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cerebis / bin3C

Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.
GNU Affero General Public License v3.0
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Building Infomap Error #31

Closed davidcalfran closed 3 years ago

davidcalfran commented 4 years ago

I am trying to follow the installation procedure and install/build Infomap and I am getting the following error:

(base) TUD1001222:bin3C dcalderonfranc$ make -f Makefile.infomap 
make -C external/infomap_repo
make[1]: Entering directory '/Volumes/DAVIDCALFRAN_HARDRIVE/TFM/Data/Paquetes/bin3C/external/infomap_repo'
Linking object files to target Infomap...
x86_64-apple-darwin13.4.0-clang++  -o Infomap build/Infomap/infomap/FlowNetwork.o build/Infomap/infomap/InfomapBase.o build/Infomap/infomap/InfomapContext.o build/Infomap/infomap/MemFlowNetwork.o build/Infomap/infomap/MemNetwork.o build/Infomap/infomap/MemoryNetworkAdapter.o build/Infomap/infomap/MultiplexNetwork.o build/Infomap/infomap/Network.o build/Infomap/infomap/NetworkAdapter.o build/Infomap/infomap/Node.o build/Infomap/infomap/TreeData.o build/Infomap/Infomap.o build/Infomap/io/BipartiteClusterReader.o build/Infomap/io/ClusterReader.o build/Infomap/io/HierarchicalNetwork.o build/Infomap/io/ProgramInterface.o build/Infomap/io/TreeDataWriter.o build/Infomap/io/version.o build/Infomap/utils/FileURI.o build/Infomap/utils/Logger.o
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
Undefined symbols for architecture x86_64:
  "__Unwind_Resume", referenced from:
      FlowNetwork::calculateFlow(Network const&, Config const&) in FlowNetwork.o
      std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in FlowNetwork.o
      std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in FlowNetwork.o
      void std::__1::vector<unsigned int, std::__1::allocator<unsigned int> >::__push_back_slow_path<unsigned int const>(unsigned int const&) in FlowNetwork.o
      InfomapBase::initNetwork() in InfomapBase.o
      InfomapBase::run(HierarchicalNetwork&) in InfomapBase.o
      InfomapBase::initNetwork(Network&) in InfomapBase.o
      ...
  "___bzero", referenced from:
      FlowNetwork::calculateFlow(Network const&, Config const&) in FlowNetwork.o
      InfomapBase::processPartitionQueue(PartitionQueue&, PartitionQueue&, bool) in InfomapBase.o
      InfomapBase::initMemoryNetwork(MemNetwork&) in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in InfomapBase.o
      std::__1::vector<unsigned int, std::__1::allocator<unsigned int> >::__append(unsigned long) in InfomapBase.o
      void InfomapContext::createInfomap<WithMemory>() in InfomapContext.o
      void InfomapContext::createInfomap<WithoutMemory>() in InfomapContext.o
      ...
  "___cxa_atexit", referenced from:
      Logger::benchmark(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, double, unsigned int, unsigned int, unsigned int, bool) in InfomapBase.o
      Logger::benchmark(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, double, unsigned int, unsigned int, unsigned int, bool) in Infomap.o
      __GLOBAL__sub_I_Logger.cpp in Logger.o
  "___stack_chk_fail", referenced from:
      InfomapBase::initNetwork(Network&) in InfomapBase.o
      InfomapBase::initMemoryNetwork(MemNetwork&) in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in InfomapBase.o
      void std::__1::__sort<IterationStatsSortSeconds&, PerIterationStats*>(PerIterationStats*, PerIterationStats*, IterationStatsSortSeconds&) in InfomapBase.o
      unsigned int std::__1::__sort5<IterationStatsSortSeconds&, PerIterationStats*>(PerIterationStats*, PerIterationStats*, PerIterationStats*, PerIterationStats*, PerIterationStats*, IterationStatsSortSeconds&) in InfomapBase.o
      bool std::__1::__insertion_sort_incomplete<IterationStatsSortSeconds&, PerIterationStats*>(PerIterationStats*, PerIterationStats*, IterationStatsSortSeconds&) in InfomapBase.o
      void std::__1::__sort<IterationStatsSortNumTopModules&, PerIterationStats*>(PerIterationStats*, PerIterationStats*, IterationStatsSortNumTopModules&) in InfomapBase.o
      ...
  "___stack_chk_guard", referenced from:
      InfomapBase::initNetwork(Network&) in InfomapBase.o
      InfomapBase::initMemoryNetwork(MemNetwork&) in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in InfomapBase.o
