Merge branch 'master' into r-updates

Clean up

.gitignore

@@ -27,9 +27,6 @@ tags
 .mypy_cache
 __pycache__
 
-/AGENTS.md
-/CLAUDE.md
-
 /pkgs/development/libraries/qt-5/*/tmp/
 /pkgs/desktops/kde-5/*/tmp/
 /pkgs/development/mobile/androidenv/xml/*

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

nixos/modules/config/xdg/portal.nix

@@ -116,8 +116,6 @@ 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`

pkgs/applications/emulators/libretro/cores/opera.nix

@@ -6,13 +6,13 @@
 }:
 mkLibretroCore {
   core = "opera";
-  version = "0-unstable-2026-07-23";
+  version = "0-unstable-2026-07-13";
 
   src = fetchFromGitHub {
     owner = "libretro";
     repo = "opera-libretro";
-    rev = "74dd2a8c6319678ffce9f31bdf36279db5681762";
-    hash = "sha256-NHXOfKItLkQJ0/jH1gLBpLFqOKBB8qgH5gMw7j1YoLw=";
+    rev = "1edda8a2a6c6b9ae259d5c7cd7d54dcba9ee7e32";
+    hash = "sha256-dc7xRjFxfSL2q9u1N0QH2j+oPbRGng2Z3U3J484lXiU=";
   };
 
   makefile = "Makefile";

pkgs/applications/emulators/libretro/cores/prboom.nix

@@ -5,13 +5,13 @@
 }:
 mkLibretroCore {
   core = "prboom";
-  version = "0-unstable-2026-07-21";
+  version = "0-unstable-2026-07-07";
 
   src = fetchFromGitHub {
     owner = "libretro";
     repo = "libretro-prboom";
-    rev = "c5b09532fa633e015ac75c0a2acfec049f65ded3";
-    hash = "sha256-13oL/U3uwNejqTIbKmITRbK8Eddg9YH5CMDIDXA6zKs=";
+    rev = "31563d6e65faa6b9b7e975754d2062370bba4342";
+    hash = "sha256-eFRzbVTL5ARf650D0ZAEFGNTxjAy1CjBiAhwSQR8vJ4=";
   };
 
   makefile = "Makefile";

pkgs/applications/emulators/libretro/cores/snes9x2005.nix

@@ -6,13 +6,13 @@
 }:
 mkLibretroCore {
   core = "snes9x2005" + lib.optionalString withBlarggAPU "-plus";
-  version = "0-unstable-2026-07-22";
+  version = "0-unstable-2026-04-20";
 
   src = fetchFromGitHub {
     owner = "libretro";
     repo = "snes9x2005";
-    rev = "deb49d80d1836e3e737480a326e31a54c46c04ae";
-    hash = "sha256-UMW+YTzcSZ5CWSyRBYc8y1cDh/CU3Am11rkjSXlyxZA=";
+    rev = "b60356971fc9caae02cd0853676dced886a08be7";
+    hash = "sha256-6IuEFyJEoCHluSAXbk5qRTXku1XJCZ6p04BhdjqZqJQ=";
   };
 
   makefile = "Makefile";

pkgs/applications/networking/mailreaders/thunderbird/packages.nix

@@ -92,8 +92,8 @@ rec {
   thunderbird-140 = common {
     applicationName = "Thunderbird ESR";
 
-    version = "140.13.0esr";
-    sha512 = "778d2fc2837ba367e90c4336f3873da5a0823c182e2f50aa9373cd1ee9ee2b5310372ad9d33e1e11978791b67de4a6952d3036ff7d57b257a06f49c8cd4a830e";
+    version = "140.12.1esr";
+    sha512 = "24e795483ba7bc112c0debe1becdaf79cc2de95703b9ee726d0216bfc1db7b33c169503f83ac867e5998a8d1d0284a6ef12c7d35d98b10d6432497c2db237477";
 
     updateScript = callPackage ./update.nix {
       attrPath = "thunderbirdPackages.thunderbird-140";

pkgs/by-name/da/datafusion-cli/package.nix

@@ -8,17 +8,17 @@
 
 rustPlatform.buildRustPackage (finalAttrs: {
   pname = "datafusion-cli";
-  version = "54.1.0";
+  version = "54.0.0";
 
   src = fetchFromGitHub {
     name = "datafusion-cli-source";
     owner = "apache";
     repo = "datafusion";
     tag = finalAttrs.version;
-    hash = "sha256-zeR6eyU4Cc5gHiE331ap8wuyYEj7s7BgqB+oOKwMfZw=";
+    hash = "sha256-BWpHiLCn7idvzI2rlsre8l23TbxQU1Ma6bCjAMxQ6m8=";
   };
 
-  cargoHash = "sha256-XXR1Turs+QwONZHq38MZHbcjv5DYZH9iqeuBl20gy3U=";
+  cargoHash = "sha256-Sj/biBiJPIYwxpL+Fua0k47vOu6gyyAhcKb4ZSUli6k=";
 
   buildAndTestSubdir = "datafusion-cli";
 

pkgs/by-name/fi/filebeat8/package.nix

@@ -8,18 +8,18 @@
 
 buildGoModule (finalAttrs: {
   pname = "filebeat";
-  version = "8.19.19";
+  version = "8.19.17";
 
   src = fetchFromGitHub {
     owner = "elastic";
     repo = "beats";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-3hvP+4U3PWlOsaLHO1MZuIpcB6YzPv2dMPlC68esiHE=";
+    hash = "sha256-Xpth1SoXMXCUh/DFf3wA+Ql6SedtUB7tCYzDElpX5Lc=";
   };
 
   proxyVendor = true; # darwin/linux hash mismatch
 
-  vendorHash = "sha256-e++Y5mhwms/uJnZCUyZNifoYqGH4TGEugSFHSGl0AQE=";
+  vendorHash = "sha256-Wxk+eI0XfBpQqqUNuskyr+/bTRqT38hszdkz/LJweQo=";
 
   subPackages = [ "filebeat" ];
 

pkgs/by-name/fl/flightgear/openscenegraph-flightgear.nix

@@ -9,6 +9,7 @@
   fetchurl,
   glib,
   libxml2,
+  pcre,
   zlib,
   libjpeg,
   giflib,
@@ -52,6 +53,7 @@ stdenv.mkDerivation {
     ++ [
       glib
       libxml2
+      pcre
       zlib
       libjpeg
       giflib

pkgs/by-name/gt/gtkwave/package.nix

@@ -18,11 +18,11 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "gtkwave";
-  version = "3.3.128";
+  version = "3.3.127";
 
   src = fetchurl {
     url = "mirror://sourceforge/gtkwave/gtkwave-gtk3-${finalAttrs.version}.tar.gz";
-    sha256 = "sha256-gX4Zf8GAj4qsNUPCwvloPLATaMkRkrjq5a9YBw7x0fg=";
+    sha256 = "sha256-8Z2i20Oye7zGaXJYQ0UZRaaMOkziMlYuNB1vY7gLVeQ=";
   };
 
   nativeBuildInputs = [

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 edd96b0..1fbdb3c 100644
+index a3ed1f3..a564046 100644
 --- a/Tools/CMake/Install.cmake
 +++ b/Tools/CMake/Install.cmake
 @@ -229,24 +229,10 @@ if(LINUX)
@@ -20,10 +20,10 @@ index edd96b0..1fbdb3c 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

pkgs/by-name/ja/jasp-desktop/module-info.json

@@ -97,9 +97,9 @@
   },
   "jaspLearnBayes": {
     "pname": "jaspLearnBayes",
-    "version": "0.95.5-release.12",
-    "tag": "0.95.5-release.12_R-4-5-2_Release",
-    "hash": "sha256-zqMcWFML/iexmegMtGWCe/OCGqwmWW98/XZfKVs6N8w="
+    "version": "0.96.5-release.0",
+    "tag": "0.96.5-release.0_R-4-5-2_Release",
+    "hash": "sha256-TdlwB2TV+YNj4Uwf4rNSIw/OtKQHEbrFKv1t2RioTmI="
   },
   "jaspLearnStats": {
     "pname": "jaspLearnStats",

pkgs/by-name/ja/jasp-desktop/package.nix

@@ -25,13 +25,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "jasp-desktop";
-  version = "0.97.1";
+  version = "0.98.1";
   src = fetchFromGitHub {
     owner = "jasp-stats";
     repo = "jasp-desktop";
     tag = "v${finalAttrs.version}";
     fetchSubmodules = true;
-    hash = "sha256-4K6ReOJJF8Pt/RdNSp2ZVH/d64ZMCFlX1RIXDAWWWBE=";
+    hash = "sha256-73RxbWVa03V6MdcW9k4Hv8EBsSNw0Feg91SioWLgC5U=";
   };
 
   patches = [
@@ -68,8 +68,7 @@ stdenv.mkDerivation (finalAttrs: {
     qt6.qtbase
     qt6.qtdeclarative
     qt6.qtwebengine
-    qt6.qtsvg
-    qt6.qt5compat
+    qt6.qthttpserver
   ];
 
