[Debian-med-packaging] Bug#861281: rnahybrid: FTBFS on armel

[Andreas Tille]

Hi Lennart,

thanks again for your analysis of the code.

On Tue, Sep 26, 2017 at 02:21:16PM -0400, Lennart Sorensen wrote:
> On Tue, Sep 26, 2017 at 02:09:56PM -0400,  wrote:
> > 
> > > > At some point I introduced an additional letter to the alphabet, the X (a masking letter; see input.h). I am not sure about the program logic anymore, whether X can actually be used for lookups in the energy tables (as the N could). In hybrid_core.c, where the energy functions are used, I check for X in a few places, so the idea was perhaps to not use X for lookups (in fact, I do not want to consider any masked sequence at all). Should that be true, ALPHASIZE being 6 would be wasteful, but it shouldn't harm otherwise. Of course, you could change the two for-loops (the k-loop in init_dr_dangle_dg_ar and the i-loop in its sibling) so that they use < instead of <=, but, while that might fix the array bound bug, it might not solve an underlying logic problem. In effect you might have a program that works technically, but produces the wrong result. Unfortunately I can't help with that. You could try fixing the loops and then do a few runs and compare the outputs, as a minimal test.
> > > 
> > > So it seems to me that it is safer to leave the loop untouched ...
> > 
> > Makes sense if the energy.h is fixed instead.
> 
> Of course it seems the change was a number of places.  ALPHASIZE was
> changed from 5 to 6, which removed the need for the +1 in a number of
> places, but of course makes the arrays a chunk larger.
> 
> I think in fact just fixing the two places that initialize the array to
> 0 to not have the <= is in fact the safer option since that will match
> the allocation.  Everywhere else that had to deal with the +1 seems to
> have already been changed in 2.1.2 to match ALPHASIZE now being 6.
> 
> Of course the larger arrays might have something to do with why the
> compile takes a bit longer than before.  But that could also just be a
> gcc change.

To summarise:  We should go with the patch you suggested originally

   https://anonscm.debian.org/git/debian-med/rnahybrid.git/tree/debian/patches/fix_loop_index.patch

to fix the bug and in addition the warnings will be fixed in

   https://anonscm.debian.org/git/debian-med/rnahybrid.git/tree/debian/patches/fix_warnings.patch

I'll be able to run the test suite on amd64 and also one arm64 box
I own.

Kind regards

       Andreas.

-- 
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