Merge commit '467ce5a9f45aaf96110b41eb863a56866e1c2c3c'

4 files changed, 38 insertions, 27 deletions

diff --git a/nixpkgs/pkgs/applications/science/math/clp/default.nix b/nixpkgs/pkgs/applications/science/math/clp/default.nix
index 5e770cec13b3..97ef3dd7543f 100644
--- a/nixpkgs/pkgs/applications/science/math/clp/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/clp/default.nix
@@ -1,11 +1,11 @@
 { stdenv, fetchurl, zlib }:
 
 stdenv.mkDerivation rec {
-  version = "1.17.5";
+  version = "1.17.6";
   pname = "clp";
   src = fetchurl {
     url = "https://www.coin-or.org/download/source/Clp/Clp-${version}.tgz";
-    sha256 = "0y5wg4lfffy5vh8gc20v68pmmv241ndi2jgm9pgvk39b00bzkaa9";
+    sha256 = "0ap1f0lxppa6pnbc4bg7ih7a96avwaki482nig8w5fr3vg9wvkzr";
   };
 
   propagatedBuildInputs = [ zlib ];
diff --git a/nixpkgs/pkgs/applications/science/math/gap/default.nix b/nixpkgs/pkgs/applications/science/math/gap/default.nix
index 87f4fa120387..04a49becc973 100644
--- a/nixpkgs/pkgs/applications/science/math/gap/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/gap/default.nix
@@ -3,7 +3,7 @@
 , fetchurl
 , fetchpatch
 , makeWrapper
-, m4
+, readline
 , gmp
 # one of
 # - "minimal" (~400M):
@@ -64,7 +64,7 @@ stdenv.mkDerivation rec {
   version = "4.10.2";
 
   src = fetchurl {
-    url = "https://www.gap-system.org/pub/gap/gap-${lib.versions.major version}.${lib.versions.minor version}/tar.bz2/gap-${version}.tar.bz2";
+    url = "https://files.gap-system.org/gap-${lib.versions.major version}.${lib.versions.minor version}/tar.bz2/gap-${version}.tar.bz2";
     sha256 = "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94";
   };
 
@@ -73,10 +73,8 @@ stdenv.mkDerivation rec {
     patchShebangs .
   '';
 
-  configureFlags = [ "--with-gmp=system" ];
-
   buildInputs = [
-    m4
+    readline
     gmp
   ];
 
@@ -91,14 +89,31 @@ stdenv.mkDerivation rec {
       url = "https://github.com/gap-system/gap/commit/3361c172e6c5ff3bb3f01ba9d6f1dd4ad42cea80.patch";
       sha256 = "1kwp9qnfvmlbpf1c3rs6j5m2jz22rj7a4hb5x1gj9vkpiyn5pdyj";
     })
+
+    # Fix for locale specific tests causing issues. Already upstream.
+    # Backport of https://github.com/gap-system/gap/pull/4022
+    # WHEN REMOVING: also remove the`rm tst/testinstall/strings.tst` line in
+    # `postPatch` below. That line is necessary since the patch is not intended
+    # for gap 4.10.
+    (fetchpatch {
+      name = "remove-locale-specific-tests.patch";
+      url = "https://github.com/gap-system/gap/commit/c18b0c4215b5212a2cc4f305e2d5b94ba716bee8.patch";
+      excludes = ["tst/testinstall/stringobj.tst"];
+      sha256 = "1mz5b4mbw2jdd1ypp5s0dy6pp0jsvwsxr2dm4kbkls20r1r192sc";
+    })
   ];
 
+  postPatch = ''
+    # File not covered by the remove-locale-specific-tests.patch patch above.
+    rm tst/testinstall/strings.tst
+  '';
+
   # "teststandard" is a superset of testinstall. It takes ~1h instead of ~1min.
   # tests are run twice, once with all packages loaded and once without
   # checkTarget = "teststandard";
 
   doInstallCheck = true;
-  installCheckTarget = "testinstall";
+  installCheckTarget = "check";
 
   preInstallCheck = ''
     # gap tests check that the home directory exists
@@ -119,16 +134,6 @@ stdenv.mkDerivation rec {
     )
   '';
 