   # needed so that the linker can find libRInside.so

pkgs/by-name/kl/kloak/package.nix

@@ -17,13 +17,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "kloak";
-  version = "0.8.6-1";
+  version = "0.8.5-1";
 
   src = fetchFromGitHub {
     owner = "Whonix";
     repo = "kloak";
     tag = finalAttrs.version;
-    hash = "sha256-zaoKVPocL8iaX6hhZh0Q+cgYg3JLWBcMgGU0nLlNcjo=";
+    hash = "sha256-fDmqA00b5ESS9LW2QIeEx3wWb0lhgkqoBYcw1XYDI7k=";
   };
 
   strictDeps = true;

pkgs/by-name/ma/matcha/package.nix

@@ -14,16 +14,16 @@ buildGoLatestModule (finalAttrs: {
   __structuredAttrs = true;
 
   pname = "matcha";
-  version = "0.44.0";
+  version = "0.43.0";
 
   src = fetchFromGitHub {
     owner = "floatpane";
     repo = "matcha";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-y1YEnqTCmf+CMKpv3wN4SZsN+lUuv3T8pKmM+zu1Ipw=";
+    hash = "sha256-x+k1/k7pwJ0MW0t31ieaOkbP8LtqDSmHOBrNEGA0K6Q=";
   };
 
-  vendorHash = "sha256-cg6R4WtDORwZlo+P16rN6qc0zZMOPtnr4VyQKV9Q2nM=";
+  vendorHash = "sha256-5smWIw8ofG61ugHxFbmQ9r9vcxi098/UmxUE15lx4wE=";
   proxyVendor = true;
 
   nativeBuildInputs = lib.optionals stdenv.hostPlatform.isLinux [

pkgs/by-name/ma/matrix-synapse-unwrapped/package.nix

@@ -14,19 +14,19 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "matrix-synapse";
-  version = "1.157.1";
+  version = "1.156.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "element-hq";
     repo = "synapse";
     rev = "v${version}";
-    hash = "sha256-yDfBtcBvIoWUfD8bqwGgeMvq4XHrr9ptVB6yKJWFX0c=";
+    hash = "sha256-x3EVmNPqcxtvt6ZaPsDCCcr7Z0LIO257s2gO3HCNmKA=";
   };
 
   cargoDeps = rustPlatform.fetchCargoVendor {
     inherit pname version src;
-    hash = "sha256-KM3j2O7J4Sad6jKF2Ca4qkRLj3w7+/UCnK6T6x8kMfs=";
+    hash = "sha256-N/JWRFz9OKcxigjp86AVVZGK63MdZmEzwHhBgBuWZcY=";
   };
 
   build-system =

pkgs/by-name/me/metals/package.nix

@@ -9,7 +9,7 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "metals";
-  version = "1.6.8";
+  version = "1.6.7";
 
   deps = stdenv.mkDerivation {
     name = "metals-deps-${finalAttrs.version}";
@@ -23,7 +23,7 @@ stdenv.mkDerivation (finalAttrs: {
     '';
     outputHashMode = "recursive";
     outputHashAlgo = "sha256";
-    outputHash = "sha256-LdZ6I7zOUTHgS/TTo0T6Dh+Kb3YpgJg8gK0UngsA7Gs=";
+    outputHash = "sha256-2ly1vO+06EalQjEekRwm/g2wfdbq26IcEQscfM14Gvc=";
   };
 
   nativeBuildInputs = [

pkgs/by-name/mu/music-assistant/package.nix

@@ -185,7 +185,7 @@ pythonPackages.buildPythonApplication (finalAttrs: {
   nativeCheckInputs =
     with pythonPackages;
     [
-      pytest9_0CheckHook
+      pytestCheckHook
       writableTmpDirAsHomeHook
     ]
     ++ lib.concatAttrValues finalAttrs.passthru.optional-dependencies

pkgs/by-name/om/omxplayer/package.nix

@@ -0,0 +1,111 @@
+{
+  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;
+  };
+}

pkgs/by-name/op/openscenegraph/package.nix

@@ -14,6 +14,7 @@
   libGL,
   glib,
   libxml2,
+  pcre,
   zlib,
   boost,
   jpegSupport ? true,
@@ -98,6 +99,7 @@ stdenv.mkDerivation (finalAttrs: {
     ++ lib.optional curlSupport curl
     ++ lib.optionals colladaSupport [
       collada-dom
+      pcre
     ]
     ++ lib.optional opencascadeSupport opencascade-occt
     ++ lib.optional ffmpegSupport ffmpeg

pkgs/by-name/pa/paperless-ngx/package.nix

@@ -118,7 +118,6 @@ pythonPackages.buildPythonApplication (finalAttrs: {
     "drf-spectacular-sidecar"
     "python-dotenv"
     "gotenberg-client"
-    "nltk"
     "redis"
     "scikit-learn"
     "tika-client"

pkgs/by-name/pi/piknik/package.nix

@@ -36,9 +36,7 @@ buildGoModule (finalAttrs: {
     homepage = "https://github.com/jedisct1/piknik";
     changelog = "https://github.com/jedisct1/piknik/blob/${finalAttrs.src.rev}/ChangeLog";
     license = lib.licenses.bsd2;
-    maintainers = with lib.maintainers; [
-      sheeeng
-    ];
+    maintainers = [ ];
     mainProgram = "piknik";
   };
 })

pkgs/by-name/r/R/package.nix

@@ -32,7 +32,7 @@
   lapack,
   curl,
   tzdata,
-  withRecommendedPackages ? true,
+  withRecommendedPackages ? false,
   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 = "4.6.0";
+  version = "4.6.1";
 
   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-uNybRUNmDHtZa4eTjfUyOUNQNgl2Un00QijuDtEuRew=";
+      hash = "sha256-TabmHSwKrF8UoufkMstfzCae/oPaQpMFC6fwPf9OLPQ=";
     };
 
   outputs = [

pkgs/by-name/sl/slack/sources.nix

@@ -1,19 +1,19 @@
 # Generated by ./update.sh - do not update manually!
-# Last updated: 2026-07-23
+# Last updated: 2026-05-14
 { fetchurl }:
 {
   aarch64-darwin = {
-    version = "4.51.180";
+    version = "4.49.89";
     src = fetchurl {
-      url = "https://downloads.slack-edge.com/desktop-releases/mac/arm64/4.51.180/Slack-4.51.180-macOS.dmg";
-      hash = "sha256-6QhuZWEwQiW8ZyYTJRLMZq5MayBgX9xlBLdhttiTaoA=";
+      url = "https://downloads.slack-edge.com/desktop-releases/mac/arm64/4.49.89/Slack-4.49.89-macOS.dmg";
+      hash = "sha256-u5NppmmRyC+6HaPIcSSGOOdVRiZdT9GE1eHvad6rYdY=";
     };
   };
   x86_64-linux = {
-    version = "4.51.180";
+    version = "4.49.89";
     src = fetchurl {
-      url = "https://downloads.slack-edge.com/desktop-releases/linux/x64/4.51.180/slack-desktop-4.51.180-amd64.deb";
-      hash = "sha256-qkXhUXlHAzdwEqmtePCyFSw2iFLghSZ65ona+1wwjqE=";
+      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=";
     };
   };
 }

pkgs/by-name/te/telemt/package.nix

@@ -5,16 +5,16 @@
 }:
 rustPlatform.buildRustPackage rec {
   pname = "telemt";
-  version = "3.4.25";
+  version = "3.4.23";
 
   src = fetchFromGitHub {
     owner = "telemt";
     repo = "telemt";
     tag = version;
-    hash = "sha256-A9+PWpVyHgQOFb/OsLc8vl4kq8J9reW1/5Hn4yTdJeI=";
+    hash = "sha256-8rKEMQPgIrvtLoM+LcSoXiYaMmCtb4OObnDUYagy+Ak=";
   };
 
-  cargoHash = "sha256-ZaaT3S3Qy7HBI2dETy8JtvWttJWnkhRNA3wWz44pTpQ=";
+  cargoHash = "sha256-wjw+FE1yQ+zc2Ta3h7B3Wtejf6bGobstTKDCjFphU+M=";
 
   checkFlags = [
     # flaky: races between MiddleClientWriterCancelled and TrafficBudgetWaitCancelled observation paths

pkgs/by-name/te/temporal-cli/package.nix

@@ -11,13 +11,13 @@
 
 buildGoModule (finalAttrs: {
   pname = "temporal-cli";
-  version = "1.8.1";
+  version = "1.8.0";
 
   src = fetchFromGitHub {
     owner = "temporalio";
     repo = "cli";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-RswHPnaWN3bLerhttVb/3G//cyz9Fr+x/B4h+/SSSqA=";
+    hash = "sha256-Z5Ba4oVQR6g/HyaBd/0iLIWq6Ht2SJAdylTVaErRFL0=";
   };
 
   vendorHash = "sha256-9lO9uhy1n85QYyoh27cKhdlcuL4GT98aCNWwe8tOwoQ=";

pkgs/by-name/tp/tpnote/package.nix

@@ -13,16 +13,16 @@
 
 rustPlatform.buildRustPackage (finalAttrs: {
   pname = "tpnote";
-  version = "1.26.7";
+  version = "1.26.6";
 
   src = fetchFromGitHub {
     owner = "getreu";
     repo = "tp-note";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-dg6IFozGnvCOHbqZ9p0Eu7CPAv7W1Yf+MqAAFxghBEg=";
+    hash = "sha256-ELRR2nIbkbD/WWS93lyHHYoPY/KLUBO9+/13UUFhA6Y=";
   };
 
-  cargoHash = "sha256-Lu4NBYxplYk5Y3IbfiCv61whW9Dk6fIScZUIB5yBdCk=";
+  cargoHash = "sha256-gFfESz0yn9AJ4QCujaUyXrFnxyHzqi3IX5Gg0Gma0DQ=";
 
   nativeBuildInputs = [
     cmake

pkgs/by-name/ya/yazi/plugins/diff/default.nix

@@ -5,13 +5,13 @@
 }:
 mkYaziPlugin {
   pname = "diff.yazi";
-  version = "0-unstable-2026-07-22";
+  version = "0-unstable-2026-07-01";
 
   src = fetchFromGitHub {
     owner = "yazi-rs";
     repo = "plugins";
-    rev = "bbac5e75b22a2893ef7cdd2bd6814b15f2abb91e";
-    hash = "sha256-lio4pvrqK575q7M+GtRr/5EdA4h2J/7gIvXK8c5rq1U=";
+    rev = "65559fd3edc33cb0fd24ec92874c763fa5f68e3e";
+    hash = "sha256-SLfwFGOcmlZIUqlSSMk7dEEUZQbKqPMidknS3vtFzPo=";
   };
 
   meta = {

pkgs/by-name/ya/yazi/plugins/gvfs/default.nix

@@ -5,13 +5,13 @@
 }:
 mkYaziPlugin {
   pname = "gvfs.yazi";
-  version = "0-unstable-2026-07-23";
+  version = "0-unstable-2026-07-13";
 
   src = fetchFromGitHub {
     owner = "boydaihungst";
     repo = "gvfs.yazi";
-    rev = "364b0a811d722a1fdb3c2bde36aa640591437967";
-    hash = "sha256-bQDcT04m1WvMRCiVIyer4WHgjYMaamMfolmH49lVSig=";
+    rev = "c5a0bb924eceeeb8b44bfc00aba0a97ba0287fa3";
+    hash = "sha256-hSHEN/F4uc1FFScB5lLRAKryLwP+O7I9vgEgobGbQyw=";
   };
 
   meta = {

pkgs/by-name/ya/yazi/plugins/restore/default.nix

@@ -5,13 +5,13 @@
 }:
 mkYaziPlugin {
   pname = "restore.yazi";
-  version = "0-unstable-2026-07-22";
+  version = "0-unstable-2026-04-04";
 
   src = fetchFromGitHub {
     owner = "boydaihungst";
     repo = "restore.yazi";
-    rev = "7bfcfcbda078b7e51d1ff9a62db9c654a3952fa4";
-    hash = "sha256-pmyS1rU5C6U9LloGoDFB8s6GwoMqG1Jve5OFooI64tU=";
+    rev = "0e0870460b9b74c5ae98b7f96c7c26a9a274ce6d";
+    hash = "sha256-rDsyMF5IEBHx+fJ0oYTCCQAlTSquUcOkFLC4Lmbuz6k=";
   };
 
   meta = {

pkgs/by-name/za/zapzap/package.nix

@@ -4,25 +4,8 @@
   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";
@@ -72,12 +55,7 @@ python3Packages.buildPythonApplication (finalAttrs: {
 
   dontWrapQtApps = true;
   preFixup = ''
-    makeWrapperArgs+=(
-      "''${qtWrapperArgs[@]}"
-      ${lib.optionalString (dictionaries != [ ]) ''
-        --set-default QTWEBENGINE_DICTIONARIES_PATH "${qtwebengineDictionaries}"
-      ''}
-    )
+    makeWrapperArgs+=("''${qtWrapperArgs[@]}")
   '';
 
   # has no tests

pkgs/development/compilers/ocaml/generic.nix

@@ -21,7 +21,6 @@ in
   ncurses,
   binutils,
   buildEnv,
-  pkgsBuildBuild,
   libunwind,
   fetchpatch,
   libx11,
@@ -178,7 +177,6 @@ stdenv.mkDerivation (
         ]
       else
         [ "nixpkgs_world" ];
-    nativeBuildInputs = optional (stdenv.hostPlatform != stdenv.targetPlatform) pkgsBuildBuild.ocaml;
     buildInputs =
       optional (lib.versionOlder version "4.07") ncurses
       ++ optionals useX11 [

pkgs/development/coq-modules/mathcomp-word/default.nix

@@ -46,7 +46,6 @@ 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=";
@@ -73,7 +72,7 @@ mkCoqDerivation {
     lib.switch
       [ coq.coq-version mathcomp.version ]
       [
-        (case (range "8.16" "9.1") (isGe "2.0") "3.5")
+        (case (range "8.16" "9.1") (isGe "2.0") "3.4")
         (case (range "8.12" "8.20") (range "1.12" "1.19") "2.4")
       ]
       null;

pkgs/development/coq-modules/multinomials/default.nix

@@ -33,7 +33,7 @@ mkCoqDerivation {
     lib.switch
       [ coq.coq-version mathcomp.version ]
       [
-        (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 "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 "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")

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" "9.3") (range "2.5" "2.6") "2.4.0")
+        (case (range "9.1" "9.2") (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")

pkgs/development/coq-modules/ssprove/default.nix

@@ -32,6 +32,7 @@
       [ 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:

pkgs/development/python-modules/nltk/default.nix

@@ -5,7 +5,6 @@
   fetchFromGitHub,
   buildPythonPackage,
   click,
-  defusedxml,
   joblib,
   regex,
   setuptools,
@@ -24,53 +23,49 @@
 
 buildPythonPackage (finalAttrs: {
   pname = "nltk";
-  version = "3.10.0";
+  version = "3.9.4";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "nltk";
     repo = "nltk";
-    tag = "v${finalAttrs.version}";
-    hash = "sha256-1iflqb3cOyaviW3IostFCuJtZ9KBZI0n9dfKfqqbcO0=";
+    tag = finalAttrs.version;
+    hash = "sha256-kDfMiqXgLq91zzDjv/qDn0XwQkYRn2sITI6E4pgWe/8=";
   };
 
