- using R version 4.3.3 (2024-02-29)
- using platform: aarch64-apple-darwin20 (64-bit)
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.4
- using session charset: UTF-8
- checking for file ‘jamba/DESCRIPTION’ ... OK
- this is package ‘jamba’ version ‘1.0.2’
- 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 ‘jamba’ can be installed ... [6s/6s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ 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 R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] 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 ... [7s/7s] OK
- checking Rd files ... [1s/1s] OK
- checking Rd metadata ... 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [5s/7s] ERROR
Running examples in ‘jamba-Ex.R’ failed
The error most likely occurred in:
> ### Name: kable_coloring
> ### Title: Extend kableExtra colorization of 'Rmarkdown' tables
> ### Aliases: kable_coloring
>
> ### ** Examples
>
> ## Don't show:
> if (all(check_pkg_installed(c("circlize", "kableExtra")))) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ expt_df <- data.frame(
+ Sample_ID="",
+ Treatment=rep(c("Vehicle", "Dex"), each=6),
+ Genotype=rep(c("Wildtype", "Knockout"), each=3),
+ Rep=paste0("rep", c(1:3)))
+ expt_df$Sample_ID <- pasteByRow(expt_df[, 2:4])
+
+ # define colors
+ colorSub <- c(Vehicle="palegoldenrod",
+ Dex="navy",
+ Wildtype="gold",
+ Knockout="firebrick",
+ nameVector(
+ color2gradient("grey48", n=3, dex=10),
+ rep("rep", 3),
+ suffix=""),
+ nameVector(
+ color2gradient(n=3,
+ c("goldenrod1", "indianred3", "royalblue3", "darkorchid4")),
+ expt_df$Sample_ID))
+ kbl <- kable_coloring(
+ expt_df,
+ caption="Experiment design table showing categorical color assignment.",
+ colorSub)
+ # Note that the HTML table is rendered in 'Rmarkdown', not pkgdown
+ kbl
+
+ # return_type="data.frame" is a data.frame with HTML contents
+ kdf3 <- kable_coloring(
+ return_type="data.frame",
+ df=expt_df,
+ colorSub=colorSub)
+ kdf3;
+ ## Don't show:
+ }) # examplesIf
> expt_df <- data.frame(Sample_ID = "", Treatment = rep(c("Vehicle", "Dex"),
+ each = 6), Genotype = rep(c("Wildtype", "Knockout"), each = 3), Rep = paste0("rep",
+ c(1:3)))
> expt_df$Sample_ID <- pasteByRow(expt_df[, 2:4])
> colorSub <- c(Vehicle = "palegoldenrod", Dex = "navy", Wildtype = "gold",
+ Knockout = "firebrick", nameVector(color2gradient("grey48", n = 3, dex = 10),
+ rep("rep", 3), suffix = ""), nameVector(color2gradient(n = 3, c("goldenrod1",
+ "indianred3", "royalblue3", "darkorchid4")), expt_df$Sample_ID))
> kbl <- kable_coloring(expt_df, caption = "Experiment design table showing categorical color assignment.",
+ colorSub)
Error in kable_coloring(expt_df, caption = "Experiment design table showing categorical color assignment.", :
kable_coloring() requires the kableExtra package.
Calls: <Anonymous> ... source -> withVisible -> eval -> eval -> kable_coloring
Execution halted
Ran 3/3 deferred expressions
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [3s/4s] OK
Running ‘testthat.R’ [3s/4s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking re-building of vignette outputs ... [7s/8s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘jamba-vignette.Rmd’ using rmarkdown
Quitting from lines 547-570 [kable_coloring] (jamba-vignette.Rmd)
Error: processing vignette 'jamba-vignette.Rmd' failed with diagnostics:
kable_coloring() requires the kableExtra package.
--- failed re-building ‘jamba-vignette.Rmd’
SUMMARY: processing the following file failed:
‘jamba-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [12s/13s] OK
- DONE
Status: 2 ERRORs
- using check arguments '--no-clean-on-error '