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Linker error when compiling SQUID #23

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Lyn16 opened this issue Sep 9, 2020 · 3 comments
Open

Linker error when compiling SQUID #23

Lyn16 opened this issue Sep 9, 2020 · 3 comments

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@Lyn16
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Lyn16 commented Sep 9, 2020

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

@Congm12
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Congm12 commented Sep 9, 2020

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.

@Lyn16
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Lyn16 commented Sep 13, 2020

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?
Thanks!

In file included from src/main.cpp:8:0: src/ReadRec.h:21:27: fatal error: api/BamReader.h: No such file or directory #include "api/BamReader.h" ^ compilation terminated. make: *** [src/main.o] Error 1

@Congm12
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Congm12 commented Sep 15, 2020

Please make sure that the correct path of bamtools installation is passed into the Makefile. This folder should be the one in cmake -DCMAKE_INSTALL_PREFIX instead of the git clone folder. You should be able to see the following contents in <bamtools_installation_folder>:

  • bin
  • include
  • lib

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