I am running a Rstudio AWS instance using the premade AMI ( http://www.louisaslett.com/RStudio_AMI/ ). Using this i am able to boot into rstudio server. I can create a default .Rmd file and knit without problem. I get the normal message at the end (pasted, the path may be relavent).
/usr/lib/rstudio-server/bin/pandoc/pandoc +RTS -K512m -RTS test.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output test.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --variable 'theme:bootstrap' --include-in-header /tmp/RtmpeN2em3/rmarkdown-str156c3b3566c1.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --no-highlight --variable highlightjs=/usr/local/lib/R/site-library/rmarkdown/rmd/h/highlight
Furthermore, i can go to shell rstudio options tools -> shell and type
Rscript -e "rmarkdown::render("test.html")"
And that knits just fine.
However, when i ssh into that same instance (git bash terminal), and try to render that same document with the same line of code. I get:
ubuntu@ip-172-31-17-88:/home/rstudio$ Rscript -e "rmarkdown::render("test.html")"
Error: pandoc version 1.12.3 or higher is required and was not found.
Execution halted
Is there a behavior about paths in ssh that i am misunderstanding?
If i type:
pandoc
The program 'pandoc' is currently not installed. You can install it by typing:
sudo apt-get install pandoc
Then how was rstudio server able to knit to html?
RStudio sets the environment variable RSTUDIO_PANDOC
to the directory that contains the pandoc
binaries shipped with the RStudio IDE/Server. When you call rmarkdown::render()
, rmarkdown tries to find pandoc
from this environment variable.
Of course, this environment variable exists when you run programs inside RStudio IDE/Server, but it is unlikely to be set outside RStudio. You either add the RStudio pandoc directory to PATH
, or run everything inside RStudio.
PATH=/usr/lib/rstudio-server/bin/pandoc/:$PATH Rscript -e "rmarkdown::render("test.Rmd")"
And you can certainly install Pandoc by yourself via apt-get install
, but I'm not sure if a sufficient version of Pandoc exists in your Ubuntu distribution.
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