Merge remote-tracking branch 'upstream/master' into nixpkgs-bump-2024…

…-05-03
msfjarvis · May 3, 2024 · abcd73e · abcd73e
2 parents 705bbe4 + cec495a
commit abcd73e
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Showing 11 changed files with 50 additions and 141 deletions.
diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng
+{ lib, stdenv, fetchurl, fetchpatch, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng
 , libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texliveSmall, tk, xz, zlib
 , less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack
 , curl, Cocoa, Foundation, libobjc, libcxx, tzdata
@@ -37,6 +37,12 @@ stdenv.mkDerivation (finalAttrs: {
 
   patches = [
     ./no-usr-local-search-paths.patch
+    (fetchpatch {
+      # https://hiddenlayer.com/research/r-bitrary-code-execution/
+      name = "CVE-2024-27322.patch";
+      url = "https://github.com/r-devel/r-svn/commit/f7c46500f455eb4edfc3656c3fa20af61b16abb7.patch";
+      hash = "sha256-CH2mMmie9E96JeGSC7UGm7/roUNhK5xv6HO53N2ixEI=";
+    })
   ];
 
   # Test of the examples for package 'tcltk' fails in Darwin sandbox. See:

diff --git a/...on-management/gitlab/gitlab-container-registry/Disable-inmemory-storage-driver-test.patch b/...on-management/gitlab/gitlab-container-registry/Disable-inmemory-storage-driver-test.patch
diff --git a/pkgs/applications/version-management/gitlab/gitlab-container-registry/default.nix b/pkgs/applications/version-management/gitlab/gitlab-container-registry/default.nix
@@ -15,11 +15,10 @@ buildGoModule rec {
 
   vendorHash = "sha256-KZWdM8Q8ipsgm7OoLyOuHo+4Vg2Nve+yZtTSUDgjOW4=";
 
-  patches = [
-    ./Disable-inmemory-storage-driver-test.patch
-  ];
-
   postPatch = ''
+    # Disable flaky inmemory storage driver test
+    rm registry/storage/driver/inmemory/driver_test.go
+
     substituteInPlace health/checks/checks_test.go \
       --replace \
         'func TestHTTPChecker(t *testing.T) {' \

diff --git a/pkgs/by-name/in/inshellisense/package.nix b/pkgs/by-name/in/inshellisense/package.nix
@@ -2,16 +2,16 @@
 
 buildNpmPackage rec {
   pname = "inshellisense";
-  version = "0.0.1-rc.14";
+  version = "0.0.1-rc.15";
 
   src = fetchFromGitHub {
     owner = "microsoft";
     repo = pname;
     rev = "refs/tags/${version}";
-    hash = "sha256-ZsEAE9EDJLREpKjHLbvqAUNM/y9eCH44g3D8NHYHiT4=";
+    hash = "sha256-/6pU8ubasONPMe1qnE+Db0nzdHRQTo9fhMr7Xxjgsos=";
   };
 
-  npmDepsHash = "sha256-p0/GnAdWNM/wjB/w+rXbOrh3Hr/smIW0IVQga7uCKYY=";
+  npmDepsHash = "sha256-rOyvFA5X3o1TCgY54XxNSg0+QotA8IUauLngTtJuRj4=";
 
   # Needed for dependency `@homebridge/node-pty-prebuilt-multiarch`
   # On Darwin systems the build fails with,

diff --git a/pkgs/development/python-modules/django-model-utils/default.nix b/pkgs/development/python-modules/django-model-utils/default.nix
@@ -8,7 +8,7 @@
 
 buildPythonPackage rec {
   pname = "django-model-utils";
-  version = "4.5.0";
+  version = "4.5.1";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -17,7 +17,7 @@ buildPythonPackage rec {
     owner = "jazzband";
     repo = "django-model-utils";
     rev = "refs/tags/${version}";
-    hash = "sha256-ZEnDk4kCXyhLvq3CZTK/zP3IK6BsNRqbkfqKAuU6Mfk=";
+    hash = "sha256-GaBTCrEwEkJyVeY5YVptPioYcmivyQtBKjs+TgC9IqA=";
   };
 
