Hi Andreas, Thanks for letting me know this. You may modify the declaration in bwt_lite.c. This fix will appear in 0.7.9 as well.
Best, Heng On May 13, 2014, at 7:46 AM, Andreas Tille <[email protected]> wrote: > Hi, > > there is some ongoing effort to enable builds with clang compiler which > has some more strict type checking than gcc and this raised some error > with bwa. I think it would be sufficient to adapt the declaration in > bwt_lite.c to enable a clean build but I would like to bring this to > your attention first. > > Kind regards and thanks for providing bwa as free software > > Andreas. > > On Tue, May 13, 2014 at 01:14:19PM +0200, Michael Tautschnig wrote: >> Package: bwa >> Version: 0.7.8-1 >> Usertags: goto-cc >> >> During a rebuild of all packages in a clean sid chroot (and >> cowbuilder+pbuilder) >> the build failed with the following error. Please note that we use our >> research >> compiler tool-chain (using tools from the cbmc package), which permits >> extended >> reporting on type inconsistencies at link time. >> >> [...] >> gcc -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat >> -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD >> QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o >> bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o >> bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa >> -L. -lbwa -lm -lz -lpthread >> >> error: conflicting function declarations "is_sa" >> old definition in module is file is.c line 191 >> signed int (const unsigned char *T, signed int *SA, signed int n) >> new definition in module bwt_lite file bwt_lite.c line 10 >> signed int (const unsigned char *, unsigned int *, signed int) >> Makefile:25: recipe for target 'bwa' failed >> make[2]: *** [bwa] Error 64 >> make[2]: Leaving directory >> '/srv/jenkins-slave/workspace/sid-goto-cc-bwa/bwa-0.7.8' >> >> The type conflict on parameter SA may be harmless (even though technically >> undefined behaviour) if the values passed around are always positive and fit >> into a signed int. Else undefined behaviour will definitively occur. >> >> Best, >> Michael >> > > > >> _______________________________________________ >> Debian-med-packaging mailing list >> [email protected] >> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > > > -- > http://fam-tille.de -- 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. -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected]
