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] Biostrings: substitution matrices disappeared?
9 messages · Martin Grigorov, Ulrich Bodenhofer, Hervé Pagès
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.bodenhofer at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Ah, thank you very much, sorry for having overlooked this! Yes, that seems the source of the problem. Herv?, 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 at gmail.com> Sent: Thursday, April 25, 2024 7:52 AM To: ulrich at bodenhofer.com Cc: bioc-devel at 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 at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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. Herv?, 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 at gmail.com> Sent: Thursday, April 25, 2024 7:52 AM To:ulrich at bodenhofer.com Cc:bioc-devel at 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 at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com [[alternative HTML version deleted]]
Great, thanks, Herv?, 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: Herv? Pag?s <hpages.on.github at gmail.com> Sent: Thursday, April 25, 2024 9:06 AM To: ulrich at bodenhofer.com; 'Martin Grigorov' <martin.grigorov at gmail.com> Cc: bioc-devel at 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. Herv?, 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 at gmail.com> <martin.grigorov at gmail.com> Sent: Thursday, April 25, 2024 7:52 AM To: ulrich at bodenhofer.com <mailto:ulrich at bodenhofer.com> Cc: bioc-devel at r-project.org <mailto:bioc-devel at 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 at gmail.com> <mailto:ulrich.bodenhofer at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com <mailto:hpages.on.github at gmail.com> [[alternative HTML version deleted]]
I'm done. Please resync you GitHub repo. Best, H.
On 4/25/24 00:14, Ulrich Bodenhofer wrote:
Great, thanks, Herv?, 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:*Herv? Pag?s <hpages.on.github at gmail.com>
*Sent:* Thursday, April 25, 2024 9:06 AM
*To:* ulrich at bodenhofer.com; 'Martin Grigorov' <martin.grigorov at gmail.com>
*Cc:* bioc-devel at 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. Herv?, 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 at gmail.com> <mailto:martin.grigorov at gmail.com>
Sent: Thursday, April 25, 2024 7:52 AM
To:ulrich at bodenhofer.com
Cc:bioc-devel at 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 at gmail.com> <mailto:ulrich.bodenhofer at 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 at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Herv? Pag?s
Bioconductor Core Team
hpages.on.github at gmail.com
Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com [[alternative HTML version deleted]]
Great, thanks, Herv?! I also made two more fixes and pushed them. Cheers, Ulrich From: Herv? Pag?s <hpages.on.github at gmail.com> Sent: Thursday, April 25, 2024 9:52 AM To: ulrich at bodenhofer.com Cc: bioc-devel at r-project.org; 'Martin Grigorov' <martin.grigorov at 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, Herv?, 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: Herv? Pag?s <mailto:hpages.on.github at gmail.com> <hpages.on.github at gmail.com> Sent: Thursday, April 25, 2024 9:06 AM To: ulrich at bodenhofer.com <mailto:ulrich at bodenhofer.com> ; 'Martin Grigorov' <mailto:martin.grigorov at gmail.com> <martin.grigorov at gmail.com> Cc: bioc-devel at r-project.org <mailto:bioc-devel at 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. Herv?, 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 at gmail.com> <martin.grigorov at gmail.com> Sent: Thursday, April 25, 2024 7:52 AM To: ulrich at bodenhofer.com <mailto:ulrich at bodenhofer.com> Cc: bioc-devel at r-project.org <mailto:bioc-devel at 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 at gmail.com> <mailto:ulrich.bodenhofer at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com <mailto:hpages.on.github at gmail.com>
Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com <mailto:hpages.on.github at gmail.com> [[alternative HTML version deleted]]
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, Herv?! I also made two more fixes and pushed them.
Cheers, Ulrich
*From:*Herv? Pag?s <hpages.on.github at gmail.com>
*Sent:* Thursday, April 25, 2024 9:52 AM
*To:* ulrich at bodenhofer.com
*Cc:* bioc-devel at r-project.org; 'Martin Grigorov'
<martin.grigorov at 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, Herv?, 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:*Herv? Pag?s <hpages.on.github at gmail.com>
<mailto:hpages.on.github at gmail.com>
*Sent:* Thursday, April 25, 2024 9:06 AM
*To:* ulrich at bodenhofer.com; 'Martin Grigorov'
<martin.grigorov at gmail.com> <mailto:martin.grigorov at gmail.com>
*Cc:* bioc-devel at 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. Herv?, 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 at gmail.com> <mailto:martin.grigorov at gmail.com>
Sent: Thursday, April 25, 2024 7:52 AM
To:ulrich at bodenhofer.com
Cc:bioc-devel at 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 at gmail.com> <mailto:ulrich.bodenhofer at 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 at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Herv? Pag?s
Bioconductor Core Team
hpages.on.github at gmail.com
--
Herv? Pag?s
Bioconductor Core Team
hpages.on.github at gmail.com
Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com [[alternative HTML version deleted]]
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: Herv? Pag?s <hpages.on.github at gmail.com> Sent: Thursday, April 25, 2024 10:11 AM To: ulrich at bodenhofer.com Cc: bioc-devel at r-project.org; 'Martin Grigorov' <martin.grigorov at gmail.com> 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, Herv?! I also made two more fixes and pushed them. Cheers, Ulrich From: Herv? Pag?s mailto:hpages.on.github at gmail.com Sent: Thursday, April 25, 2024 9:52 AM To: mailto:ulrich at bodenhofer.com Cc: mailto:bioc-devel at r-project.org; 'Martin Grigorov' mailto:martin.grigorov at 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, Herv?, 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: Herv? Pag?s mailto:hpages.on.github at gmail.com Sent: Thursday, April 25, 2024 9:06 AM To: mailto:ulrich at bodenhofer.com; 'Martin Grigorov' mailto:martin.grigorov at gmail.com Cc: mailto:bioc-devel at 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. Herv?, 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 at gmail.com Sent: Thursday, April 25, 2024 7:52 AM To: mailto:ulrich at bodenhofer.com Cc: mailto:bioc-devel at 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 at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Herv? Pag?s Bioconductor Core Team mailto:hpages.on.github at gmail.com -- Herv? Pag?s Bioconductor Core Team mailto:hpages.on.github at gmail.com
Herv? Pag?s Bioconductor Core Team mailto:hpages.on.github at gmail.com