Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
ggtree v3.0.4  For help: https://yulab-smu.top/treedata-book/

If you use ggtree in published research, please cite the most appropriate paper(s):

1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96
2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628


Loading required package: ape

Attaching package: 'ape'

The following object is masked from 'package:ggtree':

    rotate

Loading required package: maps
Warning in load_fasta(fasta.file.name) :
  Characters not in acgtnACGTN- will be treated as missing (-)...
Warning in load_fasta(woodmouse) :
  Characters not in acgtnACGTN- will be treated as missing (-)...
Read 1 item
Warning in FUN(X[[i]], ...) :
  DESCRIPTION file of package 'stats' is missing or broken
Warning in FUN(X[[i]], ...) :
  DESCRIPTION file of package 'graphics' is missing or broken
Warning in FUN(X[[i]], ...) :
  DESCRIPTION file of package 'grDevices' is missing or broken
Warning in FUN(X[[i]], ...) :
  DESCRIPTION file of package 'utils' is missing or broken
Warning in FUN(X[[i]], ...) :
  DESCRIPTION file of package 'datasets' is missing or broken
Warning in FUN(X[[i]], ...) :
  DESCRIPTION file of package 'methods' is missing or broken
Warning in FUN(X[[i]], ...) :
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Quitting from lines 173-174 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted