On 22 Feb 2016, at 01:05, William Hsiao <[email protected]> wrote:
>
> I’m trying to install Samtools 1.3 on a RHEL 6.2 system. I seemed to be able
> to install htslib 1.3 but as I try to install samtools 1.3 I encountered the
> following error when I type:
This gzopen64() problem seems to be a long-standing problem on RHEL that we
have never been able to reproduce elsewhere.
> make[1]: Entering directory
> `/usr/local/packages/samtools/samtools-1.3/htslib-1.3'
Please also cd into this .../htslib-1.3 directory and type "make htsfile". It
will be instructive to see whether this htslib-only executable also fails to
link in the same way.
> bedidx.o: In function `bed_read':
> /usr/local/packages/samtools/samtools-1.3/bedidx.c:170: undefined reference
> to `gzopen64'
Please post (or email to me) the output from
gcc -H -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I.
-Ihtslib-1.3 -c -o bedidx.o bedidx.c
(i.e., adding -H to the gcc command from your make trace that built bedidx.o.)
Hopefully with your help we can get to the bottom of this problem this time
around!
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
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