Error in Jupyter Notebook: What could be the reason? - r

Question

Recently I updated R n Jupyter Lab with homebrew.
Today, I am surprised that R failed to run on ipython notebook with error below:
Error Starting Kernel
Traceback (most recent call last):
File "/opt/anaconda3/lib/python3.7/site-packages/tornado/web.py", line 1699, in _execute
result = await result
File "/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/opt/anaconda3/lib/python3.7/site-packages/notebook/services/sessions/handlers.py", line 72, in post
type=mtype))
File "/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/opt/anaconda3/lib/python3.7/site-packages/notebook/services/sessions/sessionmanager.py", line 88, in create_session
kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
File "/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/opt/anaconda3/lib/python3.7/site-packages/notebook/services/sessions/sessionmanager.py", line 101, in start_kernel_for_session
self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
File "/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/opt/anaconda3/lib/python3.7/site-packages/notebook/services/kernels/kernelmanager.py", line 168, in start_kernel
super(MappingKernelManager, self).start_kernel(**kwargs)
File "/opt/anaconda3/lib/python3.7/site-packages/jupyter_client/multikernelmanager.py", line 110, in start_kernel
km.start_kernel(**kwargs)
File "/opt/anaconda3/lib/python3.7/site-packages/jupyter_client/manager.py", line 259, in start_kernel
**kw)
File "/opt/anaconda3/lib/python3.7/site-packages/jupyter_client/manager.py", line 204, in _launch_kernel
return launch_kernel(kernel_cmd, **kw)
File "/opt/anaconda3/lib/python3.7/site-packages/jupyter_client/launcher.py", line 138, in launch_kernel
proc = Popen(cmd, **kwargs)
File "/opt/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
restore_signals, start_new_session)
File "/opt/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/Cellar/r/3.5.3/lib/R/bin/R': '/usr/local/Cellar/r/3.5.3/lib/R/bin/R'
Appreciate your advice.

Answer 1

The interesting part of the error is.
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/Cellar/r/3.5.3/lib/R/bin/R': '/usr/local/Cellar/r/3.5.3/lib/R/bin/R'
I guess you Jupyter kernel is referencing the old installation of R that you have updated.
The first thing to do is to check what is defined in your R kernel.
Check kernel
# list all kernel
jupyter kernelspec list
#Available kernels:
# ir /opt/conda/share/jupyter/kernels/ir
# ...
You should have an ir kernel.
Check the content of the kernel definition, for example:
$ cat /opt/conda/share/jupyter/kernels/ir/kernel.json
# {"argv": ["R", "--slave", "-e", "IRkernel::main()", "--args", "{connection_file}"],
# "display_name":"R",
# "language":"R"
# }
If the command in argv is incorrect you can remove an reinstall the kernel.
Remove and reinstall the kernel
See the IRkernel installation documentation for more information.
$ jupyter kernelspec remove ir
$ R
# Install IRkernel
> install.packages('IRkernel')
# Or update it if already installed
> update.packages('IRkernel')
# Install the kernel
> IRkernel::installspec()
# Or alternatively if you want to install it system-wide
> IRkernel::installspec(user = FALSE)