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Issue Description:
I try to install ggtree_3.6.2, but it gave an error.
BiocManager::install("ggtree", force = TRUE)How to solve this error?
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
CRAN: https://mirrors.ustc.edu.cn/CRAN/
Bioconductor version 3.16 (BiocManager 1.30.27), R 4.2.3 (2023-03-15)
Installing package(s) 'ggtree'
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/ggtree_3.6.2.tar.gz'
Content type 'application/gzip' length 359692 bytes (351 KB)
==================================================
downloaded 351 KB
* installing *source* package ‘ggtree’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘is_ggplot’ is not exported by 'namespace:ggplot2'
Execution halted
ERROR: lazy loading failed for package ‘ggtree’
* removing ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/4.2/ggtree’
The downloaded source packages are in
‘/tmp/RtmpPWIMAs/downloaded_packages’Session Info
sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.12.so
locale:
[1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8 LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.4.4
loaded via a namespace (and not attached):
[1] withr_3.0.2 dplyr_1.2.0 grid_4.2.3 R6_2.6.1 lifecycle_1.0.5
[6] gtable_0.3.6 magrittr_2.0.4 scales_1.4.0 pillar_1.11.1 rlang_1.1.7
[11] cli_3.6.5 farver_2.1.2 remotes_2.5.0 rstudioapi_0.18.0 generics_0.1.4
[16] vctrs_0.7.1 RColorBrewer_1.1-3 tools_4.2.3 glue_1.8.0 compiler_4.2.3
[21] pkgconfig_2.0.3 BiocManager_1.30.27 tidyselect_1.2.1 tibble_3.3.1 By the way, I suspect that it might be a bug caused by the version of the ggplot2 package. However, due to the Seurat package's VlnPlot() function, I am unable to upgrade my ggplot2 package to version 4.0.0 or higher. Due to the error 'rect_to_poly not found', I am unable to upgrade my ggplot2 package to version 3.5.0 or higher. Please help me QAQ..
https://github.com/YuLab-SMU/ggtree/issues/601
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