[Bioc-devel] cliqueMS request for undeprecation as all errors have been fixed

2024-04-25 Thread Oriol Senan Campos 

Dear Bioconductor Core Team,

I am the maintainer of cliqueMS. The package was flagged to deprecation 
but I have been able to fix the error that was causing the failure in 
the checks. I just had to remove a dependency that is no longer on CRAN 
and replace for a package available there. After checks and passing all 
the test I could find another dependency that does a similar 
calculation. I already pushed to Bioc devel (3.18 I cannot make any more 
commits). So please remove cliqueMS from the list of deprecated packages 
for 3.19. Tomorrow we will see a new build and I expect all OS and hosts 
to pass.


Kind Regards,
Oriol Senan

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Re: [Bioc-devel] Build errors related to the new pwalign package

2024-04-25 Thread Hervé Pagès 
I forgot to mention that the BLOSUM and PAM substitution matrices have 
also moved from Biostrings to the new pwalign package.

37 software packages were affected by this move (see list below). All of 
them have been fixed. If you maintain one of them, please resync your 
GitHub repo with the repo at git.bioconductor.org.

Let me know if you have any questions.

Cheers,

H.

List of software packages that were affected by the Biostrings/pwalign 
split (in alphabetical order):

amplican
ChIPpeakAnno
ClustIRR
CNEr
crisprShiny
DECIPHER
DominoEffect
enhancerHomologSearch
girafe
GUIDEseq
hiReadsProcessor
HTSeqGenie
idpr
IMMAN
iPAC
IsoformSwitchAnalyzeR
LinTInd
MethTargetedNGS
methylscaper
motifbreakR
msa
MSA2dist
openPrimeR
QSutils
QuartPAC
R453Plus1Toolbox
Rcpi
RSVSim
sangeranalyseR
sangerseqR
scanMiR
ShortRead
SPLINTER
StructuralVariantAnnotation
svaNUMT
TFBSTools
XNAString


On 4/24/24 09:52, Hervé Pagès wrote:
>
> Hi developers,
>
> pairwiseAlignement() and stringDist() have recently moved from 
> Biostrings to the new pwalign package. This is causing a number of 
> failures today on the 3.19 report. Since yesterday I've been actively 
> repairing packages affected by this by pushing fixes to 
> git.bioconductor.org. Most packages are now fixed but this won't 
> reflect before tomorrow's report.
>
> Later in the day I'll send emails to the maintainers of packages that 
> I have touched and ask them to resync their GitHub repos with 
> git.bioconductor.org.
>
> Sorry for the inconvenience.
>
> Let me know if you have any questions.
>
> Best,
>
> H.
>
> -- 
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Biostrings: substitution matrices disappeared?

2024-04-25 Thread Ulrich Bodenhofer 
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
 
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-- 
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

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Re: [Bioc-devel] Biostrings: substitution matrices disappeared?

2024-04-25 Thread Hervé Pagès 
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 
> 
> *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  
>   
>
> 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  
>   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
>
> -- 
> Hervé Pagès
> Bioconductor Core Team
> hpages.on.git...@gmail.com

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Biostrings: substitution matrices disappeared?

2024-04-25 Thread Ulrich Bodenhofer 
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   
 
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   
 
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  
  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.git...@gmail.com  

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com  

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Re: [Bioc-devel] Biostrings: substitution matrices disappeared?

2024-04-25 Thread Hervé Pagès 
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  
>   
>
> 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  
>   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

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Biostrings: substitution matrices disappeared?

2024-04-25 Thread Ulrich Bodenhofer 
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   
 
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  
  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.git...@gmail.com  

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Biostrings: substitution matrices disappeared?

2024-04-25 Thread 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  
> 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  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

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Re: [Bioc-devel] Biostrings: substitution matrices disappeared?

2024-04-25 Thread Ulrich Bodenhofer 
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 
 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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