glog: disable optimization-dependent stacktrace test

This test fails under GCC 16. It appears to be because it makes assumptions that certain compiler optimizations do not occur. It clearly is compiler-specific and tries to work around specific compiler optimizations upstream. In particular, an analysis of the test 53d58e4531/src/stacktrace_unittest.cc (L218) shows that it would be very plausible/correct for GCC to place labels such that the `INIT_ADDRESS_RANGE` macro has `start` and `end` labels that have the same address. While the functions are labeled NOINLINE, interprocedural analysis could *plausibly* produce this result. While we are not completely certain that this is the case, it seems likely that this is not a genuine issue and just a questionable test.
assimp: never treat warnings as fatal
2026-07-25 01:50:40 +00:00 · 2026-07-24 12:59:10 -04:00 · 2026-07-24 12:59:10 -04:00 · 2026-07-24 10:52:32 -04:00 · 2026-07-24 10:52:28 -04:00 · 2026-07-24 10:52:15 -04:00
55 changed files with 7312 additions and 10605 deletions
--- 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/doc/release-notes/rl-2611.section.md
+++ b/doc/release-notes/rl-2611.section.md
@@ -16,6 +16,8 @@
  +nixpkgs.url = "https://channels.nixos.org/nixos-26.05/nixexprs.tar.zst";
  ```

+- GCC has been updated from GCC 15 to GCC 16. This introduces some backwards-incompatible changes. Refer to the [upstream porting guide](https://gcc.gnu.org/gcc-16/porting_to.html) for details.
+
 ## Backward Incompatibilities {#sec-nixpkgs-release-26.11-incompatibilities}

 <!-- To avoid merge conflicts, consider adding your item at an arbitrary place in the list instead. -->
--- 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/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/as/assimp/package.nix
+++ b/pkgs/by-name/as/assimp/package.nix
@@ -42,6 +42,7 @@ stdenv.mkDerivation (finalAttrs: {
  cmakeFlags = [
    (lib.cmakeBool "ASSIMP_BUILD_ASSIMP_TOOLS" true)
    (lib.cmakeBool "ASSIMP_BUILD_TESTS" finalAttrs.finalPackage.doCheck)
+    (lib.cmakeBool "ASSIMP_WARNINGS_AS_ERRORS" false)
  ];

  # Some matrix tests fail on non-86_64-linux:
--- a/pkgs/by-name/gl/glog/package.nix
+++ b/pkgs/by-name/gl/glog/package.nix
@@ -71,18 +71,22 @@ stdenv.mkDerivation (finalAttrs: {

  checkPhase =
    let
-      excludedTests =
-        lib.optionals stdenv.hostPlatform.isDarwin [
-          "mock-log"
-        ]
-        ++ [
-          "logging" # works around segfaults for now
-        ]
-        ++ lib.optionals (stdenv.hostPlatform.isPower64 && stdenv.hostPlatform.isBigEndian) [
-          # CHECK_STREQ failed: symbol == "non_inline_func" ((/build/source/build/symbolize_unittest+0x1000b840) vs. non_inline_func)
-          # TestWithPCInsideNonInlineFunction doesn't use TEST(), so can't exclude via GTEST_FILTER
-          "symbolize"
-        ];
+      excludedTests = [
+        "logging" # works around segfaults for now
+      ]
+      ++ lib.optionals stdenv.hostPlatform.isGnu [
+        # Test appears to make strong assumptions about compiler optimizations
+        # that appear to be broken under GCC 16.