   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 ' "/usr/share/nltk_data", ' ' "/usr/share/nltk_data", "/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")):'
   '';
 
   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-2-0
+          omw-1-4
           pl196x
           porter-test
           ptb
@@ -119,10 +114,9 @@ buildPythonPackage (finalAttrs: {
   };
 
   meta = {
-    changelog = "https://github.com/nltk/nltk/blob/${finalAttrs.src.tag}/ChangeLog";
     description = "Natural Language Processing ToolKit";
     mainProgram = "nltk";
-    homepage = "https://nltk.org/";
+    homepage = "http://nltk.org/";
     license = lib.licenses.asl20;
     maintainers = [ lib.maintainers.bengsparks ];
   };

pkgs/development/python-modules/pinecone-plugin-assistant/default.nix

@@ -0,0 +1,40 @@
+{
+  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";
+  };
+}

pkgs/development/python-modules/pinecone-plugin-interface/default.nix

@@ -0,0 +1,31 @@
+{
+  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";
+  };
+}

pkgs/development/python-modules/pinecone/default.nix

@@ -1,50 +1,47 @@
 {
   lib,
   buildPythonPackage,
-  buildPackages,
+  certifi,
   fetchFromGitHub,
-  httpx,
-  msgspec,
+  hatchling,
   orjson,
-  rustPlatform,
+  pinecone-plugin-assistant,
+  pinecone-plugin-interface,
+  python-dateutil,
+  typing-extensions,
+  urllib3,
 }:
 
 buildPythonPackage rec {
   pname = "pinecone";
-  version = "9.1.0";
+  version = "8.1.2";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "pinecone-io";
     repo = "pinecone-python-client";
     tag = "v${version}";
-    hash = "sha256-yWGW9qx4zb4FnDLXvtXREYXRO7e5Jk/KJoaQlpKMwpg=";
+    hash = "sha256-VfoSW17Bx/eFlnSxUiQZsfY/y210/sKIF5df/kb2kTc=";
   };
 
-  cargoDeps = rustPlatform.fetchCargoVendor {
-    inherit pname version src;
-    hash = "sha256-I3pIy9by+OHo6iU6OZp3VvJJPZOmJ/CYhkzoV8xHoMY=";
-  };
-
-  nativeBuildInputs = with rustPlatform; [
-    cargoSetupHook
-    maturinBuildHook
-  ];
-
-  env.PROTOC = "${lib.getExe buildPackages.protobuf}";
+  build-system = [ hatchling ];
 
   dependencies = [
-    httpx
-    msgspec
+    certifi
     orjson
+    pinecone-plugin-assistant
+    pinecone-plugin-interface
+    python-dateutil
+    typing-extensions
+    urllib3
   ];
 
   pythonImportsCheck = [ "pinecone" ];
 
   meta = {
-    description = "Pinecone Python SDK";
+    description = "Pinecone python client";
     homepage = "https://www.pinecone.io/";
-    changelog = "https://github.com/pinecone-io/python-sdk/releases/tag/${src.tag}";
+    changelog = "https://github.com/pinecone-io/pinecone-python-client/releases/tag/${src.tag}";
     license = lib.licenses.asl20;
     maintainers = with lib.maintainers; [ happysalada ];
   };

pkgs/development/r-modules/bioc-experiment-packages.json

@@ -587,9 +587,9 @@
     },
     "Hiiragi2013": {
       "name": "Hiiragi2013",
-      "version": "1.47.0",
-      "sha256": "1p2d6vpss2s61n82p6wy7nq86zjhfw0nw9wi8ws3hhq6nxs1h7pp",
-      "depends": ["Biobase", "KEGGREST", "MASS", "RColorBrewer", "affy", "boot", "clue", "cluster", "genefilter", "geneplotter", "gplots", "gtools", "lattice", "latticeExtra", "mouse4302_db", "xtable"]
+      "version": "1.48.1",
+      "sha256": "0ariib3wsc6d7a0wkgp9j303id5a31zy4h38dwgb82hvvfp29q5z",
+      "depends": ["Biobase", "MASS", "RColorBrewer", "cluster", "genefilter", "gplots", "lattice", "latticeExtra"]
     },
     "HumanAffyData": {
       "name": "HumanAffyData",
@@ -2343,6 +2343,12 @@
       "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",
@@ -3014,13 +3020,6 @@
       "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",

