sage, python313Packages.rpy2: unbreak (#441027)

      url = "https://github.com/sagemath/sage/commit/d0cbe9d353722580f98a327694f1a361c9b83ccd.patch?full_index=1";

      hash = "sha256-uV2nttxCKDsNqMf1O+lUmuoiDrx7/CfiS00JBb9kiM8=";

    })

    # https://github.com/sagemath/sage/pull/40156, landed in 10.7.beta5

    (fetchpatch2 {

      name = "cython-3.1-update.patch";

      url = "https://github.com/sagemath/sage/commit/5ea8db28977ec113aec3c4c4b208d1783e3937a7.patch?full_index=1";

      hash = "sha256-5DPPxMuidPpVHrjK8j0UVZzuwiVy9vQzFd6hBYwNAok=";

    })

    # https://github.com/sagemath/sage/pull/40175, landed in 10.7.beta8

    (fetchpatch2 {

      name = "rpy2-3.6-update.patch";

      url = "https://github.com/sagemath/sage/commit/db2d8db99d9a7dfa1972d534ecd89e3d2ba5c55b.patch?full_index=1";

      hash = "sha256-6Bk0uGlKFsiDsgv+ljMC1YnmAT+g+he6aFNkpvw2on0=";

    })

  ];

  patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;

{

  stdenv,

  lib,

  buildPythonPackage,

  fetchurl,

  isPyPy,

  R,

  rWrapper,

  xz,

  bzip2,

  zlib,

  zstd,

  icu,

  pytestCheckHook,

  setuptools,

  cffi,

}:

buildPythonPackage rec {

  version = "3.6.3";

  format = "pyproject";

  pname = "rpy2-rinterface";

  disabled = isPyPy;

  src = fetchurl {

    url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${

      builtins.replaceStrings [ "-" ] [ "_" ] pname

    }-${version}.tar.gz";

    hash = "sha256-R3vC9R0AetG4VnxdS6GvD1mVFobufxBXagbQg03ld28=";

  };

  patches = [

    # https://github.com/rpy2/rpy2/pull/1171#issuecomment-3263994962

    ./restore-initr-simple.patch

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

  '';

  buildInputs = [

    xz

    bzip2

    zlib

    zstd

    icu

  ]

  ++ rWrapper.recommendedPackages;

  nativeBuildInputs = [

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

  ];

  propagatedBuildInputs = [

    cffi

    setuptools

  ];

  nativeCheckInputs = [ pytestCheckHook ];

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

  disabledTests = [

    "test_parse_incomplete_error"

    "test_parse_error"

    "test_parse_error_when_evaluting"

  ];

  meta = {

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

    description = "Python interface to R";

    license = lib.licenses.gpl2Plus;

    platforms = lib.platforms.unix;

    maintainers = with lib; [ teams.sage ];

  };

}

diff --git a/src/rpy2/rinterface/__init__.py b/src/rpy2/rinterface/__init__.py

index 0ba46083..1f4265aa 100644

--- a/src/rpy2/rinterface/__init__.py

+++ b/src/rpy2/rinterface/__init__.py

@@ -1100,6 +1100,15 @@ NA = None

 NA_Real = None

 NA_Complex = None

+def initr_simple() -> typing.Optional[int]:

+    """Initialize R's embedded C library."""

+    with openrlib.rlock:

+        status = embedded._initr()

+        atexit.register(endr, 0)

+        _rinterface._register_external_symbols()

+        _post_initr_setup()

+        return status

+

 def initr(

         interactive: typing.Optional[bool] = None,

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', ''))

                 )

         )

+

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

index cc9f7da1..10626f13 100644

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

@@ -328,6 +328,15 @@ def _initr(

             _setinitialized()

             return None

+        # path to libraries

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

+        if existing is not None:

+        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)

         # TODO: Setting LD_LIBRARY_PATH after the process has started

         # is too late. Because of this, the line below does not help

         # address issues where calling R from the command line is working

{

  stdenv,

  lib,

  buildPythonPackage,

  fetchurl,

  fetchpatch2,

  isPyPy,

  R,

  rpy2-rinterface,

  ipython,

  jinja2,

  numpy,

  pandas,

  tzlocal,

  pytestCheckHook,

}:

buildPythonPackage rec {

  version = "3.6.2";

  format = "pyproject";

  pname = "rpy2-robjects";

  disabled = isPyPy;

  src = fetchurl {

    url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${

      builtins.replaceStrings [ "-" ] [ "_" ] pname

    }-${version}.tar.gz";

    hash = "sha256-rJGvMtXE2iNrBaPNaNr7JM2PWogPAHhim48r8CUFQjs=";

  };

  patches = [

    # https://github.com/rpy2/rpy2/pull/1171#issuecomment-3263994962

    (fetchpatch2 {

      url = "https://github.com/rpy2/rpy2/commit/524546eef9b8f7f3d61aeb76d7e7fa7beeabd2d2.patch?full_index=1";

      hash = "sha256-aR44E8wIBlD7UpQKm7B+aMn2p3FQ8dwBwLwkibIpcuM=";

      relative = "rpy2-robjects";

      revert = true;

    })

  ];

  nativeBuildInputs = [

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

  ];

  propagatedBuildInputs = [

    ipython

    jinja2

    numpy

    pandas

    rpy2-rinterface

    tzlocal

  ];

  nativeCheckInputs = [ pytestCheckHook ];

  meta = {

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

    description = "Python interface to R";

    license = lib.licenses.gpl2Plus;

    platforms = lib.platforms.unix;

    maintainers = with lib.maintainers; [ joelmo ];

  };

}