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

[Andreas Tille]

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?
 
> 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 ...
 
> I hope that helps.

Definitely.

Thanks again

      Andreas.

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