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pythonPackages.rpy2: 3.3.6 -> 3.4.1, cleanup, fix build on darwin

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Sandro Jäckel 2021-01-04 00:01:42 +01:00
parent 95aed5517d
commit 4a184896fc
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GPG Key ID: 3AF5A43A3EECC2E5
1 changed files with 19 additions and 22 deletions
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41
pkgs/development/python-modules/rpy2/default.nix
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@ -1,4 +1,5 @@
{ lib { stdenv
, lib
, python , python
, buildPythonPackage , buildPythonPackage
, fetchpatch , fetchpatch
@ -20,30 +21,37 @@
, cffi , cffi
, tzlocal , tzlocal
, simplegeneric , simplegeneric
, pytest , pytestCheckHook
, extraRPackages ? [] , extraRPackages ? []
}: }:
buildPythonPackage rec { buildPythonPackage rec {
version = "3.3.6"; version = "3.4.1";
pname = "rpy2"; pname = "rpy2";
disabled = isPyPy; disabled = isPyPy;
src = fetchPypi { src = fetchPypi {
inherit version pname; inherit version pname;
sha256 = "0xvfkxvh01r5ibd5mpisp8bz385hgpn27b988y8v65z7hqr3y1nf"; sha256 = "1qnjjlgh6i31z45jykwd29n1336gq678fn9zw7gh0rv5d6sn0hv4";
}; };
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
];
postPatch = ''
substituteInPlace 'rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
substituteInPlace 'requirements.txt' --replace 'pytest' ""
'';
buildInputs = [ buildInputs = [
R
pcre pcre
lzma lzma
bzip2 bzip2
zlib zlib
icu icu
# is in the upstream `requires` although it shouldn't be -- this is easier than patching it away
pytest
] ++ (with rPackages; [ ] ++ (with rPackages; [
# packages expected by the test framework # packages expected by the test framework
ggplot2 ggplot2
@ -58,23 +66,10 @@ buildPythonPackage rec {
tidyr tidyr
]) ++ extraRPackages ++ rWrapper.recommendedPackages; ]) ++ extraRPackages ++ rWrapper.recommendedPackages;
checkPhase = ''
pytest
'';
nativeBuildInputs = [ nativeBuildInputs = [
R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly) R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
]; ];
patches = [
# R_LIBS_SITE is used by the nix r package to point to the installed R libraries.
# This patch sets R_LIBS_SITE when rpy2 is imported.
./rpy2-3.x-r-libs-site.patch
];
postPatch = ''
substituteInPlace 'rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
'';
propagatedBuildInputs = [ propagatedBuildInputs = [
ipython ipython
jinja2 jinja2
@ -86,8 +81,10 @@ buildPythonPackage rec {
simplegeneric simplegeneric
]; ];
doCheck = !stdenv.isDarwin;
checkInputs = [ checkInputs = [
pytest pytestCheckHook
]; ];
meta = { meta = {