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Linker error when compiling SQUID

Open Lyn16 opened this issue 3 years ago • 3 comments

Here is the error message when I run make on the Makefile of squid

src/ReadRec.o: In function BuildChimericSBamRecord(std::vector<ReadRec_t, std::allocator<ReadRec_t> >&, 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&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >)': ReadRec.cpp:(.text+0x34f9): undefined reference to BamTools::BamAlignment::BamAlignment(BamTools::BamAlignment const&)' src/SegmentGraph.o: In function SegmentGraph_t::BuildNode_STAR(std::vector<int, std::allocator > const&, std::vector<ReadRec_t, std::allocator<ReadRec_t> >&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >)': SegmentGraph.cpp:(.text+0x2a1f): undefined reference to BamTools::BamAlignment::BamAlignment(BamTools::BamAlignment const&)' src/SegmentGraph.o: In function SegmentGraph_t::BuildNode_BWA(std::vector<int, std::allocator > const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >)': SegmentGraph.cpp:(.text+0x9355): undefined reference to BamTools::BamAlignment::BamAlignment(BamTools::BamAlignment const&)' src/SegmentGraph.o: In function SegmentGraph_t::RawEdgesOther(std::vector<ReadRec_t, std::allocator<ReadRec_t> >&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >)': SegmentGraph.cpp:(.text+0x1225e): undefined reference to BamTools::BamAlignment::BamAlignment(BamTools::BamAlignment const&)' src/SegmentGraph.o: In function SegmentGraph_t::RawEdges(std::vector<ReadRec_t, std::allocator<ReadRec_t> >&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >)': SegmentGraph.cpp:(.text+0x13b99): undefined reference to BamTools::BamAlignment::BamAlignment(BamTools::BamAlignment const&)' collect2: error: ld returned 1 exit status make: *** [bin/squid] Error 1

Lyn16 avatar Sep 09 '20 07:09 Lyn16