commit def736708ef2dc2efe800e0205901da23c2b6eb0 · pyrox.dev/nixpkgs

+9 -77

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

···

       4
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         buildPythonPackage,

     

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       5
        
         fetchPypi,

     

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         isPyPy,

     

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       7
       -
         R,

     

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         libdeflate,

     

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         rWrapper,

     

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         rPackages,

     

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       -
         pcre,

     

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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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         ipython,

     

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         jinja2,

     

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         pytz,

     

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         pandas,

     

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         numpy,

     

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         cffi,

     

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         tzlocal,

     

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         simplegeneric,

     

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       +
         rpy2-rinterface,

     

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         rpy2-robjects,

     

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         pytestCheckHook,

     

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         extraRPackages ? [ ],

     

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       }:

     

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       buildPythonPackage rec {

     

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         version = "3.6.2";

     

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         format = "setuptools";

     

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       +
         version = "3.6.3";

     

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         format = "pyproject";

     

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         pname = "rpy2";

     

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         disabled = isPyPy;

     

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         src = fetchPypi {

     

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           inherit version pname;

     

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           hash = "sha256-F06ld2qR0Ds13VYRiJlg4PVFHp0KvqSr/IwL5qhTd9A=";

     

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       +
           hash = "sha256-lCYYoSUhljAG0i6IqqTUgakjghwDoXQsmb7uci6w/Fo=";

     

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         };

     

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         patches = [

     

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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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         ];

     

       45
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       -
       

     

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         postPatch = ''

     

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

     

       48
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           substituteInPlace 'requirements.txt' --replace 'pytest' ""

     

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         '';

     

       50
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       -
       

     

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         buildInputs = [

     

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           pcre

     

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           xz

     

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           bzip2

     

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           zlib

     

       56
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           zstd

     

       57
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           icu

     

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           libdeflate

     

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         ]

     

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         ++ (with rPackages; [

     

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           # packages expected by the test framework

     

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           ggplot2

     

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           dplyr

     

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           RSQLite

     

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           broom

     

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           DBI

     

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           dbplyr

     

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           hexbin

     

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           lazyeval

     

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           lme4

     

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           tidyr

     

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         ])

     

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         ++ extraRPackages

     

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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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       -
       

     

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         propagatedBuildInputs = [

     

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           ipython

     

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           jinja2

     

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           pytz

     

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           pandas

     

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           numpy

     

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           cffi

     

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           tzlocal

     

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           simplegeneric

     

       24
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       +
           rpy2-rinterface

     

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           rpy2-robjects

     

       89
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         ];

     

       90
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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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         pythonImportsCheck = [

     

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           "rpy2"

     

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         ];

     

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       -
       

     

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         nativeCheckInputs = [ pytestCheckHook ];

     

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         meta = {

     

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

-21

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

···

       1
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       diff --git a/rpy2/rinterface_lib/embedded.py b/rpy2/rinterface_lib/embedded.py

     

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       index ccd3a315..51fb5da4 100644

     

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

     

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

     

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

     

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

     

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                        )

     

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                )

     

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

     

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                n_options = len(options_c)

     

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

+1 -1

pkgs/top-level/python-packages.nix

···

       16111
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       16112
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         rpmfluff = callPackage ../development/python-modules/rpmfluff { };

     

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

     

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

     

       16115
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         rpy2-rinterface = callPackage ../development/python-modules/rpy2-rinterface {

     

       16117
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           inherit (pkgs) zstd;