+        "stacktrace"
+      ]
+      ++ lib.optionals stdenv.hostPlatform.isDarwin [
+        "mock-log"
+      ]
+      ++ lib.optionals (stdenv.hostPlatform.isPower64 && stdenv.hostPlatform.isBigEndian) [
+        # CHECK_STREQ failed: symbol == "non_inline_func" ((/build/source/build/symbolize_unittest+0x1000b840) vs. non_inline_func)
+        # TestWithPCInsideNonInlineFunction doesn't use TEST(), so can't exclude via GTEST_FILTER
+        "symbolize"
+      ];
      excludedTestsRegex = lib.optionalString (
        excludedTests != [ ]
      ) "(${lib.concatStringsSep "|" excludedTests})";
--- a/pkgs/by-name/gr/grub2/package.nix
+++ b/pkgs/by-name/gr/grub2/package.nix
@@ -583,6 +583,13 @@ stdenv.mkDerivation rec {
      url = "https://git.savannah.gnu.org/cgit/grub.git/patch/?id=ac1512b872af8567b408518a7efa01607a0219ae";
      hash = "sha256-deyp6Yatlgv86bYMt7WcWhKg8J6StDPUEy4UPHqJYIc=";
    })
+    # Required to build grub2_efi with GCC 16, or fails with "error: 'regparm'
+    # attribute ignored [-Werror=attributes]"
+    (fetchpatch {
+      name = "gcc16_make_regparm_attribute_more_conditional.patch";
+      url = "https://git.savannah.gnu.org/cgit/grub.git/patch/?id=9922ed133c2c754ec9f37198da2b3e3e8a4fd5ff";
+      hash = "sha256-V2vffDxL/qQ14YN5scc3CFPBFBWvkh57dc5/hWd/6F4=";
+    })
  ];

  postPatch =
--- 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/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/je/jemalloc/package.nix
+++ b/pkgs/by-name/je/jemalloc/package.nix
@@ -2,6 +2,7 @@
  lib,
  stdenv,
  fetchFromGitHub,
+  fetchpatch,
  autoreconfHook,
  # By default, jemalloc puts a je_ prefix onto all its symbols on OSX, which
  # then stops downstream builds (mariadb in particular) from detecting it. This
@@ -59,6 +60,16 @@ stdenv.mkDerivation (finalAttrs: {
    # A (longer) patch addressing the failure posted upstream at:
    # https://github.com/jemalloc/jemalloc/pull/2954
    ./skip-extent-test-with-prof-active.patch
+
+    # the nonstandard `std::__throw_bad_alloc` is no longer exposed in gcc 16.
+    # this makes it conditional on exceptions and defers to either
+    # `throw std::bad_alloc()` or `std::terminate` as appropriate.
+    # https://github.com/jemalloc/jemalloc/pull/2900
+    (fetchpatch {
+      name = "jemalloc-dont-use-nonstandard-throw-bad-alloc.patch";
+      url = "https://github.com/jemalloc/jemalloc/commit/1a15fe33a48c52bfe26ea83e49f0d317a47da3ea.patch";
+      hash = "sha256-pL9fo8UMSbFlHCo3LFFkw0qBsdrVHcEJIkLutZYa2Yg=";
+    })
  ];

  nativeBuildInputs = [
--- a/pkgs/by-name/li/libfaketime/package.nix
+++ b/pkgs/by-name/li/libfaketime/package.nix
@@ -34,6 +34,15 @@ stdenv.mkDerivation (finalAttrs: {

  patches = [
    ./nix-store-date.patch
+
+    # GCC 16's unused variable analysis is more advanced than previous
+    # versions, and detects that these variables are unused.
+    # https://github.com/wolfcw/libfaketime/pull/528
+    (fetchpatch {
+      name = "libfaketime-silence-unused-variable-warning.patch";
+      url = "https://github.com/wolfcw/libfaketime/commit/712733e5f01e45372f3160cfdbcfd91520cb093d.patch";
+      hash = "sha256-Gu13gFhgvkncj8aowAnSRbHbUCctF5sakbX4uRwdy+A=";
+    })
  ]
  ++ lib.optionals stdenv.hostPlatform.isDarwin [
    (fetchpatch {
--- a/pkgs/by-name/li/libsystemtap/package.nix
+++ b/pkgs/by-name/li/libsystemtap/package.nix
@@ -7,14 +7,14 @@
  elfutils,
 }:

-stdenv.mkDerivation {
+stdenv.mkDerivation (finalAttrs: {
  pname = "libsystemtap";
-  version = "5.3";
+  version = "5.5";

  src = fetchgit {
    url = "git://sourceware.org/git/systemtap.git";
-    rev = "release-5.3";
-    hash = "sha256-W9iJ+hyowqgeq1hGcNQbvPfHpqY0Yt2W/Ng/4p6asxc=";
+    rev = "release-${finalAttrs.version}";
+    hash = "sha256-olN98hjIYZmQvI7Fn1v5ZwRl7yaCAPRGr2g33oMq7VQ=";
  };

  dontBuild = true;
@@ -43,4 +43,4 @@ stdenv.mkDerivation {
    badPlatforms = elfutils.meta.badPlatforms or [ ];
    maintainers = [ lib.maintainers.workflow ];
  };
-}
+})
--- 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/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/on/onetbb/package.nix
+++ b/pkgs/by-name/on/onetbb/package.nix
@@ -76,6 +76,9 @@ stdenv.mkDerivation (finalAttrs: {

  cmakeFlags = [
    (lib.cmakeBool "TBB_DISABLE_HWLOC_AUTOMATIC_SEARCH" false)
+    # Treating compiler errors as warnings creates churn each compiler update,
+    # and provides little utility to us downstream.
