[Bioc-devel] Package version did not update correctly

[Kinnary Shah]

Thank you for the quick response, this is very helpful!

On Thu, Jun 13, 2024 at 1:19 PM Kern, Lori <Lori.Shepherd using 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-bounces using r-project.org> on behalf of
> Kinnary Shah <kinnaryshahh using gmail.com>
> *Sent:* Thursday, June 13, 2024 1:04 PM
> *To:* bioc-devel using r-project.org <bioc-devel using 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
>
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