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{ 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 ];
};
}
|