.github: Bump actions/checkout from 6.0.3 to 7.0.1

Bumps [actions/checkout](https://github.com/actions/checkout) from 6.0.3 to 7.0.1. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](df4cb1c069...3d3c42e5aa) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
xfsprogs: 7.0.1 -> 7.1.1 (#523070 )
2026-07-25 10:00:28 +00:00 · 2026-07-24 11:22:46 +00:00 · 2026-07-24 11:12:32 +00:00 · 2026-07-24 10:49:13 +00:00 · 2026-07-24 10:48:52 +00:00 · 2026-07-24 10:09:58 +00:00
84 changed files with 7342 additions and 10685 deletions
--- a/.github/workflows/backport.yml
+++ b/.github/workflows/backport.yml
@@ -36,7 +36,7 @@ jobs:
          permission-pull-requests: write
          permission-workflows: write

-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          ref: ${{ github.event.pull_request.head.sha }}
          token: ${{ steps.app-token.outputs.token }}
--- a/.github/workflows/bot.yml
+++ b/.github/workflows/bot.yml
@@ -42,7 +42,7 @@ jobs:
    runs-on: ubuntu-slim
    if: github.event_name != 'schedule' || github.repository_owner == 'NixOS'
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: |
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -49,7 +49,7 @@ jobs:
    runs-on: ${{ matrix.runner }}
    timeout-minutes: 60
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: .github/actions
--- a/.github/workflows/check.yml
+++ b/.github/workflows/check.yml
@@ -43,7 +43,7 @@ jobs:
    runs-on: ubuntu-slim
    timeout-minutes: 3
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          path: trusted
@@ -96,7 +96,7 @@ jobs:
    runs-on: ubuntu-24.04-arm
    timeout-minutes: 8
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          path: trusted
@@ -138,7 +138,7 @@ jobs:
    runs-on: ubuntu-24.04-arm
    timeout-minutes: 5
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: .github/actions
--- a/.github/workflows/comment.yml
+++ b/.github/workflows/comment.yml
@@ -23,7 +23,7 @@ jobs:
    timeout-minutes: 2
    if: contains(github.event.comment.body, '@NixOS/nixpkgs-merge-bot merge')
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: |
--- a/.github/workflows/eval.yml
+++ b/.github/workflows/eval.yml
@@ -50,7 +50,7 @@ jobs:
      ciPinBumpCommit: ${{ steps.find-pinned-commit.outputs.ciPinBumpCommit }}
      ciPinBumpCommitShort: ${{ steps.find-pinned-commit.outputs.ciPinBumpCommitShort }}
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          path: trusted
@@ -58,7 +58,7 @@ jobs:
            ci/supportedVersions.nix

      - name: Check out the PR at the test merge commit
-        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          ref: ${{ inputs.mergedSha }}
@@ -174,7 +174,7 @@ jobs:
          sudo mkswap /swap
          sudo swapon /swap

-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: .github/actions
@@ -259,7 +259,7 @@ jobs:
      statuses: write # creating 'Eval Summary' commit statuses
    timeout-minutes: 5
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: .github/actions
@@ -476,7 +476,7 @@ jobs:
    runs-on: ubuntu-24.04-arm
    timeout-minutes: 10
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: .github/actions
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -26,7 +26,7 @@ jobs:
    runs-on: ubuntu-24.04-arm
    timeout-minutes: 10
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: .github/actions
@@ -61,7 +61,7 @@ jobs:
    runs-on: ubuntu-24.04-arm
    timeout-minutes: 10
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: .github/actions
@@ -90,7 +90,7 @@ jobs:
    runs-on: ubuntu-24.04-arm
    timeout-minutes: 10
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: .github/actions
@@ -134,7 +134,7 @@ jobs:
    runs-on: ubuntu-24.04-arm
    timeout-minutes: 8
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: true # Needed to run git fetch for large PRs.
          path: trusted
--- a/.github/workflows/merge-group.yml
+++ b/.github/workflows/merge-group.yml
@@ -25,7 +25,7 @@ jobs:
      targetSha: ${{ steps.prepare.outputs.targetSha }}
      systems: ${{ steps.prepare.outputs.systems }}
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: |
--- a/.github/workflows/periodic-merge.yml
+++ b/.github/workflows/periodic-merge.yml
@@ -34,7 +34,7 @@ jobs:
          permission-contents: write
          permission-pull-requests: write

-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false

--- a/.github/workflows/pull-request-target.yml
+++ b/.github/workflows/pull-request-target.yml
@@ -36,7 +36,7 @@ jobs:
      systems: ${{ steps.prepare.outputs.systems }}
      touched: ${{ steps.prepare.outputs.touched }}
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout-cone-mode: true # default, for clarity
--- a/.github/workflows/review.yml
+++ b/.github/workflows/review.yml
@@ -20,7 +20,7 @@ jobs:
    runs-on: ubuntu-slim
    timeout-minutes: 2
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: |
--- a/.github/workflows/teams.yml
+++ b/.github/workflows/teams.yml
@@ -30,7 +30,7 @@ jobs:
          permission-pull-requests: write

      - name: Fetch source
-        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout: |
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -19,7 +19,7 @@ jobs:
      push: ${{ steps.files.outputs.push }}
      targetSha: ${{ steps.prepare.outputs.targetSha }}
    steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
        with:
          persist-credentials: false
          sparse-checkout-cone-mode: true # default, for clarity
--- a/.gitignore
+++ b/.gitignore
@@ -27,6 +27,9 @@ tags
 .mypy_cache
 __pycache__

+/AGENTS.md
+/CLAUDE.md
+
 /pkgs/development/libraries/qt-5/*/tmp/
 /pkgs/desktops/kde-5/*/tmp/
 /pkgs/development/mobile/androidenv/xml/*
--- a/ci/OWNERS
+++ b/ci/OWNERS
@@ -211,7 +211,7 @@ nixos/modules/installer/tools/nix-fallback-paths.nix  @Artturin @Ericson2314 @lo
 /pkgs/development/perl-modules      @stigtsp @marcusramberg

 # R
-/pkgs/by-name/r/R   @jbedo
+/pkgs/applications/science/math/R   @jbedo
 /pkgs/development/r-modules         @jbedo

 # Rust
--- a/nixos/modules/config/xdg/portal.nix
+++ b/nixos/modules/config/xdg/portal.nix
@@ -116,6 +116,8 @@ in
      packages = [ pkgs.xdg-desktop-portal ] ++ cfg.extraPortals;
    in
    mkIf cfg.enable {
+      programs.fuse.enable = true;
+
      warnings = lib.optional (cfg.configPackages == [ ] && cfg.config == { }) ''
        xdg-desktop-portal 1.17 reworked how portal implementations are loaded, you
        should either set `xdg.portal.config` or `xdg.portal.configPackages`
--- a/pkgs/applications/emulators/libretro/cores/opera.nix
+++ b/pkgs/applications/emulators/libretro/cores/opera.nix
@@ -6,13 +6,13 @@
 }:
 mkLibretroCore {
  core = "opera";
-  version = "0-unstable-2026-07-13";
+  version = "0-unstable-2026-07-23";

  src = fetchFromGitHub {
    owner = "libretro";
    repo = "opera-libretro";
-    rev = "1edda8a2a6c6b9ae259d5c7cd7d54dcba9ee7e32";
-    hash = "sha256-dc7xRjFxfSL2q9u1N0QH2j+oPbRGng2Z3U3J484lXiU=";
+    rev = "74dd2a8c6319678ffce9f31bdf36279db5681762";
+    hash = "sha256-NHXOfKItLkQJ0/jH1gLBpLFqOKBB8qgH5gMw7j1YoLw=";
  };

  makefile = "Makefile";
--- a/pkgs/applications/emulators/libretro/cores/prboom.nix
+++ b/pkgs/applications/emulators/libretro/cores/prboom.nix
@@ -5,13 +5,13 @@
 }:
 mkLibretroCore {
  core = "prboom";
-  version = "0-unstable-2026-07-07";
+  version = "0-unstable-2026-07-21";

  src = fetchFromGitHub {
    owner = "libretro";
    repo = "libretro-prboom";
-    rev = "31563d6e65faa6b9b7e975754d2062370bba4342";
-    hash = "sha256-eFRzbVTL5ARf650D0ZAEFGNTxjAy1CjBiAhwSQR8vJ4=";
+    rev = "c5b09532fa633e015ac75c0a2acfec049f65ded3";
+    hash = "sha256-13oL/U3uwNejqTIbKmITRbK8Eddg9YH5CMDIDXA6zKs=";
  };

  makefile = "Makefile";
--- a/pkgs/applications/emulators/libretro/cores/snes9x2005.nix
+++ b/pkgs/applications/emulators/libretro/cores/snes9x2005.nix
@@ -6,13 +6,13 @@
 }:
 mkLibretroCore {
  core = "snes9x2005" + lib.optionalString withBlarggAPU "-plus";
-  version = "0-unstable-2026-04-20";
+  version = "0-unstable-2026-07-22";

  src = fetchFromGitHub {
    owner = "libretro";
    repo = "snes9x2005";
-    rev = "b60356971fc9caae02cd0853676dced886a08be7";
-    hash = "sha256-6IuEFyJEoCHluSAXbk5qRTXku1XJCZ6p04BhdjqZqJQ=";
+    rev = "deb49d80d1836e3e737480a326e31a54c46c04ae";
+    hash = "sha256-UMW+YTzcSZ5CWSyRBYc8y1cDh/CU3Am11rkjSXlyxZA=";
  };

  makefile = "Makefile";
--- a/pkgs/applications/networking/mailreaders/thunderbird/packages.nix
+++ b/pkgs/applications/networking/mailreaders/thunderbird/packages.nix
@@ -92,8 +92,8 @@ rec {
  thunderbird-140 = common {
    applicationName = "Thunderbird ESR";

-    version = "140.12.1esr";
-    sha512 = "24e795483ba7bc112c0debe1becdaf79cc2de95703b9ee726d0216bfc1db7b33c169503f83ac867e5998a8d1d0284a6ef12c7d35d98b10d6432497c2db237477";
+    version = "140.13.0esr";
+    sha512 = "778d2fc2837ba367e90c4336f3873da5a0823c182e2f50aa9373cd1ee9ee2b5310372ad9d33e1e11978791b67de4a6952d3036ff7d57b257a06f49c8cd4a830e";

    updateScript = callPackage ./update.nix {
      attrPath = "thunderbirdPackages.thunderbird-140";
--- a/pkgs/applications/science/math/R/default.nix
+++ b/pkgs/applications/science/math/R/default.nix
@@ -32,7 +32,7 @@
  lapack,
  curl,
  tzdata,
-  withRecommendedPackages ? false,
+  withRecommendedPackages ? true,
  enableStrictBarrier ? false,
  enableMemoryProfiling ? false,
  # R as of writing does not support outputting both .so and .a files; it outputs:
@@ -45,7 +45,7 @@ assert (!blas.isILP64) && (!lapack.isILP64);

 stdenv.mkDerivation (finalAttrs: {
  pname = "R";
-  version = "4.6.1";
+  version = "4.6.0";

  src =
    let
@@ -53,7 +53,7 @@ stdenv.mkDerivation (finalAttrs: {
    in
    fetchurl {
      url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
-      hash = "sha256-TabmHSwKrF8UoufkMstfzCae/oPaQpMFC6fwPf9OLPQ=";
+      hash = "sha256-uNybRUNmDHtZa4eTjfUyOUNQNgl2Un00QijuDtEuRew=";
    };

  outputs = [
--- a/pkgs/applications/science/math/R/no-usr-local-search-paths.patch
+++ b/pkgs/applications/science/math/R/no-usr-local-search-paths.patch
--- a/pkgs/applications/science/math/R/setup-hook.sh
+++ b/pkgs/applications/science/math/R/setup-hook.sh
--- a/pkgs/by-name/co/copilot-language-server/package.nix
+++ b/pkgs/by-name/co/copilot-language-server/package.nix
@@ -10,11 +10,11 @@
 }:
 stdenvNoCC.mkDerivation (finalAttrs: {
  pname = "copilot-language-server";
-  version = "1.521.0";
+  version = "1.526.0";

  src = fetchzip {
    url = "https://github.com/github/copilot-language-server-release/releases/download/${finalAttrs.version}/copilot-language-server-js-${finalAttrs.version}.zip";
-    hash = "sha256-uHt22/756jxh34HhIbMEu3nGebbTF1325ylWuKzZzEI=";
+    hash = "sha256-T1DYN/mVqISYtNGD1KBitXPgEIcrKQMqxquC7CywDo4=";
    stripRoot = false;
  };

--- a/pkgs/by-name/cr/crush/package.nix
+++ b/pkgs/by-name/cr/crush/package.nix
@@ -11,16 +11,16 @@

 buildGo126Module (finalAttrs: {
  pname = "crush";
-  version = "0.81.0";
+  version = "0.86.0";

  src = fetchFromGitHub {
    owner = "charmbracelet";
    repo = "crush";
    tag = "v${finalAttrs.version}";
-    hash = "sha256-FOvkCQxDW1dipzIzgQz2uvHIv6bm/TVV1WwhrvmBDWg=";
+    hash = "sha256-dUeXU65A9/d365a9Z+eUoHOR0RnJV9SAYsks+Vtz9js=";
  };

-  vendorHash = "sha256-4gHvyEqiFhEvZ90lJbXeI/1fMMo6L19P/PD5Eu5YUmI=";
+  vendorHash = "sha256-9WkkosPMwXsj32a5Zj4ZxphuB7aVteKq/YTzxP9Xmf0=";

  ldflags = [
    "-s"
--- a/pkgs/by-name/da/datafusion-cli/package.nix
+++ b/pkgs/by-name/da/datafusion-cli/package.nix
@@ -8,17 +8,17 @@

 rustPlatform.buildRustPackage (finalAttrs: {
  pname = "datafusion-cli";
-  version = "54.0.0";
+  version = "54.1.0";

  src = fetchFromGitHub {
    name = "datafusion-cli-source";
    owner = "apache";
    repo = "datafusion";
    tag = finalAttrs.version;
-    hash = "sha256-BWpHiLCn7idvzI2rlsre8l23TbxQU1Ma6bCjAMxQ6m8=";
+    hash = "sha256-zeR6eyU4Cc5gHiE331ap8wuyYEj7s7BgqB+oOKwMfZw=";
  };

-  cargoHash = "sha256-Sj/biBiJPIYwxpL+Fua0k47vOu6gyyAhcKb4ZSUli6k=";
+  cargoHash = "sha256-XXR1Turs+QwONZHq38MZHbcjv5DYZH9iqeuBl20gy3U=";

  buildAndTestSubdir = "datafusion-cli";

--- a/pkgs/by-name/fi/filebeat8/package.nix
+++ b/pkgs/by-name/fi/filebeat8/package.nix
@@ -8,18 +8,18 @@

 buildGoModule (finalAttrs: {
  pname = "filebeat";
-  version = "8.19.17";
+  version = "8.19.19";

  src = fetchFromGitHub {
    owner = "elastic";
    repo = "beats";
    tag = "v${finalAttrs.version}";
-    hash = "sha256-Xpth1SoXMXCUh/DFf3wA+Ql6SedtUB7tCYzDElpX5Lc=";
+    hash = "sha256-3hvP+4U3PWlOsaLHO1MZuIpcB6YzPv2dMPlC68esiHE=";
  };

  proxyVendor = true; # darwin/linux hash mismatch

-  vendorHash = "sha256-Wxk+eI0XfBpQqqUNuskyr+/bTRqT38hszdkz/LJweQo=";
+  vendorHash = "sha256-e++Y5mhwms/uJnZCUyZNifoYqGH4TGEugSFHSGl0AQE=";

  subPackages = [ "filebeat" ];

--- a/pkgs/by-name/fl/flightgear/openscenegraph-flightgear.nix
+++ b/pkgs/by-name/fl/flightgear/openscenegraph-flightgear.nix
@@ -9,7 +9,6 @@
  fetchurl,
  glib,
  libxml2,
-  pcre,
  zlib,
  libjpeg,
  giflib,
@@ -53,7 +52,6 @@ stdenv.mkDerivation {
    ++ [
      glib
      libxml2
-      pcre
      zlib
      libjpeg
      giflib
--- a/pkgs/by-name/gi/gitoxide/package.nix
+++ b/pkgs/by-name/gi/gitoxide/package.nix
@@ -18,16 +18,16 @@ let
 in
 rustPlatform.buildRustPackage (finalAttrs: {
  pname = "gitoxide";
-  version = "0.55.0";
+  version = "0.56.0";

  src = fetchFromGitHub {
    owner = "GitoxideLabs";
    repo = "gitoxide";
    tag = "v${finalAttrs.version}";
-    hash = "sha256-UtdXlIvX82UUhc4RWZZTBV5kz4YqfOTd4D/pGhDUfSI=";
+    hash = "sha256-2zNXe+niwH8oDZEx6It7APggOtL7vrnRGKO4OoteTIw=";
  };

