[Bioc-devel] groHMM package error

Mon Nov 25 23:49:32 CET 2024

Hi,

This same error has resurfaced. Can someone please look into this for the groHMM package.

Regards,
Tulip.

________________________________
From: Herv� Pag�s <hpages.on.github using gmail.com>
Sent: Saturday, October 28, 2023 1:51 PM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>; Kern, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] groHMM package error

Package is all green today on the 3.18 report:

  https://bioconductor.org/checkResults/3.18/bioc-LATEST/groHMM/<https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.18/bioc-LATEST/groHMM/__;!!MznTZTSvDXGV0Co!BPaBrGLFj6s1ULrvrPGL-g9u1P_xyFMmTDlj8JjuQ-UOQAVx6iJEdvKN8snzX83dFwTGJau1bFYs8EB_ull-gDtVQmUa3hlLalpPnA$>

Cheers,

H.

On 10/25/23 16:11, Herv� Pag�s wrote:

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, Herv� Pag�s wrote:

Hi Tulip,

I think this is caused by a late change in S4Vectors: https://github.com/Bioconductor/S4Vectors/commit/15349ef40f141b16df6daf3e38f3782ef54eb60c<https://urldefense.com/v3/__https://github.com/Bioconductor/S4Vectors/commit/15349ef40f141b16df6daf3e38f3782ef54eb60c__;!!MznTZTSvDXGV0Co!BPaBrGLFj6s1ULrvrPGL-g9u1P_xyFMmTDlj8JjuQ-UOQAVx6iJEdvKN8snzX83dFwTGJau1bFYs8EB_ull-gDtVQmUa3hltWFkgSA$>

This was an attempt at implementing the following feature request: https://github.com/Bioconductor/DelayedArray/issues/108<https://urldefense.com/v3/__https://github.com/Bioconductor/DelayedArray/issues/108__;!!MznTZTSvDXGV0Co!BPaBrGLFj6s1ULrvrPGL-g9u1P_xyFMmTDlj8JjuQ-UOQAVx6iJEdvKN8snzX83dFwTGJau1bFYs8EB_ull-gDtVQmUa3hkh2QcYxQ$>

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 <Lori.Shepherd using RoswellPark.org><mailto:Lori.Shepherd using RoswellPark.org>
Sent: Wednesday, October 25, 2023 6:06 AM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu><mailto:Tulip.Nandu using UTSouthwestern.edu>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org><mailto:bioc-devel using r-project.org>
Cc: Martin Grigorov <martin.grigorov using gmail.com><mailto:martin.grigorov using gmail.com>
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 <Tulip.Nandu using UTSouthwestern.edu><mailto:Tulip.Nandu using UTSouthwestern.edu>
Sent: Tuesday, October 24, 2023 3:33 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org><mailto:bioc-devel using r-project.org>
Cc: Kern, Lori <Lori.Shepherd using RoswellPark.org><mailto:Lori.Shepherd using RoswellPark.org>; Martin Grigorov <martin.grigorov using gmail.com><mailto:martin.grigorov using gmail.com>
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 <Lori.Shepherd using RoswellPark.org><mailto:Lori.Shepherd using RoswellPark.org>
Sent: Wednesday, October 18, 2023 3:45 PM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu><mailto:Tulip.Nandu using UTSouthwestern.edu>
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 <Tulip.Nandu using UTSouthwestern.edu><mailto:Tulip.Nandu using UTSouthwestern.edu>
Sent: Wednesday, October 18, 2023 4:37 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org><mailto:Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org><mailto:bioc-devel using r-project.org>; martin.grigorov using gmail.com<mailto:martin.grigorov using gmail.com> <martin.grigorov using gmail.com><mailto:martin.grigorov using 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$<https://urldefense.com/v3/__https://secure-web.cisco.com/1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fmaster.bioconductor.org*2FcheckResults*2F3.18*2Fbioc-LATEST*2FgroHMM*2Fnebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$__;JSUlJSUlJSUlJSUlJQ!!MznTZTSvDXGV0Co!BPaBrGLFj6s1ULrvrPGL-g9u1P_xyFMmTDlj8JjuQ-UOQAVx6iJEdvKN8snzX83dFwTGJau1bFYs8EB_ull-gDtVQmUa3hlyVpYVUA$><https://urldefense.com/v3/__https://secure-web.cisco.com/1gUrDMYAh-8fmjXWvwKvuTYLT1OWOtqrMJHRAccYOartRTyTWfM48qVa1VGmM9T32xk8Ev06tz3cPlPl8dhbVpA0gSoECMx0IWqDgYdqiVwUoxyxcHyTp9xTY278ELGk7n4Gd2ecxTYFUl14Ai_77fj5SpM_6Md1UsL0oZtABcTTCqYelO-Asx38NqsZVdJoRLaikZADKiDWPmSA41ghoujh8t0HCudzKSQ0zh4XZuVC6Jj0FEslvkGCns1PftCM9L9BUczFvsytbzLkKD7zsVDMbkdGlrKsYt3XMmdxBCcLDiAb9Go7EtTZqRSwI
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Let me know.

Thank you so much.

Regards,

Tulip.

________________________________
From: Kern, Lori <Lori.Shepherd using RoswellPark.org><mailto:Lori.Shepherd using RoswellPark.org>
Sent: Wednesday, October 18, 2023 3:36 PM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu><mailto:Tulip.Nandu using UTSouthwestern.edu>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org><mailto:bioc-devel using 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 branch.

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 <bioc-devel-bounces using r-project.org><mailto:bioc-devel-bounces using r-project.org> on behalf of Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu><mailto:Tulip.Nandu using UTSouthwestern.edu>
Sent: Wednesday, October 18, 2023 4:30 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org><mailto:bioc-devel using r-project.org>
Subject: [Bioc-devel] groHMM package error

Hi,

I just got an email from the Bioconductor stating,

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$<https://urldefense.com/v3/__https://secure-web.cisco.com/1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fmaster.bioconductor.org*2FcheckResults*2F3.18*2Fbioc-LATEST*2FgroHMM*2Fnebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$__;JSUlJSUlJSUlJSUlJQ!!MznTZTSvDXGV0Co!BPaBrGLFj6s1ULrvrPGL-g9u1P_xyFMmTDlj8JjuQ-UOQAVx6iJEdvKN8snzX83dFwTGJau1bFYs8EB_ull-gDtVQmUa3hlyVpYVUA$><https://urldefense.com/v3/__https://secure-web.cisco.com/1gUrDMYAh-8fmjXWvwKvuTYLT1OWOtqrMJHRAccYOartRTyTWfM48qVa1VGmM9T32xk8Ev06tz3cPlPl8dhbVpA0gSoECMx0IWqDgYdqiVwUoxyxcHyTp9xTY278ELGk7n4Gd2ecxTYFUl14Ai_77fj5SpM_6Md1UsL0oZtABcTTCqYelO-Asx38NqsZVdJoRLaikZADKiDWPmSA41ghoujh8t0HCudzKSQ0zh4XZuVC6Jj0FEslvkGCns1PftCM9L9BUczFvsytbzLkKD7zsVDMbkdGlrKsYt3XMmdxBCcLDiAb9Go7EtTZqRSwI
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I feel it's the version issue 3.17 to 3.18 and I need to release the package to 3.18 too. But moment I try to update it throws up a error message:

git checkout RELEASE_3_18
error: pathspec 'RELEASE_3_18' did not match any file(s) known to git

Can anyone help me with this update and error.

Regards,

Tulip.

________________________________

UT Southwestern

Medical Center

The future of medicine, today.

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