   build-system = [

diff --git a/pkgs/development/tools/bazel-watcher/default.nix b/pkgs/development/tools/bazel-watcher/default.nix
@@ -2,7 +2,7 @@
 , bazel_5
 , fetchFromGitHub
 , git
-, go
+, go_1_21
 , python3
 , lib, stdenv
 }:
@@ -29,16 +29,16 @@ let
 in
 buildBazelPackage rec {
   pname = "bazel-watcher";
-  version = "0.24.0";
+  version = "0.25.2";
 
   src = fetchFromGitHub {
     owner = "bazelbuild";
     repo = "bazel-watcher";
     rev = "v${version}";
-    hash = "sha256-ebNHAYKyE3226KiCc2/VSz1OSITuPwuYlAIS3JrWzj0=";
+    hash = "sha256-lreGKA0DZiOd1bJq8NNQ+80cyDwiughoXCkKu1RaZmc=";
   };
 
-  nativeBuildInputs = [ go git python3 ];
+  nativeBuildInputs = [ go_1_21 git python3 ];
   removeRulesCC = false;
 
   bazel = bazel_5;

diff --git a/pkgs/development/tools/continuous-integration/codeberg-pages/default.nix b/pkgs/development/tools/continuous-integration/codeberg-pages/default.nix
@@ -14,7 +14,10 @@ buildGoModule rec {
 
   vendorHash = "sha256-vTYB3ka34VooN2Wh/Rcj+2S1qAsA2a/VtXlILn1W7oU=";
 
-  patches = [ ./disable_httptest.patch ];
+  postPatch = ''
+    # disable httptest
+    rm server/handler/handler_test.go
+  '';
 
   ldflags = [ "-s" "-w" ];
 

diff --git a/pkgs/development/tools/continuous-integration/codeberg-pages/disable_httptest.patch b/pkgs/development/tools/continuous-integration/codeberg-pages/disable_httptest.patch
diff --git a/pkgs/servers/computing/storm/default.nix b/pkgs/servers/computing/storm/default.nix
@@ -1,50 +1,51 @@
 { stdenv, lib, fetchurl, zip, unzip
-, jdk, python2
+, jdk, python3
 , confFile ? ""
 , extraLibraryPaths ? []
 , extraJars ? []
+, testers
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "apache-storm";
-  version = "2.4.0";
-  name = "${pname}-${version}";
+  version = "2.6.2";
+  name = "${finalAttrs.pname}-${finalAttrs.version}";
 
   src = fetchurl {
-    url = "mirror://apache/storm/${name}/${name}.tar.gz";
-    sha256 = "sha256-VFNcaISPBRMGR5l/P6/pGnK7lHClDW2AmXJ00gzxwMY=";
+    url = "mirror://apache/storm/${finalAttrs.name}/${finalAttrs.name}.tar.gz";
+    hash = "sha256-ZAwsVKWTzc/++UQTNnOHdK5hiDDT5j6453DCLWi+7TA=";
   };
 
   nativeBuildInputs = [ zip unzip ];
 
   installPhase = ''
-    mkdir -p $out/share/${name}
+    mkdir -p $out/share/${finalAttrs.name}
     mv public $out/docs
-    mv examples $out/share/${name}/.
+    mv examples $out/share/${finalAttrs.name}/.
 
     mv external extlib* lib $out/.
     mv conf bin $out/.
     mv log4j2 $out/conf/.
   '';
 
   fixupPhase = ''
+    patchShebangs $out
     # Fix python reference
     sed -i \
-      -e '19iPYTHON=${python2}/bin/python' \
-      -e 's|#!/usr/bin/.*python|#!${python2}/bin/python|' \
+      -e '19iPYTHON=${python3}/bin/python' \
+      -e 's|#!/usr/bin/.*python|#!${python3}/bin/python|' \
       $out/bin/storm
     sed -i \
-      -e 's|#!/usr/bin/.*python|#!${python2}/bin/python|' \
+      -e 's|#!/usr/bin/.*python|#!${python3}/bin/python|' \
       -e "s|STORM_CONF_DIR = .*|STORM_CONF_DIR = os.getenv('STORM_CONF_DIR','$out/conf')|" \
       -e 's|STORM_LOG4J2_CONF_DIR =.*|STORM_LOG4J2_CONF_DIR = os.path.join(STORM_CONF_DIR, "log4j2")|' \
         $out/bin/storm.py
 