-  cargoHash = "sha256-Kv0NKA3OdHBn2M8DmcGyjcN2acGJYOdbczOb/nRsvDs=";
+  cargoHash = "sha256-u9O4y6W0TuwdedNaQ127Bz4d3Olw9RzV/+AzxAstJQE=";

  nativeBuildInputs = [
    cmake
--- a/pkgs/by-name/gt/gtkwave/package.nix
+++ b/pkgs/by-name/gt/gtkwave/package.nix
@@ -18,11 +18,11 @@

 stdenv.mkDerivation (finalAttrs: {
  pname = "gtkwave";
-  version = "3.3.127";
+  version = "3.3.128";

  src = fetchurl {
    url = "mirror://sourceforge/gtkwave/gtkwave-gtk3-${finalAttrs.version}.tar.gz";
-    sha256 = "sha256-8Z2i20Oye7zGaXJYQ0UZRaaMOkziMlYuNB1vY7gLVeQ=";
+    sha256 = "sha256-gX4Zf8GAj4qsNUPCwvloPLATaMkRkrjq5a9YBw7x0fg=";
  };

  nativeBuildInputs = [
--- a/pkgs/by-name/hm/hmcl/0001-nix-use-terracotta-from-nix.patch
+++ b/pkgs/by-name/hm/hmcl/0001-nix-use-terracotta-from-nix.patch
@@ -4,14 +4,14 @@ Date: Wed, 4 Feb 2026 15:36:17 +0800
 Subject: [PATCH 1/2] nix: use terracotta from nix

 ---
- .../hmcl/terracotta/TerracottaBundle.java     | 21 +++----------------
- 1 file changed, 3 insertions(+), 18 deletions(-)
+ .../hmcl/terracotta/TerracottaBundle.java     | 19 ++-----------------
+ 1 file changed, 2 insertions(+), 17 deletions(-)

 diff --git a/HMCL/src/main/java/org/jackhuang/hmcl/terracotta/TerracottaBundle.java b/HMCL/src/main/java/org/jackhuang/hmcl/terracotta/TerracottaBundle.java
-index 727edde9b..5b6e8b02f 100644
+index ecc99f3..b46ada0 100644
 --- a/HMCL/src/main/java/org/jackhuang/hmcl/terracotta/TerracottaBundle.java
 +++ b/HMCL/src/main/java/org/jackhuang/hmcl/terracotta/TerracottaBundle.java
-@@ -139,26 +139,11 @@ public final class TerracottaBundle {
+@@ -147,26 +147,11 @@ public final class TerracottaBundle {
     }
 
     public Path locate(String file) {
@@ -33,20 +33,13 @@ index 727edde9b..5b6e8b02f 100644
 -                return AbstractTerracottaProvider.Status.LEGACY_VERSION;
 -            }
 -        } catch (IOException e) {
-            Logger.LOG.warning("Cannot determine whether legacy versions exist.", e);
+-            LOG.warning("Cannot determine whether legacy versions exist.", e);
 -        }
 -        return AbstractTerracottaProvider.Status.NOT_EXIST;
 +        return AbstractTerracottaProvider.Status.READY;
     }
 
     private boolean isLocalBundleValid() throws IOException { // FIXME: Make control flow clearer.
-@@ -188,4 +173,4 @@ public final class TerracottaBundle {
-         }
-         return true;
-     }
-}
-+}
-\ No newline at end of file
 -- 
 2.52.0

--- a/pkgs/by-name/hm/hmcl/package.nix
+++ b/pkgs/by-name/hm/hmcl/package.nix
@@ -50,13 +50,13 @@ let
 in
 stdenv.mkDerivation (finalAttrs: {
  pname = "hmcl";
-  version = "3.15.3";
+  version = "3.16.2";

  src = fetchurl {
    # HMCL has built-in keys, such as the Microsoft OAuth secret and the CurseForge API key.
    # See https://github.com/HMCL-dev/HMCL/blob/refs/tags/release-3.6.12/.github/workflows/gradle.yml#L26-L28
    url = "https://github.com/HMCL-dev/HMCL/releases/download/v${finalAttrs.version}/HMCL-${finalAttrs.version}.jar";
-    hash = "sha256-/7RLhSHCnxtKxmusjnrfUEweYXzOoKcQO3G9+loBofk=";
+    hash = "sha256-kvQDDZwA2sy8UQLZG4FqGmSh0sDcEuSg5CM6uy0DzCc=";
  };

  # - HMCL prompts users to download prebuilt Terracotta binary for
@@ -71,12 +71,12 @@ stdenv.mkDerivation (finalAttrs: {
  terracottaBundleJava = fetchurl {
    name = "hmcl-terracotta-bundle-java-${finalAttrs.version}";
    url = "https://raw.githubusercontent.com/HMCL-dev/HMCL/v${finalAttrs.version}/${finalAttrs.terracottaBundleJavaPath}";
-    hash = "sha256-1o/CUDeywtDlhAxqInk77aUwGCCYeZ84VMIyouN49uU=";
+    hash = "sha256-dZHRim/7VNW0/nA6I8r3t5zGfzIMxG2lzdZ//dzv2Gs=";
  };
  macOSProviderJava = fetchurl {
    name = "hmcl-macos-provider-java-${finalAttrs.version}";
    url = "https://raw.githubusercontent.com/HMCL-dev/HMCL/v${finalAttrs.version}/${finalAttrs.macOSProviderJavaPath}";
-    hash = "sha256-+Zji2B8ksT7P+IObyrM9q7vHPJVl5ZtH+v/J8Mfr0Q4=";
+    hash = "sha256-7vI2U8vx3GYwlshoHJF/J8n2RS6TZ/cvoAivqYtW23Q=";
  };
  terracottaBundleJavaPath = "HMCL/src/main/java/org/jackhuang/hmcl/terracotta/TerracottaBundle.java";
  macOSProviderJavaPath = "HMCL/src/main/java/org/jackhuang/hmcl/terracotta/provider/MacOSProvider.java";
--- a/pkgs/by-name/ja/jasp-desktop/disable-module-install-logic.patch
+++ b/pkgs/by-name/ja/jasp-desktop/disable-module-install-logic.patch
@@ -1,5 +1,5 @@
 diff --git a/Tools/CMake/Install.cmake b/Tools/CMake/Install.cmake
-index a3ed1f3..a564046 100644
+index edd96b0..1fbdb3c 100644
 --- a/Tools/CMake/Install.cmake
 +++ b/Tools/CMake/Install.cmake
@@ -229,24 +229,10 @@ if(LINUX)
@@ -20,10 +20,10 @@ index a3ed1f3..a564046 100644
 -  #install(DIRECTORY ${MODULES_RENV_ROOT_PATH}/
 -  #        DESTINATION ${JASP_INSTALL_PREFIX}/lib64/renv-root)
 -
-  if(NOT FLATPAK_USED) #because flatpak already puts renv-cache in /app/lib64 anyway
-    install(DIRECTORY ${MODULES_RENV_CACHE_PATH}/
+-if(NOT FLATPAK_USED) #because flatpak already puts renv-cache in /app/lib64 anyway
+-  install(DIRECTORY ${MODULES_RENV_CACHE_PATH}/
 -          DESTINATION ${JASP_INSTALL_PREFIX}/lib64/renv-cache)
-  endif()
+-endif()
 
   #Flatpak wrapper that sets some environment variables that JASP needs
   install(PROGRAMS ${CMAKE_SOURCE_DIR}/Tools/flatpak/org.jaspstats.JASP
--- a/pkgs/by-name/ja/jasp-desktop/module-info.json
+++ b/pkgs/by-name/ja/jasp-desktop/module-info.json
@@ -97,9 +97,9 @@
  },
  "jaspLearnBayes": {
    "pname": "jaspLearnBayes",
-    "version": "0.96.5-release.0",
-    "tag": "0.96.5-release.0_R-4-5-2_Release",
-    "hash": "sha256-TdlwB2TV+YNj4Uwf4rNSIw/OtKQHEbrFKv1t2RioTmI="
+    "version": "0.95.5-release.12",
+    "tag": "0.95.5-release.12_R-4-5-2_Release",
+    "hash": "sha256-zqMcWFML/iexmegMtGWCe/OCGqwmWW98/XZfKVs6N8w="
  },
  "jaspLearnStats": {
    "pname": "jaspLearnStats",
--- a/pkgs/by-name/ja/jasp-desktop/package.nix
+++ b/pkgs/by-name/ja/jasp-desktop/package.nix
@@ -25,13 +25,13 @@

 stdenv.mkDerivation (finalAttrs: {
  pname = "jasp-desktop";
-  version = "0.98.1";
+  version = "0.97.1";
  src = fetchFromGitHub {
    owner = "jasp-stats";
    repo = "jasp-desktop";
    tag = "v${finalAttrs.version}";
    fetchSubmodules = true;
-    hash = "sha256-73RxbWVa03V6MdcW9k4Hv8EBsSNw0Feg91SioWLgC5U=";
+    hash = "sha256-4K6ReOJJF8Pt/RdNSp2ZVH/d64ZMCFlX1RIXDAWWWBE=";
  };

  patches = [
@@ -68,7 +68,8 @@ stdenv.mkDerivation (finalAttrs: {
    qt6.qtbase
    qt6.qtdeclarative
    qt6.qtwebengine
-    qt6.qthttpserver
+    qt6.qtsvg
+    qt6.qt5compat
  ];

  # needed so that the linker can find libRInside.so
--- a/pkgs/by-name/kl/kloak/package.nix
+++ b/pkgs/by-name/kl/kloak/package.nix
@@ -17,13 +17,13 @@

 stdenv.mkDerivation (finalAttrs: {
  pname = "kloak";
-  version = "0.8.5-1";
+  version = "0.8.6-1";

  src = fetchFromGitHub {
    owner = "Whonix";
    repo = "kloak";
    tag = finalAttrs.version;
-    hash = "sha256-fDmqA00b5ESS9LW2QIeEx3wWb0lhgkqoBYcw1XYDI7k=";
+    hash = "sha256-zaoKVPocL8iaX6hhZh0Q+cgYg3JLWBcMgGU0nLlNcjo=";
  };

  strictDeps = true;
--- a/pkgs/by-name/li/librevna/package.nix
+++ b/pkgs/by-name/li/librevna/package.nix
@@ -0,0 +1,84 @@
+{
+  stdenv,
+  lib,
+  fetchFromGitHub,
+  apple-sdk_14,
+  git,
+  pkg-config,
+  qt6,
+  libusb1,
+  udev,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "librevna";
+  version = "1.6.5";
+  __structuredAttrs = true;
+
+  src = fetchFromGitHub {
+    owner = "jankae";
+    repo = "LibreVNA";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-uPVnjhbFXP1Z+pJuWDX4xqQGcmbJI8ElHq8fVXN0Qcc=";
+  };
+
+  sourceRoot = "${finalAttrs.src.name}/Software/PC_Application/LibreVNA-GUI";
+
+  postPatch = ''
+    substituteInPlace resources/librevna.desktop \
+      --replace-fail Exec=/opt/LibreVNA-GUI Exec=$out/bin/LibreVNA-GUI
+  '';
+
+  nativeBuildInputs = [
+    git
+    pkg-config
+    qt6.qmake
+    qt6.qtsvg
+    qt6.wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    qt6.qtbase
+    libusb1
+  ]
+  ++ lib.optional stdenv.hostPlatform.isLinux udev
+  ++ lib.optional stdenv.hostPlatform.isDarwin apple-sdk_14;
+
+  strictDeps = true;
+
+  installPhase =
+    if stdenv.hostPlatform.isDarwin then
+      ''
+        runHook preInstall
+
+        mkdir -p $out/{Applications,bin}
+        mv LibreVNA-GUI.app $out/Applications
+        ln -s $out/Applications/LibreVNA-GUI.app/Contents/MacOS/LibreVNA-GUI $out/bin/LibreVNA-GUI
+
+        runHook postInstall
+      ''
+    else
+      ''
+        runHook preInstall
+
+        install -Dm755 LibreVNA-GUI -t $out/bin
+        install -Dm644 ../51-vna.rules -t $out/etc/udev/rules.d
+        install -Dm644 resources/librevna.desktop -t $out/share/applications
+        install -Dm644 resources/librevna.png -t $out/share/pixmaps
+
+        runHook postInstall
+      '';
+
+  meta = {
+    changelog = "https://github.com/jankae/LibreVNA/releases/tag/v${finalAttrs.version}";
+    homepage = "https://github.com/jankae/LibreVNA/";
+    description = "100kHz to 6GHz 2 port USB based VNA";
+    mainProgram = "LibreVNA-GUI";
+    license = lib.licenses.gpl3Only;
+    platforms = lib.platforms.unix;
+
+    maintainers = with lib.maintainers; [
+      dunxen
+    ];
+  };
+})
--- a/pkgs/by-name/ma/matcha/package.nix
+++ b/pkgs/by-name/ma/matcha/package.nix
@@ -14,16 +14,16 @@ buildGoLatestModule (finalAttrs: {
  __structuredAttrs = true;

  pname = "matcha";
-  version = "0.43.0";
+  version = "0.44.0";

  src = fetchFromGitHub {
    owner = "floatpane";
    repo = "matcha";
    tag = "v${finalAttrs.version}";
-    hash = "sha256-x+k1/k7pwJ0MW0t31ieaOkbP8LtqDSmHOBrNEGA0K6Q=";
+    hash = "sha256-y1YEnqTCmf+CMKpv3wN4SZsN+lUuv3T8pKmM+zu1Ipw=";
  };

-  vendorHash = "sha256-5smWIw8ofG61ugHxFbmQ9r9vcxi098/UmxUE15lx4wE=";
+  vendorHash = "sha256-cg6R4WtDORwZlo+P16rN6qc0zZMOPtnr4VyQKV9Q2nM=";
  proxyVendor = true;

  nativeBuildInputs = lib.optionals stdenv.hostPlatform.isLinux [
--- a/pkgs/by-name/ma/matomo/package.nix
+++ b/pkgs/by-name/ma/matomo/package.nix
@@ -10,11 +10,11 @@

 stdenv.mkDerivation (finalAttrs: {
  pname = "matomo";
-  version = "5.10.0";
+  version = "5.12.0";

  src = fetchurl {
    url = "https://builds.matomo.org/matomo-${finalAttrs.version}.tar.gz";
-    hash = "sha256-i7nRQRY2gAzMQmRNGaksq4B516MsQuXQZbzlEUWEsQw=";
+    hash = "sha256-yiQUXb9yGgJ8PFOL1tyXtXEmgCviaqCtN0DwxKcGZV0=";
  };

  nativeBuildInputs = [ makeWrapper ];
--- a/pkgs/by-name/ma/matrix-synapse-unwrapped/package.nix
+++ b/pkgs/by-name/ma/matrix-synapse-unwrapped/package.nix
@@ -14,19 +14,19 @@

 python3Packages.buildPythonApplication rec {
  pname = "matrix-synapse";
-  version = "1.156.0";
+  version = "1.157.1";
  pyproject = true;

  src = fetchFromGitHub {
    owner = "element-hq";
    repo = "synapse";
    rev = "v${version}";
-    hash = "sha256-x3EVmNPqcxtvt6ZaPsDCCcr7Z0LIO257s2gO3HCNmKA=";
+    hash = "sha256-yDfBtcBvIoWUfD8bqwGgeMvq4XHrr9ptVB6yKJWFX0c=";
  };

  cargoDeps = rustPlatform.fetchCargoVendor {
    inherit pname version src;
-    hash = "sha256-N/JWRFz9OKcxigjp86AVVZGK63MdZmEzwHhBgBuWZcY=";
+    hash = "sha256-KM3j2O7J4Sad6jKF2Ca4qkRLj3w7+/UCnK6T6x8kMfs=";
  };

  build-system =
--- a/pkgs/by-name/ma/mattermost/package.nix
+++ b/pkgs/by-name/ma/mattermost/package.nix
@@ -27,10 +27,10 @@
    #
    # Ensure you also check ../mattermostLatest/package.nix.
    regex = "^v(11\\.7\\.[0-9]+)$";
-    version = "11.7.6";
-    srcHash = "sha256-oMjfSX45+sEQwNpNVDTOlCBUK7OSBCCKpaUMMrRzdQM=";
+    version = "11.7.7";
+    srcHash = "sha256-dV+U+2yYX4IrM/EMaBAMwhW9WJh976WGDWFNOqnkTE8=";
    vendorHash = "sha256-XaXqQN20c3DhW2/L0zhTA8dLeRp4MyBxUKpiMVwp/7s=";
-    npmDepsHash = "sha256-F7o+AVM1WiuHKDQaqHbxDjWT1vAiddh4/D8EktxncAs=";
+    npmDepsHash = "sha256-8ZEe2TM2bevzdn04YIcVICWFSaa8HZTVS4gKn6aFcqM=";
  },
  ...
 }:
--- a/pkgs/by-name/me/metals/package.nix
+++ b/pkgs/by-name/me/metals/package.nix
@@ -9,7 +9,7 @@

 stdenv.mkDerivation (finalAttrs: {
  pname = "metals";
-  version = "1.6.7";
+  version = "1.6.8";

  deps = stdenv.mkDerivation {
    name = "metals-deps-${finalAttrs.version}";
@@ -23,7 +23,7 @@ stdenv.mkDerivation (finalAttrs: {
    '';
    outputHashMode = "recursive";
    outputHashAlgo = "sha256";
-    outputHash = "sha256-2ly1vO+06EalQjEekRwm/g2wfdbq26IcEQscfM14Gvc=";
+    outputHash = "sha256-LdZ6I7zOUTHgS/TTo0T6Dh+Kb3YpgJg8gK0UngsA7Gs=";
  };

