On 25 Nov 2016, at 18:09, yincl2013 <[email protected]> wrote:
> Recently, when i installed the samtools-1.2 on redhat 6.6 system, i got the
> following problem:
> gcc -pthread -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 cut_target.o phase.o bam2depth.o padding.o
> bedcov.o bamshuf.o faidx.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 libbam.a
> htslib-1.2.1/libhts.a -lcurses -lm -lz
> bedidx.o: In function `bed_read':
> bedidx.c:(.text+0x1650): undefined reference to `gzopen64'
Please try again with the current release, version 1.3.1. I suspect the
problem you are seeing is a known problem with the system zlib on this Linux
distribution, for which samtools 1.3.1 contains a workaround.
John
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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