Merge commit '8e4fe32876ca15e3d5eb3ecd3ca0b224417f5f17'

6 files changed, 44 insertions, 54 deletions

diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/wcslib/default.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/wcslib/default.nix
index b16ba1117f4e..58c2744605a2 100644
--- a/nixpkgs/pkgs/development/libraries/science/astronomy/wcslib/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/astronomy/wcslib/default.nix
@@ -2,22 +2,19 @@
 
 stdenv.mkDerivation rec {
   pname = "wcslib";
-  version = "7.5";
+  version = "7.6";
 
   src = fetchurl {
     url = "ftp://ftp.atnf.csiro.au/pub/software/wcslib/${pname}-${version}.tar.bz2";
-    sha256 = "1536gmcpm6pckn9xrb6j8s4pm1vryjhzvhfaj9wx3jwxcpbdy0dw";
+    sha256 = "sha256-VLuMkhZ6fxP4qnP8S4oJeFJW0smCE0Z968eigqQxMYs=";
   };
 
-  buildInputs = [ flex ];
-
-  prePatch = ''
-    substituteInPlace GNUmakefile --replace 2775 0775
-    substituteInPlace C/GNUmakefile --replace 2775 0775
-  '';
+  nativeBuildInputs = [ flex ];
 
   enableParallelBuilding = true;
 
+  outputs = [ "out" "man" ];
+
   meta = with lib; {
     homepage = "https://www.atnf.csiro.au/people/mcalabre/WCS/";
     description = "World Coordinate System library for astronomy";
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix
index 0bdcbf5a828a..5cf63e342242 100644
--- a/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix
@@ -2,16 +2,14 @@
 
 stdenv.mkDerivation rec {
   pname = "bicpl";
-  version = "unstable-2017-09-10";
-
-  owner = "BIC-MNI";
+  version = "unstable-2020-10-15";
 
   # current master is significantly ahead of most recent release, so use Git version:
   src = fetchFromGitHub {
-    inherit owner;
+    owner  = "BIC-MNI";
     repo   = pname;
-    rev    = "612a63e740fadb162fcf27ee00da6a18dec4d5a9";
-    sha256 = "1vv9gi184bkvp3f99v9xmmw1ly63ip5b09y7zdjn39g7kmwzrga7";
+    rev    = "a58af912a71a4c62014975b89ef37a8e72de3c9d";
+    sha256 = "0iw0pmr8xrifbx5l8a0xidfqbm1v8hwzqrw0lcmimxlzdihyri0g";
   };
 
   nativeBuildInputs = [ cmake ];
@@ -23,7 +21,7 @@ stdenv.mkDerivation rec {
   # internal_volume_io.h: No such file or directory
 
   meta = with lib; {
-    homepage = "https://github.com/${owner}/${pname}";
+    homepage = "https://github.com/BIC-MNI/bicpl";
     description = "Brain Imaging Centre programming library";
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix
index 626e6475ba18..7f1112311d6b 100644
--- a/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix
@@ -1,28 +1,36 @@
-{ lib, stdenv, fetchFromGitHub, cmake, libminc, bicpl, arguments, pcre-cpp }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, libminc
+, bicpl
+, arguments
+, pcre-cpp }:
 
 stdenv.mkDerivation rec {
   pname = "oobicpl";
-  version = "unstable-2016-03-02";
-
-  owner = "BIC-MNI";
+  version = "unstable-2020-08-12";
 
   src = fetchFromGitHub {
-    inherit owner;
+    owner  = "BIC-MNI";
     repo   = pname;
-    rev    = "bc062a65dead2e58461f5afb37abedfa6173f10c";
-    sha256 = "05l4ml9djw17bgdnrldhcxydrzkr2f2scqlyak52ph5azj5n4zsx";
+    rev    = "a9409da8a5bb4925438f32aff577b6333faec28b";
+    sha256 = "0b4chjhr32wbb1sash8cq1jfnr7rzdq84hif8anlrjqd3l0gw357";
   };
 
   nativeBuildInputs = [ cmake ];
+
   buildInputs = [ libminc bicpl arguments pcre-cpp ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake"
-                 "-DBICPL_DIR=${bicpl}/lib"
-                 "-DARGUMENTS_DIR=${arguments}/lib"
-                 "-DOOBICPL_BUILD_SHARED_LIBS=TRUE" ];
+  cmakeFlags = [
+    "-DLIBMINC_DIR=${libminc}/lib/cmake"
+    "-DBICPL_DIR=${bicpl}/lib"
+    "-DARGUMENTS_DIR=${arguments}/lib"
+    "-DOOBICPL_BUILD_SHARED_LIBS=TRUE"
+  ];
 
