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Cufflinks building problems

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  • Cufflinks building problems

    I'm trying to install Cufflinks. After "make", several errors were found.

    make  all-recursive
    make[1]: Entering directory `/usr/local/src/cufflinks-1.0.3'
    Making all in src
    make[2]: Entering directory `/usr/local/src/cufflinks-1.0.3/src'
    g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3  -DNDEBUG  -pthread -I/usr/local/boost/include -I/usr/local/samtools-0.1.17/include   -o cufflinks -L/usr/local/boost/lib -L/usr/local/samtools-0.1.17/lib  cufflinks.o libcufflinks.a libgc.a -lboost_thread -lbam  -lz 
    /usr/local/boost/lib/libboost_thread.a(thread.o): In function `_ZN5boost2CV23simple_exception_policyItLt1ELt31ENS_9gregorian16bad_day_of_monthEE8on_errorEttNS0_14violation_enumE.clone.79':
    thread.cpp:(.text+0x5d3): undefined reference to `__sync_fetch_and_add_4'
    /usr/local/boost/lib/libboost_thread.a(thread.o): In function `_ZN5boost2CV23simple_exception_policyItLt1400ELt10000ENS_9gregorian8bad_yearEE8on_errorEttNS0_14violation_enumE.clone.96':
    thread.cpp:(.text+0x107b): undefined reference to `__sync_fetch_and_add_4'
    /usr/local/boost/lib/libboost_thread.a(thread.o): In function `_ZN5boost2CV23simple_exception_policyItLt1ELt12ENS_9gregorian9bad_monthEE8on_errorEttNS0_14violation_enumE.clone.97':
    thread.cpp:(.text+0x13df): undefined reference to `__sync_fetch_and_add_4'
    /usr/local/boost/lib/libboost_thread.a(thread.o): In function `_ZN5boost9date_time14microsec_clockINS_10posix_time5ptimeEE11create_timeEPFP2tmPKlS6_E.clone.111':
    thread.cpp:(.text+0x1e3d): undefined reference to `__sync_fetch_and_add_4'
    collect2: ld returned 1 exit status
    make[2]: *** [cufflinks] Error 1
    make[2]:Leaving directory `/usr/local/src/cufflinks-1.0.3/src'
    make[1]: *** [all-recursive] Error 1
    make[1]:Leaving directory `/usr/local/src/cufflinks-1.0.3'
    make: *** [all] Error 2
    What should I do? Wish help! Thanks very much!
    Last edited by aquleaf; 07-29-2011, 07:03 AM.

  • #2
    Help! Does anyone know how to solve the problem?

    Thanks so much in advance.


    • #3
      It looks like an issue with the boost install. What is the configure command you are using before initiating the make command?

      Make sure you have a PATH directory folder with PATHdirectory/include/bam and PATHdirectory/lib were the boost files are in include and lib and the samtools bam file is in the bam folder.

      Check my intro thread if you need detailed instructions


      • #4
        Instruction has a typo

        I found a type in the manual of compiling cufflinks.
        When building the Boost library, it says

        bjam --prefix=<YOUR_BOOST_INSTALL_DIRECTORY> --toolset=gcc architecture=x86 address_model=64 link=static runtime-link=static stage install

        However, the correct command is here:

        bjam --prefix=<YOUR_BOOST_INSTALL_DIRECTORY> --toolset=gcc architecture=x86 address-model=64 link=static runtime-link=static stage install

        "address_model" is wrong, correctly, "address-model".