CODEWITHSUNDEEP
rwindowsanaconda
user3005422
user3005422

Reputation: 51

specifying R library path for RKernel in Anaconda Jupyter notebook

First let me preface this with the disclaimer that I'm new to R, but a longtime Python power user. Given that I love the conda ecosystem and the Jupyter notebook, I'm trying to set them up as my R development environment as well.

So using the instructions at: https://www.continuum.io/blog/developer/jupyter-and-conda-r I've set up a Jupyter Notbook that using an RKernel that should be hitting the installation of R installed in my Anaconda folder (I would think anyway).

Getting it setup was easy peasy and everything is working great for standard R stuff but my analysis requires some R libraries that are not available in r-essentials channel. No problem, I think I know how to install an R library. I go to "C:\Anaconda\R\bin\x64\Rgui.exe" and install rgdal, dismo, and some other packages. To check my work I looked in C:\Anaconda\R\library and there they are.

But when I run a jupyter notebook from the Anaconda command prompt. And start a new R notebook I get a "Error in library(dismo): there is no package called 'dismo'" Wait a sec, I run a ".libPaths()" from the notebook and it looks like its pointing

Upvotes: 2

Views: 6852

Answers (2)

Dan Luba
Dan Luba

Reputation: 124

You can find out the path to your library with installed.packages()

Upvotes: 0

Flo
Flo

Reputation: 1565

You can add .libPaths('path_where_your_packages_are') in a code cell at the beginning of your notebook to tell jupyter where your packages are. For me that was .libPaths('~/R/win-library/3.2') (work-around from discnerd who filed this issue on github).

To find out the path to your packages, just install a random package in R and wait for the location to be printed to the console.

More details (likely specific to my system/installations): When running .libPaths() in R, I got 2 locations: one for which admin rights were required for writing, and one for which admin rights were not required for writing. While packages installed through R land in the location where admin rights are not required, jupyter looks at the location where admin rights are required.

Upvotes: 6

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