pythonPackages.rpy2: various fixes (#51084)
- make sure libreadline is found at runtime - make sure python libraries are found at runtime - add libraries necessary to pass the testsuite and standard libraries
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63b39af496
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@ -1,10 +1,13 @@
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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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@ -13,7 +16,11 @@
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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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@ -38,18 +45,54 @@ buildPythonPackage rec {
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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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]) ++ extraRPackages ++ rWrapper.recommendedPackages;
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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 rpy/rinterface/__init__.py --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
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'';
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propagatedBuildInputs = [
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singledispatch
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six
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jinja2
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pytz
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numpy
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];
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checkInputs = [ pytest ];
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# Tests fail with `assert not _relpath.startswith('..'), "Path must be within the project"`
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# in the unittest `loader.py`. I don't know what causes this.
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checkInputs = [
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pytest
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mock
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];
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# One remaining test failure caused by different unicode encoding.
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# https://bitbucket.org/rpy2/rpy2/issues/488
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doCheck = false;
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# without this tests fail when looking for libreadline.so
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LD_LIBRARY_PATH = lib.makeLibraryPath buildInputs;
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checkPhase = ''
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${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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20
pkgs/development/python-modules/rpy2/r-libs-site.patch
Normal file
20
pkgs/development/python-modules/rpy2/r-libs-site.patch
Normal file
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@ -0,0 +1,20 @@
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diff --git a/rpy/rinterface/__init__.py b/rpy/rinterface/__init__.py
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index 9362e57..1af258e 100644
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--- a/rpy/rinterface/__init__.py
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+++ b/rpy/rinterface/__init__.py
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@@ -43,6 +43,15 @@ if not R_HOME:
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if not os.environ.get("R_HOME"):
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os.environ['R_HOME'] = R_HOME
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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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if sys.platform == 'win32':
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_load_r_dll(R_HOME)
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@ -5,6 +5,9 @@ stdenv.mkDerivation {
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buildInputs = [makeWrapper R] ++ recommendedPackages ++ packages;
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# Make the list of recommended R packages accessible to other packages such as rpy2
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passthru.recommendedPackages = recommendedPackages;
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unpackPhase = ":";
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installPhase = ''
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