[Bioc-devel] Biostrings: substitution matrices disappeared?

[Hervé Pagès]

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>
> *Sent:* Thursday, April 25, 2024 9:06 AM
> *To:* ulrich using bodenhofer.com; 'Martin Grigorov' <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

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