Hi Aaron,
Aaron M. Ucko, on 2024-11-20:
> AFAICT, the relevant change is in blastdbcmd error output and the
> following patch suffices (perhaps with a line break thrown in):
Thank you for your patch, I have verified that it resolves the
issue raised by the test item in bioperl-run and I plan to a
Étienne Mollier writes:
> Thanks for the additional input, naively I would think the undef
> could have to do with a subtle change in makeblastdb output, but
AFAICT, the relevant change is in blastdbcmd error output and the
following patch suffices (perhaps with a line break thrown in):
--- a/l
Control: severity -1 normal
Greetings,
Étienne Mollier, on 2024-08-01:
> 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 wi
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
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 t
Control: tags -1 confirmed upstream
Control: forwarded -1 https://github.com/bioperl/bioperl-run/issues/62
Hi,
I think I pinpointed the test failure in bioperl-run stems from
ongoing ncbi-blast+ upgrade to version 2.16.0. bioperl-run is
still building properly on testing, but if I bump ncbi-blas
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