Unverified Commit e7d6f2fd authored by Justin Bedő's avatar Justin Bedő Committed by GitHub
Browse files

Merge pull request #315015 from NixOS/r-updates 

rPackages, R: R 4.3.3 -> 4.4.1 and bump rPackages
parents 8c811054 6f3340bf

pkgs/applications/science/math/R/default.nix

+3 −9
Original line number Diff line number Diff line 
{ lib, stdenv, fetchurl, fetchpatch, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng

{ lib, stdenv, fetchurl, 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
@@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64); 


stdenv.mkDerivation (finalAttrs: {

  pname = "R";

  version = "4.3.3";

  version = "4.4.1";



  src = let

    inherit (finalAttrs) pname version;

  in fetchurl {

    url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";

    sha256 = "sha256-gIUSMTk7hb84d+6eObKC51Dthkxexgy9aObhOfBSAzA=";

    sha256 = "sha256-tMtnXequtymdOyZdIYzeQ/GSlRzluJt7saUUijay2U0=";

  };



  outputs = [ "out" "tex" ];
@@ -37,12 +37,6 @@ 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:

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

+3 −0
Original line number Diff line number Diff line
@@ -33,6 +33,9 @@ let 


    env.INCLUDE_DIR = "../inst/include/jaspColumnEncoder";



    # necessary for R 4.4.0

    hardeningDisable = [ "format" ];



    postPatch = ''

      mkdir -p inst/include

      cp -r --no-preserve=all ${jaspColumnEncoder-src} inst/include/jaspColumnEncoder

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

+3 −0
Original line number Diff line number Diff line
@@ -66,6 +66,9 @@ stdenv.mkDerivation { 
    "-DCUSTOM_R_PATH=${customREnv}"

  ];



  # necessary for R 4.4.0

  hardeningDisable = [ "format" ];



  nativeBuildInputs = [

    cmake

    ninja

pkgs/development/python-modules/rpy2/default.nix

+9 −0
Original line number Diff line number Diff line
@@ -5,6 +5,7 @@ 
  fetchPypi,

  isPyPy,

  R,

  libdeflate,

  rWrapper,

  rPackages,

  pcre,
@@ -53,6 +54,7 @@ buildPythonPackage rec { 
      bzip2

      zlib

      icu

      libdeflate

    ]

    ++ (with rPackages; [

      # packages expected by the test framework
@@ -87,6 +89,13 @@ buildPythonPackage rec { 


  doCheck = !stdenv.isDarwin;



  # https://github.com/rpy2/rpy2/issues/1111

  disabledTests = [

    "test_parse_incomplete_error"

    "test_parse_error"

    "test_parse_error_when_evaluting"

  ];



  nativeCheckInputs = [ pytestCheckHook ];



  meta = {

pkgs/development/r-modules/bioc-annotation-packages.nix

+59 −54

File changed.

Preview size limit exceeded, changes collapsed.