Add 'nixpkgs/' from commit '2436c27541b2f52deea3a4c1691216a02152e729'

git-subtree-dir: nixpkgs
git-subtree-mainline: 1148b1d122bc03e9a3665856c9b7bb96bd4e3994
git-subtree-split: 2436c27541b2f52deea3a4c1691216a02152e729

2 files changed, 128 insertions, 0 deletions

diff --git a/nixpkgs/pkgs/development/python-modules/rpy2/default.nix b/nixpkgs/pkgs/development/python-modules/rpy2/default.nix
new file mode 100644
index 00000000000..1b4ab4d40db
--- /dev/null
+++ b/nixpkgs/pkgs/development/python-modules/rpy2/default.nix
@@ -0,0 +1,108 @@
+{ 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 = if isPy27 then
+      "2.8.6" # python2 support dropped in 2.9.x
+    else
+      "2.9.5";
+    pname = "rpy2";
+    disabled = isPyPy;
+    src = fetchPypi {
+      inherit version pname;
+      sha256 = if isPy27 then
+        "162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80" # 2.8.x
+      else
+        "1nrj8pgyxrwrfdrxzb4j3z1adjwjx1mr8d1n5cmrz4nhlzy8w7xr"; # 2.9.x
+    };
+    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
+    ]) ++ 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 rpy/rinterface/__init__.py --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
+    '';
+
+    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.tests'
+    '';
+
+    # 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 = {
+      homepage = http://rpy.sourceforge.net/rpy2;
+      description = "Python interface to R";
+      license = lib.licenses.gpl2Plus;
+      platforms = lib.platforms.unix;
+      maintainers = with lib.maintainers; [ joelmo ];
+    };
+  }
diff --git a/nixpkgs/pkgs/development/python-modules/rpy2/r-libs-site.patch b/nixpkgs/pkgs/development/python-modules/rpy2/r-libs-site.patch
new file mode 100644
index 00000000000..a55b6038bb4
--- /dev/null
+++ b/nixpkgs/pkgs/development/python-modules/rpy2/r-libs-site.patch
@@ -0,0 +1,20 @@
+diff --git a/rpy/rinterface/__init__.py b/rpy/rinterface/__init__.py
+index 9362e57..1af258e 100644
+--- a/rpy/rinterface/__init__.py
++++ b/rpy/rinterface/__init__.py
+@@ -43,6 +43,15 @@ if not R_HOME:
+ if not os.environ.get("R_HOME"):
+     os.environ['R_HOME'] = R_HOME
+ 
++# path to libraries
++existing = os.environ.get('R_LIBS_SITE')
++if existing is not None:
++    prefix = existing + ':'
++else:
++    prefix = ''
++additional = '@NIX_R_LIBS_SITE@'
++os.environ['R_LIBS_SITE'] = prefix + additional
++
+ if sys.platform == 'win32':
+     _load_r_dll(R_HOME)
+