Closed HenrikBengtsson closed 1 year ago
I'm really surprised that this is not picked up by the Bioc check servers;
Surprise gone; ggplot2 3.4.0 was released today.
FYI, this looks urgent because it's breaking quite a few packages on CRAN and Bioconductor.
CRAN packages that will break immediately:
$ wget https://cran.r-project.org/src/contrib/PACKAGES
$ grep -B 4 -E "Imports:.*ggtree" PACKAGES | grep -E "(Package:|ggtree)"
Package: ggmotif
Imports: tidyverse, dplyr, XML, magrittr, ggplot2, stringr, ggtree,
Package: harrietr
Imports: ape (>= 4.1), ggtree (>= 1.8.1), magrittr (>= 1.5), lazyeval
Package: Platypus
Imports: BiocGenerics, Biostrings, cowplot, dplyr, ggplot2, ggtree,
Package: STraTUS
Imports: ape, phangorn, igraph, gmp, ggplot2, ggtree (>= 2.0.0),
Package: SurvivalPath
Imports: ggplot2, ggtree, treeio, dplyr, rms, survival, survminer,
Package: Sysrecon
Imports: ape, dplyr, ggplot2, ggtree, methods, patchwork, plyr,
I'm quite sure the maintainers of these package will get a two-week noticed from CRAN rather soon about removal. I think also the maintainers of their reverse dependencies will get a heads-up that their packages will be dropped as a side effect.
Eventually will also the following soft reverse dependencies:
$ grep -B 5 -E "Suggests:.*ggtree" PACKAGES | grep -E "(Package:|ggtree)"
Package: aplot
Suggests: ggtree
Package: CoOL
Suggests: ggtree, imager
Package: ggimage
Suggests: ape, ggtree, gridGraphics, httr, rsvg
Package: idiogramFISH
Suggests: rentrez, ggplot2, ggpubr, ggtree, phytools, treeio,
Package: PCMBase
Suggests: testthat, knitr, rmarkdown, abind, ggtree, cowplot, covr,
Package: rhierbaps
Suggests: knitr, rmarkdown, ggtree, phytools, testthat, formatR
Package: treestructure
Suggests: ggtree,ggplot2,knitr
Package: yatah
Suggests: dplyr, ggtree, knitr, rmarkdown, spelling, testthat (>=
I'm curious, did you get a email from the ggplot2 maintainers that your package breaks with ggplot2 3.4.0? I'd expect so, because they tend to run revdep checks, but maybe they didn't because you imported these internal functions.
With all CRAN and Bioconductor packages up-to-date, I get the following installation error on R 4.2.2 with Bioconductor 3.16:
This is because ggtree import at least two non-existing functions from ggplot2:
https://github.com/YuLab-SMU/ggtree/blob/403d9f6b3ac69766c019e8ab72abafeda3f8333b/R/geom_hilight.R#L477-L480
I'm really surprised that this is not picked up by the Bioc check servers;