[Bioc-devel] groHMM package error

Tue Oct 24 21:33:37 CEST 2023

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$<https://urldefense.com/v3/__https://secure-web.cisco.com/1krdleRu6rYX6knRc68ATtEj9N0jlIT2CFwqtkCoRkKdk1S9TJQrflUq-SqjwBR50ykjFHesLhPCllgM4ZWaR2oBzfwtLaw4dyPhxtk_xyGHn6Bkj6-o8kxAysmVIdiiFgnlLvok0W1_6vyPWWWWha7q8lYQvcupFRKoXiYSJ9AcelAcfw29j_ukt8hYLA5ntk1fihRrN6_f5GaQWmlSjC2BiDl4hbtErRHupbsU-GUwdvUm01qd_x1XDQNcyIvhpukhaHPCH_4LOdAa3LxHPkzC3fCqGB2jCF0HLmOYd3wSl91OV4UNbDho1eQ6L-qti/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2F*2A2Fmaster.bioconductor.org*2A2FcheckResults*2A2F3.18*2A2Fbioc-LATEST*2A2FgroHMM*2A2Fnebbiolo2-buildsrc.html__*3B*21*21MznTZTSvDXGV0Co*21EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA*24__*3BJSUlJSUlJSUlJSUlJQ*21*21MznTZTSvDXGV0Co*21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkL-19PXfs*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!CQdmhYdq0-C37GWMJwm0wPXgYZ1GnTG7CF0IRkSRTERUe6dO7rjL0BmYoLwlckm2Wv7nflkFw_L1HG3YfODPak8pDp4iLo6V_zcxPRo$>

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$<https://urldefense.com/v3/__https://secure-web.cisco.com/1krdleRu6rYX6knRc68ATtEj9N0jlIT2CFwqtkCoRkKdk1S9TJQrflUq-SqjwBR50ykjFHesLhPCllgM4ZWaR2oBzfwtLaw4dyPhxtk_xyGHn6Bkj6-o8kxAysmVIdiiFgnlLvok0W1_6vyPWWWWha7q8lYQvcupFRKoXiYSJ9AcelAcfw29j_ukt8hYLA5ntk1fihRrN6_f5GaQWmlSjC2BiDl4hbtErRHupbsU-GUwdvUm01qd_x1XDQNcyIvhpukhaHPCH_4LOdAa3LxHPkzC3fCqGB2jCF0HLmOYd3wSl91OV4UNbDho1eQ6L-qti/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2F*2A2Fmaster.bioconductor.org*2A2FcheckResults*2A2F3.18*2A2Fbioc-LATEST*2A2FgroHMM*2A2Fnebbiolo2-buildsrc.html__*3B*21*21MznTZTSvDXGV0Co*21EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA*24__*3BJSUlJSUlJSUlJSUlJQ*21*21MznTZTSvDXGV0Co*21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkL-19PXfs*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!CQdmhYdq0-C37GWMJwm0wPXgYZ1GnTG7CF0IRkSRTERUe6dO7rjL0BmYoLwlckm2Wv7nflkFw_L1HG3YfODPak8pDp4iLo6V_zcxPRo$>

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.

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
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://urldefense.com/v3/__https://secure-web.cisco.com/1RMLblrjfbaF1NsYWdKMO_dcIU_pe5b5SdV9gZJjxY6kfyhczntKmvf74_0V1VnHrBTfrhv-7bIfnFSzsgKVQqdFeYKc1CTe1oBe3VRRBfHFDRvXTmvP8cz3BMuCdiH5fLofKgi8b8vUYErmzGTCMLZrv-xKAXx8cBiVr_Pis_aznTgs8Cf5EOOD0ICYL2ogF9pj-yuCV96-3mQ3hDOE7DO7sU0max9WydlMdUzBt_RY5dh_-6VrqCFJA-Iymw9J6aDDJ-ZggxPWTV3IHbQ88j_eZTwg3QOCUZDoqorEC9WUtUQihiVmfXCv6WRynfwxu/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1o-3kGonW8iymDY6hzo2pojCCdKoWNydSzBaeOshxpTMWcS-dfzElfuIu8M6bbKbMgi9xSSJNDZtNYzec3LEB3zPMDzCle8b1h-Fc9Goghdj-wU3b8HUAJvLrOTG1Gs6zfqGVytcKWBIRFjUd9kjTeKm1JvCR_QYqe21uwsn_e4-v_2AdgIHKp5qyT5CMLbvwOwyAHj9xeF8Qqi864p1xNwWxd8Rd49ErwRK84EOd3mBa90GB3kipbWY-Vp4HHnOXwYpiGjJybSbbjglSCDpbNiSmgphgVB7d1FhGX8Vfzs9-rdd3hN-A1rjRgggBFW5v*2Fhttps*2A3A*2A2F*2A2Fstat.ethz.ch*2A2Fmailman*2A2Flistinfo*2A2Fbioc-devel__*3BJSUlJSUl*21*21MznTZTSvDXGV0Co*21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkLI-p7bho*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!CQdmhYdq0-C37GWMJwm0wPXgYZ1GnTG7CF0IRkSRTERUe6dO7rjL0BmYoLwlckm2Wv7nflkFw_L1HG3YfODPak8pDp4iLo6VJZOUmB4$>

This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.

This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: =?utf-8?B?U2NyZWVuc2hvdCAyMDIzLTEwLTI0IGF0IDIuMzEuMjLigK9QTS5wbmc=?=
Type: image/png
Size: 109395 bytes
Desc: =?utf-8?B?U2NyZWVuc2hvdCAyMDIzLTEwLTI0IGF0IDIuMzEuMjLigK9QTS5wbmc=?=
URL: <https://stat.ethz.ch/pipermail/bioc-devel/attachments/20231024/072c2b90/attachment.png>