一. 报错

在运行ggtree脚本的时候出现报错：

Error in `stat_tree()`:

! Problem while converting geom to grob.

ℹ Error occurred in the 1st layer.

Caused by error in `is.waive()`:

! could not find function "is.waive"

Backtrace:

     ▆

  1. ├─base::print(p)

  2. ├─ggplot2 (local) `print.ggplot2::ggplot`(p)

  3. │ ├─ggplot2::ggplot_gtable(data)

  4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)

  5. │   └─ggplot2:::by_layer(...)

  6. │     ├─rlang::try_fetch(...)

  7. │     │ ├─base::tryCatch(...)

  8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)

  9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])

 10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)

 11. │     │ └─base::withCallingHandlers(...)

 12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])

 13. │       └─l$draw_geom(d, layout)

 14. │         └─ggplot2 (local) draw_geom(..., self = self)

 15. │           └─self$geom$draw_layer(...)

 16. │             └─ggplot2 (local) draw_layer(..., self = self)

 17. │               └─base::lapply(...)

 18. │                 └─ggplot2 (local) FUN(X[[i]], ...)

 19. │                   ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))

 20. │                   └─self$draw_panel(...)

 21. │                     └─ggtree (local) draw_panel(...)

 22. │                       └─ggplot2:::empty(data)

 23. └─base::.handleSimpleError(...)

 24.   └─rlang (local) h(simpleError(msg, call))

 25.     └─handlers[[1L]](cnd)

 26.       └─cli::cli_abort(...)

 27.         └─rlang::abort(...)

Execution halted

归根结底错误就是这个：! could not find function "is.waive"

二. 解决方案

remotes::install_version("ggplot2", version = "3.5.1")

remotes::install_github("YuLab-SMU/ggtree")

remotes::install_github("YuLab-SMU/ggtree", dependencies = TRUE, upgrade = "always")

if (!exists("is.waive")) {
  is.waive <- \(x) inherits(x, "waiver") # nolint
}