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

[Charles Plessy]

Le Tue, Jul 30, 2024 at 10:19:32PM +0200, Étienne Mollier a écrit :
> Control: forwarded -1 https://github.com/bioperl/bioperl-run/issues/62
 
> The test includes several calls to the makeblastdb command,
> through various "factories" (in the sense of design patterns).
> My impression is that the test suite may have to adjust its
> makeblastdb invocation, at least the one spanning lines 55-58,
> as it seems to include the faulty windowmasker invocation.  As
> it very much feels like the test may need update, I informed
> upstream of the issue.

Hi all,

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.

`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.

Have a nice day,

Charles

-- 
Charles Plessy                         Nagahama, Yomitan, Okinawa, Japan
Debian Med packaging team         http://www.debian.org/devel/debian-med
Tooting from home                  https://framapiaf.org/@charles_plessy
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