      void std::__1::__sort<IterationStatsSortSeconds&, PerIterationStats*>(PerIterationStats*, PerIterationStats*, IterationStatsSortSeconds&) in InfomapBase.o
      unsigned int std::__1::__sort5<IterationStatsSortSeconds&, PerIterationStats*>(PerIterationStats*, PerIterationStats*, PerIterationStats*, PerIterationStats*, PerIterationStats*, IterationStatsSortSeconds&) in InfomapBase.o
      bool std::__1::__insertion_sort_incomplete<IterationStatsSortSeconds&, PerIterationStats*>(PerIterationStats*, PerIterationStats*, IterationStatsSortSeconds&) in InfomapBase.o
      void std::__1::__sort<IterationStatsSortNumTopModules&, PerIterationStats*>(PerIterationStats*, PerIterationStats*, IterationStatsSortNumTopModules&) in InfomapBase.o
      ...
  "_atof", referenced from:
      MemNetwork::parseStateLink(char*, int&, unsigned int&, unsigned int&, double&) in MemNetwork.o
      Network::parseLink(char*, unsigned int&, unsigned int&, double&) in Network.o
  "_atoi", referenced from:
      MemNetwork::parseStateLink(char*, int&, unsigned int&, unsigned int&, double&) in MemNetwork.o
      Network::parsePajekNetworkWithoutIOStreams(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in Network.o
      Network::parseLink(char*, unsigned int&, unsigned int&, double&) in Network.o
  "_clock", referenced from:
      InfomapBase::run(HierarchicalNetwork&) in InfomapBase.o
      Logger::benchmark(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, double, unsigned int, unsigned int, unsigned int, bool) in InfomapBase.o
      Logger::benchmark(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, double, unsigned int, unsigned int, unsigned int, bool) in Infomap.o
      run(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in Infomap.o
  "_difftime", referenced from:
      InfomapBase::printClusterNumbers(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in InfomapBase.o
      InfomapGreedyTypeSpecialized<FlowUndirected, WithMemory>::printClusterNumbers(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in InfomapContext.o
      InfomapGreedyTypeSpecialized<FlowDirectedNonDetailedBalance, WithMemory>::printClusterNumbers(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in InfomapContext.o
      InfomapGreedyTypeSpecialized<FlowDirectedWithTeleportation, WithMemory>::printClusterNumbers(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in InfomapContext.o
      InfomapGreedyTypeSpecialized<FlowDirectedNonDetailedBalanceWithTeleportation, WithMemory>::printClusterNumbers(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in InfomapContext.o
      run(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in Infomap.o
      HierarchicalNetwork::writeClu(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) in HierarchicalNetwork.o
      ...
  "_exit", referenced from:
      ProgramInterface::exitWithUsage(bool) in ProgramInterface.o
      ProgramInterface::exitWithVersionInformation() in ProgramInterface.o
      ProgramInterface::exitWithError(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in ProgramInterface.o
  "_exp2", referenced from:
      InfomapBase::run(HierarchicalNetwork&) in InfomapBase.o
  "_fclose", referenced from:
      SafeOutFile::SafeOutFile(char const*, unsigned int) in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::~basic_filebuf() in InfomapBase.o
      SafeOutFile::~SafeOutFile() in InfomapBase.o
      SafeInFile::SafeInFile(char const*, unsigned int) in MemNetwork.o
      SafeOutFile::SafeOutFile(char const*, unsigned int) in MemNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::~basic_filebuf() in MemNetwork.o
      SafeInFile::~SafeInFile() in MemNetwork.o
      ...
  "_fflush", referenced from:
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in MemNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in MemoryNetworkAdapter.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in MultiplexNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in Network.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in NetworkAdapter.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in Infomap.o
      ...
  "_fgetc", referenced from:
      Network::parsePajekNetworkWithoutIOStreams(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in Network.o
  "_fgets", referenced from:
      Network::parsePajekNetworkWithoutIOStreams(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in Network.o
