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 -- 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. ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help