Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • fail to make tophat 2.0.7 because of boost

    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!

  • #2
    Have you installed the boost libraries from: http://www.boost.org/ and made sure they are in your default path?

    Comment


    • #3
      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

      Comment


      • #4
        Originally posted by wjyzidane View Post
        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

        Comment


        • #5
          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)

          Comment


          • #6
            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.

            Comment


            • #7
              Originally posted by wjyzidane View Post

              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?

              Comment


              • #8
                Originally posted by alec View Post
                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?

                Comment


                • #9
                  Originally posted by wjyzidane View Post
                  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)

                  Comment


                  • #10
                    Originally posted by GenoMax View Post
                    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.

                    Comment


                    • #11
                      Originally posted by wjyzidane View Post
                      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?

                      Comment


                      • #12
                        Originally posted by alec View Post
                        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.

                        Comment


                        • #13
                          Originally posted by GenoMax View Post
                          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

                          Comment


                          • #14
                            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

                            Comment


                            • #15
                              Originally posted by lucapinello View Post

                              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.

                              Comment

                              Latest Articles

                              Collapse

                              • seqadmin
                                Strategies for Sequencing Challenging Samples
                                by seqadmin


                                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                                03-22-2024, 06:39 AM
                              • seqadmin
                                Techniques and Challenges in Conservation Genomics
                                by seqadmin



                                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                                Avian Conservation
                                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                                03-08-2024, 10:41 AM

                              ad_right_rmr

                              Collapse

                              News

                              Collapse

                              Topics Statistics Last Post
                              Started by seqadmin, Yesterday, 06:37 PM
                              0 responses
                              7 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, Yesterday, 06:07 PM
                              0 responses
                              7 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 03-22-2024, 10:03 AM
                              0 responses
                              49 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 03-21-2024, 07:32 AM
                              0 responses
                              66 views
                              0 likes
                              Last Post seqadmin  
                              Working...
                              X