[Bioc-devel] Package version did not update correctly
A few things. 1. Please keep in mind there is a delay from pushing to the Bioconductor git and when it will be available via BiocManager. The package must first get built and propagated on our system. The checkResults page shows the timings of these reports currently twice a week. https://bioconductor.org/checkResults/ ??????We hope to have devel builds back to daily builds soon. 1. There are always two active branches of Bioconductor the release and devel branches. If you push to default, which based on your versioning is where you pushed, this updates the devel branch only. You would also need to push to RELEASE_3_19 to have changes visible on the release 3.19 branch. This versioning would be 1.0.0 to 1.0.1 as we generally keep version_x.y.z of a package the y odd in devel and even in release. 1. As far as the ERROR from github install. You can check to see if it also occurs on our build system once the builds pick up the pushed devel version but without digging into the code its hard to say if its used properly or not. I will say that I just tried installing from github using install_github and it seemed to install properly. Hope this helps 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 <bioc-devel-bounces at r-project.org> on behalf of Kinnary Shah <kinnaryshahh at gmail.com>
Sent: Thursday, June 13, 2024 1:04 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Package version did not update correctly
Sent: Thursday, June 13, 2024 1:04 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Package version did not update correctly
Hello, I made some small changes to a function in my package, "spoon", and wanted to update the patch version number to build the changes. https://secure-web.cisco.com/1zR5ERV81i3b1mbOVu4UUbWz7ccIbJzxw57R4EwygH5zgpfDlIjiFYWxi7jwY58iI-zQdwLnRqEcXoweBgmAu67NkxQi97-YNcDpGtjwvk7kaIAqVwU9gVCB9JRpfGKQOXijjUnkTN3lX3cE8T9S_DV1HGAgdWxNr4vcrKLeWPQPzUpSg5Bw_rlyH4lgCDBQIp8UJEyqQetzL8OKfdn9PDYDQDcwu6lk-AXuBB7hJCK060miWJYWvPeQ34yjGVK9eJhErf-u88mMHMNmEsye-Mf2HrErTKxlnVlsoRZ7u2_rpd1VTfOPPWD1gO9fGS7xJ/https%3A%2F%2Fgithub.com%2Fkinnaryshah%2Fspoon%2Ftree%2Fmain I updated the version from 1.1.0 to 1.1.1 and pushed the changes to the Bioconductor and GitHub repositories. When I try to install through BiocManager with Bioconductor 3.19, it installs 1.0.0. When I install using remotes to install from GitHub in R 4.4, it gives me the following error and does not install: Error: Failed to install 'spoon' from GitHub: $ operator is invalid for atomic vectors In addition: Warning message: In FUN(X[[i]], ...) : DESCRIPTION file of package 'spoon' is missing or broken I have used the $ operator in the changes that I have made, but it is valid in the way that it has been used. I had to merge the DESCRIPTION file change before updating the version number (https://secure-web.cisco.com/1lj-E4tKIE1gqbIbd-TXxhNEHvtvREem72CgM4xPTwLEbxueLXtMO2TEQkWIqQmD6LH_P8NhVRk0fC0XSRyk9C1ipm1nAiWJQYLqzPxQRMG4fm6ucgkikMDwwloEcpALlul7LIFMV_OvebyuJjDpTIZpBUkqVzbaRu9bTdo9Me9j0KuhEJRtqv4wqRBwlk_qM-1kvlPZjFL4xfYAaLBvyEFTkKc-XQk5ikzbJP4Su-RBxxDAkqUB_2DehkzXc0zakmdWOoxq08cuIypiypxbxdEKAxaFKutmwrOSbh9VdFN-Udor2UU8czJd-3WxgLKkr/https%3A%2F%2Fgithub.com%2Fkinnaryshah%2Fspoon%2Fcommits%2Fmain%2F) because I incorrectly updated the version at first, so I'm not sure if this messed up the overall version updating. Please advise if more context is needed or if there are suggestions about how to proceed. Thank you, Kinnary [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1B2Yk76Mm1iHQ_Nmihc4Age46SuKiOo_4WziH4pnTC-Xqh0njN-uFshW_QkTTXwCkbTjwhfy8iLj5OziNNLg-MafGJT2O_9KikyH1CIObPJYc1r6_PXHxJrRpdxDF9qboG8DmIGwKGGxH3QCC32LYLqMrHWSBvxkL3_LN8X6htuHkc_aRAD5yOrvu7aoJBOPdXihgjOLFTgX2dSm9Z4gbsSC1EupHFX4DWynFdmobWzo0Pb7eEMB8kYpJIxqvfmvutN0kcENLeaaTIlCqgbvy_TIfFoFqdSZGlc2IsfzEM7GqP7zWkY_06P6b9m1ANSWg/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.