fail to make tophat 2.0.7 because of boost

[wjyzidane]

while i am making tophat after correct configuring:

make: Warning: File `Makefile' has modification time 1.5e+03 s in the future
make all-recursive
make[1]: Entering directory `/data1/qwu/tophat-2.0.7'
make[1]: Warning: File `Makefile' has modification time 1.5e+03 s in the future
Making all in src
make[2]: Entering directory `/data1/qwu/tophat-2.0.7/src'
make[2]: Warning: File `Makefile' has modification time 1.5e+03 s in the future
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/data1/qwu/boost/boost/boost_1_52_0/boost/include -I/data1/qwu/samtools/include -I./SeqAn-1.3 -o segment_juncs -L/data1/qwu/boost/boost/boost_1_52_0/boost/lib -L/data1/qwu/samtools/lib segment_juncs.o ../src/libtophat.a -lbam -lz -L/data1/qwu/boost/boost/boost_1_52_0/stage/lib
segment_juncs.o: In function `__static_initialization_and_destruction_0':
/data1/qwu/boost/boost/boost_1_52_0/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
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> > > >&)':
/data1/qwu/tophat-2.0.7/src/segment_juncs.cpp:4949: undefined reference to `boost::thread::join()'
segment_juncs.o: In function `~thread':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:179: undefined reference to `boost::thread::detach()'
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> > > >&)':
/data1/qwu/tophat-2.0.7/src/segment_juncs.cpp:5026: undefined reference to `boost::thread::join()'
segment_juncs.o: In function `~thread':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:179: undefined reference to `boost::thread::detach()'
segment_juncs.o: In function `thread_exception':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
segment_juncs.o: In function `~thread_data':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o: In function `thread_data_base':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/pthread/thread_data.hpp:125: undefined reference to `vtable for boost::detail::thread_data_base'
segment_juncs.o: In function `thread_exception':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
segment_juncs.o: In function `thread_data':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:72: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o: In function `thread<SegmentSearchWorker>':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:223: undefined reference to `boost::thread::start_thread()'
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 `/data1/qwu/tophat-2.0.7/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/data1/qwu/tophat-2.0.7'
make: *** [all] Error 2


i try to add export LD_LIBRARY_PATH=/data1/qwu/bin:$LD_LIBRARY_PATH
to my .bash_profile, but it doesnt work.
desperately ask for help, thanks!

[GenoMax]

Have you installed the boost libraries from: http://www.boost.org/ and made sure they are in your default path?

[wjyzidane]

yes, i have installed the boost in the path /data1/qwu/boost/boost/boost_1_52_0

my configure command is:
./configure --prefix=/data1/qwu/tophat_new --with-boost=/data1/qwu/boost/boost/boost_1_52_0/ --with-bam=/data1/qwu/samtools

it seems that the makefile doesn't match the boost path

[GenoMax]

yes, i have installed the boost in the path /data1/qwu/boost/boost/boost_1_52_0

my configure command is:
./configure --prefix=/data1/qwu/tophat_new --with-boost=/data1/qwu/boost/boost/boost_1_52_0/ --with-bam=/data1/qwu/samtools

it seems that the makefile doesn't match the boost path

The boost library files are likely down a level below the main boost directory. Try exporting the library path as below (make sure the "lib" directory is there):

export LD_LIBRARY_PATH=/data1/qwu/boost/boost/boost_1_52_0/lib:$LD_LIBRARY_PATH

[wjyzidane]

i changed it, but it still doesn't work.
my bash_profile is like this:
# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi

# User specific environment and startup programs

PATH=$PATH:$HOME/bin
#Cufflinks
export LIBS="-L/data1/qwu/boost/boost/boost_1_52_0/stage/lib"
export CPPFLAGS="-I/data1/qwu/boost/boost/boost_1_52_0/"
export LD_LIBRARY_PATH=/data1/qwu/boost/boost/boost_1_52_0/stage/lib:$LD_LIBRARY_PATH


export PATH


data1/qwu/boost/boost/boost_1_52_0/stage/lib is the library that contains many files ending up with .so or .a

another problem is that I find the readout (as show before) contains
-I/data1/qwu/boost/boost/boost_1_52_0/boost/include
-L/data1/qwu/boost/boost/boost_1_52_0/boost/lib

but actually i don't have these two directories in my system.

and the most strange thing is that it can be made successfully if I operate on the node where I LOGIN, but fail if I rsh to another node.(I am not the administer so i install all these softwares under my account)

[alec]

Just a guess, but I think rsh loads your bashrc file rather than bash_profile. If that doesn't work, try printing your environment with rsh and comparing to the local environment.

[GenoMax]

and the most strange thing is that it can be made successfully if I operate on the node where I LOGIN, but fail if I rsh to another node.(I am not the administer so i install all these softwares under my account)

Since it can be made successfully on the login node means you have all the pieces available there.

What kind of a cluster is this? Can you explicitly source your bash profile like "source ~/.bash_profile" after you rsh?

[wjyzidane]

Just a guess, but I think rsh loads your bashrc file rather than bash_profile. If that doesn't work, try printing your environment with rsh and comparing to the local environment.

so you mean i need to add it to my bashrc file?

[alec]

so you mean i need to add it to my bashrc file?

Yes, or set your environment some other way after you rsh (like `source ~/.bash_profile` as GenoMax suggested)

[wjyzidane]

Since it can be made successfully on the login node means you have all the pieces available there.

What kind of a cluster is this? Can you explicitly source your bash profile like "source ~/.bash_profile" after you rsh?

i wrote and sourced it after i rsh.
we have one host for administration and multiple host computers for compute. so i login on the administration host first and rsh to computational node to operate.

[GenoMax]

i wrote and sourced it after i rsh.
we have one host for administration and multiple host computers for compute. so i login on the administration host first and rsh to computational node to operate.

Interesting. So this is not a real cluster with a job queuing system/cluster OS?

Did "source"ing the bash_profile work?

[wjyzidane]

Yes, or set your environment some other way after you rsh (like `source ~/.bash_profile` as GenoMax suggested)

sorry for replying late as i cannot login our server during the new year holiday.
I tried but faild.

[wjyzidane]

Interesting. So this is not a real cluster with a job queuing system/cluster OS?

Did "source"ing the bash_profile work?

sorry for replying late as i cannot login our server during the new year holiday.
it failed and i give up to install this new version of TOPHAT, and try to map with the older version (2.0.6). it worked fine if i remove the -G option(removing the annotation gtf file).

I install the new one previously becausue the mapping faild and reported as below:
[2012-12-27 17:25:26] Joining segment hits
[FAILED]
Error running 'long_spanning_reads':Warning: 74283 malformed closure

[lucapinello]

Solution!

I found a solution.

I installed first BOOST from scarch in my home using the --prefix=/path/to/yourhome option

then I installed tophat using
./configure --with-boost=/path/to/yourhome --prefix=/path/to/yourhome


Hope this help

Luca

http://about.me/lucapinello

[JamieHeather]

then I installed tophat using
./configure --with-boost=/path/to/yourhome --prefix=/path/to/yourhome

Just for future reference, this thread describes the same problem I was having, and this solution got me past the same block.