Pandoc: error 1, binary file does not exist

Question

I'm having problems knitting an .rmd file to a .html (and pdf for that matter) file using rmarkdown. The report that I'm trying to knit in the following example is just the example report you get when starting a new rmakrdown document.

This is the error message I get:

==> rmarkdown::render('C:/Users/***/Documents/test/test.Rmd',  encoding = 'UTF-8');


processing file: test.Rmd
  |..........                                                            |  14%
  ordinary text without R code

  |....................                                                  |  29%
label: setup (with options) 
List of 1
 $ include: logi FALSE

  |..............................                                        |  43%
  ordinary text without R code

  |........................................                              |  57%
label: cars
  |..................................................                    |  71%
  ordinary text without R code

  |............................................................          |  86%
label: pressure (with options) 
List of 1
 $ echo: logi FALSE

  |......................................................................| 100%
  ordinary text without R code


output file: test.knit.md

"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output test.html --email-obfuscation none --self-contained --standalone --section-divs --template "\\storage-***.se\home$\****\My Documents\R\win-library\4.0\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable "theme:bootstrap" --include-in-header "C:\Users\*****\AppData\Local\Temp\Rtmpc1mrLs\rmarkdown-str511010115ff7.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --lua-filter "\\storage-****.se/home$/****/My Documents/R/win-library/4.0/rmarkdown/rmd/lua/pagebreak.lua" --lua-filter "\\storage-***-se/home$/*****/My Documents/R/win-library/4.0/rmarkdown/rmd/lua/latex-div.lua" 
pandoc.exe: \\: openBinaryFile: does not exist (No such file or directory)
Error: pandoc document conversion failed with error 1
Execution halted

Pandoc tries to reach a file saved on my computer but for some reason can't find it. This is my work computer where everything is saved locally and then uploaded to a server. I have talked with IT at my office and they don't know why it wont work. I have managed to get a rmarkdown report before when I moved EVERYTHING (r project, packages and the files where I do my analysis) to a map that is not uploaded to the backup server. However, this is not a safe way since there is no backup, obviously. I've tried to just have the r-project locally for the knitting but it doesn't work either. Why can't pandoc find this binary file and is there a way I can get it to work without having to risk the safety of my work? If not, is there another way of creating similar files without pandoc?

I have seen similar questions but nothing that could give me any answers. Or give the people at the IT department any clues.

Thanks! Johanna

Here is the session information:

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252   
[3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C                   
[5] LC_TIME=Swedish_Sweden.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_4.0.2  htmltools_0.5.0 tools_4.0.2     yaml_2.2.1      rmarkdown_2.3  
 [6] knitr_1.29      xfun_0.16       digest_0.6.25   rlang_0.4.7     evaluate_0.14  

Versions:

> version
               _                           
platform       x86_64-w64-mingw32          
arch           x86_64                      
os             mingw32                     
system         x86_64, mingw32             
status                                     
major          4                           
minor          0.2                         
year           2020                        
month          06                          
day            22                          
svn rev        78730                       
language       R                           
version.string R version 4.0.2 (2020-06-22)
nickname       Taking Off Again 

> pandoc_version()
[1] ‘2.7.2’

> pandoc_available()
[1] TRUE

Answer 1

I have solved the problem!

The actual problem was the path of the rmarkdown package. It was on my //storage... path. What I finally had to do was to go into system settings and add an environmental variable for R_LIBS_USER to my H:/ path. Now when pandoc is looking for the rmarkdown details it can find the path.

Answer 2

Using this link as research. try using the RELATIVE path for your file. in this one you are using the absolute path C:/Users/... and this temporarily changes R's working directory.