Your message dated Fri, 13 Jan 2017 13:43:18 +0100
with message-id <>
and subject line Re: Bug#747185: Do the conflicting return types of function 
DejaVu_create exist in new upstream version?
has caused the Debian Bug report #747185,
regarding Conflicting return types of function DejaVu_create
to be marked as done.

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If this is not the case it is now your responsibility to reopen the
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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:,27,28,30,31,32,33,34,35,36#L26

#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:

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.


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issue is done in my opinion.  Please reopen if not.

Kind regards


On Wed, Dec 14, 2016 at 07:28:05AM +0100, Andreas Tille wrote:
> Hi Michael,
> I'm currently checking older bugs and stumbled upon this one.  I
> currently can not find the said cruel mix of definitions is used for
> ALPHABET_SIZE in the code base of 2.4.0.  Could you please recheck
> and confirm whether this bug can be closed or explain in more detail
> in how far different definitions are used?
> Kind regards
>       Andreas.
> -- 
> _______________________________________________
> Debian-med-packaging mailing list


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