2019-11-28 19:58:59 +00:00
|
|
|
{ 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 = {
|
2020-04-01 02:11:51 +01:00
|
|
|
homepage = "http://rpy.sourceforge.net/rpy2";
|
2019-11-28 19:58:59 +00:00
|
|
|
description = "Python interface to R";
|
|
|
|
|
license = lib.licenses.gpl2Plus;
|
|
|
|
|
platforms = lib.platforms.unix;
|
|
|
|
|
maintainers = with lib.maintainers; [ joelmo ];
|
|
|
|
|
};
|
|
|
|
|
}
|
