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

[Matthew Fernandez]

> On Apr 17, 2020, at 04:20, Andreas Tille <andreas at an3as.eu> wrote:
> 
> 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.

As a jumping off point, the attached patch fixes some issues with logging calls in the upstream 1.2.4 source release.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: clustalo-log-format-calls.patch
Type: application/octet-stream
Size: 5513 bytes
Desc: not available
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20200417/15712489/attachment.obj>