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Undefined References From Boost When Installing Bam-Readcount

I am trying to install bam-readcount in a centralized location for our cluster, which means downloading "source" and building in a non-standard location. I built cmake 2.18.12.2 and boost 1.55.0. Then following the instructions did: cmake <path/to/source>, make deps and make.

I had to dig down and find the actual c++ statement (actually gcc), and add in the paths to the boost libraries, include, etc. and the build is down to what appears to be 4 errors (one very long). I'm not sure if my version of boost has changed some things since 1.40, or if I'm just missing some libraries. I'm getting:

  /scratch/rists/hpcapps/x86_64/boost/1.55.0/lib/libboost_program_options.a(options_description.o):
  In function
  boost::program_options::options_description::print(std::basic_ostream<char,
std::char_traits<char> >&) const':
options_description.cpp:(.text+0x2a8b): undefined reference to
std::basic_ostream<char, std::char_traits<char> >&
  std::__ostream_insert<char, std::char_traits<char>

      (std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' ...

  /scratch/rists/hpcapps/x86_64/boost/1.55.0/lib/libboost_program_options.a(options_description.o):options_description.cpp:(.text+0x2fc4):
  more undefined references to std::basic_ostream<char,
  std::char_traits<char> >& std::__ostream_insert<char,
  std::char_traits<char> >(std::basic_ostream<char,
  std::char_traits<char> >&, char const*, long)' follow

  /scratch/rists/hpcapps/x86_64/boost/1.55.0/lib/libboost_program_options.so:
  undefined reference to std::basic_ostream<char,
  std::char_traits<char> >& std::__ostream_insert<char,
  std::char_traits<char> >(std::basic_ostream<char,
  std::char_traits<char> >&, char const*, long)@GLIBCXX_3.4.9'

  /scratch/rists/hpcapps/x86_64/boost/1.55.0/lib/libboost_program_options.so:
  undefined reference to std::ctype<char>::_M_widen_init()
  const@GLIBCXX_3.4.11'

I am open to suggestions here -- I'm hoping I can just add some additional libraries to the c++ statement.

Regards,
Sally Boyd

bam-readcount
• 6,909 views • link
updated by Ram Ram • written by sally.boyd • sally.boyd

Are you compiling with gcc rather than g++? That's a frequent cause of things like undefined reference to std::basic_ostream. You might also just add -lstdc++, which ends up doing much of the same thing, but it's better to directly call g++.

• 144 views • link
written by Devon Ryan Devon Ryan

It was using /usr/bin/c++. Changed it to g++ (no path) and that worked! Thanks so much!

• 0 views • link
written by sally.boyd • sally.boyd

I am having the exact problem! Could you please explain in detail what you did? How did you change it to g++?

• 0 views • link
written by tayebwajb tayebwajb

@dpryan79 I am having the same problem. I have pasted the error messages I am getting here. Please look at them and let me know how I should install bam-readcount successfully on my system. Thanks!

• 0 views • link
updated by Ram Ram • written by tayebwajb tayebwajb

Try just setting the CXX environment variable to g++. That might solve the problem. Make sure to wipe the build tree first (i.e. start with nothing compiled).

• 0 views • link
written by Devon Ryan Devon Ryan

That didn't work for me. What finally worked was disabling auto-linking by adding to CMakeLists.txt

add_definitions(-DBOOST_ALL_NO_LIB)

and linking to the boost program options library by adding the line

link_libraries(${Boost_PROGRAM_OPTIONS_LIBRARY})
• 0 views • link
updated by Ram Ram • written by tayebwajb tayebwajb

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