filterBam compiling error
Posted: Thu Nov 19, 2015 2:51 pm
Originally posted by Willow in the old forum on 01.07.2015 - 11:04
After install bamtools successfully,I change directory to filterBam, and type make,but it returns:
(cd src;make)
make[1]: Entering directory `/home/jjian/augustus-3.1/auxprogs/filterBam/src'
g++ -I/home/jjian/bamtools-master/include -Iheaders -I/home/jjian/bamtools-master/src/toolkit -std=c++0x filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam /home/jjian/bamtools-master/lib/libbamtools.a -lz
filterBam.o: In function `std::vector<std::string, std::allocator<std::string> >::_M_range_check(unsigned long) const':
filterBam.cc:(.text._ZNKSt6vectorISsSaISsEE14_M_range_checkEm[_ZNKSt6vectorISsSaISsEE14_M_range_checkEm]+0x48): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
filterBam.o: In function `std::vector<PairednessCoverage, std::allocator<PairednessCoverage> >::_M_range_check(unsigned long) const':
filterBam.cc:(.text._ZNKSt6vectorI18PairednessCoverageSaIS0_EE14_M_range_checkEm[_ZNKSt6vectorI18PairednessCoverageSaIS0_EE14_M_range_checkEm]+0x48): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
filterBam.o: In function `std::vector<int, std::allocator<int> >::_M_range_check(unsigned long) const':
filterBam.cc:(.text._ZNKSt6vectorIiSaIiEE14_M_range_checkEm[_ZNKSt6vectorIiSaIiEE14_M_range_checkEm]+0x48): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
filterBam.o: In function `std::vector<BamTools::BamAlignment, std::allocator<BamTools::BamAlignment> >::_M_range_check(unsigned long) const':
filterBam.cc:(.text._ZNKSt6vectorIN8BamTools12BamAlignmentESaIS1_EE14_M_range_checkEm[_ZNKSt6vectorIN8BamTools12BamAlignmentESaIS1_EE14_M_range_checkEm]+0x48): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
filterBam.o: In function `std::vector<MatePairs, std::allocator<MatePairs> >::_M_range_check(unsigned long) const':
filterBam.cc:(.text._ZNKSt6vectorI9MatePairsSaIS0_EE14_M_range_checkEm[_ZNKSt6vectorI9MatePairsSaIS0_EE14_M_range_checkEm]+0x48): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
getReferenceName.o:getReferenceName.cc:(.text._ZNKSt6vectorIN8BamTools7RefDataESaIS1_EE14_M_range_checkEm[_ZNKSt6vectorIN8BamTools7RefDataESaIS1_EE14_M_range_checkEm]+0x48): more undefined references to `std::__throw_out_of_range_fmt(char const*, ...)' follow
collect2: error: ld returned 1 exit status
make[1]: *** [filterBam] Error 1
make[1]: Leaving directory `/home/jjian/augustus-3.1/auxprogs/filterBam/src'
make: *** [all] Error 2
what is the solution?
After install bamtools successfully,I change directory to filterBam, and type make,but it returns:
(cd src;make)
make[1]: Entering directory `/home/jjian/augustus-3.1/auxprogs/filterBam/src'
g++ -I/home/jjian/bamtools-master/include -Iheaders -I/home/jjian/bamtools-master/src/toolkit -std=c++0x filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam /home/jjian/bamtools-master/lib/libbamtools.a -lz
filterBam.o: In function `std::vector<std::string, std::allocator<std::string> >::_M_range_check(unsigned long) const':
filterBam.cc:(.text._ZNKSt6vectorISsSaISsEE14_M_range_checkEm[_ZNKSt6vectorISsSaISsEE14_M_range_checkEm]+0x48): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
filterBam.o: In function `std::vector<PairednessCoverage, std::allocator<PairednessCoverage> >::_M_range_check(unsigned long) const':
filterBam.cc:(.text._ZNKSt6vectorI18PairednessCoverageSaIS0_EE14_M_range_checkEm[_ZNKSt6vectorI18PairednessCoverageSaIS0_EE14_M_range_checkEm]+0x48): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
filterBam.o: In function `std::vector<int, std::allocator<int> >::_M_range_check(unsigned long) const':
filterBam.cc:(.text._ZNKSt6vectorIiSaIiEE14_M_range_checkEm[_ZNKSt6vectorIiSaIiEE14_M_range_checkEm]+0x48): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
filterBam.o: In function `std::vector<BamTools::BamAlignment, std::allocator<BamTools::BamAlignment> >::_M_range_check(unsigned long) const':
filterBam.cc:(.text._ZNKSt6vectorIN8BamTools12BamAlignmentESaIS1_EE14_M_range_checkEm[_ZNKSt6vectorIN8BamTools12BamAlignmentESaIS1_EE14_M_range_checkEm]+0x48): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
filterBam.o: In function `std::vector<MatePairs, std::allocator<MatePairs> >::_M_range_check(unsigned long) const':
filterBam.cc:(.text._ZNKSt6vectorI9MatePairsSaIS0_EE14_M_range_checkEm[_ZNKSt6vectorI9MatePairsSaIS0_EE14_M_range_checkEm]+0x48): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
getReferenceName.o:getReferenceName.cc:(.text._ZNKSt6vectorIN8BamTools7RefDataESaIS1_EE14_M_range_checkEm[_ZNKSt6vectorIN8BamTools7RefDataESaIS1_EE14_M_range_checkEm]+0x48): more undefined references to `std::__throw_out_of_range_fmt(char const*, ...)' follow
collect2: error: ld returned 1 exit status
make[1]: *** [filterBam] Error 1
make[1]: Leaving directory `/home/jjian/augustus-3.1/auxprogs/filterBam/src'
make: *** [all] Error 2
what is the solution?