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", "preseqR", "randomForest", "rtracklayer"]
+      "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "ChIPpeakAnno", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "GenomicScores", "IRanges", "KernSmooth", "Rsamtools", "S4Vectors", "edgeR", "limma", "motifStack", "randomForest", "rtracklayer"]
     },
     "ATACseqTFEA": {
       "name": "ATACseqTFEA",
@@ -275,8 +275,8 @@
     },
     "AnVILGCP": {
       "name": "AnVILGCP",
-      "version": "1.6.0",
-      "sha256": "1z4nmvx0sjpby2m1z3a9mw8sg74xw5nihhcjq6dsfxkn997qd3j4",
+      "version": "1.6.2",
+      "sha256": "0fcqbh2ykbdjybbc1l893dk4s6v9ag1lpmhh04lpkn5zr4lb8jys",
       "depends": ["AnVILBase", "BiocBaseUtils", "GCPtools", "dplyr", "httr", "jsonlite", "rlang", "tibble", "tidyr"]
     },
     "AnVILPublish": {
@@ -317,8 +317,8 @@
     },
     "AnnotationHub": {
       "name": "AnnotationHub",
-      "version": "4.2.0",
-      "sha256": "0ra9cya4kln8fhsff0qbpp8fjx8i68ka9xrm2vjv2nw2yw8klzk4",
+      "version": "4.2.2",
+      "sha256": "0ai9m9yd0hs6vzgz4ri3vbnifd31ffzwy8fhaby9kzy9n51x92d5",
       "depends": ["AnnotationDbi", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "RSQLite", "S4Vectors", "curl", "dplyr", "httr2", "rappdirs", "yaml"]
     },
     "AnnotationHubData": {
@@ -365,8 +365,8 @@
     },
     "BASiCStan": {
       "name": "BASiCStan",
-      "version": "1.14.0",
-      "sha256": "1224zcj5imy7r24w0qbmyb13yc4hf907d980nbp38yrv6ynw3in0",
+      "version": "1.14.1",
+      "sha256": "0lrfzxjhvq0dhind9783q69r7kabrjj6nvv5kn2c8d986dz6n0p0",
       "depends": ["BASiCS", "BH", "Rcpp", "RcppEigen", "RcppParallel", "SingleCellExperiment", "StanHeaders", "SummarizedExperiment", "glmGamPoi", "rstan", "rstantools", "scran", "scuttle"]
     },
     "BBCAnalyzer": {
@@ -509,8 +509,8 @@
     },
     "BatChef": {
       "name": "BatChef",
-      "version": "1.0.1",
-      "sha256": "0n792nj9hs9vh9n25ckfav4birlgbn994wfki5gxckcd4k0bmf0a",
+      "version": "1.0.2",
+      "sha256": "0qmg53dls168nfhlzvak5nx35wif0s5l4l9na1xpkd3iqpjif8fm",
       "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": "1.14.0",
-      "sha256": "143k126qn1n86kfqsbxwkamnph6hv1w52cqrsjk2ym4swp9794vc",
+      "version": "1.14.2",
+      "sha256": "1fijpvdy26sqqk3m16yan7k8yw5rky3dwy2adnchz1ql43dnixyi",
       "depends": []
     },
     "BiocBook": {
@@ -671,14 +671,14 @@
     },
     "BiocBuildReporter": {
       "name": "BiocBuildReporter",
-      "version": "1.0.0",
-      "sha256": "0zxrg8qizpr8vic7snazwvbfnhdcpxxvsampk1ryvs69iymi6zgn",
+      "version": "1.0.1",
+      "sha256": "1kmy3lh4lp6raav8yzq7fk96bqgprslzi816vcj657glgiiir6aa",
       "depends": ["BiocFileCache", "arrow", "dplyr"]
     },
     "BiocCheck": {
       "name": "BiocCheck",
-      "version": "1.48.0",
-      "sha256": "149avgqaslz276hhihr062agsgkar0imfyjg3in2xib7257dki3r",
+      "version": "1.48.1",
+      "sha256": "02df2w2b6ivj1j9fpjlvfgsccm9prwygyzc7ywdnbcfvmdjf115b",
       "depends": ["BiocBaseUtils", "BiocFileCache", "BiocManager", "biocViews", "callr", "cli", "codetools", "commonmark", "graph", "httr2", "knitr", "rvest", "stringdist", "xml2"]
     },
     "BiocFHIR": {
@@ -1211,8 +1211,8 @@
     },
     "CatsCradle": {
       "name": "CatsCradle",
-      "version": "1.6.0",
-      "sha256": "0vhwcmdlsp1kji13sv18plrc6s7ql42njagc2qb5crmrh8rx295n",
+      "version": "1.6.1",
+      "sha256": "1slc2nfv168nbzyc55r6vhabnsxjbr9sw655w1nssrx3i7x3v5kx",
       "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": "1.0.0",
-      "sha256": "00cdp9qw5isx7bixw8cjxa3f24h0rqabz1bdxwsy4x99z3sn03nw",
+      "version": "1.0.1",
+      "sha256": "0qyck58dbgglyfqdjn9y24ipmbib4mcqr3vzmvj8vh7iq93z5a8h",
       "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": "1.12.0",
-      "sha256": "1jgx62zla9jn1246hjvdgxx7k1605p7kgyv3wm24p4abxglxwy5y",
+      "version": "1.12.1",
+      "sha256": "1574vbv2xn9a1a1qbxvabidhk0zhsgihvdbypznvzbpj18bap9fr",
       "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": "0.38.1",
-      "sha256": "1gpbamzchzqg1czpf0krkr3qpp1fkmj86kmjvg09gmq8l69qm1d6",
+      "version": "0.38.2",
+      "sha256": "1zg3xy6bx76h429lvqvp2dv2dhix854w2ym4m55dygcfixgiklyr",
       "depends": ["BiocGenerics", "IRanges", "Matrix", "MatrixGenerics", "S4Arrays", "S4Vectors", "SparseArray"]
     },
     "DelayedDataFrame": {
@@ -2111,8 +2111,8 @@
     },
     "ENmix": {
       "name": "ENmix",
-      "version": "1.48.0",
-      "sha256": "1rbv95gqhklm6mjl2d2cz7dfiyvgrzbsxnwdcynyi6a5zysn2zih",
+      "version": "1.48.3",
+      "sha256": "1g9mdi2bmx12jsvcbrsp9mpyzrhr6a3n11hmgyn9za7dzibq7dnj",
       "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": "1.2.0",
-      "sha256": "1ajb8awl6l6af37dpn2zn8yi6wgc5kg61i3vx59jq2s8xvxwnf5r",
+      "version": "1.2.1",
+      "sha256": "035fii0lrzqardv3dnb68vr5gnhx21xciqnigldm8wz0a41c71wq",
       "depends": ["AnVILBase", "BiocBaseUtils", "dplyr", "httr", "rlang", "tibble", "tidyr"]
     },
     "GDCRNATools": {
@@ -2489,8 +2489,8 @@
     },
     "GOSemSim": {
       "name": "GOSemSim",
-      "version": "2.38.0",
-      "sha256": "1bfrxb6zm9lms264wb4xzxdb50py97zdr6lh3mharzxnngbri4d7",
+      "version": "2.38.3",
+      "sha256": "0i6nkhplfwim60qxs3f5n8pr5fz1pslw09f278vgc0sj6wy6q9b7",
       "depends": ["AnnotationDbi", "DBI", "GO_db", "Rcpp", "digest", "rlang", "yulab_utils"]
     },
     "GOTHiC": {
@@ -2867,8 +2867,8 @@
     },
     "Glimma": {
       "name": "Glimma",
-      "version": "2.21.0",
-      "sha256": "1n3x7nm65mszjz558zcfs8hrpc1wd0vf91xrh2r0pcjbgwqkmg9b",
+      "version": "2.22.1",
+      "sha256": "1qks28b7skw8rzd2yd2xyhglxqscp5cpv0ffrnm57b83a6izy0i6",
       "depends": ["DESeq2", "S4Vectors", "SummarizedExperiment", "edgeR", "htmlwidgets", "jsonlite", "limma"]
     },
     "GloScope": {
@@ -2909,8 +2909,8 @@
     },
     "GraphExperiment": {
       "name": "GraphExperiment",
-      "version": "1.0.0",
-      "sha256": "1ijqk2bxqmkqnqbnqqbx3vrwpy5csqwyh7mrnqgwc5a4xz2zqgih",
+      "version": "1.0.2",
+      "sha256": "0ayyfzq27a7w67w8qi9limpphpdg44503pf1kw43gh4apn4dcr5s",
       "depends": ["BiocBaseUtils", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "igraph"]
     },
     "GreyListChIP": {
@@ -3167,8 +3167,8 @@
     },
     "HuBMAPR": {
       "name": "HuBMAPR",
-      "version": "1.6.1",
-      "sha256": "0kvc79f23i91p2cv4wq618zbqvrp1s2x1dqkk912d59l96nrdf0n",
+      "version": "1.6.2",
+      "sha256": "0hfxpmnkhspfv0cm0mmdzpzkndpijzdzjmmnbl8nj3pw0r1cwn55",
       "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", "HDCI", "Matrix", "MatrixExtra", "S4Vectors", "SummarizedExperiment", "doParallel", "doRNG", "foreach", "glmnet", "mathjaxr", "parallelly", "stringr"]
+      "depends": ["DescTools", "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", "depmixS4", "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", "dplyr", "flock", "future", "future_apply", "ggplot2", "limma", "magrittr", "parallelly", "plyranges", "preprocessCore", "readr", "reshape2"]
     },
     "InTAD": {
       "name": "InTAD",
