I can't knit my rmarkdown files - pandoc error

Question

My university provided laptop was recently replaced and now when I try to knit my Rmd files if get the following error:

pandoc.exe: \\: openBinaryFile: invalid argument (Invalid argument)
Error: pandoc document conversion failed with error 1
Execution halted

These files used to knit perfectly on my old laptop and all of the code blocks within the file still run without errors.

The pandoc_available() function returns TRUE

The answers to similar questions that I have searched suggest it is something to do with the file paths but I am not familiar enough with this to make sense of what I should do. I tried mapping a network drive (Z:) to the folder where the Rmd file is stored and then changing the working directory in RStudio to that drive but it hasn't helped (and now I don't know how to change it back to ~ or what that referred to in the first place)

I have also tried downloading the latest version of Pandoc and a search on Windows Explorer shows that has installed in my user directory but I also have a version in C:\Program Files\RStudio\bin. That has also not helped.

I'm not sure if this is relevant but here is the information on the R version that I am running:

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit)

Can you tell me what other information is required to diagnose the problem and I will edit to include.

I am sorry this question is so poorly specified and would appreciate any help to improve it.

**** UPDATE ****

I have found that if I

(i) specify that I want a .md file in the YAML header,

(ii) create an .md file by knitting the markdown file,

(iii) copy that .md file manually to the Pandoc directory

(iv) run pandoc.exe -s -o test.knit.md test.html from the MSDOS command prompt within the Pandoc directory,

then I can create the html output file.

However, changing the working directory for RStudio to the Pandoc directory and running

x <- rmarkdown::render("test.Rmd", run_pandoc = FALSE, clean = FALSE)
knit_meta <- attr(x, "knit_meta")
rmarkdown::render(   input = 'test.knit.md'    , knit_meta = knit_meta )

as per https://stackoverflow.com/questions/38908766/how-to-generate-an-md-file-from-a-rmarkdown-file-containing-an-htmlwidget gives the same error as shown in my original post.

Does this prompt any thoughts that might lead to a solution to my problem?

Answer 1

The university IT people were able to solve my problem by uninstalling R and RStudio from the network drive and installing it on the C: drive and I am now able to knit successfully.