Unverified Commit b6beee67 authored by Ryan Lahfa's avatar Ryan Lahfa Committed by GitHub
Browse files

Merge pull request #233336 from smancill/shogun-fix-build 

shogun: fix build
parents 101fe71a 70b3662a

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

+31 −14
Original line number Diff line number Diff line
@@ -50,21 +50,21 @@ let 


  srcs = {

    toolbox = fetchFromGitHub {

      owner = pname + "-toolbox";

      repo = pname;

      rev = pname + "_" + version;

      sha256 = "05s9dclmk7x5d7wnnj4qr6r6c827m72a44gizcv09lxr28pr9inz";

      owner = "shogun-toolbox";

      repo = "shogun";

      rev =  "shogun_${version}";

      sha256 = "sha256-38aULxK50wQ2+/ERosSpRyBmssmYSGv5aaWfWSlrSRc=";

      fetchSubmodules = true;

    };



    # The CMake external projects expect the packed archives

    rxcpp = fetchurl {

      url = "https://github.com/Reactive-Extensions/RxCpp/archive/v${rxcppVersion}.tar.gz";

      sha256 = "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh";

      sha256 = "sha256-UOc5WrG8KgAA3xJsaSCjbdPE7gSnFJay9MEK31DWUXg=";

    };

    gtest = fetchurl {

      url = "https://github.com/google/googletest/archive/release-${gtestVersion}.tar.gz";

      sha256 = "1n5p1m2m3fjrjdj752lf92f9wq3pl5cbsfrb49jqbg52ghkz99jq";

      sha256 = "sha256-WKb0J3yivIVlIis7vVihd2CenEiOinJkk1m6UUUNt9g=";

    };

  };

in
@@ -77,13 +77,6 @@ stdenv.mkDerivation rec { 
  src = srcs.toolbox;



  patches = [

    # Fix compile errors with json-c

    # https://github.com/shogun-toolbox/shogun/pull/4104

    (fetchpatch {

      url = "https://github.com/shogun-toolbox/shogun/commit/365ce4c4c700736d2eec8ba6c975327a5ac2cd9b.patch";

      sha256 = "158hqv4xzw648pmjbwrhxjp7qcppqa7kvriif87gn3zdn711c49s";

    })



    # Fix compile errors with GCC 9+

    # https://github.com/shogun-toolbox/shogun/pull/4811

    (fetchpatch {
@@ -95,6 +88,20 @@ stdenv.mkDerivation rec { 
      sha256 = "sha256-AgJJKQA8vc5oKaTQDqMdwBR4hT4sn9+uW0jLe7GteJw=";

    })



    # Fix virtual destruction

    (fetchpatch {

      url = "https://github.com/shogun-toolbox/shogun/commit/ef0e4dc1cc4a33c9e6b17a108fa38a436de2d7ee.patch";

      sha256 = "sha256-a9Rm0ytqkSAgC3dguv8m3SwOSipb+VByBHHdmV0d63w=";

    })

    ./fix-virtual-destruction.patch



    # Fix compile errors with json-c

    # https://github.com/shogun-toolbox/shogun/pull/4104

    (fetchpatch {

      url = "https://github.com/shogun-toolbox/shogun/commit/365ce4c4c700736d2eec8ba6c975327a5ac2cd9b.patch";

      sha256 = "sha256-OhEWwrHtD/sOcjHmPY/C9zJ8ruww8yXrRcTw38nGEJU=";

    })



    # Fix compile errors with Eigen 3.4

    ./eigen-3.4.patch
@@ -126,6 +133,16 @@ stdenv.mkDerivation rec { 


  cmakeFlags = let

    enableIf = cond: if cond then "ON" else "OFF";

    excludeTestsRegex = lib.concatStringsSep "|" [

      # sporadic segfault

      "TrainedModelSerialization"

      # broken by openblas 0.3.21

      "mathematics_lapack"

      # these take too long on CI

      "evaluation_cross_validation"

      "modelselection_combined_kernel"

      "modelselection_grid_search"

    ];

  in [

    "-DBUILD_META_EXAMPLES=ON"

    "-DCMAKE_DISABLE_FIND_PACKAGE_ARPACK=ON"
@@ -134,7 +151,7 @@ stdenv.mkDerivation rec { 
    "-DCMAKE_DISABLE_FIND_PACKAGE_Mosek=ON"

    "-DCMAKE_DISABLE_FIND_PACKAGE_TFLogger=ON"

    "-DCMAKE_DISABLE_FIND_PACKAGE_ViennaCL=ON"

    "-DCMAKE_CTEST_ARGUMENTS='--exclude-regex;TrainedModelSerialization'"  # Sporadic segfault

    "-DCMAKE_CTEST_ARGUMENTS=--exclude-regex;'${excludeTestsRegex}'"

    "-DENABLE_TESTING=${enableIf doCheck}"

    "-DDISABLE_META_INTEGRATION_TESTS=ON"

    "-DTRAVIS_DISABLE_META_CPP=ON"

pkgs/applications/science/machine-learning/shogun/fix-virtual-destruction.patch

0 → 100644
+20 −0
Original line number Diff line number Diff line 
From: Sebastián Mancilla <smancill@smancill.dev>

Subject: Fix virtual destruction



---

 src/shogun/solver/LDASolver.h | 2 +-

 1 file changed, 1 insertion(+), 1 deletion(-)



diff --git a/src/shogun/solver/LDASolver.h b/src/shogun/solver/LDASolver.h

index 9300a85c5..d500eca5d 100644

--- a/src/shogun/solver/LDASolver.h

+++ b/src/shogun/solver/LDASolver.h

@@ -87,7 +87,7 @@ namespace shogun

 			compute_within_cov();

 		}

 

-		~LDASolver()

+		virtual ~LDASolver()

 		{

 			SG_UNREF(m_features)

 			SG_UNREF(m_labels)