commit b4413a7ea14e3ac3df6c2147f5575149c79383b0 · pyrox.dev/nixpkgs

+14

pkgs/by-name/sa/sage/sage-src.nix

···

       82
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             url = "https://github.com/sagemath/sage/commit/d0cbe9d353722580f98a327694f1a361c9b83ccd.patch?full_index=1";

     

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

     

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           })

     

       85
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       +
       

     

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

     

       87
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       +
           (fetchpatch2 {

     

       88
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       +
             name = "cython-3.1-update.patch";

     

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

     

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       +
             hash = "sha256-5DPPxMuidPpVHrjK8j0UVZzuwiVy9vQzFd6hBYwNAok=";

     

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       +
           })

     

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       +
       

     

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

     

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       +
           (fetchpatch2 {

     

       95
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       +
             name = "rpy2-3.6-update.patch";

     

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

     

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

     

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       +
           })

     

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         ];

     

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         patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;

+79

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

···

       1
       1
       +
       {

     

       2
       2
       +
         stdenv,

     

       3
       3
       +
         lib,

     

       4
       4
       +
         buildPythonPackage,

     

       5
       5
       +
         fetchurl,

     

       6
       6
       +
         isPyPy,

     

       7
       7
       +
         R,

     

       8
       8
       +
         rWrapper,

     

       9
       9
       +
         xz,

     

       10
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       +
         bzip2,

     

       11
       11
       +
         zlib,

     

       12
       12
       +
         zstd,

     

       13
       13
       +
         icu,

     

       14
       14
       +
         pytestCheckHook,

     

       15
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       +
         setuptools,

     

       16
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       +
         cffi,

     

       17
       17
       +
       }:

     

       18
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       +
       

     

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       +
       buildPythonPackage rec {

     

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       +
         version = "3.6.3";

     

       21
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       +
         format = "pyproject";

     

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       +
         pname = "rpy2-rinterface";

     

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       +
       

     

       24
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       +
         disabled = isPyPy;

     

       25
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       +
         src = fetchurl {

     

       26
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       +
           url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${

     

       27
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       +
             builtins.replaceStrings [ "-" ] [ "_" ] pname

     

       28
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       +
           }-${version}.tar.gz";

     

       29
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       +
           hash = "sha256-R3vC9R0AetG4VnxdS6GvD1mVFobufxBXagbQg03ld28=";

     

       30
       30
       +
         };

     

       31
       31
       +
       

     

       32
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       +
         patches = [

     

       33
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       +
           # https://github.com/rpy2/rpy2/pull/1171#issuecomment-3263994962

     

       34
       34
       +
           ./restore-initr-simple.patch

     

       35
       35
       +
       

     

       36
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       +
           # R_LIBS_SITE is used by the nix r package to point to the installed R libraries.

     

       37
       37
       +
           # This patch sets R_LIBS_SITE when rpy2 is imported.

     

       38
       38
       +
           ./rpy2-3.x-r-libs-site.patch

     

       39
       39
       +
         ];

     

       40
       40
       +
       

     

       41
       41
       +
         postPatch = ''

     

       42
       42
       +
           substituteInPlace 'src/rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"

     

       43
       43
       +
         '';

     

       44
       44
       +
       

     

       45
       45
       +
         buildInputs = [

     

       46
       46
       +
           xz

     

       47
       47
       +
           bzip2

     

       48
       48
       +
           zlib

     

       49
       49
       +
           zstd

     

       50
       50
       +
           icu

     

       51
       51
       +
         ]

     

       52
       52
       +
         ++ rWrapper.recommendedPackages;

     

       53
       53
       +
       

     

       54
       54
       +
         nativeBuildInputs = [

     

       55
       55
       +
           R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)

     

       56
       56
       +
         ];

     

       57
       57
       +
       

     

       58
       58
       +
         propagatedBuildInputs = [

     

       59
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       +
           cffi

     

       60
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       +
           setuptools

     

       61
       61
       +
         ];

     

       62
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       +
       

     

       63
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       +
         nativeCheckInputs = [ pytestCheckHook ];

     

       64
       64
       +
       

     

       65
       65
       +
         # https://github.com/rpy2/rpy2/issues/1111

     

       66
       66
       +
         disabledTests = [

     

       67
       67
       +
           "test_parse_incomplete_error"

     

       68
       68
       +
           "test_parse_error"

     

       69
       69
       +
           "test_parse_error_when_evaluting"

     

       70
       70
       +
         ];

     

       71
       71
       +
       

     

       72
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       +
         meta = {

     

       73
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       +
           homepage = "https://rpy2.github.io/";

     

       74
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       +
           description = "Python interface to R";

     

       75
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       +
           license = lib.licenses.gpl2Plus;

