Re: [Bioc-devel] Biostrings: substitution matrices disappeared?
No, that’s absolutely fine. I actually had forgotten that substitution matrices were also used in the examples of msaMuscle(). Thanks for fixing! Cheers, Ulrich From: Hervé Pagès Sent: Thursday, April 25, 2024 10:11 AM To: ulr...@bodenhofer.com Cc: bioc-devel@r-project.org; 'Martin Grigorov' Subject: Re: [Bioc-devel] Biostrings: substitution matrices disappeared? 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 mailto:hpages.on.git...@gmail.com Sent: Thursday, April 25, 2024 9:52 AM To: mailto:ulr...@bodenhofer.com Cc: mailto:bioc-devel@r-project.org; 'Martin Grigorov' mailto:martin.grigo...@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.git...@gmail.com Sent: Thursday, April 25, 2024 9:06 AM To: mailto:ulr...@bodenhofer.com; 'Martin Grigorov' mailto:martin.grigo...@gmail.com Cc: mailto:bioc-devel@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.grigo...@gmail.com Sent: Thursday, April 25, 2024 7:52 AM To: mailto:ulr...@bodenhofer.com Cc: mailto: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 mailto:hpages.on.git...@gmail.com -- Hervé Pagès Bioconductor Core Team mailto:hpages.on.git...@gmail.com -- Hervé Pagès Bioconductor Core Team mailto:hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Biostrings: substitution matrices disappeared?
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 > *Sent:* Thursday, April 25, 2024 9:52 AM > *To:* ulr...@bodenhofer.com > *Cc:* bioc-devel@r-project.org; 'Martin Grigorov' > > *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.git...@gmail.com> > *Sent:* Thursday, April 25, 2024 9:06 AM > *To:* ulr...@bodenhofer.com; 'Martin Grigorov' > <mailto:martin.grigo...@gmail.com> > *Cc:* bioc-devel@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.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> > <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 <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 > > -- > Hervé Pagès > Bioconductor Core Team > hpages.on.git...@gmail.com -- 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
Re: [Bioc-devel] Biostrings: substitution matrices disappeared?
Great, thanks, Hervé! I also made two more fixes and pushed them. Cheers, Ulrich From: Hervé Pagès Sent: Thursday, April 25, 2024 9:52 AM To: ulr...@bodenhofer.com Cc: bioc-devel@r-project.org; 'Martin Grigorov' 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.git...@gmail.com> Sent: Thursday, April 25, 2024 9:06 AM To: ulr...@bodenhofer.com <mailto:ulr...@bodenhofer.com> ; 'Martin Grigorov' <mailto:martin.grigo...@gmail.com> Cc: bioc-devel@r-project.org <mailto:bioc-devel@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.grigo...@gmail.com> Sent: Thursday, April 25, 2024 7:52 AM To: ulr...@bodenhofer.com <mailto:ulr...@bodenhofer.com> Cc: bioc-devel@r-project.org <mailto: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> <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 <mailto:hpages.on.git...@gmail.com> -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 > *Sent:* Thursday, April 25, 2024 9:06 AM > *To:* ulr...@bodenhofer.com; 'Martin Grigorov' > *Cc:* bioc-devel@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.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> > <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 <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 -- 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
Re: [Bioc-devel] Biostrings: substitution matrices disappeared?
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 Sent: Thursday, April 25, 2024 9:06 AM To: ulr...@bodenhofer.com; 'Martin Grigorov' Cc: bioc-devel@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.grigo...@gmail.com> Sent: Thursday, April 25, 2024 7:52 AM To: ulr...@bodenhofer.com <mailto:ulr...@bodenhofer.com> Cc: bioc-devel@r-project.org <mailto: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> <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 <mailto:hpages.on.git...@gmail.com> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 > 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
Re: [Bioc-devel] Biostrings: substitution matrices disappeared?
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 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 < 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 > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Biostrings: substitution matrices disappeared?
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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
