nixpkgs/pkgs/development/python-modules/rpy2/2.nix
Timo Kaufmann ef43cd3d42 python3.pkgs.rpy2: 2.9.5 -> 3.2.2
There have been significant changes, therefore it doesn't make sense
anymore to maintain the python2 and python3 version in the same file.
We'll be able to drop the python2 version soon, some time after we have
switched sage to python3.
2019-12-01 00:07:12 +01:00

109 lines
2.6 KiB
Nix

{ 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 ];
};
}