Hello nice helpers,
I'm currently trying to install samtools-1.3.1 on an iMac 10.6.8. Everything
seems to be ok after the "./configure" command, but I'm facing with the
following make error and I didn't manage to find a related thread on the
samtools-help list:
make
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_index.o bam_index.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_plcmd.o bam_plcmd.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o sam_view.o sam_view.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_cat.o bam_cat.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_md.o bam_md.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_reheader.o bam_reheader.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_sort.o bam_sort.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bedidx.o bedidx.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o kprobaln.o kprobaln.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_rmdup.o bam_rmdup.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_rmdupse.o bam_rmdupse.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_color.o bam_color.c
echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bamtk.o bamtk.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o errmod.o errmod.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o sample.o sample.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o sam_opts.o sam_opts.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o cut_target.o cut_target.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o phase.o phase.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam2depth.o bam2depth.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o padding.o padding.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bedcov.o bedcov.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bamshuf.o bamshuf.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o faidx.o faidx.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o dict.o dict.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o stats.o stats.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o stats_isize.o stats_isize.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_flags.o bam_flags.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_split.o bam_split.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_tview.o bam_tview.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_tview_curses.o bam_tview_curses.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_tview_html.o bam_tview_html.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_lpileup.o bam_lpileup.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_quickcheck.o bam_quickcheck.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_addrprg.o bam_addrprg.c
bam_addrprg.c: In function ‘get_rg_line’:
bam_addrprg.c:149: warning: incompatible implicit declaration of built-in
function ‘strndup’
bam_addrprg.c: In function ‘confirm_rg’:
bam_addrprg.c:186: warning: incompatible implicit declaration of built-in
function ‘strndup’
bam_addrprg.c: In function ‘get_first_rgid’:
bam_addrprg.c:208: warning: incompatible implicit declaration of built-in
function ‘strndup’
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_aux.o bam_aux.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam.o bam.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_import.o bam_import.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o sam.o sam.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o sam_header.o sam_header.c
gcc -g -O2 -I. -Ihtslib-1.3.1 -c -o bam_plbuf.o bam_plbuf.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
gcc -pthread -rdynamic -o samtools bam_index.o bam_plcmd.o sam_view.o
bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o
bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o
bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o
padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o
bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o
bam_quickcheck.o bam_addrprg.o libbam.a htslib-1.3.1/libhts.a -lncurses -lm -lz
-ldl
Undefined symbols:
"_strndup", referenced from:
_get_rg_line in bam_addrprg.o
_confirm_rg in bam_addrprg.o
_main_addreplacerg in bam_addrprg.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [samtools] Error 1
Do you know where it could come from and what I could do to overcome this
error, please?
Many thanks in advance!
Béatrice
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