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Linker error when compiling SQUID #23
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This error is related to the update of bamtools. We update the installation instruction according to the latest bamtools. Please replace the Makefile with the latest version (update the path to boost, glpk accordingly), and reinstall bamtools according to the latest instruction. Let us know if there are further problems. |
Hi, thanks a lot for the last replying. I think i still have a problem with compiling the squid; I followed the latest instruction for installing bamtools and for everything else. And I did update the Makefile accordingly, this time I got a different error message(attached below), I wonder if it's still a problem from the installation of bamtools?
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Please make sure that the correct path of bamtools installation is passed into the Makefile. This folder should be the one in
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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
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