      Network::parseLinkListWithoutIOStreams(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in Network.o
  "_floor", referenced from:
      operator<<(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, ElapsedTime const&) in InfomapBase.o
      operator<<(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, ElapsedTime const&) in InfomapContext.o
      operator<<(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, ElapsedTime const&) in Infomap.o
      operator<<(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, ElapsedTime const&) in HierarchicalNetwork.o
  "_fopen", referenced from:
      SafeOutFile::SafeOutFile(char const*, unsigned int) in InfomapBase.o
      SafeInFile::SafeInFile(char const*, unsigned int) in MemNetwork.o
      SafeOutFile::SafeOutFile(char const*, unsigned int) in MemNetwork.o
      SafeInFile::SafeInFile(char const*, unsigned int) in MemoryNetworkAdapter.o
      SafeInFile::SafeInFile(char const*, unsigned int) in MultiplexNetwork.o
      Network::parsePajekNetworkWithoutIOStreams(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in Network.o
      SafeInFile::SafeInFile(char const*, unsigned int) in Network.o
      ...
  "_fread", referenced from:
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in MemNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in MemoryNetworkAdapter.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in MultiplexNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in Network.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in NetworkAdapter.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in Infomap.o
      ...
  "_fseek", referenced from:
      SafeOutFile::SafeOutFile(char const*, unsigned int) in InfomapBase.o
      SafeInFile::SafeInFile(char const*, unsigned int) in MemNetwork.o
      SafeOutFile::SafeOutFile(char const*, unsigned int) in MemNetwork.o
      SafeInFile::SafeInFile(char const*, unsigned int) in MemoryNetworkAdapter.o
      SafeInFile::SafeInFile(char const*, unsigned int) in MultiplexNetwork.o
      SafeInFile::SafeInFile(char const*, unsigned int) in Network.o
      SafeOutFile::SafeOutFile(char const*, unsigned int) in Network.o
      ...
  "_fseeko", referenced from:
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekpos(std::__1::fpos<__mbstate_t>, unsigned int) in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in MemNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekpos(std::__1::fpos<__mbstate_t>, unsigned int) in MemNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in MemNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in MemoryNetworkAdapter.o
      ...
  "_ftell", referenced from:
      HierarchicalNetwork::writeStreamableTree(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, bool) in HierarchicalNetwork.o
  "_ftello", referenced from:
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in MemNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in MemoryNetworkAdapter.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in MultiplexNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in Network.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in NetworkAdapter.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in Infomap.o
      ...
  "_fwrite", referenced from:
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::overflow(int) in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in MemNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::overflow(int) in MemNetwork.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in MemoryNetworkAdapter.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::overflow(int) in MemoryNetworkAdapter.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in MultiplexNetwork.o
      ...
  "_localtime", referenced from:
      operator<<(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, Date const&) in InfomapBase.o
      operator<<(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, Date const&) in Infomap.o
  "_log2", referenced from:
      InfomapBase::run(HierarchicalNetwork&) in InfomapBase.o
      InfomapBase::initNetwork(Network&) in InfomapBase.o
      InfomapBase::calcEntropyRate() in InfomapBase.o
      InfomapGreedyCommon<InfomapGreedyTypeSpecialized<FlowUndirected, WithMemory> >::initConstantInfomapTerms() in InfomapContext.o
      InfomapGreedyTypeSpecialized<FlowUndirected, WithMemory>::calcCodelengthOnRootOfLeafNodes(NodeBase const&) in InfomapContext.o
