I actually had a similar issue.
You don't say that here, but when I tried installing screeps on my PI 3b+ itcaused my PI to completely freeze up right around module_handle.o I had to replug it to get it back up and running.
This was actually caused by the compiler running out of RAM. You can see your RAM usage during compilation using htop:

sudo apt-get install htop
htop

if you also notice that you are running out of RAM, the easiest way to fix it is to increase the swap file size (the amount of disk space to use, when the RAM is full) I increased my swap file to 2GB and now screeps is compiling fine (even though it still takes quite some time, swap files are slow).
I don't know the exact command to do this of the top of my head, but a quick google search should help.

I had the same issue on a vps with only 2GB memory.

To create a swap file and activate it, do as follow as root (or sudo) user :
dd if=/dev/zero of=/swapper bs=1M count=2048
mkswap /swapper
swapon /swapper

To check if the swap file is activated :
free -m

Then, as screeps user, you can :
npm install screeps

After completion of the install process
you can delete your swap partition as root (or sudo) user :
swapoff /swapper
rm /swapper

That sounds like an isolated-vm issue, are you able to install it alone? If it doesn't install either, please create the issue at ivm module page.