Re: Bug#861281: rnahybrid: FTBFS on armel
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
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