Bug#663743: fails to link on powerpc

Soeren Sonnenburg sonne at debian.org
Tue Mar 13 18:33:40 UTC 2012 

Package: clang
Version: 3.0-6
Severity: grave

I am compiling the shogun package with clang (due to its much smaller
memory footprint)



clang++   ./evaluation/MulticlassAccuracy.cpp.o ./evaluation/CrossValidation.cpp.o ./evaluation/MeanAbsoluteError.cpp.o ./evaluation/ContingencyTableEvaluation.cpp.o ./evaluation/MeanSquaredError.cpp.o ./evaluation/ROCEvaluation.cpp.o ./evaluation/SplittingStrategy.cpp.o ./evaluation/PRCEvaluation.cpp.o ./evaluation/StratifiedCrossValidationSplitting.cpp.o ./modelselection/GridSearchModelSelection.cpp.o ./modelselection/ParameterCombination.cpp.o ./modelselection/ModelSelection.cpp.o ./modelselection/ModelSelectionParameters.cpp.o ./base/init.cpp.o ./base/Parameter.cpp.o ./base/SGObject.cpp.o ./base/Version.cpp.o ./base/class_list.cpp.o ./base/ParameterMap.cpp.o ./base/Parallel.cpp.o ./io/SerializableXmlFile.cpp.o ./io/HDF5File.cpp.o ./io/File.cpp.o ./io/SerializableAsciiFile.cpp.o ./io/AsciiFile.cpp.o ./io/SerializableJsonFile.cpp.o ./io/IOBuffer.cpp.o ./io/SerializableHdf5Reader00.cpp.o ./io/SerializableAsciiReader00.cpp.o ./io/StreamingAsciiFile.cpp.o ./io/BinaryFile.cpp.o ./io/StreamingVwCacheFile.cpp.o ./io/SerializableXmlReader00.cpp.o ./io/SerializableFile.cpp.o ./io/SerializableHdf5File.cpp.o ./io/StreamingFile.cpp.o ./io/SerializableJsonReader00.cpp.o ./io/StreamingVwFile.cpp.o ./io/StreamingFileFromFeatures.cpp.o ./io/SGIO.cpp.o ./classifier/GaussianNaiveBayes.cpp.o ./classifier/Perceptron.cpp.o ./classifier/LPBoost.cpp.o ./classifier/LPM.cpp.o ./classifier/mkl/MKLMultiClassOptimizationBase.cpp.o ./classifier/mkl/MKLMultiClassGradient.cpp.o ./classifier/mkl/MKLClassification.cpp.o ./classifier/mkl/MKLOneClass.cpp.o ./classifier/mkl/MKL.cpp.o ./classifier/mkl/MKLMultiClass.cpp.o ./classifier/mkl/MKLMultiClassGLPK.cpp.o ./classifier/svm/SVMOcas.cpp.o ./classifier/svm/SVM_linear.cpp.o ./classifier/svm/ScatterSVM.cpp.o ./classifier/svm/GMNPLib.cpp.o ./classifier/svm/GPBTSVM.cpp.o ./classifier/svm/OnlineSVMSGD.cpp.o ./classifier/svm/gpdtsolve.cpp.o ./classifier/svm/LibLinear.cpp.o ./classifier/svm/SVMLin.cpp.o ./classifier/svm/MPDSVM.cpp.o ./classifier/svm/SGDQN.cpp.o ./classifier/svm/gpdt.cpp.o ./classifier/svm/SVM_libsvm.cpp.o ./classifier/svm/LibSVM.cpp.o ./classifier/svm/Tron.cpp.o ./classifier/svm/SVMLightOneClass.cpp.o ./classifier/svm/MultiClassSVM.cpp.o ./classifier/svm/DomainAdaptationSVM.cpp.o ./classifier/svm/gpm.cpp.o ./classifier/svm/OnlineLibLinear.cpp.o ./classifier/svm/GMNPSVM.cpp.o ./classifier/svm/pr_loqo.cpp.o ./classifier/svm/LaRank.cpp.o ./classifier/svm/DomainAdaptationSVMLinear.cpp.o ./classifier/svm/LibSVMOneClass.cpp.o ./classifier/svm/GNPPSVM.cpp.o ./classifier/svm/SVMSGD.cpp.o ./classifier/svm/GNPPLib.cpp.o ./classifier/svm/SVM.cpp.o ./classifier/svm/SubGradientSVM.cpp.o ./classifier/svm/libocas.cpp.o ./classifier/svm/SVMLight.cpp.o ./classifier/svm/WDSVMOcas.cpp.o ./classifier/svm/ssl.cpp.o ./classifier/svm/CPLEXSVM.cpp.o ./classifier/svm/QPBSVMLib.cpp.o ./classifier/svm/libqp_splx.cpp.o ./classifier/svm/LibSVMMultiClass.cpp.o ./classifier/SubGradientLPM.cpp.o ./classifier/vw/VowpalWabbit.cpp.o ./classifier/vw/vw_example.cpp.o ./classifier/vw/vw_label.cpp.o ./classifier/vw/VwRegressor.cpp.o ./classifier/vw/VwEnvironment.cpp.o ./classifier/vw/learners/VwAdaptiveLearner.cpp.o ./classifier/vw/learners/VwNonAdaptiveLearner.cpp.o ./classifier/vw/VwParser.cpp.o ./classifier/vw/vw_math.cpp.o ./classifier/vw/cache/VwNativeCacheWriter.cpp.o ./classifier/vw/cache/VwCacheWriter.cpp.o ./classifier/vw/cache/VwNativeCacheReader.cpp.o ./classifier/vw/cache/VwCacheReader.cpp.o ./classifier/KNN.cpp.o ./classifier/PluginEstimate.cpp.o ./classifier/AveragedPerceptron.cpp.o ./classifier/LDA.cpp.o ./lib/Compressor.cpp.o ./lib/Time.cpp.o ./lib/ShogunException.cpp.o ./lib/Trie.cpp.o ./lib/memory.cpp.o ./lib/Hash.cpp.o ./lib/Signal.cpp.o ./lib/FibonacciHeap.cpp.o ./lib/HashSet.cpp.o ./lib/DataType.cpp.o ./kernel/SalzbergWordStringKernel.cpp.o ./kernel/HistogramWordStringKernel.cpp.o ./kernel/Chi2Kernel.cpp.o ./kernel/SphericalKernel.cpp.o ./kernel/SimpleLocalityImprovedStringKernel.cpp.o ./kernel/WeightedCommWordStringKernel.cpp.o ./kernel/CauchyKernel.cpp.o ./kernel/BesselKernel.cpp.o ./kernel/DiagKernel.cpp.o ./kernel/HistogramIntersectionKernel.cpp.o ./kernel/WeightedDegreeRBFKernel.cpp.o ./kernel/CircularKernel.cpp.o ./kernel/GaussianShiftKernel.cpp.o ./kernel/SpectrumMismatchRBFKernel.cpp.o ./kernel/SpectrumRBFKernel.cpp.o ./kernel/MultiquadricKernel.cpp.o ./kernel/CommUlongStringKernel.cpp.o ./kernel/OligoStringKernel.cpp.o ./kernel/DistanceKernel.cpp.o ./kernel/LocalityImprovedStringKernel.cpp.o ./kernel/InverseMultiQuadricKernel.cpp.o ./kernel/WaveKernel.cpp.o ./kernel/ExponentialKernel.cpp.o ./kernel/SNPStringKernel.cpp.o ./kernel/CommWordStringKernel.cpp.o ./kernel/LogKernel.cpp.o ./kernel/WaveletKernel.cpp.o ./kernel/PowerKernel.cpp.o ./kernel/ConstKernel.cpp.o ./kernel/RationalQuadraticKernel.cpp.o ./kernel/CustomKernel.cpp.o ./kernel/AUCKernel.cpp.o ./kernel/PolyKernel.cpp.o ./kernel/MatchWordStringKernel.cpp.o ./kernel/RegulatoryModulesStringKernel.cpp.o ./kernel/Kernel.cpp.o ./kernel/LocalAlignmentStringKernel.cpp.o ./kernel/LinearKernel.cpp.o ./kernel/GaussianShortRealKernel.cpp.o ./kernel/SparseSpatialSampleStringKernel.cpp.o ./kernel/GaussianKernel.cpp.o ./kernel/DistantSegmentsKernel.cpp.o ./kernel/PolyMatchWordStringKernel.cpp.o ./kernel/WeightedDegreeStringKernel.cpp.o ./kernel/FixedDegreeStringKernel.cpp.o ./kernel/WeightedDegreePositionStringKernel.cpp.o ./kernel/SigmoidKernel.cpp.o ./kernel/TStudentKernel.cpp.o ./kernel/PolyMatchStringKernel.cpp.o ./kernel/ANOVAKernel.cpp.o ./kernel/PyramidChi2.cpp.o ./kernel/SplineKernel.cpp.o ./kernel/LinearStringKernel.cpp.o ./kernel/TensorProductPairKernel.cpp.o ./kernel/CombinedKernel.cpp.o ./kernel/GaussianMatchStringKernel.cpp.o ./regression/KRR.cpp.o ./regression/svr/SVRLight.cpp.o ./regression/svr/LibSVR.cpp.o ./regression/svr/MKLRegression.cpp.o ./converter/KernelLocallyLinearEmbedding.cpp.o ./converter/KernelLocalTangentSpaceAlignment.cpp.o ./converter/LocalityPreservingProjections.cpp.o ./converter/Isomap.cpp.o ./converter/EmbeddingConverter.cpp.o ./converter/LocallyLinearEmbedding.cpp.o ./converter/NeighborhoodPreservingEmbedding.cpp.o ./converter/MultidimensionalScaling.cpp.o ./converter/HessianLocallyLinearEmbedding.cpp.o ./converter/LocalTangentSpaceAlignment.cpp.o ./converter/LaplacianEigenmaps.cpp.o ./converter/DiffusionMaps.cpp.o ./converter/LinearLocalTangentSpaceAlignment.cpp.o ./distributions/Histogram.cpp.o ./distributions/Gaussian.cpp.o ./distributions/LinearHMM.cpp.o ./distributions/HMM.cpp.o ./distributions/GHMM.cpp.o ./distributions/PositionalPWM.cpp.o ./distributions/Distribution.cpp.o ./features/StringFileFeatures.cpp.o ./features/WDFeatures.cpp.o ./features/StreamingDotFeatures.cpp.o ./features/LBPPyrDotFeatures.cpp.o ./features/SparseFeatures.cpp.o ./features/CombinedDotFeatures.cpp.o ./features/StreamingSimpleFeatures.cpp.o ./features/Subset.cpp.o ./features/DummyFeatures.cpp.o ./features/CombinedFeatures.cpp.o ./features/HashedWDFeaturesTransposed.cpp.o ./features/SparsePolyFeatures.cpp.o ./features/ExplicitSpecFeatures.cpp.o ./features/StreamingFeatures.cpp.o ./features/StreamingSparseFeatures.cpp.o ./features/HashedWDFeatures.cpp.o ./features/TOPFeatures.cpp.o ./features/RealFileFeatures.cpp.o ./features/SNPFeatures.cpp.o ./features/StringFeatures.cpp.o ./features/Alphabet.cpp.o ./features/PolyFeatures.cpp.o ./features/StreamingVwFeatures.cpp.o ./features/ImplicitWeightedSpecFeatures.cpp.o ./features/StreamingStringFeatures.cpp.o ./features/Labels.cpp.o ./features/Features.cpp.o ./features/AttributeFeatures.cpp.o ./features/DotFeatures.cpp.o ./features/SimpleFeatures.cpp.o ./features/FKFeatures.cpp.o ./structure/SegmentLoss.cpp.o ./structure/DynProg.cpp.o ./structure/PlifArray.cpp.o ./structure/Plif.cpp.o ./structure/IntronList.cpp.o ./structure/PlifMatrix.cpp.o ./machine/KernelMachine.cpp.o ./machine/OnlineLinearMachine.cpp.o ./machine/DistanceMachine.cpp.o ./machine/Machine.cpp.o ./machine/LinearMachine.cpp.o ./distance/HammingWordDistance.cpp.o ./distance/BrayCurtisDistance.cpp.o ./distance/CosineDistance.cpp.o ./distance/CustomDistance.cpp.o ./distance/GeodesicMetric.cpp.o ./distance/Distance.cpp.o ./distance/ManhattanWordDistance.cpp.o ./distance/MinkowskiMetric.cpp.o ./distance/CanberraWordDistance.cpp.o ./distance/TanimotoDistance.cpp.o ./distance/ManhattanMetric.cpp.o ./distance/ChiSquareDistance.cpp.o ./distance/CanberraMetric.cpp.o ./distance/ChebyshewMetric.cpp.o ./distance/SparseEuclidianDistance.cpp.o ./distance/EuclidianDistance.cpp.o ./distance/JensenMetric.cpp.o ./distance/KernelDistance.cpp.o ./distance/AttenuatedEuclidianDistance.cpp.o ./ui/GUITime.cpp.o ./ui/GUIHMM.cpp.o ./ui/GUIStructure.cpp.o ./ui/GUIClassifier.cpp.o ./ui/GUIKernel.cpp.o ./ui/GUIMath.cpp.o ./ui/GUIFeatures.cpp.o ./ui/GUIDistance.cpp.o ./ui/GUIPreprocessor.cpp.o ./ui/GUILabels.cpp.o ./ui/SGInterface.cpp.o ./ui/GUIPluginEstimate.cpp.o ./preprocessor/LogPlusOne.cpp.o ./preprocessor/PCA.cpp.o ./preprocessor/SortWordString.cpp.o ./preprocessor/SortUlongString.cpp.o ./preprocessor/NormOne.cpp.o ./preprocessor/DecompressString.cpp.o ./preprocessor/RandomFourierGaussPreproc.cpp.o ./preprocessor/SimplePreprocessor.cpp.o ./preprocessor/DimensionReductionPreprocessor.cpp.o ./preprocessor/PruneVarSubMean.cpp.o ./preprocessor/KernelPCA.cpp.o ./clustering/GMM.cpp.o ./clustering/Hierarchical.cpp.o ./clustering/KMeans.cpp.o ./loss/SmoothHingeLoss.cpp.o ./loss/HingeLoss.cpp.o ./loss/LogLossMargin.cpp.o ./loss/SquaredHingeLoss.cpp.o ./loss/LogLoss.cpp.o ./loss/SquaredLoss.cpp.o ./mathematics/lapack.cpp.o ./mathematics/Cplex.cpp.o ./mathematics/arpack.cpp.o ./mathematics/Statistics.cpp.o ./mathematics/Math.cpp.o -Xlinker --no-undefined  -o libshogun.so.11.0 -lm -pthread -lhdf5 -ljson   -lxml2   -llapack -lblas -lglpk -lm -llzo2 -lz -llzma -fPIC -Xlinker -soname=libshogun.so.11 -shared -Wl,-export-dynamic
./kernel/SpectrumMismatchRBFKernel.cpp.o: In function `shogun::CSpectrumMismatchRBFKernel::compute_all()':
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumMismatchRBFKernel.cpp:351: undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, unsigned long, std::allocator<char> const&)'
./kernel/SpectrumMismatchRBFKernel.cpp.o: In function `std::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)':
/usr/include/c++/4.6/bits/basic_string.h:2363: undefined reference to `std::string::append(unsigned long, char)'
./kernel/SpectrumRBFKernel.cpp.o: In function `shogun::CSpectrumRBFKernel::read_profiles_and_sequences()':
