python313Packages.rpy2: 3.6.2 -> 3.6.3, unbreak

  buildPythonPackage,

  fetchPypi,

  isPyPy,

  R,

  libdeflate,

  rWrapper,

  rPackages,

  pcre,

  xz,

  bzip2,

  zlib,

  zstd,

  icu,

  ipython,

  jinja2,

  pytz,

  pandas,

  numpy,

  cffi,

  tzlocal,

  simplegeneric,

  rpy2-rinterface,

  rpy2-robjects,

  pytestCheckHook,

  extraRPackages ? [ ],

}:

buildPythonPackage rec {

  version = "3.6.2";

  format = "setuptools";

  version = "3.6.3";

  format = "pyproject";

  pname = "rpy2";

  disabled = isPyPy;

  src = fetchPypi {

    inherit version pname;

    hash = "sha256-F06ld2qR0Ds13VYRiJlg4PVFHp0KvqSr/IwL5qhTd9A=";

    hash = "sha256-lCYYoSUhljAG0i6IqqTUgakjghwDoXQsmb7uci6w/Fo=";

  };

  patches = [

    # R_LIBS_SITE is used by the nix r package to point to the installed R libraries.

    # This patch sets R_LIBS_SITE when rpy2 is imported.

    ./rpy2-3.x-r-libs-site.patch

  ];

  postPatch = ''

    substituteInPlace 'rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"

    substituteInPlace 'requirements.txt' --replace 'pytest' ""

  '';

  buildInputs = [

    pcre

    xz

    bzip2

    zlib

    zstd

    icu

    libdeflate

  ]

  ++ (with rPackages; [

    # packages expected by the test framework

    ggplot2

    dplyr

    RSQLite

    broom

    DBI

    dbplyr

    hexbin

    lazyeval

    lme4

    tidyr

  ])

  ++ extraRPackages

  ++ rWrapper.recommendedPackages;

  nativeBuildInputs = [

    R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)

  ];

  propagatedBuildInputs = [

    ipython

    jinja2

    pytz

    pandas

    numpy

    cffi

    tzlocal

    simplegeneric

    rpy2-rinterface

    rpy2-robjects

  ];

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

  disabledTests = [

    "test_parse_incomplete_error"

    "test_parse_error"

    "test_parse_error_when_evaluting"

  pythonImportsCheck = [

    "rpy2"

  ];

  nativeCheckInputs = [ pytestCheckHook ];

  meta = {

    homepage = "https://rpy2.github.io/";

    description = "Python interface to R";

diff --git a/rpy2/rinterface_lib/embedded.py b/rpy2/rinterface_lib/embedded.py

index ccd3a315..51fb5da4 100644

--- a/rpy2/rinterface_lib/embedded.py

+++ b/rpy2/rinterface_lib/embedded.py

@@ -276,6 +276,16 @@ def _initr(

                  os.environ.get('LD_LIBRARY_PATH', ''))

                 )

         )

+

+        # path to libraries

+        existing = os.environ.get('R_LIBS_SITE')

+        if existing is not None:

+            prefix = existing + ':'

+        else:

+            prefix = ''

+        additional = '@NIX_R_LIBS_SITE@'

+        os.environ['R_LIBS_SITE'] = prefix + additional

+

         options_c = [ffi.new('char[]', o.encode('ASCII')) for o in _options]

         n_options = len(options_c)

         n_options_c = ffi.cast('int', n_options)

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

  rpy2 = callPackage ../development/python-modules/rpy2 { inherit (pkgs) zstd; };

  rpy2 = callPackage ../development/python-modules/rpy2 { };

  rpy2-rinterface = callPackage ../development/python-modules/rpy2-rinterface {

    inherit (pkgs) zstd;