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

[Andreas Tille]

Control: tags -1 help

Hi,

as it can be seen on the recent build log of clustalo on mips[1] the
build fails with


# Run additional test from python-biopython package to verify that
# this will work as well
src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force
make[1]: *** [debian/rules:25: override_dh_auto_test-arch] Bus error


I injected that extra test since this very test failed inside the
python-biopython package.  To track it down I logged in to
eller.debian.org tried to build the package and was able to reproduce
the error.  Thus I fired up gdb in this session and got:


(sid_mipsel-dchroot)tille at eller:~/clustalo-1.2.4$ gdb --args src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force
GNU gdb (Debian 9.1-3) 9.1
...
Reading symbols from src/clustalo...
(gdb) run
Starting program: /home/tille/clustalo-1.2.4/src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/mipsel-linux-gnu/libthread_db.so.1".

Program received signal SIGBUS, Bus error.
0x5556a188 in PairDistances (distmat=0x7fff278c, mseq=0x55692a38, pairdist_type=<optimized out>, bPercID=<optimized out>, istart=0, iend=3, jstart=0, jend=3, fdist_in=0x0, fdist_out=0x0) at pair_dist.c:346
346                 NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),
(gdb)


So it seems the bus error occures somehow here:

   https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/pair_dist.c#L346


I have no idea how to continue from here.  I'm hoping that someone with
some more detailed knowledge might have a clue how to fix this issue on
mipsel.  Otherwise I personally do not see any better solution than to
remove clustalo from mipsel architecture.

Kind regards

      Andreas.

[1] https://buildd.debian.org/status/fetch.php?pkg=clustalo&arch=mipsel&ver=1.2.4-5&stamp=1586883766&raw=0

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