Rscript not working with packaged R for AWS Lambda - r

Question

I'm trying to run an R script on the command line of an AWS EC2 instance using packaged R binaries and libraries (without installation) -- the point is to test the script for deployment to AWS Lambda. I followed these instructions. The instructions are for packaging up all the R binaries and libraries in a zip file and moving everything to a Amazon EC2 instance for testing. I unzipped everything on the new machine, ran 'sudo yum update' on the machine, and set R's environment variables to point to the proper location:
export R_HOME=$HOME
export LD_LIBRARY_PATH=$HOME/lib
NOTE: $HOME is equal to /home/ec2-user.
I created this hello_world.R file to test:
#!/home/ec2-user/bin/Rscript
print ("Hello World!")
But when I ran this:
ec2-user$ Rscript hello_world.R
I got the following error:
Rscript execution error: No such file or directory
So I checked the path, but everything checks out:
ec2-user$ whereis Rscript
Rscript: /home/ec2-user/bin/Rscript
ec2-user$ whereis R
R: /home/ec2-user/bin/R /home/ec2-user/R
But when I tried to evaluate an expression using Rscript at the command line, I got this:
ec2-user$ Rscript -e "" --verbose
running
'/usr/lib64/R/bin/R --slave --no-restore -e '
Rscript execution error: No such file or directory
It seems Rscript is still looking for R in the default location '/usr/lib64/R/bin/R' even though my R_HOME variable is set to '/home/ec2-user':
ec2-user$ echo $R_HOME
/home/ec2-user
I've found sprinkles of support, but I can't find anything that addresses my specific issue. Some people have suggested reinstalling R, but my understanding is, for the purposes of Lambda, everything needs to be self-contained so I installed R on a separate EC2 instance, then packaged it up. I should mention that everything runs fine on the machine where R was installed with the package manager.
SOLUTION: Posted my solution in the answers.

Answer 1

It thinkt it is staring at you right there:
ec2-user$ whereis R
R: /home/ec2-user/bin/R /home/ec2-user/R
is where you put R -- however it was built for / expects this:
ec2-user$ Rscript -e "" --verbose
running
'/usr/lib64/R/bin/R --slave --no-restore -e '
These paths are not the same. The real error may be your assumption that you could just relocate the built and configured R installation to a different directory. You can't.
You could build R for the new (known) path and install that. On a system where the configured-for and installed-at path are the same, all is good:
$ Rscript -e "q()" --verbose
running
'/usr/lib/R/bin/R --slave --no-restore -e q()'
$

Answer 2

This blog post walks through a similar problem and offers a potential solution. I also had to implement part of the solution from this post.
I changed the very first line of R's source code from this:
#!/bin/sh
# Shell wrapper for R executable.
R_HOME_DIR=${R_ROOT_DIR}/lib64${R_ROOT_DIR}
To this:
R_HOME_DIR=${RHOME}/lib64${R_ROOT_DIR}
I'll explain why below.
NOTE -- The rest of the code is:
if test "${R_HOME_DIR}" = "${R_ROOT_DIR}/lib64${R_ROOT_DIR}"; then
case "linux-gnu" in
linux*)
run_arch=`uname -m`
case "$run_arch" in
x86_64|mips64|ppc64|powerpc64|sparc64|s390x)
libnn=lib64
libnn_fallback=lib
;;
*)
libnn=lib
libnn_fallback=lib64
;;
esac
if [ -x "${R_ROOT_DIR}/${libnn}${R_ROOT_DIR}/bin/exec${R_ROOT_DIR}" ]; then
R_HOME_DIR="${R_ROOT_DIR}/${libnn}${R_ROOT_DIR}"
elif [ -x "${R_ROOT_DIR}/${libnn_fallback}${R_ROOT_DIR}/bin/exec${R_ROOT_DIR}" ]; then
R_HOME_DIR="${R_ROOT_DIR}/${libnn_fallback}${R_ROOT_DIR}"
## else -- leave alone (might be a sub-arch)
fi
;;
esac
fi
if test -n "${R_HOME}" && \
test "${R_HOME}" != "${R_HOME_DIR}"; then
echo "WARNING: ignoring environment value of R_HOME"
fi
R_HOME="${R_HOME_DIR}"
export R_HOME
You can see at the bottom, the code sets R_HOME equal to R_HOME_DIR, which it originally assigned based on R_ROOT_DIR.
No matter what you set the R_HOME_DIR or R_HOME variable to, R resets everything using the R_ROOT_DIR variable.
With the change, I can set all my environment variables:
export RHOME=$PWD/R #/home/ec2-user/R
export R_HOME=$PWD/R #/home/ec2-user/R
export R_ROOT_DIR=/R #/R
I set RHOME to my working directory where the R package sits. RHOME basically acts as a prefix, in my case, it's /home/ec2-user/.
Also, Rscript appends /R/bin to whatever RHOME is, so now I can properly run...
Rscript hello_world.R
...on the command line. Rscript knows where to find R, which knows where to find all it's stuff.
I feel like packaging up R to run in a portable self-contained folder, without using Docker or something, should be easier than this, so if anyone has a better way of doing this, I'd really appreciate it.

Answer 3

Another more quickly method:
create same folder /usr/lib/R/bin/
then put R into this folder.