Closed bschilder closed 1 year ago
devtools
to 2.4.5
(latest version on CRAN) did not seem to help.devtools
to 2.4.5.9000
(dev version from GitHub) did not seem to help.pkgdown
to 2.0.7
(latest version on CRAN) did not seem to help.pkgdown
to 2.0.7.9000
(dev version from GitHub) did not seem to help.rmarkdown
to 2.20
(latest version on CRAN) did not seem to help.rmarkdown
to 2.20.1
(dev version from GitHub) did not seem to help.Also, noting that it's strange that this only occurs on line 251 (the picard_files
step) even though the step before it (peak_info
) is nearly identical (just a slightly different dataframe).
```{r peak_info}
peak_info_df <- peak_info(peaklist = peaklist,
blacklist = blacklist)
download_button(object = peak_info_df,
filename = "peak_info_df",
output_extension = ".csv")
# Print table
knitr::kable(peak_info_df, format = "markdown")
# Save output
save_output(save_output = params$save_output,
file = peak_info_df,
file_type = "data.frame",
filename = "peak_info",
outpath = outfile_dir)
# Remove variable
remove(peak_info_df)
vs.
```{r picard_files}
if (!is.null(params$picard_files)){
fragment_info_df <- fragment_info(picard_list = params$picard_files)
download_button(object = fragment_info_df,
filename = "fragment_info",
output_extension = ".csv")
# Print data frame
knitr::kable(fragment_info_df, format = "markdown")
save_output(save_output = params$save_output,
file = fragment_info_df,
file_type = "data.frame",
filename = "fragment_info",
outpath = outfile_dir)
remove(fragment_info_df)
}
Based on some clues from here https://github.com/r-lib/pkgdown/issues/825, tried removing my custom.css from the EpiCompare.Rmd template. But didn't seem to have any effect.
Tried updating pandoc
on my Mac system and then restarting R:
brew install pandoc
pandoc -v
# pandoc 3.1
# Features: +server +lua
# Scripting engine: Lua 5.4
# User data directory: /Users/schilder/.local/share/pandoc
# Copyright (C) 2006-2023 John MacFarlane. Web: https://pandoc.org
# This is free software; see the source for copying conditions. There is no
# warranty, not even for merchantability or fitness for a particular purpose.
Had no effect.
Tried adding self_contained: true
to yaml header based on some clues from here https://github.com/rstudio/rmarkdown/pull/2095
No effect.
Note that devtools::check(vignettes=F)
does circumvent these issues. This confirms it is purely an issue with rendering the vignettes (not running the example/test code).
Indeed, all checks pass when running this way:
Suddenly all checks are now passing with the default devtools::check()
in Rstudio, despite running the vignettes. No idea how this fixed itself, but it must have been related to one of the other fixes I made along the way!
1. Bug description
Error occurs during
devtools::check
when building the EpiCompare.Rmd vignette, but not while running manually. So this is mostly just an issue for us (the developers) rather than the users.Console output
Expected behaviour
Runs in both cases
2. Reproducible example
Code
(Please add the steps to reproduce the bug here. See here for an intro to making a reproducible example (i.e. reprex) and why they're important! This will help us to help you much faster.)
3. Session info
(Add output of the R function
utils::sessionInfo()
below. This helps us assess version/OS conflicts which could be causing bugs.)