diff options
author | Katharina Fey <kookie@spacekookie.de> | 2020-01-12 01:00:12 +0000 |
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committer | Katharina Fey <kookie@spacekookie.de> | 2020-01-12 01:00:12 +0000 |
commit | eeaf5d25d5f6ae7ae1f5bf8a3dee4559693f8147 (patch) | |
tree | afc41ca8dde96b41089ca324533084aef570322f /nixpkgs/pkgs/development/python-modules/rpy2 | |
parent | 63c4c4dda49dc69e5812faa7ef8406180998f3ae (diff) | |
parent | e4134747f5666bcab8680aff67fa3b63384f9a0f (diff) |
Merge commit 'e4134747f5666bcab8680aff67fa3b63384f9a0f'
Diffstat (limited to 'nixpkgs/pkgs/development/python-modules/rpy2')
3 files changed, 152 insertions, 33 deletions
diff --git a/nixpkgs/pkgs/development/python-modules/rpy2/2.nix b/nixpkgs/pkgs/development/python-modules/rpy2/2.nix new file mode 100644 index 00000000000..aef184d4afc --- /dev/null +++ b/nixpkgs/pkgs/development/python-modules/rpy2/2.nix @@ -0,0 +1,108 @@ +{ lib +, python +, buildPythonPackage +, fetchPypi +, isPyPy +, isPy27 +, readline +, R +, rWrapper +, rPackages +, pcre +, lzma +, bzip2 +, zlib +, icu +, singledispatch +, six +, jinja2 +, pytz +, numpy +, pytest +, mock +, extraRPackages ? [] +}: + +buildPythonPackage rec { + version = "2.8.6"; # python2 support dropped in 2.9.x + pname = "rpy2"; + disabled = isPyPy; + src = fetchPypi { + inherit version pname; + sha256 = "162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80"; + }; + buildInputs = [ + readline + R + pcre + lzma + bzip2 + zlib + icu + ] ++ (with rPackages; [ + # packages expected by the test framework + ggplot2 + dplyr + RSQLite + broom + DBI + dbplyr + hexbin + lme4 + tidyr + + # is in upstream's `requires` although it shouldn't be -- this is easier than patching it away + pytest + ]) ++ extraRPackages ++ rWrapper.recommendedPackages; + + nativeBuildInputs = [ + R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly) + ]; + + 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. + ./r-libs-site.patch + ]; + postPatch = '' + substituteInPlace ${ if isPy27 then "rpy/rinterface/__init__.py" else "rpy2/rinterface_lib/embedded.py" } --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE" + ''; + + doPatchelf = false; # fails because of "missing filename" + patchelfPhase = ""; + + propagatedBuildInputs = [ + singledispatch + six + jinja2 + pytz + numpy + ]; + + checkInputs = [ + pytest + mock + ]; + # One remaining test failure caused by different unicode encoding. + # https://bitbucket.org/rpy2/rpy2/issues/488 + doCheck = false; + checkPhase = '' + ${python.interpreter} -m 'rpy2' + ''; + + # For some reason libreadline.so is not found. Curiously `ldd _rinterface.so | grep readline` shows two readline entries: + # libreadline.so.6 => not found + # libreadline.so.6 => /nix/store/z2zhmrg6jcrn5iq2779mav0nnq4vm2q6-readline-6.3p08/lib/libreadline.so.6 (0x00007f333ac43000) + # There must be a better way to fix this, but I don't know it. + postFixup = '' + patchelf --add-needed ${readline}/lib/libreadline.so "$out/${python.sitePackages}/rpy2/rinterface/"_rinterface*.so + ''; + + meta = { + homepage = http://rpy.sourceforge.net/rpy2; + description = "Python interface to R"; + license = lib.licenses.gpl2Plus; + platforms = lib.platforms.unix; + maintainers = with lib.maintainers; [ joelmo ]; + }; + } diff --git a/nixpkgs/pkgs/development/python-modules/rpy2/default.nix b/nixpkgs/pkgs/development/python-modules/rpy2/default.nix index 1b4ab4d40db..5a00b18557a 100644 --- a/nixpkgs/pkgs/development/python-modules/rpy2/default.nix +++ b/nixpkgs/pkgs/development/python-modules/rpy2/default.nix @@ -3,8 +3,6 @@ , buildPythonPackage , fetchPypi , isPyPy -, isPy27 -, readline , R , rWrapper , rPackages @@ -13,38 +11,38 @@ , bzip2 , zlib , icu -, singledispatch -, six +, ipython , jinja2 , pytz +, pandas , numpy +, cffi +, tzlocal +, simplegeneric , pytest -, mock , extraRPackages ? [] }: buildPythonPackage rec { - version = if isPy27 then - "2.8.6" # python2 support dropped in 2.9.x - else - "2.9.5"; + version = "3.2.4"; pname = "rpy2"; + disabled = isPyPy; src = fetchPypi { inherit version pname; - sha256 = if isPy27 then - "162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80" # 2.8.x - else - "1nrj8pgyxrwrfdrxzb4j3z1adjwjx1mr8d1n5cmrz4nhlzy8w7xr"; # 2.9.x + sha256 = "3daf1a4b28c4e354ef989093f03b066908bf6e5082a6f4af72cc3fd928a28dc6"; }; + buildInputs = [ - readline R pcre lzma bzip2 zlib icu + + # is in the upstream `requires` although it shouldn't be -- this is easier than patching it away + pytest ] ++ (with rPackages; [ # packages expected by the test framework ggplot2 @@ -58,6 +56,10 @@ buildPythonPackage rec { tidyr ]) ++ extraRPackages ++ rWrapper.recommendedPackages; + checkPhase = '' + pytest + ''; + nativeBuildInputs = [ R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly) ]; @@ -65,38 +67,26 @@ buildPythonPackage rec { 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. - ./r-libs-site.patch + ./rpy2-3.x-r-libs-site.patch ]; postPatch = '' - substituteInPlace rpy/rinterface/__init__.py --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE" + substituteInPlace 'rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE" ''; propagatedBuildInputs = [ - singledispatch - six + ipython jinja2 pytz + pandas numpy + cffi + tzlocal + simplegeneric ]; checkInputs = [ pytest - mock ]; - # One remaining test failure caused by different unicode encoding. - # https://bitbucket.org/rpy2/rpy2/issues/488 - doCheck = false; - checkPhase = '' - ${python.interpreter} -m 'rpy2.tests' - ''; - - # For some reason libreadline.so is not found. Curiously `ldd _rinterface.so | grep readline` shows two readline entries: - # libreadline.so.6 => not found - # libreadline.so.6 => /nix/store/z2zhmrg6jcrn5iq2779mav0nnq4vm2q6-readline-6.3p08/lib/libreadline.so.6 (0x00007f333ac43000) - # There must be a better way to fix this, but I don't know it. - postFixup = '' - patchelf --add-needed ${readline}/lib/libreadline.so "$out/${python.sitePackages}/rpy2/rinterface/"_rinterface*.so - ''; meta = { homepage = http://rpy.sourceforge.net/rpy2; diff --git a/nixpkgs/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch b/nixpkgs/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch new file mode 100644 index 00000000000..177e4f9a83d --- /dev/null +++ b/nixpkgs/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch @@ -0,0 +1,21 @@ +diff --git a/rpy2/rinterface_lib/embedded.py b/rpy2/rinterface_lib/embedded.py +index cc32b6d..3969ad0 100644 +--- a/rpy2/rinterface_lib/embedded.py ++++ b/rpy2/rinterface_lib/embedded.py +@@ -113,6 +113,16 @@ def _initr(interactive: bool = True, + if isinitialized(): + return None + os.environ['R_HOME'] = openrlib.R_HOME ++ ++ # 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) |