• using R Under development (unstable) (2025-09-15 r88835)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘genekitr/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘genekitr’ version ‘1.2.8’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘genekitr’ can be installed ... [60s/111s] OK See the install log for details.
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [18s/43s] OK
• checking whether the package can be loaded with stated dependencies ... [18s/49s] OK
• checking whether the package can be unloaded cleanly ... [18s/49s] OK
• checking whether the namespace can be loaded with stated dependencies ... [17s/41s] OK
• checking whether the namespace can be unloaded cleanly ... [18s/42s] OK
• checking loading without being on the library search path ... [18s/42s] OK
• checking whether startup messages can be suppressed ... [19s/38s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [89s/247s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [24s/81s] 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
• checking PDF version of manual ... [9s/20s] OK
• checking HTML version of manual ... [1s/33s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR