Question: Error Installing Cufflinks
0
gravatar for lin.barnum
6.6 years ago by
lin.barnum230
lin.barnum230 wrote:

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.

ubuntu cufflinks • 3.3k views
ADD COMMENTlink written 6.6 years ago by lin.barnum230

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!

ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by Geparada1.3k
1
gravatar for Niek De Klein
6.6 years ago by
Niek De Klein2.4k
Netherlands
Niek De Klein2.4k wrote:

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.

ADD COMMENTlink written 6.6 years ago by Niek De Klein2.4k
1
gravatar for Geparada
6.6 years ago by
Geparada1.3k
Cambridge
Geparada1.3k wrote:

You can download the pre-compiled version of Cufflinks,

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

Cheers,

ADD COMMENTlink written 6.6 years ago by Geparada1.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 726 users visited in the last hour