   meta = with lib; {
-    homepage = "https://github.com/${owner}/${pname}";
+    homepage = "https://github.com/BIC-MNI/oobicpl";
     description = "Brain Imaging Centre object-oriented programming library (and tools)";
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;
diff --git a/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix b/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix
index eb91e0a3d222..26659ffc1661 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix
@@ -17,13 +17,13 @@ let
   blasIntSize = if blas64 then "64" else "32";
 in stdenv.mkDerivation rec {
   pname = "blis";
-  version = "0.8.0";
+  version = "0.8.1";
 
   src = fetchFromGitHub {
     owner = "flame";
     repo = "blis";
     rev = version;
-    sha256 = "0fp0nskydan3i7sj7qkabwc9sjh7mw73pjpgzh50qchkkcv0s3n1";
+    sha256 = "sha256-D5T/itq9zyD5TkeJ4Ae1vS4yEWU51omyJoIkKQ2NLhY=";
   };
 
   inherit blas64;
diff --git a/nixpkgs/pkgs/development/libraries/science/math/cudnn/default.nix b/nixpkgs/pkgs/development/libraries/science/math/cudnn/default.nix
index b8aac46d9194..d4c7fcac9785 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/cudnn/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/cudnn/default.nix
@@ -1,4 +1,4 @@
-{ callPackage, cudatoolkit_9_0, cudatoolkit_9_1, cudatoolkit_9_2, cudatoolkit_10_0, cudatoolkit_10_1, cudatoolkit_10_2, cudatoolkit_11_0, cudatoolkit_11_1, cudatoolkit_11_2 }:
+{ callPackage, cudatoolkit_10_0, cudatoolkit_10_1, cudatoolkit_10_2, cudatoolkit_11_0, cudatoolkit_11_1, cudatoolkit_11_2 }:
 
 let
   generic = args: callPackage (import ./generic.nix (removeAttrs args ["cudatoolkit"])) {
@@ -6,29 +6,6 @@ let
   };
 
 in rec {
-  cudnn_cudatoolkit_9_0 = generic rec {
-    version = "7.3.0";
-    cudatoolkit = cudatoolkit_9_0;
-    srcName = "cudnn-${cudatoolkit.majorVersion}-linux-x64-v7.3.0.29.tgz";
-    sha256 = "16z4vgbcmbayk4hppz0xshgs3g07blkp4j25cxcjqyrczx1r0gs0";
-  };
-
-  cudnn_cudatoolkit_9_1 = generic rec {
-    version = "7.1.3";
-    cudatoolkit = cudatoolkit_9_1;
-    srcName = "cudnn-${cudatoolkit.majorVersion}-linux-x64-v7.1.tgz";
-    sha256 = "0a0237gpr0p63s92njai0xvxmkbailzgfsvh7n9fnz0njhvnsqfx";
-  };
-
-  cudnn_cudatoolkit_9_2 = generic rec {
-    version = "7.2.1";
-    cudatoolkit = cudatoolkit_9_2;
-    srcName = "cudnn-${cudatoolkit.majorVersion}-linux-x64-v7.2.1.38.tgz";
-    sha256 = "1sf215wm6zgr17gs6sxfhw61b7a0qmcxiwhgy1b4nqdyxpqgay1y";
-  };
-
-  cudnn_cudatoolkit_9 = cudnn_cudatoolkit_9_2;
-
   cudnn_cudatoolkit_10_0 = generic rec {
     version = "7.4.2";
     cudatoolkit = cudatoolkit_10_0;
diff --git a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
index 23a82f483dc6..c66e4ba44ef9 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, perl, which
+{ lib, stdenv, fetchFromGitHub, fetchpatch, perl, which
 # Most packages depending on openblas expect integer width to match
 # pointer width, but some expect to use 32-bit integers always
 # (for compatibility with reference BLAS).
@@ -124,6 +124,16 @@ stdenv.mkDerivation rec {
     sha256 = "14jxh0v3jfbw4mfjx4mcz4dd51lyq7pqvh9k8dg94539ypzjr2lj";
   };
 
+  # apply https://github.com/xianyi/OpenBLAS/pull/3060 to fix a crash on arm
+  # remove this when updating to 0.3.14 or newer
+  patches = [
+    (fetchpatch {
+      name = "label-get_cpu_ftr-as-volatile.patch";
+      url = "https://github.com/xianyi/OpenBLAS/commit/6fe0f1fab9d6a7f46d71d37ebb210fbf56924fbc.diff";
+      sha256 = "06gwh73k4sas1ap2fi3jvpifbjkys2vhmnbj4mzrsvj279ljsfdk";
+    })
+  ];
+
   inherit blas64;
 
   # Some hardening features are disabled due to sporadic failures in