wise eternal compilation error!

[aloliveira]

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

[GenoMax]

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

[aloliveira]

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.

[GenoMax]

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

[aloliveira]

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' "{}" +;

[GenoMax]

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?