shogun: 6.0.0 -> 6.1.4

Also migrate to opencv3 to address #72739, the PR didn't build for me.
Disable testing and ccache since they were broken.

Co-authored-by: Robert Scott <code@humanleg.org.uk>

pkgs/applications/science/machine-learning/shogun/default.nix

@@ -1,8 +1,8 @@
-{ stdenv, lib, fetchFromGitHub, fetchpatch, ccache, cmake, ctags, swig
+{ stdenv, lib, fetchFromGitHub, fetchpatch, fetchurl, cmake, ctags, swig
 # data, compression
 , bzip2, curl, hdf5, json_c, lzma, lzo, protobuf, snappy
 # maths
-, openblasCompat, eigen, nlopt, lp_solve, colpack
+, openblasCompat, eigen, nlopt, lp_solve, colpack, liblapack, glpk
 # libraries
 , libarchive, libxml2
 # extra support
@@ -13,47 +13,79 @@
 assert pythonSupport -> pythonPackages != null;
 assert opencvSupport -> opencv != null;
 
-stdenv.mkDerivation rec {
+let
   pname = "shogun";
-  version = "6.0.0";
-
-  src = fetchFromGitHub {
-    owner = pname + "-toolbox";
-    repo = pname;
-    rev = pname + "_" + version;
-    sha256 = "0f2zwzvn5apvwypkfkq371xp7c5bdb4g1fwqfh8c2d57ysjxhmgf";
-    fetchSubmodules = true;
+  version = "6.1.4";
+  rxcppVersion = "4.0.0";
+  gtestVersion = "1.8.0";
+  srcs = {
+    toolbox = fetchFromGitHub {
+      owner = pname + "-toolbox";
+      repo = pname;
+      rev = pname + "_" + version;
+      sha256 = "38aULxK50wQ2+/ERosSpRyBmssmYSGv5aaWfWSlrSRc=";
+      fetchSubmodules = true;
+    };
+    # we need the packed archive
+    rxcpp = fetchurl {
+      url = "https://github.com/Reactive-Extensions/RxCpp/archive/v${rxcppVersion}.tar.gz";
+      sha256 = "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh";
+    };
+    gtest = fetchurl {
+      url = "https://github.com/google/googletest/archive/release-${gtestVersion}.tar.gz";
+      sha256 = "1n5p1m2m3fjrjdj752lf92f9wq3pl5cbsfrb49jqbg52ghkz99jq";
+    };
   };
+in
+
+stdenv.mkDerivation rec {
+
+  inherit pname version;
+
+  src = srcs.toolbox;
+
+  postUnpack = ''
+    mkdir -p $sourceRoot/third_party/{rxcpp,gtest}
+    ln -s ${srcs.rxcpp} $sourceRoot/third_party/rxcpp/v${rxcppVersion}.tar.gz
+    ln -s ${srcs.gtest} $sourceRoot/third_party/gtest/release-${gtestVersion}.tar.gz
+  '';
+
+  # broken
+  doCheck = false;
 
   patches = [
-    (fetchpatch {
-      name = "Fix-meta-example-parser-bug-in-parallel-builds.patch";
-      url = "https://github.com/shogun-toolbox/shogun/commit/ecd6a8f11ac52748e89d27c7fab7f43c1de39f05.patch";
-      sha256 = "1hrwwrj78sxhwcvgaz7n4kvh5y9snfcc4jf5xpgji5hjymnl311n";
-    })
     (fetchpatch {
       url = "https://github.com/awild82/shogun/commit/365ce4c4c700736d2eec8ba6c975327a5ac2cd9b.patch";
       sha256 = "158hqv4xzw648pmjbwrhxjp7qcppqa7kvriif87gn3zdn711c49s";
     })
   ];
 
+  CCACHE_DISABLE="1";
   CCACHE_DIR=".ccache";
 
   buildInputs = with lib; [
-      openblasCompat bzip2 ccache cmake colpack curl ctags eigen hdf5 json_c lp_solve lzma lzo
-      protobuf nlopt snappy swig (libarchive.dev) libxml2
+      openblasCompat bzip2 cmake colpack curl ctags eigen hdf5 json_c lp_solve lzma lzo
+      protobuf nlopt snappy swig (libarchive.dev) libxml2 liblapack glpk
     ]
     ++ optionals (pythonSupport) (with pythonPackages; [ python ply numpy ])
     ++ optional  (opencvSupport) opencv;
 
-  cmakeFlags = with lib; []
-    ++ (optional (pythonSupport) "-DPythonModular=ON")
-    ++ (optional (opencvSupport) "-DOpenCV=ON")
-    ;
+  NIX_CFLAGS_COMPILE="-faligned-new";
 
-  # Previous attempts to fix parallel builds (see patch above) were not entirely successful.
-  # Sporadic build failures still exist. Dislable parallel builds for now.
-  enableParallelBuilding = false;
+  cmakeFlags =
+  let
+      onOff = b: if b then "ON" else "OFF";
+      flag = n: b: "-D"+n+"="+onOff b;
+  in
+  with lib; [
+    (flag "ENABLE_TESTING" doCheck)
+    (flag "BUILD_META_EXAMPLES" doCheck)
+    (flag "CMAKE_VERBOSE_MAKEFILE:BOOL" doCheck)
+    (flag "PythonModular" pythonSupport)
+    (flag "OpenCV" opencvSupport)
+  ];
+
+  enableParallelBuilding = true;
 
   meta = with stdenv.lib; {
     description = "A toolbox which offers a wide range of efficient and unified machine learning methods";

pkgs/top-level/all-packages.nix

@@ -20608,6 +20608,15 @@ in
 
   shogun = callPackage ../applications/science/machine-learning/shogun {
     stdenv = gcc8Stdenv;
+
+    # Workaround for the glibc abi version mismatch.
+    # Please note that opencv builds are by default disabled.
+    opencv = opencv3.override {
+      stdenv = gcc8Stdenv;
+      openexr = openexr.override {
+        stdenv = gcc8Stdenv;
+      };
+    };
   };
 
   sky = callPackage ../applications/networking/instant-messengers/sky {};