Dear James, Thank you very much for your help! It appears indeed that strndup is not available on mac os x (10.6.8) and gcc i686-apple-darwin10-gcc-4.2.1. It was only added to OS X in version 10.7. But following your advice and by modifying a little bit the makefile, I've managed to reach the end of the installation process without any additional error.
Cheers, Béatrice Le Lundi 13 Juin 2016 12:51 CEST, James Bonfield <j...@sanger.ac.uk> a écrit: > 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
