uboot: (firmwareOdroidC2/C4) don't invoke patch tool, use patches = [] instead
https://github.com/NixOS/nixpkgs/blob/master/pkgs/stdenv/generic/setup.sh#L948 this can do it nicely. Signed-off-by: Anton Arapov <anton@deadbeef.mx>
This commit is contained in:
Anton Arapov
Alan Daniels
commit
56de2bcd43
30691 changed files with 3076956 additions and 0 deletions
192
pkgs/applications/science/machine-learning/shogun/default.nix
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192
pkgs/applications/science/machine-learning/shogun/default.nix
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@ -0,0 +1,192 @@
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{ lib
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, stdenv
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, fetchFromGitHub
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, fetchpatch
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, fetchurl
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# build
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, cmake
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, ctags
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, python3Packages
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, swig
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# math
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, eigen
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, blas
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, lapack
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, glpk
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# data
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, protobuf
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, json_c
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, libxml2
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, hdf5
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, curl
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# compression
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, libarchive
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, bzip2
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, xz
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, snappy
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, lzo
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# more math
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, nlopt
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, lp_solve
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, colpack
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# extra support
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, pythonSupport ? false
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, opencvSupport ? false
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, opencv ? null
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, withSvmLight ? false
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}:
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assert pythonSupport -> python3Packages != null;
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assert opencvSupport -> opencv != null;
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assert (!blas.isILP64) && (!lapack.isILP64);
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let
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pname = "shogun";
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version = "6.1.4";
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rxcppVersion = "4.0.0";
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gtestVersion = "1.8.0";
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srcs = {
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toolbox = fetchFromGitHub {
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owner = pname + "-toolbox";
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repo = pname;
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rev = pname + "_" + version;
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sha256 = "05s9dclmk7x5d7wnnj4qr6r6c827m72a44gizcv09lxr28pr9inz";
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fetchSubmodules = true;
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};
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# The CMake external projects expect the packed archives
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rxcpp = fetchurl {
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url = "https://github.com/Reactive-Extensions/RxCpp/archive/v${rxcppVersion}.tar.gz";
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sha256 = "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh";
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};
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gtest = fetchurl {
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url = "https://github.com/google/googletest/archive/release-${gtestVersion}.tar.gz";
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sha256 = "1n5p1m2m3fjrjdj752lf92f9wq3pl5cbsfrb49jqbg52ghkz99jq";
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};
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};
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in
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stdenv.mkDerivation rec {
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inherit pname version;
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outputs = [ "out" "dev" "doc" ];
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src = srcs.toolbox;
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patches = [
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# Fix compile errors with json-c
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# https://github.com/shogun-toolbox/shogun/pull/4104
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(fetchpatch {
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url = "https://github.com/shogun-toolbox/shogun/commit/365ce4c4c700736d2eec8ba6c975327a5ac2cd9b.patch";
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sha256 = "158hqv4xzw648pmjbwrhxjp7qcppqa7kvriif87gn3zdn711c49s";
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})
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# Fix compile errors with GCC 9+
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# https://github.com/shogun-toolbox/shogun/pull/4811
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(fetchpatch {
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url = "https://github.com/shogun-toolbox/shogun/commit/c8b670be4790e0f06804b048a6f3d77c17c3ee95.patch";
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sha256 = "sha256-MxsR3Y2noFQevfqWK3nmX5iK4OVWeKBl5tfeDNgjcXk=";
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})
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(fetchpatch {
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url = "https://github.com/shogun-toolbox/shogun/commit/5aceefd9fb0e2132c354b9a0c0ceb9160cc9b2f7.patch";
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sha256 = "sha256-AgJJKQA8vc5oKaTQDqMdwBR4hT4sn9+uW0jLe7GteJw=";
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})
