Comments (6)
Are you using the precompiled binaries for Cufflinks?
from cufflinks.
Yes.
from cufflinks.
So I'm no longer able to reproduce this with Bowtie 2.2.5, TopHat 2.1.0, and the current head of the develop branch. Have you tried with a recent build from source?
from cufflinks.
Sorry, this is hard to test at the moment. I updated Bowtie2 and Tophat, but without updating Cufflinks I'm still seeing the problem. Building from source is a bit more involved, and it may take a few days for me to brave the build instructions.
from cufflinks.
It's been a mess, but I've been able to install the prerequisites (including the outdated Boost 1.55 alongside the latest Boost) without breaking anything else on my system. However, make
fails on its final steps--it appears unable to link to the libbam library.
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -DNDEBUG -pthread -I/usr/local/opt/boost155/include -I/usr/local/include -I/usr/local/include/Eigen/include -L/usr/local/opt/samtools/lib -L/usr/local/opt/boost155/lib -L/usr/local/lib -L/usr/local/opt/samtools/lib -o gtf_to_sam gtf_to_sam.o libcufflinks.a libgc.a -lboost_thread-mt -lboost_system-mt -lboost_serialization-mt -lbam -lz
...
...
skipping 1000s of lines of warning messages
...
...
Undefined symbols for architecture x86_64:
Undefined symbols for architecture x86_64:
"_bam_aux2A", referenced from:
"_bam_aux2A", referenced from:
BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
"_bam_aux2i", referenced from:
"_bam_aux2i", referenced from:
BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
"_bam_aux_get", referenced from:
"_bam_aux_get", referenced from:
BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
"_bam_destroy1", referenced from:
"_bam_destroy1", referenced from:
_sampileup in libbam.a(sam.o)
_sampileup in libbam.a(sam.o)
"_bam_hdr_destroy", referenced from:
"_bam_hdr_destroy", referenced from:
_samclose in libbam.a(sam.o)
_samclose in libbam.a(sam.o)
"_bam_init1", referenced from:
"_bam_init1", referenced from:
_sampileup in libbam.a(sam.o)
_sampileup in libbam.a(sam.o)
"_bam_plp_destroy", referenced from:
"_bam_plp_destroy", referenced from:
_bam_plbuf_destroy in libbam.a(bam_plbuf.o)
_bam_plbuf_destroy in libbam.a(bam_plbuf.o)
"_bam_plp_init", referenced from:
"_bam_plp_init", referenced from:
_bam_plbuf_init in libbam.a(bam_plbuf.o)
_bam_plbuf_init in libbam.a(bam_plbuf.o)
"_bam_plp_next", referenced from:
"_bam_plp_next", referenced from:
_bam_plbuf_push in libbam.a(bam_plbuf.o)
_bam_plbuf_push in libbam.a(bam_plbuf.o)
"_bam_plp_push", referenced from:
"_bam_plp_push", referenced from:
_bam_plbuf_push in libbam.a(bam_plbuf.o)
_bam_plbuf_push in libbam.a(bam_plbuf.o)
"_bam_plp_reset", referenced from:
"_bam_plp_reset", referenced from:
_bam_plbuf_reset in libbam.a(bam_plbuf.o)
_bam_plbuf_reset in libbam.a(bam_plbuf.o)
"_bgzf_mt", referenced from:
"_bgzf_mt", referenced from:
_samthreads in libbam.a(sam.o)
_samthreads in libbam.a(sam.o)
"_bgzf_seek", referenced from:
"_bgzf_seek", referenced from:
BAMHitFactory::reset() in libcufflinks.a(hits.o)
BAMHitFactory::undo_hit() in libcufflinks.a(hits.o)
BAMHitFactory::reset() in libcufflinks.a(hits.o)
BAMHitFactory::undo_hit() in libcufflinks.a(hits.o)
"_fai_build", referenced from:
"_fai_build", referenced from:
_samfaipath in libbam.a(sam.o)
_samfaipath in libbam.a(sam.o)
"_hts_close", referenced from:
"_hts_close", referenced from:
_samclose in libbam.a(sam.o)
_samclose in libbam.a(sam.o)
"_hts_get_format", referenced from:
"_hts_get_format", referenced from:
_samthreads in libbam.a(sam.o)
_samopen in libbam.a(sam.o)
_samthreads in libbam.a(sam.o)
_samopen in libbam.a(sam.o)
"_hts_open", referenced from:
"_hts_open", referenced from:
_samopen in libbam.a(sam.o)
_samopen in libbam.a(sam.o)
"_hts_set_fai_filename", referenced from:
"_hts_set_fai_filename", referenced from:
_samopen in libbam.a(sam.o)
_samopen in libbam.a(sam.o)
"_hts_verbose", referenced from:
"_hts_verbose", referenced from:
_samopen in libbam.a(sam.o)
_samfaipath in libbam.a(sam.o)
_samopen in libbam.a(sam.o)
_samfaipath in libbam.a(sam.o)
"_sam_hdr_read", referenced from:
"_sam_hdr_read", referenced from:
_samopen in libbam.a(sam.o)
_samopen in libbam.a(sam.o)
"_sam_hdr_write", referenced from:
"_sam_hdr_write", referenced from:
_samopen in libbam.a(sam.o)
_samopen in libbam.a(sam.o)
"_sam_read1", referenced from:
"_sam_read1", referenced from:
BAMHitFactory::next_record(char const*&, unsigned long&) in libcufflinks.a(hits.o)
BAMHitFactory::next_record(char const*&, unsigned long&) in libcufflinks.a(hits.o)
_sampileup in libbam.a(sam.o)
_sampileup in libbam.a(sam.o)
ld: symbol(s) not found for architecture x86_64
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Samtools is installed in the default location, so I have no idea what the issue is.
$ ls /usr/local/include/bam
bam.h bam_endian.h bam_plbuf.h errmod.h sam.h sample.h stats_isize.h
bam2bcf.h bam_lpileup.h bam_tview.h kprobaln.h sam_header.h samtools.h version.h
$
$ ls /usr/local/lib/libbam.a
/usr/local/lib/libbam.a
from cufflinks.
I have now tried to install cufflinks on 2 separate mac systems and ended up with the same problem above. Has this issue been resolved?
from cufflinks.
Related Issues (20)
- Please use std::fabs instead of just fabs in C++ to avoid conflicts
- The https version of cufflinks website looks broken
- Please add the corresponding ifdef for the code meant only for MinGW
- -m64 breaks build on architectures other than amd64
- configure error: We could not detect the bam libraries
- error: reference to 'thread' is ambiguous HOT 1
- Correlation between replicates
- Nondeterministic segfault on OSX
- 0 ReadHits still live
- Intron not within scaffold warnings HOT 1
- license clarification
- Cuffmerge:ValueError: can't have unbuffered text I/O HOT 5
- cuffmerge
- Cuffmerge GTF error
- Performance data of cufflinks in computing speed.
- Cufflinks - Inconsistent Results for SAM/BAM File Sorted by Reference Position
- cuffdiff error: number of labels must match number of conditions
- multithreading
- # coverage and -g and -G
- Unusual behavior of cufflinks when a colon is present in the contig names
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from cufflinks.