Merge branch 'master' into closure-size

6 files changed, 28 insertions, 40 deletions

diff --git a/pkgs/applications/science/electronics/eagle/default.nix b/pkgs/applications/science/electronics/eagle/default.nix
index da4894c11a85..71bc58af7c03 100644
--- a/pkgs/applications/science/electronics/eagle/default.nix
+++ b/pkgs/applications/science/electronics/eagle/default.nix
@@ -1,24 +1,34 @@
 { stdenv, fetchurl, makeDesktopItem, patchelf, zlib, freetype, fontconfig
 , openssl, libXrender, libXrandr, libXcursor, libX11, libXext, libXi
+, libxcb, cups, xkeyboardconfig
 }:
 
 let
 
   libPath = stdenv.lib.makeLibraryPath
     [ zlib freetype fontconfig openssl libXrender libXrandr libXcursor libX11
-      libXext libXi
+      libXext libXi libxcb cups
     ];
 
 in
 
 stdenv.mkDerivation rec {
   name = "eagle-${version}";
-  version = "6.6.0";
+  version = "7.5.0";
 
-  src = fetchurl {
-    url = "ftp://ftp.cadsoft.de/eagle/program/6.6/eagle-lin-${version}.run";
-    sha256 = "0m5289daah85b2rwpivnh2z1573v6j4alzjy9hg78fkb9jdgbn0x";
-  };
+  src =
+    if stdenv.system == "i686-linux" then
+      fetchurl {
+        url = "ftp://ftp.cadsoft.de/eagle/program/7.5/eagle-lin32-${version}.run";
+        sha256 = "1yfpfv2bqppc95964dhn38g0hq198wnz88lq2dmh517z7jlq9j5g";
+      }
+    else if stdenv.system == "x86_64-linux" then
+      fetchurl {
+        url = "ftp://ftp.cadsoft.de/eagle/program/7.5/eagle-lin64-${version}.run";
+        sha256 = "0msd0sn8yfln96mf7j5rc3b8amprxn87vmpq4wsz2cnmgd8xq0s9";
+      }
+    else
+      throw "Unsupported system: ${stdenv.system}";
 
   desktopItem = makeDesktopItem {
     name = "eagle";
@@ -65,6 +75,7 @@ stdenv.mkDerivation rec {
     #!${stdenv.shell}
     export LD_LIBRARY_PATH="${stdenv.cc.cc}/lib:${libPath}"
     export LD_PRELOAD="$out/lib/eagle_fixer.so"
+    export QT_XKB_CONFIG_ROOT="${xkeyboardconfig}/share/X11/xkb"
     exec "$dynlinker" "$out/eagle-${version}/bin/eagle" "\$@"
     EOF
     chmod a+x "$out"/bin/eagle
diff --git a/pkgs/applications/science/logic/why3/default.nix b/pkgs/applications/science/logic/why3/default.nix
index d1fb853ee9e1..0313467ed789 100644
--- a/pkgs/applications/science/logic/why3/default.nix
+++ b/pkgs/applications/science/logic/why3/default.nix
@@ -1,12 +1,12 @@
-{ fetchurl, stdenv, ocaml, ocamlPackages, coq }:
+{ fetchurl, stdenv, ocamlPackages, coq }:
 
 stdenv.mkDerivation rec {
   name    = "why3-${version}";
-  version = "0.86.1";
+  version = "0.86.2";
 
   src = fetchurl {
-    url    = https://gforge.inria.fr/frs/download.php/file/34797/why3-0.86.1.tar.gz;
-    sha256 = "129kzq79n8h480zrlphgh1ixvwp3wm18nbcky9bp4wdnr6zaibd7";
+    url    = https://gforge.inria.fr/frs/download.php/file/35214/why3-0.86.2.tar.gz;
+    sha256 = "08sa7dmp6yp29xn0m6h98nic4q47vb4ahvaid5drwh522pvwvg10";
   };
 
   buildInputs = with ocamlPackages;
diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix
index 7c8e76d676b7..183a1f503753 100644
--- a/pkgs/applications/science/math/R/default.nix
+++ b/pkgs/applications/science/math/R/default.nix
@@ -6,11 +6,11 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "R-3.2.2";
+  name = "R-3.2.3";
 
   src = fetchurl {
     url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
-    sha256 = "07a6s865bjnh7w0fqsrkv1pva76w99v86w0w787qpdil87km54cw";
+    sha256 = "b93b7d878138279234160f007cb9b7f81b8a72c012a15566e9ec5395cfd9b6c1";
   };
 
   buildInputs = [ bzip2 gfortran libX11 libXmu libXt
@@ -19,8 +19,7 @@ stdenv.mkDerivation rec {
     which jdk openblas curl
   ];
 
