Running examples in ‘genekitr-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotVenn
> ### Title: Venn plot for groups of genes
> ### Aliases: plotVenn
> 
> ### ** Examples
> 
> k1 = requireNamespace("ComplexUpset",quietly = TRUE)
> k2 = requireNamespace("futile.logger",quietly = TRUE)
> k3 = requireNamespace("ggsci",quietly = TRUE)
> k4 = requireNamespace("RColorBrewer",quietly = TRUE)
> if(k1&k2&k3&k4){
+ library(ggplot2)
+ set1 <- paste0(rep("gene", 30), sample(1:1000, 30))
+ set2 <- paste0(rep("gene", 40), sample(1:1000, 40))
+ set3 <- paste0(rep("gene", 50), sample(1:1000, 50))
+ set4 <- paste0(rep("gene", 60), sample(1:1000, 60))
+ set5 <- paste0(rep("gene", 70), sample(1:1000, 70))
+ sm_gene_list <- list(gset1 = set1, gset2 = set2, gset3 = set3)
+ la_gene_list <- list(
+   gset1 = set1, gset2 = set2, gset3 = set3,
+   gset4 = set4, gset5 = set5
+ )
+ plotVenn(sm_gene_list,
+   use_venn = TRUE,
+   alpha_degree = 0.5,
+   main_text_size = 3,
+   border_thick = 0,
+   venn_percent = TRUE
+ )
+ plotVenn(la_gene_list,
+   use_venn = FALSE,
+   main_text_size = 15,
+   legend_text_size = 8,
+   legend_position = 'left'
+ )
+ }
Color length should be same with venn_list, auto assign colors...
Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the genekitr package.
  Please report the issue at <https://github.com/GangLiLab/genekitr/issues>.
Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the genekitr package.
  Please report the issue at <https://github.com/GangLiLab/genekitr/issues>.
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
ℹ The deprecated feature was likely used in the genekitr package.
  Please report the issue at <https://github.com/GangLiLab/genekitr/issues>.
Warning: themes$intersections_matrix is not a valid theme.
Please use `theme()` to construct themes.
Warning: `legend.margin` must be specified using `margin()`
ℹ For the old behavior use `legend.spacing`
Warning: themes$intersections_matrix is not a valid theme.
Please use `theme()` to construct themes.
Error in `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`:
! Can't merge the `text` theme element.
Caused by error:
! `object` must be an <S7_object>, not a S3<element_text/element>
Backtrace:
     ▆
  1. ├─genekitr::plotVenn(...)
  2. │ └─ComplexUpset::upset(...)
  3. │   └─S7:::Ops.S7_object(...)
  4. │     ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
  5. │     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6. │     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. │     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8. │     └─base_ops[[.Generic]](e1, e2)
  9. │       ├─S7::S7_dispatch()
 10. │       └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
 11. │         └─ggplot2:::add_ggplot(e1, e2, e2name)
 12. │           ├─ggplot2::ggplot_add(object, p, objectname)
 13. │           └─ggplot2:::ggplot_add.default(object, p, objectname)
 14. │             └─ggplot2::update_ggplot(object = object, plot = plot, ...)
 15. │               ├─S7::S7_dispatch()
 16. │               └─ggplot2 (local) `method(update_ggplot, list(class_list, ggplot2::ggplot))`(...)
 17. │                 ├─ggplot2::ggplot_add(o, plot, object_name)
 18. │                 └─ggplot2:::ggplot_add.default(o, plot, object_name)
 19. │                   └─ggplot2::update_ggplot(object = object, plot = plot, ...)
 20. │                     ├─S7::S7_dispatch()
 21. │                     └─ggplot2 (local) `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`(object = `<theme>`, plot = `<ggplt2::>`, ...)
 22. │                       ├─S7::set_props(plot, theme = add_theme(plot@theme, object))
 23. │                       └─ggplot2:::add_theme(plot@theme, object)
 24. │                         ├─rlang::try_fetch(...)
 25. │                         │ ├─base::tryCatch(...)
 26. │                         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 27. │                         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 28. │                         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 29. │                         │ └─base::withCallingHandlers(...)
 30. │                         └─ggplot2::merge_element(t2[[item]], t1[[item]])
 31. │                           ├─S7::S7_dispatch()
 32. │                           └─ggplot2 (local) `method(merge_element, list(ggplot2::element, class_any))`(...)
 33. │                             └─S7::props(old, idx)
 34. │                               └─S7::check_is_S7(object)
 35. │                                 └─base::stop(msg, call. = FALSE)
 36. └─base::.handleSimpleError(...)
 37.   └─rlang (local) h(simpleError(msg, call))
 38.     └─handlers[[1L]](cnd)
 39.       └─cli::cli_abort(...)
 40.         └─rlang::abort(...)
Execution halted