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

[Andreas Tille]

Hi Matthew,

On Fri, Apr 17, 2020 at 08:18:29AM -0700, Matthew Fernandez wrote:
> > Thanks for the patch which I applied to packaging Git.  I assume you
> > want to express that while these fixes are definitely good coding
> > practice the bus error problem is not fixed by it, right?
> 
> Thanks, Andreas. It may fix the bus error, but I don’t have a MIPS machine
> to test on. Some of those logging calls had the potential to leave you with
> a misaligned stack pointer. IIUC unaligned loads on MIPS could cause such a
> bus error.

I tried with hope ... but failed:

(sid_mipsel-dchroot)tille at eller:~/clustalo$ 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/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),


Thank you for the fixes anyway

     Andreas.

-- 
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