+    (lib.cmakeBool "TBB_STRICT" false)
    (lib.cmakeBool "TBB_TEST" finalAttrs.finalPackage.doCheck)
  ]
  ++ lib.optionals stdenv.hostPlatform.isDarwin [
@@ -83,10 +86,6 @@ stdenv.mkDerivation (finalAttrs: {
  ];

  env = {
-    # Fix build with modern gcc
-    # In member function 'void std::__atomic_base<_IntTp>::store(__int_type, std::memory_order) [with _ITp = bool]',
-    NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isGNU "-Wno-error=stringop-overflow";
-
    # Fix undefined reference errors with version script under LLVM.
    NIX_LDFLAGS = lib.optionalString (
      stdenv.cc.bintools.isLLVM && lib.versionAtLeast stdenv.cc.bintools.version "17"
--- 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/protobufc/package.nix
+++ b/pkgs/by-name/pr/protobufc/package.nix
@@ -36,6 +36,21 @@ stdenv.mkDerivation (finalAttrs: {
    zlib
  ];

+  # The upstream macro is vendored from a very old autoconf archive:
+  # https://github.com/protobuf-c/protobuf-c/commit/42612b4ba4b11d48b76e3643fa6d42f617e661b6
+  # and the build system appears to arbitrarily require C++17 specifically:
+  # https://github.com/protobuf-c/protobuf-c/blob/4719fdd7760624388c2c5b9d6759eb6a47490626/configure.ac#L72
+  # However, the default standard version used by GCC continues to increase
+  # (e.g. C++20 for GCC 16), and so protobuf-c's dependencies do as well. In
+  # particular, abseil-cpp has headers that protobuf-c includes and are
+  # sensitive to the standard version. While we could override the standard
+  # version used by these dependents, it is simpler to drop the requirement and
+  # allow the compiler default standard to be used.
+  postPatch = ''
+    substituteInPlace configure.ac --replace-fail \
+      "AX_CXX_COMPILE_STDCXX(17, noext, mandatory)" ""
+  '';
+
  env.PROTOC = lib.getExe buildPackages.protobuf_33;

  meta = {
--- a/pkgs/by-name/sb/sbsigntool/package.nix
+++ b/pkgs/by-name/sb/sbsigntool/package.nix
@@ -61,6 +61,10 @@ stdenv.mkDerivation (finalAttrs: {
    automake --add-missing -Wno-portability
  '';

+  # GCC 16's unused variable analysis is more advanced, leading to a build
+  # failure since sbsigntool builds with -Wno-error.
+  configureFlags = [ "CFLAGS=-Wno-error=unused-but-set-variable" ];
+
  makeFlags = [
    "AR=${stdenv.cc.targetPrefix}ar"
  ];
--- a/pkgs/by-name/so/sourceHighlight/gcc16-disambiguate-regex-ranges-test.patch
+++ b/pkgs/by-name/so/sourceHighlight/gcc16-disambiguate-regex-ranges-test.patch
@@ -0,0 +1,57 @@
+diff --git a/lib/tests/test_regexranges_main.cpp b/lib/tests/test_regexranges_main.cpp
+index 567d79230c..e28bba47e5 100644
+--- a/lib/tests/test_regexranges_main.cpp
+++ b/lib/tests/test_regexranges_main.cpp
+@@ -12,26 +12,26 @@
+ using namespace std;
+ using namespace srchilite;
+ 
+-RegexRanges ranges;
+RegexRanges regexRanges;
+ 
+ void check_range_regex(const string &s, bool expectedTrue = true) {
+     cout << "checking " << s << endl;
+     if (expectedTrue)
+-        assertTrue(ranges.addRegexRange(s));
+        assertTrue(regexRanges.addRegexRange(s));
+     else
+-        assertFalse(ranges.addRegexRange(s));
+        assertFalse(regexRanges.addRegexRange(s));
+ }
+ 
+ void check_match(const string &line, const string &expected = "") {
+     cout << "searching inside " << line;
+     const boost::regex *matched = 0;
+     if (expected != "") {
+-        matched = ranges.matches(line);
+        matched = regexRanges.matches(line);
+         assertTrue(matched != 0);
+         assertEquals(expected, matched->str());
+         cout << " found " << *matched << endl;
+     } else {
+-        assertTrue(ranges.matches(line) == 0);
+        assertTrue(regexRanges.matches(line) == 0);
+         cout << " not found" << endl;
+     }
+ }
+@@ -39,9 +39,9 @@
+ void check_in_range(const string &s, bool expectedTrue = true) {
+     cout << "checking " << s << "... ";
+     if (expectedTrue) {
+-        assertTrue(ranges.isInRange(s));
+        assertTrue(regexRanges.isInRange(s));
+     } else {
+-        assertFalse(ranges.isInRange(s));
+        assertFalse(regexRanges.isInRange(s));
+     }
+     cout << expectedTrue << endl;
+ }
+@@ -57,7 +57,7 @@
+     check_range_regex("{notclosed");
+ 
+     // reset regular expressions
+-    ranges.clear();
+    regexRanges.clear();
+ 
+     check_range_regex("/// foo");
+     check_range_regex("/// bar");
--- a/pkgs/by-name/so/sourceHighlight/package.nix
+++ b/pkgs/by-name/so/sourceHighlight/package.nix
@@ -37,6 +37,11 @@ stdenv.mkDerivation rec {
      url = "https://git.savannah.gnu.org/cgit/src-highlite.git/patch/?id=ab9fe5cb9b85c5afab94f2a7f4b6d7d473c14ee9";
      hash = "sha256-wmSLgLnLuFE+IC6AjxzZp/HEnaOCS1VfY2cac0T7Y+w=";
    })
+
+    # GCC 16 detects ambiguity in the `ranges` name in a test (conflicts with
+    # `namespace std::range { }` from GCC), so we rename the variable to
+    # disambiguate.
+    ./gcc16-disambiguate-regex-ranges-test.patch
  ]
  ++ lib.optionals stdenv.cc.isClang [
    # Adds compatibility with C++17 by removing the `register` storage class specifier.
--- a/pkgs/by-name/sy/systemtap-unwrapped/package.nix
+++ b/pkgs/by-name/sy/systemtap-unwrapped/package.nix
@@ -12,21 +12,14 @@

 stdenv.mkDerivation (finalAttrs: {
  pname = "systemtap";
-  version = "5.4";
+  version = "5.5";

  src = fetchgit {
    url = "git://sourceware.org/git/systemtap.git";
    rev = "release-${finalAttrs.version}";
-    hash = "sha256-11ecQFiBaWOZcbS5Qqf/41heiJM1wSttx0eMoVQImZc=";
+    hash = "sha256-olN98hjIYZmQvI7Fn1v5ZwRl7yaCAPRGr2g33oMq7VQ=";
  };

-  patches = lib.optionals stdenv.hostPlatform.is32bit [
-    # Fix 32bit build
-    # https://sourceware.org/git/?p=systemtap.git;a=commit;h=94efb7c4eb02de0e3565cb165b53963602d3dcb6
-    # does not apply with fetchpatch because of gitweb encoding issues
-    ./systemtap-elaborate-fix-32bit-build.patch
-  ];
-
  nativeBuildInputs = [
    pkg-config
    cpio
--- a/pkgs/by-name/sy/systemtap-unwrapped/systemtap-elaborate-fix-32bit-build.patch