@@ -3413,8 +3413,8 @@
     },
     "KEGGREST": {
       "name": "KEGGREST",
-      "version": "1.52.0",
-      "sha256": "1z9xp4pkpqcyadbrzam7qxqcrrqy29pn926n3nqni6cpypbv7jj4",
+      "version": "1.52.2",
+      "sha256": "1jp9b8r51z3a8644xclk165rmkd6gj9lfj4j7v73dj5a67prhslf",
       "depends": ["Biostrings", "httr", "png"]
     },
     "KEGGgraph": {
@@ -3983,9 +3983,9 @@
     },
     "MeLSI": {
       "name": "MeLSI",
-      "version": "1.0.0",
-      "sha256": "09nmljg69s80851vl3frzdc6xp36rnkhga1r6nf90i0ildky848b",
-      "depends": ["ggplot2", "phyloseq", "vegan"]
+      "version": "1.0.1",
+      "sha256": "02k9qbbss9lrzrradxnlh8wz44wqs3g70pigs0314hgy3q1zqmnb",
+      "depends": ["Rcpp", "ggplot2"]
     },
     "MeSHDbi": {
       "name": "MeSHDbi",
@@ -4187,8 +4187,8 @@
     },
     "Moonlight2R": {
       "name": "Moonlight2R",
-      "version": "1.10.0",
-      "sha256": "1c8lin5gf4k7kyqs7gcp1hbx890wd01xihjgc33qzmlhnm0d293y",
+      "version": "1.10.1",
+      "sha256": "0w996b523823w8838r7a4drckpny43p7sar08ix46d65sxzi5cr9",
       "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": "2.4.0",
-      "sha256": "1nra87n4pnzy8shg7s2gg82n4xrczdvfafqmi0i9iywgbm5f47i5",
+      "version": "2.4.1",
+      "sha256": "10bjv6zjal5wszqrmr0xcg5c38dvr7ilwngaf5mlf9gsf3j97m83",
       "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": "2.0.0",
-      "sha256": "1mygyari0xinmw7kiwb258z4f3qjkm4bvhjqm9hl89jc7qx356s0",
+      "version": "2.0.1",
+      "sha256": "1m8sgy7pfqpyf5ipjdzc1zgxsnz9k5jzxvhawk84csyz9azgy2wf",
       "depends": ["R_utils", "curl", "jsonlite", "lifecycle", "paws_storage"]
     },
     "RbcBook1": {
@@ -5531,8 +5531,8 @@
     },
     "Rega": {
       "name": "Rega",
-      "version": "1.0.0",
-      "sha256": "184cxjfm0hiik4d3l4fylch0m7gg0wyv7gj9hdkasf8vj57fqy2s",
+      "version": "1.0.2",
+      "sha256": "0zfc86qjhlhhv5g6f8xwdf50yyg1p7p66fprgmhrpb0ggp7f53fg",
       "depends": ["askpass", "httr2", "jsonlite", "jsonvalidate", "keyring", "readxl", "rlang", "stringr", "tibble", "tidyr", "validate", "yaml"]
     },
     "RegionalST": {
@@ -5927,9 +5927,9 @@
     },
     "SPONGE": {
       "name": "SPONGE",
-      "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"]
+      "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"]
     },
     "SPOTlight": {
       "name": "SPOTlight",
@@ -6035,8 +6035,8 @@
     },
     "SeqArray": {
       "name": "SeqArray",
-      "version": "1.52.0",
-      "sha256": "1nk1xbm10057abm3x5f1z8p0pylr1rhcjbkjvrj0ks85m627i2wf",
+      "version": "1.52.1",
+      "sha256": "00sdj7xr8rlb22c51c1dbb0hfh1fza729ngmzhsdxi032asi10b0",
       "depends": ["Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "digest", "gdsfmt"]
     },
     "SeqGSEA": {
@@ -6257,8 +6257,8 @@
     },
     "Spectra": {
       "name": "Spectra",
-      "version": "1.22.0",
-      "sha256": "19310y9g2jp3a75a1k4yb4b8n306b7pbhycwjgwrhpvn2xxz5lz4",
+      "version": "1.22.2",
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       "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", "PRIMME", "cluster", "dplyr", "magrittr"]
+      "depends": ["BiocParallel", "GenomicRanges", "HiCcompare", "Matrix", "cluster", "dplyr", "magrittr"]
     },
     "SpectriPy": {
       "name": "SpectriPy",
@@ -6409,7 +6409,7 @@
       "name": "TADCompare",
       "version": "1.22.0",
       "sha256": "05lrx7qhkybnw9x8i35xsnrbgb3riwiqqb9n7n60jr2sadlm1cwm",
-      "depends": ["HiCcompare", "Matrix", "PRIMME", "RColorBrewer", "cluster", "cowplot", "dplyr", "ggplot2", "ggpubr", "magrittr", "reshape2", "tidyr"]
+      "depends": ["HiCcompare", "Matrix", "RColorBrewer", "cluster", "cowplot", "dplyr", "ggplot2", "ggpubr", "magrittr", "reshape2", "tidyr"]
     },
     "TAPseq": {
       "name": "TAPseq",
@@ -6437,8 +6437,8 @@
     },
     "TCGAutils": {
       "name": "TCGAutils",
-      "version": "1.32.0",
-      "sha256": "1skm8rlsrc9k95z0zglc82622sjjxq19wxwm55vyq7450gnw2n0k",
+      "version": "1.32.2",
+      "sha256": "1rphdzyr8f9z5z7i1lryjzcv0g1m1dj8ygx7jahdjwf3f4819m5d",
       "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": "1.12.0",
-      "sha256": "08bs3jiv355035kdzsjwn8zd0lwdlz0jy3l33y70j1pjq2ss0zzb",
+      "version": "1.12.1",
+      "sha256": "114q6vcy45w8y5ir7x0wwzd27l2n2sn041z38vnd9641ih0pw1xc",
       "depends": ["Rcpp", "Rhdf5lib", "S4Vectors", "alabaster_schemas", "assorthead", "jsonlite", "jsonvalidate", "rhdf5"]
     },
     "alabaster_bumpy": {
@@ -7271,8 +7271,8 @@
     },
     "assorthead": {
       "name": "assorthead",
-      "version": "1.6.1",
-      "sha256": "1j3c29d0j9612ayjy18q3clqdq85lym1y0gfq0vnl72jcwpzdynh",
+      "version": "1.6.3",
+      "sha256": "0vh175mpwmdjw30if09ddzlnvrh8r8lr2gxi5l0bjhwxc2xhdhvm",
       "depends": []
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     "asuri": {
@@ -8759,8 +8759,8 @@
     },
     "edgeR": {
       "name": "edgeR",
-      "version": "4.10.0",
-      "sha256": "0qd089xydha4vx2hdg9yzy1zc8hr29qaf804rj79gfh8krih4bxh",
+      "version": "4.10.1",
+      "sha256": "0yh5w155izrzby1p4nyiwlxzzy2jha8dri6w94831kz1lvl8wgkg",
       "depends": ["limma", "locfit"]
     },
     "eds": {
@@ -8801,8 +8801,8 @@
     },
     "ensembldb": {
       "name": "ensembldb",
-      "version": "2.36.0",
-      "sha256": "1x5yxmsbvrd9a60jc2cmybr5kd5jw3d187312afflwjl08p7y4vq",
+      "version": "2.36.1",
+      "sha256": "1rzx68kk6rfjlrax8yqyasx8dw4sgwngd7w99cylxzbq9fxh5ynn",
       "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": "1.16.1",
-      "sha256": "1m4fzj5bmd5dh44nz0as6a4a5pkrijp3p542y5dq5pyafisl1a5v",
+      "version": "1.16.2",
+      "sha256": "0zmnqhraa58y5vap1jp92bjxjdihfib7xd2x260dx4p7mcd4yr8r",
       "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": "1.10.0",
-      "sha256": "0982ibfn3j8g4ccra40yd0knwigvj7jaq2zpx3ivd0ra5phr49vw",
+      "version": "1.10.1",
+      "sha256": "0b6s97laal3lc5fibhz4fb40fi5gwlpx3kv3yl5rv0pscq36j73l",
       "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": "1.12.0",
-      "sha256": "0xd511igjmj1bb4g8kw4557cy1kj377gklwkm6dlhfkigi7m398y",
+      "version": "1.12.1",
+      "sha256": "1lq1qripvykp27m9llyy2jlpci37aj5c3hfhd7i3sflfgdyf929i",
       "depends": ["BiocManager", "dplyr", "flowCore", "flowWorkspace", "ggcyto", "ggplot2", "purrr", "rlang", "shiny", "tibble"]
     },
     "flowGraph": {
@@ -9383,8 +9383,8 @@
     },
     "gatom": {
       "name": "gatom",
-      "version": "1.10.0",
-      "sha256": "0lvyd3bjwzvs0alzxs2zzmsd432f45a2x38c28n7qlx4ckgd0g2h",
+      "version": "1.10.2",
+      "sha256": "1c9w586rci3l5mhlzhkb8afgpb5hc3b2hxagqf1fbkivqiq6hj48",
       "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": "1.48.1",
-      "sha256": "001l93k5912fgiqp7a6h1lmlxvwn5kbgs1cal9qyl2v1i5q6ggbr",
+      "version": "1.48.2",
+      "sha256": "1clql2dqr1gr8jh6ddn9cbrb5aj4f96z9yvn1hxxp87fs3kiym91",
       "depends": []
     },
     "geNetClassifier": {
@@ -9611,8 +9611,8 @@
     },
     "ggtreeExtra": {
       "name": "ggtreeExtra",
-      "version": "1.22.0",
-      "sha256": "196hz0xxaqmipqkv51q4w3fsv8rc6yxn6svgyzxxq6zn1wlwhqwn",
