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

[Michael Tautschnig]

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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