Merge branch 'master' into package-petsc-p4est

3 files changed, 37 insertions, 8 deletions

diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix
index 92606f3f909ce..5d2158843ede8 100644
--- a/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/pkgs/applications/science/chemistry/jmol/default.nix
@@ -17,14 +17,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "14.31.42";
+  version = "14.31.44";
   pname = "jmol";
 
   src = let
     baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
   in fetchurl {
     url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
-    sha256 = "sha256-q81dUSxrKT3nzX0bFclolsyguQxXKlsiX9GCwEvOpAw=";
+    sha256 = "sha256-MHfqoQzUEL7nje7Y/hbaA8iktxfN7464TJXum5B6OCc=";
   };
 
   patchPhase = ''
diff --git a/pkgs/applications/science/math/glsurf/default.nix b/pkgs/applications/science/math/glsurf/default.nix
index 208bb95f930e5..58b2a617bd63f 100644
--- a/pkgs/applications/science/math/glsurf/default.nix
+++ b/pkgs/applications/science/math/glsurf/default.nix
@@ -1,7 +1,12 @@
-{ lib, stdenv, fetchurl, ocamlPackages, libGLU, libGL, freeglut, giflib
-, libmysqlclient, mpfr, gmp, libtiff, libjpeg, libpng
+{ lib, stdenv, fetchurl, ocamlPackages, makeWrapper
+, libGLU, libGL, freeglut, mpfr, gmp
+, pkgsHostTarget
 }:
 
+let
+  inherit (pkgsHostTarget.targetPackages.stdenv) cc;
+in
+
 stdenv.mkDerivation {
   name = "glsurf-3.3.1";
 
@@ -10,17 +15,32 @@ stdenv.mkDerivation {
     sha256 = "0w8xxfnw2snflz8wdr2ca9f5g91w5vbyp1hwlx1v7vg83d4bwqs7";
   };
 
-  buildInputs = [ freeglut libGLU libGL libmysqlclient mpfr giflib gmp
-    libtiff libjpeg libpng ]
-  ++ (with ocamlPackages; [
-    ocaml findlib ocaml_mysql lablgl camlimages_4_1_2 mlgmpidl
+  nativeBuildInputs = [
+    makeWrapper
+  ] ++ (with ocamlPackages; [
+    ocaml findlib
+  ]);
+
+  buildInputs = [
+    freeglut libGL libGLU mpfr gmp
+  ] ++ (with ocamlPackages; [
+    camlp4 lablgl camlimages_4_2_4
   ]);
 
+  postPatch = ''
+    for f in callbacks*/Makefile src/Makefile; do
+      substituteInPlace "$f" --replace "+camlp4" \
+        "${ocamlPackages.camlp4}/lib/ocaml/${ocamlPackages.ocaml.version}/site-lib/camlp4"
+    done
+  '';
+
   installPhase = ''
     mkdir -p $out/bin $out/share/doc/glsurf
     cp ./src/glsurf.opt $out/bin/glsurf
     cp ./doc/doc.pdf $out/share/doc/glsurf
     cp -r ./examples $out/share/doc/glsurf
+
+    wrapProgram "$out/bin/glsurf" --set CC "${cc}/bin/${cc.targetPrefix}cc"
   '';
 
   meta = {
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index 1ed174ebd4607..218ab920a8724 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -126,6 +126,15 @@ stdenv.mkDerivation rec {
       rev = "bc84af8c795b7da433d2000afc3626ee65ba28b8";
       sha256 = "sha256-5Kvs9jarC8xRIU1rdmvIWxQLC25ehiTLJpg5skh8WNM=";
     })
+
+    # eclib 20210625 update
+    # https://trac.sagemath.org/ticket/31443
+    (fetchSageDiff {
+      base = "9.4.beta3";
+      name = "eclib-20210625.patch";
+      rev = "789550ca04c94acfb1e803251538996a34962038";
+      sha256 = "sha256-VlyEn5hg3joG8t/GwiRfq9TzJ54AoHxLolsNQ3shc2c=";
+    })
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;