[Debian-med-packaging] Bug#747185: Conflicting return types of function DejaVu_create

[Michael Tautschnig]

Package: exonerate
Version: 2.2.0-6
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.

error: conflicting function declarations "DejaVu_create"
old definition in module bsam file ../../src/struct/dejavu.h line 42
DejaVu *DejaVu_create(gchar *seq, gint len)
new definition in module dejavu file dejavu.c line 26
DejaVu *DejaVu_create(gchar *seq, gint len)

reason for conflict at nil.symbol_list in types listed below (array/array):

signed int [2048]
signed int [256]

This is with the following code in dejavu.h:

http://sources.debian.net/src/exonerate/2.2.0-6/src/struct/dejavu.h?hl=26,27,28,30,31,32,33,34,35,36#L26

#ifndef ALPHABET_SIZE
#define ALPHABET_SIZE (1 << CHAR_BIT)
#endif /* ALPHABET_SIZE */

typedef struct {
       gchar *seq;
        gint  len;
        gint *next;
        gint  symbol_list[ALPHABET_SIZE];
        gint  symbol_list_len;
} DejaVu;

Unfortunately, however, a cruel mix of definitions is used for ALPHABET_SIZE
throughout the codebase of exonerate:

http://codesearch.debian.net/search?q=package%3Aexonerate+ALPHABET_SIZE

Any code relying on the size of the symbol_list array will break as it will
access invalid memory; accesses to the symbol_list_len element are invalid as
its offset will be wrong.

Best,
Michael

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