'The kernel for server .... appears to have died' when using %%R in Jupyter Notebook - what can I do?

I am executing the following code

%%R -i data_mat -i input_groups -o size_factors
require(scran)

size_factors = computeSumFactors(data_mat, clusters=input_groups, min.mean=0.1)

...then it takes the kernel ~25 min to work and give me the following as output:

Kernel Restarting The Kernel for... appears to have died. It will restart automatically

I already tried using pip install ipykernel --upgrade - but nothing seems to change when executing the code..