beaker-notebook

Adding new R packages to hosted Beaker Lab notebook

I'd like to use an R package that is not included in the default installation of the hosted version of Beaker, Beaker Lab. The code:

install.packages("raster")

fails with the message:

Error
Installing package into '/usr/local/lib/R/site-library'

Is there a way to install new libraries in Beaker Lab?

Solution

  • To install R packages:

    1) Open scratch space, click BROWSE and create a directory rpackages

    2) Create a blank R notebook

    3) Type :

    install.packages(‘packagename’, ‘/mnt/scratch/rpackages’, repos=’http://cran.us.r-project.org’)

    and run the cell

    4) Wait for installation to finish

    5) If installation hangs for some time it means that something malfunctioned -> reload browser, close notebook, reopen notebook and redo the install command. This will continue from where it was before blocking.

    To use installed packages:

    In your R notebook, in the first cell (or cell before you use the package) type:

    .libPaths(c(‘/mnt/scratch/rpackages’,.libPaths()))

    And run the cell

    Here's an example in Beaker Lab

    https://lab.beakernotebook.com/approval/view/8645c600-3ec4-11e6-b811-8b63dac7dd4c