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# Fix compile errors with Eigen 3.4
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./eigen-3.4.patch
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] ++ lib.optional (!withSvmLight) ./svmlight-scrubber.patch;
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nativeBuildInputs = [ cmake swig ctags ]
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++ (with python3Packages; [ python jinja2 ply ]);
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buildInputs = [
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eigen
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blas
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lapack
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glpk
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protobuf
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json_c
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libxml2
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hdf5
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curl
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libarchive
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bzip2
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xz
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snappy
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lzo
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nlopt
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lp_solve
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colpack
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] ++ lib.optionals pythonSupport (with python3Packages; [ python numpy ])
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++ lib.optional opencvSupport opencv;
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cmakeFlags = let
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enableIf = cond: if cond then "ON" else "OFF";
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in [
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"-DBUILD_META_EXAMPLES=ON"
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"-DCMAKE_DISABLE_FIND_PACKAGE_ARPACK=ON"
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"-DCMAKE_DISABLE_FIND_PACKAGE_ARPREC=ON"
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"-DCMAKE_DISABLE_FIND_PACKAGE_CPLEX=ON"
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"-DCMAKE_DISABLE_FIND_PACKAGE_Mosek=ON"
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"-DCMAKE_DISABLE_FIND_PACKAGE_TFLogger=ON"
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"-DCMAKE_DISABLE_FIND_PACKAGE_ViennaCL=ON"
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"-DCMAKE_SKIP_BUILD_RPATH=OFF"
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"-DCMAKE_CTEST_ARGUMENTS='--exclude-regex;TrainedModelSerialization'" # Sporadic segfault
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"-DENABLE_TESTING=${enableIf doCheck}"
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"-DDISABLE_META_INTEGRATION_TESTS=ON"
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"-DTRAVIS_DISABLE_META_CPP=ON"
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"-DINTERFACE_PYTHON=${enableIf pythonSupport}"
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"-DOpenCV=${enableIf opencvSupport}"
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"-DUSE_SVMLIGHT=${enableIf withSvmLight}"
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];
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CXXFLAGS = "-faligned-new";
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doCheck = true;
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postUnpack = ''
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mkdir -p $sourceRoot/third_party/{rxcpp,GoogleMock}
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ln -s ${srcs.rxcpp} $sourceRoot/third_party/rxcpp/v${rxcppVersion}.tar.gz
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ln -s ${srcs.gtest} $sourceRoot/third_party/GoogleMock/release-${gtestVersion}.tar.gz
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'';
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postPatch = ''
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# Fix preprocessing SVMlight code
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sed -i \
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-e 's@#ifdef SVMLIGHT@#ifdef USE_SVMLIGHT@' \
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-e '/^#ifdef USE_SVMLIGHT/,/^#endif/ s@#endif@#endif //USE_SVMLIGHT@' \
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src/shogun/kernel/string/CommUlongStringKernel.cpp
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sed -i -e 's/#if USE_SVMLIGHT/#ifdef USE_SVMLIGHT/' src/interfaces/swig/Machine.i
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sed -i -e 's@// USE_SVMLIGHT@//USE_SVMLIGHT@' src/interfaces/swig/Transfer.i
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sed -i -e 's@/\* USE_SVMLIGHT \*/@//USE_SVMLIGHT@' src/interfaces/swig/Transfer_includes.i
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'' + lib.optionalString (!withSvmLight) ''
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# Run SVMlight scrubber
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patchShebangs scripts/light-scrubber.sh
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echo "removing SVMlight code"
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./scripts/light-scrubber.sh
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'';
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postInstall = ''
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mkdir -p $doc/share/doc/shogun/examples
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mv $out/share/shogun/examples/cpp $doc/share/doc/shogun/examples
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cp ../examples/undocumented/libshogun/*.cpp $doc/share/doc/shogun/examples/cpp
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rm -r $out/share
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'';
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postFixup = ''
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# CMake incorrectly calculates library path from dev prefix
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substituteInPlace $dev/lib/cmake/shogun/ShogunTargets-release.cmake \
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--replace "\''${_IMPORT_PREFIX}/lib/" "$out/lib/"
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'';
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meta = with lib; {
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description = "A toolbox which offers a wide range of efficient and unified machine learning methods";
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homepage = "http://shogun-toolbox.org/";
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license = if withSvmLight then licenses.unfree else licenses.gpl3Plus;
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maintainers = with maintainers; [ edwtjo smancill ];
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};
