maffilter install failed
于振朋
Dear jydu,
When I installed the maffilter meet following warnings：
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/
-- Found /bin/gzip compression program, using file extension .gz
-- bpp-core 4.1.0 found:
-- static lib: /usr/local/lib64/libbpp-core.a
-- shared lib: /usr/local/lib64/libbpp-core.so.4.1.0
-- includes: /usr/local/include
-- bpp-seq 12.0.0 found:
-- static lib: /usr/local/lib64/libbpp-seq.a
-- shared lib: /usr/local/lib64/libbpp-seq.so.12.0.0
-- includes: /usr/local/include
-- bpp-seq-omics 3.0.0 found:
-- static lib: /usr/local/lib64/libbpp-seq-omics.a
-- shared lib: /usr/local/lib64/libbpp-seq-omics.so.3.0.0
-- includes: /usr/local/include
-- bpp-phyl 12.0.0 found:
-- static lib: /usr/local/lib64/libbpp-phyl.a
-- shared lib: /usr/local/lib64/libbpp-phyl.so.12.0.0
-- includes: /usr/local/include
-- bpp-phyl-omics 3.0.0 found:
-- static lib: /usr/local/lib64/libbpp-phyl-omics.a
-- shared lib: /usr/local/lib64/libbpp-phyl-omics.so.3.0.0
-- includes: /usr/local/include
-- Boost version: 1.41.0
-- Found the following Boost libraries:
-- iostreams
-- Boost libraries found here:
includes: /usr/include
dynamic libraries: /usr/lib64/libboost_iostreams-mt.so
-- Library z found here:
includes: /usr/include
dynamic libraries: /usr/lib64/libz.so
-- Library bz2 found here:
includes: /usr/include
dynamic libraries: /usr/lib64/libbz2.so
-- makeinfo program not found: 'info' and 'html' target disabled (builds info/html doc)
-- Configuring done
-- Generating done
-- Build files have been written to: /Bio/home/Yanglab/Yuzhenpeng/opt/softwares/maffilter-1.3.1
make install
Scanning dependencies of target maffilter
[ 20%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/MafFilter.cpp.o
[ 40%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/OutputAsFeaturesMafIterator.cpp.o
[ 60%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/SystemCallMafIterator.cpp.o
[ 80%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/TreeBuildingSystemCallMafIterator.cpp.o
Linking CXX executable maffilter
CMakeFiles/maffilter.dir/MafFilter.cpp.o: In function bpp::BasicSequenceFeature::getAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const': CMakeFiles/maffilter.dir/MafFilter.cpp.o: In functionbpp::BasicSequenceFeature::getAttribute(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const':
/usr/local/include/Bpp/Seq/Feature/SequenceFeature.h:350: undefined reference to _ZN3bpp15SequenceFeature16NO_ATTRIBUTE_SETB5cxx11E' CMakeFiles/maffilter.dir/MafFilter.cpp.o: In functionbpp::PolymorphismMafStatistics::PolymorphismMafStatistics(std::vector<std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > >, std::allocator<std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > > > const&)':
/usr/local/include/Bpp/Seq/Io/Maf/MafStatistics.h:663: undefined reference to bpp::AbstractSpeciesMultipleSelectionMafStatistics::AbstractSpeciesMultipleSelectionMafStatistics(std::vector<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::allocator<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)' CMakeFiles/maffilter.dir/MafFilter.cpp.o: In functionbasic_string':
/opt/sysoft/gcc-5.5.0/include/c++/5.5.0/bits/basic_string.h:109: undefined reference to _ZN3bpp38MaximumLikelihoodModelFitMafStatistics11NO_PROPERTYB5cxx11E' /opt/sysoft/gcc-5.5.0/include/c++/5.5.0/bits/basic_string.h:195: undefined reference to_ZN3bpp38MaximumLikelihoodModelFitMafStatistics11NO_PROPERTYB5cxx11E'
/opt/sysoft/gcc-5.5.0/include/c++/5.5.0/bits/basic_string.h:109: undefined reference to _ZN3bpp38MaximumLikelihoodModelFitMafStatistics11NO_PROPERTYB5cxx11E' /opt/sysoft/gcc-5.5.0/include/c++/5.5.0/bits/basic_string.h:195: undefined reference to_ZN3bpp38MaximumLikelihoodModelFitMafStatistics11NO_PROPERTYB5cxx11E'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::SequenceMask::MASK' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference tobpp::TextTools::resizeRight(std::string const&, unsigned long, char)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::EdSymbolList::addElement(std::string const&)' /usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference to bpp::NodePException::NodePException(std::string const&, bpp::Node const*)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::VectorSequenceContainer::setSequencesNames(std::vector<std::string, std::allocator<std::string> > const&, bool)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference tobpp::AbstractAlphabet::charToInt(std::string const&) const'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::EdSymbolList::getChar(unsigned long) const' /usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference tobpp::SiteContainerTools::computeSimilarityMatrix(bpp::SiteContainer const&, bool, std::string const&, bool)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::AbstractAlphabet::getSupportedChars() const' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::SiteContainerTools::SIMILARITY_NOGAP'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::AbstractAlphabet::isCharInAlphabet(std::string const&) const' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::AbstractAlphabet::getName(int) const'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::SequenceWithAnnotation::getAnnotationTypes() const' /usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference to bpp::OptimizationTools::OPTIMIZATION_NEWTON'
/usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference to bpp::OptimizationTools::optimizeNumericalParameters2(bpp::DiscreteRatesAcrossSitesTreeLikelihood*, bpp::ParameterList const&, bpp::OptimizationListener*, double, unsigned int, bpp::OutputStream*, bpp::OutputStream*, bool, bool, unsigned int, std::string const&)' /usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference to bpp::UnrootedTreeException::UnrootedTreeException(std::string const&, bpp::Tree const*)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::SiteContainerTools::computeSimilarity(bpp::Sequence const&, bpp::Sequence const&, bool, std::string const&, bool)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference tobpp::TextTools::removeSurroundingWhiteSpaces(std::string const&)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::EdSymbolList::setContent(std::vector<std::string, std::allocator<std::string> > const&)' /usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference tobpp::DistanceMatrix::getNameIndex(std::string const&) const'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::ApplicationTools::displayUnlimitedGauge(unsigned long, std::string const&)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference tobpp::KeyvalTools::multipleKeyvals(std::string const&, std::map<std::string, std::string, std::lessstd::string, std::allocator<std::pair<std::string const, std::string> > >&, std::string const&, bool)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::SequenceWithAnnotation::append(std::vector<std::string, std::allocator<std::string> > const&)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference tobpp::TextTools::replaceAll(std::string&, std::string const&, std::string const&)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::ApplicationTools::displayTask(std::string const&, bool)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::SequenceWithAnnotation::setContent(std::string const&)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::AbstractAlphabet::getStateIndex(std::string const&) const' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::AbstractAlphabet::intToChar(int) const'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::VectorSiteContainer::VectorSiteContainer(std::vector<std::string, std::allocator<std::string> > const&, bpp::Alphabet const*)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference tobpp::ApplicationTools::displayMessage(std::string const&)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::EdSymbolList::toString() const' /usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference tobpp::NodePException::NodePException(std::string const&, bpp::Node const*)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::AbstractAlphabet::getResolvedChars() const' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::IndexOutOfBoundsException::IndexOutOfBoundsException(std::string, unsigned long, unsigned long, unsigned long)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::AbstractAlphabet::getGeneric(std::vector<std::string, std::allocator<std::string> > const&) const' /usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference tobpp::ParameterList::getParameterNames() const'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::OutOfRangeException::OutOfRangeException(std::string, double, double, double)' /usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference tobpp::OptimizationTools::estimateDistanceMatrix(bpp::DistanceEstimation&, bpp::ParameterList const&, std::string const&, unsigned int)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::SequenceQuality::QUALITY_SCORE' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference tobpp::SequenceWithAnnotation::append(std::string const&)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::Exception::Exception(std::string)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::EdSymbolList::setElement(unsigned long, std::string const&)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::SequenceWithAnnotation::SequenceWithAnnotation(std::string const&, std::string const&, bpp::Alphabet const*)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference tobpp::BadCharException::BadCharException(std::string const&, std::string const&, bpp::Alphabet const*)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::StringTokenizer::StringTokenizer(std::string const&, std::string const&, bool, bool)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference tobpp::Exception::Exception(std::string)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::AbstractAlphabet::getName(std::string const&) const' /usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference tobpp::NodeNotFoundException::NodeNotFoundException(std::string const&, std::string const&)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::AbstractAlphabet::getAlias(std::string const&) const' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::AlphabetException::AlphabetException(std::string const&, bpp::Alphabet const*)'
/usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference to bpp::TreeTemplateTools::getLeavesNames(bpp::Node const&)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::AbstractAlphabet::getState(std::string const&) const'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::BadIntegerException::BadIntegerException(std::string, int)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::TextTools::resizeLeft(std::string const&, unsigned long, char)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::TextTools::isEmpty(std::string const&)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference tobpp::ApplicationTools::displayGauge(unsigned long, unsigned long, char, std::string const&)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::TextTools::toDouble(std::string const&, char, char)' /usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference tobpp::ApplicationTools::displayWarning(std::string const&)'
/usr/local/lib64/libbpp-seq-omics.so.3.0.0: undefined reference to bpp::EdSymbolList::addElement(unsigned long, std::string const&)' /usr/local/lib64/libbpp-phyl-omics.so.3.0.0: undefined reference tobpp::ParameterList::deleteParameters(std::vector<std::string, std::allocatorstd::string > const&, bool)'
collect2: error: ld returned 1 exit status
make[2]: *** [MafFilter/maffilter] Error 1
make[1]: *** [MafFilter/CMakeFiles/maffilter.dir/all] Error 2
make: *** [all] Error 2
I do not know why. Could you give me some suggests.