  nativeBuildInputs = [
--- a/pkgs/by-name/mu/music-assistant/package.nix
+++ b/pkgs/by-name/mu/music-assistant/package.nix
@@ -185,7 +185,7 @@ pythonPackages.buildPythonApplication (finalAttrs: {
  nativeCheckInputs =
    with pythonPackages;
    [
-      pytestCheckHook
+      pytest9_0CheckHook
      writableTmpDirAsHomeHook
    ]
    ++ lib.concatAttrValues finalAttrs.passthru.optional-dependencies
--- a/pkgs/by-name/om/omxplayer/package.nix
+++ b/pkgs/by-name/om/omxplayer/package.nix
@@ -1,111 +0,0 @@
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  fetchurl,
-  raspberrypifw,
-  pcre,
-  boost,
-  freetype,
-  zlib,
-}:
-
-let
-  ffmpeg = stdenv.mkDerivation rec {
-    pname = "ffmpeg";
-    version = "1.1.3";
-
-    src = fetchurl {
-      url = "http://www.ffmpeg.org/releases/ffmpeg-${version}.tar.bz2";
-      sha256 = "03s1zsprz5p6gjgwwqcf7b6cvzwwid6l8k7bamx9i0f1iwkgdm0j";
-    };
-
-    configurePlatforms = [ ];
-    configureFlags = [
-      "--arch=${stdenv.hostPlatform.parsed.cpu.name}"
-    ]
-    ++ lib.optionals stdenv.hostPlatform.isAarch32 [
-      # TODO be better with condition
-      "--cpu=arm1176jzf-s"
-    ]
-    ++ [
-      "--disable-muxers"
-      "--enable-muxer=spdif"
-      "--enable-muxer=adts"
-      "--disable-encoders"
-      "--enable-encoder=ac3"
-      "--enable-encoder=aac"
-      "--disable-decoder=mpeg_xvmc"
-      "--disable-devices"
-      "--disable-ffprobe"
-      "--disable-ffplay"
-      "--disable-ffserver"
-      "--disable-ffmpeg"
-      "--enable-shared"
-      "--disable-doc"
-      "--enable-postproc"
-      "--enable-gpl"
-      "--enable-protocol=http"
-      "--enable-pthreads"
-      "--disable-runtime-cpudetect"
-      "--enable-pic"
-      "--disable-armv5te"
-      "--disable-neon"
-      "--enable-armv6t2"
-      "--enable-armv6"
-      "--enable-hardcoded-tables"
-      "--disable-runtime-cpudetect"
-      "--disable-debug"
-      "--arch=${stdenv.hostPlatform.parsed.cpu.name}"
-      "--target_os=${stdenv.hostPlatform.parsed.kernel.name}"
-    ]
-    ++ lib.optionals (stdenv.hostPlatform != stdenv.buildPlatform) [
-      "--cross-prefix=${stdenv.cc.targetPrefix}"
-      "--enable-cross-compile"
-    ];
-
-    enableParallelBuilding = true;
-
-    meta = {
-      homepage = "http://www.ffmpeg.org/";
-      description = "Complete, cross-platform solution to record, convert and stream audio and video";
-    };
-  };
-in
-stdenv.mkDerivation {
-  pname = "omxplayer";
-  version = "0-unstable-2013-03-28";
-
-  src = fetchFromGitHub {
-    owner = "huceke";
-    repo = "omxplayer";
-    rev = "fbee325dc20441138d04d8d2022ad85956302e97";
-    sha256 = "0fkvv8il7ffqxki2gp8cxa5shh6sz9jsy5vv3f4025g4gss6afkg";
-  };
-
-  postPatch = ''
-    sed -i 1d Makefile
-    export INCLUDES="-I${raspberrypifw}/include/interface/vcos/pthreads -I${raspberrypifw}/include/interface/vmcs_host/linux/"
-  '';
-
-  installPhase = ''
-    mkdir -p $out/bin
-    cp omxplayer.bin $out/bin
-  '';
-
-  buildInputs = [
-    raspberrypifw
-    ffmpeg
-    pcre
-    boost
-    freetype
-    zlib
-  ];
-
-  meta = {
-    homepage = "https://github.com/huceke/omxplayer";
-    description = "Commandline OMX player for the Raspberry Pi";
-    license = lib.licenses.gpl2Plus;
-    platforms = lib.platforms.arm;
-  };
-}
--- a/pkgs/by-name/op/openscenegraph/package.nix
+++ b/pkgs/by-name/op/openscenegraph/package.nix
@@ -14,7 +14,6 @@
  libGL,
  glib,
  libxml2,
-  pcre,
  zlib,
  boost,
  jpegSupport ? true,
@@ -99,7 +98,6 @@ stdenv.mkDerivation (finalAttrs: {
    ++ lib.optional curlSupport curl
    ++ lib.optionals colladaSupport [
      collada-dom
-      pcre
    ]
    ++ lib.optional opencascadeSupport opencascade-occt
    ++ lib.optional ffmpegSupport ffmpeg
--- a/pkgs/by-name/pa/paperless-ngx/package.nix
+++ b/pkgs/by-name/pa/paperless-ngx/package.nix
@@ -118,6 +118,7 @@ pythonPackages.buildPythonApplication (finalAttrs: {
    "drf-spectacular-sidecar"
    "python-dotenv"
    "gotenberg-client"
+    "nltk"
    "redis"
    "scikit-learn"
    "tika-client"
--- a/pkgs/by-name/pi/piknik/package.nix
+++ b/pkgs/by-name/pi/piknik/package.nix
@@ -36,7 +36,9 @@ buildGoModule (finalAttrs: {
    homepage = "https://github.com/jedisct1/piknik";
    changelog = "https://github.com/jedisct1/piknik/blob/${finalAttrs.src.rev}/ChangeLog";
    license = lib.licenses.bsd2;
-    maintainers = [ ];
+    maintainers = with lib.maintainers; [
+      sheeeng
+    ];
    mainProgram = "piknik";
  };
 })
--- a/pkgs/by-name/pr/protoc-gen-grpc-java/data.nix
+++ b/pkgs/by-name/pr/protoc-gen-grpc-java/data.nix
@@ -1,14 +1,14 @@
 {
-  version = "1.82.2";
+  version = "1.83.0";
  hashes = {
-    linux-aarch_64 = "sha256-RVdT8rpH1WHd5vQb+o3BP81ipuwFZ/Bv8Hr8BC7shwA=";
-    linux-ppcle_64 = "sha256-Jcjpo21XWjCeCMcWmjM5tPtQYwd5JZ0pUsfFXMAF95Q=";
-    linux-s390_64 = "sha256-Oe9brWzFO1aP3xcVhR8Uq40nJFTzyxDAtp0+3ErynjI=";
-    linux-x86_32 = "sha256-AlnBc3VBeV+jMn6T0QFWurd+0hywSihi7snop81bO2E=";
-    linux-x86_64 = "sha256-5SKpbtVprxNAXhzqODcPZ+I7U81RSjELWQKQ71/lYF4=";
-    osx-aarch_64 = "sha256-LNFM4zTJiLO5XHWT/iaipbQWgN2HwyjNxTMps/XlzYo=";
-    osx-x86_64 = "sha256-LNFM4zTJiLO5XHWT/iaipbQWgN2HwyjNxTMps/XlzYo=";
-    windows-x86_32 = "sha256-yrbPXrPSn+iaI16zCPh1rteFh1Q18sQuR9UWo+xMToQ=";
-    windows-x86_64 = "sha256-vfdo65O6o8ctW+qVdcWuH5sQDXypn4ktNHMCv6uJ0gw=";
+    linux-aarch_64 = "sha256-Nwnk4Upg8VZCVbR/bpJDct/wI6GGaTICK+Sh711ZVEM=";
+    linux-ppcle_64 = "sha256-xUwugnrRQQqEkupYFh7SPtqtNmXmNCjAE+msHskmPXY=";
+    linux-s390_64 = "sha256-hj+QMaSxtX+hs6G5qCxf7ON2bDvpEGovt9iuVFwsXAQ=";
+    linux-x86_32 = "sha256-qJ034I7Im1pEn5u6W16y662y4+d7ZpB9EQtd7hkSCG4=";
+    linux-x86_64 = "sha256-oZrnSqTLA+HQEmlWKsYWXsMqhIp769AyrqmguVaXGLo=";
+    osx-aarch_64 = "sha256-w+3q+DtvfVzsqm9PfeMq6WyUn0jJorp0NngnH6HQh3I=";
+    osx-x86_64 = "sha256-w+3q+DtvfVzsqm9PfeMq6WyUn0jJorp0NngnH6HQh3I=";
+    windows-x86_32 = "sha256-fwDjhD8Jhy7M7qPSc8vJSUA8H/OhWeOyV/69uuZX+9Y=";
+    windows-x86_64 = "sha256-MER2cr8kaMO3zVTLujYr4jPX8jcbBqbHf9/Fxb0CbJY=";
  };
 }
--- a/pkgs/by-name/sl/slack/sources.nix
+++ b/pkgs/by-name/sl/slack/sources.nix
@@ -1,19 +1,19 @@
 # Generated by ./update.sh - do not update manually!
-# Last updated: 2026-05-14
+# Last updated: 2026-07-23
 { fetchurl }:
 {
  aarch64-darwin = {
-    version = "4.49.89";
+    version = "4.51.180";
    src = fetchurl {
-      url = "https://downloads.slack-edge.com/desktop-releases/mac/arm64/4.49.89/Slack-4.49.89-macOS.dmg";
-      hash = "sha256-u5NppmmRyC+6HaPIcSSGOOdVRiZdT9GE1eHvad6rYdY=";
+      url = "https://downloads.slack-edge.com/desktop-releases/mac/arm64/4.51.180/Slack-4.51.180-macOS.dmg";
+      hash = "sha256-6QhuZWEwQiW8ZyYTJRLMZq5MayBgX9xlBLdhttiTaoA=";
    };
  };
  x86_64-linux = {
-    version = "4.49.89";
+    version = "4.51.180";
    src = fetchurl {
-      url = "https://downloads.slack-edge.com/desktop-releases/linux/x64/4.49.89/slack-desktop-4.49.89-amd64.deb";
-      hash = "sha256-Shf4/igTudAwg0ve8iGjpLIS8AL/k90RDN92JyAMGy8=";
+      url = "https://downloads.slack-edge.com/desktop-releases/linux/x64/4.51.180/slack-desktop-4.51.180-amd64.deb";
+      hash = "sha256-qkXhUXlHAzdwEqmtePCyFSw2iFLghSZ65ona+1wwjqE=";
    };
  };
 }
--- a/pkgs/by-name/te/telemt/package.nix
+++ b/pkgs/by-name/te/telemt/package.nix
@@ -5,16 +5,16 @@
 }:
 rustPlatform.buildRustPackage rec {
  pname = "telemt";
-  version = "3.4.23";
+  version = "3.4.25";

  src = fetchFromGitHub {
    owner = "telemt";
    repo = "telemt";
    tag = version;
-    hash = "sha256-8rKEMQPgIrvtLoM+LcSoXiYaMmCtb4OObnDUYagy+Ak=";
+    hash = "sha256-A9+PWpVyHgQOFb/OsLc8vl4kq8J9reW1/5Hn4yTdJeI=";
  };

-  cargoHash = "sha256-wjw+FE1yQ+zc2Ta3h7B3Wtejf6bGobstTKDCjFphU+M=";
+  cargoHash = "sha256-ZaaT3S3Qy7HBI2dETy8JtvWttJWnkhRNA3wWz44pTpQ=";

  checkFlags = [
    # flaky: races between MiddleClientWriterCancelled and TrafficBudgetWaitCancelled observation paths
--- a/pkgs/by-name/te/temporal-cli/package.nix
+++ b/pkgs/by-name/te/temporal-cli/package.nix
@@ -11,13 +11,13 @@

 buildGoModule (finalAttrs: {
  pname = "temporal-cli";
-  version = "1.8.0";
+  version = "1.8.1";

  src = fetchFromGitHub {
    owner = "temporalio";
    repo = "cli";
    tag = "v${finalAttrs.version}";
-    hash = "sha256-Z5Ba4oVQR6g/HyaBd/0iLIWq6Ht2SJAdylTVaErRFL0=";
+    hash = "sha256-RswHPnaWN3bLerhttVb/3G//cyz9Fr+x/B4h+/SSSqA=";
  };

  vendorHash = "sha256-9lO9uhy1n85QYyoh27cKhdlcuL4GT98aCNWwe8tOwoQ=";
--- a/pkgs/by-name/tp/tpnote/package.nix
+++ b/pkgs/by-name/tp/tpnote/package.nix
@@ -13,16 +13,16 @@

 rustPlatform.buildRustPackage (finalAttrs: {
  pname = "tpnote";
-  version = "1.26.6";
+  version = "1.26.7";

  src = fetchFromGitHub {
    owner = "getreu";
    repo = "tp-note";
    tag = "v${finalAttrs.version}";
-    hash = "sha256-ELRR2nIbkbD/WWS93lyHHYoPY/KLUBO9+/13UUFhA6Y=";
+    hash = "sha256-dg6IFozGnvCOHbqZ9p0Eu7CPAv7W1Yf+MqAAFxghBEg=";
  };

-  cargoHash = "sha256-gFfESz0yn9AJ4QCujaUyXrFnxyHzqi3IX5Gg0Gma0DQ=";
+  cargoHash = "sha256-Lu4NBYxplYk5Y3IbfiCv61whW9Dk6fIScZUIB5yBdCk=";

  nativeBuildInputs = [
    cmake
--- a/pkgs/by-name/xf/xfsprogs/package.nix
+++ b/pkgs/by-name/xf/xfsprogs/package.nix
@@ -17,11 +17,11 @@

 stdenv.mkDerivation (finalAttrs: {
  pname = "xfsprogs";
-  version = "7.0.1";
+  version = "7.1.1";

  src = fetchurl {
    url = "mirror://kernel/linux/utils/fs/xfs/xfsprogs/xfsprogs-${finalAttrs.version}.tar.xz";
-    hash = "sha256-SoyoOnrLjNksmX1jtprmTxcAVrNmopJKdT5H1LtLiwY=";
+    hash = "sha256-Bj7cMbqOhclcf6+b5GWgSJi7p8bmIv3ZsUbu1MpUFeg=";
  };

  postPatch = ''
--- a/pkgs/by-name/ya/yazi/plugins/diff/default.nix
+++ b/pkgs/by-name/ya/yazi/plugins/diff/default.nix
@@ -5,13 +5,13 @@
 }:
 mkYaziPlugin {
  pname = "diff.yazi";
-  version = "0-unstable-2026-07-01";
+  version = "0-unstable-2026-07-22";

  src = fetchFromGitHub {
    owner = "yazi-rs";
    repo = "plugins";
-    rev = "65559fd3edc33cb0fd24ec92874c763fa5f68e3e";
-    hash = "sha256-SLfwFGOcmlZIUqlSSMk7dEEUZQbKqPMidknS3vtFzPo=";
+    rev = "bbac5e75b22a2893ef7cdd2bd6814b15f2abb91e";
+    hash = "sha256-lio4pvrqK575q7M+GtRr/5EdA4h2J/7gIvXK8c5rq1U=";
  };

  meta = {
--- a/pkgs/by-name/ya/yazi/plugins/gvfs/default.nix
+++ b/pkgs/by-name/ya/yazi/plugins/gvfs/default.nix
@@ -5,13 +5,13 @@
 }:
 mkYaziPlugin {
  pname = "gvfs.yazi";
-  version = "0-unstable-2026-07-13";
+  version = "0-unstable-2026-07-23";

  src = fetchFromGitHub {
    owner = "boydaihungst";
    repo = "gvfs.yazi";
-    rev = "c5a0bb924eceeeb8b44bfc00aba0a97ba0287fa3";
-    hash = "sha256-hSHEN/F4uc1FFScB5lLRAKryLwP+O7I9vgEgobGbQyw=";
+    rev = "364b0a811d722a1fdb3c2bde36aa640591437967";
+    hash = "sha256-bQDcT04m1WvMRCiVIyer4WHgjYMaamMfolmH49lVSig=";
  };

  meta = {
--- a/pkgs/by-name/ya/yazi/plugins/restore/default.nix
+++ b/pkgs/by-name/ya/yazi/plugins/restore/default.nix
@@ -5,13 +5,13 @@
 }:
 mkYaziPlugin {
  pname = "restore.yazi";
-  version = "0-unstable-2026-04-04";
+  version = "0-unstable-2026-07-22";

  src = fetchFromGitHub {
    owner = "boydaihungst";
    repo = "restore.yazi";
-    rev = "0e0870460b9b74c5ae98b7f96c7c26a9a274ce6d";
-    hash = "sha256-rDsyMF5IEBHx+fJ0oYTCCQAlTSquUcOkFLC4Lmbuz6k=";
+    rev = "7bfcfcbda078b7e51d1ff9a62db9c654a3952fa4";
+    hash = "sha256-pmyS1rU5C6U9LloGoDFB8s6GwoMqG1Jve5OFooI64tU=";
  };

  meta = {
--- a/pkgs/by-name/za/zapzap/package.nix
+++ b/pkgs/by-name/za/zapzap/package.nix
@@ -4,8 +4,25 @@
  fetchpatch,
  python3Packages,
  qt6,
+  linkFarm,
+  hunspellDictsChromium,
+  dictionaries ? [
+    hunspellDictsChromium.en-us
+    hunspellDictsChromium.en-gb
+    hunspellDictsChromium.de-de
+    hunspellDictsChromium.fr-fr
+    hunspellDictsChromium.sv-se
+  ],
 }:

