SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat 2.0.6 installation error sudheer.svss Bioinformatics 0 02-18-2013 09:50 PM
tophat installation error bob-loblaw Bioinformatics 2 12-17-2012 12:59 PM
Installation error of tophat-2.0.0 fortunezhang General 0 04-18-2012 05:02 AM
TopHat installation vinay052003 Bioinformatics 5 11-22-2011 12:54 PM
solid2srf installation error? zxl124 SOLiD 0 01-27-2011 07:36 AM

Reply
 
Thread Tools
Old 05-23-2013, 08:00 PM   #1
canhu
Member
 
Location: beijing,china

Join Date: May 2013
Posts: 11
Question Tophat 2.0.8b installation error

I install tophat-2.0.8b to rerun the mapping. but when i make it, the error appears like this.
make[1]: Entering directory `/media/chenzz/software/tophat-2.0.8b'
Making all in src
make[2]: Entering directory `/media/chenzz/software/tophat-2.0.8b/src'
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/usr/include -I/usr/local/include -I./SeqAn-1.3 -o segment_juncs -L/usr/lib -L/usr/local/lib segment_juncs.o ../src/libtophat.a -lbam -lz
segment_juncs.o: In function `__static_initialization_and_destruction_0':
/usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
/usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
/usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
segment_juncs.o: In function `boost::thread::get_id() const':
/usr/local/include/boost/thread/detail/thread.hpp:725: undefined reference to `boost::thread::native_handle()'
segment_juncs.o: In function `boost::thread::join()':
/usr/local/include/boost/thread/detail/thread.hpp:751: undefined reference to `boost::thread::join_noexcept()'
segment_juncs.o: In function `~thread':
/usr/local/include/boost/thread/detail/thread.hpp:255: undefined reference to `boost::thread::detach()'
segment_juncs.o: In function `boost::thread::start_thread()':
/usr/local/include/boost/thread/detail/thread.hpp:180: undefined reference to `boost::thread::start_thread_noexcept()'
/usr/local/include/boost/thread/detail/thread.hpp:180: undefined reference to `boost::thread::start_thread_noexcept()'
segment_juncs.o: In function `boost::thread::get_id() const':
/usr/local/include/boost/thread/detail/thread.hpp:725: undefined reference to `boost::thread::native_handle()'
segment_juncs.o: In function `boost::thread::join()':
/usr/local/include/boost/thread/detail/thread.hpp:751: undefined reference to `boost::thread::join_noexcept()'
segment_juncs.o: In function `~thread':
/usr/local/include/boost/thread/detail/thread.hpp:255: undefined reference to `boost::thread::detach()'
segment_juncs.o: In function `thread_exception':
/usr/local/include/boost/thread/exceptions.hpp:51: undefined reference to `boost::system::system_category()'
segment_juncs.o: In function `~thread_data':
/usr/local/include/boost/thread/detail/thread.hpp:93: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/usr/local/include/boost/thread/detail/thread.hpp:93: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/usr/local/include/boost/thread/detail/thread.hpp:93: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/usr/local/include/boost/thread/detail/thread.hpp:93: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o: In function `thread_data_base':
/usr/local/include/boost/thread/pthread/thread_data.hpp:142: undefined reference to `vtable for boost::detail::thread_data_base'
segment_juncs.o: In function `thread_data':
/usr/local/include/boost/thread/detail/thread.hpp:111: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o.rodata._ZTIN5boost6detail11thread_dataI19SegmentSearchWorkerEE[typeinfo for boost::detail::thread_data<SegmentSearchWorker>]+0x10): undefined reference to `typeinfo for boost::detail::thread_data_base'
collect2: ld returned 1 exit status
make[2]: *** [segment_juncs] Error 1
make[2]: Leaving directory `/media/chenzz/software/tophat-2.0.8b/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/media/chenzz/software/tophat-2.0.8b'
make: *** [all] Error 2
__________________
canhu is offline   Reply With Quote
Old 05-24-2013, 01:22 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,033
Default

You either did not install the "Boost" libraries or if you did, then they did not install correctly.

Details on the boost installation are included on the tophat getting started page: http://tophat.cbcb.umd.edu/tutorial.shtml
GenoMax is offline   Reply With Quote
Old 05-24-2013, 02:09 AM   #3
canhu
Member
 
Location: beijing,china

Join Date: May 2013
Posts: 11
Smile

Quote:
Originally Posted by GenoMax View Post
You either did not install the "Boost" libraries or if you did, then they did not install correctly.

Details on the boost installation are included on the tophat getting started page: http://tophat.cbcb.umd.edu/tutorial.shtml
Thanks for your reply, it works well until i re-install boost
__________________
canhu is offline   Reply With Quote
Reply

Tags
install error, tophat 2.0.8b

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:17 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO