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build fails: undefined reference boost::program_options #5

@ptrebert

Description

@ptrebert

Hi,
following build env:
Debian 9 "Stretch" running Kernel 4.9.91
ldd --version: (Debian GLIBC 2.24-11+deb9u3) 2.24
Followed setup/build instruction as given in git readme

Situation 1:
Existing Conda environment with htslib=1.9 as dependency for other tools; additionally, installed boost=1.67.0 and cmake=3.12.2 into environment to build Mosaicatcher. Minor issue/suggestion for doc update: needed to run cmake -DBOOST_INCLUDEDIR=/PATH/TO/conda/envs/ENVNAME/include ../src/ for a successful configure. Subsequent make failed with something like /build/htslib/lib/libhts.so: undefined reference "memcpy@GLIBC_2.14" - I realized that despite the existing htslib in the environment, the setup routine downloads htslib nevertheless. No idea about the internals, of course, but I suspected this to be the source of the problem; leads to...

Situation 2:
New Conda environment containing boost=1.67.0, cmake=3.12.2 and make=4.2.1, nothing else. Cmake as above succeeds, subsequent make now seems to get past the htslib issue, but fails with this:

[ 90%] Linking CXX executable mosaic
[...tons of output...]
CMakeFiles/mosaic.dir/main.cpp.o:(.data.rel.ro._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30):
undefined reference to
`boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'

collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/mosaic.dir/build.make:90: mosaic] Error 1
make[1]: *** [CMakeFiles/Makefile2:73: CMakeFiles/mosaic.dir/all] Error 2
make: *** [Makefile:84: all] Error 2

Any advice?

Best,
Peter

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