Rmarkdown not working on Win 10 machine: openBinaryFile: does not exist (No such file or directory)

Question

I am not able to knit html, pdf, or word. Same error each time:

"C:/Users/bosr/AppData/Local/Pandoc/pandoc" +RTS -K512m -RTS test.utf8.md --to docx --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output test.docx --highlight-style tango 
pandoc.exe: test.utf8.md: openBinaryFile: does not exist (No such file or directory)
Error: pandoc document conversion failed with error 1
Execution halted

I know there are many questions of this nature, but none that I have found have fixed my issue.

I installed R 3.6.1 and RStudio 1.2.1578 on a new Win 10 machine w/o admin rights. Managed to get everything working except Rmarkdown. My sessionInfo() is below. If I open a command prompt, pandoc is findable:

C:\>pandoc --version
pandoc 2.7.3
Compiled with pandoc-types 1.17.5.4, texmath 0.11.2.2, skylighting 0.8.1
Default user data directory: C:\Users\bosr\AppData\Roaming\pandoc
Copyright (C) 2006-2019 John MacFarlane
Web:  http://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.

I have pandoc installed at C:\Users\bosr\AppData\Local\Pandoc\

I also tried @kevinushey's solution mentioned here which resulted in a second pandoc install at H:\rstudio-pandoc\

Both pandoc installs are in my path (user) environment variable which I am allowed to set.

I would be very grateful for any suggestions.

- Session info -------------------------------------------------------
 setting  value                       
 version  R version 3.6.1 (2019-07-05)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_United States.1252  
 ctype    English_United States.1252  
 tz       America/New_York            
 date     2019-09-24                  

- Packages -----------------------------------------------------------
 package   * version date       lib source                      
 base64enc   0.1-3   2015-07-28 [1] CRAN (R 3.6.1)              
 digest      0.6.21  2019-09-20 [1] CRAN (R 3.6.1)              
 evaluate    0.14    2019-05-28 [1] CRAN (R 3.6.1)              
 glue        1.3.1   2019-03-12 [1] CRAN (R 3.6.1)              
 highr       0.8     2019-03-20 [1] CRAN (R 3.6.1)              
 htmltools   0.3.6   2017-04-28 [1] CRAN (R 3.6.1)              
 jsonlite    1.6     2018-12-07 [1] CRAN (R 3.6.1)              
 knitr       1.25.1  2019-09-24 [1] Github (yihui/knitr@11ddfc6)
 magrittr    1.5     2014-11-22 [1] CRAN (R 3.6.1)              
 markdown    1.1     2019-08-07 [1] CRAN (R 3.6.1)              
 mime        0.7     2019-06-11 [1] CRAN (R 3.6.0)              
 Rcpp        1.0.2   2019-07-25 [1] CRAN (R 3.6.1)              
 rmarkdown   1.15    2019-08-21 [1] CRAN (R 3.6.1)              
 stringi     1.4.3   2019-03-12 [1] CRAN (R 3.6.0)              
 stringr     1.4.0   2019-02-10 [1] CRAN (R 3.6.1)              
 tinytex     0.16    2019-09-17 [1] CRAN (R 3.6.1)              
 xfun        0.9     2019-08-21 [1] CRAN (R 3.6.1)              
 yaml        2.2.0   2018-07-25 [1] CRAN (R 3.6.0)              

[1] C:/Users/bosr/R/R-3.6.1/library
[2] C:/pit

Update: I had IT install pandoc using the admin password, and I am still getting the same error:

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS riskNotes.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output riskReport_20190925.tex --table-of-contents --toc-depth 2 --template "C:\Users\bosr\R\R-3.6.1\library\rmarkdown\rmd\latex\default-1.17.0.2.tex" --no-highlight --pdf-engine pdflatex --variable graphics=yes --variable "compact-title:yes" 
pandoc.exe: riskNotes.utf8.md: openBinaryFile: does not exist (No such file or directory)
Error: pandoc document conversion failed with error 1
In addition: There were 22 warnings (use warnings() to see them)

Noeminoesis

For me an easy solution was to remove all spaces in named chunks. I use underscore to join words in the names, but some had trailing spaces. For large documents, Rstudio may have gone as far as generating the markdown *.md file, an you can continue from it in rmarkdown::render(my_md_file.md) , but you have to rename the intermediate files in the png's folder for the project. hope it helps – Crag

Answer 1

Ok, I see now this is due to the file being saved on a network drive. See here. There is no fix yet. Too bad.

Noeminoesis

By "the file", do you refer to the .Rmd that you are trying to knit? – Drainpipe

Yes, if the .Rmd file is on a local drive it knits file, but if it is on a network drive, you get a cryptic error that "openBinaryFile: does not exist". I just tried it again with R 3.6.2 and rmarkdown_2.1. – Noeminoesis

Answer 2

I have had a similar error and resolved it by uninstalling all stand-alone versions of Pandoc. In my case I had a separate Pandoc version 2.9.2.1 installed, verified by running the following in R Studio:

rmarkdown::pandoc_version()
# 2.9.2.1
rmarkdown::pandoc_exec()
# "C:/Program File~/pandoc/pandoc"

Uninstalling this version allowed me to render even network files and yielded the folowing after a reboot:

rmarkdown::pandoc_version()
# 1.19.2.1
rmarkdown::pandoc_exec()
# "C:/Program Files/RStudio/bin/pandoc/pandoc"

Tenebrae

I also had a separate version of pandoc installed, but your solution didn't work for me. Using the latest version of Rstudio 1.3.959 I get a much higher versionof pandoc: rmarkdown::pandoc_version() [1] ‘2.7.3’ rmarkdown::pandoc_exec() [1] "C:/Users/bosr/RStudio/bin/pandoc/pandoc" – Noeminoesis

Strange you have a higher version of Pandoc since I have a higher version of Rstudio (1.1.463) and thought I updated all packages with a recent installation of R 4.0.1. My version for rmarkdown is 2.3.1 – Tenebrae

Strange indeed @RDavey. I updated R to 4.0.2, R-Studio to 1.3.1056, Pandoc still 2.7.3, and still no joy. As far as I can tell this is the version of Pandoc that comes with Rstudio and is the only version installed. My network drive is also mapped to a drive letter.. – Noeminoesis

Answer 3

I had the same problem. The reason was that there was an old .RHistory file in the same folder as the RMarkdown document, which was taken over into a new project due to copying an old folder. By deleting this .RHistory file, I was able to fix the problem.

Ingalls