[Debian-med-packaging] Bug#1077454: Bug#1077454: bioperl-run: t/SABlastPlus.t failure

[Étienne Mollier]

Hi Charles,

Charles Plessy, on 2024-08-01:
> I had a closer look at the source code yesterday and I could not
> understand the reason for the error.
> 
> One of the failing statement is:
> 
>     is ($fac->db_type, 'nucl', "right type");
> 
> The `db_type` method just looks at the `_db_type` slot of the object,
> which records the `-dbtype` parameter passed to `makeblastdb`, which
> must be `nucl` or `prot`, and this has not changed in the latest
> `ncbi-blast+` package.

Thanks for the additional input, naively I would think the undef
could have to do with a subtle change in makeblastdb output, but
I haven't checked closely the first test failure to be honest.

Anyway:
> `bioperl-run` has no activity on GitHub for the past 4 years, and no
> other Debian Med packages depend on it.  If us or upstream can not fix
> that bug on time, I think that it is probably fine to release without it
> and to consider removing package go if we do not get complains.

Good point, if that drains too much energy, "let it fade" may be
an adequate course of action.  I will tackle other bugs in the
meantime, and get back to it once RC bugs are under control.

> Have a nice day,

Likewise,  :)
-- 
  .''`.  Étienne Mollier <emollier at debian.org>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/0, please excuse my verbosity
   `-    on air: Yes - Fly From Here

> - You  do not have  my permission  to use  this email  to train  an AI -
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 833 bytes
Desc: not available
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20240801/ea3c0da9/attachment-0001.sig>