Comments (4)
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
from hicaptools.
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.
from hicaptools.
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
.
from hicaptools.
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
from hicaptools.
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