diff options
Diffstat (limited to 'nixpkgs/pkgs/development/python-modules/rpy2/default.nix')
| -rw-r--r-- | nixpkgs/pkgs/development/python-modules/rpy2/default.nix | 56 |
1 files changed, 23 insertions, 33 deletions
diff --git a/nixpkgs/pkgs/development/python-modules/rpy2/default.nix b/nixpkgs/pkgs/development/python-modules/rpy2/default.nix index 1b4ab4d40db9..5a00b18557a6 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; |