When knitting: invalid version specification ‘getAppUserDataDirectory:sHGetFolderPath:’

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1

Hi all,

I have written up and am trying to knit an R Markdown file. The file is formatted correctly, with no offending code in the body that might cause an error. However, when I try to knit the file (using the "knit" button), I encounter the error

pandoc.exe: getAppUserDataDirectory:sHGetFolderPath: illegal operation (unsupported operation)
Error in strsplit(info, "\n")[[1]] : subscript out of bounds
Calls: <Anonymous> ... pandoc_available -> find_pandoc -> lapply -> FUN -> get_pandoc_version
In addition: Warning message:
In system(paste(shQuote(path), "--version"), intern = TRUE) :
  running command '"D:/Program Files/Pandoc/pandoc.exe" --version' had status 1
Execution halted

While debugging, I tried using rmarkdown::find_pandoc() and rmarkdown::pandoc_available, which also yield similar errors:

> rmarkdown::find_pandoc()
Error: invalid version specification ‘getAppUserDataDirectory:sHGetFolderPath:’
In addition: Warning message:
In system(paste(shQuote(path), "--version"), intern = TRUE) :
  running command '"D:/Program Files/Pandoc/pandoc.exe" --version' had status 1

> rmarkdown::pandoc_available()
Error: invalid version specification ‘getAppUserDataDirectory:sHGetFolderPath:’
In addition: Warning message:
In system(paste(shQuote(path), "--version"), intern = TRUE) :
  running command '"D:/Program Files/Pandoc/pandoc.exe" --version' had status 1

Other things I have tried:

  • Set the RSTUDIO_PANDOC path to a custom installation of pandoc
  • Reinstalled RStudio
  • Followed the suggestions/hints here and here, to no avail

Has anyone encountered a similar problem, or have any insights into what I can do?

2

It seems that your Pandoc binary is not working correctly, or at least as we expect.

Can you try running pandoc.exe --version from your terminal on Windows from where it is installed ? (or use full path instead of pandoc.exe

Also can you try

rmarkdown:::find_program("pandoc")

what is the returned value ?

3

Both commands seem to recognise my installation of pandoc.

Running pandoc.exe --version in my windows terminal yields

C:\Windows\System32>pandoc.exe --version

pandoc.exe 2.18
Compiled with pandoc-types 1.22.2, texmath 0.12.5, skylighting 0.12.3,
citeproc 0.7, ipynb 0.2, hslua 2.2.0
Scripting engine: Lua 5.4
User data directory: C:\Users\Timothy\AppData\Roaming\pandoc
Copyright (C) 2006-2022 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.

And rmarkdown:::find_program("pandoc") yields

> rmarkdown:::find_program("pandoc")
                                 pandoc 
"D:\\Program Files\\Pandoc\\pandoc.exe"
4

That is not the same version as found by rmarkdown

Does this binary exists on your system ? Does it work ?
Is RSTUDIO_PANDOC set to this pandoc binary ?

5

Hi cderv,

I mentioned in my original post that I had installed pandoc separately to see if this would resolve my issues - this is why the version was v2.18 (latest pandoc version) and not v2.17 (the version included with RStudio).

I have now reverted to v2.17 by uninstalling v2.18 and repeated the steps you mentioned. RSTUDIO_PANDOC now points to the default directory:

> Sys.getenv("RSTUDIO_PANDOC")
[1] "D:/Program Files/RStudio/bin/quarto/bin"

And I confirmed this by checking in cmd:

C:\Users\Timothy>"D:/Program Files/RStudio/bin/quarto/bin/pandoc.exe" --version
pandoc.exe 2.17.1.1
Compiled with pandoc-types 1.22.1, texmath 0.12.4, skylighting 0.12.2,
citeproc 0.6.0.1, ipynb 0.2
User data directory: C:\Users\Timothy\AppData\Roaming\pandoc
Copyright (C) 2006-2022 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.

But when I try looking for pandoc in R, nothing is there:

> rmarkdown:::find_program('pandoc')
pandoc 
    ""

Using other commands in rmarkdown invokes errors identical to the ones described in the original post:

> rmarkdown:::pandoc_available()
Error: invalid version specification ‘getAppUserDataDirectory:sHGetFolderPath:’
In addition: Warning message:
In system(paste(shQuote(path), "--version"), intern = TRUE) :
  running command '"D:/Program Files/RStudio/bin/quarto/bin/pandoc.exe" --version' had status 1

> rmarkdown:::find_pandoc()
Error: invalid version specification ‘getAppUserDataDirectory:sHGetFolderPath:’
In addition: Warning message:
In system(paste(shQuote(path), "--version"), intern = TRUE) :
  running command '"D:/Program Files/RStudio/bin/quarto/bin/pandoc.exe" --version' had status 1
6

This is really an uncommon error, and I believe it comes from Pandoc. I think if you try pandoc --version in your terminal without R you'll get the same issue.

Which OS / environment are you on ?

I found some similar issue on Windows AZURE (Pandoc on Microsoft Azure gives getAppUserDataDirectory error - Super User and Pandoc on Microsoft Azure gives getAppUserDataDirectory error · Issue #7486 · jgm/pandoc · GitHub)

it seems that somehow, the user data dir is not correctly found. Pandoc uses a default data dir (Pandoc - Pandoc User’s Guide) which should be on Windows: C:\Users\USERNAME\AppData\Roaming\pandoc
Are you on windows ?

Modifying the --data-dir could solve the issue. (Using pandoc_args in each YAML header for you document) or setting probably XDG_DATA_HOME env var.
However, I am not sure why this does not work on your system. This would be an issue for Pandoc

7

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