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Old 12-17-2012, 08:50 AM   #1
bob-loblaw
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Default tophat installation error

Hi All,

I've been having some trouble installing tophat and I was hoping you could help, from everything is fine up until I run make, then what's below gets spit out at me). From what I see it seems to be that the boost libraries are not installed properly, I did some googling and went back and reinstalled them specifically stating to include the thread library but still no dice. Can anyone help? Thanks in advance

make all-recursive
make[1]: Entering directory `/home/tuxedo/tophat-2.0.6'
Making all in src
make[2]: Entering directory `/home/tuxedo/tophat-2.0.6/src'
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I../boost_1_52_0/boost.1.52.0//include -I../samtools_0.1.18//include -I./SeqAn-1.3 -o segment_juncs -L../boost_1_52_0/boost.1.52.0//lib -L../samtools_0.1.18//lib segment_juncs.o ../src/libtophat.a -lbam -lz
segment_juncs.o: In function `driver(std::basic_istream<char, std::char_traits<char> >&, _IO_FILE*, _IO_FILE*, _IO_FILE*, _IO_FILE*, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
/home/tuxedo/tophat-2.0.6/src/segment_juncs.cpp:4949: undefined reference to `boost::thread::join()'
/home/tuxedo/tophat-2.0.6/src/segment_juncs.cpp:4950: undefined reference to `boost::thread::~thread()'
/home/tophat-2.0.6/src/segment_juncs.cpp:5026: undefined reference to `boost::thread::join()'
/home/tuxedo/tophat-2.0.6/src/segment_juncs.cpp:5027: undefined reference to `boost::thread::~thread()'
/home/tuxedo/tophat-2.0.6/src/segment_juncs.cpp:4942: undefined reference to `boost::thread::thread(boost::function0<void, std::allocator<boost::function_base> > const&)'
/home/tuxedo/tophat-2.0.6/src/segment_juncs.cpp:5019: undefined reference to `boost::thread::thread(boost::function0<void, std::allocator<boost::function_base> > const&)'
collect2: ld returned 1 exit status
make[2]: *** [segment_juncs] Error 1
make[2]: Leaving directory `/home/tuxedo/tophat-2.0.6/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/tuxedo/tophat-2.0.6'
make: *** [all] Error 2
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Old 12-17-2012, 09:45 AM   #2
aafc
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It looks likes you've "made a huge mistake" . . .




I think I had this exact problem when I was first trying to install cufflinks. Try this, in order:

1) Make sure LD_LIBRARY_PATH is set to the location of your boost dynamic library files (the .so files)

2) If step 1 fails, install boost version 1.47 and do the step above
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Old 12-17-2012, 12:59 PM   #3
bob-loblaw
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Quote:
Originally Posted by aafc View Post
It looks likes you've "made a huge mistake" . . .


I think I had this exact problem when I was first trying to install cufflinks. Try this, in order:

1) Make sure LD_LIBRARY_PATH is set to the location of your boost dynamic library files (the .so files)

2) If step 1 fails, install boost version 1.47 and do the step above
haha, thanks, I'll try that!
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