title: 'The kernel for server .... appears to have died' when using %%R in Jupyter Notebook - what can I do?
body: <p>I am executing the following code</p>
  <pre><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)
  </code></pre>
  <p>...then it takes the kernel ~25 min to work and give me the following as output:</p>
  <p><em>Kernel Restarting
  The Kernel for... appears to have died. It will restart automatically</em></p>
  <p>I already tried using <code>pip install ipykernel --upgrade</code> - but nothing seems to change when executing the code..</p>