+let
+  qtwebengineDictionaries = linkFarm "zapzap-qtwebengine-dictionaries" (
+    map (d: {
+      name = d.dictFileName;
+      path = d;
+    }) dictionaries
+  );
+in
 python3Packages.buildPythonApplication (finalAttrs: {
  pname = "zapzap";
  version = "7.0";
@@ -55,7 +72,12 @@ python3Packages.buildPythonApplication (finalAttrs: {

  dontWrapQtApps = true;
  preFixup = ''
-    makeWrapperArgs+=("''${qtWrapperArgs[@]}")
+    makeWrapperArgs+=(
+      "''${qtWrapperArgs[@]}"
+      ${lib.optionalString (dictionaries != [ ]) ''
+        --set-default QTWEBENGINE_DICTIONARIES_PATH "${qtwebengineDictionaries}"
+      ''}
+    )
  '';

  # has no tests
--- a/pkgs/development/compilers/ocaml/generic.nix
+++ b/pkgs/development/compilers/ocaml/generic.nix
@@ -21,6 +21,7 @@ in
  ncurses,
  binutils,
  buildEnv,
+  pkgsBuildBuild,
  libunwind,
  fetchpatch,
  libx11,
@@ -177,6 +178,7 @@ stdenv.mkDerivation (
        ]
      else
        [ "nixpkgs_world" ];
+    nativeBuildInputs = optional (stdenv.hostPlatform != stdenv.targetPlatform) pkgsBuildBuild.ocaml;
    buildInputs =
      optional (lib.versionOlder version "4.07") ncurses
      ++ optionals useX11 [
--- a/pkgs/development/coq-modules/mathcomp-word/default.nix
+++ b/pkgs/development/coq-modules/mathcomp-word/default.nix
@@ -46,6 +46,7 @@ mkCoqDerivation {

  releaseRev = v: "v${v}";

+  release."3.5".hash = "sha256-ur6XGhTUQ1XdcyC6RERYaTwyzL58mWwdihY/yemjfQg=";
  release."3.4".hash = "sha256-AnyiM5B7JJZI5LR0vSi6baVIx9SibYRiho7UBg1uV5w=";
  release."3.3".hash = "sha256-Zn9245fr0OhgaXjWlIO1QwSxrQYetj7qPHwZAXTdqNc=";
  release."3.2".hash = "sha256-4HOFFQzKbHIq+ktjJaS5b2Qr8WL1eQ26YxF4vt1FdWM=";
@@ -72,7 +73,7 @@ mkCoqDerivation {
    lib.switch
      [ coq.coq-version mathcomp.version ]
      [
-        (case (range "8.16" "9.1") (isGe "2.0") "3.4")
+        (case (range "8.16" "9.1") (isGe "2.0") "3.5")
        (case (range "8.12" "8.20") (range "1.12" "1.19") "2.4")
      ]
      null;
--- a/pkgs/development/coq-modules/multinomials/default.nix
+++ b/pkgs/development/coq-modules/multinomials/default.nix
@@ -33,7 +33,7 @@ mkCoqDerivation {
    lib.switch
      [ coq.coq-version mathcomp.version ]
      [
-        (case (range "9.0" "9.2") (range "2.6.0" "2.6.0") "2.5.0") # also works on MC 2.4 and 2.5 but breaks validsdp
+        (case (range "9.0" "9.3") (range "2.6.0" "2.6.0") "2.5.0") # also works on MC 2.4 and 2.5 but breaks validsdp
        (case (range "8.18" "9.1") (range "2.1.0" "2.5.0") "2.4.0")
        (case (range "8.17" "9.0") (range "2.1.0" "2.3.0") "2.3.0")
        (case (range "8.17" "8.20") (isGe "2.1.0") "2.2.0")
--- a/pkgs/development/coq-modules/odd-order/default.nix
+++ b/pkgs/development/coq-modules/odd-order/default.nix
@@ -34,7 +34,7 @@ mkCoqDerivation {
    lib.switch
      [ coq.coq-version mathcomp-character.version ]
      [
-        (case (range "9.1" "9.2") (range "2.5" "2.6") "2.4.0")
+        (case (range "9.1" "9.3") (range "2.5" "2.6") "2.4.0")
        (case (range "9.0" "9.1") (range "2.5" "2.5") "2.3.0")
        (case (range "8.16" "9.1") (range "2.2.0" "2.4.0") "2.2.0")
        (case (range "8.16" "9.0") (range "2.1.0" "2.3.0") "2.1.0")
--- a/pkgs/development/coq-modules/ssprove/default.nix
+++ b/pkgs/development/coq-modules/ssprove/default.nix
@@ -32,7 +32,6 @@
      [ coq.coq-version mathcomp-boot.version ]
      [
        (case (range "8.20" "9.1") (range "2.3.0" "2.5.0") "0.3.1")
-        (case (range "8.18" "9.1") (range "2.3.0" "2.4.0") "0.2.4")
        (case (range "8.18" "8.20") (range "2.3.0" "2.3.0") "0.2.3")
        (case (range "8.18" "8.20") (range "2.1.0" "2.2.0") "0.2.2")
        # This is the original dependency:
--- a/pkgs/development/python-modules/nltk/default.nix
+++ b/pkgs/development/python-modules/nltk/default.nix
@@ -5,6 +5,7 @@
  fetchFromGitHub,
  buildPythonPackage,
  click,
+  defusedxml,
  joblib,
  regex,
  setuptools,
@@ -23,49 +24,53 @@

 buildPythonPackage (finalAttrs: {
  pname = "nltk";
-  version = "3.9.4";
+  version = "3.10.0";
  pyproject = true;

  src = fetchFromGitHub {
    owner = "nltk";
    repo = "nltk";
-    tag = finalAttrs.version;
-    hash = "sha256-kDfMiqXgLq91zzDjv/qDn0XwQkYRn2sITI6E4pgWe/8=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-1iflqb3cOyaviW3IostFCuJtZ9KBZI0n9dfKfqqbcO0=";
  };

  postPatch = ''
    # In the nix store we trust
    substituteInPlace nltk/pathsec.py \
-      --replace-fail 'if not (target == scoped_root or target.is_relative_to(scoped_root)):' 'if not (target == scoped_root or target.is_relative_to(scoped_root) or target.is_relative_to("/nix/store")):'
+      --replace-fail 'if not (target == scoped_root or target.is_relative_to(scoped_root)):' \
+                     'if not (target == scoped_root or target.is_relative_to(scoped_root) or target.is_relative_to("/nix/store")):' \
+      --replace-fail ' "/usr/share/nltk_data", ' ' "/usr/share/nltk_data", "/nix/store", '
  '';

  build-system = [ setuptools ];

  dependencies = [
    click
+    defusedxml
    joblib
    regex
    tqdm
  ];

-  # Use new passthru function to pass dependencies required for testing
  preInstallCheck = ''
    export NLTK_DATA=${
      nltk.dataDir (
        d: with d; [
          averaged-perceptron-tagger-eng
          averaged-perceptron-tagger-rus
+          bcp47
          brown
          cess-cat
          cess-esp
          conll2007
          floresta
          gutenberg
+          ieer
          inaugural
          indian
          large-grammars
          nombank-1-0
-          omw-1-4
+          omw-2-0
          pl196x
          porter-test
          ptb
@@ -114,9 +119,10 @@ buildPythonPackage (finalAttrs: {
  };

  meta = {
+    changelog = "https://github.com/nltk/nltk/blob/${finalAttrs.src.tag}/ChangeLog";
    description = "Natural Language Processing ToolKit";
    mainProgram = "nltk";
-    homepage = "http://nltk.org/";
+    homepage = "https://nltk.org/";
    license = lib.licenses.asl20;
    maintainers = [ lib.maintainers.bengsparks ];
  };
--- a/pkgs/development/python-modules/pinecone-plugin-assistant/default.nix
+++ b/pkgs/development/python-modules/pinecone-plugin-assistant/default.nix
@@ -1,40 +0,0 @@
-{
-  buildPythonPackage,
-  lib,
-  fetchPypi,
-  poetry-core,
-  requests,
-}:
-
-buildPythonPackage rec {
-  pname = "pinecone-plugin-assistant";
-  version = "3.0.3";
-
-  pyproject = true;
-
-  src = fetchPypi {
-    pname = "pinecone_plugin_assistant";
-    inherit version;
-    hash = "sha256-U/VI7eYKldef9I14ZaPQr9Zlztnnd1gnLmK6DGxjvSY=";
-  };
-
-  build-system = [
-    poetry-core
-  ];
-
-  dependencies = [
-    requests
-  ];
-
-  pythonRelaxDeps = [
-    "packaging"
-  ];
-
-  meta = {
-    homepage = "https://www.pinecone.io/";
-    maintainers = with lib.maintainers; [ codgician ];
-    license = lib.licenses.asl20;
-    platforms = lib.platforms.unix;
-    description = "Assistant plugin for Pinecone SDK";
-  };
-}
--- a/pkgs/development/python-modules/pinecone-plugin-interface/default.nix
+++ b/pkgs/development/python-modules/pinecone-plugin-interface/default.nix
@@ -1,31 +0,0 @@
-{
-  buildPythonPackage,
-  lib,
-  fetchPypi,
-  poetry-core,
-}:
-
-buildPythonPackage rec {
-  pname = "pinecone-plugin-interface";
-  version = "0.0.7";
-
-  pyproject = true;
-
-  src = fetchPypi {
-    pname = "pinecone_plugin_interface";
-    inherit version;
-    hash = "sha256-uOZnXkGEczOqE5I8xE2qP4VnbXFXMkaC3BZAWIqYKEY=";
-  };
-
-  build-system = [
-    poetry-core
-  ];
-
-  meta = {
-    homepage = "https://www.pinecone.io/";
-    maintainers = with lib.maintainers; [ bot-wxt1221 ];
-    license = lib.licenses.asl20;
-    platforms = lib.platforms.unix;
-    description = "Plugin interface for the Pinecone python client";
-  };
-}
--- a/pkgs/development/python-modules/pinecone/default.nix
+++ b/pkgs/development/python-modules/pinecone/default.nix
@@ -1,47 +1,50 @@
 {
  lib,
  buildPythonPackage,
-  certifi,
+  buildPackages,
  fetchFromGitHub,
-  hatchling,
+  httpx,
+  msgspec,
  orjson,
-  pinecone-plugin-assistant,
-  pinecone-plugin-interface,
-  python-dateutil,
-  typing-extensions,
-  urllib3,
+  rustPlatform,
 }:

 buildPythonPackage rec {
  pname = "pinecone";
-  version = "8.1.2";
+  version = "9.1.0";
  pyproject = true;

  src = fetchFromGitHub {
    owner = "pinecone-io";
    repo = "pinecone-python-client";
    tag = "v${version}";
-    hash = "sha256-VfoSW17Bx/eFlnSxUiQZsfY/y210/sKIF5df/kb2kTc=";
+    hash = "sha256-yWGW9qx4zb4FnDLXvtXREYXRO7e5Jk/KJoaQlpKMwpg=";
  };

-  build-system = [ hatchling ];
+  cargoDeps = rustPlatform.fetchCargoVendor {
+    inherit pname version src;
+    hash = "sha256-I3pIy9by+OHo6iU6OZp3VvJJPZOmJ/CYhkzoV8xHoMY=";
+  };
+
+  nativeBuildInputs = with rustPlatform; [
+    cargoSetupHook
+    maturinBuildHook
+  ];
+
+  env.PROTOC = "${lib.getExe buildPackages.protobuf}";

  dependencies = [
-    certifi
+    httpx
+    msgspec
    orjson
-    pinecone-plugin-assistant
-    pinecone-plugin-interface
-    python-dateutil
-    typing-extensions
-    urllib3
  ];

  pythonImportsCheck = [ "pinecone" ];