+      "version": "1.22.1",
+      "sha256": "17zlm3bpibd18qbs8s6w84j8kpb2zm5b2n0lzj1rgnyq6cb6vxhj",
       "depends": ["cli", "ggnewscale", "ggplot2", "ggtree", "magrittr", "rlang", "tidytree", "yulab_utils"]
     },
     "ggtreeSpace": {
@@ -10067,8 +10067,8 @@
     },
     "igblastr": {
       "name": "igblastr",
-      "version": "1.2.2",
-      "sha256": "0g6qirgvgpqpmklw2n2y19mjirp2djx8vvxaaqfx8pf17c20fh14",
+      "version": "1.2.12",
+      "sha256": "1xbnnzdi5nrc60v9w4xgp5f6nr7fpgzwy6wpx78djxf8w605g3bc",
       "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "IRanges", "R_utils", "S4Vectors", "curl", "httr", "jsonlite", "rvest", "tibble", "xml2", "xtable"]
     },
     "igvR": {
@@ -10337,8 +10337,8 @@
     },
     "limma": {
       "name": "limma",
-      "version": "3.68.3",
-      "sha256": "0xvqvp8582n890ndjx656qpgkyncfrcsy887a2k9ff1sm19q2dhx",
+      "version": "3.68.4",
+      "sha256": "0452k5p1v01qjzk6jlip6ix871dfyn0prvxjxpjxdnjl4zbkrz3v",
       "depends": ["statmod"]
     },
     "limmaGUI": {
@@ -11075,8 +11075,8 @@
     },
     "motifTestR": {
       "name": "motifTestR",
-      "version": "1.8.0",
-      "sha256": "1y40m4pldm1q3iwa24j8h9yvknj0d826w186mkf809xmscy2xk02",
+      "version": "1.8.1",
+      "sha256": "0mcxcr45d08lq0rdxbisc9niwqhqcrdc5b2aky955di86asdh3nl",
       "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", "depmixS4", "magrittr"]
+      "depends": ["AnnotationHub", "BiocStyle", "GenomicRanges", "Seurat", "SingleCellExperiment", "data_table", "magrittr"]
     },
     "pathMED": {
       "name": "pathMED",
@@ -11825,8 +11825,8 @@
     },
     "pipeComp": {
       "name": "pipeComp",
-      "version": "1.22.0",
-      "sha256": "19qzv5060a9vf1p25iwryv6adfpbdbzh2h1smv6i1wb3zr374x1a",
+      "version": "1.22.1",
+      "sha256": "06hzffzg73x90zw9czjqvw1z432n5nq5bc749bi4syb0n4r9zw16",
       "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": {
@@ -12027,6 +12027,12 @@
       "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",
@@ -12053,8 +12059,8 @@
     },
     "psichomics": {
       "name": "psichomics",
-      "version": "1.38.0",
-      "sha256": "1fxrhxb9nidg3dq2qm45sa0dnsqg2pcwp74a5ybpm61kj7bfihqn",
+      "version": "1.38.1",
+      "sha256": "1phvwnb0mzikhj1mj76p1ymlrdv80ahqb8kg7cana6v6m6c1lg4d",
       "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": {
@@ -12389,9 +12395,9 @@
     },
     "rfaRm": {
       "name": "rfaRm",
-      "version": "1.23.0",
-      "sha256": "1v4zv4spfvnj4wsq5bkcv4mf0xl4g98n87b3xrl4w2lyr6s2sg19",
-      "depends": ["Biostrings", "IRanges", "S4Vectors", "data_table", "httr", "jsonlite", "magick", "rsvg", "rvest", "stringi", "xml2"]
+      "version": "1.24.1",
+      "sha256": "1jam21z522ara21xr8yhwsxg0w7mi9w3qmys65mnly1ry25s79hi",
+      "depends": ["Biostrings", "IRanges", "S4Vectors", "data_table", "httr", "magick", "rsvg", "rvest", "stringi", "xml2"]
     },
     "rgoslin": {
       "name": "rgoslin",
@@ -12413,8 +12419,8 @@
     },
     "rhdf5client": {
       "name": "rhdf5client",
-      "version": "1.34.0",
-      "sha256": "1vmw9zcsrw5kj02k3syvwxk4xvkaawqjhjk7z3h2fap8mg7h08z0",
+      "version": "1.34.2",
+      "sha256": "1147i9164kvh01fkginqjmrshbq7bd66mjih1iv6nvgwc81w2n02",
       "depends": ["DelayedArray", "data_table", "httr", "rjson"]
     },
     "rhdf5filters": {
@@ -12689,9 +12695,9 @@
     },
     "scDblFinder": {
       "name": "scDblFinder",
-      "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"]
+      "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"]
     },
     "scDesign3": {
       "name": "scDesign3",
@@ -12713,8 +12719,8 @@
     },
     "scECODA": {
       "name": "scECODA",
-      "version": "1.0.0",
-      "sha256": "1lglmsinwpmwb48547bphd0fpl2c6qcjvnm36a1vib2w5qydx5id",
+      "version": "1.0.1",
+      "sha256": "0vcqyxzzybcs7a5gbrb785vbagqdcyqwad84x2nhdnrqj4q7rr5w",
       "depends": ["BiocGenerics", "DESeq2", "Matrix", "S4Vectors", "SummarizedExperiment", "cluster", "corrplot", "dplyr", "factoextra", "ggplot2", "ggpubr", "ggrepel", "gtools", "mclust", "pheatmap", "plotly", "rlang", "rstatix", "stringr", "tidyr", "vegan"]
     },
     "scFeatureFilter": {
@@ -12779,8 +12785,8 @@
     },
     "scMitoMut": {
       "name": "scMitoMut",
-      "version": "1.7.0",
-      "sha256": "1h4hpg1h0f39fhlffz7lw9a2ryrbygicnaz13r50lmwjqqmj41v4",
+      "version": "1.8.0",
+      "sha256": "0p39pcm68hwm557i7wqi2s4wsy5xrzzm43ivmwq5hn1f874whz8h",
       "depends": ["RColorBrewer", "Rcpp", "RcppArmadillo", "data_table", "ggplot2", "magrittr", "pheatmap", "plyr", "readr", "rhdf5", "stringr"]
     },
     "scMultiSim": {
@@ -12829,7 +12835,7 @@
       "name": "scRecover",
       "version": "1.28.0",
       "sha256": "0mp91i8ar6blbilamm7gblcyj1zkah74y5mdv7z71jhvzh6rijmi",
-      "depends": ["BiocParallel", "MASS", "Matrix", "SAVER", "bbmle", "doParallel", "foreach", "gamlss", "kernlab", "penalized", "preseqR", "pscl", "rsvd"]
+      "depends": ["BiocParallel", "MASS", "Matrix", "SAVER", "bbmle", "doParallel", "foreach", "gamlss", "kernlab", "penalized", "pscl", "rsvd"]
     },
     "scRepertoire": {
       "name": "scRepertoire",
@@ -12899,9 +12905,9 @@
     },
     "scater": {
       "name": "scater",
-      "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"]
+      "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"]
     },
     "scatterHatch": {
       "name": "scatterHatch",
@@ -13103,8 +13109,8 @@
     },
     "sesame": {
       "name": "sesame",
-      "version": "1.30.0",
-      "sha256": "081rjiqip0aqxc23pvzp0vwiyn7lnca2z33jyan629w70nfxy2bb",
+      "version": "1.30.1",
+      "sha256": "09g9aw0drswg80g10427739sg8birkalscpq22v11srx31483hvd",
       "depends": ["BiocFileCache", "BiocParallel", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "Seqinfo", "SummarizedExperiment", "dplyr", "ggplot2", "preprocessCore", "readr", "reshape2", "sesameData", "stringr", "tibble", "wheatmap"]
     },
     "sevenC": {
@@ -13699,7 +13705,7 @@
       "name": "tLOH",
       "version": "1.19.0",
       "sha256": "0p6vpkj8v749jxrhbldkrl0rci26pbg8cwic0zj1irp3k0rxpds8",
-      "depends": ["GenomicRanges", "MatrixGenerics", "VariantAnnotation", "bestNormalize", "data_table", "depmixS4", "dplyr", "ggplot2", "naniar", "purrr", "scales", "stringr"]
+      "depends": ["GenomicRanges", "MatrixGenerics", "VariantAnnotation", "bestNormalize", "data_table", "dplyr", "ggplot2", "naniar", "purrr", "scales", "stringr"]
     },
     "tRNA": {
       "name": "tRNA",
@@ -13949,8 +13955,8 @@
     },
     "transmogR": {
       "name": "transmogR",
-      "version": "1.8.0",
-      "sha256": "1pc0k73k1ls9v7iqlb0khmvcylds2cs0y1s46pjaw1hk3aq37r8l",
+      "version": "1.8.1",
+      "sha256": "0fbgzdb3kz5cwp1l7wp8fays9nyiq5i1ympr2r236vf6m4yzlv25",
       "depends": ["BSgenome", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "data_table", "ggplot2", "jsonlite", "matrixStats", "patchwork", "scales"]
     },
     "transomics2cytoscape": {
@@ -17710,13 +17716,6 @@
       "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",

