On Thu, Jul 14, 2016 at 03:07:47PM +0200, Andreas Tille wrote: > > > gcc -L/<<BUILDDIR>>/staden-2.0.0+b10/lib -Wl,-z,relro > > > -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o eba qual.o conf.o > > > -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm > > > -lpthread -lcurl -lz -lmisc -lm -lm > > > conf.o: In function `probFromQual': > > > /<<BUILDDIR>>/staden-2.0.0+b10/eba/conf.c:385: undefined reference to > > > `min' > > > /<<BUILDDIR>>/staden-2.0.0+b10/eba/conf.c:385: undefined reference to > > > `min' > > > /<<BUILDDIR>>/staden-2.0.0+b10/eba/conf.c:385: undefined reference to > > > `min' > > > /<<BUILDDIR>>/staden-2.0.0+b10/eba/conf.c:385: undefined reference to > > > `min' > > > collect2: error: ld returned 1 exit status
I think the problem here is trying to use the old Staden release with a much more modern io_lib release. It's a mistake that we broke backwards compatibility, but trivially fixed in eba itself. See commit https://sourceforge.net/p/staden/code/4067/: Due to io_lib changes, change from min() to MIN(). --- a/staden/trunk/src/eba/conf.c +++ b/staden/trunk/src/eba/conf.c @@ -382,7 +382,7 @@ char probFromQual(float qual) { - return (char)(100.0*(1.0 - min(qual,1.0))); + return (char)(100.0*(1.0 - MIN(qual,1.0))); } There is a 2.0.0b11 release now which I think incorporates this change. The Staden Package as a whole is pretty much on life support. The only tool that gets any real updates is Gap5, and they have slowed up a lot in the last couple years. Things like "eba" are long since dead really, but basic things like fixing compilation errors is OK to solve. James -- 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.
