Hello, On Fri, Jun 10, 2016 at 04:44:15PM +0200, CHANE-WOON-MING B?atrice (VIE) 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: ... > Undefined symbols: > "_strndup", referenced from: > _get_rg_line in bam_addrprg.o > _confirm_rg in bam_addrprg.o > _main_addreplacerg in bam_addrprg.o
Do you have a newer version of gcc or clang available? According to the XOpen documentation strndup has been a standard function since 2006. http://pubs.opengroup.org/onlinepubs/9699919799/functions/strdup.html Your MacOS X 10.6.8 was released in 2011, but I assume came with an older compiler or at least a compiler that hadn't yet incorporated all of that XOpen specification. If you don't have a newer compiler available, you can however just add a copy of strndup to one of your C and headers files. Apple themselves seem to have a trivial copy here: http://opensource.apple.com//source/gcc/gcc-5666.3/libiberty/strndup.c James PS. However perhaps we should check for this in autoconf, or just use a workaround that doesn't require use of strndup. -- James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- 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
