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methodical #3169

Closed richardheery closed 8 months ago

richardheery commented 1 year ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Confirm the following by editing each check box to '[x]'

I am familiar with the essential aspects of Bioconductor software management, including:

For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: methodical_0.99.20.tar.gz Linux (Ubuntu 22.04.2 LTS): methodical_0.99.20.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/methodical to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 9 months ago

Please ignore the bioc-devel mailing list ERROR; I can confirm the email is registered and we are looking into why BiocCheck is reporting an ERROR in mistake.

DarioS commented 9 months ago

The package has been substantially improved.

bioc-issue-bot commented 9 months ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

lshep commented 8 months ago

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/richardheery.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("methodical"). The package 'landing page' will be created at

https://bioconductor.org/packages/methodical

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

lshep commented 5 months ago

Your package has been failing on our devel builders for over 6 weeks. Please fix to avoid removal from Bioconductor

richardheery commented 5 months ago

Hello,

Sure I will take a look at the issues in the coming days.

Best wishes,

Richard

On Tue 9 Apr 2024, 14:56 lshep, @.***> wrote:

Your package has been failing on our devel builders for over 6 weeks. Please fix to avoid removal from Bioconductor

— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3169#issuecomment-2045239130, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMP6CXDQTOTEDLA5ZMWEGMTY4PXO7AVCNFSM6AAAAAA5JUOCO6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBVGIZTSMJTGA . You are receiving this because you were mentioned.Message ID: @.***>

richardheery commented 5 months ago

Since my package is on the devel version of Bioconductor, do I need to still push any changes to the devel branch of Bioconductor at git@git.bioconductor.org:packages or is it enough just to my Git repository?

Is there also a way to trigger a BBS build report without waiting for the nightly build?

lshep commented 5 months ago

You need to push to git.bioconductor.org. Bioconductor no longer makes any connection or reference to the github repo. You will need to push changes to git.bioconductor.org with a valid version bump in order for them to appear and propagate to users

lshep commented 5 months ago

Currently builds are only once a day. But I encourage you to run R CMD build and R CMD check on your own, perhaps with the bioconductor docker image to test changes.