I am trying to link a .Rmd file on a private ubuntu amazon ec2 instance with 15 GB of memory. I installed rstudio (RStudio 0.99.903 - Ubuntu 12.04 + / Debian 8+ (64-bit)) from the source without any problems, and then linked the companion version of pandoc after.
$ sudo ln -s /usr/lib/rstudio/bin/pandoc/pandoc /usr/local/bin
$ sudo ln -s /usr/lib/rstudio/bin/pandoc/pandoc-citeproc /usr/local/bin
And confirmed it in PATH
ubuntu@ip-172-31-46-87:~$ pandoc -v
pandoc 1.15.2
Calling knitr from the command line
Rscript -e "rmarkdown::render('Observed.Rmd')" &> run.txt
I can successfully knit small test runs.
However, when I try to do a larger run, I get an error
/usr/local/bin/pandoc +RTS -K512m -RTS SingleSpecies.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output SingleSpecies.html --smart --email-obfuscation none --self-contained -M2GB +RTS -K64m -RTS --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.3/rmarkdown/rmd/h/default.html --number-sections --variable 'theme:spacelab' --include-in-header /tmp/RtmpWXb9A4/rmarkdown-str58570a61934.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --no-highlight --variable highlightjs=/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.3/rmarkdown/rmd/h/highlight --variable navigationjs=/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.3/rmarkdown/rmd/h/navigation-1.0
Error: pandoc document conversion failed with error 127
Execution halted
Warning message:
system call failed: Cannot allocate memory
I tried to increase heap size following another SO question by adding in YAML
output:
html_document:
keep_md: yes
number_sections: yes
theme: spacelab
toc: yes
pandoc_args: [
"-M2GB", "+RTS", "-K64m", "-RTS"
]
I also tried
self_contained: no
From which I see that figures knit only 40 MB
ubuntu@ip-172-31-21-194:~/Whales$ du SingleSpecies_files/ -sh
40M SingleSpecies_files/
In e2c, I track memory in increments of five minutes.
, knitr ( pandoc) , 10 . ? , , ggmap, . , , . .
, , knitr rstudio, rstudio , knitr?