Skip to content

build fails: undefined reference boost::program_options #5

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

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions