SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Compile cufflinks in MacOSX10.7 (Lion)--error in make mrbirdy857 Bioinformatics 2 01-19-2012 05:49 AM
cufflinks quantification problem Trudy Bioinformatics 0 06-13-2011 03:20 AM
strange problem for cufflinks sterding Bioinformatics 3 12-03-2010 10:44 AM
any help for this compile problem with SRA_SDK? feng Bioinformatics 6 10-28-2010 01:10 AM
Cufflinks on Solaris (compile error) luxmare Bioinformatics 1 06-04-2010 02:00 AM

Reply
 
Thread Tools
Old 03-10-2015, 11:54 PM   #1
tedwong
Member
 
Location: Sydney

Join Date: Mar 2015
Posts: 13
Default 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?
tedwong is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:50 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO