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.na...@utsouthwestern.edu>
Sent: Tuesday, October 24, 2023 3:33 PM
To: bioc-devel@r-project.org <bioc-devel@r-project.org>
Cc: Kern, Lori <lori.sheph...@roswellpark.org>; Martin Grigorov
<martin.grigo...@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.sheph...@roswellpark.org>
Sent: Wednesday, October 18, 2023 3:45 PM
To: Tulip Nandu <tulip.na...@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.na...@utsouthwestern.edu>
Sent: Wednesday, October 18, 2023 4:37 PM
To: Kern, Lori <lori.sheph...@roswellpark.org>; bioc-devel@r-project.org
<bioc-devel@r-project.org>; martin.grigo...@gmail.com
<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$<https://secure-web.cisco.com/1gUrDMYAh-8fmjXWvwKvuTYLT1OWOtqrMJHRAccYOartRTyTWfM48qVa1VGmM9T32xk8Ev06tz3cPlPl8dhbVpA0gSoECMx0IWqDgYdqiVwUoxyxcHyTp9xTY278ELGk7n4Gd2ecxTYFUl14Ai_77fj5SpM_6Md1UsL0oZtABcTTCqYelO-Asx38NqsZVdJoRLaikZADKiDWPmSA41ghoujh8t0HCudzKSQ0zh4XZuVC6Jj0FEslvkGCns1PftCM9L9BUczFvsytbzLkKD7zsVDMbkdGlrKsYt3XMmdxBCcLDiAb9Go7EtTZqRSwIPxdg/https%3A%2F%2Furldefens
e.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__%2
A3B%2A21%2A21MznTZTSvDXGV0Co%2A21EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA%2A24__%2A3BJSUlJSUlJSUlJSUlJQ%2A21%2A21MznTZTSvDXGV0Co%2A21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkL-19PXfs%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl%21%21MznTZTSvDXGV0Co%21CQdmhYdq0-C37GWMJwm0wPXgYZ1GnTG7CF0IRkSRTERUe6dO7rjL0BmYoLwlckm2Wv7nflkFw_L1HG3YfODPak8pDp4iLo6V_zcxPRo%24>
Let me know.
Thank you so much.
Regards,
Tulip.
________________________________
From: Kern, Lori <lori.sheph...@roswellpark.org>
Sent: Wednesday, October 18, 2023 3:36 PM
To: Tulip Nandu <tulip.na...@utsouthwestern.edu>; bioc-devel@r-project.org
<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 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-boun...@r-project.org> on behalf of Tulip Nandu
<tulip.na...@utsouthwestern.edu>
Sent: Wednesday, October 18, 2023 4:30 PM
To: bioc-devel@r-project.org <bioc-devel@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://secure-web.cisco.com/1gUrDMYAh-8fmjXWvwKvuTYLT1OWOtqrMJHRAccYOartRTyTWfM48qVa1VGmM9T32xk8Ev06tz3cPlPl8dhbVpA0gSoECMx0IWqDgYdqiVwUoxyxcHyTp9xTY278ELGk7n4Gd2ecxTYFUl14Ai_77fj5SpM_6Md1UsL0oZtABcTTCqYelO-Asx38NqsZVdJoRLaikZADKiDWPmSA41ghoujh8t0HCudzKSQ0zh4XZuVC6Jj0FEslvkGCns1PftCM9L9BUczFvsytbzLkKD7zsVDMbkdGlrKsYt3XMmdxBCcLDiAb9Go7EtTZqRSwIPxdg/https%3A%2F%2Furldefens
e.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__%2
A3B%2A21%2A21MznTZTSvDXGV0Co%2A21EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA%2A24__%2A3BJSUlJSUlJSUlJSUlJQ%2A21%2A21MznTZTSvDXGV0Co%2A21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkL-19PXfs%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl%21%21MznTZTSvDXGV0Co%21CQdmhYdq0-C37GWMJwm0wPXgYZ1GnTG7CF0IRkSRTERUe6dO7rjL0BmYoLwlckm2Wv7nflkFw_L1HG3YfODPak8pDp4iLo6V_zcxPRo%24>
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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https://secure-web.cisco.com/1o-3kGonW8iymDY6hzo2pojCCdKoWNydSzBaeOshxpTMWcS-dfzElfuIu8M6bbKbMgi9xSSJNDZtNYzec3LEB3zPMDzCle8b1h-Fc9Goghdj-wU3b8HUAJvLrOTG1Gs6zfqGVytcKWBIRFjUd9kjTeKm1JvCR_QYqe21uwsn_e4-v_2AdgIHKp5qyT5CMLbvwOwyAHj9xeF8Qqi864p1xNwWxd8Rd49ErwRK84EOd3mBa90GB3kipbWY-Vp4HHnOXwYpiGjJybSbbjglSCDpbNiSmgphgVB7d1FhGX8Vfzs9-rdd3hN-A1rjRgggBFW5v/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel<https://secure-web.cisco.com/1td0EkI2g1ZyyIzNVYIaU-VUiHDiSr91F-inGjEawFZvB5JViUNifU0EALPtUw7ReHHjiMqy2HeqdlZB8zk0NxSDwWcQH2O_-Oh_P0cqwFek8ufqImlClbyeCwtqunO2lbB9apd3mRpL2Eb1geANGnQO8NgQXcnnd0EC1E_SJ2o_KbgtuMzZV2Q7wXfq5Im4QGsohIu9spjaJOHLLrPXx50W_vfkxSr8VSEAck07wZAFdxhLxGnVDQJXwirbDihP6Pq1PD7MkTh232Q7_1j3hzXuFmibt5X0lgCTpCURbfH9vI8_zSznz2px08tRx8DOI/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1RMLblrjfbaF1NsYWdKMO_dcIU_pe5b5SdV9gZJjxY6kfyhczntKmvf74_0V1VnHrBTfrhv-7bIfnFSzsgKVQqdFeYKc1CTe1oBe3VRRBfHFDRvXTmvP8cz3BMuCdiH5fLofKgi8b8vUYErmzGTCMLZrv-xKAXx8
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