Install DESeq2 through anaconda
Ultimately my colleague helped me to solve the issue by following the steps:


Created environment: conda create --name myenv
Activated it: source activate myenv
Edited .condarc to set the priority of the channels to be the following (top to bottom): conda-forge, bioconda, r, default
Checked that the channels are set in the correct order: conda config --get channels
conda install r=3.5.1
conda install r-essentials
conda install rstudio
Installation of all of the bioconductor packages through bioconda and never install anything from inside R or Rstudio (I guess that is how it was broken)


Then launching rstudio from within the environment. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to.