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  • problem installing cufflinks

    there was no problem configuring Cufflinks v2.02 but when i make it i get an error like this

    make  all-recursive
    make[1]: Entering directory `/media/sda8/bharat/genomes/cufflinks-2.0.2'
    Making all in src
    make[2]: Entering directory `/media/sda8/bharat/genomes/cufflinks-2.0.2/src'
    if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I usr/local/include -I/usr/local/include  -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \
            then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
    if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I usr/local/include -I/usr/local/include  -MT differential.o -MD -MP -MF ".deps/differential.Tpo" -c -o differential.o differential.cpp; \
            then mv -f ".deps/differential.Tpo" ".deps/differential.Po"; else rm -f ".deps/differential.Tpo"; exit 1; fi
    In file included from hits.h:21:0,
                     from abundances.h:23,
                     from differential.cpp:17:
    common.h:25:25: error: 'boost::BOOST_FOREACH' has not been declared
    In file included from differential.h:29:0,
                     from differential.cpp:18:
    replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)':
    replicates.h:152:50: warning: unused variable 's2' [-Wunused-variable]
    In file included from differential.cpp:18:0:
    differential.h: In constructor 'FPKMContext::FPKMContext(double, double, double,                                                                                uble, AbundanceStatus, const StatusPerReplicateTable&)':
    differential.h:142:21: warning: 'FPKMContext::status' will be initialized after
    differential.h:139:29: warning:   'StatusPerReplicateTable FPKMContext::status_p
    differential.h:131:2: warning:   when initialized here [-Wreorder]
    differential.cpp: In member function 'void TestLauncher::perform_testing(std::ve
    differential.cpp:212:31: warning: unused variable 's2' [-Wunused-variable]
    differential.cpp: In member function 'void TestLauncher::record_tracking_data(st
    differential.cpp:240:31: warning: unused variable 's2' [-Wunused-variable]
    differential.cpp: In function 'SampleDifference get_ds_tests(const AbundanceGrou
    differential.cpp:790:16: warning: unused variable 'name' [-Wunused-variable]
    differential.cpp: In function 'void test_differential(const string&, const std::
    differential.cpp:1771:83: warning: comparison between signed and unsigned intege
    differential.cpp:1772:83: warning: comparison between signed and unsigned intege
    differential.cpp:1814:83: warning: comparison between signed and unsigned intege
    differential.cpp:1815:83: warning: comparison between signed and unsigned intege
    differential.cpp:1856:83: warning: comparison between signed and unsigned intege
    differential.cpp:1857:83: warning: comparison between signed and unsigned intege
    make[2]: *** [differential.o] Error 1
    make[2]: Leaving directory `/media/sda8/bharat/genomes/cufflinks-2.0.2/src'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/media/sda8/bharat/genomes/cufflinks-2.0.2'
    make: *** [all] Error 2

    I dont understand where to troubleshoot. All boost1.52 and Eigen libraries are copied in /usr/local/lib
    Last edited by bharat_iyengar; 12-16-2012, 09:36 PM.

  • #2
    Try using boost version 1.47. I think I had a similar issue when trying using the latest version of boost, which was 1.51. The version specified by cufflinks in the manual is 1.47, I think.


    • #3
      I had corrected that particular problem,which was because of improper definition of a variable. But then another one appeared which is perhaps because boost_system library is not linked during compilation.

      this is what is written in Cufflinks Manual.

      If you see any errors during configuration, verify that you are using Boost version 1.47 or higher
      I shall nonetheless try 1.47/48

      I have observed that this is a general problem with others using boost libraries.
      Last edited by bharat_iyengar; 12-17-2012, 08:06 AM.


      • #4
        Unless the developers of cufflinks tested every single release of boost beyond 1.47, that statement doesn't really mean much. It is possible for newer libraries to not work on software that was designed on older versions of those libraries.

        I just confirmed that my system has 1.47 installed - try that version.


        • #5
          i shall try. thanks


          • #6
            Also, make sure $LD_LIBRARY_PATH is defined as the path to the dynamic boost library files (the .so files)


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