  meta = {
-    description = "Pinecone python client";
+    description = "Pinecone Python SDK";
    homepage = "https://www.pinecone.io/";
-    changelog = "https://github.com/pinecone-io/pinecone-python-client/releases/tag/${src.tag}";
+    changelog = "https://github.com/pinecone-io/python-sdk/releases/tag/${src.tag}";
    license = lib.licenses.asl20;
    maintainers = with lib.maintainers; [ happysalada ];
  };
--- a/pkgs/development/r-modules/bioc-experiment-packages.json
+++ b/pkgs/development/r-modules/bioc-experiment-packages.json
@@ -587,9 +587,9 @@
    },
    "Hiiragi2013": {
      "name": "Hiiragi2013",
-      "version": "1.48.1",
-      "sha256": "0ariib3wsc6d7a0wkgp9j303id5a31zy4h38dwgb82hvvfp29q5z",
-      "depends": ["Biobase", "MASS", "RColorBrewer", "cluster", "genefilter", "gplots", "lattice", "latticeExtra"]
+      "version": "1.47.0",
+      "sha256": "1p2d6vpss2s61n82p6wy7nq86zjhfw0nw9wi8ws3hhq6nxs1h7pp",
+      "depends": ["Biobase", "KEGGREST", "MASS", "RColorBrewer", "affy", "boot", "clue", "cluster", "genefilter", "geneplotter", "gplots", "gtools", "lattice", "latticeExtra", "mouse4302_db", "xtable"]
    },
    "HumanAffyData": {
      "name": "HumanAffyData",
@@ -2343,12 +2343,6 @@
      "sha256": "0n66amxlcr9ddi8b7mjld4xjsqdca185nms32yi7nwqpz81ncjfk",
      "depends": ["Biobase", "oligo", "puma"]
    },
-    "qPLEXdata": {
-      "name": "qPLEXdata",
-      "version": "1.30.1",
-      "sha256": "190jaz16fd8h2njpyb151i83y6ygv8pa5nhiprh84bx6q25kgs3z",
-      "depends": ["MSnbase", "dplyr", "knitr", "qPLEXanalyzer"]
-    },
    "raerdata": {
      "name": "raerdata",
      "version": "1.10.0",
@@ -3020,6 +3014,13 @@
      "depends": ["ExperimentHub"],
      "broken": true
    },
+    "qPLEXdata": {
+      "name": "qPLEXdata",
+      "version": "1.27.0",
+      "sha256": "15fq5yzpipp2g7fx6nh766ykq84rr82yi6cccq7kqi9c1aywgwbf",
+      "depends": ["MSnbase", "dplyr", "knitr", "qPLEXanalyzer"],
+      "broken": true
+    },
    "rRDPData": {
      "name": "rRDPData",
      "version": "1.30.0",
--- a/pkgs/development/r-modules/bioc-packages.json
+++ b/pkgs/development/r-modules/bioc-packages.json
@@ -175,7 +175,7 @@
      "name": "ATACseqQC",
      "version": "1.36.0",
      "sha256": "1flikjhvjml25hwwhmm67ymch0ppmgxx12dl43rfw5y8bzb1gm7p",
-      "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "ChIPpeakAnno", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "GenomicScores", "IRanges", "KernSmooth", "Rsamtools", "S4Vectors", "edgeR", "limma", "motifStack", "randomForest", "rtracklayer"]
+      "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "ChIPpeakAnno", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "GenomicScores", "IRanges", "KernSmooth", "Rsamtools", "S4Vectors", "edgeR", "limma", "motifStack", "preseqR", "randomForest", "rtracklayer"]
    },
    "ATACseqTFEA": {
      "name": "ATACseqTFEA",
@@ -275,8 +275,8 @@
    },
    "AnVILGCP": {
      "name": "AnVILGCP",
-      "version": "1.6.2",
-      "sha256": "0fcqbh2ykbdjybbc1l893dk4s6v9ag1lpmhh04lpkn5zr4lb8jys",
+      "version": "1.6.0",
+      "sha256": "1z4nmvx0sjpby2m1z3a9mw8sg74xw5nihhcjq6dsfxkn997qd3j4",
      "depends": ["AnVILBase", "BiocBaseUtils", "GCPtools", "dplyr", "httr", "jsonlite", "rlang", "tibble", "tidyr"]
    },
    "AnVILPublish": {
@@ -317,8 +317,8 @@
    },
    "AnnotationHub": {
      "name": "AnnotationHub",
-      "version": "4.2.2",
-      "sha256": "0ai9m9yd0hs6vzgz4ri3vbnifd31ffzwy8fhaby9kzy9n51x92d5",
+      "version": "4.2.0",
+      "sha256": "0ra9cya4kln8fhsff0qbpp8fjx8i68ka9xrm2vjv2nw2yw8klzk4",
      "depends": ["AnnotationDbi", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "RSQLite", "S4Vectors", "curl", "dplyr", "httr2", "rappdirs", "yaml"]
    },
    "AnnotationHubData": {
@@ -365,8 +365,8 @@
    },
    "BASiCStan": {
      "name": "BASiCStan",
-      "version": "1.14.1",
-      "sha256": "0lrfzxjhvq0dhind9783q69r7kabrjj6nvv5kn2c8d986dz6n0p0",
+      "version": "1.14.0",
+      "sha256": "1224zcj5imy7r24w0qbmyb13yc4hf907d980nbp38yrv6ynw3in0",
      "depends": ["BASiCS", "BH", "Rcpp", "RcppEigen", "RcppParallel", "SingleCellExperiment", "StanHeaders", "SummarizedExperiment", "glmGamPoi", "rstan", "rstantools", "scran", "scuttle"]
    },
    "BBCAnalyzer": {
@@ -509,8 +509,8 @@
    },
    "BatChef": {
      "name": "BatChef",
-      "version": "1.0.2",
-      "sha256": "0qmg53dls168nfhlzvak5nx35wif0s5l4l9na1xpkd3iqpjif8fm",
+      "version": "1.0.1",
+      "sha256": "0n792nj9hs9vh9n25ckfav4birlgbn994wfki5gxckcd4k0bmf0a",
      "depends": ["Matrix", "RANN", "Rcpp", "RcppArmadillo", "S4Vectors", "Seurat", "SeuratObject", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "anndata", "aricode", "batchelor", "bluster", "cluster", "e1071", "fitdistrplus", "ggplot2", "harmony", "leidenAlg", "limma", "mclust", "purrr", "reticulate", "rliger", "scCustomize", "scMerge", "scrapper", "sf", "splatter", "sva", "transport", "zellkonverter"]
    },
    "BatchQC": {
@@ -659,8 +659,8 @@
    },
    "BiocBaseUtils": {
      "name": "BiocBaseUtils",
-      "version": "1.14.2",
-      "sha256": "1fijpvdy26sqqk3m16yan7k8yw5rky3dwy2adnchz1ql43dnixyi",
+      "version": "1.14.0",
+      "sha256": "143k126qn1n86kfqsbxwkamnph6hv1w52cqrsjk2ym4swp9794vc",
      "depends": []
    },
    "BiocBook": {
@@ -671,14 +671,14 @@
    },
    "BiocBuildReporter": {
      "name": "BiocBuildReporter",
-      "version": "1.0.1",
-      "sha256": "1kmy3lh4lp6raav8yzq7fk96bqgprslzi816vcj657glgiiir6aa",
+      "version": "1.0.0",
+      "sha256": "0zxrg8qizpr8vic7snazwvbfnhdcpxxvsampk1ryvs69iymi6zgn",
      "depends": ["BiocFileCache", "arrow", "dplyr"]
    },
    "BiocCheck": {
      "name": "BiocCheck",
-      "version": "1.48.1",
-      "sha256": "02df2w2b6ivj1j9fpjlvfgsccm9prwygyzc7ywdnbcfvmdjf115b",
+      "version": "1.48.0",
+      "sha256": "149avgqaslz276hhihr062agsgkar0imfyjg3in2xib7257dki3r",
      "depends": ["BiocBaseUtils", "BiocFileCache", "BiocManager", "biocViews", "callr", "cli", "codetools", "commonmark", "graph", "httr2", "knitr", "rvest", "stringdist", "xml2"]
    },
    "BiocFHIR": {
@@ -1211,8 +1211,8 @@
    },
    "CatsCradle": {
      "name": "CatsCradle",
-      "version": "1.6.1",
-      "sha256": "1slc2nfv168nbzyc55r6vhabnsxjbr9sw655w1nssrx3i7x3v5kx",
+      "version": "1.6.0",
+      "sha256": "0vhwcmdlsp1kji13sv18plrc6s7ql42njagc2qb5crmrh8rx295n",
      "depends": ["EBImage", "Matrix", "Rfast", "S4Vectors", "Seurat", "SeuratObject", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "abind", "data_table", "geometry", "ggplot2", "igraph", "msigdbr", "networkD3", "pheatmap", "pracma", "rdist", "reshape2", "stringr"]
    },
    "CausalR": {
@@ -1247,8 +1247,8 @@
    },
    "CellMentor": {
      "name": "CellMentor",
-      "version": "1.0.1",
-      "sha256": "0qyck58dbgglyfqdjn9y24ipmbib4mcqr3vzmvj8vh7iq93z5a8h",
+      "version": "1.0.0",
+      "sha256": "00cdp9qw5isx7bixw8cjxa3f24h0rqabz1bdxwsy4x99z3sn03nw",
      "depends": ["BiocParallel", "MLmetrics", "Matrix", "RMTstat", "Seurat", "SingleCellExperiment", "SingleR", "aricode", "cluster", "data_table", "entropy", "ggplot2", "irlba", "lsa", "magrittr", "nnls", "progress", "skmeans", "sparsesvd", "tibble"]
    },
    "CellMixS": {
@@ -1475,8 +1475,8 @@
    },
    "CoSIA": {
      "name": "CoSIA",
-      "version": "1.12.1",
-      "sha256": "1574vbv2xn9a1a1qbxvabidhk0zhsgihvdbypznvzbpj18bap9fr",
+      "version": "1.12.0",
+      "sha256": "1jgx62zla9jn1246hjvdgxx7k1605p7kgyv3wm24p4abxglxwy5y",
      "depends": ["AnnotationDbi", "ExperimentHub", "RColorBrewer", "annotationTools", "biomaRt", "dplyr", "ggplot2", "homologene", "magrittr", "org_Ce_eg_db", "org_Dm_eg_db", "org_Dr_eg_db", "org_Hs_eg_db", "org_Mm_eg_db", "org_Rn_eg_db", "plotly", "readr", "stringr", "tibble", "tidyr", "tidyselect"]
    },
    "Cogito": {
@@ -1901,8 +1901,8 @@
    },
    "DelayedArray": {
      "name": "DelayedArray",
-      "version": "0.38.2",
-      "sha256": "1zg3xy6bx76h429lvqvp2dv2dhix854w2ym4m55dygcfixgiklyr",
+      "version": "0.38.1",
+      "sha256": "1gpbamzchzqg1czpf0krkr3qpp1fkmj86kmjvg09gmq8l69qm1d6",
      "depends": ["BiocGenerics", "IRanges", "Matrix", "MatrixGenerics", "S4Arrays", "S4Vectors", "SparseArray"]
    },
    "DelayedDataFrame": {
@@ -2111,8 +2111,8 @@
    },
    "ENmix": {
      "name": "ENmix",
-      "version": "1.48.3",
-      "sha256": "1g9mdi2bmx12jsvcbrsp9mpyzrhr6a3n11hmgyn9za7dzibq7dnj",
+      "version": "1.48.0",
+      "sha256": "1rbv95gqhklm6mjl2d2cz7dfiyvgrzbsxnwdcynyi6a5zysn2zih",
      "depends": ["AnnotationHub", "Biobase", "ExperimentHub", "IRanges", "RPMM", "S4Vectors", "SummarizedExperiment", "doParallel", "dynamicTreeCut", "foreach", "genefilter", "geneplotter", "gplots", "gtools", "illuminaio", "impute", "irlba", "matrixStats", "minfi", "quadprog"]
    },
    "ERSSA": {
@@ -2387,8 +2387,8 @@
    },
    "GCPtools": {
      "name": "GCPtools",
-      "version": "1.2.1",
-      "sha256": "035fii0lrzqardv3dnb68vr5gnhx21xciqnigldm8wz0a41c71wq",
+      "version": "1.2.0",
+      "sha256": "1ajb8awl6l6af37dpn2zn8yi6wgc5kg61i3vx59jq2s8xvxwnf5r",
      "depends": ["AnVILBase", "BiocBaseUtils", "dplyr", "httr", "rlang", "tibble", "tidyr"]
    },
    "GDCRNATools": {
@@ -2489,8 +2489,8 @@
    },
    "GOSemSim": {
      "name": "GOSemSim",
-      "version": "2.38.3",
-      "sha256": "0i6nkhplfwim60qxs3f5n8pr5fz1pslw09f278vgc0sj6wy6q9b7",
+      "version": "2.38.0",
+      "sha256": "1bfrxb6zm9lms264wb4xzxdb50py97zdr6lh3mharzxnngbri4d7",
      "depends": ["AnnotationDbi", "DBI", "GO_db", "Rcpp", "digest", "rlang", "yulab_utils"]
    },
    "GOTHiC": {
@@ -2867,8 +2867,8 @@
    },
    "Glimma": {
      "name": "Glimma",
-      "version": "2.22.1",
-      "sha256": "1qks28b7skw8rzd2yd2xyhglxqscp5cpv0ffrnm57b83a6izy0i6",
+      "version": "2.21.0",
+      "sha256": "1n3x7nm65mszjz558zcfs8hrpc1wd0vf91xrh2r0pcjbgwqkmg9b",
      "depends": ["DESeq2", "S4Vectors", "SummarizedExperiment", "edgeR", "htmlwidgets", "jsonlite", "limma"]
    },
    "GloScope": {
@@ -2909,8 +2909,8 @@
    },
    "GraphExperiment": {
      "name": "GraphExperiment",
-      "version": "1.0.2",
-      "sha256": "0ayyfzq27a7w67w8qi9limpphpdg44503pf1kw43gh4apn4dcr5s",
+      "version": "1.0.0",
+      "sha256": "1ijqk2bxqmkqnqbnqqbx3vrwpy5csqwyh7mrnqgwc5a4xz2zqgih",
      "depends": ["BiocBaseUtils", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "igraph"]
    },
    "GreyListChIP": {
@@ -3167,8 +3167,8 @@
    },
    "HuBMAPR": {
      "name": "HuBMAPR",
-      "version": "1.6.2",
-      "sha256": "0hfxpmnkhspfv0cm0mmdzpzkndpijzdzjmmnbl8nj3pw0r1cwn55",
+      "version": "1.6.1",
+      "sha256": "0kvc79f23i91p2cv4wq618zbqvrp1s2x1dqkk912d59l96nrdf0n",
      "depends": ["dplyr", "httr2", "purrr", "rjsoncons", "rlang", "stringr", "tibble", "tidyr", "whisker"]
    },
    "HubPub": {
@@ -3193,7 +3193,7 @@
      "name": "IFAA",
      "version": "1.14.0",
      "sha256": "0r7ywvzw1vglaw485j1szz5wh2z6ff33rgzcsncpi9i2m0mfqhd2",
-      "depends": ["DescTools", "Matrix", "MatrixExtra", "S4Vectors", "SummarizedExperiment", "doParallel", "doRNG", "foreach", "glmnet", "mathjaxr", "parallelly", "stringr"]
+      "depends": ["DescTools", "HDCI", "Matrix", "MatrixExtra", "S4Vectors", "SummarizedExperiment", "doParallel", "doRNG", "foreach", "glmnet", "mathjaxr", "parallelly", "stringr"]
    },
    "IHW": {
      "name": "IHW",
@@ -3331,7 +3331,7 @@
      "name": "InPAS",
      "version": "2.20.0",
      "sha256": "1fwqg8a9zhbkblhvghqqv7idiav4z2iw7kswx1man31hbgc76fwr",
-      "depends": ["AnnotationDbi", "BSgenome", "Biobase", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "Seqinfo", "batchtools", "cleanUpdTSeq", "dplyr", "flock", "future", "future_apply", "ggplot2", "limma", "magrittr", "parallelly", "plyranges", "preprocessCore", "readr", "reshape2"]
+      "depends": ["AnnotationDbi", "BSgenome", "Biobase", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "Seqinfo", "batchtools", "cleanUpdTSeq", "depmixS4", "dplyr", "flock", "future", "future_apply", "ggplot2", "limma", "magrittr", "parallelly", "plyranges", "preprocessCore", "readr", "reshape2"]
    },
    "InTAD": {
      "name": "InTAD",
@@ -3413,8 +3413,8 @@
    },
    "KEGGREST": {
      "name": "KEGGREST",
-      "version": "1.52.2",
-      "sha256": "1jp9b8r51z3a8644xclk165rmkd6gj9lfj4j7v73dj5a67prhslf",
+      "version": "1.52.0",
+      "sha256": "1z9xp4pkpqcyadbrzam7qxqcrrqy29pn926n3nqni6cpypbv7jj4",
      "depends": ["Biostrings", "httr", "png"]
    },
    "KEGGgraph": {
@@ -3983,9 +3983,9 @@
    },
    "MeLSI": {
      "name": "MeLSI",
-      "version": "1.0.1",
-      "sha256": "02k9qbbss9lrzrradxnlh8wz44wqs3g70pigs0314hgy3q1zqmnb",
-      "depends": ["Rcpp", "ggplot2"]
+      "version": "1.0.0",
+      "sha256": "09nmljg69s80851vl3frzdc6xp36rnkhga1r6nf90i0ildky848b",
+      "depends": ["ggplot2", "phyloseq", "vegan"]
    },
    "MeSHDbi": {
      "name": "MeSHDbi",
@@ -4187,8 +4187,8 @@
    },
    "Moonlight2R": {
      "name": "Moonlight2R",
-      "version": "1.10.1",
-      "sha256": "0w996b523823w8838r7a4drckpny43p7sar08ix46d65sxzi5cr9",
+      "version": "1.10.0",
+      "sha256": "1c8lin5gf4k7kyqs7gcp1hbx890wd01xihjgc33qzmlhnm0d293y",
      "depends": ["AnnotationHub", "Biobase", "BiocGenerics", "ComplexHeatmap", "DOSE", "EpiMix", "ExperimentHub", "GEOquery", "GenomicRanges", "HiveR", "RColorBrewer", "RISmed", "circlize", "clusterProfiler", "data_table", "doParallel", "dplyr", "easyPubMed", "fgsea", "foreach", "fuzzyjoin", "ggplot2", "gplots", "magrittr", "org_Hs_eg_db", "parmigene", "purrr", "qpdf", "randomForest", "readr", "rlang", "rtracklayer", "seqminer", "stringr", "tibble", "tidyHeatmap", "tidyr", "withr"]
    },
    "MoonlightR": {
@@ -4859,8 +4859,8 @@
    },
    "PhyloProfile": {
      "name": "PhyloProfile",
-      "version": "2.4.1",
-      "sha256": "10bjv6zjal5wszqrmr0xcg5c38dvr7ilwngaf5mlf9gsf3j97m83",
+      "version": "2.4.0",
+      "sha256": "1nra87n4pnzy8shg7s2gg82n4xrczdvfafqmi0i9iywgbm5f47i5",
      "depends": ["BiocStyle", "Biostrings", "DT", "RColorBrewer", "RCurl", "Rfast", "ape", "bioDist", "bsplus", "colourpicker", "data_table", "dplyr", "energy", "fastcluster", "ggplot2", "gridExtra", "htmlwidgets", "pbapply", "plotly", "scattermore", "shiny", "shinyFiles", "shinycssloaders", "shinyjs", "stringr", "svglite", "tsne", "umap", "xml2", "yaml", "zoo"]
    },
    "Pigengene": {
@@ -5411,8 +5411,8 @@
    },
    "Rarr": {
      "name": "Rarr",
-      "version": "2.0.1",
-      "sha256": "1m8sgy7pfqpyf5ipjdzc1zgxsnz9k5jzxvhawk84csyz9azgy2wf",
+      "version": "2.0.0",
+      "sha256": "1mygyari0xinmw7kiwb258z4f3qjkm4bvhjqm9hl89jc7qx356s0",
      "depends": ["R_utils", "curl", "jsonlite", "lifecycle", "paws_storage"]
    },
    "RbcBook1": {
@@ -5531,8 +5531,8 @@
    },
    "Rega": {
      "name": "Rega",
-      "version": "1.0.2",
-      "sha256": "0zfc86qjhlhhv5g6f8xwdf50yyg1p7p66fprgmhrpb0ggp7f53fg",
+      "version": "1.0.0",
+      "sha256": "184cxjfm0hiik4d3l4fylch0m7gg0wyv7gj9hdkasf8vj57fqy2s",
      "depends": ["askpass", "httr2", "jsonlite", "jsonvalidate", "keyring", "readxl", "rlang", "stringr", "tibble", "tidyr", "validate", "yaml"]
    },
    "RegionalST": {
@@ -5927,9 +5927,9 @@
    },
    "SPONGE": {
      "name": "SPONGE",
-      "version": "1.34.1",
-      "sha256": "03iiwv7kf7kj94fbnshvlqd6ldsj0b49g2vvpl0c1ggrbmkcc1xp",
-      "depends": ["Biobase", "ComplexHeatmap", "MASS", "MetBrewer", "biomaRt", "caret", "cvms", "data_table", "doRNG", "dplyr", "expm", "foreach", "gRbase", "ggplot2", "ggpubr", "ggridges", "glmnet", "igraph", "iterators", "logger", "ppcor", "randomForest", "rlang", "stringr", "tibble", "tidyr", "tnet"]
+      "version": "1.34.0",
+      "sha256": "0q5pngbdj2n3bz706qzs7smcs23a4avx6fp6p6zsxygwbmv1679k",
+      "depends": ["Biobase", "ComplexHeatmap", "MASS", "MetBrewer", "biomaRt", "caret", "cvms", "data_table", "doRNG", "dplyr", "expm", "foreach", "gRbase", "ggplot2", "ggpubr", "ggridges", "glmnet", "igraph", "iterators", "logging", "ppcor", "randomForest", "rlang", "stringr", "tidyr", "tidyverse", "tnet"]
    },
    "SPOTlight": {
      "name": "SPOTlight",
@@ -6035,8 +6035,8 @@
    },
    "SeqArray": {
      "name": "SeqArray",
-      "version": "1.52.1",
-      "sha256": "00sdj7xr8rlb22c51c1dbb0hfh1fza729ngmzhsdxi032asi10b0",
+      "version": "1.52.0",
+      "sha256": "1nk1xbm10057abm3x5f1z8p0pylr1rhcjbkjvrj0ks85m627i2wf",
      "depends": ["Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "digest", "gdsfmt"]
    },
    "SeqGSEA": {
@@ -6257,8 +6257,8 @@
    },
    "Spectra": {
      "name": "Spectra",
-      "version": "1.22.2",
-      "sha256": "0zpy23zr8vzji4g05y51hfc9snf9l8zb4bbg5pyh6jzvqj6m759a",
+      "version": "1.22.0",
+      "sha256": "19310y9g2jp3a75a1k4yb4b8n306b7pbhycwjgwrhpvn2xxz5lz4",
      "depends": ["BiocGenerics", "BiocParallel", "IRanges", "MetaboCoreUtils", "MsCoreUtils", "ProtGenerics", "S4Vectors", "data_table", "fs"]
    },
    "SpectraQL": {
@@ -6271,7 +6271,7 @@
      "name": "SpectralTAD",
      "version": "1.28.0",
      "sha256": "1nxl509zd4fxmx5sq5w324wdll61nchi62ivv2wcq2lz7h7hfl25",
-      "depends": ["BiocParallel", "GenomicRanges", "HiCcompare", "Matrix", "cluster", "dplyr", "magrittr"]
+      "depends": ["BiocParallel", "GenomicRanges", "HiCcompare", "Matrix", "PRIMME", "cluster", "dplyr", "magrittr"]
    },
    "SpectriPy": {
      "name": "SpectriPy",
@@ -6409,7 +6409,7 @@
      "name": "TADCompare",
      "version": "1.22.0",
      "sha256": "05lrx7qhkybnw9x8i35xsnrbgb3riwiqqb9n7n60jr2sadlm1cwm",
-      "depends": ["HiCcompare", "Matrix", "RColorBrewer", "cluster", "cowplot", "dplyr", "ggplot2", "ggpubr", "magrittr", "reshape2", "tidyr"]
+      "depends": ["HiCcompare", "Matrix", "PRIMME", "RColorBrewer", "cluster", "cowplot", "dplyr", "ggplot2", "ggpubr", "magrittr", "reshape2", "tidyr"]
    },
    "TAPseq": {
      "name": "TAPseq",
@@ -6437,8 +6437,8 @@
    },
    "TCGAutils": {
      "name": "TCGAutils",
-      "version": "1.32.2",
-      "sha256": "1rphdzyr8f9z5z7i1lryjzcv0g1m1dj8ygx7jahdjwf3f4819m5d",
+      "version": "1.32.0",
+      "sha256": "1skm8rlsrc9k95z0zglc82622sjjxq19wxwm55vyq7450gnw2n0k",
      "depends": ["AnnotationDbi", "BiocBaseUtils", "BiocGenerics", "GenomeInfoDb", "GenomicDataCommons", "GenomicFeatures", "GenomicRanges", "IRanges", "MultiAssayExperiment", "RaggedExperiment", "S4Vectors", "Seqinfo", "SummarizedExperiment", "glue", "rvest", "stringr", "xml2"]
    },
    "TCseq": {
@@ -7049,8 +7049,8 @@
    },
    "alabaster_base": {
      "name": "alabaster.base",
-      "version": "1.12.1",
-      "sha256": "114q6vcy45w8y5ir7x0wwzd27l2n2sn041z38vnd9641ih0pw1xc",
+      "version": "1.12.0",
+      "sha256": "08bs3jiv355035kdzsjwn8zd0lwdlz0jy3l33y70j1pjq2ss0zzb",
      "depends": ["Rcpp", "Rhdf5lib", "S4Vectors", "alabaster_schemas", "assorthead", "jsonlite", "jsonvalidate", "rhdf5"]
    },
    "alabaster_bumpy": {
@@ -7271,8 +7271,8 @@
    },
    "assorthead": {
      "name": "assorthead",
-      "version": "1.6.3",
-      "sha256": "0vh175mpwmdjw30if09ddzlnvrh8r8lr2gxi5l0bjhwxc2xhdhvm",
+      "version": "1.6.1",
+      "sha256": "1j3c29d0j9612ayjy18q3clqdq85lym1y0gfq0vnl72jcwpzdynh",
      "depends": []
    },
    "asuri": {
@@ -8759,8 +8759,8 @@
    },
    "edgeR": {
      "name": "edgeR",
-      "version": "4.10.1",
-      "sha256": "0yh5w155izrzby1p4nyiwlxzzy2jha8dri6w94831kz1lvl8wgkg",
+      "version": "4.10.0",
+      "sha256": "0qd089xydha4vx2hdg9yzy1zc8hr29qaf804rj79gfh8krih4bxh",
      "depends": ["limma", "locfit"]
    },
    "eds": {
@@ -8801,8 +8801,8 @@
    },
    "ensembldb": {
      "name": "ensembldb",
-      "version": "2.36.1",
-      "sha256": "1rzx68kk6rfjlrax8yqyasx8dw4sgwngd7w99cylxzbq9fxh5ynn",
+      "version": "2.36.0",
+      "sha256": "1x5yxmsbvrd9a60jc2cmybr5kd5jw3d187312afflwjl08p7y4vq",
      "depends": ["AnnotationDbi", "AnnotationFilter", "Biobase", "BiocGenerics", "Biostrings", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "ProtGenerics", "RSQLite", "Rsamtools", "S4Vectors", "Seqinfo", "curl", "rtracklayer"]
    },
    "epiNEM": {
@@ -8951,8 +8951,8 @@
    },
    "extraChIPs": {
      "name": "extraChIPs",
-      "version": "1.16.2",
-      "sha256": "0zmnqhraa58y5vap1jp92bjxjdihfib7xd2x260dx4p7mcd4yr8r",
+      "version": "1.16.1",
+      "sha256": "1m4fzj5bmd5dh44nz0as6a4a5pkrijp3p542y5dq5pyafisl1a5v",
      "depends": ["BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "RColorBrewer", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "csaw", "dplyr", "edgeR", "forcats", "ggplot2", "ggrepel", "ggside", "glue", "matrixStats", "patchwork", "rlang", "rtracklayer", "scales", "stringr", "tibble", "tidyr", "tidyselect", "vctrs"]
    },
    "fCCAC": {
@@ -9047,8 +9047,8 @@
    },
    "fenr": {
      "name": "fenr",
-      "version": "1.10.1",
-      "sha256": "0b6s97laal3lc5fibhz4fb40fi5gwlpx3kv3yl5rv0pscq36j73l",
+      "version": "1.10.0",
+      "sha256": "0982ibfn3j8g4ccra40yd0knwigvj7jaq2zpx3ivd0ra5phr49vw",
      "depends": ["BiocFileCache", "assertthat", "dplyr", "ggplot2", "httr2", "progress", "purrr", "readr", "rlang", "rvest", "shiny", "stringr", "tibble", "tidyr", "tidyselect"]
    },
    "ffpe": {
@@ -9155,8 +9155,8 @@
    },
    "flowGate": {
      "name": "flowGate",
-      "version": "1.12.1",
-      "sha256": "1lq1qripvykp27m9llyy2jlpci37aj5c3hfhd7i3sflfgdyf929i",
+      "version": "1.12.0",
+      "sha256": "0xd511igjmj1bb4g8kw4557cy1kj377gklwkm6dlhfkigi7m398y",
      "depends": ["BiocManager", "dplyr", "flowCore", "flowWorkspace", "ggcyto", "ggplot2", "purrr", "rlang", "shiny", "tibble"]
    },
    "flowGraph": {
@@ -9383,8 +9383,8 @@
    },
    "gatom": {
      "name": "gatom",
-      "version": "1.10.2",
-      "sha256": "1c9w586rci3l5mhlzhkb8afgpb5hc3b2hxagqf1fbkivqiq6hj48",
+      "version": "1.10.0",
+      "sha256": "0lvyd3bjwzvs0alzxs2zzmsd432f45a2x38c28n7qlx4ckgd0g2h",
      "depends": ["BioNet", "XML", "data_table", "ggnetwork", "ggplot2", "htmltools", "htmlwidgets", "igraph", "intergraph", "mwcsr", "network", "plyr", "scales", "shinyCyJS", "sna"]
    },
    "gcapc": {
@@ -9407,8 +9407,8 @@
    },
    "gdsfmt": {
      "name": "gdsfmt",
-      "version": "1.48.2",
-      "sha256": "1clql2dqr1gr8jh6ddn9cbrb5aj4f96z9yvn1hxxp87fs3kiym91",
+      "version": "1.48.1",
+      "sha256": "001l93k5912fgiqp7a6h1lmlxvwn5kbgs1cal9qyl2v1i5q6ggbr",
      "depends": []
    },
    "geNetClassifier": {
@@ -9611,8 +9611,8 @@
    },
    "ggtreeExtra": {
      "name": "ggtreeExtra",
-      "version": "1.22.1",
-      "sha256": "17zlm3bpibd18qbs8s6w84j8kpb2zm5b2n0lzj1rgnyq6cb6vxhj",
+      "version": "1.22.0",
+      "sha256": "196hz0xxaqmipqkv51q4w3fsv8rc6yxn6svgyzxxq6zn1wlwhqwn",
      "depends": ["cli", "ggnewscale", "ggplot2", "ggtree", "magrittr", "rlang", "tidytree", "yulab_utils"]
    },
    "ggtreeSpace": {
@@ -10067,8 +10067,8 @@
    },
    "igblastr": {
      "name": "igblastr",
-      "version": "1.2.12",
-      "sha256": "1xbnnzdi5nrc60v9w4xgp5f6nr7fpgzwy6wpx78djxf8w605g3bc",
+      "version": "1.2.2",
+      "sha256": "0g6qirgvgpqpmklw2n2y19mjirp2djx8vvxaaqfx8pf17c20fh14",
      "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "IRanges", "R_utils", "S4Vectors", "curl", "httr", "jsonlite", "rvest", "tibble", "xml2", "xtable"]
    },
    "igvR": {
@@ -10337,8 +10337,8 @@
    },
    "limma": {
      "name": "limma",
-      "version": "3.68.4",
-      "sha256": "0452k5p1v01qjzk6jlip6ix871dfyn0prvxjxpjxdnjl4zbkrz3v",
+      "version": "3.68.3",
+      "sha256": "0xvqvp8582n890ndjx656qpgkyncfrcsy887a2k9ff1sm19q2dhx",
      "depends": ["statmod"]
    },
    "limmaGUI": {
@@ -11075,8 +11075,8 @@
    },
    "motifTestR": {
      "name": "motifTestR",
-      "version": "1.8.1",
-      "sha256": "0mcxcr45d08lq0rdxbisc9niwqhqcrdc5b2aky955di86asdh3nl",
+      "version": "1.8.0",
+      "sha256": "1y40m4pldm1q3iwa24j8h9yvknj0d826w186mkf809xmscy2xk02",
      "depends": ["Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "ggplot2", "harmonicmeanp", "matrixStats", "patchwork", "rlang", "universalmotif"]
    },
    "motifcounter": {
@@ -11653,7 +11653,7 @@
      "name": "partCNV",
      "version": "1.9.0",
      "sha256": "0ln46gcj4mxpqf2v46zgsxn8lx1b2zw31bjhc0vwm9c2wcs08nfd",
-      "depends": ["AnnotationHub", "BiocStyle", "GenomicRanges", "Seurat", "SingleCellExperiment", "data_table", "magrittr"]
+      "depends": ["AnnotationHub", "BiocStyle", "GenomicRanges", "Seurat", "SingleCellExperiment", "data_table", "depmixS4", "magrittr"]
    },
    "pathMED": {
      "name": "pathMED",
@@ -11825,8 +11825,8 @@
    },
    "pipeComp": {
      "name": "pipeComp",
-      "version": "1.22.1",
-      "sha256": "06hzffzg73x90zw9czjqvw1z432n5nq5bc749bi4syb0n4r9zw16",
+      "version": "1.22.0",
+      "sha256": "19qzv5060a9vf1p25iwryv6adfpbdbzh2h1smv6i1wb3zr374x1a",
      "depends": ["BiocParallel", "ComplexHeatmap", "Matrix", "RColorBrewer", "Rtsne", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "aricode", "circlize", "clue", "cluster", "cowplot", "dplyr", "ggplot2", "intrinsicDimension", "knitr", "matrixStats", "randomcoloR", "reshape2", "scales", "scater", "scran", "uwot", "viridisLite"]
    },
    "pipeFrame": {
@@ -12027,12 +12027,6 @@
      "sha256": "0lf2yb97a2a2zx93cwkrr782zirdsdwcm34vj88z78wgr922mmda",
      "depends": ["BiocGenerics", "Rcpp"]
    },
-    "profileplyr": {
-      "name": "profileplyr",
-      "version": "1.28.3",
-      "sha256": "1qvd02br16xjbs0vd0c18a4rxfvjzij6fh0ibdf2iyigh6fn00q4",
-      "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "ChIPseeker", "ComplexHeatmap", "EnrichedHeatmap", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "R_utils", "Rsamtools", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "TxDb_Mmusculus_UCSC_mm10_knownGene", "TxDb_Mmusculus_UCSC_mm9_knownGene", "circlize", "dplyr", "ggplot2", "magrittr", "org_Hs_eg_db", "org_Mm_eg_db", "pheatmap", "plyranges", "rGREAT", "rjson", "rlang", "rtracklayer", "tidyr", "tiff", "txdbmaker"]
-    },
    "progeny": {
      "name": "progeny",
      "version": "1.34.0",
@@ -12059,8 +12053,8 @@
    },
    "psichomics": {
      "name": "psichomics",
-      "version": "1.38.1",
-      "sha256": "1phvwnb0mzikhj1mj76p1ymlrdv80ahqb8kg7cana6v6m6c1lg4d",
+      "version": "1.38.0",
+      "sha256": "1fxrhxb9nidg3dq2qm45sa0dnsqg2pcwp74a5ybpm61kj7bfihqn",
      "depends": ["AnnotationDbi", "AnnotationHub", "BiocFileCache", "DT", "R_utils", "Rcpp", "Rfast", "SummarizedExperiment", "XML", "cluster", "colourpicker", "data_table", "digest", "dplyr", "edgeR", "fastICA", "fastmatch", "ggplot2", "ggrepel", "highcharter", "htmltools", "httr", "jsonlite", "limma", "pairsD3", "plyr", "purrr", "recount", "reshape2", "shiny", "shinyBS", "shinyjs", "stringr", "survival", "xtable"]
    },
    "ptairMS": {
@@ -12395,9 +12389,9 @@
    },
    "rfaRm": {
      "name": "rfaRm",
-      "version": "1.24.1",
-      "sha256": "1jam21z522ara21xr8yhwsxg0w7mi9w3qmys65mnly1ry25s79hi",
-      "depends": ["Biostrings", "IRanges", "S4Vectors", "data_table", "httr", "magick", "rsvg", "rvest", "stringi", "xml2"]
+      "version": "1.23.0",
+      "sha256": "1v4zv4spfvnj4wsq5bkcv4mf0xl4g98n87b3xrl4w2lyr6s2sg19",
+      "depends": ["Biostrings", "IRanges", "S4Vectors", "data_table", "httr", "jsonlite", "magick", "rsvg", "rvest", "stringi", "xml2"]
    },
    "rgoslin": {
      "name": "rgoslin",
@@ -12419,8 +12413,8 @@
    },
    "rhdf5client": {
      "name": "rhdf5client",
-      "version": "1.34.2",
-      "sha256": "1147i9164kvh01fkginqjmrshbq7bd66mjih1iv6nvgwc81w2n02",
+      "version": "1.34.0",
+      "sha256": "1vmw9zcsrw5kj02k3syvwxk4xvkaawqjhjk7z3h2fap8mg7h08z0",
      "depends": ["DelayedArray", "data_table", "httr", "rjson"]
    },
    "rhdf5filters": {
@@ -12695,9 +12689,9 @@
    },
    "scDblFinder": {
      "name": "scDblFinder",
-      "version": "1.26.7",
-      "sha256": "0ng0mvcl9ydnfp7bc62mskp6ih7q68vpfnj3x51c9sncjwypb6s2",
-      "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "Matrix", "Rsamtools", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bluster", "igraph", "rtracklayer", "scater", "scran", "scrapper", "scuttle", "xgboost"]
+      "version": "1.26.0",
+      "sha256": "1hdzipp4ncc474la668yrickazv4apwks3jg7rbsc368c8hxvwfh",
+      "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "Matrix", "Rsamtools", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bluster", "igraph", "rtracklayer", "scater", "scran", "scuttle", "xgboost"]
    },
    "scDesign3": {
      "name": "scDesign3",
@@ -12719,8 +12713,8 @@
    },
    "scECODA": {
      "name": "scECODA",
-      "version": "1.0.1",
-      "sha256": "0vcqyxzzybcs7a5gbrb785vbagqdcyqwad84x2nhdnrqj4q7rr5w",
+      "version": "1.0.0",
+      "sha256": "1lglmsinwpmwb48547bphd0fpl2c6qcjvnm36a1vib2w5qydx5id",
      "depends": ["BiocGenerics", "DESeq2", "Matrix", "S4Vectors", "SummarizedExperiment", "cluster", "corrplot", "dplyr", "factoextra", "ggplot2", "ggpubr", "ggrepel", "gtools", "mclust", "pheatmap", "plotly", "rlang", "rstatix", "stringr", "tidyr", "vegan"]
    },
    "scFeatureFilter": {
@@ -12785,8 +12779,8 @@
    },
    "scMitoMut": {
      "name": "scMitoMut",
-      "version": "1.8.0",
-      "sha256": "0p39pcm68hwm557i7wqi2s4wsy5xrzzm43ivmwq5hn1f874whz8h",
+      "version": "1.7.0",
+      "sha256": "1h4hpg1h0f39fhlffz7lw9a2ryrbygicnaz13r50lmwjqqmj41v4",
      "depends": ["RColorBrewer", "Rcpp", "RcppArmadillo", "data_table", "ggplot2", "magrittr", "pheatmap", "plyr", "readr", "rhdf5", "stringr"]
    },
    "scMultiSim": {
@@ -12835,7 +12829,7 @@
      "name": "scRecover",
      "version": "1.28.0",
      "sha256": "0mp91i8ar6blbilamm7gblcyj1zkah74y5mdv7z71jhvzh6rijmi",
-      "depends": ["BiocParallel", "MASS", "Matrix", "SAVER", "bbmle", "doParallel", "foreach", "gamlss", "kernlab", "penalized", "pscl", "rsvd"]
+      "depends": ["BiocParallel", "MASS", "Matrix", "SAVER", "bbmle", "doParallel", "foreach", "gamlss", "kernlab", "penalized", "preseqR", "pscl", "rsvd"]
    },
    "scRepertoire": {
      "name": "scRepertoire",
@@ -12905,9 +12899,9 @@
    },
    "scater": {
      "name": "scater",
-      "version": "1.40.2",
-      "sha256": "0ra4pkm7ikdd8w3kgb5dqv2di3yw0p4wsizqna55c17g3ila14cm",
-      "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "Matrix", "MatrixGenerics", "RColorBrewer", "RcppML", "Rtsne", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "beachmat", "ggbeeswarm", "ggplot2", "ggrepel", "pheatmap", "rlang", "scuttle", "uwot", "viridis"]
+      "version": "1.40.1",
+      "sha256": "0kd72ba3nbrrmbphlznrhm937jz9l7lav7qrrvawlp7xlrpq6izf",
+      "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "Matrix", "MatrixGenerics", "RColorBrewer", "RcppML", "Rtsne", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "beachmat", "ggbeeswarm", "ggplot2", "ggrastr", "ggrepel", "pheatmap", "rlang", "scuttle", "uwot", "viridis"]
    },
    "scatterHatch": {
      "name": "scatterHatch",
@@ -13109,8 +13103,8 @@
    },
    "sesame": {
      "name": "sesame",
-      "version": "1.30.1",
-      "sha256": "09g9aw0drswg80g10427739sg8birkalscpq22v11srx31483hvd",
+      "version": "1.30.0",
+      "sha256": "081rjiqip0aqxc23pvzp0vwiyn7lnca2z33jyan629w70nfxy2bb",
      "depends": ["BiocFileCache", "BiocParallel", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "Seqinfo", "SummarizedExperiment", "dplyr", "ggplot2", "preprocessCore", "readr", "reshape2", "sesameData", "stringr", "tibble", "wheatmap"]
    },
    "sevenC": {
@@ -13705,7 +13699,7 @@
      "name": "tLOH",
      "version": "1.19.0",
      "sha256": "0p6vpkj8v749jxrhbldkrl0rci26pbg8cwic0zj1irp3k0rxpds8",
-      "depends": ["GenomicRanges", "MatrixGenerics", "VariantAnnotation", "bestNormalize", "data_table", "dplyr", "ggplot2", "naniar", "purrr", "scales", "stringr"]
+      "depends": ["GenomicRanges", "MatrixGenerics", "VariantAnnotation", "bestNormalize", "data_table", "depmixS4", "dplyr", "ggplot2", "naniar", "purrr", "scales", "stringr"]
    },
    "tRNA": {
      "name": "tRNA",
@@ -13955,8 +13949,8 @@
    },
    "transmogR": {
      "name": "transmogR",
-      "version": "1.8.1",
-      "sha256": "0fbgzdb3kz5cwp1l7wp8fays9nyiq5i1ympr2r236vf6m4yzlv25",
+      "version": "1.8.0",
+      "sha256": "1pc0k73k1ls9v7iqlb0khmvcylds2cs0y1s46pjaw1hk3aq37r8l",
      "depends": ["BSgenome", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "data_table", "ggplot2", "jsonlite", "matrixStats", "patchwork", "scales"]
    },
    "transomics2cytoscape": {
@@ -17716,6 +17710,13 @@
      "depends": ["Biobase", "BiocParallel", "minpack_lm", "missForest", "pracma", "ropls", "xcms"],
      "broken": true
    },
+    "profileplyr": {
+      "name": "profileplyr",
+      "version": "1.24.1",
+      "sha256": "02y423r6g9bi7g5izvrwmxmrxrkyah8496pdrm1xhq97i9k8pdba",
+      "depends": ["BiocGenerics", "BiocParallel", "ChIPseeker", "ComplexHeatmap", "EnrichedHeatmap", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "R_utils", "Rsamtools", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "TxDb_Mmusculus_UCSC_mm10_knownGene", "TxDb_Mmusculus_UCSC_mm9_knownGene", "circlize", "dplyr", "ggplot2", "magrittr", "org_Hs_eg_db", "org_Mm_eg_db", "pheatmap", "rGREAT", "rjson", "rlang", "rtracklayer", "soGGi", "tidyr", "tiff"],
+      "broken": true
+    },
    "prot2D": {
      "name": "prot2D",
      "version": "1.8.0",
--- a/pkgs/development/r-modules/cran-packages.json
+++ b/pkgs/development/r-modules/cran-packages.json
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
--- a/pkgs/development/r-modules/generic-builder.nix
+++ b/pkgs/development/r-modules/generic-builder.nix
@@ -38,14 +38,8 @@ stdenv.mkDerivation (

