[Debian-med-packaging] Clustalo fix for loop going outof-bounds

[Christian Ehrhardt]

Hi Clustalo/Omega Team,
as discussed on the Ubuntu bug [1] and eventually found in [2] (thanks
IBM s390x team) it seems that Clustalo causes a segfault by broken
iChunkEnds handling. There was a fix suggested that I wanted to pass
on to you.

diff --git a/src/clustal/pair_dist.c.orig b/src/clustal/pair_dist.c
index e6dbdc3..bb79e61 100644
--- a/src/clustal/pair_dist.c.orig
+++ b/src/clustal/pair_dist.c
@@ -321,7 +321,7 @@ PairDistances(symmatrix_t **distmat, mseq_t *mseq,
int pairdist_type, bool bPerc

/* FIXME: can get rid of iChunkStart, iChunkEnd now that we're using
the arrays */
iChunkStart = iend;
- for(iChunk = 0; iChunk <= iNumberOfThreads; iChunk++)
+ for(iChunk = 0; iChunk < iNumberOfThreads; iChunk++)
{
iChunkEnd = iChunkStart;
if (iChunk == iNumberOfThreads - 1){

This also is discussed on Debian in [3].
Missing a mailing list or bug tracker I'd appreciate if you could
comment in [1] or [3] or both about your upstream-opinion on that
change.

[1]: https://bugs.launchpad.net/ubuntu/+source/clustalo/+bug/1903817
[2]: https://bugs.launchpad.net/ubuntu/+source/clustalo/+bug/1903817/comments/15
[3]: https://salsa.debian.org/med-team/clustalo/-/merge_requests/1

-- 
Christian Ehrhardt
Staff Engineer, Ubuntu Server
Canonical Ltd