretchr-testify
+           go-github-com-davecgh-go-spew
+           go-go-uber-org-goleak))
+    (propagated-inputs
+     (list go-github-com-eapache-go-resiliency
+           go-github-com-eapache-queue
+           go-github-com-jcmturner-gofork
+           go-github-com-jcmturner-gokrb5-v8
+           go-github-com-klauspost-compress
+           go-github-com-pierrec-lz4-v4
+           go-github-com-rcrowley-go-metrics
+           go-golang-org-x-net
+           go-golang-org-x-sync
+           go-golang-org-x-sys))
+    (home-page "https://github.com/IBM/sarama")
+    (synopsis "Go library for Apache Kafka")
+    (description
+     "Package sarama is a pure Go client library for dealing with Apache Kafka
+(versions 0.8 and later).  It includes a high-level API for easily producing
+and consuming messages, and a low-level API for controlling bytes on the wire
+when the high-level API is insufficient.  Usage examples for the high-level
+APIs are provided inline with their full documentation.")
+    (license license:expat)))
+
 (define-public go-github-com-igungor-gofakes3
   (package
     (name "go-github-com-igungor-gofakes3")
@@ -13629,24 +14076,24 @@ standard library.")
     (build-system go-build-system)
     (arguments
      (list
-      ;; TODO: Enable tests and build when all missing inputs are packages, use
-      ;; as source only package for Kubo.
-      #:skip-build? #t
-      #:tests? #f
-      #:import-path "github.com/openzipkin/zipkin-go"))
+      #:import-path "github.com/openzipkin/zipkin-go"
+      ;; span_test.go:56: expected valid endpoint, got error: host lookup
+      ;; failure: lookup www.google.com on [::1]:53: read udp
+      ;; [::1]:56302->[::1]:53: read: connection refused
+      #:test-flags #~(list "-skip" "TestRemoteEndpoint|TestHTTPClient")))
     (native-inputs
      (list go-github-com-onsi-ginkgo-v2
            go-github-com-onsi-gomega))
     (propagated-inputs
-     (list ;; go-github-com-ibm-sarama
-           ;; go-github-com-rabbitmq-amqp091-go
+     (list go-github-com-ibm-sarama
+           go-github-com-rabbitmq-amqp091-go
            go-google-golang-org-grpc
            go-google-golang-org-protobuf))
     (home-page "https://github.com/openzipkin/zipkin-go")
     (synopsis "Zipkin Library for Go")
     (description
      "Package zipkin implements a native Zipkin instrumentation library for
-Go.")
+Go.  @url{https://zipkin.io/, Zipkin} is a distributed tracing system.")
     (license license:asl2.0)))
 
 (define-public go-github-com-oracle-oci-go-sdk-v65
@@ -15574,6 +16021,38 @@ currently implements
 of the specification.")
       (license license:expat)))
 
+(define-public go-github-com-rabbitmq-amqp091-go
+  (package
+    (name "go-github-com-rabbitmq-amqp091-go")
+    (version "1.11.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/rabbitmq/amqp091-go")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1xn0ykx08l8gg66qk6jhz2md4as8n9fqm0smzcbislyqp4d3gpr8"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/rabbitmq/amqp091-go"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-examples
+            (lambda* (#:key tests? import-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" import-path)
+                (delete-file-recursively "_examples")))))))
+    (native-inputs
+     (list go-go-uber-org-goleak))
+    (home-page "https://github.com/rabbitmq/amqp091-go")
+    (synopsis "Go RabbitMQ Client Library")
+    (description
+     "Package amqp091 is an @acronym{Advanced Message Queuing Protocol, AMQP}
+0.9.1 client with @code{RabbitMQ} extensions.")
+    (license license:bsd-2)))
+
 (define-public go-github-com-rasky-go-xdr
   (package
     (name "go-github-com-rasky-go-xdr")
@@ -16233,6 +16712,7 @@ and consumers to transparently record signed metadata to a ledger.")
       #:test-subdirs
       #~(list "internal/algorithmregistry"
               "internal/safeint"
+              "pkg/client/read"
               "pkg/client/write"
               "pkg/types/dsse"
               "pkg/types/hashedrekord"
@@ -16247,7 +16727,8 @@ and consumers to transparently record signed metadata to a ledger.")
            go-github-com-stretchr-testify
            go-sigs-k8s-io-release-utils))
     (propagated-inputs
-     (list go-cloud-google-com-go-storage
+     (list go-cloud-google-com-go-spanner
+           go-cloud-google-com-go-storage
            go-github-com-aws-aws-sdk-go-v2
            go-github-com-aws-aws-sdk-go-v2-config
            go-github-com-aws-aws-sdk-go-v2-credentials
@@ -16264,12 +16745,14 @@ and consumers to transparently record signed metadata to a ledger.")
            go-github-com-sigstore-sigstore
            ;; go-github-com-sigstore-sigstore-go                 ;cycles
            go-github-com-sigstore-sigstore-pkg-signature-kms-aws
+           go-github-com-chainguard-dev-clog
            go-github-com-sigstore-sigstore-pkg-signature-kms-gcp
            go-github-com-tink-crypto-tink-go-awskms-v2
            go-github-com-tink-crypto-tink-go-gcpkms-v2
            go-github-com-tink-crypto-tink-go-v2
            go-github-com-transparency-dev-formats
            go-github-com-transparency-dev-merkle
+           go-github-com-transparency-dev-tessera
            go-go-opentelemetry-io-otel
            go-go-opentelemetry-io-otel-exporters-prometheus
            go-go-opentelemetry-io-otel-sdk-metric
@@ -16283,9 +16766,6 @@ and consumers to transparently record signed metadata to a ledger.")
            go-k8s-io-klog-v2
 
            ;; TODO: Complete packaging.
-           ;; go-cloud-google-com-go-spanner
-           ;; go-github-com-chainguard-dev-clog
-           ;; go-github-com-transparency-dev-tessera
            #;go-go-step-sm-crypto))
     (home-page "https://github.com/sigstore/rekor-tiles")
     (synopsis "Tile-based transparency log for Sigstore")
@@ -17917,7 +18397,95 @@ caching protocol.  It provides support to programmatically store and retrieve
 build caches, instead of relying on the standard actions/cache YAML step.")
     (license license:expat)))
 
+(define-public go-github-com-transparency-dev-tessera
+  (package
+    (name "go-github-com-transparency-dev-tessera")
+    (version "1.0.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/transparency-dev/tessera")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "101y83j67g7r1bqk49qj8mwxgys88wkxz5lf7pvjp4c6b10w5gck"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/transparency-dev/tessera"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-access-to-state-tree-state
+            (lambda* (#:key import-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" import-path)
+                (make-file-writable "testdata/log/.state/treeState.lock"))))
+          (add-after 'check 'remove-testdata
+            (lambda* (#:key import-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" import-path)
+                (delete-file-recursively "testdata")))))))
+    (native-inputs
+     (list strace
+           ;; XXX: Remove when cycle is fixed.
+           go-github-com-envoyproxy-go-control-plane))
+    (propagated-inputs
+     (list go-cloud-google-com-go-spanner
+           go-cloud-google-com-go-storage
+           go-github-com-avast-retry-go-v4
+           go-github-com-aws-aws-sdk-go-v2
+           go-github-com-aws-aws-sdk-go-v2-config
+           go-github-com-aws-aws-sdk-go-v2-credentials
+           go-github-com-aws-aws-sdk-go-v2-service-s3
+           go-github-com-aws-smithy-go
+           go-github-com-bitfield-script
+           go-github-com-cenkalti-backoff-v5
+           go-github-com-charmbracelet-bubbletea
+           go-github-com-charmbracelet-lipgloss
+           go-github-com-dgraph-io-badger-v4
+           go-github-com-dustin-go-humanize
+           go-github-com-gdamore-tcell-v2
+           go-github-com-go-sql-driver-mysql
+           go-github-com-google-go-cmp
+           go-github-com-googlecloudplatform-opentelemetry-operations-go-exporter-metric
+           go-github-com-googlecloudplatform-opentelemetry-operations-go-exporter-trace
+           go-github-com-hashicorp-golang-lru-v2
+           go-github-com-muesli-termenv
+           go-github-com-rivo-tview
+           go-github-com-robinus2-golang-moving-average
+           go-github-com-transparency-dev-formats
+           go-github-com-transparency-dev-merkle
+           go-go-opentelemetry-io-contrib-detectors-aws-ec2-v2
+           go-go-opentelemetry-io-contrib-detectors-aws-ecs
+           go-go-opentelemetry-io-contrib-detectors-gcp
+           go-go-opentelemetry-io-contrib-propagators-aws
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-exporters-otlp-otlpmetric-otlpmetricgrpc
+           go-go-opentelemetry-io-otel-exporters-otlp-otlptrace-otlptracegrpc
+           go-go-opentelemetry-io-otel-metric
+           go-go-opentelemetry-io-otel-sdk
+           go-go-opentelemetry-io-otel-sdk-metric
+           go-golang-org-x-crypto
+           go-golang-org-x-exp
+           go-golang-org-x-mod
+           go-golang-org-x-net
+           go-golang-org-x-sync
+           go-golang-org-x-time
+           go-google-golang-org-api
+           go-google-golang-org-grpc
+           go-k8s-io-klog-v2))
+    (home-page "https://github.com/transparency-dev/tessera")
+    (synopsis "Go library for building tile-based transparency logs (tlogs)")
+    (description
+     "Tessera is a Go library for building tile-based transparency logs (tlogs).
+ It is the logical successor to the approach
+@url{https://github.com/google/trillian, Trillian v1} takes in building and
+operating logs.  The implementation and its APIs bake-in current
+best-practices based on the lessons learned over the past decade of building
+and operating transparency logs in production environments and at scale.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-tv42-httpunix
+
   (let ((commit "2ba4b9c3382c77e7b9ea89d00746e6111d142a22")
         (revision "0"))
     (package
@@ -19686,6 +20254,101 @@ lists)
      "Package sdk provides an auto-instrumentable @code{OpenTelemetry} SDK.")
     (license license:asl2.0)))
 
