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 Connect with the Bioconductor community at our conferences: * EuroBioC 2025 (September 17-19, Barcelona, Spain)<https://eurobioc2025.bioconductor.org/> From: Bioc-devel <[email protected]> on behalf of Leonardo Collado Torres <[email protected]> Date: Wednesday, 17 September 2025 at 02:36 To: Bioc-devel <[email protected]> Subject: [Bioc-devel] ggplot2 v4.0.0 related errors; related to ggbio and maybe other packages WARNING: EXTERNAL EMAIL This email was sent by a person from outside University of Limerick. Exercise caution when clicking links, opening attachments or taking further action, before validating its authenticity. Use the Report Phishing button to report suspicious emails. 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 [email protected] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://stat.ethz.ch/mailman/listinfo/bioc-devel> [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
