Folder created automatically when knitting R Markdown

ejlatour · April 4, 2019, 8:39pm

A new behavior has started happening when I knit a .Rmd file to HTML. RStudio seems to automatically create a new folder with the images saved to it.

It did not used to do this for me and I have not changed YAML or other chunk options that should be having this effect.

Has anyone else experienced this or is anyone aware of why this might be happening?

When I delete the folder, it will also delete the knitted HTML like they are linked somehow. Super weird

andresrcs · April 4, 2019, 8:48pm

I can confirm that this is happening, even when knitting with self_contained = TRUE option, an empty folder gets created.

render(rmd_path,
       output_format = "html_document",
       output_options = c("self_contained = TRUE"),
       quiet = TRUE)

ejlatour · April 9, 2019, 3:48am

I had posted this hoping that someone from RStudio might see and have some kind of comment/suggestion. This behavior is a little worrisome

cderv · April 9, 2019, 7:35am

What is the version of Rmarkdown and knitr we are talking about here ? Did you manage find when it changed ? There were several bugs fixed and this may be a side effect of one of them.

cderv · April 9, 2019, 9:17am

I think there is an issue opened about this

github.com/rstudio/rmarkdown

rmarkdown creates _files directory not cleared

opened 11:01PM - 18 Mar 19 UTC

closed 03:17PM - 12 Apr 19 UTC

wxli0

bug

Hello, I was playing with rmarkdown::render() function. After that, I found k…nit in rmarkdown always created an empty "_files" directory, which I do not want. Is there any commands that can help me get rid of this directory automatically? I have attached the all the render commands I have tried. ```library(rmarkdown) # output_dir <- "result" # render() # rmarkdown::render("6_1p_CSC05a_onset.Rmd", output_file = "result/6_1p_CSC05a_onset.pdf") # rmarkdown::render('6_1p_CSC05a_onset.Rmd', # output_file='6_1p_CSC05a_onset.md') # rmarkdown::render("6_1p_CSC05a_onset.Rmd") # knit("doc.Rmd", "papers/doc.md") # knit("6_1p_CSC05a_onset.Rmd", "result/6_1p_CSC05a_onset.md") # opts_knit$set(output.dir="result") # must place in the folder as iRaster.R due to source(...) # rmarkdown::render("6_1p_CSC05a_onset.Rmd", output_format = "all", clean = TRUE) ``` In my case, it always created 6_1p_CSC05a_onset_files folder in the same folder as 6_1p_CSC05a_onset.pdf. Any help would be appreciated!

I will look into this.

cderv · April 9, 2019, 2:50pm

Know that this is a confirmed bug that will be fixed in next version. (see this answer)

ejlatour · April 9, 2019, 6:42pm

@cderv Thank you so much! I had not found any discussion along this issue and I very much appreciate that you were able to track it down!!

system · April 30, 2019, 6:42pm

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