     

       76
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       +
           platforms = lib.platforms.unix;

     

       77
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       +
           maintainers = with lib; [ teams.sage ];

     

       78
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       +
         };

     

       79
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       +
       }

+20

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

···

       1
       1
       +
       diff --git a/src/rpy2/rinterface/__init__.py b/src/rpy2/rinterface/__init__.py

     

       2
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       +
       index 0ba46083..1f4265aa 100644

     

       3
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       +
       --- a/src/rpy2/rinterface/__init__.py

     

       4
       4
       +
       +++ b/src/rpy2/rinterface/__init__.py

     

       5
       5
       +
       @@ -1100,6 +1100,15 @@ NA = None

     

       6
       6
       +
        NA_Real = None

     

       7
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       +
        NA_Complex = None

     

       8
       8
       +
        

     

       9
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       +
       +def initr_simple() -> typing.Optional[int]:

     

       10
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       +
       +    """Initialize R's embedded C library."""

     

       11
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       +
       +    with openrlib.rlock:

     

       12
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       +
       +        status = embedded._initr()

     

       13
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       +
       +        atexit.register(endr, 0)

     

       14
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       +
       +        _rinterface._register_external_symbols()

     

       15
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       +
       +        _post_initr_setup()

     

       16
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       +
       +        return status

     

       17
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       +
       +

     

       18
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       +
        

     

       19
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       +
        def initr(

     

       20
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       +
                interactive: typing.Optional[bool] = None,

+19

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

···

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

     

       2
       2
       +
       index cc9f7da1..10626f13 100644

     

       3
       3
       +
       --- a/src/rpy2/rinterface_lib/embedded.py b/src/rpy2/rinterface_lib/embedded.py

     

       4
       4
       +
       @@ -328,6 +328,15 @@ def _initr(

     

       5
       5
       +
                    _setinitialized()

     

       6
       6
       +
                    return None

     

       7
       7
       +
        

     

       8
       8
       +
       +        # path to libraries

     

       9
       9
       +
       +        existing = os.environ.get('R_LIBS_SITE')

     

       10
       10
       +
       +        if existing is not None:

     

       11
       11
       +
       +            prefix = existing + ':'

     

       12
       12
       +
       +        else:

     

       13
       13
       +
       +            prefix = ''

     

       14
       14
       +
       +        additional = '@NIX_R_LIBS_SITE@'

     

       15
       15
       +
       +        os.environ['R_LIBS_SITE'] = prefix + additional

     

       16
       16
       +
       +

     

       17
       17
       +
                # TODO: Setting LD_LIBRARY_PATH after the process has started

     

       18
       18
       +
                # is too late. Because of this, the line below does not help

     

       19
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       +
                # address issues where calling R from the command line is working

+63

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

···

       1
       1
       +
       {

     

       2
       2
       +
         stdenv,

     

       3
       3
       +
         lib,

     

       4
       4
       +
         buildPythonPackage,

     

       5
       5
       +
         fetchurl,

     

       6
       6
       +
         fetchpatch2,

     

       7
       7
       +
         isPyPy,

     

       8
       8
       +
         R,

     

       9
       9
       +
         rpy2-rinterface,

     

       10
       10
       +
         ipython,

     

       11
       11
       +
         jinja2,

     

       12
       12
       +
         numpy,

     

       13
       13
       +
         pandas,

     

       14
       14
       +
         tzlocal,

     

       15
       15
       +
         pytestCheckHook,

     

       16
       16
       +
       }:

     

       17
       17
       +
       

     

       18
       18
       +
       buildPythonPackage rec {

     

       19
       19
       +
         version = "3.6.2";

     

       20
       20
       +
         format = "pyproject";

     

       21
       21
       +
         pname = "rpy2-robjects";

     

       22
       22
       +
       

     

       23
       23
       +
         disabled = isPyPy;

     

       24
       24
       +
         src = fetchurl {

     

       25
       25
       +
           url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${

     

       26
       26
       +
             builtins.replaceStrings [ "-" ] [ "_" ] pname

     

       27
       27
       +
           }-${version}.tar.gz";

     

       28
       28
       +
           hash = "sha256-rJGvMtXE2iNrBaPNaNr7JM2PWogPAHhim48r8CUFQjs=";

     

       29
       29
       +
         };

     

       30
       30
       +
       

     

       31
       31
       +
         patches = [

     

       32
       32
       +
           # https://github.com/rpy2/rpy2/pull/1171#issuecomment-3263994962

     

       33
       33
       +
           (fetchpatch2 {

     

       34
       34
       +
             url = "https://github.com/rpy2/rpy2/commit/524546eef9b8f7f3d61aeb76d7e7fa7beeabd2d2.patch?full_index=1";

     

       35
       35
       +
             hash = "sha256-aR44E8wIBlD7UpQKm7B+aMn2p3FQ8dwBwLwkibIpcuM=";

     

       36
       36
       +
             relative = "rpy2-robjects";

     

       37
       37
       +
             revert = true;

     

       38
       38
       +
           })

     

       39
       39
       +
         ];

     

       40
       40
       +
       

     

       41
       41
       +
         nativeBuildInputs = [

     

       42
       42
       +
           R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)

     

       43
       43
       +
         ];

     

       44
       44
       +
       

     

       45
       45
       +
         propagatedBuildInputs = [

     

       46
       46
       +
           ipython

     

       47
       47
       +
           jinja2

     

       48
       48
       +
           numpy

     

       49
       49
       +
           pandas

     

       50
       50
       +
           rpy2-rinterface

     

       51
       51
       +
           tzlocal

     

       52
       52
       +
         ];

     

       53
       53
       +
       

     

       54
       54
       +
         nativeCheckInputs = [ pytestCheckHook ];

     

       55
       55
       +
       

     

       56
       56
       +
         meta = {

     

       57
       57
       +
           homepage = "https://rpy2.github.io/";

     

       58
       58
       +
           description = "Python interface to R";

     

       59
       59
       +
           license = lib.licenses.gpl2Plus;

     

       60
       60
       +
           platforms = lib.platforms.unix;

     

       61
       61
       +
           maintainers = with lib.maintainers; [ joelmo ];

     

       62
       62
       +
         };

     

       63
       63
       +
       }

+9 -77

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

···

       4
       4
        
         buildPythonPackage,

     

       5
       5
        
         fetchPypi,

     

       6
       6
        
         isPyPy,

     

       7
       7
       -
         R,

     

       8
       8
       -
         libdeflate,

     

       9
       9
       -
         rWrapper,

     

       10
       10
       -
         rPackages,

     

       11
       11
       -
         pcre,

     

       12
       12
       -
         xz,

     

       13
       13
       -
         bzip2,

     

       14
       14
       -
         zlib,

     

       15
       15
       -
         zstd,

     

       16
       16
       -
         icu,

     

       17
       17
       -
         ipython,

     

       18
       18
       -
         jinja2,

     

       19
       19
       -
         pytz,

     

       20
       20
       -
         pandas,

     

       21
       21
       -
         numpy,

     

       22
       22
       -
         cffi,

     

       23
       23
       -
         tzlocal,

     

       24
       24
       -
         simplegeneric,

     

       7
       7
       +
         rpy2-rinterface,

     

       8
       8
       +
         rpy2-robjects,

     

       25
       9
        
         pytestCheckHook,

     

       26
       26
       -
         extraRPackages ? [ ],

     

       27
       10
        
       }:

     

       28
       11
        
       

     

       29
       12
        
       buildPythonPackage rec {

     

       30
       30
       -
         version = "3.6.2";

     

       31
       31
       -
         format = "setuptools";

     

       13
       13
       +
         version = "3.6.3";

     

       14
       14
       +
         format = "pyproject";

     

       32
       15
        
         pname = "rpy2";

     

       33
       16
        
       

     

       34
       17
        
         disabled = isPyPy;

     

       35
       18
        
         src = fetchPypi {

     

       36
       19
        
           inherit version pname;

     

       37
       37
       -
           hash = "sha256-F06ld2qR0Ds13VYRiJlg4PVFHp0KvqSr/IwL5qhTd9A=";

     

       20
       20
       +
           hash = "sha256-lCYYoSUhljAG0i6IqqTUgakjghwDoXQsmb7uci6w/Fo=";

     

       38
       21
        
         };

     

       39
       22
        
       

     

       40
       40
       -
         patches = [

     

       41
       41
       -
           # R_LIBS_SITE is used by the nix r package to point to the installed R libraries.

     

       42
       42
       -
           # This patch sets R_LIBS_SITE when rpy2 is imported.