+(define-public go-go-opentelemetry-io-contrib-detectors-aws-ec2-v2
+  (package
+    (name "go-go-opentelemetry-io-contrib-detectors-aws-ec2-v2")
+    (version "2.5.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/open-telemetry/opentelemetry-go-contrib")
+              (commit (go-version->git-ref version
+                                           #:subdir "detectors/aws/ec2"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nh7g1zxr3drqcbhsnnkqaz2hn1rnawg8jalixng23c9hwfgqaly"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "detectors/aws" "ec2")
+            (delete-all-but "detectors" "aws")
+            (delete-all-but "." "detectors")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "go.opentelemetry.io/contrib/detectors/aws/ec2/v2"
+      #:unpack-path "go.opentelemetry.io/contrib"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (propagated-inputs
+     (list go-github-com-aws-aws-sdk-go-v2
+           go-github-com-aws-aws-sdk-go-v2-config
+           go-github-com-aws-aws-sdk-go-v2-feature-ec2-imds
+           go-github-com-aws-smithy-go
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-sdk))
+    (home-page "https://github.com/open-telemetry/opentelemetry-go-contrib")
+    (synopsis "Resource detector for EC2 instances")
+    (description
+     "Package ec2 provides a resource detector for @acronym{Amazon Elastic
+Compute Cloud, EC2} instances using @code{aws-sdk-go-v2}.")
+    (license license:asl2.0)))
+
+(define-public go-go-opentelemetry-io-contrib-detectors-aws-ecs
+  (package
+    (name "go-go-opentelemetry-io-contrib-detectors-aws-ecs")
+    (version "1.43.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/open-telemetry/opentelemetry-go-contrib")
+              (commit (go-version->git-ref version
+                                           #:subdir "detectors/aws/ecs"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nh7g1zxr3drqcbhsnnkqaz2hn1rnawg8jalixng23c9hwfgqaly"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "detectors/aws" "ecs")
+            (delete-all-but "detectors" "aws")
+            (delete-all-but "." "detectors")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "go.opentelemetry.io/contrib/detectors/aws/ecs"
+      #:unpack-path "go.opentelemetry.io/contrib"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (propagated-inputs
+     (list go-github-com-brunoscheufler-aws-ecs-metadata-go
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-sdk))
+    (home-page "https://go.opentelemetry.io/contrib")
+    (synopsis "OTLP resource detector for AWS ECS instances")
+    (description
+     "Package ecs provides a resource detector for AWS @acronym{Elastic
+Container Service, ECS} instances.")
+    (license license:asl2.0)))
+
 (define-public go-go-opentelemetry-io-contrib-detectors-gcp
   (package
     (name "go-go-opentelemetry-io-contrib-detectors-gcp")
@@ -20289,7 +20952,7 @@ protobuf payloads.")
 (define-public go-go-opentelemetry-io-otel-exporters-otlp-otlptrace-otlptracegrpc
   (package
     (name "go-go-opentelemetry-io-otel-exporters-otlp-otlptrace-otlptracegrpc")
-    (version "1.36.0")
+    (version "1.43.0")
     (source
      (origin
        (method git-fetch)
@@ -20299,15 +20962,12 @@ protobuf payloads.")
                                            #:subdir "exporters/otlp/otlptrace/otlptracegrpc"))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1kvfbqc56p1h9rh9cvgn37ya6k10613r0f2rhjiwrrkgs2mszk30"))
+        (base32 "0583dw99k25k07pnq8hhhb45kwqhsx30lbk9yxsh4m50ji65wl8h"))
        (modules '((guix build utils)
                   (ice-9 ftw)
                   (srfi srfi-26)))
        (snippet
         #~(begin
-            ;; XXX: 'delete-all-but' is copied from the turbovnc package.
-            ;; Consider implementing it as a reusable procedure in
-            ;; guix/build/utils or guix/build-system/go.
             (define (delete-all-but directory . preserve)
               (with-directory-excursion directory
                 (let* ((pred (negate (cut member <>
@@ -20315,23 +20975,27 @@ protobuf payloads.")
                        (items (scandir "." pred)))
                   (for-each (cut delete-file-recursively <>) items))))
             (delete-all-but "exporters/otlp/otlptrace" "otlptracegrpc")
+            (delete-all-but "exporters/otlp" "otlptrace")
             (delete-all-but "." "exporters")))))
     (build-system go-build-system)
     (arguments
      (list
-      ;; TODO: Enable when all missing inputs are available, use as source
-      ;; only package for Boxo.
-      #:skip-build? #t
-      #:tests? #f
       #:import-path
       "go.opentelemetry.io/otel/exporters/otlp/otlptrace/otlptracegrpc"
       #:unpack-path "go.opentelemetry.io/otel"))
     (native-inputs
-     (list go-github-com-stretchr-testify))
+     (list go-github-com-stretchr-testify
+           go-go-uber-org-goleak))
     (propagated-inputs
      (list go-github-com-cenkalti-backoff-v5
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-exporters-otlp-otlptrace
+           go-go-opentelemetry-io-otel-metric
+           go-go-opentelemetry-io-otel-metric-x
+           go-go-opentelemetry-io-otel-sdk
+           go-go-opentelemetry-io-otel-sdk-metric
+           go-go-opentelemetry-io-otel-trace
            go-go-opentelemetry-io-proto-otlp
-           go-go-uber-org-goleak
            go-google-golang-org-genproto-googleapis-rpc
            go-google-golang-org-grpc
            go-google-golang-org-protobuf))
@@ -20646,6 +21310,50 @@ logging library.  Instead, install one of the bridges listed in the
      "Package metric provides an implementation of the metric part of the
 OpenTelemetry API.")))
 
+(define-public go-go-opentelemetry-io-otel-metric-x
+  (package
+    (name "go-go-opentelemetry-io-otel-metric-x")
+    (version "0.0.0-20260424084752-468c62dac625")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/open-telemetry/opentelemetry-go")
+              (commit (go-version->git-ref version #:subdir "metric/x"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16x0aw116dadi73vzh8bcwasy79sblvh6k1q7yfx8n841x48ry8r"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "metric" "x")
+            (delete-all-but "." "metric")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "go.opentelemetry.io/otel/metric/x"
+      #:unpack-path "go.opentelemetry.io/otel"))
+    (propagated-inputs
+     (list go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-metric
+           go-go-opentelemetry-io-otel-trace))
+    (home-page "https://github.com/open-telemetry/opentelemetry-go")
+    (synopsis "Experimental Metric Options")
+    (description
+     "This package contains experimental options for the OpenTelemetry metric
+package.  These options are currently under development and not part of the
+stable API. They may be changed in backwards-incompatible ways, or removed
+entirely.")
+    (license license:asl2.0)))
+
 (define-public go-go-opentelemetry-io-otel-sdk
   (package
     (name "go-go-opentelemetry-io-otel-sdk")
@@ -22770,6 +23478,34 @@ carries no encryption keys and cannot decode the traffic that it proxies.")))
     (propagated-inputs '())
     (inputs '())))
 
+(define-public sarama-tools
+  (package/inherit go-github-com-ibm-sarama
+    (name "sarama-tools")
+    (arguments
+     (substitute-keyword-arguments arguments
+       ((#:install-source? _ #t) #f)
+       ((#:skip-build? _ #t) #f)
+       ((#:tests? _ #t) #f)
+       ((#:import-path _) "github.com/IBM/sarama/tools/...")))
+    (native-inputs (package-propagated-inputs go-github-com-ibm-sarama))
+    (propagated-inputs '())
+    (inputs '())
+    (description
+     "This package contains applications that are useful for exploration of
+Kafka cluster, or instrumentation.  Some of these tools mirror tools that ship
+with Kafka, but these tools won't require installing the JVM to function.
+
+@itemize
+@item @command{kafka-console-producer}: a command line tool to produce a
+single message to your Kafka custer.
+@item @command{kafka-console-partitionconsumer}: a command line
+tool to consume a single partition of a topic on your Kafka cluster.
+@item @command{kafka-console-consumer}: a command line tool to consume
+arbitrary partitions of a topic on your Kafka cluster.
+@item @command{kafka-producer-performance}: a command line tool to performance
+test producers (sync and async) on your Kafka cluster.
+@end itemize")))
+
 (define-public snowflake-proxy
   (package/inherit
       go-gitlab-torproject-org-tpo-anti-censorship-pluggable-transports-snowflake-v2

gnu/packages/golang-xyz.scm

@@ -525,6 +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")
@@ -613,6 +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")
@@ -2981,6 +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")
@@ -4433,6 +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")
@@ -8967,6 +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")
@@ -30438,8 +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))
@@ -30451,7 +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/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.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/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/maths.scm

@@ -2475,6 +2475,9 @@ similar to MATLAB, GNU Octave or SciPy.")
                    ;; "--enable-doxygen"
                    "--enable-dot"
                    "--enable-netcdf-4"
+                   #$@(if (or (target-x86-32?) (target-arm32?))
+                          '("CFLAGS=-Wno-error=incompatible-pointer-types")
+                          '())
                    (string-append "--with-plugin-dir=" #$output "/lib/hdf5-plugins"))
            #:phases
            #~(modify-phases %standard-phases
@@ -2486,7 +2489,15 @@ similar to MATLAB, GNU Octave or SciPy.")
                      (("testurl.sh") ""))
                    (substitute* "nczarr_test/Makefile.in"
                      (("/bin/bash")
-                      (search-input-file inputs "bin/bash")))))
+                      (search-input-file inputs "bin/bash")))
+                   ;; This test fails on 32 bit platforms.
+                   #$@(if (or (target-x86-32?) (target-arm32?))
+                          '((substitute* '("ncdump/tst_netcdf4_4.sh"
+                                           "ncdump/tst_nccopy4.sh")
+                              (("#!/bin/sh" m) (string-append m "\nexit 0\n")))
+                            (substitute* "ncdump/Makefile.in"
+                              (("tst_netcdf4_4.log") "")))
+                          '())))
                (add-before 'configure 'fix-source-date
                  (lambda _
                    ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
@@ -11458,7 +11469,7 @@ expression parsing and evaluation.")
 (define-public highs
   (package
     (name "highs")
-    (version "1.10.0")
+    (version "1.14.0")
     (source
      (origin
        (method git-fetch)
@@ -11467,14 +11478,14 @@ expression parsing and evaluation.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "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

@@ -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/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/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-0.124.0-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/prolog.scm

@@ -237,7 +237,7 @@ it.")
 (define-public trealla
   (package
     (name "trealla")
-    (version "2.93.2")
+    (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 "0rsqka6i51ky74mzf2xlzdzss2xnldyk1wm0f5ilas6ic6pw3hir"))
+        (base32 "050x9m79j1bi17mj7zzbhlnn7ia26k51qrhp5z43wsx0rpp0hfqb"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (inputs

gnu/packages/rust-sources.scm

@@ -1537,6 +1537,168 @@ repository, used as dependencies by codex-acp.")
 and runtime for AI-assisted coding.")
      (license license:asl2.0))))
 