+++ b/pkgs/by-name/sy/systemtap-unwrapped/systemtap-elaborate-fix-32bit-build.patch
@@ -1,102 +0,0 @@
-From 94efb7c4eb02de0e3565cb165b53963602d3dcb6 Mon Sep 17 00:00:00 2001
-From: Sergei Trofimovich <slyich@gmail.com>
-Date: Sun, 30 Nov 2025 20:58:01 +0000
-Subject: [PATCH] elaborate.cxx: fix 32-bit build
-
-Without the change the build fails on i686-linux as:
-
-    elaborate.cxx:5119:33: error:
-      format '%ld' expects argument of type 'long int',
-      but argument 2 has type 'int64_t' {aka 'long long int'} [-Werror=format=]
-     5119 |       session.print_warning (_F("Collapsing unresolved @define to %ld [stapprobes]", value), e->tok);
-          |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
---
- elaborate.cxx    | 2 +-
- po/cs.po         | 2 +-
- po/en.po         | 2 +-
- po/fr.po         | 2 +-
- po/pl.po         | 2 +-
- po/systemtap.pot | 2 +-
- 6 files changed, 6 insertions(+), 6 deletions(-)
-
-diff --git a/elaborate.cxx b/elaborate.cxx
-index 93ecffa1a..3ad3614e7 100644
--- a/elaborate.cxx
-+++ b/elaborate.cxx
-@@ -5116,7 +5116,7 @@ const_folder::visit_defined_op (defined_op* e)
-       // Don't be greedy... we'll only collapse one at a time so type
-       // resolution can have another go at it.
-       relaxed_p = false;
-      session.print_warning (_F("Collapsing unresolved @define to %ld [stapprobes]", value), e->tok);
-+      session.print_warning (_F("Collapsing unresolved @define to %lld [stapprobes]", (long long)value), e->tok);
-       literal_number* n = new literal_number (value);
-       n->tok = e->tok;
-       n->visit (this);
-diff --git a/po/cs.po b/po/cs.po
-index df6412772..92fdef7ad 100644
--- a/po/cs.po
-+++ b/po/cs.po
-@@ -2039,7 +2039,7 @@ msgstr "Zahazuji kontrolu '@defined' bez vedlejších účinků "
- 
- #: elaborate.cxx:5119
- #, fuzzy, c-format
-msgid "Collapsing unresolved @define to %ld [stapprobes]"
-+msgid "Collapsing unresolved @define to %lld [stapprobes]"
- msgstr "Zahazuji kontrolu '@defined' bez vedlejších účinků "
- 
- #: elaborate.cxx:5127
-diff --git a/po/en.po b/po/en.po
-index 8847639e8..1db2292bd 100644
--- a/po/en.po
-+++ b/po/en.po
-@@ -2050,7 +2050,7 @@ msgstr ""
- 
- #: elaborate.cxx:5119
- #, c-format
-msgid "Collapsing unresolved @define to %ld [stapprobes]"
-+msgid "Collapsing unresolved @define to %lld [stapprobes]"
- msgstr ""
- 
- #: elaborate.cxx:5127
-diff --git a/po/fr.po b/po/fr.po
-index b8677707b..55e409919 100644
--- a/po/fr.po
-+++ b/po/fr.po
-@@ -2090,7 +2090,7 @@ msgstr ""
- 
- #: elaborate.cxx:5119
- #, c-format
-msgid "Collapsing unresolved @define to %ld [stapprobes]"
-+msgid "Collapsing unresolved @define to %lld [stapprobes]"
- msgstr ""
- 
- #: elaborate.cxx:5127
-diff --git a/po/pl.po b/po/pl.po
-index e3b6700ee..0b35880c1 100644
--- a/po/pl.po
-+++ b/po/pl.po
-@@ -1977,7 +1977,7 @@ msgstr ""
- 
- #: elaborate.cxx:5119
- #, c-format
-msgid "Collapsing unresolved @define to %ld [stapprobes]"
-+msgid "Collapsing unresolved @define to %lld [stapprobes]"
- msgstr ""
- 
- #: elaborate.cxx:5127
-diff --git a/po/systemtap.pot b/po/systemtap.pot
-index 32ddb2290..4ec0d9a8c 100644
--- a/po/systemtap.pot
-+++ b/po/systemtap.pot
-@@ -1973,7 +1973,7 @@ msgstr ""
- 
- #: elaborate.cxx:5119
- #, c-format
-msgid "Collapsing unresolved @define to %ld [stapprobes]"
-+msgid "Collapsing unresolved @define to %lld [stapprobes]"
- msgstr ""
- 
- #: elaborate.cxx:5127
-- 
-2.52.0
-
--- 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/to/toml11/package.nix
+++ b/pkgs/by-name/to/toml11/package.nix
@@ -37,6 +37,11 @@ stdenv.mkDerivation (finalAttrs: {
    cmake
  ];
  cmakeFlags = [
+    # GCC 16 warns that various uses of `fmt` in value.hpp are used
+    # uninitialized. This may be a true failure, but it does not seem like a
+    # major concern, so we silence it for now.