     

       43
       43
       -
           ./rpy2-3.x-r-libs-site.patch

     

       44
       44
       -
         ];

     

       45
       45
       -
       

     

       46
       46
       -
         postPatch = ''

     

       47
       47
       -
           substituteInPlace 'rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"

     

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

     

       49
       49
       -
         '';

     

       50
       50
       -
       

     

       51
       51
       -
         buildInputs = [

     

       52
       52
       -
           pcre

     

       53
       53
       -
           xz

     

       54
       54
       -
           bzip2

     

       55
       55
       -
           zlib

     

       56
       56
       -
           zstd

     

       57
       57
       -
           icu

     

       58
       58
       -
           libdeflate

     

       59
       59
       -
         ]

     

       60
       60
       -
         ++ (with rPackages; [

     

       61
       61
       -
           # packages expected by the test framework

     

       62
       62
       -
           ggplot2

     

       63
       63
       -
           dplyr

     

       64
       64
       -
           RSQLite

     

       65
       65
       -
           broom

     

       66
       66
       -
           DBI

     

       67
       67
       -
           dbplyr

     

       68
       68
       -
           hexbin

     

       69
       69
       -
           lazyeval

     

       70
       70
       -
           lme4

     

       71
       71
       -
           tidyr

     

       72
       72
       -
         ])

     

       73
       73
       -
         ++ extraRPackages

     

       74
       74
       -
         ++ rWrapper.recommendedPackages;

     

       75
       75
       -
       

     

       76
       76
       -
         nativeBuildInputs = [

     

       77
       77
       -
           R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)

     

       78
       78
       -
         ];

     

       79
       79
       -
       

     

       80
       23
        
         propagatedBuildInputs = [

     

       81
       81
       -
           ipython

     

       82
       82
       -
           jinja2

     

       83
       83
       -
           pytz

     

       84
       84
       -
           pandas

     

       85
       85
       -
           numpy

     

       86
       86
       -
           cffi

     

       87
       87
       -
           tzlocal

     

       88
       88
       -
           simplegeneric

     

       24
       24
       +
           rpy2-rinterface

     

       25
       25
       +
           rpy2-robjects

     

       89
       26
        
         ];

     

       90
       27
        
       

     

       91
       91
       -
         # https://github.com/rpy2/rpy2/issues/1111

     

       92
       92
       -
         disabledTests = [

     

       93
       93
       -
           "test_parse_incomplete_error"

     

       94
       94
       -
           "test_parse_error"

     

       95
       95
       -
           "test_parse_error_when_evaluting"

     

       28
       28
       +
         pythonImportsCheck = [

     

       29
       29
       +
           "rpy2"

     

       96
       30
        
         ];

     

       97
       97
       -
       

     

       98
       98
       -
         nativeCheckInputs = [ pytestCheckHook ];

     

       99
       31
        
       

     

       100
       32
        
         meta = {

     

       101
       33
        
           homepage = "https://rpy2.github.io/";

-21

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

···

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

     

       2
       2
       -
       index ccd3a315..51fb5da4 100644

     

       3
       3
       -
       --- a/rpy2/rinterface_lib/embedded.py

     

       4
       4
       -
       +++ b/rpy2/rinterface_lib/embedded.py

     

       5
       5
       -
       @@ -276,6 +276,16 @@ def _initr(

     

       6
       6
       -
                         os.environ.get('LD_LIBRARY_PATH', ''))

     

       7
       7
       -
                        )

     

       8
       8
       -
                )

     

       9
       9
       -
       +

     

       10
       10
       -
       +        # path to libraries

     

       11
       11
       -
       +        existing = os.environ.get('R_LIBS_SITE')

     

       12
       12
       -
       +        if existing is not None:

     

       13
       13
       -
       +            prefix = existing + ':'

     

       14
       14
       -
       +        else:

     

       15
       15
       -
       +            prefix = ''

     

       16
       16
       -
       +        additional = '@NIX_R_LIBS_SITE@'

     

       17
       17
       -
       +        os.environ['R_LIBS_SITE'] = prefix + additional

     

       18
       18
       -
       +

     

       19
       19
       -
                options_c = [ffi.new('char[]', o.encode('ASCII')) for o in _options]

     

       20
       20
       -
                n_options = len(options_c)

     

       21
       21
       -
                n_options_c = ffi.cast('int', n_options)

+7 -1

pkgs/top-level/python-packages.nix

···

       16135
       16135
        
       

     

       16136
       16136
        
         rpmfluff = callPackage ../development/python-modules/rpmfluff { };

     

       16137
       16137
        
       

     

       16138
       16138
       -
         rpy2 = callPackage ../development/python-modules/rpy2 { inherit (pkgs) zstd; };

     

       16138
       16138
       +
         rpy2 = callPackage ../development/python-modules/rpy2 { };

     

       16139
       16139
       +
       

     

       16140
       16140
       +
         rpy2-rinterface = callPackage ../development/python-modules/rpy2-rinterface {

     

       16141
       16141
       +
           inherit (pkgs) zstd;

     

       16142
       16142
       +
         };

     

       16143
       16143
       +
       

     

       16144
       16144
       +
         rpy2-robjects = callPackage ../development/python-modules/rpy2-robjects { };

     

       16139
       16145
        
       

     

       16140
       16146
        
         rpyc = callPackage ../development/python-modules/rpyc { };

     

       16141
       16147