[Bioc-devel] Bioconductor packages and upcoming changes to ggplot2

[Maria.Doyle]

Thanks Teun for the heads-up and for engaging with the community.

To support developers and users, we�ve published a blog post summarising the upcoming ggplot2 changes and how to test packages:.

https://blog.bioconductor.org/posts/2025-07-07-ggplot2-update/

Happy to update it if further issues or fixes come in.

Maria Doyle, PhD
Bioconductor Community Manager

Connect with the Bioconductor community at our conferences:

  *   EuroBioC 2025 (September 17-19, Barcelona, Spain)<https://eurobioc2025.bioconductor.org/>

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Message: 1
Date: Thu, 3 Jul 2025 11:42:13 +0200
From: Teun van den Brand <teun.vandenbrand using posit.co>
To: bioc-devel using r-project.org
Subject: [Bioc-devel] Bioconductor packages and upcoming changes to
        ggplot2
Message-ID:
        <CAG386wdf1oZ-Rreo_YL2UzRd28Jibe+KC4gvu6FN9yb_iBzQhA using mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi everyone,

We've been preparing a new major version of ggplot2 and expect that some
packages might be broken.
If you do not maintain a package that depends on ggplot2, you can safely
skip reading this.

Unfortunately, our own reverse dependency testing infrastructure based on
the revdepcheck package has some issues checking Bioconductor packages.
We're not confident we can fix the infrastructure within a short timeframe,
which is why I'm reaching out to you in this aspecific manner.
If you maintain a package that uses ggplot2, we're asking if you can test
your package against the new version.
You can test your code with the development version of ggplot2 by
installing it as follows:

```r
# install.packages("pak")
pak::pak("tidyverse/ggplot2")
```

If you find any problems, either with ggplot2 or perhaps in the interaction
with your package, please do not hesitate to reach out. You can file a
possible bug report at https://github.com/tidyverse/ggplot2/issues<https://github.com/tidyverse/ggplot2/issues> or tag
@teunbrand on GitHub if you want me to take a look. Below you can find a
list of common issues and possible solutions, where you're also welcome to
raise discussion:

* https://github.com/tidyverse/ggplot2/issues/6498<https://github.com/tidyverse/ggplot2/issues/6498>
* https://github.com/tidyverse/ggplot2/issues/6504<https://github.com/tidyverse/ggplot2/issues/6504>
* https://github.com/tidyverse/ggplot2/issues/6505<https://github.com/tidyverse/ggplot2/issues/6505>
* https://github.com/tidyverse/ggplot2/issues/6507<https://github.com/tidyverse/ggplot2/issues/6507>
* https://github.com/tidyverse/ggplot2/issues/6515<https://github.com/tidyverse/ggplot2/issues/6515>

I'm happy to assist in the run-up to the release, but I'd need help finding
the places where assistance is needed. We aim to release the new ggplot2
version in about 2 weeks. Hopefully this will give you notice in a timely
manner.

Best wishes,
Teun

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