[Bioc-devel] Biostrings: substitution matrices disappeared?

[Hervé Pagès]

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
>
> *From:*Hervé Pagès <hpages.on.github using gmail.com>
> *Sent:* Thursday, April 25, 2024 9:52 AM
> *To:* ulrich using bodenhofer.com
> *Cc:* bioc-devel using r-project.org; 'Martin Grigorov' 
> <martin.grigorov using gmail.com>
> *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 <hpages.on.github using gmail.com>
>     <mailto:hpages.on.github using gmail.com>
>     *Sent:* Thursday, April 25, 2024 9:06 AM
>     *To:* ulrich using bodenhofer.com; 'Martin Grigorov'
>     <martin.grigorov using gmail.com> <mailto:martin.grigorov using gmail.com>
>     *Cc:* bioc-devel using r-project.org
>     *Subject:* Re: [Bioc-devel] Biostrings: substitution matrices
>     disappeared?
>
>     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 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?
>
>           
>
>         Thanks and best regards,
>
>         Ulrich
>
>           
>
>           
>
>         From: Martin Grigorov<martin.grigorov using gmail.com>  <mailto:martin.grigorov using gmail.com>  
>
>         Sent: Thursday, April 25, 2024 7:52 AM
>
>         To:ulrich using bodenhofer.com
>
>         Cc:bioc-devel using r-project.org
>
>         Subject: Re: [Bioc-devel] Biostrings: substitution matrices disappeared?
>
>           
>
>         Hi,
>
>           
>
>         Yesterday there was another email about Biostrings -https://stat.ethz.ch/pipermail/bioc-devel/2024-April/020395.html
>
>         I thought it might be related to your problem.
>
>           
>
>         Regards,
>
>         Martin
>
>           
>
>         On Thu, Apr 25, 2024 at 8:23 AM Ulrich Bodenhofer<mailto:ulrich.bodenhofer using gmail.com>  <mailto:ulrich.bodenhofer using gmail.com>  wrote:
>
>         Dear colleagues, dear BioC core team,
>
>           
>
>         One of my packages in the devel branch, the ‘msa’ package seems broken since
>
>         yesterday. The vignette does not run anymore (therefore, the package does
>
>         not build), and the reason is that the BLOSUM62 substitution matrix cannot
>
>         be loaded form the ‘Biostrings’ package anymore. I checked the ‘Biostrings’
>
>         package. In Version 2.70.3 in the release branch, the substitution matrices
>
>         were still in the ‘data/’ directory. In the current devel version 2.71.6,
>
>         they have disappeared. I found no hint to that in the NEWS file. So, I want
>
>         to kindly ask the maintainers of the ‘Biostrings’ package to give me some
>
>         advice how to fix that on my side or, in case that this is an error in the
>
>         current devel version of the ‘Biostrings’ package, to have a look into this.
>
>           
>
>         Thanks a lot in advance, best regards,
>
>         Ulrich
>
>           
>
>         _______________________________________________
>
>         mailto:Bioc-devel using r-project.org  <mailto:Bioc-devel using r-project.org>  mailing list
>
>         https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>           
>
>     -- 
>
>     Hervé Pagès
>
>       
>
>     Bioconductor Core Team
>
>     hpages.on.github using gmail.com
>
> -- 
> Hervé Pagès
> Bioconductor Core Team
> hpages.on.github using gmail.com

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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