[Bioc-devel] groHMM package error

Wed Oct 25 23:03:36 CEST 2023

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>
Sent: Wednesday, October 25, 2023 6:06 AM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Cc: Martin Grigorov <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>
Sent: Tuesday, October 24, 2023 3:33 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Cc: Kern, Lori <Lori.Shepherd using RoswellPark.org>; Martin Grigorov <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>
Sent: Wednesday, October 18, 2023 3:45 PM
To: Tulip Nandu <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>
Sent: Wednesday, October 18, 2023 4:37 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org <bioc-devel using r-project.org>; martin.grigorov using gmail.com <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/1gUrDMYAh-8fmjXWvwKvuTYLT1OWOtqrMJHRAccYOartRTyTWfM48qVa1VGmM9T32xk8Ev06tz3cPlPl8dhbVpA0gSoECMx0IWqDgYdqiVwUoxyxcHyTp9xTY278ELGk7n4Gd2ecxTYFUl14Ai_77fj5SpM_6Md1UsL0oZtABcTTCqYelO-Asx38NqsZVdJoRLaikZADKiDWPmSA41ghoujh8t0HCudzKSQ0zh4XZuVC6Jj0FEslvkGCns1PftCM9L9BUczFvsytbzLkKD7zsVDMbkdGlrKsYt3XMmdxBCcLDiAb9Go7EtTZqRSwIPxdg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1krdleRu6rYX6knRc68ATtEj9N0jlIT2CFwqtkCoRkKdk1S9TJQrflUq-SqjwBR50ykjFHesLhPCllgM4ZWaR2oBzfwtLaw4dyPhxtk_xyGHn6Bkj6-o8kxAysmVIdiiFgnlLvok0W1_6vyPWWWWha7q8lYQvcupFRKoXiYSJ9AcelAcfw29j_ukt8hYLA5ntk1fihRrN6_f5GaQWmlSjC2BiDl4hbtErRHupbsU-GUwdvUm01qd_x1XDQNcyIvhpukhaHPCH_4LOdAa3LxHPkzC3fCqGB2jCF0HLmOYd3wSl91OV4UNbDho1eQ6L-qti*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2F*2A2Fsecure-web.cisco.com*2A2F1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Furldefense.com*2A2A2Fv3*2A2A2F__https*2A2A3A*2A2A2F*2A2A2Fmaster.bioconductor.org*2A2A2FcheckResults*2A2A2F3.18*2A2A2Fbioc-LATEST*2A2A2FgroHMM*2A2A2Fnebbiolo2-buildsrc.html__*2A3B*2A21*2A21MznTZTSvDXGV0Co*2A21EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA*2A24__*2A3BJSUlJSUlJSUlJSUlJQ*2A21*2A21MznTZTSvDXGV0Co*2A21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkL-19PXfs*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl*21*21MznTZTSvDXGV0Co*21CQdmhYdq0-C37GWMJwm0wPXgYZ1GnTG7CF0IRkSRTERUe6dO7rjL0BmYoLwlckm2Wv7nflkFw_L1HG3YfODPak8pDp4iLo6V_zcxPRo*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!Amw3xom-SM3e3cfsWyoJb1tzyz6v_ttMAIJJAnoGProVnS0LgDu4QJfuSTSyUZHPs-in3lbx4Z6LeOXbhAEEj53cdAHd6Y_xqKS9fsU$>

Let me know.

Thank you so much.

Regards,

Tulip.

________________________________
From: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Wednesday, October 18, 2023 3:36 PM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>; bioc-devel using r-project.org <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> on behalf of Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>
Sent: Wednesday, October 18, 2023 4:30 PM
To: bioc-devel using r-project.org <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/1gUrDMYAh-8fmjXWvwKvuTYLT1OWOtqrMJHRAccYOartRTyTWfM48qVa1VGmM9T32xk8Ev06tz3cPlPl8dhbVpA0gSoECMx0IWqDgYdqiVwUoxyxcHyTp9xTY278ELGk7n4Gd2ecxTYFUl14Ai_77fj5SpM_6Md1UsL0oZtABcTTCqYelO-Asx38NqsZVdJoRLaikZADKiDWPmSA41ghoujh8t0HCudzKSQ0zh4XZuVC6Jj0FEslvkGCns1PftCM9L9BUczFvsytbzLkKD7zsVDMbkdGlrKsYt3XMmdxBCcLDiAb9Go7EtTZqRSwIPxdg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1krdleRu6rYX6knRc68ATtEj9N0jlIT2CFwqtkCoRkKdk1S9TJQrflUq-SqjwBR50ykjFHesLhPCllgM4ZWaR2oBzfwtLaw4dyPhxtk_xyGHn6Bkj6-o8kxAysmVIdiiFgnlLvok0W1_6vyPWWWWha7q8lYQvcupFRKoXiYSJ9AcelAcfw29j_ukt8hYLA5ntk1fihRrN6_f5GaQWmlSjC2BiDl4hbtErRHupbsU-GUwdvUm01qd_x1XDQNcyIvhpukhaHPCH_4LOdAa3LxHPkzC3fCqGB2jCF0HLmOYd3wSl91OV4UNbDho1eQ6L-qti*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2F*2A2Fsecure-web.cisco.com*2A2F1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Furldefense.com*2A2A2Fv3*2A2A2F__https*2A2A3A*2A2A2F*2A2A2Fmaster.bioconductor.org*2A2A2FcheckResults*2A2A2F3.18*2A2A2Fbioc-LATEST*2A2A2FgroHMM*2A2A2Fnebbiolo2-buildsrc.html__*2A3B*2A21*2A21MznTZTSvDXGV0Co*2A21EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA*2A24__*2A3BJSUlJSUlJSUlJSUlJQ*2A21*2A21MznTZTSvDXGV0Co*2A21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkL-19PXfs*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl*21*21MznTZTSvDXGV0Co*21CQdmhYdq0-C37GWMJwm0wPXgYZ1GnTG7CF0IRkSRTERUe6dO7rjL0BmYoLwlckm2Wv7nflkFw_L1HG3YfODPak8pDp4iLo6V_zcxPRo*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!Amw3xom-SM3e3cfsWyoJb1tzyz6v_ttMAIJJAnoGProVnS0LgDu4QJfuSTSyUZHPs-in3lbx4Z6LeOXbhAEEj53cdAHd6Y_xqKS9fsU$>

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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