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YuLab-SMU / ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees
https://yulab-smu.top/contribution-tree-data/
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BiocManager::install("ggtree"), Error in get(x, envir = ns, inherits = FALSE) : object 'rect_to_poly' not found #625

Open danli349 opened 2 months ago

danli349 commented 2 months ago

Hi:

BiocManager::install("ggtree")

How to solve this error?

Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.0 (2023-04-21)
Installing package(s) 'ggtree'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/ggtree_3.8.2.tar.gz'
Content type 'application/gzip' length 360923 bytes (352 KB)
==================================================
downloaded 352 KB

* installing *source* package ‘ggtree’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in get(x, envir = ns, inherits = FALSE) :
  object 'rect_to_poly' not found
Error: unable to load R code in package ‘ggtree’
Execution halted
ERROR: lazy loading failed for package ‘ggtree’
* removing ‘/home/dan/R/x86_64-pc-linux-gnu-library/4.03/ggtree’

Thanks a lot

xiangpin commented 2 months ago

The issue was fixed in the newest released version (ggtree == 3.12.0 with Bioconductor version 3.19). But your Bioconductor version is 3.17. You should first update your Bioconductor version by updating your R to 4.4.0. Or you can try to install the development version by remotes::install_github("YuLab-SMU/ggtree").

danli349 commented 2 months ago

@xiangpin Yes. Bioconductor version 3.19 solved this problem. Thanks