Fail to generate file in Rmarkdwon. OpenBinaryFile: does not exist (No such file or directory)

lamontbeau · July 9, 2019, 4:29am

Hi everyone,

When I knitr to PDF, R markdown failed to generate a PDF output and following error messages occurred.

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

And the error message:

"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS test.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output test.tex --template "C:\R\R-3.5.2\library\rmarkdown\rmd\latex\default-1.17.0.2.tex" --highlight-style tango --pdf-engine pdflatex --variable graphics=yes --variable "geometry:margin=1in" --variable "compact-title:yes" 
pandoc.exe: test.utf8.md: openBinaryFile: does not exist (No such file or directory)
Error: pandoc document conversion failed with error 1
Execution halted

And the rmarkdown session information is such that

> sessionInfo("rmarkdown")
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

Matrix products: default

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

attached base packages:
character(0)

other attached packages:
[1] rmarkdown_1.13

loaded via a namespace (and not attached):
 [1] compiler_3.6.0  graphics_3.6.0  htmltools_0.3.6
 [4] tools_3.6.0     utils_3.6.0     yaml_2.2.0     
 [7] grDevices_3.6.0 Rcpp_1.0.1      stats_3.6.0    
[10] datasets_3.6.0  knitr_1.23      methods_3.6.0  
[13] xfun_0.7        digest_0.6.19   base_3.6.0     
[16] evaluate_0.14

Could anyone advise what I should do in this regard?

leilalam · July 18, 2019, 5:57pm

I am having the same issue and am interested in any ideas for solutions

yihui · July 24, 2019, 7:19pm

This might be the same issue as

github.com/rstudio/rmarkdown

pandoc: openFile: does not exist (No such file or directory)

opened 06:07AM - 24 Feb 18 UTC

harryprince

bug help wanted

I am trying to server Rmd using shiny server. However, it seems rmarkdown or pan…doc is buggy. It works well on Rstudio but fails deploy on rstudio connect too. yaml config: ``` output: flexdashboard::flex_dashboard: social: menu source: embed storyboard: yes ``` Rmarkdown version: ``` packageVersion("rmarkdown") [1] ‘1.8’ ``` ``` shiny-server --version Shiny Server v1.5.3.838 Node.js v6.10.0 ``` pandoc version ``` /opt/shiny-server/ext/pandoc/pandoc --version pandoc 1.12.3 Compiled with texmath 0.6.6, highlighting-kate 0.5.6. ``` sessionInfo(): ``` R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base ``` here is the shiny server log: ``` processing file: index.Rmd output file: /tmp/rmarkdown/e01d3e5bbe48ef364e37eb0580046563/index.knit.md pandoc: /tmp/RtmpWH829n/rmarkdown-str67a94810a85d.html: openFile: does not exist (No such file or directory) Warning: Error in : pandoc document conversion failed with error 1 Stack trace (innermost first): 115: pandoc_convert 114: convert 113: <Anonymous> 112: do.call 111: contextFunc 110: .getReactiveEnvironment()$runWith 109: shiny::maskReactiveContext 108: <reactive> 95: doc 94: shiny::renderUI 93: func 92: force 91: withVisible 90: withCallingHandlers 89: globals$domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 83: tryCatch 82: do 81: hybrid_chain 80: origRenderFunc 79: output$__reactivedoc__ 3: <Anonymous> 2: do.call 1: rmarkdown::run ```

and

github.com/rstudio/rmarkdown

pandoc error with pdf when .Rmd is on network file share (NFS)

opened 04:33PM - 19 May 16 UTC

GeorgeTomlinson

I am on OSX El Capitain and have a network file share mounted using sshfs. When… I run markdown::render() (or use the menu item knit->PDF in Studio) on a .Rmd file on my local drive it works fine. When the .Rmd is located on the file share, it will generate a PDF, but it terminates with the message below. This in itself is usually not a problem but there are two side effects: (1) The PDF does not open in the internal viewer in RStudio. I have to open the PDF directly with another application. (2) When I use the "keep_tex: true" option in the preamble, I don't get a .tex file One possible clue: path names to files and directories are not case-sensitive on my local drive (OSX) but are case-sensitive on the file share drive. Error message: pandoc: InterimReportMay18.pdf: hClose: invalid argument (Bad file descriptor) Error: pandoc document conversion failed with error 1 Execution halted

Is your Rmd on a network drive?

system · July 31, 2019, 7:19pm

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