+    # https://github.com/ToruNiina/toml11/issues/313
+    (lib.cmakeFeature "CMAKE_CXX_FLAGS" "-Wno-error=maybe-uninitialized")
    (lib.cmakeBool "TOML11_BUILD_TOML_TESTS" finalAttrs.finalPackage.doCheck)
  ];
  checkInputs = [
--- 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/us/usrsctp/package.nix
+++ b/pkgs/by-name/us/usrsctp/package.nix
@@ -38,6 +38,11 @@ stdenv.mkDerivation (finalAttrs: {

  nativeBuildInputs = [ cmake ];

+  # GCC 16's unused variable analysis is more advanced, leading to a build
+  # failure since usrsctp builds with -Wno-error.
+  # https://github.com/sctplab/usrsctp/pull/744
+  cmakeFlags = [ (lib.cmakeFeature "CMAKE_C_FLAGS" "-Wno-error=unused-but-set-variable") ];
+
  # https://github.com/sctplab/usrsctp/issues/662
  postPatch = ''
    substituteInPlace usrsctplib/CMakeLists.txt \
--- a/pkgs/by-name/we/webrtc-audio-processing/package.nix
+++ b/pkgs/by-name/we/webrtc-audio-processing/package.nix
@@ -3,7 +3,7 @@
  stdenv,
  fetchFromGitLab,
  fetchpatch,
-  abseil-cpp,
+  abseil-cpp_202601,
  meson,
  ninja,
  pkg-config,
@@ -46,7 +46,11 @@ stdenv.mkDerivation (finalAttrs: {
  ];

  propagatedBuildInputs = [
-    abseil-cpp
+    # webrtc-audio-processing specifies C++17, so abseil must match. Otherwise,
+    # abseil exposes a different (incompatible) interface based on the default
+    # C++ standard of the compiler.
+    # https://gitlab.freedesktop.org/pulseaudio/webrtc-audio-processing/-/blob/d0569cfa50c1858ee279d77b3fc8870be6902441/meson.build#L7
+    (abseil-cpp_202601.override { cxxStandard = "17"; })
  ];

  mesonFlags =
--- 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/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/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/os-specific/linux/minimal-bootstrap/gcc/glibc.nix
+++ b/pkgs/os-specific/linux/minimal-bootstrap/gcc/glibc.nix
@@ -22,7 +22,7 @@
 }:
 let
  pname = "gcc";
-  version = "15.3.0";
+  version = "16.1.0";
  linkerName =
    {
      i686-linux = "ld-linux.so.2";
@@ -32,7 +32,7 @@ let

  src = fetchurl {
    url = "mirror://gnu/gcc/gcc-${version}/gcc-${version}.tar.xz";
-    hash = "sha256-+lnBvu+JlfJ8TXHB3yJ1hxiTFdPm+v8btDBuYbDFMOs=";
+    hash = "sha256-UO+02Uwzl6/zsNYaWr10i03THZ0/Kre+BbFx02pRD3k=";
  };

  gmpVersion = "6.3.0";
--- a/pkgs/os-specific/linux/minimal-bootstrap/gcc/latest.nix
+++ b/pkgs/os-specific/linux/minimal-bootstrap/gcc/latest.nix
@@ -21,11 +21,11 @@
 }:
 let
  pname = "gcc";
-  version = "15.3.0";
+  version = "16.1.0";

  src = fetchurl {
    url = "mirror://gnu/gcc/gcc-${version}/gcc-${version}.tar.xz";
-    hash = "sha256-+lnBvu+JlfJ8TXHB3yJ1hxiTFdPm+v8btDBuYbDFMOs=";
+    hash = "sha256-UO+02Uwzl6/zsNYaWr10i03THZ0/Kre+BbFx02pRD3k=";
  };

  gmpVersion = "6.3.0";
--- 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/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -3266,7 +3266,7 @@ with pkgs;
  gerbilPackages-unstable = pkgs.gerbil-support.gerbilPackages-unstable; # NB: don't recurseIntoAttrs for (unstable!) libraries
  glow-lang = pkgs.gerbilPackages-unstable.glow-lang;

-  default-gcc-version = 15;
+  default-gcc-version = 16;
  gcc = pkgs.${"gcc${toString default-gcc-version}"};
  gccFun = callPackage ../development/compilers/gcc;
  gcc-unwrapped = gcc.cc;
@@ -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
