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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