Dear John, Many thanks for your help too and the patch you gave me. Everything is resolved now and the installation (a new one, just to test) went well after applying it.
Cheers, Béatrice Le Lundi 13 Juin 2016 18:38 CEST, John Marshall <[email protected]> a écrit: > On 10 Jun 2016, at 15:44, CHANE-WOON-MING Béatrice (VIE) > <[email protected]> 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 [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
