src/rnaeffective.c | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 fix build error with gcc-4.8 by adding string.h

src/Makefile.am | 3 3 + 0 - 0 !
1 file changed, 3 insertions(+)

 propagate hardening options

man/RNAcalibrate.1 | 1 0 + 1 - 0 !
man/RNAeffective.1 | 1 0 + 1 - 0 !
man/RNAhybrid.1 | 1 0 + 1 - 0 !
3 files changed, 3 deletions(-)

 fix manpage syntax

src/rnacalibrate.c | 7 6 + 1 - 0 !
src/rnaeffective.c | 6 5 + 1 - 0 !
2 files changed, 11 insertions(+), 2 deletions(-)

 check if file exists before opening

src/energy.c | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 fix issues that are becoming visible on arm but might be
 a problem on all architectures.
 .
 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 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.

src/fasta.h | 1 1 + 0 - 0 !
src/hybrid_core.h | 2 2 + 0 - 0 !
src/numerical.c | 2 2 + 0 - 0 !
src/plot.c | 2 2 + 0 - 0 !
src/plot.h | 3 3 + 0 - 0 !
src/random.c | 1 1 + 0 - 0 !
src/rnacalibrate.c | 24 14 + 10 - 0 !
src/rnaeffective.c | 22 13 + 9 - 0 !
src/rnahybrid.c | 1 1 + 0 - 0 !
9 files changed, 39 insertions(+), 19 deletions(-)

 fix spurious warnings that might in fact be errors