Re: [Bioc-devel] groHMM package error
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$<https://urldefense.com/v3/__https://secure-web.cisco.com/1gUrDMYAh-8fmjXWvwKvuTYLT1OWOtqrMJHRAccYOartRTyTWfM48qVa1VGmM9T32xk8Ev06tz3cPlPl8dhbVpA0gSoECMx0IWqDgYdqiVwUoxyxcHyTp9xTY278ELGk7n4Gd2ecxTYFUl14Ai_77fj5SpM_6Md1UsL0oZtABcTTCqYelO-Asx38NqsZVdJoRLaikZADKiDWPmSA41ghoujh8t0HCudzKSQ0zh4XZuVC6Jj0FEslvkGCns1PftCM9L9BUczFvsytbzLkKD7zsVDMbkdGlrKsYt3XMmdxBCcLDiAb9Go7EtTZqRSwI Pxdg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1krdleRu6rYX6knRc68ATtEj9N0jlIT2CFwqtkCoRkKdk1S9TJQrflUq-SqjwBR50ykjFHesLhPCllgM4ZWaR2oBzfwtLaw4dyPhxtk_xyGHn6Bkj6-o8kxAysmVIdiiFgnlLvok0W1_6vyPha7q8lYQvcupFRKoXiYSJ9AcelAcfw29j_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*2A2A2 Fnebbiolo2-buildsrc.html__*2A3B*2A21*2A21MznTZTSvDXGV0Co*2A21EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA*2A24__*2A3BJSUlJSUlJSUlJSUlJQ*2A21*2A21MznTZTSvDXGV0Co*2A21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkL-19PXfs*2A24__*3BJS
Re: [Bioc-devel] 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-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEX pU28/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$__;JSUlJSUlJSUlJSUlJQ!!MznTZTSvDXGV0Co!FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkL-19PXfs$> 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 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 on behalf of Tulip Nandu Sent: Wednesday, October 18, 2023 4:30 PM To: 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$<https://urldefense.com/v3/__https://secure-web.cisco.com/1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEX pU28/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fmaster.bioconductor.org*2FcheckResults*2F3.18*2Fbioc-LATEST*2FgroHMM*2Fnebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$__;JSUlJSUlJSUlJSUlJQ!!MznTZTSvDXGV0Co!FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkL-19PXfs$> I feel it's the version issue 3.17 to 3.18 and I need to release the package to 3.18 too. But moment I try to update it throws up a error message: git checkout RELEASE_3_18 error: pathspec 'RELEASE_3_18' did not match any file(s) known to git Can anyone help me with this update and error. Regards, Tulip. UT Southwestern Medical Center The future of medicine, today. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing
[Bioc-devel] groHMM package error
Hi, I just got an email from the Bioconductor stating, According to the Multiple platform build/check report for BioC 3.18, the groHMM package has the following problem(s): o ERROR for 'R CMD build' on nebbiolo2. See the details here: https://urldefense.com/v3/__https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/groHMM/nebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$ 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] New maintainer for package - Updating a R package and pushing the commit
Hi Kern, Anusha no longer is associated with the lab. So I will need to have access to the package. If you can create an account on GitCredentials that would be great. I do have a github account. tulipnandu is the username. https://github.com/tulipnandu [https://avatars.githubusercontent.com/u/1099843?v=4?s=400]<https://github.com/tulipnandu> tulipnandu - Overview<https://github.com/tulipnandu> tulipnandu has 10 repositories available. Follow their code on GitHub. github.com Also I would need to push the changes in the src file to master on bioconductor/git. If I can get some help with that, it would be great too. Regards, Tulip. From: Kern, Lori Sent: Thursday, September 29, 2022 6:52 AM To: Tulip Nandu ; bioc-devel@r-project.org ; Anusha Nagari Subject: Re: New maintainer for package - Updating a R package and pushing the commit EXTERNAL MAIL This message was sent securely using Zix�<http://www.zixcorp.com/get-started/> a few points: Normally only one person has maintainer access to a package this currently was Anusha Nagari . Should they also retain maintainer access? Anusha was assigned because that is who is listed with Authors@R. You currently have a mixure of using Authors@R and Maintainer/Author field. Please remove Author/Maintainer fields and only use Authors@R. In a normal procedure the currently listed maintainer would request the switch or additional access. Since I see you listed in the Maintainer field, we can ignore this step for this situation. I will need to create an account on our GitCredentials where you can manage your ssh keys for access. We can link a github account for access. Do you have a personal github account you would like associated with; if so please provide your github username? Cheers, 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 Tulip Nandu Sent: Wednesday, September 28, 2022 5:15 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] New maintainer for package - Updating a R package and pushing the commit Hi, I'm the new maintainer of the groHMM package which is having issues in its build. In that view I would like to update the package but it won't allow me since my email is not on file with the maintainer of bioconductor package. Can you please list the steps to have me listed as a maintainer and update the package on bioconductor/git. Let me know. Regards, Tulip. UT Southwestern Medical Center The future of medicine, today. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/153TPO9q9LgJcIfq7xj6UvgBc8nFbtHT8ZYZQGFIIs9ZSk4A7ilw0CeI7TbK_V6bYIx6ThYomprV1f_aLbd2S7a4YeVDdjcKH03QZSE2kEv9_cNUrEpbkAGk1iajxtenYsDmTonDkJbZIeg-IoB4g0iaPG_jCRjh5agFEcsI__iP6x9liTUj5A10Dg00kng9WU4FVkpjP43oIF598TjRkpatlZZje1T_Uia_oVEIB40G8FCCId7tn4Ma2qwItlJv02H_hbkaC51OFRBiEs01TpHluUuNezGZ0_C3uhIT4KIFVO5xO4VHhGZplznuonJ4r/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel 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. This message was secured by Zix<http://www.zixcorp.com>�. CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] groHMM package error check report error
Hi, I received the following email, "According to the Multiple platform build/check report for BioC 3.16, the groHMM package has the following problem(s): o ERROR for 'R CMD check' on nebbiolo2. See the details here: https://master.bioconductor.org/checkResults/3.16/bioc-LATEST/groHMM/nebbiolo2-checksrc.html o ERROR for 'R CMD INSTALL' on nebbiolo2. See the details here: https://master.bioconductor.org/checkResults/3.16/bioc-LATEST/groHMM/nebbiolo2-install.html Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org Notes: * This was the status of your package at the time this email was sent to you. Given that the online report is updated daily (in normal conditions) you could see something different when you visit the URL(s) above, especially if you do so several days after you received this email. * It is possible that the problems reported in this report are false positives, either because another package (from CRAN or Bioconductor) breaks your package (if yours depends on it) or because of a Build System problem. If this is the case, then you can ignore this email. * Please check the report again 24h after you've committed your changes to the package and make sure that all the problems have gone. * If you have questions about this report or need help with the maintenance of your package, please use the Bioc-devel mailing list: https://bioconductor.org/help/mailing-list/ (all package maintainers are requested to subscribe to this list) For immediate notification of package build status, please subscribe to your package's RSS feed. Information is at: https://bioconductor.org/developers/rss-feeds/ Thanks for contributing to the Bioconductor project! CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying." When I checked at my end, the groHMM package is being installed correctly without any problems. Can you check again if there is an issue and if all dependencies are installed correctly? Let me know. Regards, Tulip. UT Southwestern Medical Center The future of medicine, today. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
