Re: [Bioc-devel] groHMM package error

2023-10-25 Thread Hervé Pagès 
Addressed in S4Vectors 0.40.1. Today's builds have started already so 
the fix won't be reflected on tomorrow's report (Thursday), only on Friday.

Sorry again for the inconvenience.

Best,

H.

On 10/25/23 15:34, Hervé Pagès wrote:
>
> Hi Tulip,
>
> I think this is caused by a late change in S4Vectors: 
> https://github.com/Bioconductor/S4Vectors/commit/15349ef40f141b16df6daf3e38f3782ef54eb60c
>
> This was an attempt at implementing the following feature request: 
> https://github.com/Bioconductor/DelayedArray/issues/108
>
> Sorry that this change broken your subsetting operation kgChr7[de==1, ].
>
> Honestly, it's hard (if not impossible) to anticipate that some code 
> somewhere would use a Nx1 TestResults object (this is what 'de==1' 
> is!) as a subscript to subset a Vector derivative like your GRanges 
> object kgChr7. It was just luck that this was working so far. Anyways, 
> I think we can make this work again. A patch is coming.
>
> Best,
>
> H.
>
> On 10/25/23 14:03, Tulip Nandu wrote:
>> Hi Lori,
>>
>> Thank you for your prompt response. I haven't changed anything in the 
>> development package (on git on anywhere else) then why the error message has 
>> suddenly come up. As per the package what exactly they want me to change so 
>> it passes the R CMD Check goes on without errors.
>>
>> Regards,
>>
>> Tulip.
>>
>> 
>> From: Kern, Lori
>> Sent: Wednesday, October 25, 2023 6:06 AM
>> To: Tulip Nandu;bioc-devel@r-project.org  
>> 
>> Cc: Martin Grigorov
>> Subject: Re: groHMM package error
>>
>> You should make sure you are using the latest version of R and have updated 
>> Bioconductor/CRAN packages by running BiocManager::valid and/or 
>> BiocManager:install .  I can reproduce this locally.
>>
>> Running your vignette it has to do with this line:
>>
>>> upGenes <- kgChr7[de==1,]
>> Error: invalid subscript
>>
>>
>>
>>
>>
>> Lori Shepherd - Kern
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>> 
>> From: Tulip Nandu
>> Sent: Tuesday, October 24, 2023 3:33 PM
>> To:bioc-devel@r-project.org  
>> Cc: Kern, Lori; Martin 
>> Grigorov
>> Subject: Re: groHMM package error
>>
>> Hi,
>>
>>
>> Can someone explain as why has this error suddenly come up. I haven't 
>> changed anything from my end.
>>
>> Also, please if someone can help me tackle the error it would be great.
>>
>>
>> Thanks.
>>
>> Regards,
>>
>> Tulip.
>>
>> 
>> From: Kern, Lori
>> Sent: Wednesday, October 18, 2023 3:45 PM
>> To: Tulip Nandu
>> Subject: Re: groHMM package error
>>
>> As Martin also responded,  The ERROR should not be neglected but you should 
>> push to the "devel" branch instead of "RELEASE_3_18".
>>
>>
>>
>>
>>
>> Lori Shepherd - Kern
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>> 
>> From: Tulip Nandu
>> Sent: Wednesday, October 18, 2023 4:37 PM
>> To: Kern, Lori;bioc-devel@r-project.org  
>> ;martin.grigo...@gmail.com  
>> 
>> Subject: Re: groHMM package error
>>
>> Is this error to be neglected then?
>>
>> Package: groHMM
>> Version: 1.35.0
>> Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs 
>> --no-resave-data groHMM
>> StartedAt: 2023-10-17 17:05:26 -0400 (Tue, 17 Oct 2023)
>> EndedAt: 2023-10-17 17:07:18 -0400 (Tue, 17 Oct 2023)
>> EllapsedTime: 112.0 seconds
>> RetCode: 1
>> Status:   ERROR
>> PackageFile: None
>> PackageFileSize: NA
>>
>>
>> According to the Multiple platform build/check report for BioC 3.18,
>> the groHMM package has the following problem(s):
>>
>>   o ERROR for 'R CMD build' on nebbiolo2. See the details here:
>>   
>> https://secure-web.cisco.com/1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.18%2Fbioc-LATEST%2FgroHMM%2Fnebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$>  
>>

