On 10 Jun 2016, at 15:44, CHANE-WOON-MING Béatrice (VIE)
<b.chanewoonm...@ibmc-cnrs.unistra.fr> wrote:
> 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:
[...]
> 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’
This hasn't come up before because the use of this function is limited to
bam_addrprg.c, which is relatively new in samtools (only since 1.3). And, as
James noted, your compiler is somewhat unusual in not supporting it.
Anyway, it's easy for samtools to avoid using this function. I've fixed this
in the git repository, and you will be able to compile on your machine by
applying this patch to your 1.3.1 directory:
https://github.com/samtools/samtools/commit/f3178b7462c4890e586266615b96d75e4805f83e.patch
Thanks for reporting this problem.
John
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