When I create a new instance following the directions here https://cloud.google.com/architecture/data-science-with-r-on-gcp-eda, the notebook cannot connect to the R kernel. It says initializing, then connecting then it disconnects.
When I SSH to the server and call curl http://127.0.0.1:8080/api/kernelspecs, I get the following output.
{
"default": "python3",
"kernelspecs": {
"python3": {
"name": "python3",
"spec": {
"argv": [
"/opt/conda/bin/python", "-m","ipykernel_launcher", "-f", "{connection_file}"
],
"env": {},
"display_name": "Python 3",
"language": "python",
"interrupt_mode": "signal",
"metadata": {"debugger": true}
},
"resources": {
"logo-32x32": "/kernelspecs/python3/logo-32x32.png",
"logo-64x64": "/kernelspecs/python3/logo-64x64.png"
}
},
"ir": {
"name": "ir",
"spec": {
"argv": [
"/usr/lib/R/bin/R", "--slave", "-e", "IRkernel::main()", "--args", "{connection_file}"
],
"env": {},
"display_name": "R",
"language": "R",
"interrupt_mode": "signal",
"metadata": {}
},
"resources": {
"kernel.js": "/kernelspecs/ir/kernel.js",
"logo-64x64": "/kernelspecs/ir/logo-64x64.png"}
},
"conda-root-py": {
"name": "conda-root-py",
"spec": {
"argv": ["/opt/conda/bin/python", "-m", "ipykernel_launcher", "-f", "{connection_file}"
],
"env": {},
"display_name":
"Python [conda env:root] *",
"language": "python",
"interrupt_mode": "signal",
"metadata": {
"debugger": true,
"conda_env_name": "root",
"conda_env_path": "/opt/conda"
}
},
"resources": {
"logo-32x32": "/kernelspecs/conda-root-py/logo-32x32.png",
"logo-64x64": "/kernelspecs/conda-root-py/logo-64x64.png"
}
}
}
}root@r-ma5832xxxxxxxxx
Is this right for an instance that was created using the R4.0 environment option?
When I checked the server logs I found this:
Error: package ‘IRkernel’ was installed before R 4.0.0: please re-install it
I opened an ssh console to the server and cd'd to /etc/R, then started R by typing 'R'.
I then tried to install the package using install.packages('IRkernel') as per instructions here: https://github.com/IRkernel/IRkernel only I ran into a whole lot of missing dependencies. I tried to update my version of R by following the instructions here: https://cran.r-project.org/bin/linux/debian/#debian-buster-stable but it turned out I was up to date. The only thing left was to update all my packages. I followed the instructions from the cran website and then went back to my jupyter notebook and could connect to the kernel.
IN the end, all I had to do was run the command below in R on my server to unlock the kernel.
update.packages(lib.loc="/usr/local/lib/R/site-library", ask = FALSE, checkBuilt = TRUE, Ncpus = 16)