[Debian-med-packaging] Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)

[Matthew Fernandez]

> On Apr 30, 2020, at 00:31, Andreas Tille <andreas at fam-tille.de> wrote:
> 
> On Wed, Apr 29, 2020 at 05:51:26PM -0700, Matthew Fernandez wrote:
> 
>> The other option I suggested was Valgrind, but if you can’t run apt-file you probably can’t install Valgrind either.
> 
> Well, I guess apt-get is permitted for sudo but not apt-file.  So I can
> probably install valgrind inside the chroot environment.  I've never
> worked with valgrind.  What am I supposed to do?

Valgrind, in its default mode, checks for a variety of memory issues (use-after-free, write out-of bounds, …). You don’t need any special configure/build options, but you probably want to enable debug symbols (`export CFLAGS=-g; export CXXFLAGS=-g`). Then you can prefix the test you’re running with Valgrind: `valgrind ./src/clustalo -i debian/tests/biopython_testdata/f002 …`.

Valgrind and ASan serve roughly the same purpose in this scenario, but I usually tend to prefer ASan because it is more efficient and tends to give you more accurate debugging clues.

> On the other hand:  Is valgrind possibly able to uncover issues also
> on any other architecture?

You mean if we were to use Valgrind to debug this on e.g. x86? In my own experiments on amd64, both ASan and Valgrind found multiple issues in both Clustal Omega and its dependency, argtable2. However I don’t believe any of the remaining ones I was seeing after the last patches I sent you could be causing the mipsel bus error; they were all memory leaks.