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  • GenoMax
    replied
    If you used apt-get then the library should be in the default path. Can you try adding library option "-lglib-2.0" instead of the modification you tried?

    Leave a comment:


  • aloliveira
    replied
    The libglib2-0 was installed via apt-get, and I modified the make file with the following command lines:

    find ./ -type f -name "makefile" -exec sed -i.old 's/glib-config --libs/pkg-config --libs glib-2.0/g' "{}" +;
    find ./ -type f -name "makefile" -exec sed -i.old 's/glib-config --cflags/pkg-config --cflags glib-2.0/g' "{}" +;

    Leave a comment:


  • GenoMax
    replied
    Where did you install the libglib2-0? How did you modify the makefile?

    Leave a comment:


  • aloliveira
    replied
    GeneMax I'm running in Ubuntu-Linux. I already installed that library and modified the makefile to include the libglib2.0 during the compilation, but still the error persists.

    Leave a comment:


  • GenoMax
    replied
    What OS are you doing this compilation on? You may have to install libglib2.0-dev package based on the errors above.

    Leave a comment:


  • aloliveira
    started a topic wise eternal compilation error!

    wise eternal compilation error!

    Hello,

    I am trying to run CEGMA, but I am not able to compile genewise in order to do so. I've followed so many different tutorials, but still I could find the answer for my problem. I am Biology guy, so I have no idea what is happening. I will appreciate any help because I've tried so many things without any success.

    The problem in the compilation is in this specific command:

    gcc -g -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm

    And the output is:

    ../dynlibsrc//libdyna_glib.a(hsp.o): In function `Wise2_add_pair_HSPmanager':
    hsp.c.text+0x1432): undefined reference to `g_hash_table_lookup'
    hsp.c.text+0x1568): undefined reference to `g_hash_table_insert'
    ../dynlibsrc//libdyna_glib.a(hsp.o): In function `Wise2_add_new_HSP_HSPmanager':
    hsp.c.text+0x1618): undefined reference to `g_hash_table_lookup'
    hsp.c.text+0x16b8): undefined reference to `g_hash_table_insert'
    ../dynlibsrc//libdyna_glib.a(hsp.o): In function `Wise2_free_HSPmanager':
    [.......]

    collect2: error: ld returned 1 exit status
    make[1]: *** [estwise] Error 1
    make[1]: Leaving directory `/home/oliveira/Downloads/wise2.2.3-rc7/src/models'
    make: *** [realall] Error 2

    Thank you very much and I'm looking forward for any help,
    Best regards André

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