Issues with Shiny and Leaflet on an AWS EC2

[nicojacgo]

As described in the title, I'm having issues with installing the package 'leaflet' on my shiny server (on an EC2).

** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggplot2)
* installing *source* package ‘viridis’ ...
** package ‘viridis’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (viridis)
ERROR: dependency ‘raster’ is not available for package ‘leaflet’
* removing ‘/home/shiny/R/x86_64-pc-linux-gnu-library/3.4/leaflet’

The downloaded source packages are in
	‘/tmp/RtmpeFj1fk/downloaded_packages’
Warning message:
In install.packages("leaflet") :
  installation of package ‘leaflet’ had non-zero exit status
> install.packages("raster")
Installing package into ‘/home/shiny/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Warning message:
package ‘raster’ is not available (for R version 3.4.4) 
> 

A dependency for leaflet, 'raster', is not available; however, I am also unable to download it as a package through R, as demonstrated.

Could someone kindly address this issue for me?

[andresrcs]

The raster package depends on R >= 3.5.0 so you need to update your R version.

[nicojacgo]

That's what I had assumed, but I'm unsure how I would go about doing this on this Ubuntu 18.04 instance -- and I have added a public key to the system I believe.

[andresrcs]

You have to add a repository to your /etc/apt/sources.list file

sudo nano /etc/apt/sources.list

Add this line and save the file

deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/

Then add the apt key

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9

update your apt cache and install R

sudo apt update
sudo apt install r-base r-base-dev

[nicojacgo]

@andresrcs

sudo apt install r-base r-base-dev

It also seems that I have this issue:

g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RasterModule.cpp -o RasterModule.o

Freezes on this chunk of code, which I believe had also happened earlier. Any idea what this could be?

I appreciate the help though!

Edit: In the monitoring portion of my AWS instance, it seems as though the CPU reaches ~100% utilization when trying to install the "leaflet" library, which leads to this crash.

EDIT: Seems as though the basic ec2.micro's memory is the issue here...

[andresrcs]

Sorry but you are not showing any error message, if the cpu is working then maybe you simply have to wait longer, a t2.micro is a very underpowered instance but it is more than capable of compiling leaflet (I have tested it), if your issue where lack of memory then the compiler should stop with a kill message, but even if that was the case you could add swap memory to solve it.

[nicojacgo]

I was able to debug successfully; ended up upgrading to a t2.medium to download the packages. Everything is running just fine as of now!