R, Python: install packages on rpy2

Ricardo's answer no longer works.

To install from Python, we can use the utils.install_packages function:

from rpy2.robjects.packages import importr
utils = importr('utils')

(That utils package is the R.utils package whose pdf documentation can be found here: https://CRAN.R-project.org/package=R.utils - or, more directly here, is the more verbose install.packages function documentation that we use: https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packages. It is renamed to install_packages in Python because the . is not part of a legal Python name as it is in R.)

Next, you need to decide which repo to get the package from.

You can declare the repo when calling utils.install_packages with the repos argument:

utils.install_packages('DirichletReg', repos="https://cloud.r-project.org")

Or you can set the mirror before calling utils.install_packages with

utils.chooseCRANmirror(ind=1) # select the first mirror in the list

or

utils.chooseBioCmirror(ind=1) # select the first mirror in the list

otherwise Python/R will attempt to launch the interactive mirror selector (which may or may not work with your setup).

And then, for a single package:

utils.install_packages('DirichletReg')

Or for multiple packages, pass it a character vector:

from rpy2.robjects.vectors import StrVector

package_names = ('ggplot2', 'hexbin')
utils.install_packages(StrVector(package_names))

These examples were adapted from the rpy2 documentation and the install.packages documentation - and as of my last edit, the documentation still says to do this.

When running pytest, Aaron's answer makes my Python hang and R keep giving error messages, probably because of this:

Calling install_packages() without first choosing a mirror will require the user to interactively choose a mirror.

According to rpy2 documentation, I used this which worked:

from rpy2 import robjects
import rpy2.robjects.packages as rpackages

utils = rpackages.importr('utils')
utils.chooseCRANmirror(ind=1)
utils.install_packages("DirichletReg")
DirichletReg = rpackages.importr("DirichletReg")