It looks like a major update to {ggplot2} is coming (version 4.0.0), where Posit is switching the internals from S3 to S7. This will break many reverse dependencies of {ggplot2} (a reverse dependency is a package that depends on {ggplot2}), and so Posit is following the recommendation of the CRAN policies, which state that they should give a heads-up to devs of reverse dependencies and give them enough time to fix their packages. Posit even goes beyond that and is opening PRs to offer fixes themselves, which I think is really great.

However, this seems to be a bit trickier in the case of R packages hosted on Bioconductor: my understanding of Bioconductor is that they have two releases per year, and packages cannot be updated in between releases. Now I’m not entirely sure if that is exactly the case, or if some exceptions can be made and packages can perhaps be fixed in between releases. That being said, it seems like this upgrade will cause some issues, and there is apparently quite a heated discussion on Bioconductor’s community chat (which I don’t have access to).

Whatever is going to happen, and whatever is going on in this discussion, and whatever you think of Posit, CRAN, or Bioconductor, as an end-user, there are not a million things that you can do to make sure that upgrading to the latest {ggplot2} (or whichever packages) won’t break projects you’re currently working on:

• only use dependency-free packages like those from the tinyverse or even just base R
• use something like {renv} or {groundhog} to snapshot package versions, or better yet, Nix using my {rix} package
• just don’t care and hope for the best.

Ultimately, it is on YOU to ensure that your projects are reproducible, and that you can work with stable environments. Relying on infrastructure or upstream developers you don’t control is not a valid strategy.