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}
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@ -0,0 +1,74 @@
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From: Sebastián Mancilla <smancill@smancill.dev>
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Subject: [PATCH] Fix compile errors when using Eigen 3.4
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---
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.../machine/gp/MultiLaplaceInferenceMethod.cpp | 18 +++++++++---------
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1 file changed, 9 insertions(+), 9 deletions(-)
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diff --git a/src/shogun/machine/gp/MultiLaplaceInferenceMethod.cpp b/src/shogun/machine/gp/MultiLaplaceInferenceMethod.cpp
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index 2e27678d2..60050afea 100644
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--- a/src/shogun/machine/gp/MultiLaplaceInferenceMethod.cpp
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+++ b/src/shogun/machine/gp/MultiLaplaceInferenceMethod.cpp
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@@ -84,9 +84,9 @@ class CMultiPsiLine : public func_base
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float64_t result=0;
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for(index_t bl=0; bl<C; bl++)
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{
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- eigen_f.block(bl*n,0,n,1)=K*alpha->block(bl*n,0,n,1)*CMath::exp(log_scale*2.0);
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- result+=alpha->block(bl*n,0,n,1).dot(eigen_f.block(bl*n,0,n,1))/2.0;
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- eigen_f.block(bl*n,0,n,1)+=eigen_m;
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+ eigen_f.segment(bl*n,n)=K*alpha->segment(bl*n,n)*CMath::exp(log_scale*2.0);
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+ result+=alpha->segment(bl*n,n).dot(eigen_f.segment(bl*n,n))/2.0;
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+ eigen_f.segment(bl*n,n)+=eigen_m;
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}
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// get first and second derivatives of log likelihood
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@@ -272,7 +272,7 @@ void CMultiLaplaceInferenceMethod::update_alpha()
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{
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Map<VectorXd> alpha(m_alpha.vector, m_alpha.vlen);
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for(index_t bl=0; bl<C; bl++)
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- eigen_mu.block(bl*n,0,n,1)=eigen_ktrtr*CMath::exp(m_log_scale*2.0)*alpha.block(bl*n,0,n,1);
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+ eigen_mu.segment(bl*n,n)=eigen_ktrtr*CMath::exp(m_log_scale*2.0)*alpha.segment(bl*n,n);
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//alpha'*(f-m)/2.0
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Psi_New=alpha.dot(eigen_mu)/2.0;
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@@ -316,7 +316,7 @@ void CMultiLaplaceInferenceMethod::update_alpha()
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for(index_t bl=0; bl<C; bl++)
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{
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- VectorXd eigen_sD=eigen_dpi.block(bl*n,0,n,1).cwiseSqrt();
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+ VectorXd eigen_sD=eigen_dpi.segment(bl*n,n).cwiseSqrt();
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LLT<MatrixXd> chol_tmp((eigen_sD*eigen_sD.transpose()).cwiseProduct(eigen_ktrtr*CMath::exp(m_log_scale*2.0))+
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MatrixXd::Identity(m_ktrtr.num_rows, m_ktrtr.num_cols));
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MatrixXd eigen_L_tmp=chol_tmp.matrixU();
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@@ -341,11 +341,11 @@ void CMultiLaplaceInferenceMethod::update_alpha()
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VectorXd tmp2=m_tmp.array().rowwise().sum();
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for(index_t bl=0; bl<C; bl++)
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- eigen_b.block(bl*n,0,n,1)+=eigen_dpi.block(bl*n,0,n,1).cwiseProduct(eigen_mu.block(bl*n,0,n,1)-eigen_mean_bl-tmp2);
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+ eigen_b.segment(bl*n,n)+=eigen_dpi.segment(bl*n,n).cwiseProduct(eigen_mu.segment(bl*n,n)-eigen_mean_bl-tmp2);
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Map<VectorXd> &eigen_c=eigen_W;
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for(index_t bl=0; bl<C; bl++)
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- eigen_c.block(bl*n,0,n,1)=eigen_E.block(0,bl*n,n,n)*(eigen_ktrtr*CMath::exp(m_log_scale*2.0)*eigen_b.block(bl*n,0,n,1));
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+ eigen_c.segment(bl*n,n)=eigen_E.block(0,bl*n,n,n)*(eigen_ktrtr*CMath::exp(m_log_scale*2.0)*eigen_b.segment(bl*n,n));
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Map<MatrixXd> c_tmp(eigen_c.data(),n,C);
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@@ -409,7 +409,7 @@ float64_t CMultiLaplaceInferenceMethod::get_derivative_helper(SGMatrix<float64_t
|
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{
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result+=((eigen_E.block(0,bl*n,n,n)-eigen_U.block(0,bl*n,n,n).transpose()*eigen_U.block(0,bl*n,n,n)).array()
|
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*eigen_dK.array()).sum();
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- result-=(eigen_dK*eigen_alpha.block(bl*n,0,n,1)).dot(eigen_alpha.block(bl*n,0,n,1));
|
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+ result-=(eigen_dK*eigen_alpha.segment(bl*n,n)).dot(eigen_alpha.segment(bl*n,n));
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}
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return result/2.0;
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@@ -489,7 +489,7 @@ SGVector<float64_t> CMultiLaplaceInferenceMethod::get_derivative_wrt_mean(
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result[i]=0;
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//currently only compute the explicit term
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for(index_t bl=0; bl<C; bl++)
|
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- result[i]-=eigen_alpha.block(bl*n,0,n,1).dot(eigen_dmu);
|
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+ result[i]-=eigen_alpha.segment(bl*n,n).dot(eigen_dmu);
|
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}
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return result;
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|
|
@ -0,0 +1,76 @@
|
|||
From: Sebastián Mancilla <smancill@smancill.dev>
|
||||
Subject: Update SVMlight scrubber script
|
||||
|
||||
This requires previously fixing a few wrong preprocessor directives that
|
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are supposed to fence code using SVMlight.
