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

[Andreas Tille]

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.