Which is the best way to install R packages?

[brorio]

On the Amazon AMI I can install from inside R, but then I have this problem:
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
Warning in install.packages("jsonlite", repos = "http://cran.r-project.org") :
'lib = "/usr/lib64/R/library"' is not writable
Would you like to use a personal library instead? (y/n)

I can install it this way also:
wget https://cran.r-project.org/src/contrib/jsonlite_1.5.tar.gz
sudo R CMD INSTALL jsonlite_1.5.tar.gz

which probably is the best way, or run R as sudo..

[MikeBadescu]

Packages to be installed are supposed to be listed in the variable R_PACKAGES (originally defined in settings_default.sh).

The code to install them is located in the second part of the script 11_install_packages.sh which indicates the lib path, etc.

[brorio]

Yes, I read the code in all the files under /scripts, but I could not find out how exactly how it's supposed to work and which syntax to use.

[MikeBadescu]

how exactly how it's supposed to work

In setup_user.sh define a variable R_PACKAGES as shown in settings_default.sh. For example:

# do not use commas or quotes, leave spaces before and after each package name
R_PACKAGES=( jsonlite purrr digest )

Then, you can run the main script 01_main.sh.

If you want to use the auto-setup, run any of scripts 21_setup_vpc.sh, 22_setup_custom_ami.sh, 23_setup_s3.sh, 24_setup_lambda.sh, as needed before runnig the main script.

[brorio]

Great! Thanks! I only intend to use 11 and 12 (or if it was 13..). Then shut the EC2 down and develop on my local computer with AWS SAM. I already have aws-sam-cli, R and Python on my Mac, so I just have to invoke the phyton lambda to see that it works and then deploy it.

Unfortunately, the python aws sam has bugs that stop that scenario.