Merge remote-tracking branch 'upstream/master' into HEAD

4 files changed, 40 insertions, 9 deletions

diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix
index d6e00659c1a9..406f42e9ad7b 100644
--- a/pkgs/applications/science/biology/bedtools/default.nix
+++ b/pkgs/applications/science/biology/bedtools/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "bedtools-${version}";
-  version = "2.26.0";
+  version = "2.27.1";
 
   src = fetchFromGitHub {
     owner = "arq5x";
     repo = "bedtools2";
     rev = "v${version}";
-    sha256 = "1j2ia68rmcw3qksjm5gvv1cb84bh76vmln59mvncr2an23f5a3ss";
+    sha256 = "1pk68y052rm2m24yfmy82ms8p6kd6xcqxxgi7n0a1sbh89wllm6s";
   };
 
   buildInputs = [ zlib python ];
diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix
index bc13032f1aac..d1dbacf053fb 100644
--- a/pkgs/applications/science/biology/bwa/default.nix
+++ b/pkgs/applications/science/biology/bwa/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name    = "bwa-${version}";
-  version = "0.7.16a";
+  version = "0.7.17";
 
   src = fetchurl {
     url = "mirror://sourceforge/bio-bwa/${name}.tar.bz2";
-    sha256 = "0w61zxh6b4isydw5qp6pdb1mc50jg1h8vhahw2xm24w7i1gxpv4g";
+    sha256 = "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy";
   };
 
   buildInputs = [ zlib ];
diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix
index d2188673fb7d..725b3f342c3e 100644
--- a/pkgs/applications/science/math/R/default.nix
+++ b/pkgs/applications/science/math/R/default.nix
@@ -19,10 +19,14 @@ stdenv.mkDerivation rec {
     pango pcre perl readline texLive xz zlib less texinfo graphviz icu
     pkgconfig bison imake which jdk openblas curl
   ] ++ stdenv.lib.optionals (!stdenv.isDarwin) [ tcl tk ]
-    ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa Foundation cf-private libobjc ];
+    ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc ];
 
   patches = [ ./no-usr-local-search-paths.patch ];
 
+  prePatch = stdenv.lib.optionalString stdenv.isDarwin ''
+    substituteInPlace configure --replace "-install_name libR.dylib" "-install_name $out/lib/R/lib/libR.dylib"
+  '';
+
   preConfigure = ''
     configureFlagsArray=(
       --disable-lto
@@ -40,8 +44,8 @@ stdenv.mkDerivation rec {
       --enable-R-shlib
       AR=$(type -p ar)
       AWK=$(type -p gawk)
-      CC=$(type -p gcc)
-      CXX=$(type -p g++)
+      CC=$(type -p cc)
+      CXX=$(type -p c++)
       FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran"
       JAVA_HOME="${jdk}"
       RANLIB=$(type -p ranlib)
@@ -50,8 +54,6 @@ stdenv.mkDerivation rec {
       --without-tcltk
       --without-aqua
       --disable-R-framework
-      CC="clang"
-      CXX="clang++"
       OBJC="clang"
   '' + ''
     )
diff --git a/pkgs/applications/science/math/almonds/default.nix b/pkgs/applications/science/math/almonds/default.nix
new file mode 100644
index 000000000000..fb76699b0c83
--- /dev/null
+++ b/pkgs/applications/science/math/almonds/default.nix
@@ -0,0 +1,29 @@
+{ stdenv, buildPythonApplication, fetchFromGitHub, ncurses, pillow, pytest }:
+
+let
+  version = "1.25b";
+in
+
+buildPythonApplication {
+  name = "almonds-${version}";
+  src = fetchFromGitHub {
+    owner = "Tenchi2xh";
+    repo = "Almonds";
+    rev = version;
+    sha256 = "0j8d8jizivnfx8lpc4w6sbqj5hq35nfz0vdg7ld80sc5cs7jr3ws";
+  };
+
+  nativeBuildInputs = [ pytest ];
+  buildInputs = [ ncurses ];
+  propagatedBuildInputs = [ pillow ];
+
+  checkPhase = "py.test";
+
+  meta = with stdenv.lib; {
+    description = "Terminal Mandelbrot fractal viewer";
+    homepage = https://github.com/Tenchi2xh/Almonds;
+    # No license has been specified
+    license = licenses.unfree;
+    maintainers = with maintainers; [ infinisil ];
+  };
+}