Introduction
Bioconductor is moving towards using R-universe for it’s daily build system. See previous blog post Collaborating between Bioconductor and R-universe on Development of Common Infrastructure. As we move in this direction it was also necessary to update the submission process for Bioconductor packages. While the daily builders are still transitioning, the new submission process location is now live. The new system utilizes GitHub Actions to trigger review milestones and R-Universe as the build/check backend. The new system is a smoother experience; It is more automated and avoids administrative steps that have historically bottlenecked the review process.
Information
Location:
The new location for submitting new packages to Bioconductor for review is BiocContributions. This replaces the old location at Bioconductor/Contributions.
Documentation
There is documentation on What to Expect as well as a detailed Slide Deck.
There is also a FAQ for commonly asked questions, concerns, or troubleshooting.
If you need to report an issue with the new system, please open an Issue on the BiocSubmissionProcess GitHub repository.
What about Bioconductor/Contributions
The submission location at Bioconductor/Contributions has been frozen and will no longer accept new issues. The BiocContributions replaces this location. If you already submitted to the old location, if you are assigned a reviewer, your review will finish there. If you have not been assigned a reviewer yet, we will be posting shortly to close out your submission and move to the new location.
Easier Reproducibility
One of the frequent comments we receive is how do we reproduce the results of the build reports Bioconductor creates. The switch to using R-universe as the building and checking backend allows for a reproducible testing environment. Any maintainer can apply R-Universe checking on their personal GitHub repository for a Bioconductor package by following these instructions. This allows for a maintainer to test before submitting to Bioconductor and testing any future changes before pushing directly to Bioconductor.
Thank you!
We appreicate you patience and understanding as we transition to the new system.
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