    configurePhase = ''
      runHook preConfigure
-
      export MAKEFLAGS+="''${enableParallelBuilding:+-j$NIX_BUILD_CORES}"
      export R_LIBS_SITE="$R_LIBS_SITE''${R_LIBS_SITE:+:}$out/library"
-
-      if [ -f ./configure ] && [ -z "''${dontPatchShebangsInConfigure:-}" ]; then
-        patchShebangs --build ./configure
-      fi
-
      runHook postConfigure
    '';

--- a/pkgs/development/rocq-modules/hierarchy-builder/default.nix
+++ b/pkgs/development/rocq-modules/hierarchy-builder/default.nix
@@ -17,7 +17,7 @@ let
      in
      with lib.versions;
      lib.switch rocq-core.rocq-version [
-        (case (range "9.0" "9.2") "1.10.3")
+        (case (range "9.0" "9.3") "1.10.3")
        (case (range "9.0" "9.1") "1.10.2")
        (case (range "9.0" "9.1") "1.10.0")
        (case (range "9.0" "9.1") "1.9.1")
--- a/pkgs/development/rocq-modules/mathcomp-bigenough/default.nix
+++ b/pkgs/development/rocq-modules/mathcomp-bigenough/default.nix
@@ -25,7 +25,7 @@ mkRocqDerivation {
    in
    with lib.versions;
    lib.switch rocq-core.rocq-version [
-      (case (range "9.0" "9.2") "1.0.4")
+      (case (range "9.0" "9.3") "1.0.4")
    ] null;

  propagatedBuildInputs = [ mathcomp-boot ];
--- a/pkgs/development/rocq-modules/mathcomp-finmap/default.nix
+++ b/pkgs/development/rocq-modules/mathcomp-finmap/default.nix
@@ -29,7 +29,7 @@ mkRocqDerivation {
    lib.switch
      [ rocq-core.rocq-version mathcomp-boot.version ]
      [
-        (case (range "9.2" "9.2") (range "2.5" "2.6") "2.2.4") # also compiles on Rocq 9.0 and 9.1 (but requires graph-theory update)
+        (case (range "9.2" "9.3") (range "2.5" "2.6") "2.2.4") # also compiles on Rocq 9.0 and 9.1 (but requires graph-theory update)
        (case (range "9.0" "9.1") (range "2.3" "2.5") "2.2.2")
      ]
      null;
--- a/pkgs/development/rocq-modules/mathcomp-real-closed/default.nix
+++ b/pkgs/development/rocq-modules/mathcomp-real-closed/default.nix
@@ -35,7 +35,7 @@ mkRocqDerivation {
    lib.switch
      [ rocq-core.version mathcomp.version ]
      [
-        (case (range "9.0" "9.2") (isGe "2.6.0") "2.0.6")
+        (case (range "9.0" "9.3") (isGe "2.6.0") "2.0.6")
        (case (range "9.0" "9.2") (isEq "2.5.0") "2.0.5")
      ]
      null;
--- a/pkgs/development/rocq-modules/mathcomp/default.nix
+++ b/pkgs/development/rocq-modules/mathcomp/default.nix
@@ -35,7 +35,7 @@ let
      inherit (lib.versions) range;
    in
    lib.switch rocq-core.rocq-version [
-      (case (range "9.2" "9.2") "2.6.0") # also compiles on Rocq 9.0 and 9.1
+      (case (range "9.2" "9.3") "2.6.0") # also compiles on Rocq 9.0 and 9.1
      (case (range "9.0" "9.1") "2.5.0")
    ] null;
  release = {
--- a/pkgs/development/rocq-modules/micromega-plugin/default.nix
+++ b/pkgs/development/rocq-modules/micromega-plugin/default.nix
@@ -15,10 +15,12 @@ mkRocqDerivation {
    in
    with lib.versions;
    lib.switch rocq-core.rocq-version [
+      (case (range "9.0" "9.3") "1.1.1")
      (case (range "9.0" "9.2") "1.1.0")
    ] null;

  release = {
+    "1.1.1".hash = "sha256-TIUbrMRoPkLx3QcBGTAEdnzqt4HcKOHaQwJWUtBXUQA=";
    "1.1.0".hash = "sha256-CWMbGErC5bu20Yu9eskgslLkzmSof6klNlOYEkQjUjc=";
  };
  releaseRev = v: "v${v}";
--- a/pkgs/development/rocq-modules/rocq-elpi/default.nix
+++ b/pkgs/development/rocq-modules/rocq-elpi/default.nix
@@ -17,7 +17,7 @@ let
      in
      with lib.versions;
      lib.switch rocq-core.rocq-version [
-        (case (range "9.0" "9.2") "3.7.1")
+        (case (range "9.0" "9.3") "3.7.1")
        (case (range "9.0" "9.1") "3.4.5")
        (case (range "9.0" "9.1") "2.0.7")
      ] rocq-core.ocamlPackages.elpi.version;
@@ -37,11 +37,13 @@ let
      in
      with lib.versions;
      lib.switch rocq-core.rocq-version [
+        (case (range "9.0" "9.3") "3.5.0")
        (case (range "9.0" "9.2") "3.4.0")
        (case (range "9.0" "9.1") "3.2.0")
        (case (range "9.0" "9.1") "2.6.0")
        (case "9.0" "2.5.2")
      ] null;
+    release."3.5.0".sha256 = "sha256-k6kbkFRngQmKUP0owiFOxJzdJVRte5IlZWG4Tpqd3YU=";
    release."3.4.0".sha256 = "sha256-8x2Sa/+pUpXEqB+NdyfOyw6Yyzp6Q1k5LnhrjG/qJNM=";
    release."3.3.0".sha256 = "sha256-wcsUpw7S+H9CaXuz+W3g22IFWO2cLllJ4xm2qLTG0nM=";
    release."3.2.0".sha256 = "sha256-FyYG/8lEyt1L/paMez8jYAnnUE+sxIp4Da5MztmwJ/c=";
--- a/pkgs/development/rocq-modules/rocqnavi/default.nix
+++ b/pkgs/development/rocq-modules/rocqnavi/default.nix
@@ -17,7 +17,7 @@ mkRocqDerivation {
    in
    with versions;
    switch rocq-core.rocq-version [
-      (case (range "9.0" "9.2") "0.5.0")
+      (case (range "9.0" "9.3") "0.5.0")
    ] null;
  release = {
    "0.5.0".hash = "sha256-pmK4gD5ccerjr2UVgwGIVbjH/RiXdYQq79/XFetiHZg=";
--- a/pkgs/tools/text/nltk-data/default.nix
+++ b/pkgs/tools/text/nltk-data/default.nix
@@ -7,7 +7,7 @@
 }:
 let
  base = {
-    version = "0-unstable-2024-07-29";
+    version = "0-unstable-2026-07-01";
    nativeBuildInputs = [ unzip ];
    dontBuild = true;
    dontFixup = true;
@@ -30,9 +30,10 @@ let
    }:
    let
      src = fetchFromGitHub {
+        name = "nltk-${location}";
        owner = "nltk";
        repo = "nltk_data";
-        rev = "cfe82914f3c2d24363687f1db3b05e8b9f687e2b";
+        rev = "550b6625bcef1f2abff2ff770a5a0d272c9c6b2a";
        inherit hash;
        sparseCheckout = [ "packages/${location}/${pname}.zip" ];
      };
@@ -60,7 +61,7 @@ let
    makeNltkDataPackage {
      inherit pname;
      location = "chunkers";
-      hash = "sha256-kemjqaCM9hlKAdMw8oVJnp62EAC9rMQ50dKg7wlAwEc=";
+      hash = "sha256-+n0TkS+/NHk0OqFZNQBLIcO/9uw56Mn7/AyNkRDGZEQ=";
    };

  makeCorpus =
@@ -68,7 +69,7 @@ let
    makeNltkDataPackage {
      inherit pname;
      location = "corpora";
-      hash = "sha256-8lMjW5YI8h6dHJ/83HVY2OYGDyKPpgkUAKPISiAKqqk=";
+      hash = "sha256-7uiTXZ+eMyBtH135NsYoAjLV6R/DG2hVV+RJwYDmu50=";
    };

  makeGrammar =
@@ -76,7 +77,7 @@ let
    makeNltkDataPackage {
      inherit pname;
      location = "grammars";
-      hash = "sha256-pyLEcX3Azv8j1kCGvVYonuiNgVJxtWt7veU0S/yNbIM=";
+      hash = "sha256-KoZ1q0F2X7bSFdbw1qK/jzZ3iuMJXTYHfogylO7nHEY=";
    };

  makeHelp =
@@ -84,7 +85,7 @@ let
    makeNltkDataPackage {
      inherit pname;
      location = "help";
-      hash = "sha256-97mYLNES5WujLF5gD8Ul4cJ6LqSzz+jDzclUsdBeHNE=";
+      hash = "sha256-2x3kemPdipHAj0TGYCm6Il5Aapx+fuo/jlNT9+XWbss=";
    };

  makeMisc =
@@ -92,7 +93,7 @@ let
    makeNltkDataPackage {
      inherit pname;
      location = "misc";
-      hash = "sha256-XtizfEsc8TYWqvvC/eSFdha2ClC5/ZiJM8nue0vXLb4=";
+      hash = "sha256-edBgrWM+eQgEGWq7oBHTebtvJPZcofCzzXSu3S9Fa1o=";
    };

  makeModel =
@@ -100,7 +101,7 @@ let
    makeNltkDataPackage {
      inherit pname;
      location = "models";
-      hash = "sha256-iq3weEgCci6rgLW2j28F2eRLprJtInGXKe/awJPSVG4=";
+      hash = "sha256-uTRr9pBfL1KZ7z8WTQPAiWlMn/os4ISa9tj/Si/RmtI=";
    };

  makeTagger =
@@ -108,7 +109,7 @@ let
    makeNltkDataPackage {
      inherit pname;
      location = "taggers";
-      hash = "sha256-tl3Cn2okhBkUtTXvAmFRx72Brez6iTGRdmFTwFmpk3M=";
+      hash = "sha256-V5bs0JUQgr4ijs2NaF5JXzVwT1e/ZYnlU0TZXeoqfM4=";
    };

  makeTokenizer =
@@ -116,7 +117,7 @@ let
    makeNltkDataPackage {
      inherit pname;
      location = "tokenizers";
-      hash = "sha256-OzMkruoYbFKqzuimOXIpE5lhHz8tmSqOFoLT+fjdTVg=";
+      hash = "sha256-V/Qs8wJbCZB8gp5pAAM1JK8aAfcHorNyvAkHUat56uY=";
    };

  makeStemmer =
@@ -124,7 +125,7 @@ let
    makeNltkDataPackage {
      inherit pname;
      location = "stemmers";
-      hash = "sha256-mNefwOPVJGz9kXV3LV4DuV7FJpNir/Nwg4ujd0CogEk=";
+      hash = "sha256-6sQQCA8r8jWRFImpiBovUt/IzHjh13W6X8yLpn61cs0=";
    };
 in
 lib.makeScope newScope (self: {
@@ -152,6 +153,7 @@ lib.makeScope newScope (self: {
  crubadan = makeCorpus "crubadan";
  dependency-treebank = makeCorpus "dependency_treebank";
  dolch = makeCorpus "dolch";
+  english_wordnet = makeCorpus "english_wordnet";
  europarl-raw = makeCorpus "europarl_raw";
  extended-omw = makeCorpus "extended_omw";
  floresta = makeCorpus "floresta";
@@ -170,6 +172,7 @@ lib.makeScope newScope (self: {
  mac-morpho = makeCorpus "mac_morpho";
  machado = makeCorpus "machado";
  masc-tagged = makeCorpus "masc_tagged";
+  mock_corpus = makeCorpus "mock_corpus";
  movie-reviews = makeCorpus "movie_reviews";
  mte-teip5 = makeCorpus "mte_teip5";
  names = makeCorpus "names";
@@ -178,6 +181,7 @@ lib.makeScope newScope (self: {
  nps-chat = makeCorpus "nps_chat";
  omw = makeCorpus "omw";
  omw-1-4 = makeCorpus "omw-1.4";
+  omw-2-0 = makeCorpus "omw-2.0";
  opinion-lexicon = makeCorpus "opinion_lexicon";
  panlex-swadesh = makeCorpus "panlex_swadesh";
  paradigms = makeCorpus "paradigms";
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -1728,6 +1728,7 @@ mapAliases {
  oil = throw "'oil' has been renamed to/replaced by 'oils-for-unix'"; # Converted to throw 2025-10-27
  olaris-server = throw "'olaris-server' has been removed as it failed to build since 2024"; # Added 2026-01-15
  olive-editor = throw "'olive-editor' has been removed as it is unmaintained upstream and broken"; # Added 2026-05-22
+  omxplayer = throw "'omxplayer' has been removed because it depends on a severely outdated upstream, a severely outdated FFmpeg, and the new upstream was deprecated since 2020. Please use 'vlc' instead."; # Added 2026-07-24
  oneDNN = onednn; # Added 2026-02-08
  oneDNN_2 = onednn_2; # Added 2026-02-08
  onevpl-intel-gpu = throw "'onevpl-intel-gpu' has been renamed to/replaced by 'vpl-gpu-rt'"; # Converted to throw 2025-10-27
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -7104,6 +7104,11 @@ with pkgs;

