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samtools doesn't compile on Mountain Lion. bam_qa.c produces this error
bam_qa.c: In function 'main_qa':
bam_qa.c:88: warning: implicit declaration of function 'getopt'
bam_qa.c:92: error: 'optarg' undeclared (first use in this function)
bam_qa.c:92: error: (Each undeclared identifier is reported only once
bam_qa.c:92: error: for each function it appears in.)
bam_qa.c:96: error: 'optind' undeclared (first use in this function)
make[1]: *** [bam_qa.o] Error 1
make: *** [all-recur] Error 1
clang -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 bam_qa.o padding.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz
Undefined symbols for architecture x86_64:
"___ks_insertsort_heap", referenced from:
_ks_combsort_heap in libbam.a(bam_sort.o)
_ks_introsort_heap in libbam.a(bam_sort.o)
"___ks_insertsort_sort", referenced from:
_ks_combsort_sort in libbam.a(bam_sort.o)
_ks_introsort_sort in libbam.a(bam_sort.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
The latter error is not raised if gcc is used, but clang is the default compiler for OSX 10.8 (and latest FreeBSD too). One simple (and correct) solution is to make the inlined function static.
The distributed objective file will leads to linker errors on some
platform. This commit applies a upstream patch (lh3/samtools#15) to
allow compiling samtools from source. Copying `CRISP` to the base
directory will cause error on case-insensitive file systems and thus is
disabled.
samtools doesn't compile on Mountain Lion. bam_qa.c produces this error
This is easily solved with this patch
in addition, linking produces this error:
The latter error is not raised if gcc is used, but clang is the default compiler for OSX 10.8 (and latest FreeBSD too). One simple (and correct) solution is to make the inlined function static.
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