|
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|
||||
- The script was too eager and removing *.light files in SVMlight format
|
||||
that are used by other tests. The code reading those files doesn't use
|
||||
any SVMlight code so it should be fine to keep it and run the tests.
|
||||
|
||||
- The Python test *domainadaptationsvm.py was not removed because of
|
||||
wrong globbing.
|
||||
|
||||
- Remove a couple of examples using SVMlight that were missed.
|
||||
|
||||
- The script is actually modifying (and breaking) itself because the
|
||||
grep for the USE_SVMLIGHT macro is too eager again and matches itself
|
||||
(and the version stored in upstream's Debian package control tarball
|
||||
is broken because of it). Just fix it by grepping for preprocessor
|
||||
directives only.
|
||||
|
||||
- No need to fix the Transfer_includes.i file in the script with a final
|
||||
%} when its preprocessor directives have been fixed.
|
||||
|
||||
- The Swig files were moved to a new directory at some point but the
|
||||
script was not updated accordingly.
|
||||
---
|
||||
scripts/light-scrubber.sh | 16 ++++++----------
|
||||
1 file changed, 6 insertions(+), 10 deletions(-)
|
||||
|
||||
diff a/scripts/light-scrubber.sh b/scripts/light-scrubber.sh
|
||||
--- a/scripts/light-scrubber.sh
|
||||
+++ b/scripts/light-scrubber.sh
|
||||
@@ -26,14 +26,16 @@
|
||||
# You should have received a copy of the GNU General Public License
|
||||
# along with this program. If not, see <http://www.gnu.org/licenses/>.
|
||||
#
|
||||
-rm -rf examples/*/*/{*light*,*_domainadaptationsvm_*} \
|
||||
+rm -rf examples/*/*/{*light*.*,*domainadaptationsvm*} \
|
||||
examples/undocumented/matlab_and_octave/tests/*light* \
|
||||
+ examples/undocumented/python/serialization_string_kernels.py \
|
||||
+ examples/undocumented/python/mkl_binclass.py \
|
||||
src/shogun/classifier/svm/SVMLight.* \
|
||||
src/shogun/classifier/svm/SVMLightOneClass.* \
|
||||
src/shogun/regression/svr/SVRLight.* \
|
||||
doc/md/LICENSE_SVMlight*
|
||||
|
||||
-for _file in `grep -rl USE_SVMLIGHT .`
|
||||
+grep -rl '^#ifdef USE_SVMLIGHT' . | while read -r _file
|
||||
do
|
||||
sed -i.orig -e \
|
||||
'/\#ifdef USE_SVMLIGHT/,/\#endif \/\/USE_SVMLIGHT/c \\' ${_file} && \
|
||||
@@ -41,7 +43,7 @@ do
|
||||
rm -rf ${_file}.orig
|
||||
done
|
||||
|
||||
-for _file in `find . -depth -name 'CMakeLists.txt'`
|
||||
+find . -depth -name 'CMakeLists.txt' | while read -r _file
|
||||
do
|
||||
sed -i.orig -e 's!.*_sv[mr]light_.*!!g' ${_file} && \
|
||||
touch -r ${_file}.orig ${_file} && \
|
||||
@@ -56,13 +58,7 @@ do
|
||||
rm -rf ${_file}.orig
|
||||
done
|
||||
|
||||
-_file="src/interfaces/modular/Transfer_includes.i" && \
|
||||
-cp -a ${_file} ${_file}.orig && \
|
||||
-echo '%}' >> ${_file} && \
|
||||
-touch -r ${_file}.orig ${_file} && \
|
||||
-rm -rf ${_file}.orig
|
||||
-
|
||||
-_file="src/interfaces/modular/Machine.i" && \
|
||||
+_file="src/interfaces/swig/Machine.i" && \
|
||||
sed -i.orig -e '/.*CSVRLight.*/d' ${_file} && \
|
||||
touch -r ${_file}.orig ${_file} && \
|
||||
rm -rf ${_file}.orig
|
||||
Loading…
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Reference in a new issue