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fritzsedlazeck / SURVIVOR_ant

A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)
MIT License
13 stars 2 forks source link

installation error #3

Closed jungminchoilab closed 6 years ago

jungminchoilab commented 6 years ago

Hello,

Thanks for sharing this software. Looking great for the annotation of structural variants. I am hoping to try it but encountered the error while installing it. Could you kindly look into this?

Best, Jungmin

[jc2545@c13n01 build]$ make
Scanning dependencies of target zlibstatic
[  3%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/adler32.o
[  6%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/compress.o
[ 10%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/crc32.o
[ 13%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/deflate.o
[ 16%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzclose.o
[ 20%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzlib.o
[ 23%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzread.o
[ 26%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzwrite.o
[ 30%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inflate.o
[ 33%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/infback.o
[ 36%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inftrees.o
[ 40%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inffast.o
[ 43%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/trees.o
[ 46%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/uncompr.o
[ 50%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/zutil.o
[ 53%] Linking C static library libz.a
[ 53%] Built target zlibstatic
Scanning dependencies of target survivor_ant
[ 56%] Building CXX object src/CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o
[ 60%] Building CXX object src/CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o
[ 63%] Building CXX object src/CMakeFiles/survivor_ant.dir/Parser/BEDParser.cpp.o
[ 66%] Building CXX object src/CMakeFiles/survivor_ant.dir/Parser/GFFParser.cpp.o
[ 70%] Building CXX object src/CMakeFiles/survivor_ant.dir/Parser/VCFParser.cpp.o
[ 73%] Building CXX object src/CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o
[ 76%] Linking CXX executable ../../bin/survivor_ant-core-0.1.0/survivor_ant
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::overlap(position_str, position_str, short, SVS_Node*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::overlap(position_str, position_str, short, SVS_Node*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::overlap(position_str, position_str, short, SVS_Node*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::overlap(position_str, position_str, short, SVS_Node*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::insert(position_str, position_str, short, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool, TNode*&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::insert(position_str, position_str, short, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool, TNode*&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::insert(position_str, position_str, short, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool, TNode*&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::insert(position_str, position_str, short, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool, TNode*&): error: undefined reference to 'operator delete(void*, unsigned long)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::inorder_addanno(position_str, position_str, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, TNode*, TNode*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::StdOutput::spacePrint(std::ostream&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, int) const [clone .constprop.189]: error: undefined reference to 'std::__throw_out_of_range_fmt(char const*, ...)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::add(TCLAP::Arg*) [clone .constprop.187]: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::add(TCLAP::Arg*) [clone .constprop.186]: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::HelpVisitor::~HelpVisitor(): error: undefined reference to 'operator delete(void*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::VersionVisitor::~VersionVisitor(): error: undefined reference to 'operator delete(void*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::IgnoreRestVisitor::~IgnoreRestVisitor(): error: undefined reference to 'operator delete(void*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::operator==(TCLAP::Arg const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::ArgException::what() const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::ArgException::what() const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::ArgException::what() const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::trimFlag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) const: error: undefined reference to 'std::__throw_out_of_range_fmt(char const*, ...)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::SwitchArg::combinedSwitchesMatch(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char, unsigned long) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::add(TCLAP::Arg*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::missingArgsException(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::missingArgsException(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::substr(unsigned long, unsigned long) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::missingArgsException(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::missingArgsException(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::assign(char const*)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::missingArgsException(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::assign(char const*)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::longID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct(unsigned long, char)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::longID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct(unsigned long, char)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::shortID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::shortID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::shortID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct(unsigned long, char)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::shortID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::Arg(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, TCLAP::Visitor*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char const*, unsigned long, unsigned long) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::StdOutput::_shortUsage(TCLAP::CmdLineInterface&, std::ostream&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::StdOutput::_longUsage(TCLAP::CmdLineInterface&, std::ostream&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::StdOutput::_longUsage(TCLAP::CmdLineInterface&, std::ostream&) const: error: undefined reference to 'std::__throw_out_of_range_fmt(char const*, ...)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::StdOutput::_longUsage(TCLAP::CmdLineInterface&, std::ostream&) const: error: undefined reference to 'std::__throw_out_of_range_fmt(char const*, ...)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function Parameter::parse_intput(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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'VTT for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'VTT for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::_M_sync(char*, unsigned long, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_istringstream()'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/Parser/BEDParser.cpp.o:BEDParser.cpp:function BEDParser::parse_bed(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/Parser/BEDParser.cpp.o:BEDParser.cpp:function BEDParser::parse_bed(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/Parser/BEDParser.cpp.o:BEDParser.cpp:function BEDParser::parse_bed(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/Parser/GFFParser.cpp.o:GFFParser.cpp:function GFFParser::parse_gff(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace_aux(unsigned long, unsigned long, unsigned long, char)'
CMakeFiles/survivor_ant.dir/Parser/VCFParser.cpp.o:VCFParser.cpp:function VCFParser::parse_stop(char const*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/Parser/VCFParser.cpp.o:VCFParser.cpp:function VCFParser::assign_lines(std::vector<SVS_Node*, std::allocator<SVS_Node*> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/Parser/VCFParser.cpp.o:VCFParser.cpp:function VCFParser::parse_entries(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char const*, unsigned long, unsigned long) const'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_entry(SVS_Node*, int, std::pair<int, int>&): error: undefined reference to 'std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()'
collect2: error: ld returned 1 exit status
make[2]: *** [../bin/survivor_ant-core-0.1.0/survivor_ant] Error 1
make[1]: *** [src/CMakeFiles/survivor_ant.dir/all] Error 2
make: *** [all] Error 2
jungminchoilab commented 6 years ago

I was able to build it with the gcc 4.8.5 instead of gcc 6.3.0.

Thanks!

fritzsedlazeck commented 6 years ago

ah great. sorry I am traveling and therefore the slow response.