Re: [Bioc-devel] groHMM package error

2023-10-25 Thread Tulip Nandu 
Hi Lori,

Thank you for your prompt response. I haven't changed anything in the 
development package (on git on anywhere else) then why the error message has 
suddenly come up. As per the package what exactly they want me to change so it 
passes the R CMD Check goes on without errors.

Regards,

Tulip.


From: Kern, Lori 
Sent: Wednesday, October 25, 2023 6:06 AM
To: Tulip Nandu ; bioc-devel@r-project.org 

Cc: Martin Grigorov 
Subject: Re: groHMM package error

You should make sure you are using the latest version of R and have updated 
Bioconductor/CRAN packages by running BiocManager::valid and/or 
BiocManager:install .  I can reproduce this locally.

Running your vignette it has to do with this line:

> upGenes <- kgChr7[de==1,]
Error: invalid subscript





Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Tulip Nandu 
Sent: Tuesday, October 24, 2023 3:33 PM
To: bioc-devel@r-project.org 
Cc: Kern, Lori ; Martin Grigorov 

Subject: Re: groHMM package error

Hi,


Can someone explain as why has this error suddenly come up. I haven't changed 
anything from my end.

Also, please if someone can help me tackle the error it would be great.


Thanks.

Regards,

Tulip.


From: Kern, Lori 
Sent: Wednesday, October 18, 2023 3:45 PM
To: Tulip Nandu 
Subject: Re: groHMM package error

As Martin also responded,  The ERROR should not be neglected but you should 
push to the "devel" branch instead of "RELEASE_3_18".





Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Tulip Nandu 
Sent: Wednesday, October 18, 2023 4:37 PM
To: Kern, Lori ; bioc-devel@r-project.org 
; martin.grigo...@gmail.com 

Subject: Re: groHMM package error

Is this error to be neglected then?

Package: groHMM
Version: 1.35.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs 
--no-resave-data groHMM
StartedAt: 2023-10-17 17:05:26 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 17:07:18 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 112.0 seconds
RetCode: 1
Status:   ERROR
PackageFile: None
PackageFileSize: NA


According to the Multiple platform build/check report for BioC 3.18,
the groHMM package has the following problem(s):

 o ERROR for 'R CMD build' on nebbiolo2. See the details here:
 
https://secure-web.cisco.com/1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.18%2Fbioc-LATEST%2FgroHMM%2Fnebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$

[Bioc-devel] Bioconductor 3.18 is Released!

2023-10-25 Thread Kern, Lori via Bioc-devel 
Thanks to all developers and community members for contributing to the project!
Please see the full release announcement:
https://bioconductor.org/news/bioc_3_18_release/

Cheers,
Sent on behalf of the Bioconductor Core Team



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] groHMM package error

2023-10-25 Thread Kern, Lori via Bioc-devel 
You should make sure you are using the latest version of R and have updated 
Bioconductor/CRAN packages by running BiocManager::valid and/or 
BiocManager:install .  I can reproduce this locally.

Running your vignette it has to do with this line:

> upGenes <- kgChr7[de==1,]
Error: invalid subscript





Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Tulip Nandu 
Sent: Tuesday, October 24, 2023 3:33 PM
To: bioc-devel@r-project.org 
Cc: Kern, Lori ; Martin Grigorov 

Subject: Re: groHMM package error

Hi,


Can someone explain as why has this error suddenly come up. I haven't changed 
anything from my end.

Also, please if someone can help me tackle the error it would be great.


Thanks.

Regards,

Tulip.


