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  • problem running Dindel on MacOSX 10.6.4

    Hi all,

    I am experiencing problems executing the binary file or building a executable for version 1.01 on a MAC. When the pre-built binary file was executed I receive the following error message:

    sh-3.2# ./dindel-1.01-mac-os-x
    dyld: Library not loaded: libboost_program_options-xgcc40-mt-1_37.dylib
    Referenced from: /Users/johnsoong/Downloads/dindel-1.01-mac-os-x/binaries/./dindel-1.01-mac-os-x
    Reason: image not found
    Trace/BPT trap


    When I try to rebuild from source (and having successfully installed BOOST libraries), I still receive error messages with the final lines (the build cannot produce a static library?) :

    sh-3.2# make
    g++ -o dindel -I/Users/johnsoong/Downloads/samtools-0.1.9/ -Iseqan_library/ -I./ -Wno-deprecated -O3 DInDel.o HapBlock.o HaplotypeDistribution.o ObservationModelFB.o GetCandidates.o Faster.o -L/Users/johnsoong/Downloads/samtools-0.1.9/ -lbam -lz -lboost_program_options -static
    ld: library not found for -lcrt0.o
    collect2: ld returned 1 exit status


    So I modified the Makefile file deleting the -static in LDFLAG. Still, the build failed with the following last line:

    ld: symbol(s) not found
    collect2: ld returned 1 exit status


    I have specified the correct path to samtools source...
    Would anyone know how to solve the issue? Thanks in advance.

    csoong

  • #2
    problem resolved. I removed the -static in LDFLAG and the build worked. I don't know how I got this to work because I tried this several times and didn't work. Dindel is working properly now.

    Comment


    • #3
      I want to add a note for users experiencing similar problems. I ran into the issue again on another mac pro today. And this time instead of not knowing how it suddenly worked, I actually made it work. First of all, my configuration for boost library was done through macport and i have samtools installed as well.

      It turns out that the linker and compiler could not find out the correct path to the installed boost library and its headers, so in the Makefile i had to speciafically add in the path that points to booth library, both for the header path as well as the linker path. usually the included path should look like this if using mac ports:
      /opt/local/lib for linker path
      /opt/local/include for header path

      good luck.

      oh yes... remember to remove the static flag in Makefile as well.

      Comment


      • #4
        Could you please paste your Makefile here, that would be a great help. Thanks.

        Comment


        • #5
          SAMTOOLDIR=/Users/rich/Downloads/samtools-0.1.12a/
          #/nfs/users/nfs_c/caa/source/samtools/
          SEQANDIR=seqan_library/

          CPPFLAGS= -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL
          CXXFLAGS= -I$(SAMTOOLDIR) -I$(SEQANDIR) -I./ -I/opt/local/include/ -I/opt/local/lib/ -Wno-deprecated -O3
          LDFLAGS= -L$(SAMTOOLDIR) -L/opt/local/lib/ -lbam -lz -lboost_program_options

          SRCSDINDEL=DInDel.cpp HapBlock.cpp HaplotypeDistribution.cpp ObservationModelFB.cpp GetCandidates.cpp Faster.cpp
          OBJSDINDEL=$(SRCSDINDEL:%.cpp=%.o)

          dindel:$(OBJSDINDEL) Read.hpp DInDel.hpp HapBlock.hpp Haplotype.hpp HaplotypeDistribution.hpp MyBam.hpp GetCandidates.hpp Variant.hpp Fasta.hpp OutputData.hpp MLAlignment.hpp ObservationModelSeqAn.hpp VariantFile.hpp ReadIndelErrorModel.hpp Library.hpp Faster.hpp
          $(CXX) -o $@ $(CXXFLAGS) $(DINDELFLAGS) $(OBJSDINDEL) $(LDFLAGS)

          clean:
          rm -f $(OBJSDINDEL) $(OBJSCOMPAREVARIANTS) $(OBJSMAKEGLF)

          Comment


          • #6
            Thanks for the information. I got dindel installed.

            Comment

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