[Debian-med-packaging] Bug#747970: Parameter declarations of function is_sa differ in signedness

[Andreas Tille]

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
> 



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