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

[Lennart Sorensen]

On Tue, Sep 26, 2017 at 09:57:09AM +0100, Edmund Grimley Evans wrote:
> The infinite loop is still there with gcc-7. I've created bug #876825.
> 
> Before you exclude armel, you could perhaps try doing something about
> this warning, which is given not just on armel and may or may not be
> related to the compiler going into an infinite loop:
> 
> energy.c:539:104: warning: iteration 6 invokes undefined behavior
> [-Waggressive-loop-optimizations]

Is it because of this:
energy.c:539:53: note: within this loop
   for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<=ALPHASIZE;k++) dr_dangle_dg_ar[i][j][k] = 0;

Perhaps that that k<= in the k loop should be < like in the i and j loops so it doesn't go beyond the end of the array.

ALPHASIZE is 6, so the k loop would try go one too far.  Every array allocated with ALPHASIZE certainly don't add one anywhere, so any look going from 0 to ALPHASIZE must use < not <= so there are two places in the file that are wrong.

I think this might help:

--- rnahybrid-2.1.2.orig/src/energy.c   2013-08-25 11:51:20.000000000 -0400
+++ rnahybrid-2.1.2/src/energy.c        2017-09-26 11:04:34.747986466 -0400
@@ -536,7 +536,7 @@
 void init_dr_dangle_dg_ar()
 {
   int i,j,k;
-  for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<=ALPHASIZE;k++) dr_dangle_dg_ar[i][j][k] = 0;
+  for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<ALPHASIZE;k++) dr_dangle_dg_ar[i][j][k] = 0;
 
   dr_dangle_dg_ar[A][U][A] = -0.700;
   dr_dangle_dg_ar[A][U][C] = -0.100;
@@ -568,7 +568,7 @@
 void init_dl_dangle_dg_ar()
 {
   int i,j,k;
-  for(i=0;i<=ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<ALPHASIZE;k++) dl_dangle_dg_ar[i][j][k] = 0;
+  for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<ALPHASIZE;k++) dl_dangle_dg_ar[i][j][k] = 0;
 
   dl_dangle_dg_ar[A][A][U] = -0.300;
   dl_dangle_dg_ar[C][A][U] = -0.300;

> There are other warnings, too, but undefined behaviour is particularly scary.

The pointers being converted to integers concern me a bit.  That might
cause big problems on 64 bit systems.

It sure looks like some seriously sloppy coding.

-- 
Len Sorensen