Fails to build with `undefined reference to `BamTools::BamReader::Open(…)`

[sahlenlab]

Fails to build with `undefined reference to `BamTools::BamReader::Open(…)`

[paulmenzel]

The actual command by CMake looks like below (make VERBOSE=1).

/usr/bin/cmake -E cmake_link_script CMakeFiles/HiCapTools.dir/link.txt --verbose=1
/usr/bin/c++    -rdynamic CMakeFiles/HiCapTools.dir/src/BackgroundInteractionFrequency.cpp.o CMakeFiles/HiCapTools.dir/src/CallHiCUP.cpp.o CMakeFiles/HiCapTools.dir/src/DesignProbes.cpp.o CMakeFiles/HiCapTools.dir/src/Features.cpp.o CMakeFiles/HiCapTools.dir/src/Find_Interactions.cpp.o CMakeFiles/HiCapTools.dir/src/NegativeProbeDesign.cpp.o CMakeFiles/HiCapTools.dir/src/ProbeDesignMain.cpp.o CMakeFiles/HiCapTools.dir/src/ProbeFeatureClass.cpp.o CMakeFiles/HiCapTools.dir/src/Probes.cpp.o CMakeFiles/HiCapTools.dir/src/ProcessPairs.cpp.o CMakeFiles/HiCapTools.dir/src/ProxDetectMain.cpp.o CMakeFiles/HiCapTools.dir/src/Proximities.cpp.o CMakeFiles/HiCapTools.dir/src/RESitesCount.cpp.o CMakeFiles/HiCapTools.dir/src/RepeatOverlaps.cpp.o CMakeFiles/HiCapTools.dir/src/bioioMod.cpp.o CMakeFiles/HiCapTools.dir/src/main.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/alglibinternal.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/alglibmisc.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/ap.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/dataanalysis.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/diffequations.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/fasttransforms.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/integration.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/interpolation.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/linalg.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/optimization.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/solvers.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/specialfunctions.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/statistics.cpp.o  -o ../bin/HiCapTools ../bamtools/libbamtools.so.2.4.1 -lz

[paulmenzel]

I wonder, why there is add_library(libbamtools STATIC IMPORTED) in CMakeLists.txt instead of SHARED. The library seems to be a shared library.

$ file bamtools/libbamtools.so.2.4.1
bamtools/libbamtools.so.2.4.1: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, not stripped

But changing that line, doesn’t make any difference.

[paulmenzel]

By the way, the included bamtools library seems to contain the references, the linker does not find.

$ nm bamtools/libbamtools.so.2.4.1 | c++filt | grep BamReader::Open
0000000000023180 T BamTools::BamReader::Open(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
0000000000023190 T BamTools::BamReader::OpenIndex(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)

In our system, we have bamtools 2.5.1 and the static library. I was able to link everything with the command below.

/usr/bin/c++    -rdynamic CMakeFiles/HiCapTools.dir/src/BackgroundInteractionFrequency.cpp.o CMakeFiles/HiCapTools.dir/src/CallHiCUP.cpp.o CMakeFiles/HiCapTools.dir/src/DesignProbes.cpp.o CMakeFiles/HiCapTools.dir/src/Features.cpp.o CMakeFiles/HiCapTools.dir/src/Find_Interactions.cpp.o CMakeFiles/HiCapTools.dir/src/NegativeProbeDesign.cpp.o CMakeFiles/HiCapTools.dir/src/ProbeDesignMain.cpp.o CMakeFiles/HiCapTools.dir/src/ProbeFeatureClass.cpp.o CMakeFiles/HiCapTools.dir/src/Probes.cpp.o CMakeFiles/HiCapTools.dir/src/ProcessPairs.cpp.o CMakeFiles/HiCapTools.dir/src/ProxDetectMain.cpp.o CMakeFiles/HiCapTools.dir/src/Proximities.cpp.o CMakeFiles/HiCapTools.dir/src/RESitesCount.cpp.o CMakeFiles/HiCapTools.dir/src/RepeatOverlaps.cpp.o CMakeFiles/HiCapTools.dir/src/bioioMod.cpp.o CMakeFiles/HiCapTools.dir/src/main.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/alglibinternal.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/alglibmisc.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/ap.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/dataanalysis.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/diffequations.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/fasttransforms.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/integration.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/interpolation.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/linalg.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/optimization.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/solvers.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/specialfunctions.cpp.o CMakeFiles/HiCapTools.dir/ExterAlg/statistics.cpp.o  -o ../bin/HiCapTools -L /package/sequencer/bamtools/2.5.1/lib64/ -lbamtools -lz

So, instead of ../bamtools/libbamtools.so.2.4.1 I used -L /package/sequencer/bamtools/2.5.1/lib64/ -lbamtools.

[jwakely]

By the way, the included bamtools library seems to contain the references, the linker does not find.

No it doesn't, that's a different symbol. Read it more carefully.

You need to read https://gcc.gnu.org/onlinedocs/libstdc++/manual/using_dual_abi.html