whispers	a06d109d48	glog: disable optimization-dependent stacktrace test This test fails under GCC 16. It appears to be because it makes assumptions that certain compiler optimizations do not occur. It clearly is compiler-specific and tries to work around specific compiler optimizations upstream. In particular, an analysis of the test `53d58e4531/src/stacktrace_unittest.cc (L218)` shows that it would be very plausible/correct for GCC to place labels such that the `INIT_ADDRESS_RANGE` macro has `start` and `end` labels that have the same address. While the functions are labeled NOINLINE, interprocedural analysis could plausibly produce this result. While we are not completely certain that this is the case, it seems likely that this is not a genuine issue and just a questionable test.	2026-07-24 12:59:10 -04:00
whispers	c465430f82	assimp: never treat warnings as fatal assimp sometimes has warnings that are triggered by new compiler or library versions. since assimp builds with -Werror by default, this requires workaround in Nixpkgs until they cut a release. this is the case with unused variable warnings in GCC 16. instead of dealing with this, we simply disable -Werror via the cmake flag it offers to do so.	2026-07-24 12:59:10 -04:00
whispers	1e10b67e35	protobufc: unpin standard version to fix build with gcc 16 protobufc pins a specific version of the C++ standard and does so using an ancient vendored macro from the autoconf archive. this causes a failure to build on gcc 16, as it defaults to C++20 and protobufc uses C++17. this particularly causes problems with abseil, which has headers which depend on the C++ standard to compile. accordingly, to avoid having to manually specify and update a version each time the default standard version updates, we unpin it completely and allow the compiler to choose what it uses by default. alternatively, we could override the abseil that ends up in protobufc by way of protobuf_33 to use the C++17 standard instead. this would work, but this seems more fragile and subject to compiler version churn. it is also our understanding that mixing and matching versions of standards in dependents can be messy, and using the default seems the least likely to cause problems.	2026-07-24 10:52:32 -04:00
whispers	6aa36277ff	webrtc-audio-processing: explicitly specify C++17 for abseil-cpp abseil exposes different interfaces depending on what is available in `std` in a given C++ standard. gcc 16 defaults to C++20, thus causing the default abseil-cpp to expose a different interface than the one webrtc-audio-processing (built with C++17) expects. this leads to a great deal of "error: 'partial_ordering' has not been declared in 'std'" and similar originating from abseil's types/compare.h. thus, we explicitly override abseil to specify the desired C++ standard.	2026-07-24 10:52:28 -04:00
whispers	d457a15860	grub2_efi: apply patch for gcc 16 gcc 16 gains stricter analysis of whether attributes are ignored, leading to build failures when built with -Werror. we could silence the error, but this was fixed in a trivial commit upstream that is obviously correct, so we pull it in: https://cgit.git.savannah.gnu.org/cgit/grub.git/commit/?id=9922ed133c2c754ec9f37198da2b3e3e8a4fd5ff	2026-07-24 10:52:15 -04:00
whispers	75c304b0e0	toml11: make maybe-uninitialized non-fatal for gcc 16 GCC 16 flags various calls here as if they're uninitialized, but they appear (to me as a non-C++ expert) to be false positives. Accordingly, we make those non-fatal. This fixes the build on GCC 16.	2026-07-24 10:52:05 -04:00
