I can't knit Rmd-files to pdf

rotalk · August 23, 2019, 10:07pm

Error Information:

Description of issue -

When I try to knit Rmd-files to pdf in Rstudio I get an error message. Before summer it worked well, but for about a month now it has not worked. I can still knit to word.

I get the same problem with any Rmd-file, for example this one:

---
title: "Untitled"
output:
  pdf_document: default
---

This is a test.

I get the following error message:

processing file: test.Rmd
  |.................................................................| 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 latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output test.tex --template "\\hig-ad\personal\homes\R\win-library\3.6\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" 
Could not fetch http://?/UNC/hig-ad/personal/homes/R/win-library/3.6/rmarkdown/rmd/latex/default-1.17.0.2.tex
HttpExceptionRequest Request {
  host                 = ""
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/"
  queryString          = "?/UNC/hig-ad/personal/homes/R/win-library/3.6/rmarkdown/rmd/latex/default-1.17.0.2.tex"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InvalidDestinationHost "")
Error: pandoc document conversion failed with error 61
Execution halted

Steps taken so far -

I gave the computer to IT-support where I work. They reinstalled everything, including Windows 10 and Rstudio. This did not solve the problem. I still got the same error message.

System Information:

RStudio Edition: Desktop
RStudio Version: 1.2.1335.
OS Version: Windows 10
R Version: R i386 3.6.0 and R x64 3.6.0

Also:

Your sessionInfo():

R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
locale:
[1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252    LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C                    LC_TIME=Swedish_Sweden.1252    

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

other attached packages:
[1] lmerTest_3.1-0 lme4_1.1-21    Matrix_1.2-17 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2          knitr_1.24          splines_3.6.0       MASS_7.3-51.4       munsell_0.5.0       colorspace_1.4-1    lattice_0.20-38     rlang_0.4.0         minqa_1.2.4        
[10] tools_3.6.0         grid_3.6.0          gtable_0.3.0        nlme_3.1-139        xfun_0.8            htmltools_0.3.6     yaml_2.2.0          digest_0.6.20       lazyeval_0.2.2     
[19] tibble_2.1.3        numDeriv_2016.8-1.1 crayon_1.3.4        nloptr_1.2.1        ggplot2_3.2.1       evaluate_0.14       rmarkdown_1.14      compiler_3.6.0      pillar_1.4.2       
[28] scales_1.0.0        boot_1.3-22         pkgconfig_2.0.2

From Troubleshooting Guide: Using RStudio

technocrat · August 24, 2019, 1:55pm

The same error message is reported on stackoverflow, ironically also from UNC.

The nub of the problem is that pandoc is trying to fetch the required \LaTeX style file over an HTTP connection. Either the proxy server, if there is one, or the target server doesn't recognize the request because pandoc doesn't automatically include a request-header User-Agent= ... (at least)

So, it's a configuration problem with the \LaTeX installation, which is where default-1.17.0.2.tex lives. I'm not sure what UNC did to point pandoc to the default-1.17.0.2.tex file over an HTTP connection.

rotalk · August 28, 2019, 11:06am

Thank you @technocrat for your answer. In the link to stackoverflow that you sent I read that I should "remove the package 'rmarkdown', and reinstall it". I have now removed rmarkdown by writing remove.packages('rmarkdown') and then installed it again by writing install.packages('rmarkdown'). I still have the same problem and get the same error message...

technocrat · August 28, 2019, 3:40pm

Sorry that I was unclear; my link was just to show that a similar problem had come up involving UNC. The default pandoc - \LaTeX configuration is that pandoc looks for the default-1.17.0.2,tex in the local file system. pandoc can find http files, but to do that it has to be configured to pass the minimum required client side http protocol request headers and, in the case of what's probably a password-protected site, login-credentials.

cderv · August 30, 2019, 9:24pm

I think this is related to this Pandoc issue

github.com/jgm/pandoc

Windows UNC Paths Broken

opened 04:55PM - 05 Dec 18 UTC

closed 05:35AM - 20 Sep 20 UTC

KeenRivals

platform:windows

When running Pandoc 2.5 against a UNC path in Windows, I get a file not found er…ror. The problem does not occur in Pandoc 2.2.3.2. Here's a sample Pandoc 2.2.3.2 session, which works: ``` C:\Users\me>pandoc -t html5 -s -o \\example-nas.org\private\out.html \\example-nas.org\private\in.txt C:\Users\me> ``` Here's Pandoc 2.5: ``` C:\Users\me>pandoc -t html5 -s -o \\example-nas.org\private\out.html \\example-nas.org\private\in.txt pandoc.exe: \\example-nas.org\private\in.txt: openBinaryFile: does not exist (No such file or directory) C:\Users\me> ``` I'm running Windows 10 64-bit, 1809. Using 64-bit versions of pandoc, but I've had the same behavior on 32-bit versions. The problem also occurs if the cwd is inside the network folder. I was also able to recreate the issue on Pandoc 2.4. The target network shares I've had it happen on are a samba share and a Windows file server.

It seems to be fixed since Pandoc 2.7.2. You should check your version and install newer binary if necessary. (rmarkdown::pandoc_version()) See Release note
https://pandoc.org/releases.html#pandoc-2.7.2-5-april-2019

Text.Pandoc.Class: fetchItem : don’t treat UNC paths as protocol-relative URLs (#5127). These are paths beginning //?/UNC/... .

Seems related to what you observe with UNC path.

If it does not work, maybe there is something to report back to pandoc...

Hope it helps !

rotalk · September 3, 2019, 3:56pm

Thank you @cderv for this advise. I have now installed pandoc 2.7.3. The error message has changed as a result. When I try to knit Rmd-files I now get this error message:

processing file: test.Rmd
|.................................................................| 100%
ordinary text without R code

output file: test.knit.md

"C:/Users/rotalk/AppData/Local/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 "\hig-ad\personal\homes\R\win-library\3.6\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: \: openBinaryFile: does not exist (No such file or directory)
Error: pandoc document conversion failed with error 1
Execution halted

cderv · September 4, 2019, 6:00am

There is still something of with the fact your libraries are not on a local directory. rmarkdown package is on the shared dir I guess and if you don't get the UNC error, there is still a reading error from this directory.
Maybe the fix in pandoc is not enough. You can check the discussion in the issue to see what they say...

hamzatu · September 4, 2019, 9:04am

Try installing the tinytex package.

system · September 25, 2019, 9:04am

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