[Debian-med-packaging] Bug#825461: staden: FTBFS in testing

[Andreas Tille]

Hi,

after dealing with the actual issue reported in bug #825461[1] I noticed
that more strict gcc fails at other parts.  I fixed an implicit declaration
issue[2] and I'm now stumbling upon

...
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST  -I/build/staden-2.0.0+b10/./gap5 -I/build/staden-2.0.0+b10/./Misc -I"/usr
sam_index.c:321:14: error: conflicting types for 'append_int'
 static char *append_int(char *cp, int i) {
              ^
In file included from /usr/include/io_lib/scram.h:52:0,
                 from sam_pileup.h:4,
                 from sam_index.c:17:
/usr/include/io_lib/bam.h:758:16: note: previous declaration of 'append_int' was here
 unsigned char *append_int(unsigned char *cp, int32_t i);
                ^
sam_index.c: In function 'parse_sam_or_bam':
sam_index.c:2268:6: warning: implicit declaration of function 'contig_visible_start' [-Wimplicit-function-declaration]
      contig_visible_start(io, bio->c->rec, CITER_CSTART);
      ^
sam_index.c:2269:6: warning: implicit declaration of function 'contig_visible_end' [-Wimplicit-function-declaration]
      contig_visible_end  (io, bio->c->rec, CITER_CEND);
      ^
/build/staden-2.0.0+b10/./gap5/../global.mk:388: recipe for target 'sam_index.o' failed


which is caused by staden-io-lib version 1.14.8.  The function
append_int is defined in staden-io-lib io_lib/bam.c differently from
staden gap5/sam_index.c.  It would be great if you could sort this
out.

Kind regards

       Andreas.

[1] https://bugs.debian.org/825461
[2] https://anonscm.debian.org/git/debian-med/staden.git/tree/debian/patches/fix_implicit_declaration.patch

-- 
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