compiling samtools in mac

[meritxellop]

Hi all,

I'm trying to install samtools-0.1.18 on Mac OS X 10.6.8.
The the error raised when trying to compile is attached at the end of this post.

I guess it's an error produced by a missing library, so I have included all the libraries in the maste library (sam.h) with no success...

Can sb give me a hand, please?

Thanks

Meri
______

gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
Undefined symbols:
"_egzopen", referenced from:
_loadpos in phase.o
_bed_read in libbam.a(bedidx.o)
_sam_open in libbam.a(bam_import.o)
___bam_get_lines in libbam.a(bam_import.o)
_sam_header_read2 in libbam.a(bam_import.o)
"_egzread", referenced from:
_ks_getuntil2 in phase.o
_loadpos in phase.o
_ks_getuntil2 in libbam.a(bedidx.o)
_bed_read in libbam.a(bedidx.o)
_ks_getuntil2 in libbam.a(bam_import.o)
_sam_header_read2 in libbam.a(bam_import.o)
"_einflate", referenced from:
_bgzf_read_block in libbam.a(bgzf.o)
__razf_read in libbam.a(razf.o)
"_egzclose", referenced from:
_loadpos in phase.o
_bed_read in libbam.a(bedidx.o)
_sam_close in libbam.a(bam_import.o)
___bam_get_lines in libbam.a(bam_import.o)
_sam_header_read2 in libbam.a(bam_import.o)
"_edeflate", referenced from:
_deflate_block in libbam.a(bgzf.o)
__razf_write in libbam.a(razf.o)
_razf_write in libbam.a(razf.o)
_razf_close in libbam.a(razf.o)
"_einflateEnd", referenced from:
_bgzf_read_block in libbam.a(bgzf.o)
_bgzf_read_block in libbam.a(bgzf.o)
_razf_open_r in libbam.a(razf.o)
_razf_close in libbam.a(razf.o)
"_einflateReset", referenced from:
__razf_reset_read in libbam.a(razf.o)
"_einflateInit2_", referenced from:
_bgzf_read_block in libbam.a(bgzf.o)
_razf_open_r in libbam.a(razf.o)
"_ecrc32", referenced from:
_deflate_block in libbam.a(bgzf.o)
_deflate_block in libbam.a(bgzf.o)
"_edeflateInit2_", referenced from:
_deflate_block in libbam.a(bgzf.o)
_razf_open_w in libbam.a(razf.o)
"_egzdopen", referenced from:
_loadpos in phase.o
_bed_read in libbam.a(bedidx.o)
_sam_open in libbam.a(bam_import.o)
___bam_get_lines in libbam.a(bam_import.o)
_sam_header_read2 in libbam.a(bam_import.o)
"_edeflateEnd", referenced from:
_deflate_block in libbam.a(bgzf.o)
_deflate_block in libbam.a(bgzf.o)
_razf_close in libbam.a(razf.o)
"_edeflateSetHeader", referenced from:
_razf_open_w in libbam.a(razf.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [samtools] Error 1
make: *** [all-recur] Error 1

[adaptivegenome]

I think you might need to change the makefile so that instead of "-lcurses" it points to "-lncurses".

[lifeng.tian]

Meri,
The same problem was reported for compiling BWA, see

BWA make error on Macbook pro
egzclose/open BWA0.5.7 install

to check which zlib.h was used, try:
gcc -E phase.c -o phase.i

then grep 'zlib'. On my Lion (10.7.2), I see "/usr/include/zlib.h". what's yours?

Lifeng

[Carlos Borroto]

You might also want to check out Homebrew

To install samtools using Homebrew:

$ brew install samtools