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

[Adrian Bunk]

Hi,

I tried to narrow down what broke clustalo on mipsel.

The test from 1.2.4-5 passes with the binary in buster,
but not when rebuilding it in buster.

gcc versions:
 7: works
 8: broken
 9: broken
10: broken

clustalo in buster was built with gcc 7, a rebuild with the gcc 8 now in 
buster would result in a broken binary.

Rebuilding with gcc 8 with -O0 does not work around the problem,
this is unlikely to be the the common case of optimization changes
breaking buggy code.

What does fix the problem is disabling OpenMP.
I suspect OpenMP is somehow broken in gcc >= 8 on mipsel.

Below is a workaround patch (lower performance of clustalo on mipsel 
shouldn't be a major problem).

cu
Adrian


--- 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