From: Kern, Lori 
Sent: Wednesday, October 18, 2023 3:45 PM
To: Tulip Nandu 
Subject: Re: groHMM package error

As Martin also responded,  The ERROR should not be neglected but you should 
push to the "devel" branch instead of "RELEASE_3_18".





Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Tulip Nandu 
Sent: Wednesday, October 18, 2023 4:37 PM
To: Kern, Lori ; bioc-devel@r-project.org 
; martin.grigo...@gmail.com 

Subject: Re: groHMM package error

Is this error to be neglected then?

Package: groHMM
Version: 1.35.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs 
--no-resave-data groHMM
StartedAt: 2023-10-17 17:05:26 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 17:07:18 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 112.0 seconds
RetCode: 1
Status:   ERROR
PackageFile: None
PackageFileSize: NA


According to the Multiple platform build/check report for BioC 3.18,
the groHMM package has the following problem(s):

 o ERROR for 'R CMD build' on nebbiolo2. See the details here:
 
https://secure-web.cisco.com/1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.18%2Fbioc-LATEST%2FgroHMM%2Fnebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$

Let me know.

Thank you so much.

Regards,

Tulip.



From: Kern, Lori 
Sent: Wednesday, October 18, 2023 3:36 PM
To: Tulip Nandu ; bioc-devel@r-project.org 

Subject: Re: groHMM package error


EXTERNAL MAIL

There is no RELEASE_3_18 branch until the release next week (created 
automatically by the core team on release day) .  All updates should be pushed 
to the devel

Re: [Bioc-devel] Macarron Next BiocRelease

2023-10-25 Thread Kern, Lori via Bioc-devel 
yes. Please push to both devel and RELEASE_3_18 with your changes.  remember to 
pull first as there will be version bumps from the core team from yesterdays 
Bioc 3.18 creation.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of sagun maharjan 

Sent: Tuesday, October 24, 2023 9:38 PM
To: Bioc-devel@r-project.org 
Cc: abho...@hsph.harvard.edu 
Subject: [Bioc-devel] Macarron Next BiocRelease

Hi Bioc Team,

We have fixed the windows build error for the Macarron package for the next
BioC release
https://secure-web.cisco.com/1S70TTR97-wShq8IvFc34VN9ip4v6t_wYXj_wS1QoWqOrjibe3VlRUMyU-UgIzpNIQ8IC9k4HM1X5rPkcbRfXEkCB3pWJ9J7g6tYPYt64PlTmhkibxEuhqdcD0dG9kJn99bqPgIZUVHTlmt_jC5ninrPHUJQ-FxET1YgXlZgPTgB30RTkR1NaKMEPpoPlbxdRKnRaWda4E-BA9kjfxDeaS53X96JxOH-cPoa6Q4MgRW5uGskCE3zdAlJE95Eb9FrbOnkPFbiR8LlIZ8ahskveY-Dt41spDU1HQTAKAQ6Ko11SH9F2PdCeg8tupVXpCQjl/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FMacarron%2F

Are the next steps to push the Macarron github changes into the new BioC
release branch following the tutorial below?
https://secure-web.cisco.com/1hhFkD10h_N0hYNvcKOc2BrzN6B4G0g3KklZzsCYpmiElj3SHLu20q_vwDemOnp1RTC7ylv7LmJudNE9DfzuD7oUDjrsYeNHFVsLFNOp4d7oOgFvBOBEVyAG2H1sVvE5_7gsU3mw7JoGKNV9uwYAt4GEKmxcnC5nn0oKyT1E1sWTlwRUfh0snt45TToectYSLdIRpL1WGKIlD8QoP-9ixOJLexatIUrXHNr9s7I-EFo9Wa9CXwaB_F4ucJFRhCUJ2u3RP7_Sb_nUZ3eRAWm792XoYFUoEyvxBFD9Vc1_Ex-B7YNHEP87UywkEyJEZiDe8/https%3A%2F%2Fcontributions.bioconductor.org%2Fgit-version-control.html%23sync-existing-repositories


Please suggest.

Regards,
Sagun

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