Error(s) in re-building vignettes:
--- re-building ‘ggmsa.Rmd’ using rmarkdown
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Loading required package: dplyr

Attaching package: 'dplyr'

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    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
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ggtree v3.0.2  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



Attaching package: 'ggtree'

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Warning: Unknown or uninitialised column: `name`.
Warning: Unknown or uninitialised column: `name`.
Loading required package: gggenes
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replace the existing scale.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
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Error: processing vignette 'ggmsa.Rmd' failed with diagnostics:
there is no package called 'ggtreeExtra'
--- failed re-building ‘ggmsa.Rmd’

SUMMARY: processing the following file failed:
  ‘ggmsa.Rmd’

Error: Vignette re-building failed.
Execution halted