  ### DEVELOPMENT / R MODULES

+  R = callPackage ../applications/science/math/R {
+    # TODO: split docs into a separate output
+    withRecommendedPackages = false;
+  };
+
  rWrapper = callPackage ../development/r-modules/wrapper.nix {
    recommendedPackages = with rPackages; [
      boot
--- a/pkgs/top-level/python-aliases.nix
+++ b/pkgs/top-level/python-aliases.nix
@@ -439,6 +439,8 @@ mapAliases {
  pilight = throw "'pilight' has been removed, because it is unmaintained since 2019 and the integration was removed from Home Assistant."; # added 2026-05-06
  pillow-avif-plugin = throw "'pillow-avif-plugin' has been removed because 'pillow' has native avif support since 11.3"; # added 2025-11-26
  pinecone-client = warnAlias "'pinecone-client' has been renamed to 'pinecone'" pinecone; # added 2026-07-22
+  pinecone-plugin-assistant = throw "'pinecone-plugin-assistant' has been integrated into 'pinecone-client'"; # Added 2026-07-22
+  pinecone-plugin-interface = throw "'pinecone-plugin-interface' has been removed because the plugin discovery system was retired in 'pinecone-client' 9"; # Added 2026-07-22
  pizzapi = throw "pizzapi was removed because it no longer works"; # added 2025-12-03
  pkuseg = throw "'pkuseg' has been removed because it was not supported on newer versions of Python"; # added 2026-01-20
  ploomber-extension = throw "'ploomber-extension' has been removed since the upstream repo was archived"; # added 2026-02-16
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -13199,10 +13199,6 @@ self: super: with self; {

  pinecone = callPackage ../development/python-modules/pinecone { };

-  pinecone-plugin-assistant = callPackage ../development/python-modules/pinecone-plugin-assistant { };
-
-  pinecone-plugin-interface = callPackage ../development/python-modules/pinecone-plugin-interface { };
-
  ping3 = callPackage ../development/python-modules/ping3 { };

  pingouin = callPackage ../development/python-modules/pingouin { };
Author	SHA1	Message	Date
dependabot[bot]	7079e863e7	.github: Bump actions/checkout from 6.0.3 to 7.0.1 Bumps [actions/checkout](https://github.com/actions/checkout) from 6.0.3 to 7.0.1. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](`df4cb1c069...3d3c42e5aa`) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>	2026-07-24 11:22:46 +00:00
ajs124	b6afca8e77	xfsprogs: 7.0.1 -> 7.1.1 (#523070 )	2026-07-24 11:12:32 +00:00
nixpkgs-ci[bot]	fd10d5017a	protoc-gen-grpc-java: 1.82.2 -> 1.83.0 (#545107 )	2026-07-24 10:49:13 +00:00
nixpkgs-ci[bot]	bceeca55de	gitoxide: 0.55.0 -> 0.56.0 (#544919 )	2026-07-24 10:48:52 +00:00
Sizhe Zhao	10061cf0f7	hmcl: 3.15.3 -> 3.16.2 (#544737 )	2026-07-24 10:09:58 +00:00
kirillrdy	dae023c345	librevna: init at 1.6.5 (#446590 )	2026-07-24 09:59:51 +00:00
nixpkgs-ci[bot]	242d36d7b7	crush: 0.81.0 -> 0.86.0 (#545172 )	2026-07-24 09:57:23 +00:00
nixpkgs-ci[bot]	9bd9d121dc	copilot-language-server: 1.521.0 -> 1.526.0 (#545112 )	2026-07-24 09:57:04 +00:00
nixpkgs-ci[bot]	905f8f74bd	matomo: 5.10.0 -> 5.12.0 (#532827 )	2026-07-24 09:56:34 +00:00
@mjones	da6063cbe1	mattermost: 11.7.6 -> 11.7.7 (#544725 )	2026-07-24 09:27:07 +00:00
Vincent Laporte	a76040f2df	rocqPackages.rocq-elpi: 3.4.0 -> 3.5.0 (#545143 )	2026-07-24 09:20:00 +00:00
Duncan Dean	fae658c82c	librevna: init at 1.6.5	2026-07-24 11:16:56 +02:00
Grimmauld	8c1d4dd32e	omxplayer: drop (#545162 )	2026-07-24 09:16:04 +00:00
kirillrdy	805b05500e	slack: 4.49.89 -> 4.51.180 (#533086 )	2026-07-24 09:15:01 +00:00
R. Ryantm	9599335283	crush: 0.81.0 -> 0.86.0	2026-07-24 09:13:56 +00:00
Grimmauld	e4f1329ede	omxplayer: drop part of #356387 Why would anyone use this? - Old rpi 1 stuff - Upstream is unmaintained since 2013 - The more maintained fork is deprecated since 2020 [1] - uses pcre - uses FFmpeg 1.1.3 from 2013 - only 2 non-treewide commits to the package since introduction, not a single update [1] https://github.com/popcornmix/omxplayer#deprecation-warning	2026-07-24 11:10:23 +02:00
Sarah Brofeldt	f11b773a1e	filebeat8: 8.19.17 -> 8.19.19 (#538676 )	2026-07-24 08:49:22 +00:00
Vincent Laporte	16611dafa6	ocaml: fix cross-compile by adding bootstrapping ocaml (#542468 )	2026-07-24 08:34:00 +00:00
Grimmauld	d6f70286e7	openscenegraph: remove unused pcre dependency (#545154 )	2026-07-24 08:22:15 +00:00
Grimmauld	cb79c550fc	openscenegraph: remove unused pcre dependency The build output is identical apart from changed nix store paths.	2026-07-24 10:15:54 +02:00
Grimmauld	80b2f9ec36	flightgear: remove unused pcre dependency (#545043 )	2026-07-24 08:15:27 +00:00
nixpkgs-ci[bot]	88449c0e01	matcha: 0.43.0 -> 0.44.0 (#545127 )	2026-07-24 07:57:27 +00:00
Thiago Kenji Okada	551d54cfc4	libretro.prboom: 0-unstable-2026-07-07 -> 0-unstable-2026-07-21 (#545125 )	2026-07-24 07:45:58 +00:00
Thiago Kenji Okada	8e24e33451	libretro.opera: 0-unstable-2026-07-13 -> 0-unstable-2026-07-23 (#545104 )	2026-07-24 07:45:46 +00:00
Thiago Kenji Okada	640664d98d	libretro.snes9x2005: 0-unstable-2026-04-20 -> 0-unstable-2026-07-22 (#545098 )	2026-07-24 07:45:36 +00:00
Pierre Roux	54f8f8a829	rocqPackages.micromega-plugin: 1.1.0 -> 1.1.1	2026-07-24 09:41:27 +02:00
nixpkgs-ci[bot]	1a310691f9	kloak: 0.8.5-1 -> 0.8.6-1 (#545126 )	2026-07-24 07:03:56 +00:00
nixpkgs-ci[bot]	036b92ec81	telemt: 3.4.23 -> 3.4.25 (#545106 )	2026-07-24 07:03:55 +00:00
Yt	e64b9b7373	datafusion-cli: 54.0.0 -> 54.1.0 (#545114 )	2026-07-24 07:00:59 +00:00
Pierre Roux	1870911b32	rocqPackages.rocq-elpi: 3.4.0 -> 3.5.0	2026-07-24 08:37:01 +02:00
Fabián Heredia Montiel	588fe9a6f2	metals: 1.6.7 -> 1.6.8 (#545024 )	2026-07-24 06:01:17 +00:00
Vincent Laporte	335f0738cb	coqPackages.mathcomp-word: 3.4 → 3.5 (#544910 )	2026-07-24 05:48:35 +00:00
Maximilian Bosch	2836fbbd41	matrix-synapse: 1.156.0 -> 1.157.1 (#544480 )	2026-07-24 05:37:50 +00:00
Wolfgang Walther	596a0d7dc0	gitignore: add AGENTS.md and CLAUDE.md (#544374 )	2026-07-24 05:34:53 +00:00
R. Ryantm	aebf3d0f9f	matcha: 0.43.0 -> 0.44.0	2026-07-24 05:09:54 +00:00
R. Ryantm	87906566c7	kloak: 0.8.5-1 -> 0.8.6-1	2026-07-24 05:09:42 +00:00
R. Ryantm	1a12318a59	libretro.prboom: 0-unstable-2026-07-07 -> 0-unstable-2026-07-21	2026-07-24 05:04:58 +00:00
Audrey Dutcher	a515e75f6b	nixos/xdg: enable fuse for desktop portals (#543168 )	2026-07-24 05:03:17 +00:00
Vincent Laporte	c5a79bf94d	coqPackages.mathcomp-word: 3.4 → 3.5	2026-07-24 06:53:31 +02:00
Vladimír Čunát	33b11c7a18	thunderbird-140: 140.12.1esr -> 140.13.0esr (#545065 )	2026-07-24 04:29:18 +00:00
R. Ryantm	39d8a34f31	filebeat8: 8.19.17 -> 8.19.19	2026-07-24 04:12:15 +00:00
R. Ryantm	bb590c3739	datafusion-cli: 54.0.0 -> 54.1.0	2026-07-24 04:06:05 +00:00
R. Ryantm	23a6f403f9	copilot-language-server: 1.521.0 -> 1.526.0	2026-07-24 03:52:29 +00:00
R. Ryantm	43970c9823	protoc-gen-grpc-java: 1.82.2 -> 1.83.0	2026-07-24 03:20:47 +00:00
R. Ryantm	8dbada257e	telemt: 3.4.23 -> 3.4.25	2026-07-24 03:14:51 +00:00
R. Ryantm	a6c44bb0e5	libretro.opera: 0-unstable-2026-07-13 -> 0-unstable-2026-07-23	2026-07-24 03:11:59 +00:00
nixpkgs-ci[bot]	4cb9d58ac0	yaziPlugins: update on 2026-07-23 (#544999 )	2026-07-24 02:35:19 +00:00
R. Ryantm	f3c9b412ad	libretro.snes9x2005: 0-unstable-2026-04-20 -> 0-unstable-2026-07-22	2026-07-24 02:35:09 +00:00
nixpkgs-ci[bot]	4a02d63a72	zapzap: add Hunspell dictionaries for spellcheck (#544093 )	2026-07-24 02:32:26 +00:00
Yt	c6b4f51ed2	python3Packages.pinecone: 8.1.2 -> 9.1.0 (#544751 )	2026-07-24 01:31:50 +00:00
Yt	11666f06dc	python314Packages.nltk: 3.9.4 -> 3.10.0 (#545023 )	2026-07-24 01:29:56 +00:00
Martin Weinelt	1ce8afeba2	music-assistant: fix pytestCheckPhase by pinning pytest to 9.0.x (#545018 )	2026-07-24 01:15:49 +00:00
Michael Daniels	3d238b4d3b	piknik: adopt (#543919 )	2026-07-24 01:06:43 +00:00
nixpkgs-ci[bot]	1ea2a247f0	tpnote: 1.26.6 -> 1.26.7 (#545031 )	2026-07-24 00:52:48 +00:00
nixpkgs-ci[bot]	f82c92cf1f	temporal-cli: 1.8.0 -> 1.8.1 (#544819 )	2026-07-24 00:52:44 +00:00
nixpkgs-ci[bot]	2ffb4d3f41	gtkwave: 3.3.127 -> 3.3.128 (#544756 )	2026-07-24 00:52:38 +00:00
Ihar Hrachyshka	c9b84ce04d	python3Packages.pinecone-plugin-interface: drop	2026-07-23 19:41:01 -04:00
Ihar Hrachyshka	f73579b2d5	python3Packages.pinecone-plugin-assistant: drop	2026-07-23 19:41:00 -04:00
Ihar Hrachyshka	9494ab4bd9	python3Packages.pinecone: 8.1.2 -> 9.1.0	2026-07-23 19:40:57 -04:00
Ihar Hrachyshka	3addee54fd	thunderbird-140: 140.12.1esr -> 140.13.0esr https://www.thunderbird.net/en-US/thunderbird/140.13.0esr/releasenotes/	2026-07-23 19:16:52 -04:00
Kirill Radzikhovskyy	dace4d93f1	flightgear: remove unused pcre dependency part of #356387	2026-07-24 07:51:16 +10:00
Sandro Jäckel	f107f71070	paperless-ngx: relax nltk dependency	2026-07-23 23:06:51 +02:00
Maximilian Bosch	8751b9fd7c	matrix-synapse: 1.156.0 -> 1.157.1 ChangeLog: * https://github.com/element-hq/synapse/releases/tag/v1.157.0 * https://github.com/element-hq/synapse/releases/tag/v1.157.1	2026-07-23 23:02:20 +02:00
R. Ryantm	e25fe7a968	tpnote: 1.26.6 -> 1.26.7	2026-07-23 20:57:36 +00:00
Jaakko Paju	0ede4d7c4f	metals: 1.6.7 -> 1.6.8	2026-07-23 23:57:22 +03:00
Sandro Jäckel	9494ef5d2c	python314Packages.nltk: 3.9.4 -> 3.10.0 Diff: https://github.com/nltk/nltk/compare/3.9.4...v3.10.0	2026-07-23 22:47:21 +02:00
emilylange	962224d36a	music-assistant: fix pytestCheckPhase by pinning pytest to 9.0.x https://hydra.nixos.org/build/338544626	2026-07-23 22:34:11 +02:00
Sandro Jäckel	60bf249d13	nltk-data: 0-unstable-2024-07-29 -> 0-unstable-2026-07-01 Diff: `cfe82914f3...550b6625bc`	2026-07-23 21:48:08 +02:00
R. Ryantm	5a59a1d155	xfsprogs: 7.0.1 -> 7.1.1	2026-07-23 18:17:31 +00:00
R. Ryantm	c2c67711a3	gitoxide: 0.55.0 -> 0.56.0	2026-07-23 16:15:58 +00:00
R. Ryantm	86c123c30b	slack: 4.49.89 -> 4.51.180 Co-authored-by: teutat3s <10206665+teutat3s@users.noreply.github.com>	2026-07-23 15:14:05 +02:00
R. Ryantm	c73eaa6a58	temporal-cli: 1.8.0 -> 1.8.1	2026-07-23 09:15:21 +00:00
Austin Horstman	a718e78415	yaziPlugins.restore: 0-unstable-2026-04-04 → 0-unstable-2026-07-22 Compare: `0e0870460b...7bfcfcbda0`	2026-07-23 03:02:25 -05:00
Austin Horstman	87024b4b71	yaziPlugins.gvfs: 0-unstable-2026-07-13 → 0-unstable-2026-07-23 Compare: `c5a0bb924e...364b0a811d`	2026-07-23 03:01:42 -05:00
Austin Horstman	07b25d7bda	yaziPlugins.diff: 0-unstable-2026-07-01 → 0-unstable-2026-07-22 Compare: `65559fd3ed...bbac5e75b2`	2026-07-23 03:01:23 -05:00
Rine Amakawa	6e3f8c5fd1	hmcl: 3.15.3 -> 3.16.2 Changelog: https://docs.hmcl.net/changelog/stable.html	2026-07-23 10:12:34 +09:00
R. Ryantm	3dc4b3fbc7	gtkwave: 3.3.127 -> 3.3.128	2026-07-23 00:40:36 +00:00
R. Ryantm	cf6603d435	mattermost: 11.7.6 -> 11.7.7	2026-07-23 00:27:48 +00:00
Eman Resu	9b6be193ad	gitignore: add AGENTS.md and CLAUDE.md	2026-07-21 21:05:33 -04:00
eymeric	6f508907ef	zapzap: add Hunspell dictionaries for spellcheck	2026-07-22 08:04:33 +07:00
Leonard Sheng Sheng Lee	2f7a8a8ae4	piknik: adopt This commit is part of https://github.com/NixOS/nixpkgs/issues/458096. Signed-off-by: Leonard Sheng Sheng Lee <leonard.sheng.sheng.lee@gmail.com>	2026-07-20 19:39:36 +02:00
Gerhard Schwanzer	e4d9d6766f	nixos/xdg: enable fuse for desktop portals xdg-document-portal mounts a FUSE filesystem and libfuse expects /run/wrappers/bin/fusermount3. Enable programs.fuse with the portal now that FUSE is no longer enabled globally. Closes #542790 Assisted-by: pi coding agent / Mika (OpenAI gpt-5.6-sol) Suggested-by: Audrey Dutcher <audrey@rhelmot.io>	2026-07-18 11:08:29 +02:00
·𐑑𐑴𐑕𐑑𐑩𐑤	def7d4d5df	ocaml: fix cross-compile by adding bootstrapping ocaml Fixes cross compilation looking for ocamlc: checking if the installed OCaml compiler can build the cross compiler... ./configure: line 4348: ocamlc: command not found no (5.4.1 vs ) configure: error: exiting Assisted-by: DeepSeek V4 Flash	2026-07-16 12:08:22 +07:00
R. Ryantm	93c5137c1c	matomo: 5.10.0 -> 5.12.0	2026-07-14 04:45:08 +00:00