R, Python: install packages on rpy2

Question

I'm using R in my Python script through the rpy2 library and I need a package that is not in the default installation of R. How can I install it?

install.packages("DirichletReg", repos="http://r-forge.r-project.org")

won't work.

On Python:

>>> install.packages("DirichletReg", repos="http://r-forge.r-project.org") 
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
NameError: name 'install' is not defined

And from R:

> install.packages("DirichletReg", repos="http://r-forge.r-project.org")
Installing package(s) into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘DirichletReg’ is not available (for R version 2.14.1)

Answer 1

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.