Thank you for the quick response, this is very helpful! On Thu, Jun 13, 2024 at 1:19 PM Kern, Lori <lori.sheph...@roswellpark.org> wrote:
> 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. > > > 2. 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. > > > > 3. 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-boun...@r-project.org> on behalf of > Kinnary Shah <kinnarysh...@gmail.com> > *Sent:* Thursday, June 13, 2024 1:04 PM > *To:* bioc-devel@r-project.org <bioc-devel@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@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. > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
