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-   -   Problem compile cufflinks on Xcode (http://seqanswers.com/forums/showthread.php?t=50900)

tedwong 03-10-2015 10:54 PM

Problem compile cufflinks on Xcode
 
I have installed all requirements for compiling cufflinks. I'm compiling the sources with their provided Xcode project.

Everything goes well but during the linking phase:

ld: warning: directory not found for option '-L/opt/local/libIntel64'
Undefined symbols for architecture x86_64:
"_bam_aux2A", referenced from:
BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in hits.o
"_bam_aux2i", referenced from:
BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in hits.o
"_bam_aux_get", referenced from:
BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in hits.o
"_bam_destroy1", referenced from:
_sampileup in libbam.a(sam.o)
"_bam_hdr_destroy", referenced from:
_samclose in libbam.a(sam.o)
"_bam_init1", referenced from:
_sampileup in libbam.a(sam.o)
"_bam_plp_destroy", referenced from:
_bam_plbuf_destroy in libbam.a(bam_plbuf.o)
"_bam_plp_init", referenced from:
_bam_plbuf_init in libbam.a(bam_plbuf.o)
"_bam_plp_next", referenced from:
_bam_plbuf_push in libbam.a(bam_plbuf.o)
"_bam_plp_push", referenced from:
_bam_plbuf_push in libbam.a(bam_plbuf.o)
"_bam_plp_reset", referenced from:
_bam_plbuf_reset in libbam.a(bam_plbuf.o)
"_bgzf_mt", referenced from:
_samthreads in libbam.a(sam.o)

The libbam.a was compiled directly in gcc (by typing make in the samtools directory in terminal). My guess is that the symbols compiled with gcc can't be used with Xcode but I could be wrong.

Anyone, any idea? Cufflink developers, can you shed some hint on how to compile the sources with Xcode on MacOSX?


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