diff options
author | Timo Kaufmann <timokau@zoho.com> | 2018-11-27 18:24:37 +0100 |
---|---|---|
committer | GitHub <noreply@github.com> | 2018-11-27 18:24:37 +0100 |
commit | 63b39af496505034fd5125f9a94dccd795d1b648 (patch) | |
tree | 44d32bbf025f24439426dc2828a0efaa5de19b43 /pkgs/development/python-modules/rpy2/default.nix | |
parent | be8569be499490fc04eff48c2d27dd9d89aaa60d (diff) |
pythonPackages.rpy2: various fixes (#51084)
- make sure libreadline is found at runtime
- make sure python libraries are found at runtime
- add libraries necessary to pass the testsuite and standard libraries
Diffstat (limited to '')
-rw-r--r-- | pkgs/development/python-modules/rpy2/default.nix | 53 |
1 files changed, 48 insertions, 5 deletions
diff --git a/pkgs/development/python-modules/rpy2/default.nix b/pkgs/development/python-modules/rpy2/default.nix index 61447e740265..cefd155353ac 100644 --- a/pkgs/development/python-modules/rpy2/default.nix +++ b/pkgs/development/python-modules/rpy2/default.nix @@ -1,10 +1,13 @@ { lib +, python , buildPythonPackage , fetchPypi , isPyPy , isPy27 , readline , R +, rWrapper +, rPackages , pcre , lzma , bzip2 @@ -13,7 +16,11 @@ , singledispatch , six , jinja2 +, pytz +, numpy , pytest +, mock +, extraRPackages ? [] }: buildPythonPackage rec { @@ -38,18 +45,54 @@ buildPythonPackage rec { bzip2 zlib icu + ] ++ (with rPackages; [ + # packages expected by the test framework + ggplot2 + dplyr + RSQLite + broom + DBI + dbplyr + hexbin + lme4 + tidyr + ]) ++ extraRPackages ++ rWrapper.recommendedPackages; + + 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 rpy/rinterface/__init__.py --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE" + ''; + propagatedBuildInputs = [ singledispatch six jinja2 + pytz + numpy ]; - checkInputs = [ pytest ]; - # Tests fail with `assert not _relpath.startswith('..'), "Path must be within the project"` - # in the unittest `loader.py`. I don't know what causes this. + + checkInputs = [ + pytest + mock + ]; + # One remaining test failure caused by different unicode encoding. + # https://bitbucket.org/rpy2/rpy2/issues/488 doCheck = false; - # without this tests fail when looking for libreadline.so - LD_LIBRARY_PATH = lib.makeLibraryPath buildInputs; + 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; |