[Bioc-devel] Biostrings: substitution matrices disappeared?

[Hervé Pagès]

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>  
> 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>  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
>
> _______________________________________________
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>
-- 
Hervé Pagès

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

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