-  patches = [ ./no-usr-local-search-paths.patch
-              ./fix-tests-without-recommended-packages.patch ];
+  patches = [ ./no-usr-local-search-paths.patch ];
 
   preConfigure = ''
     configureFlagsArray=(
diff --git a/pkgs/applications/science/math/R/fix-tests-without-recommended-packages.patch b/pkgs/applications/science/math/R/fix-tests-without-recommended-packages.patch
deleted file mode 100644
index c736c7098a30..000000000000
--- a/pkgs/applications/science/math/R/fix-tests-without-recommended-packages.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff -Naur R-3.2.2-upstream/tests/reg-packages.R R-3.2.2/tests/reg-packages.R
---- R-3.2.2-upstream/tests/reg-packages.R	2015-08-05 17:45:05.000000000 -0430
-+++ R-3.2.2/tests/reg-packages.R	2015-10-01 02:11:05.484992903 -0430
-@@ -82,7 +82,8 @@
- ## pkgB tests an empty R directory
- dir.create(file.path(pkgPath, "pkgB", "R"), recursive = TRUE,
- 	   showWarnings = FALSE)
--p.lis <- if("Matrix" %in% row.names(installed.packages(.Library)))
-+matrixIsInstalled <- "Matrix" %in% row.names(installed.packages(.Library))
-+p.lis <- if(matrixIsInstalled)
- 	     c("pkgA", "pkgB", "exNSS4") else "exNSS4"
- for(p. in p.lis) {
-     cat("building package", p., "...\n")
-@@ -111,8 +112,8 @@
-   tools::assertError(is.null(pkgA:::nilData))
- }
- 
--if(dir.exists(file.path("myLib", "exNSS4"))) {
--    for(ns in c("pkgB", "pkgA", "Matrix", "exNSS4")) unloadNamespace(ns)
-+if(matrixIsInstalled && dir.exists(file.path("myLib", "exNSS4"))) {
-+    for(ns in c(rev(p.lis), "Matrix")) unloadNamespace(ns)
-     ## Both exNSS4 and Matrix define "atomicVector" *the same*,
-     ## but  'exNSS4'  has it extended - and hence *both* are registered in cache -> "conflicts"
-     requireNamespace("exNSS4", lib= "myLib")
diff --git a/pkgs/applications/science/math/mathematica/default.nix b/pkgs/applications/science/math/mathematica/default.nix
index 233323fceef9..05c6f2622934 100644
--- a/pkgs/applications/science/math/mathematica/default.nix
+++ b/pkgs/applications/science/math/mathematica/default.nix
@@ -96,6 +96,8 @@ stdenv.mkDerivation rec {
 
   preFixup = ''
     echo "=== PatchElfing away ==="
+    # This code should be a bit forgiving of errors, unfortunately
+    set +e
     find $out/libexec/Mathematica/SystemFiles -type f -perm -0100 | while read f; do
       type=$(readelf -h "$f" 2>/dev/null | grep 'Type:' | sed -e 's/ *Type: *\([A-Z]*\) (.*/\1/')
       if [ -z "$type" ]; then
diff --git a/pkgs/applications/science/spyder/default.nix b/pkgs/applications/science/spyder/default.nix
index 4bc160a2c284..9e74a2332365 100644
--- a/pkgs/applications/science/spyder/default.nix
+++ b/pkgs/applications/science/spyder/default.nix
@@ -9,12 +9,12 @@
 
 buildPythonPackage rec {
   name = "spyder-${version}";
-  version = "2.3.7";
+  version = "2.3.8";
   namePrefix = "";
 
   src = fetchurl {
     url = "https://pypi.python.org/packages/source/s/spyder/${name}.zip";
-    sha256 = "0ywgvgcp9s64ys25nfscd2648f7di8544a21b5lb59d4f48z028h";
+    sha256 = "99fdae2cea325c0f2842c77bd67dd22db19fef3d9c0dde1545b1a2650eae517e";
   };
 
   # NOTE: sphinx makes the build fail with: ValueError: ZIP does not support timestamps before 1980