[Bioc-devel] ggplot2 v4.0.0 related errors; related to ggbio and maybe other packages

[Maria.Doyle]

Thanks for highlighting this Leo!

Just linking back to the Bioconductor blog post from July that flagged potential reverse dependency issues ahead of the release: https://blog.bioconductor.org/posts/2025-07-07-ggplot2-update/
Hopefully useful context for anyone reviewing package checks or planning updates.

Maria Doyle, PhD
Bioconductor Community Manager

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From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Leonardo Collado Torres <lcolladotor using gmail.com>
Date: Wednesday, 17 September 2025 at 02:36
To: Bioc-devel <bioc-devel using r-project.org>
Subject: [Bioc-devel] ggplot2 v4.0.0 related errors; related to ggbio and maybe other packages
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Hi bioc-devel (cc Michael Lawrence),

As some of you might be aware of, ggplot2 just had a major version
release described in detail at
https://www.tidyverse.org/blog/2025/09/ggplot2-4-0-0/<https://www.tidyverse.org/blog/2025/09/ggplot2-4-0-0/>.

I see that several of my Bioconductor packages that make
visualizations with ggplot2 (either directly or under the hood through
other packages such as ggbio) are now failing in bioc-release and
bioc-devel.

* spatialLIBD: https://bioconductor.org/checkResults/3.22/data-experiment-LATEST/spatialLIBD/nebbiolo2-checksrc.html<https://bioconductor.org/checkResults/3.22/data-experiment-LATEST/spatialLIBD/nebbiolo2-checksrc.html>
seems like can fix by changing a unit test. I actually just did by
making the unit test more versatile so it works with older versions of
ggplot2 too: https://github.com/LieberInstitute/spatialLIBD/commit/910497195987e09ebef745437056a09b53c7a464<https://github.com/LieberInstitute/spatialLIBD/commit/910497195987e09ebef745437056a09b53c7a464>.
* regionReport:
https://bioconductor.org/checkResults/3.22/bioc-LATEST/regionReport/nebbiolo2-checksrc.html<https://bioconductor.org/checkResults/3.22/bioc-LATEST/regionReport/nebbiolo2-checksrc.html>.
Failing because ggbio is failing.
* derfinderPlot: uses regionReport, which uses ggbio.
https://bioconductor.org/checkResults/3.22/bioc-LATEST/derfinderPlot/nebbiolo2-buildsrc.html<https://bioconductor.org/checkResults/3.22/bioc-LATEST/derfinderPlot/nebbiolo2-buildsrc.html>

Michael seems to have recently (< 24 hrs ago) been made aware of this
issue at https://github.com/lawremi/ggbio/issues/175<https://github.com/lawremi/ggbio/issues/175>.

But well, other Bioconductor packages might also be having related
ggplot2 v4.0.0 issues, which is why I'm sending this email to
bioc-devel. Just as a heads up!

Best,
Leo


Leonardo Collado Torres, Ph. D.
Investigator, LIEBER INSTITUTE for BRAIN DEVELOPMENT
Assistant Professor, Department of Biostatistics
Johns Hopkins Bloomberg School of Public Health
855 N. Wolfe St., Room 382
Baltimore, MD 21205
lcolladotor.github.io
lcolladotor using gmail.com

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