108 lines
2.1 KiB
Nix
108 lines
2.1 KiB
Nix
|
{ lib
|
||
|
|
, python
|
||
|
|
, buildPythonPackage
|
||
|
|
, fetchpatch
|
||
|
|
, fetchPypi
|
||
|
|
, isPyPy
|
||
|
|
, R
|
||
|
|
, rWrapper
|
||
|
|
, rPackages
|
||
|
|
, pcre
|
||
|
|
, lzma
|
||
|
|
, bzip2
|
||
|
|
, zlib
|
||
|
|
, icu
|
||
|
|
, ipython
|
||
|
|
, jinja2
|
||
|
|
, pytz
|
||
|
|
, pandas
|
||
|
|
, numpy
|
||
|
|
, cffi
|
||
|
|
, tzlocal
|
||
|
|
, simplegeneric
|
||
|
|
, pytest
|
||
|
|
, extraRPackages ? []
|
||
|
|
}:
|
||
|
|
|
||
|
|
buildPythonPackage rec {
|
||
|
|
version = "3.2.6";
|
||
|
|
pname = "rpy2";
|
||
|
|
|
||
|
|
disabled = isPyPy;
|
||
|
|
src = fetchPypi {
|
||
|
|
inherit version pname;
|
||
|
|
sha256 = "1p990cqx3p2pd1rc9wn66m56wahaq8dlr88frz49vb7nv4zw4a8q";
|
||
|
|
};
|
||
|
|
|
||
|
|
buildInputs = [
|
||
|
|
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
|
||
|
|
dplyr
|
||
|
|
RSQLite
|
||
|
|
broom
|
||
|
|
DBI
|
||
|
|
dbplyr
|
||
|
|
hexbin
|
||
|
|
lme4
|
||
|
|
tidyr
|
||
|
|
]) ++ extraRPackages ++ rWrapper.recommendedPackages;
|
||
|
|
|
||
|
|
checkPhase = ''
|
||
|
|
pytest
|
||
|
|
'';
|
||
|
|
|
||
|
|
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.
|
||
|
|
./rpy2-3.x-r-libs-site.patch
|
||
|
|
|
||
|
|
# pandas 1.x compatibility, already merged upstream
|
||
|
|
# https://github.com/rpy2/rpy2/issues/636
|
||
|
|
(fetchpatch {
|
||
|
|
name = "pandas-1.x.patch";
|
||
|
|
url = "https://github.com/rpy2/rpy2/commit/fbd060e364b70012e8d26cc74df04ee53f769379.patch";
|
||
|
|
sha256 = "19rdqydwjmqg25ibmsbx7lggrr9fsyjn283zgvz1wj4iyfjwp1za";
|
||
|
|
})
|
||
|
|
];
|
||
|
|
postPatch = ''
|
||
|
|
substituteInPlace 'rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
|
||
|
|
'';
|
||
|
|
|
||
|
|
propagatedBuildInputs = [
|
||
|
|
ipython
|
||
|
|
jinja2
|
||
|
|
pytz
|
||
|
|
pandas
|
||
|
|
numpy
|
||
|
|
cffi
|
||
|
|
tzlocal
|
||
|
|
simplegeneric
|
||
|
|
];
|
||
|
|
|
||
|
|
checkInputs = [
|
||
|
|
pytest
|
||
|
|
];
|
||
|
|
|
||
|
|
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 ];
|
||
|
|
};
|
||
|
|
}
|