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:158: undefined reference to `std::string::find(char, unsigned long) const'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:161: undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&, unsigned long, unsigned long)'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:180: undefined reference to `std::string::find_first_not_of(char, unsigned long) const'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:180: undefined reference to `std::string::find(char, unsigned long) const'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:182: undefined reference to `std::string::find_first_not_of(char, unsigned long) const'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:182: undefined reference to `std::string::find(char, unsigned long) const'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:184: undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&, unsigned long, unsigned long)'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:195: undefined reference to `std::string::find_first_not_of(char, unsigned long) const'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:195: undefined reference to `std::string::find(char, unsigned long) const'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:208: undefined reference to `std::string::find_first_not_of(char, unsigned long) const'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:208: undefined reference to `std::string::find(char, unsigned long) const'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:210: undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&, unsigned long, unsigned long)'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:200: undefined reference to `std::string::find_first_not_of(char, unsigned long) const'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/SpectrumRBFKernel.cpp:200: undefined reference to `std::string::find(char, unsigned long) const'
./kernel/OligoStringKernel.cpp.o: In function `shogun::COligoStringKernel::encodeOligo(std::string const&, unsigned int, std::string const&, std::vector<std::pair<int, double>, std::allocator<std::pair<int, double> > >&)':
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/OligoStringKernel.cpp:83: undefined reference to `std::string::find(char, unsigned long) const'
./kernel/OligoStringKernel.cpp.o: In function `shogun::COligoStringKernel::compute(int, int)':
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/OligoStringKernel.cpp:241: undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, unsigned long, std::allocator<char> const&)'
/build/buildd-shogun_1.1.0-4-powerpc-jF5gk9/shogun-1.1.0/src/shogun/kernel/OligoStringKernel.cpp:242: undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, unsigned long, std::allocator<char> const&)'
./kernel/OligoStringKernel.cpp.o: In function `std::pair<std::pair<int, double>*, long> std::get_temporary_buffer<std::pair<int, double> >(long)':
/usr/include/c++/4.6/bits/stl_tempbuf.h:95: undefined reference to `operator new(unsigned long, std::nothrow_t const&)'
/usr/include/c++/4.6/bits/stl_tempbuf.h:95: undefined reference to `operator new(unsigned long, std::nothrow_t const&)'
clang: error: linker command failed with exit code 1 (use -v to see invocation)

https://buildd.debian.org/status/fetch.php?pkg=shogun&arch=powerpc&ver=1.1.0-4&stamp=1331629900

-- System Information:
Debian Release: wheezy/sid
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'unstable'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.3.0-rc5-sonne+ (SMP w/2 CPU cores; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages clang depends on:
ii  libc6                2.13-27
ii  libclang-common-dev  3.0-6
ii  libffi5              3.0.10-3
ii  libgcc1              1:4.6.3-1
ii  libllvm3.0           3.0-7
ii  libstdc++6           4.6.3-1
ii  libstdc++6-4.6-dev   4.6.3-1

Versions of packages clang recommends:
ii  llvm-3.0-dev  3.0-7
ii  python        2.7.2-10

clang suggests no packages.

-- no debconf information

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