Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)

On Thu, Apr 30, 2020 at 10:33 AM Matthew Fernandez
<[email protected]> wrote:
>
> > On Apr 30, 2020, at 00:31, Andreas Tille <[email protected]> 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 …`.

One small issue... Valgrind recommends -O0 or -O1:

<QUOTE>
Compile your program with -g to include debugging information so that
Memcheck's error messages include exact line numbers. Using -O0 is
also a good idea, if you can tolerate the slowdown. With -O1 line
numbers in error messages can be inaccurate, although generally
speaking running Memcheck on code compiled at -O1 works fairly well,
and the speed improvement compared to running -O0 is quite
significant. Use of -O2 and above is not recommended as Memcheck
occasionally reports uninitialised-value errors which don't really
exist.
</QUOTE>

Also see the Valgrind Quick Start Guide, Section 2. Preparing Your
Programs, at http://valgrind.org/docs/manual/QuickStart.html.

Jeff