Merge pull request #74537 from timokau/rpy2-3.2.2
python3.pkgs.rpy2: 2.9.5 -> 3.2.2
This commit is contained in:
Timo Kaufmann
GitHub
commit
28cb34d538
108
pkgs/development/python-modules/rpy2/2.nix
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108
pkgs/development/python-modules/rpy2/2.nix
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@ -0,0 +1,108 @@
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{ lib
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, python
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, buildPythonPackage
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, fetchPypi
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, isPyPy
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, isPy27
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, readline
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, R
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, rWrapper
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, rPackages
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, pcre
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, lzma
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, bzip2
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, zlib
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, icu
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, singledispatch
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, six
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, jinja2
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, pytz
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, numpy
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, pytest
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, mock
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, extraRPackages ? []
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}:
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buildPythonPackage rec {
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version = "2.8.6"; # python2 support dropped in 2.9.x
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pname = "rpy2";
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disabled = isPyPy;
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src = fetchPypi {
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inherit version pname;
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sha256 = "162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80";
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};
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buildInputs = [
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readline
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R
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pcre
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lzma
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bzip2
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zlib
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icu
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] ++ (with rPackages; [
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# packages expected by the test framework
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ggplot2
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dplyr
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RSQLite
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broom
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DBI
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dbplyr
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hexbin
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lme4
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tidyr
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# is in upstream's `requires` although it shouldn't be -- this is easier than patching it away
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pytest
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]) ++ extraRPackages ++ rWrapper.recommendedPackages;
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nativeBuildInputs = [
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R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
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];
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patches = [
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# R_LIBS_SITE is used by the nix r package to point to the installed R libraries.
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# This patch sets R_LIBS_SITE when rpy2 is imported.
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./r-libs-site.patch
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];
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postPatch = ''
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substituteInPlace ${ if isPy27 then "rpy/rinterface/__init__.py" else "rpy2/rinterface_lib/embedded.py" } --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
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'';
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doPatchelf = false; # fails because of "missing filename"
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patchelfPhase = "";
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propagatedBuildInputs = [
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singledispatch
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six
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jinja2
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pytz
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numpy
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];
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checkInputs = [
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pytest
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mock
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];
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# One remaining test failure caused by different unicode encoding.
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# https://bitbucket.org/rpy2/rpy2/issues/488
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doCheck = false;
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checkPhase = ''
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${python.interpreter} -m 'rpy2'
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'';
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# For some reason libreadline.so is not found. Curiously `ldd _rinterface.so | grep readline` shows two readline entries:
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# libreadline.so.6 => not found
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# libreadline.so.6 => /nix/store/z2zhmrg6jcrn5iq2779mav0nnq4vm2q6-readline-6.3p08/lib/libreadline.so.6 (0x00007f333ac43000)
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# There must be a better way to fix this, but I don't know it.
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postFixup = ''
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patchelf --add-needed ${readline}/lib/libreadline.so "$out/${python.sitePackages}/rpy2/rinterface/"_rinterface*.so
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'';
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meta = {
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homepage = http://rpy.sourceforge.net/rpy2;
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description = "Python interface to R";
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license = lib.licenses.gpl2Plus;
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platforms = lib.platforms.unix;
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maintainers = with lib.maintainers; [ joelmo ];
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};
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}
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@ -3,8 +3,6 @@
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, buildPythonPackage
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, fetchPypi
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, isPyPy
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, isPy27
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, readline
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, R
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, rWrapper
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, rPackages
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@ -13,38 +11,38 @@
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, bzip2
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, zlib
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, icu
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, singledispatch
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, six
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, ipython
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, jinja2
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, pytz
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, pandas
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, numpy
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, cffi
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, tzlocal
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, simplegeneric
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, pytest
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, mock
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, extraRPackages ? []
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}:
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buildPythonPackage rec {
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version = if isPy27 then
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"2.8.6" # python2 support dropped in 2.9.x
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else
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"2.9.5";
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version = "3.2.2";
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pname = "rpy2";
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disabled = isPyPy;
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src = fetchPypi {
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inherit version pname;
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sha256 = if isPy27 then
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"162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80" # 2.8.x
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else
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"1nrj8pgyxrwrfdrxzb4j3z1adjwjx1mr8d1n5cmrz4nhlzy8w7xr"; # 2.9.x
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sha256 = "0b3jpn9x7m2pccriyzgfsdb68qp6nq4ffhvjy1q2ar8wdxvmf5xp";
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};
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buildInputs = [
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readline
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R
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pcre
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lzma
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bzip2
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zlib
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icu
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# is in the upstream `requires` although it shouldn't be -- this is easier than patching it away
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pytest
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] ++ (with rPackages; [
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# packages expected by the test framework
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ggplot2
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@ -58,6 +56,10 @@ buildPythonPackage rec {
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tidyr
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]) ++ extraRPackages ++ rWrapper.recommendedPackages;
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checkPhase = ''
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pytest
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'';
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nativeBuildInputs = [
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R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
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];
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@ -65,38 +67,26 @@ buildPythonPackage rec {
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patches = [
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# R_LIBS_SITE is used by the nix r package to point to the installed R libraries.
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# This patch sets R_LIBS_SITE when rpy2 is imported.
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./r-libs-site.patch
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./rpy2-3.x-r-libs-site.patch
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];
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postPatch = ''
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substituteInPlace rpy/rinterface/__init__.py --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
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substituteInPlace 'rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
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'';
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propagatedBuildInputs = [
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singledispatch
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six
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ipython
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jinja2
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pytz
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pandas
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numpy
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cffi
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tzlocal
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simplegeneric
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];
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checkInputs = [
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pytest
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mock
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];
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# One remaining test failure caused by different unicode encoding.
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# https://bitbucket.org/rpy2/rpy2/issues/488
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doCheck = false;
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checkPhase = ''
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${python.interpreter} -m 'rpy2.tests'
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'';
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# For some reason libreadline.so is not found. Curiously `ldd _rinterface.so | grep readline` shows two readline entries:
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# libreadline.so.6 => not found
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# libreadline.so.6 => /nix/store/z2zhmrg6jcrn5iq2779mav0nnq4vm2q6-readline-6.3p08/lib/libreadline.so.6 (0x00007f333ac43000)
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# There must be a better way to fix this, but I don't know it.
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postFixup = ''
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patchelf --add-needed ${readline}/lib/libreadline.so "$out/${python.sitePackages}/rpy2/rinterface/"_rinterface*.so
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'';
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meta = {
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homepage = http://rpy.sourceforge.net/rpy2;
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@ -0,0 +1,21 @@
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diff --git a/rpy2/rinterface_lib/embedded.py b/rpy2/rinterface_lib/embedded.py
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index cc32b6d..3969ad0 100644
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--- a/rpy2/rinterface_lib/embedded.py
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+++ b/rpy2/rinterface_lib/embedded.py
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@@ -113,6 +113,16 @@ def _initr(interactive: bool = True,
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if isinitialized():
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return None
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os.environ['R_HOME'] = openrlib.R_HOME
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+
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+ # path to libraries
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+ existing = os.environ.get('R_LIBS_SITE')
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+ if existing is not None:
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+ prefix = existing + ':'
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+ else:
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+ prefix = ''
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+ additional = '@NIX_R_LIBS_SITE@'
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+ os.environ['R_LIBS_SITE'] = prefix + additional
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+
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options_c = [ffi.new('char[]', o.encode('ASCII')) for o in _options]
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n_options = len(options_c)
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n_options_c = ffi.cast('int', n_options)
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@ -5042,7 +5042,9 @@ in {
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rpmfluff = callPackage ../development/python-modules/rpmfluff {};
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rpy2 = callPackage ../development/python-modules/rpy2 {};
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rpy2 = if isPy3k
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then callPackage ../development/python-modules/rpy2 { }
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else callPackage ../development/python-modules/rpy2/2.nix { };
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rtslib = callPackage ../development/python-modules/rtslib {};
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