> On Apr 17, 2020, at 04:20, Andreas Tille <andr...@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@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.
clustalo-log-format-calls.patch
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