      InfomapGreedyTypeSpecialized<FlowUndirected, WithMemory>::calcCodelengthOnModuleOfLeafNodes(NodeBase const&) in InfomapContext.o
      InfomapGreedyTypeSpecialized<FlowUndirected, WithMemory>::calcCodelengthOnModuleOfModules(NodeBase const&) in InfomapContext.o
      ...
  "_memcmp", referenced from:
      std::__1::__tree_iterator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Option*>, std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Option*>, void*>*, long> std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Option*>, std::__1::__map_value_compare<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Option*>, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Option*> > >::find<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in ProgramInterface.o
      std::__1::__tree_node_base<void*>*& std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Option*>, std::__1::__map_value_compare<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Option*>, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Option*> > >::__find_equal<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(std::__1::__tree_end_node<std::__1::__tree_node_base<void*>*>*&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in ProgramInterface.o
  "_memcpy", referenced from:
      FlowNetwork::calculateFlow(Network const&, Config const&) in FlowNetwork.o
      void std::__1::vector<unsigned int, std::__1::allocator<unsigned int> >::__push_back_slow_path<unsigned int const>(unsigned int const&) in FlowNetwork.o
      InfomapBase::findSuperModulesIterativelyFast(PartitionQueue&) in InfomapBase.o
      std::__1::vector<NodeBase*, std::__1::allocator<NodeBase*> >::reserve(unsigned long) in InfomapBase.o
      void std::__1::vector<NodeBase*, std::__1::allocator<NodeBase*> >::__push_back_slow_path<NodeBase* const>(NodeBase* const&) in InfomapBase.o
      void std::__1::vector<Edge<NodeBase>*, std::__1::allocator<Edge<NodeBase>*> >::__push_back_slow_path<Edge<NodeBase>* const>(Edge<NodeBase>* const&) in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekpos(std::__1::fpos<__mbstate_t>, unsigned int) in InfomapBase.o
      ...
  "_memmove", referenced from:
      std::__1::deque<PendingModule, std::__1::allocator<PendingModule> >::__add_back_capacity(unsigned long) in InfomapBase.o
      std::__1::__split_buffer<PendingModule*, std::__1::allocator<PendingModule*> >::push_front(PendingModule* const&) in InfomapBase.o
      std::__1::__split_buffer<PendingModule*, std::__1::allocator<PendingModule*>&>::push_front(PendingModule* const&) in InfomapBase.o
      std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in InfomapBase.o
      std::__1::deque<unsigned int, std::__1::allocator<unsigned int> >::__add_back_capacity() in InfomapBase.o
      std::__1::__split_buffer<unsigned int*, std::__1::allocator<unsigned int*> >::push_front(unsigned int* const&) in InfomapBase.o
      std::__1::__split_buffer<unsigned int*, std::__1::allocator<unsigned int*>&>::push_front(unsigned int* const&) in InfomapBase.o
      ...
  "_memset", referenced from:
      std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in FlowNetwork.o
      std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > io::padValue<unsigned int>(unsigned int, unsigned long, bool, char) in InfomapBase.o
      std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > io::padValue<double>(double, unsigned long, bool, char) in InfomapBase.o
      std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in InfomapBase.o
      std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in InfomapContext.o
      std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in MemFlowNetwork.o
      MemNetwork::simulateMemoryToIncompleteData() in MemNetwork.o
      ...
  "_memset_pattern16", referenced from:
      Network::parseVertices(std::__1::basic_ifstream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool) in Network.o
  "_remove", referenced from:
      isDirectoryWritable(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in Infomap.o
     (maybe you meant: __ZNSt3__113__tree_removeIPNS_16__tree_node_baseIPvEEEEvT_S5_)
  "_snprintf", referenced from:
      Network::parsePajekNetworkWithoutIOStreams(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in Network.o
      Network::initNodeNames() in Network.o
