Jupyter notebook with rpy2 RMagic can't find a bioconductor library

[Arnaud Mounier]

Hello,

I have a env with a ipython kernel 3.6 and R, some R packages and the bridge for this 2 languages rpy2. In the notebook, I load the extension rpy2.ipython.

I have to load 2 library from R in a notebooks : tidyverse and dada2. Tidyverse come from a regular anaconda r channel whereas dada2 come from bioconductor. This 2 packages are both in /opt/conda/envs/my_env/lib/R/library but when I try to load it tidyverse works fine but the system say it can't find dada2 and I don't know why.

%%R

library(dada2)

R[write to console]: Error in library(dada2) : aucun package nommé ‘dada2’ n'est trouvé

Have I miss a configuration in the notebook ?

Thank you,

arnome.

[Arnaud Mounier]

Hello,

I find the error, the R_HOME env variable was wrong (/usr/lib/R) and I change it like this :

os.environ['R_HOME'] = "/opt/conda/envs/<my_env>/lib/R"

before load the extention rp2.extension

arnome.