Error Installing Cufflinks

Question

[lin.barnum]

I am trying to install Cufflinks on Ubuntu 11.10 and and running into the following error which I cannot figure out. What am I missing here?

make  all-recursive
make[1]: Entering directory `/home/software/cufflinks-1.3.0'
Making all in src
make[2]: Entering directory `/home/software/cufflinks-1.3.0/src'
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I/usr/include -I/usr/local/include   -o cufflinks -L/usr/lib -L/usr/local/lib  cufflinks.o libcufflinks.a libgc.a  -lbam  -lz 
cufflinks.o: In function `sleep<boost::date_time::subsecond_duration<boost::posix_time::time_duration, 1000l> >':
/usr/include/boost/thread/pthread/thread_data.hpp:138: undefined reference to `boost::this_thread::sleep(boost::posix_time::ptime const&)'
cufflinks.o: In function `thread_data_base':
/usr/include/boost/thread/pthread/thread_data.hpp:67: undefined reference to `vtable for boost::detail::thread_data_base'
cufflinks.o: In function `thread<void (*)(const RefSequenceTable&, HitBundle*, BiasLearner*, long double, _IO_FILE*, _IO_FILE*, _IO_FILE*, _IO_FILE*), boost::reference_wrapper<const RefSequenceTable>, HitBundle*, BiasLearner*, long double, _IO_FILE*, _IO_FILE*, _IO_FILE*, _IO_FILE*>':
/usr/include/boost/thread/detail/thread.hpp:300: undefined reference to `boost::thread::start_thread()'
cufflinks.o: In function `assemble_hits(BundleFactory&, BiasLearner*)':
/home/software/cufflinks-1.3.0/src/cufflinks.cpp:1465: undefined reference to `boost::thread::~thread()'
cufflinks.o: In function `sleep<boost::date_time::subsecond_duration<boost::posix_time::time_duration, 1000l> >':
/usr/include/boost/thread/pthread/thread_data.hpp:138: undefined reference to `boost::this_thread::sleep(boost::posix_time::ptime const&)'
cufflinks.o: In function `assemble_hits(BundleFactory&, BiasLearner*)':
/home/software/cufflinks-1.3.0/src/cufflinks.cpp:1465: undefined reference to `boost::thread::~thread()'
cufflinks.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:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
cufflinks.o:/usr/include/boost/thread/tss.hpp:84: more undefined references to `boost::detail::get_tss_data(void const*)' follow
cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::reset(std::basic_string<char, std::char_traits<char>, std::allocator<char> >*)':
/usr/include/boost/thread/tss.hpp:105: undefined reference to `boost::detail::set_tss_data(void const*, boost::shared_ptr<boost::detail::tss_cleanup_function>, void*, bool)'
cufflinks.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:84: undefined reference to `boost::detail::get_tss_data(void const*)'
cufflinks.o: In function `at_thread_exit<void (*)()>':
/usr/include/boost/thread/detail/thread.hpp:521: undefined reference to `boost::detail::add_thread_exit_function(boost::detail::thread_exit_function_base*)'
cufflinks.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:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
cufflinks.o: In function `~thread_data':
/usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
cufflinks.o:(.rodata._ZTIN5boost6detail11thread_dataINS_3_bi6bind_tIvPFvRK16RefSequenceTableP9HitBundleP11BiasLearnereP8_IO_FILESC_SC_SC_ENS2_5list8INS_17reference_wrapperIS5_EENS2_5valueIS8_EENSI_ISA_EENSI_IeEENSI_ISC_EESM_SM_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*, _IO_FILE*), boost::_bi::list8<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*>, boost::_bi::value<_IO_FILE*> > > >]+0x10): undefined reference to `typeinfo for boost::detail::thread_data_base'
libcufflinks.a(common.o): In function `~thread_specific_ptr':
/usr/include/boost/thread/tss.hpp:79: 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> > >::operator->() const':
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
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:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
libcufflinks.a(assemble.o):/usr/include/boost/thread/tss.hpp:84: more undefined references to `boost::detail::get_tss_data(void const*)' follow
collect2: ld returned 1 exit status
make[2]: *** [cufflinks] Error 1
make[2]: Leaving directory `/home/software/cufflinks-1.3.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/software/cufflinks-1.3.0'
make: *** [all] Error 2

Apologies for the long post.

[Geparada]

Did you tried to run the make command as a root? ---> sudo make all-recursive

Do you have the gcc compiler installed? I'll try to install Cufflinks later, and I'll tell you if I have the same trouble... good luck!

Answer 1

[Niek De Klein]

Try installing libboost-thread package for ubuntu and/or setting the following option

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

when you run your configure script.

Answer 2

[Geparada]

You can download the pre-compiled version of Cufflinks,

I have the same version of Ubuntu and I had no problem!

Cheers,