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/.
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 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. * regionReport: 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 Michael seems to have recently (< 24 hrs ago) been made aware of this issue at 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
