[Debian-med-packaging] Bug#751277: python-biopython: FTBFS on mips* powerpc s390x

[Dejan Latinovic]

Hello,
I took a look at test failures on mips/mipsel.

Test that fails is based on a result of dnal tool.
dnal is part of a debian package wise.

In file: Bio/Wise/__init__.py,
an error was raised because the return value from dnal
is greater than 1.

If you look at dnal.c:

>   alb = make_align_dnaalign(one,two,mat,dse,-gap,-ext,-gap,-ext,dpri);
> 
>   printf("Score %d\n",alb->score);
> 
>   if( alb == NULL )
>     fatal("Could not build alignment!");
> 
>   if( show_pretty == TRUE )
>      write_pretty_seq_align(alb,one,two,12,60,stdout);
> 
>   if( show_alb == TRUE )
>     dump_ascii_AlnBlock(alb,stdout);
> }

you can see that there is no return statement.
In this case the return value of dnal usually will be the return value 
of last used function.
This behavior is mutable.
It can not be guaranteed on all architectures,
or if different optimization flags are used.
Further, using dnal with different options, last used function
could be changed.

Adding
> return 0;
at the end of main function in dnal.c,
test_align (test_Wise.TestWise) successfully passes
on mips/mipsel.


With this fix, package python-biopython
successfully builds for mipsel.
Patch that includes this fix is attached.


Unfortunately, on mips (BE)
test test_Cluster.py failed under Python 3.4.
Any progress on this issue?


Best Regards,
Dejan

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