Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
Hi,
On Wed, Apr 29, 2020 at 10:30:35AM +0800, 黄佳文 wrote:
> I am a developer from Loongson company (R & D CPU/mip64el), I've been
> looking at this recently.
Very nice to see mips developers to care for biological software. :-)
> I did two experiments, and I found that when I used Python 3,7 to compile
> python-biopython, Build successfully.
> In the same environment, I just upgrade Python 3.7 to Python 3.8, and then
> compile python-biopytho, Build fails, but not bus error.
> I found through online query that some symbol tables were added and deleted
> in upgrading Python 3.7 to 3.8. The following are symbol tables:
Sorry to insist here - I do not think that it is a Python version problem
at all. The issue can be reproduced in clustalo only which is pure C code.
May be you have a look at
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956324#59
and the following discussion. Despite Matthew has found some issues inside
the C code it did not helped to prevent:
Starting program: /home/tille/clustalo/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.
0x5556a1b8 in PairDistances (distmat=0x7fff278c, mseq=0x55692a30, 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),
That's the issue we need to care about here.
Kind regards and thanks a lot for the attempt to help
Andreas.
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