[Bioc-devel] Biostrings: substitution matrices disappeared?

[Ulrich Bodenhofer]

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  <mailto:hpages.on.github using gmail.com> <hpages.on.github using gmail.com> 
Sent: Thursday, April 25, 2024 9:06 AM
To: ulrich using bodenhofer.com <mailto:ulrich using bodenhofer.com> ; 'Martin Grigorov'  <mailto:martin.grigorov using gmail.com> <martin.grigorov using gmail.com>
Cc: bioc-devel using r-project.org <mailto: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  <mailto:martin.grigorov using gmail.com> <martin.grigorov using gmail.com> 
Sent: Thursday, April 25, 2024 7:52 AM
To: ulrich using bodenhofer.com <mailto:ulrich using bodenhofer.com> 
Cc: bioc-devel using r-project.org <mailto: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
 
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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com <mailto:hpages.on.github using gmail.com> 

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com <mailto:hpages.on.github using gmail.com> 

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