pkgs/development/r-modules/generic-builder.nix

@@ -38,8 +38,14 @@ 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
     '';
 

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" "9.3") "1.10.3")
+        (case (range "9.0" "9.2") "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")

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" "9.3") "1.0.4")
+      (case (range "9.0" "9.2") "1.0.4")
     ] null;
 
   propagatedBuildInputs = [ mathcomp-boot ];

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" "9.3") (range "2.5" "2.6") "2.2.4") # also compiles on Rocq 9.0 and 9.1 (but requires graph-theory update)
+        (case (range "9.2" "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 "9.0" "9.1") (range "2.3" "2.5") "2.2.2")
       ]
       null;

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" "9.3") (isGe "2.6.0") "2.0.6")
+        (case (range "9.0" "9.2") (isGe "2.6.0") "2.0.6")
         (case (range "9.0" "9.2") (isEq "2.5.0") "2.0.5")
       ]
       null;

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" "9.3") "2.6.0") # also compiles on Rocq 9.0 and 9.1
+      (case (range "9.2" "9.2") "2.6.0") # also compiles on Rocq 9.0 and 9.1
       (case (range "9.0" "9.1") "2.5.0")
     ] null;
   release = {

pkgs/development/rocq-modules/micromega-plugin/default.nix

@@ -15,12 +15,10 @@ 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}";

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" "9.3") "3.7.1")
+        (case (range "9.0" "9.2") "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;
@@ -37,13 +37,11 @@ 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=";

pkgs/development/rocq-modules/rocqnavi/default.nix

@@ -17,7 +17,7 @@ mkRocqDerivation {
     in
     with versions;
     switch rocq-core.rocq-version [
-      (case (range "9.0" "9.3") "0.5.0")
+      (case (range "9.0" "9.2") "0.5.0")
     ] null;
   release = {
     "0.5.0".hash = "sha256-pmK4gD5ccerjr2UVgwGIVbjH/RiXdYQq79/XFetiHZg=";

pkgs/tools/text/nltk-data/default.nix

@@ -7,7 +7,7 @@
 }:
 let
   base = {
-    version = "0-unstable-2026-07-01";
+    version = "0-unstable-2024-07-29";
     nativeBuildInputs = [ unzip ];
     dontBuild = true;
     dontFixup = true;
@@ -30,10 +30,9 @@ let
     }:
     let
       src = fetchFromGitHub {
-        name = "nltk-${location}";
         owner = "nltk";
         repo = "nltk_data";
-        rev = "550b6625bcef1f2abff2ff770a5a0d272c9c6b2a";
+        rev = "cfe82914f3c2d24363687f1db3b05e8b9f687e2b";
         inherit hash;
         sparseCheckout = [ "packages/${location}/${pname}.zip" ];
       };
@@ -61,7 +60,7 @@ let
     makeNltkDataPackage {
       inherit pname;
       location = "chunkers";
-      hash = "sha256-+n0TkS+/NHk0OqFZNQBLIcO/9uw56Mn7/AyNkRDGZEQ=";
+      hash = "sha256-kemjqaCM9hlKAdMw8oVJnp62EAC9rMQ50dKg7wlAwEc=";
     };
 
   makeCorpus =
@@ -69,7 +68,7 @@ let
     makeNltkDataPackage {
       inherit pname;
       location = "corpora";
-      hash = "sha256-7uiTXZ+eMyBtH135NsYoAjLV6R/DG2hVV+RJwYDmu50=";
+      hash = "sha256-8lMjW5YI8h6dHJ/83HVY2OYGDyKPpgkUAKPISiAKqqk=";
     };
 
   makeGrammar =
@@ -77,7 +76,7 @@ let
     makeNltkDataPackage {
       inherit pname;
       location = "grammars";
-      hash = "sha256-KoZ1q0F2X7bSFdbw1qK/jzZ3iuMJXTYHfogylO7nHEY=";
+      hash = "sha256-pyLEcX3Azv8j1kCGvVYonuiNgVJxtWt7veU0S/yNbIM=";
     };
 
   makeHelp =
@@ -85,7 +84,7 @@ let
     makeNltkDataPackage {
       inherit pname;
       location = "help";
-      hash = "sha256-2x3kemPdipHAj0TGYCm6Il5Aapx+fuo/jlNT9+XWbss=";
+      hash = "sha256-97mYLNES5WujLF5gD8Ul4cJ6LqSzz+jDzclUsdBeHNE=";
     };
 
   makeMisc =
@@ -93,7 +92,7 @@ let
     makeNltkDataPackage {
       inherit pname;
       location = "misc";
-      hash = "sha256-edBgrWM+eQgEGWq7oBHTebtvJPZcofCzzXSu3S9Fa1o=";
+      hash = "sha256-XtizfEsc8TYWqvvC/eSFdha2ClC5/ZiJM8nue0vXLb4=";
     };
 
   makeModel =
@@ -101,7 +100,7 @@ let
     makeNltkDataPackage {
       inherit pname;
       location = "models";
-      hash = "sha256-uTRr9pBfL1KZ7z8WTQPAiWlMn/os4ISa9tj/Si/RmtI=";
+      hash = "sha256-iq3weEgCci6rgLW2j28F2eRLprJtInGXKe/awJPSVG4=";
     };
 
   makeTagger =
@@ -109,7 +108,7 @@ let
     makeNltkDataPackage {
       inherit pname;
       location = "taggers";
-      hash = "sha256-V5bs0JUQgr4ijs2NaF5JXzVwT1e/ZYnlU0TZXeoqfM4=";
+      hash = "sha256-tl3Cn2okhBkUtTXvAmFRx72Brez6iTGRdmFTwFmpk3M=";
     };
 
   makeTokenizer =
@@ -117,7 +116,7 @@ let
     makeNltkDataPackage {
       inherit pname;
       location = "tokenizers";
-      hash = "sha256-V/Qs8wJbCZB8gp5pAAM1JK8aAfcHorNyvAkHUat56uY=";
+      hash = "sha256-OzMkruoYbFKqzuimOXIpE5lhHz8tmSqOFoLT+fjdTVg=";
     };
 
   makeStemmer =
@@ -125,7 +124,7 @@ let
     makeNltkDataPackage {
       inherit pname;
       location = "stemmers";
-      hash = "sha256-6sQQCA8r8jWRFImpiBovUt/IzHjh13W6X8yLpn61cs0=";
+      hash = "sha256-mNefwOPVJGz9kXV3LV4DuV7FJpNir/Nwg4ujd0CogEk=";
     };
 in
 lib.makeScope newScope (self: {
@@ -153,7 +152,6 @@ 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";
@@ -172,7 +170,6 @@ 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";
@@ -181,7 +178,6 @@ 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";

pkgs/top-level/aliases.nix

@@ -1728,7 +1728,6 @@ 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

pkgs/top-level/all-packages.nix

@@ -7104,11 +7104,6 @@ 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

pkgs/top-level/python-aliases.nix

@@ -439,8 +439,6 @@ 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

pkgs/top-level/python-packages.nix

@@ -13199,6 +13199,10 @@ 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 { };