[Bioc-devel] ggplot2 v4.0.0 related errors; related to ggbio and maybe other packages
Dear Bioconductor developers, Unfortunately the update from ggplot2 3.5.2 to 4.0.0 breaks the 77 Bioconductor packages listed below, in devel and release! Please make sure to fix your package in devel **and** release?in a timely fashion?in order to avoid deprecation. Let us know if you have concerns or need help with this. Best, H. List of packages broken by the recent update from ggplot2 3.5.2 to 4.0.0, as of Sep 22, 2025: AlphaMissenseR AlpsNMR annotatr APAlyzer barcodetrackR BPRMeth BubbleTree CaDrA cageminer CEMiTool ceRNAnetsim comapr CPSM cummeRbund DEGreport demuxSNP derfinderPlot destiny dittoSeq enrichViewNet EpiCompare extraChIPs GEOexplorer ggbio gINTomics GladiaTOX granulator hicVennDiagram HPiP idr2d IMAS iPath isomiRs limpca Maaslin2 maaslin3 Macarron methodical MetNet mfa miaViz MicrobiotaProcess microSTASIS mitology Moonlight2R MOSClip MultiRNAflow NanoStringNCTools orthogene peakPantheR PRONE qsvaR receptLoss regionReport RNAdecay Sconify scQTLtools ScreenR scRepertoire scruff SGCP SigFuge singleCellTK singscore soGGi SpaceTrooper SpatialOmicsOverlay spatzie SPOTlight TCGAbiolinks transite transmogR UMI4Cats vidger XAItest Please refer to the daily build reports for more information about the errors: - daily report for BioC 3.22 (devel): https://bioconductor.org/checkResults/3.22/bioc-LATEST/ - semiweekly report for BioC 3.21 (release): https://bioconductor.org/checkResults/3.22/bioc-LATEST/
On 17/09/2025 05:55, Maria.Doyle via Bioc-devel wrote:
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<bioc-devel-bounces at r-project.org> on behalf of Leonardo Collado Torres<lcolladotor at gmail.com> Date: Wednesday, 17 September 2025 at 02:36 To: Bioc-devel<bioc-devel at r-project.org> 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 athttps://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 at gmail.com
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