ngs-bits: Compile Error - undefined references to BamTools functions

Hello,

First, I am using a version of qt greater than 5.5. Here is the output of qmake -v:

QMake version 3.0 Using Qt version 5.6.1 in /usr/lib64

I am getting the following error during the process of running make build_tools_release:

g++ -Wl,-rpath,‘$ORIGIN’ -Wl,-O1 -o …/…/bin/SamplesNGSD main.o -Lngs-bits/src/…/bin -lcppCORE -lcppXML -lcppNGS -Lngs-bits/src/…/bamtools/lib/ -lbamtools -lz -Lngs-bits/src/SamplesNGSD/…/bin -lcppNGSD -lQt5Sql -lQt5Core -lpthread ngs-bits/src/…/bin/libcppNGS.so: undefined reference to `BamTools::BamReader::GetReferenceID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const’ ngs-bits/src/…/bin/libcppNGS.so: undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)’ ngs-bits/src/…/bin/libcppNGS.so: undefined reference to `BamTools::BamAlignment::IsValidSize(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&) const’ ngs-bits/src/…/bin/libcppNGS.so: undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char*&, unsigned int const&, unsigned int&) const’ ngs-bits/src/…/bin/libcppNGS.so: undefined reference to `BamTools::BamReader::OpenIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)’ ngs-bits/src/…/bin/libcppNGS.so: undefined reference to `_ZNK8BamTools9BamReader14GetErrorStringB5cxx11Ev’ ngs-bits/src/…/bin/libcppNGS.so: undefined reference to `_ZNK8BamTools9BamReader11GetFilenameB5cxx11Ev’ collect2: error: ld returned 1 exit status make[2]: *** […/…/bin/SamplesNGSD] Error 1 make[2]: Leaving directory `ngs-bits/build-tools-Linux-Release/SamplesNGSD’ make[1]: *** [sub-SamplesNGSD-make_first] Error 2 make[1]: Leaving directory `ngs-bits/build-tools-Linux-Release’ make: *** [build_tools_release] Error 2

Any idea what the problem could be?

About this issue

  • Original URL
  • State: closed
  • Created 7 years ago
  • Comments: 15 (7 by maintainers)

Most upvoted comments

Hmm, actually I have just tried with a different gcc version (4.8.4) and it looks like it finished properly. You may still want to test it for compatibility with the newer compiler version, but I think I’m set.