-  postCheck = ''
-    # The testsuite doesn't exit with a non-zero exit code on failure.
-    # It leaves its logs in dev/log however.
-
-    # grep for error messages
-    if grep ^##### dev/log/*; then
-        exit 1
-    fi
-  '';
-
   postBuild = ''
     pushd pkg
     bash ../bin/BuildPackages.sh
@@ -170,11 +175,11 @@ stdenv.mkDerivation rec {
     ];
     platforms = platforms.all;
     broken = stdenv.isDarwin;
-    # keeping all packages increases the package size considerably, wchich
-    # is why a local build is preferable in that situation. The timeframe
-    # is reasonable and that way the binary cache doesn't get overloaded.
+    # keeping all packages increases the package size considerably, which is
+    # why a local build is preferable in that situation. The timeframe is
+    # reasonable and that way the binary cache doesn't get overloaded.
     hydraPlatforms = lib.optionals (!keepAllPackages) meta.platforms;
     license = licenses.gpl2;
-    homepage = "http://gap-system.org/";
+    homepage = "https://www.gap-system.org";
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/math/nauty/default.nix b/nixpkgs/pkgs/applications/science/math/nauty/default.nix
index 64cc4a9aa003..c1d408213b98 100644
--- a/nixpkgs/pkgs/applications/science/math/nauty/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/nauty/default.nix
@@ -4,10 +4,10 @@
 }:
 stdenv.mkDerivation rec {
   pname = "nauty";
-  version = "26r12";
+  version = "27r1";
   src = fetchurl {
     url = "http://pallini.di.uniroma1.it/nauty${version}.tar.gz";
-    sha256 = "1p4mxf8q5wm47nxyskxbqwa5p1vvkycv1zgswvnk9nsn6vff0al6";
+    sha256 = "1nym0p2djws8ylkpr0kgpxfa6fxdlh46cmvz0gn5vd02jzgs0aww";
   };
   outputs = [ "out" "dev" ];
   configureFlags = {
@@ -37,6 +37,10 @@ stdenv.mkDerivation rec {
     license = licenses.asl20;
     maintainers = with maintainers; [ raskin timokau ];
     platforms = platforms.unix;
+    # I'm not sure if the filename will remain the same for future changelog or
+    # if it will track changes to minor releases. Lets see. Better than nothing
+    # in any case.
+    changelog = "http://pallini.di.uniroma1.it/changes24-27.txt";
     homepage = "http://pallini.di.uniroma1.it/";
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/math/palp/default.nix b/nixpkgs/pkgs/applications/science/math/palp/default.nix
index 4912b82d158f..c383438002f4 100644
--- a/nixpkgs/pkgs/applications/science/math/palp/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/palp/default.nix
@@ -9,16 +9,15 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "palp";
-  version = "2.1";
+  version = "2.11";
 
   src = fetchurl {
     url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/palp-${version}.tar.gz";
-    sha256 = "1s7s2lc5f0ig1yy7ygsh3sddm3sbq4mxwybqsj8lp9wjdxs7qfrs";
+    sha256 = "00jpm73fw9jjq58z6rysr1mwv489j6rpfqqlhm9ab0dln4kyhh05";
   };
 
   hardeningDisable = [
     "format"
-    "strictoverflow" # causes runtime failure (tested in checkPhase)
   ];
 
   patchPhase = stdenv.lib.optionalString stdenv.isDarwin ''
@@ -78,6 +77,9 @@ stdenv.mkDerivation rec {
       facet enumeration compares well with existing packages.
     '';
     homepage = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html";
+    # Not really a changelog, but a one-line summary of each update that should
+    # be reviewed on update.
+    changelog = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html";
     # Just a link on the website pointing to gpl -- now gplv3. When the last
     # version was released that pointed to gplv2 however, so thats probably
     # the right license.