On 16 Dec 2015, at 10:06, Stephane Plaisance | VIB |
<stephane.plaisa...@vib.be> wrote:
> When trying compile the new release, I get the following error
>
> $ 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/libhts.a -lcurses -lm -lz
> -ldl
>
> gcc: error: unrecognized command line option '-rdynamic'
Interesting, more recent OS X clang and gcc compilers support -rdynamic in the
name of compatibility. But this is easily fixed:
1. If you aren't using HTSlib plugins, you can just delete -rdynamic (from
samtools-1.3/Makefile and if necessary htslib-1.3/config.mk).
2. Otherwise replace -rdynamic with -Wl,-export_dynamic which is the native OS
X equivalent.
John
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