  "_strchr", referenced from:
      Network::parsePajekNetworkWithoutIOStreams(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in Network.o
  "_strlen", referenced from:
      std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > io::stringify<char const*>(char const*) in InfomapBase.o
      Config::Config() in InfomapContext.o
      std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > io::stringify<char const*>(char const*) in InfomapContext.o
      std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > io::stringify<char const*>(char const*) in MemFlowNetwork.o
      std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > io::stringify<char const*>(char const*) in MemNetwork.o
      std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > io::stringify<char*>(char*) in MemNetwork.o
      MemoryNetworkAdapter::readExternalHierarchy(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in MemoryNetworkAdapter.o
      ...
  "_strncmp", referenced from:
      Network::parsePajekNetworkWithoutIOStreams(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in Network.o
  "_strrchr", referenced from:
      Network::parsePajekNetworkWithoutIOStreams(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in Network.o
  "_strtod", referenced from:
      Network::parsePajekNetworkWithoutIOStreams(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in Network.o
  "_strtok", referenced from:
      MemNetwork::parseStateLink(char*, int&, unsigned int&, unsigned int&, double&) in MemNetwork.o
      Network::parseLink(char*, unsigned int&, unsigned int&, double&) in Network.o
  "_time", referenced from:
      InfomapBase::run(HierarchicalNetwork&) in InfomapBase.o
      InfomapBase::printClusterNumbers(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in InfomapBase.o
      InfomapGreedyTypeSpecialized<FlowUndirected, WithMemory>::printClusterNumbers(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in InfomapContext.o
      Config::Config() in InfomapContext.o
      InfomapGreedyTypeSpecialized<FlowDirectedNonDetailedBalance, WithMemory>::printClusterNumbers(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in InfomapContext.o
      InfomapGreedyTypeSpecialized<FlowDirectedWithTeleportation, WithMemory>::printClusterNumbers(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in InfomapContext.o
      InfomapGreedyTypeSpecialized<FlowDirectedNonDetailedBalanceWithTeleportation, WithMemory>::printClusterNumbers(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in InfomapContext.o
      ...
  "_ungetc", referenced from:
      Network::parsePajekNetworkWithoutIOStreams(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in Network.o
**ld: symbol(s) not found for architecture x86_64
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [Makefile:38: Infomap] Error 1
make[1]: Leaving directory '/Volumes/DAVIDCALFRAN_HARDRIVE/TFM/Data/Paquetes/bin3C/external/infomap_repo'
make: *** [Makefile.infomap:5: external/infomap_repo/Infomap] Error 2**

Has anybody encountered this problem before? Thank you very much.

cerebis commented 4 years ago

bin3C was not developed to be used on OSX, as a result most branches in this repository will suffer from the same issues.

However, I just recently addressed this issue within the "extaction" development branch. You might find this works for you, but I have not tested this fix on anything except Catalina. Further, you will need to install GCC using Brew or another package manager as there are build issues with Clang for some external source-based projects.

Newer branches of bin3C can also be installed with pip and you can attempt to install the extraction branch as follows:

eg. with brew installed gcc v9.

export CXX=gcc-9
pip install git+https://github.com/cerebis/bin3C@extraction

You must set the compiler environment variable so that Infomap does not used Clang.

This approach might also work with the manual make process of the original master branch.

Note: if you plan to install bin3C on a clean system or within a virtual environment, please install Cython and Numpy first. This prerequisite does not get installed, despite my efforts to specify this in setup.py.

eg.

pip install cython "numpy<1.15"
cerebis commented 3 years ago

I believe this issue has been addressed in theextraction branch, and its decendents. Soon this will become the master.