     # Default jdk location
-    sed -i -e 's|#.*export JAVA_HOME=.*|export JAVA_HOME="${jdk.home}"|' \
+    sed -i -e 's|export JAVA_HOME=.*|export JAVA_HOME="${jdk.home}"|' \
            $out/conf/storm-env.sh
-    ls -lh $out/lib
-    unzip  $out/lib/storm-client-${version}.jar defaults.yaml;
-    zip -d $out/lib/storm-client-${version}.jar defaults.yaml;
+    unzip  $out/lib/storm-client-${finalAttrs.version}.jar defaults.yaml;
+    zip -d $out/lib/storm-client-${finalAttrs.version}.jar defaults.yaml;
     sed -i \
        -e 's|java.library.path: .*|java.library.path: "${lib.concatStringsSep ":" extraLibraryPaths}"|' \
        -e 's|storm.log4j2.conf.dir: .*|storm.log4j2.conf.dir: "conf/log4j2"|' \
@@ -59,6 +60,11 @@ stdenv.mkDerivation rec {
 
   dontStrip = true;
 
+  passthru.tests.version = testers.testVersion {
+    package = finalAttrs.finalPackage;
+    command = "storm version";
+  };
+
   meta = with lib; {
     homepage = "https://storm.apache.org/";
     description = "Distributed realtime computation system";
@@ -67,4 +73,4 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ edwtjo vizanto ];
     platforms = with platforms; unix;
   };
-}
+})
diff --git a/pkgs/tools/security/kubescape/default.nix b/pkgs/tools/security/kubescape/default.nix
@@ -10,17 +10,17 @@
 
 buildGoModule rec {
   pname = "kubescape";
-  version = "3.0.8";
+  version = "3.0.9";
 
   src = fetchFromGitHub {
     owner = "kubescape";
     repo = "kubescape";
     rev = "refs/tags/v${version}";
-    hash = "sha256-ZGDE9go8BmaXE1YFT/z5Nob90MhsKZ6oKrodDMu2npY=";
+    hash = "sha256-pAe289XwKq/PO39/Wt60uipt4Z0ZD5f73pDaOTXXwi0=";
     fetchSubmodules = true;
   };
 
-  vendorHash = "sha256-qFJVoWzU9rqpYbb8gzdK33rq///zizxVkWhsNV8OXOM=";
+  vendorHash = "sha256-UWmsS79N8ooFr4qpKqOVC14cgf5ckAQwzROHGl1smD8=";
 
   subPackages = [
     "."
@@ -49,7 +49,6 @@ buildGoModule rec {
     rm core/cautils/getter/downloadreleasedpolicy_test.go
     rm core/core/initutils_test.go
     rm core/core/list_test.go
-    rm core/pkg/resourcehandler/remotegitutils_test.go
 
     # Remove tests that use networking
     substituteInPlace core/pkg/resourcehandler/repositoryscanner_test.go \

diff --git a/pkgs/tools/security/tpm2-tools/default.nix b/pkgs/tools/security/tpm2-tools/default.nix
@@ -4,21 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname = "tpm2-tools";
-  version = "5.6";
+  version = "5.7";
 
   src = fetchurl {
     url = "https://github.com/tpm2-software/${pname}/releases/download/${version}/${pname}-${version}.tar.gz";
-    sha256 = "sha256-Usi8uq3KCCq/5et+5JZ9LWMthLFndnXy8HG20uwizsM=";
+    sha256 = "sha256-OBDTa1B5JW9PL3zlUuIiE9Q7EDHBMVON+KLbw8VwmDo=";
   };
 
-  patches = [
-    # https://github.com/tpm2-software/tpm2-tools/pull/3271
-    (fetchpatch {
-      url = "https://github.com/tpm2-software/tpm2-tools/commit/b98be08f6f88b0cca9e0667760c4e1e5eb417fbd.patch";
-      sha256 = "sha256-2sEam9i4gwscJhLwraX2EAjVM8Dh1vmNnG3zYsOF0fc=";
-    })
-  ];
-
   nativeBuildInputs = [ pandoc pkg-config makeWrapper ];
   buildInputs = [
     curl openssl tpm2-tss libuuid