+(define-public rust-codex-0.124.0
+  (hidden-package
+   (package
+     (inherit rust-codex-0.120.0)
+     (version "0.124.0")
+     (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/openai/codex")
+              (commit "e9fb49366c93a1478ec71cc41ecee415a197d036")))
+        (file-name (git-file-name "rust-codex" "0.124.0"))
+        (sha256
+         (base32 "06il60npjnc0h91afyp3wk725cgy3ywk3hx2sbvzdxx6037z6nb0"))
+        (modules '((guix build utils)))
+        (snippet '(begin
+                    ;;; These are JSON manifests with a dotslash
+                    ;;; shebang that download and run pre-built
+                    ;;; binaries (ripgrep, bash) at runtime.
+                    (delete-file "codex-cli/bin/rg")
+                    ;; Bundled bubblewrap source tree; includes a
+                    ;; compiled BPF blob (demos/flatpak.bpf).
+                    (delete-file-recursively "codex-rs/vendor/bubblewrap")))
+        (patches (search-patches
+                  "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"))))
+     (arguments
+      (substitute-keyword-arguments (package-arguments rust-codex-0.120.0)
+        ;; 0.124 differs from 0.120 by a single removal
+        ;; (codex-instructions) and ten additions placed at topo-correct
+        ;; positions; the order also shifts in a few spots to satisfy new
+        ;; deps (e.g. codex-utils-cargo-bin moves before codex-app-server-
+        ;; protocol).  Replace the whole list rather than computing a
+        ;; delta against the inherited one.
+        ((#:cargo-package-crates _)
+         ''(;; Topologically sorted by internal dependency order.
+            "codex-async-utils"
+            "codex-utils-absolute-path"
+            "codex-execpolicy"
+            "codex-utils-home-dir"
+            "codex-utils-rustls-provider"
+            "codex-network-proxy"
+            "codex-utils-cache"
+            "codex-utils-image"
+            "codex-utils-string"
+            "codex-utils-template"
+            "codex-protocol"
+            "codex-agent-identity"
+            "codex-experimental-api-macros"
+            "codex-shell-command"
+            "codex-utils-cargo-bin"
+            "codex-app-server-protocol"
+            "codex-client"
+            "codex-api"
+            "codex-otel"
+            "codex-features"
+            "codex-model-provider-info"
+            "codex-utils-path"
+            "codex-config"
+            "codex-sandboxing"
+            "codex-utils-pty"
+            "codex-exec-server"
+            "codex-git-utils"
+            "codex-keyring-store"
+            "codex-terminal-detection"
+            "codex-login"
+            "codex-utils-plugins"
+            "codex-plugin"
+            "codex-analytics"
+            "codex-ansi-escape"
+            "codex-apply-patch"
+            "codex-code-mode"
+            "codex-connectors"
+            "codex-skills"
+            "codex-utils-output-truncation"
+            "codex-core-skills"
+            "codex-core-plugins"
+            "codex-feedback"
+            "codex-hooks"
+            "codex-rmcp-client"
+            "codex-mcp"
+            "codex-aws-auth"
+            "codex-model-provider"
+            "codex-collaboration-mode-templates"
+            "codex-response-debug-context"
+            "codex-models-manager"
+            "codex-file-search"
+            "codex-state"
+            "codex-rollout"
+            "codex-rollout-trace"
+            "codex-secrets"
+            "codex-shell-escalation"
+            "codex-thread-store"
+            "codex-tools"
+            "codex-utils-readiness"
+            "codex-utils-stream-parser"
+            "codex-windows-sandbox"
+            "codex-core"
+            "codex-linux-sandbox"
+            "codex-arg0"
+            "codex-backend-openapi-models"
+            "codex-backend-client"
+            "codex-utils-cli"
+            "codex-chatgpt"
+            "codex-cloud-requirements"
+            "codex-device-key"
+            "codex-utils-json-to-toml"
+            "codex-app-server"
+            "codex-app-server-client"
+            "codex-app-server-test-client"
+            "codex-cloud-tasks-client"
+            "codex-cloud-tasks-mock-client"
+            "codex-install-context"
+            "codex-realtime-webrtc"
+            "codex-utils-approval-presets"
+            "codex-utils-elapsed"
+            "codex-utils-fuzzy-match"
+            "codex-lmstudio"
+            "codex-ollama"
+            "codex-utils-oss"
+            "codex-utils-sandbox-summary"
+            "codex-utils-sleep-inhibitor"
+            "codex-exec"
+            "codex-mcp-server"
+            "codex-process-hardening"
+            "codex-responses-api-proxy"
+            "codex-uds"
+            "codex-stdio-to-uds"
+            "codex-debug-client"
+            "codex-execpolicy-legacy"
+            "codex-test-binary-support"))
+        ((#:phases orig)
+         ;; Two changes from the inherited phases:
+         ;; (1) 'add-version-to-workspace-deps stamps the literal
+         ;;     0.120.0 version inside its substitute pattern, so we
+         ;;     swap the whole phase for one stamping 0.124.0 (and
+         ;;     using a regex that also matches the codex_windows_
+         ;;     sandbox underscore alias introduced in 0.124).
+         ;; (2) Add a new phase 'break-dev-dep-cycles to strip the
+         ;;     codex-test-binary-support dev-dep from exec-server and
+         ;;     core; it forms a cycle (test-binary-support -> arg0 ->
+         ;;     {exec-server,core} -> test-binary-support) that cargo
+         ;;     package --no-verify still rejects.
+         #~(modify-phases #$orig
+             (replace 'add-version-to-workspace-deps
+               (lambda _
+                 (let ((cargo-files (find-files "." "^Cargo\\.toml$")))
+                   (substitute* cargo-files
+                     (("(codex[_-][a-z0-9_-]+) = \\{ path = " all name)
+                      (string-append name " = { version = \"0.124.0\", path = "))
+                     (("(codex[_-][a-z0-9_-]+) = \\{ package = " all name)
+                      (string-append name " = { version = \"0.124.0\", package = "))
+                     (("^(path = \"\\.\\./[^\"]*\")" all path-line)
+                      (string-append path-line "\nversion = \"0.124.0\""))))))
+             (add-after 'add-version-to-workspace-deps 'break-dev-dep-cycles
+               (lambda _
+                 (substitute* '("exec-server/Cargo.toml" "core/Cargo.toml")
+                   (("^codex-test-binary-support = \\{[^}]*\\}\n") ""))))))))
+     (inputs (cargo-inputs 'rust-codex-0.124.0)))))
+
 ;; Also update (@ (gnu packages gnome) glycin-loaders) when updating this.
 (define-public rust-glycin-3
   (package

gnu/packages/statistics.scm

@@ -384,15 +384,15 @@ comparison and diagnostics.")
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "4.5.3")
+    (version "4.6.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
                                   (version-major version) "/R-"
-                                  version ".tar.gz"))
+                                  version ".tar.xz"))
               (sha256
                (base32
-                "1wmqnm813lb58c0vwhjymnkfih3a6mq4cr9xa6n72wiw57a1wp5a"))))
+                "09sszy5fykpl2lyzxw5rgiabb3f5l62bqamnm7g2q9d57xlv7wli"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/syncthing.scm

@@ -50,7 +50,7 @@
 (define-public syncthing
   (package
     (name "syncthing")
-    (version "2.0.14")
+    (version "2.0.16")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/syncthing/syncthing"
@@ -58,7 +58,7 @@
                                   "/syncthing-source-v" version ".tar.gz"))
               (sha256
                (base32
-                "00isf0j9nf0752wrn79nh4aj5ij5gapv1kvhrg8ydmmw1gi6rhzy"))))
+                "0sgij3i2mhl6m9n2d98cz86f17215kfdc3z913k8yz4n8gwkcf7r"))))
     ;; TODO: Build from git, remove vendor.
     (build-system go-build-system)
     ;; The primary Syncthing executable goes to "out", while the auxiliary
@@ -73,6 +73,7 @@
        #:import-path "github.com/syncthing/syncthing"
        ;; Check 'go.mod' in the source distribution for the required version of Go.
        ;; We don't need to install the source code for end-user applications.
+       #:go go-1.25
        #:install-source? #f
        #:phases
        #~(modify-phases %standard-phases

gnu/packages/syndication.scm

@@ -10,6 +10,7 @@
 ;;; Copyright © 2024 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
 ;;; Copyright © 2025 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2026 Nguyễn Gia Phong <cnx@loang.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,6 +30,7 @@
 (define-module (gnu packages syndication)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix download)
+  #:use-module (guix fossil-download)
   #:use-module (guix git-download)
   #:use-module (guix packages)
   #:use-module (guix utils)
@@ -75,6 +77,33 @@
   #:use-module (gnu packages xorg)
   #:use-module (srfi srfi-1))
 
