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

[Andreas Tille]

Hi Adrian,

thanks a lot for your investigation.

On Sun, May 10, 2020 at 11:19:27AM +0300, Adrian Bunk wrote:
> What does fix the problem is disabling OpenMP.
> I suspect OpenMP is somehow broken in gcc >= 8 on mipsel.

I wonder how we could keep this finding to other packages.  I bet it
would not the only issue but it has shown up due to intense testing.
 
> Below is a workaround patch (lower performance of clustalo on mipsel 
> shouldn't be a major problem).

Its definitely no problem - I doubt that the package is used at all on
mipsel.  Its simply of theoretical interest and might uncover hidden
issues (finally some suggestions to enhance the code were found not only
for mipsel).

> --- clustalo-1.2.4/debian/rules	2020-04-14 12:19:44.000000000 +0300
> +++ clustalo-1.2.4/debian/rules	2020-04-14 12:19:44.000000000 +0300
> @@ -9,6 +9,11 @@
>  %:
>  	dh $@
>  
> +ifneq (,$(filter $(DEB_HOST_ARCH), mipsel))
> +override_dh_auto_configure:
> +	dh_auto_configure -- --without-openmp
> +endif
> +
>  override_dh_auto_build-indep:
>  	# nothing to do here

I've now uploaded now with this patch closing the bug - but as I tried to
express I'd sleep a bit better if this issue would be recorded somewhere
else than in a closed bug.

Thanks again for your research

    Andreas.

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