whispers	2012d325a3	onetbb: never treat warnings as fatal onetbb often triggers compiler warnings upstream, and works around them in an ad-hoc, per version manner: `88482f5f1a` `bdbec20606` we encountered this failing while preparing for a gcc 16 upgrade in Nixpkgs, and the same issue came up for gcc 15 and similar (#446139). it is likely to come up again, as -Werror is extremely susceptible to compiler and library changes (though onetbb admittedly has few dependencies). additionally, while it may be useful for upstream onetbb, it seems to provide little value to us downstream; we just end up working around it. thus, we never treat warnings as errors by disabling upstream's cmake flag for this purpose.	2026-07-24 10:52:00 -04:00
whispers	1dd0a5d9e5	libfaketime: add patch for gcc 16 gcc 16's unused variable analysis is more advanced than previous versions, and detects that some variables used in tests are unused. upstream patched this away, so we fetch their patch. alternatively, we could pass `-Wno-error=unused-but-set-variable` if that is preferred.	2026-07-24 10:51:38 -04:00
whispers	fb7e01a3b6	sbsigntool: make unused-but-set-variable non-fatal for gcc 16 since sbsigntool builds with -Werror by default, and gcc 16's unused variable analysis is better than previous versions, this causes a build failure.	2026-07-24 10:50:54 -04:00
whispers	80c9a1708e	libsystemtap: 5.3 -> 5.5 Log: https://sourceware.org/git/?p=systemtap.git;a=shortlog;h=refs/tags/release-5.5	2026-07-24 10:48:57 -04:00
whispers	b57ec0fcb2	systemtap-unwrapped: 5.4 -> 5.5 Log: https://sourceware.org/git/?p=systemtap.git;a=shortlog;h=refs/tags/release-5.5	2026-07-24 10:48:57 -04:00
whispers	f7b16131d9	usrsctp: make unused-but-set-variable non-fatal for gcc 16 since usrsctp builds with -Werror by default, and gcc 16's unused variable analysis is better than previous versions, this causes a build failure. a fix for this particular variable has been submitted upstream, but this is sufficient in the interim.	2026-07-24 13:31:31 +02:00
whispers	6c37551652	jemalloc: add patch to fix build under gcc 16 jemalloc used the nonstandard `std::__throw_bad_alloc`, which is no longer visible in GCC 16. this upstream patch makes it conditional on exceptions and defers to either `throw std::bad_alloc()` or `std::terminate` as appropriate, and fixes the build.	2026-07-24 13:31:18 +02:00
whispers	aab37bd258	sourceHighlight: patch to fix build with gcc 16 The `ranges` name in the test here conflicts with the `namespace std::ranges { }` from GCC 16, causing this test to fail to build with "error: reference to 'ranges' is ambiguous". To avoid this, we simply rename the variable.	2026-07-24 13:31:06 +02:00
whispers	017fed1d63	gcc: 15 -> 16 changes: https://gcc.gnu.org/gcc-16/changes.html porting guide: https://gcc.gnu.org/gcc-16/porting_to.html	2026-07-24 13:23:18 +02:00
whispers	f46e80f6c5	minimal-bootstrap.gcc-glibc: 15.3.0 -> 16.1.0 https://gcc.gnu.org/gcc-16/changes.html	2026-07-24 13:23:18 +02:00
whispers	8c8bcc8565	minimal-bootstrap.gcc-latest: 15.3.0 -> 16.1.0 https://gcc.gnu.org/gcc-16/changes.html	2026-07-24 13:23:14 +02:00
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
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
nixpkgs-ci[bot]	4cb9d58ac0	yaziPlugins: update on 2026-07-23 (#544999 )	2026-07-24 02:35:19 +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
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
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	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
R. Ryantm	3dc4b3fbc7	gtkwave: 3.3.127 -> 3.3.128	2026-07-23 00:40:36 +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