+(define-public fead
+  (package
+    (name "fead")
+    (version "1.0.1")
+    (source
+     (origin
+       (method fossil-fetch)
+       (uri (fossil-reference
+             (uri "https://chim.loan/fead")
+             (check-in version)))
+       (sha256
+        (base32 "0fzxabmxpyd04v5ym20xhjcnh0vqdwc6z1xjrq676d2k0hr2rzz2"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f                       ;no test
+      #:make-flags #~(list (string-append "PREFIX=" #$output))
+      #:phases #~(modify-phases %standard-phases
+                   (delete 'configure))))
+    (inputs (list python))
+    (native-inputs (list help2man))
+    (home-page "https://chim.loan/fead")
+    (synopsis "Advert generator from web feeds")
+    (description "Fead a tool for advertising other blogs you like on your own
+by embedding the summary of their latest posts extracted from their web feed.")
+    (license license:agpl3+)))
+
 (define-public giara
   (package
     (name "giara")

gnu/packages/text-editors.scm

@@ -875,30 +875,29 @@ compiled, requires few libraries, and starts up quickly.")
 (define-public e3
   (package
     (name "e3")
-    (version "2.82")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://sites.google.com/site/e3editor/Home/"
-                                  "e3-" version ".tgz"))
-              (sha256
-               (base32
-                "0919kadkas020maqq37852isnzp053q2fnws2zh3mz81d1jiviak"))
-              (modules '((guix build utils)))
-
-              ;; Remove pre-built binaries.
-              (snippet '(begin
-                          (delete-file-recursively "bin")
-                          #t))))
+    (version "2.82.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://codeberg.org/museoa/e3editor")
+              (commit version)))
+       (sha256
+        (base32
+         "1l57rxin3kv6iiw91rhjzl3bpk0gkfp3nrx7wmqikk1nycmkfbhm"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f
-       #:make-flags (list (string-append "PREFIX="
-                                         (assoc-ref %outputs "out")))
-       #:phases (modify-phases %standard-phases
-                  (delete 'configure))))
+     (list
+      #:tests? #f
+      #:make-flags
+      #~(list (string-append "PREFIX=" #$output))
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure))))
     (native-inputs
      (list nasm))
-    (home-page "https://sites.google.com/site/e3editor/")
+    (supported-systems '("x86_64-linux" "i686-linux"))
+    (home-page "https://codeberg.org/museoa/e3editor")
     (synopsis "Tiny text editor written in assembly")
     (description
      "e3 is a micro text editor with an executable code size between 3800 and
@@ -907,7 +906,6 @@ of the basic functions one expects plus built in arithmetic calculations.
 UTF-8 coding of unicode characters is supported as well.  e3 can use
 Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings.  e3 can be used on
 16, 32, and 64-bit CPUs.")
-    (supported-systems '("x86_64-linux" "i686-linux"))
     (license license:gpl2+)))
 
 (define-public mg

gnu/packages/version-control.scm

@@ -3522,106 +3522,113 @@ modification time.")
     (license license:bsd-2)))
 
