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.grigo...@gmail.com> > Sent: Thursday, April 25, 2024 7:52 AM > To:ulr...@bodenhofer.com > Cc:bioc-devel@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.bodenho...@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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
