[Debian-med-packaging] Bug#746770: Conflicting declarations of function simple_aligner

[Michael Tautschnig]

Package: dialign-t
Version: 1.0.2-5
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.

http://sources.debian.net/src/dialign-t/1.0.2-5/

[...]
gcc -o ./museq \
  ./museq.o ./parameters.o ./io.o ./diag.o ./alig.o ./assemble.o ./prob.o ./orf.o ./translate.o  \
  -pipe -Wall -lm -Wl,-z,relro

error: conflicting function declarations "simple_aligner"
old definition in module museq file museq.c line 56
signed int (struct seq_col *, struct diag_col *, struct scr_matrix *, struct prob_dist *, struct alignment *, signed int)
new definition in module assemble file assemble.c line 398
char (struct seq_col *scol, struct diag_col *dcol, struct scr_matrix *smatrix, struct prob_dist *pdist, struct alignment *algn, signed int round)

The inconsistent return types will result in wrong interpretation of numeric
values, with possibly even worse results on big-endian systems.

Best,
Michael

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