 (define-public libfossil
-  (let ((ci "914ed6dcaff13bf7209c9f27ccfb77c2d8fdf36b8d2133aa1590258b0708f035")
+  (package
+    (name "libfossil")
+    (version "0.6.0")
+    (source
+     (origin
+       (method fossil-fetch)
+       (uri (fossil-reference
+             (uri "https://fossil.wanderinghorse.net/r/libfossil")
+             (check-in version)))
+       (file-name (fossil-file-name name version))
+       (sha256
+        (base32 "0haaczpjnjpkiikf0q70nfabm2csdk6dl9rh80j0sh90wfvkyqwm"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "autosetup" "proj.tcl" "wh-common.tcl")
+            (delete-file-recursively "extsrc")
+            ;; Re-create Fossil check-out manifests,
+            ;; whose content does not affect in semantics.
+            (for-each
+              (lambda (file)
+                (call-with-output-file file (const #t)))
+              '("manifest" "manifest.uuid"))))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:configure-flags
+           #~(list "--no-debug" "--no-fnc" ;TODO: C++ and Tcl binding?
+                   (string-append "--with-sqlite="
+                                  #$(this-package-input "sqlite"))
+                   (string-append "--soname=libfossil.so"))
+           #:phases
+           #~(modify-phases %standard-phases
+               (replace 'configure
+                 (lambda* (#:key configure-flags #:allow-other-keys)
+                   (apply invoke "autosetup"
+                          (string-append "--prefix=" #$output)
+                          configure-flags)))
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (substitute* "sanity-checks.sh"
+                       ;; FIXME: these tests requires a Fossil checkout.
+                       (("\\./f-sanity.*") "")
+                       (("\\./f-parseparty.*") ""))
+                     (setenv "LD_LIBRARY_PATH" (getcwd))
+                     (invoke "./sanity-checks.sh")))))))
+    (native-inputs (list autosetup))
+    (inputs (list sqlite-next zlib))
+    (home-page "https://fossil.wanderinghorse.net/r/libfossil")
+    (synopsis "Unofficial Fossil SCM Library API")
+    (description
+     "@code{libfossil} is an alternative interface into Fossil repositories,
+as opposed to a replacement for the core fossil application,
+intended for new ways to access and manipulate fossil repositories.")
+    (license license:bsd-2)))
+
+(define-public fnc
+  (let ((check-in
+         "c158d7ac2175078b4b783157be92de38aa627dc1a237febab9ec92093420cedb")
         (revision "0"))
     (package
-      (name "libfossil")
-      (version (fossil-version "0.6.0" revision ci))
+      (name "fnc")
+      (version (fossil-version "0.19" revision check-in))
       (source
        (origin
          (method fossil-fetch)
          (uri (fossil-reference
-               (uri "https://fossil.wanderinghorse.net/r/libfossil")
-               (check-in ci)))
+               (uri "https://fnc.sh")
+               (check-in check-in)))
          (file-name (fossil-file-name name version))
          (sha256
-          (base32 "0a0ycnnba2izmiqjj8hgvjgjdwhpn0x36lhy3vmw4j7bhny0df52"))
-         (patches (search-patches "libfossil-skip-amalgamation.patch"))
-         (modules '((guix build utils)
-                    (ice-9 ftw)
-                    (srfi srfi-26)))
-         (snippet
-          #~(begin
-              (define (delete-all-but directory . preserve)
-                (with-directory-excursion directory
-                  (let* ((pred (negate (cut member <>
-                                            (cons* "." ".." preserve))))
-                         (items (scandir "." pred)))
-                    (for-each (cut delete-file-recursively <>) items))))
-              (delete-all-but "autosetup" "proj.tcl" "wh-common.tcl")
-              (delete-file-recursively "extsrc")
-              ;; Re-create Fossil check-out manifests,
-              ;; whose content does not affect in semantics.
-              (for-each
-                (lambda (file)
-                  (call-with-output-file file (const #t)))
-                '("manifest" "manifest.uuid"))))))
+          (base32 "09m0bgzy0yjglsgrqq03sdq4p2rwi3y8m84979j066z1c5b444iz"))
+         (modules '((guix build utils)))
+         (snippet #~(begin
+                      (delete-file-recursively "lib")
+                      (substitute* (find-files "." "\\.c$")
+                        (("^#include \"libfossil.h\"")
+                         "#include <fossil-scm/libfossil.h>"))
+                      (substitute* "fnc.bld.mk"
+                        ((" \\$\\{SQLITE_OBJS\\} \\$\\{FOSSIL_OBJS\\}") "")
+                        (("-lm -lutil -lz ") "")
+                        ;; Fix cross-compiling.
+                        (("install -s") "install"))))))
       (build-system gnu-build-system)
       (arguments
-       (list #:configure-flags
-             #~(list "--no-debug" "--no-fnc" ;TODO: C++ and Tcl binding?
-                     (string-append "--with-sqlite="
-                                    #$(this-package-input "sqlite"))
-                     (string-append "--soname=libfossil.so"))
-             #:phases
-             #~(modify-phases %standard-phases
-                 (replace 'configure
-                   (lambda* (#:key configure-flags #:allow-other-keys)
-                     (apply invoke "autosetup"
-                            (string-append "--prefix=" #$output)
-                            configure-flags)))
-                 (replace 'check
-                   (lambda* (#:key tests? #:allow-other-keys)
-                     (when tests?
-                       (substitute* "sanity-checks.sh"
-                         ;; FIXME: these tests requires a Fossil checkout.
-                         (("\\./f-sanity.*") "")
-                         (("\\./f-parseparty.*") ""))
-                       (setenv "LD_LIBRARY_PATH" (getcwd))
-                       (invoke "./sanity-checks.sh")))))))
-      (native-inputs (list autosetup))
-      (inputs (list sqlite-next zlib))
-      (home-page "https://fossil.wanderinghorse.net/r/libfossil")
-      (synopsis "Unofficial Fossil SCM Library API")
-      (description
-       "@code{libfossil} is an alternative interface into Fossil repositories,
-as opposed to a replacement for the core fossil application,
-intended for new ways to access and manipulate fossil repositories.")
-      (license license:bsd-2))))
-
-(define-public fnc
-  (package
-    (name "fnc")
-    (version "0.18")
-    (source (origin
-              (method url-fetch)
-              (uri
-               (string-append "https://fnc.bsdbox.org/uv/dl/fnc-"
-                              version ".tar.gz"))
-              (sha256
-               (base32
-                "1067rr4nqngld1nqa8c7imp9n3w5fp7rpc7khh6l84q2w1klrya9"))))
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:phases #~(modify-phases %standard-phases
-                   (delete 'configure)
-                   ;; fix cross-compiling.
-                   (add-after 'unpack 'don-t-use-install-s
-                     (lambda _
-                       (substitute* "fnc.bld.mk"
-                         (("install -s")
-                          "install")))))
-      #:tests? #f                       ; no tests
-      #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
-                           (string-append "PREFIX=" #$output))))
-    (inputs (list ncurses zlib sqlite-next))
-    (home-page "https://fnc.bsdbox.org")
-    (synopsis "Interactive text-based user interface for Fossil")
-    (description "fnc uses ncurses and libfossil to create a fossil user
+       (list
+        #:phases #~(modify-phases %standard-phases
+                     (delete 'configure))
+        #:tests? #f                     ;no tests
+        #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
+                             "LDFLAGS=-lfossil -lsqlite3"
+                             (string-append "PREFIX=" #$output))))
+      (inputs (list libfossil ncurses sqlite-next))
+      (home-page "https://fnc.sh")
+      (synopsis "Interactive text-based user interface for Fossil")
+      (description "fnc uses ncurses and libfossil to create a fossil user
 interface in the terminal.  It can view local changes at the hunk level to
 prepare atomic commits.")
-    (license license:isc)))
+      (license license:isc))))
 
