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

[Lennart Sorensen]

On Tue, Sep 26, 2017 at 02:09:56PM -0400,  wrote:
> On Tue, Sep 26, 2017 at 07:30:40PM +0200, Andreas Tille wrote:
> > Hi Marc,
> > 
> > thanks for the quick response.
> > 
> > On Tue, Sep 26, 2017 at 06:45:42PM +0200, Marc Rehmsmeier wrote:
> > > Hi Andreas,
> > > 
> > > I am not entirely sure what I was doing there and then. That seems to be version 2.1.2, correct?
> > 
> > Yes, that's correct.  We always try to package the latest upstream
> > 
> > 
> > > In version 2.1.1, the array is allocated with ALPHASIZE+1. The <= in the k-loop is originally not a mistake; the function's sibling, init_dl_dangle_dg_ar, has the <= in the first loop (the i-loop). These are the allocations in version 2.1.1:
> > > 
> > > double dr_dangle_dg_ar[ALPHASIZE][ALPHASIZE][ALPHASIZE+1];
> > > double dl_dangle_dg_ar[ALPHASIZE+1][ALPHASIZE][ALPHASIZE];
> > > 
> > > You see that there's a +1 on the corresponding sides.
> > 
> > Yes, I see.  Would you like to express that the better fix for that
> > issue would be to restore this allocation inside energy.h instead of
> > fixing the loop index?
> 
> So someone broke the allocation size in 2.1.2?
> 
> Seems like a valid fix too, especially if there is some actual use for
> the extra slot.
> 
> > > 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.

-- 
Len Sorensen