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

[Andreas Tille]

Hi Dejan,

thanks for the hint.  I'll apply your patch which looks promising.  When
checking the wise package I detected some other issues when trying to
run wise's own test suite which I need to fix before an upload.  Once
this is done I'll upload biopython with a versioned Build-Depends.  This
would leave us only with the mips Python 3.4 issue.  I wonder whether
I should cheat and skip this test for the moment to let the package
migrate to testing with this known minor issue.

Kind regards

        Andreas.

On Mon, Aug 04, 2014 at 05:10:38PM +0000, Dejan Latinovic wrote:
> 
> 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
> 

> --- wise-2.4.1.orig/src/models/dnal.c	2004-11-24 16:26:11.000000000 +0000
> +++ wise-2.4.1/src/models/dnal.c	2014-07-31 14:53:54.000000000 +0000
> @@ -75,6 +75,8 @@
>  
>    if( show_alb == TRUE )
>      dump_ascii_AlnBlock(alb,stdout);
> +
> +  return 0;
>  }
>  
>  


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