Dear Bioconductor Core Team,
I am the maintainer of cliqueMS. The package was flagged to deprecation
but I have been able to fix the error that was causing the failure in
the checks. I just had to remove a dependency that is no longer on CRAN
and replace for a package available there. After
I forgot to mention that the BLOSUM and PAM substitution matrices have
also moved from Biostrings to the new pwalign package.
37 software packages were affected by this move (see list below). All of
them have been fixed. If you maintain one of them, please resync your
GitHub repo with the repo
No, that’s absolutely fine. I actually had forgotten that substitution matrices
were also used in the examples of msaMuscle(). Thanks for fixing!
Cheers, Ulrich
From: Hervé Pagès
Sent: Thursday, April 25, 2024 10:11 AM
To: ulr...@bodenhofer.com
Cc: bioc-devel@r-project.org; 'Martin Grigorov'
Good. I also just pushed 2 additional small tweaks (commits 0e98500 and
84c8ed5) right after you pushed yours. Hopefully I didn't step on your toes.
H.
On 4/25/24 01:04, Ulrich Bodenhofer wrote:
>
> Great, thanks, Hervé! I also made two more fixes and pushed them.
>
> Cheers, Ulrich
>
>
Great, thanks, Hervé! I also made two more fixes and pushed them.
Cheers, Ulrich
From: Hervé Pagès
Sent: Thursday, April 25, 2024 9:52 AM
To: ulr...@bodenhofer.com
Cc: bioc-devel@r-project.org; 'Martin Grigorov'
Subject: Re: [Bioc-devel] Biostrings: substitution matrices disappeared?
I'm done. Please resync you GitHub repo.
Best,
H.
On 4/25/24 00:14, Ulrich Bodenhofer wrote:
>
> Great, thanks, Hervé, so I’ll simply wait for the update. If there is
> anything I should do, just let me know.
>
> Thanks and best regards,
>
> Ulrich
>
> *From:*Hervé Pagès
> *Sent:* Thursday,
Great, thanks, Hervé, so I’ll simply wait for the update. If there is anything
I should do, just let me know.
Thanks and best regards,
Ulrich
From: Hervé Pagès
Sent: Thursday, April 25, 2024 9:06 AM
To: ulr...@bodenhofer.com; 'Martin Grigorov'
Cc: bioc-devel@r-project.org
Subject:
Hi Ulrich,
Yes the substitution matrices are now in pwalign. I'm taking care of
msa. Sorry for that.
Best,
H.
On 4/24/24 23:25, Ulrich Bodenhofer wrote:
> Ah, thank you very much, sorry for having overlooked this! Yes, that seems
> the source of the problem. Hervé, should I wait for your
Ah, thank you very much, sorry for having overlooked this! Yes, that seems the
source of the problem. Hervé, should I wait for your update or rather change
the package myself? The latter won’t be a problem for me. I suppose it is just
about adding ‘pwalign’ as an additional dependency, right?
