Fwd: building cufflinks has compiler error related to boost

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Fwd: building cufflinks has compiler error related to boost

Michael Gooch
The following error is happening when I try to build cufflinks. I am on

Red Hat Enterprise Linux 6.1 and I have installed every boost package
available from the RHN repositories. (I would install directly from
boost but RHN support is usually anal about using stuff from source when
its available from them.)

Cufflinks says it uses boost 1.38, and the package version is 1.41, so
the version should be adequate.

I'm somewhat lost now. This occurred after I noticed some of the
pre-bulit binaries had issues with red-hat's version of the z-lib
library, so I was trying to see if building the package would interface
properly with the included z-lib from redhat, but then I ran into this
boost problem.

the error:

cufflinks.o:(.rodata._ZTIN5boost6detail11thread_dataINS_3_bi6bind_tIvPFvRK16RefSequenceTableP9HitBundleP11BiasLearnereP8_IO_FILESC_SC_ENS2_5list7INS_17reference_wrapperIS5_EENS2_5valueIS8_EENSI_ISA_EENSI_IeEENSI_ISC_EESM_SM_EEEEEE[typeinfo
for boost::detail::thread_data<boost::_bi::bind_t<void, void
(*)(RefSequenceTable const&, HitBundle*, BiasLearner*, long double,
_IO_FILE*, _IO_FILE*, _IO_FILE*),
boost::_bi::list7<boost::reference_wrapper<RefSequenceTable const>,
boost::_bi::value<HitBundle*>, boost::_bi::value<BiasLearner*>,
boost::_bi::value<long double>, boost::_bi::value<_IO_FILE*>,
boost::_bi::value<_IO_FILE*>, boost::_bi::value<_IO_FILE*>  >  >  >]+0x10):
undefined reference to `typeinfo for boost::detail::thread_data_base'
libcufflinks.a(common.o): In function
`boost::thread_specific_ptr<std::basic_string<char,
std::char_traits<char>, std::allocator<char>  >  >::~thread_specific_ptr()':
common.cpp:(.text._ZN5boost19thread_specific_ptrISsED2Ev[_ZN5boost19thread_specific_ptrISsED5Ev]+0x35):
undefined reference to `boost::detail::set_tss_data(void const*,
boost::shared_ptr<boost::detail::tss_cleanup_function>, void*, bool)'
libcufflinks.a(assemble.o): In function
`boost::thread_specific_ptr<std::basic_string<char,
std::char_traits<char>, std::allocator<char>  >  >::get() const':
/usr/include/boost/thread/tss.hpp:82: undefined reference to
`boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:82: undefined reference to
`boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:82: undefined reference to
`boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:82: undefined reference to
`boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:82: undefined reference to
`boost::detail::get_tss_data(void const*)'
libcufflinks.a(assemble.o):/usr/include/boost/thread/tss.hpp:82: more
undefined references to `boost::detail::get_tss_data(void const*)' follow
collect2: ld returned 1 exit status
make[2]: *** [cufflinks] Error 1


M.Gooch

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Re: Fwd: building cufflinks has compiler error related to boost

Burnce
Hi M.Gooch,

You should set the following option when you run your configure script:

--with-boost-thread=/usr/lib64/boost141/libboost_thread-mt.so

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Re: Fwd: building cufflinks has compiler error related to boost

jernest1
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