commit 50b368e4c24293da4c7c85fe16e82835ac9f11d2 · pyrox.dev/nixpkgs

+79

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

···

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       {

     

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         stdenv,

     

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         lib,

     

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         buildPythonPackage,

     

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         fetchurl,

     

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         isPyPy,

     

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         R,

     

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         rWrapper,

     

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         xz,

     

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         bzip2,

     

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         zlib,

     

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         zstd,

     

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         icu,

     

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         pytestCheckHook,

     

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         setuptools,

     

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         cffi,

     

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       }:

     

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       buildPythonPackage rec {

     

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         version = "3.6.3";

     

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         format = "pyproject";

     

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         pname = "rpy2-rinterface";

     

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         disabled = isPyPy;

     

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         src = fetchurl {

     

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

     

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

     

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

     

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           hash = "sha256-R3vC9R0AetG4VnxdS6GvD1mVFobufxBXagbQg03ld28=";

     

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         };

     

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         patches = [

     

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

     

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           ./restore-initr-simple.patch

     

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

     

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           # This patch sets R_LIBS_SITE when rpy2 is imported.

     

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

     

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         ];

     

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         postPatch = ''

     

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

     

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         '';

     

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       +
       

     

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         buildInputs = [

     

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           xz

     

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           bzip2

     

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           zlib

     

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           zstd

     

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           icu

     

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         ]

     

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         ++ rWrapper.recommendedPackages;

     

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       +
       

     

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         nativeBuildInputs = [

     

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

     

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         ];

     

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         propagatedBuildInputs = [

     

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           cffi

     

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           setuptools

     

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         ];

     

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         nativeCheckInputs = [ pytestCheckHook ];

     

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       +
       

     

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

     

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         disabledTests = [

     

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           "test_parse_incomplete_error"

     

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           "test_parse_error"

     

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           "test_parse_error_when_evaluting"

     

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         ];

     

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         meta = {

     

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

     

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           description = "Python interface to R";

     

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           license = lib.licenses.gpl2Plus;

     

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           platforms = lib.platforms.unix;

     

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           maintainers = with lib; [ teams.sage ];

     

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         };

     

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       }

+20

pkgs/development/python-modules/rpy2-rinterface/restore-initr-simple.patch

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

     

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       index 0ba46083..1f4265aa 100644

     

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

     

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

     

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

     

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        NA_Real = None

     

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        NA_Complex = None

     

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

     

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

     

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       +    with openrlib.rlock:

     

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       +        status = embedded._initr()

     

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       +        atexit.register(endr, 0)

     

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       +        _rinterface._register_external_symbols()

     

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       +        _post_initr_setup()

     

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       +        return status

     

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       +

     

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       +
        

     

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        def initr(

     

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                interactive: typing.Optional[bool] = None,

+19

pkgs/development/python-modules/rpy2-rinterface/rpy2-3.x-r-libs-site.patch

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

     

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       index cc9f7da1..10626f13 100644

     

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

     

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

     

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                    _setinitialized()

     

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                    return None

     

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       +
        

     

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       +        # path to libraries

     

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

     

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       +        if existing is not None:

     

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       +            prefix = existing + ':'

     

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       +        else:

     

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       +            prefix = ''

     

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       +        additional = '@NIX_R_LIBS_SITE@'

     

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

     

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       +

     

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                # TODO: Setting LD_LIBRARY_PATH after the process has started

     

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

     

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

pkgs/top-level/python-packages.nix

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

     

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

     

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

···

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

     

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

     

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           inherit (pkgs) zstd;

     

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         };

     

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

     

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