 (define-public myrepos
   (package

gnu/packages/vim.scm

@@ -232,39 +232,39 @@ with the editor vim.")))
     (inherit vim)
     (name "vim-full")
     (arguments
-     (cons*
-       #:configure-flags
-       #~(list (string-append "--with-lua-prefix="
-                              #$(this-package-input "lua"))
-               "--with-features=huge"
-               "--enable-python3interp=yes"
-               "--enable-perlinterp=yes"
-               "--enable-rubyinterp=yes"
-               "--enable-tclinterp=yes"
-               "--enable-luainterp=yes"
-               "--enable-cscope"
-               "--enable-sniff"
-               "--enable-multibyte"
-               "--enable-xim"
-               "--disable-selinux"
-               "--enable-gui")
-       (substitute-keyword-arguments arguments
-         ((#:phases phases)
-          #~(modify-phases #$phases
-              (add-before 'check 'skip-some-more-tests
-                (lambda _
-                  ;; Fontconfig can't figure out its cache directory.
-                  (substitute* "src/testdir/test_startup.vim"
-                    ((".*Test_progname.*" line)
-                     (string-append line "return\n")))))
-              ;; Some tests require an X server, but do not start one.
-              (add-before 'check 'start-xserver
-                (lambda _
-                  (setenv "DISPLAY" ":1")
-                  (zero? (system #$(file-append
-                                     (this-package-native-input
-                                       "xorg-server")
-                                     "/bin/Xvfb :1 &"))))))))))
+     (substitute-keyword-arguments arguments
+       ((#:configure-flags flags #~'())
+        #~(cons* (string-append "--with-lua-prefix="
+                                #$(this-package-input "lua"))
+                 "--with-features=huge"
+                 "--enable-python3interp=yes"
+                 "--enable-perlinterp=yes"
+                 "--enable-rubyinterp=yes"
+                 "--enable-tclinterp=yes"
+                 "--enable-luainterp=yes"
+                 "--enable-cscope"
+                 "--enable-sniff"
+                 "--enable-multibyte"
+                 "--enable-xim"
+                 "--disable-selinux"
+                 "--enable-gui"
+                 #$flags))
+       ((#:phases phases)
+        #~(modify-phases #$phases
+            (add-before 'check 'skip-some-more-tests
+              (lambda _
+                ;; Fontconfig can't figure out its cache directory.
+                (substitute* "src/testdir/test_startup.vim"
+                  ((".*Test_progname.*" line)
+                   (string-append line "return\n")))))
+            ;; Some tests require an X server, but do not start one.
+            (add-before 'check 'start-xserver
+              (lambda _
+                (setenv "DISPLAY" ":1")
+                (zero? (system #$(file-append
+                                   (this-package-native-input
+                                     "xorg-server")
+                                   "/bin/Xvfb :1 &")))))))))
     (native-inputs
      (modify-inputs native-inputs
        (prepend pkg-config xorg-server-for-tests)))

gnu/packages/wm.scm

@@ -3749,6 +3749,31 @@ productive, customizable lisp based systems.")
 control module for StumpWM.")
       (license license:gpl3))))
 
+(define-public sbcl-stumpwm-acpi-backlight
+  (package
+    (name "sbcl-stumpwm-acpi-backlight")
+    (version "0.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/Junker/stumpwm-acpi-backlight")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1dih6fzy77f3r60fwhsk0dw3qksadzj991k1i28z0da64fpshm0a"))))
+    (arguments
+     (list
+      #:asd-systems ''("acpi-backlight")
+      #:tests? #f)) ; There are no tests.
+    (build-system asdf-build-system/sbcl)
+    (inputs (list stumpwm))
+    (home-page "https://github.com/Junker/stumpwm-acpi-backlight")
+    (synopsis "ACPI backlight control module for StumpWM")
+    (description
+     "ACPI backlight control module for StumpWM.")
+    (license license:gpl3)))
+
 (define-public sbcl-stumpwm-binwarp
   (package
     (inherit stumpwm-contrib)
@@ -3766,6 +3791,40 @@ control module for StumpWM.")
 mouse control mode for StumpWM.")
     (license (list license:gpl2+ license:gpl3+ license:bsd-2))))
 
+(define-public sbcl-stumpwm-bluetooth
+  (package
+    (name "sbcl-stumpwm-bluetooth")
+    (version "0.1.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/Junker/stumpwm-bluetooth")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "08a028r83kd66a3smiyzi9hadk3w89qdhha7hsd9ffh3gdk5s99a"))))
+    (arguments
+     (list
+      #:asd-systems ''("bluetooth")
+      #:tests? #f ; There are no tests.
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-bin-path
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* "bluetooth.lisp"
+                (("/usr/bin/bluetoothctl")
+                 (search-input-file inputs "bin/bluetoothctl"))))))))
+    (build-system asdf-build-system/sbcl)
+    (inputs (list stumpwm
+                  bluez
+                  sbcl-bordeaux-threads))
+    (home-page "https://github.com/Junker/stumpwm-bluetooth")
+    (synopsis "StumpWM module for controlling Bluetooth devices")
+    (description
+     "StumpWM module for controlling Bluetooth devices via bluetoothctl.")
+    (license license:gpl3)))
+
 (define-public sbcl-stumpwm-stump-nm
   (package
     (inherit stumpwm-contrib)
@@ -3792,7 +3851,7 @@ not a replacement for nmtui and/or nmcli.")
 (define-public sbcl-stumpwm-tomato
   (package
     (name "sbcl-stumpwm-tomato")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
      (origin
        (method git-fetch)
@@ -3801,7 +3860,7 @@ not a replacement for nmtui and/or nmcli.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0qq11spvhrcq74gh0dw0p4859ai2mqzbxa45gjbf599kmcybp1pa"))))
+        (base32 "0r00f8qi5kzf1sxx19fxr2lvc32bw3xlz75qrnxl5vgwsl8qafr5"))))
     (build-system asdf-build-system/sbcl)
     (inputs (list stumpwm))
     (arguments
@@ -4079,6 +4138,41 @@ layouts in StumpWM.")
 one in Emacs.")
     (license license:gpl3+)))
 
+(define-public sbcl-stumpwm-wpctl
+  (package
+    (name "sbcl-stumpwm-wpctl")
+    (version "0.2.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/Junker/stumpwm-wpctl")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1c3i5z1cmhd96xnlsb40ykgk60cyignl1m4f61i9k9vq05n83pdj"))))
+    (arguments
+     (list #:asd-systems ''("wpctl")
+           #:tests? #f ; There are no tests.
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'fix-wpctl-path
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   (substitute* "wpctl.lisp"
+                     (("/usr/bin/wpctl")
+                      (search-input-file inputs "bin/wpctl"))))))))
+    (build-system asdf-build-system/sbcl)
+    (inputs
+     (list stumpwm
+           wireplumber-minimal
+           sbcl-parse-float
+           sbcl-bordeaux-threads))
+    (home-page "https://github.com/Junker/stumpwm-wpctl")
+    (synopsis "StumpWM PipeWire module")
+    (description
+     "PipeWire (WirePlumber) volume and microphone control module for StumpWM.")
+    (license license:gpl3)))
+
 (define-public sbcl-stumpwm-screenshot
   (package
     (inherit stumpwm-contrib)