Last updated on 2025-09-13 01:49:48 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.8 | 36.49 | 304.04 | 340.53 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.8 | 25.88 | 216.28 | 242.16 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.8 | OK | ||||
| r-devel-linux-x86_64-fedora-gcc | 1.2.8 | 517.43 | ERROR | |||
| r-devel-windows-x86_64 | 1.2.8 | 36.00 | 246.00 | 282.00 | OK | |
| r-patched-linux-x86_64 | 1.2.8 | 33.95 | 271.92 | 305.87 | OK | |
| r-release-linux-x86_64 | 1.2.8 | 32.72 | 273.62 | 306.34 | OK | |
| r-release-macos-arm64 | 1.2.8 | 115.00 | OK | |||
| r-release-macos-x86_64 | 1.2.8 | 362.00 | OK | |||
| r-release-windows-x86_64 | 1.2.8 | 38.00 | 240.00 | 278.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.8 | 120.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.2.8 | 278.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.2.8 | 50.00 | 330.00 | 380.00 | OK |
Version: 1.2.8
Check: examples
Result: ERROR
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: 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 ggvenn package.
Please report the issue to the authors.
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: 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
Flavor: r-devel-linux-x86_64-fedora-gcc