rvenv 0.2

Install and manage R packages in a python virtualenv

Install and manage R packages in a python virtualenv.

Why?

I need someplace to put project-specific R packages. The python virtualenv I inevitably have installed in any given project/analysis/pipeline seems as good a place as any.

Installation

Install to an active virtualenv using pip (or simply copy rvenv to $VIRTUAL_ENV/bin):

% virtualenv r-env
% source r-env/bin/activate
% pip install rvenv

Or to install from the GitHub repository:

% pip install git+https://github.com/nhoffman/rvenv.git

You can use the rvenv script from the command line to install packages to $VIRTUAL_ENV/lib/R.%v-library:

% rvenv dplyr

Including the following lines in an R script will set the library path to use locally-installed packages:

#!/usr/bin/env Rscript
if(Sys.getenv("VIRTUAL_ENV") == ""){ stop("An active virtualenv is required") }
source(file.path(Sys.getenv('VIRTUAL_ENV'), 'bin', 'rvenv'))

Loading rvenv as above prepends $VIRTUAL_ENV/lib/R.%v-library to the library search path. See example script script.R

To start an interactive R session with the library path defined:

% eval $(rvenv -e)
% R

And to define the library path within an already running R session:

> Sys.setenv(VIRTUAL_ENV='some/path/to/virtualenv')
> source(file.path(Sys.getenv("VIRTUAL_ENV"), "bin", "rvenv"))

usage

usage: ./rvenv [-h] [-r REQUIREMENTS] [--rm] [-U] [-l] [-e] [-R REPOS] [-v]
               [packages [packages ...]]

Install R packages to a python virtualenv

Include the following in an R script to add "$VIRTUAL_ENV/lib/R.%v-library"
to the library search path:

  #!/usr/bin/env Rscript
  if(Sys.getenv("VIRTUAL_ENV") == ""){ stop("An active virtualenv is required") }
  source(file.path(Sys.getenv("VIRTUAL_ENV"), "bin", "rvenv"))

Also see https://github.com/nhoffman/rvenv

positional arguments:
  packages              one or more package names

optional arguments:
  -h, --help            show this help message and exit
  -r REQUIREMENTS, --requirements REQUIREMENTS
                        a file listing packages
  --rm                  remove listed packages
  -U, --update          update existing packages
  -l, --list            list packages installed locally
  -e, --environ         print shell command to set R_LIBS
  -R REPOS, --repos REPOS
                        value for "install.packages(repos)" [http://cran.fhcrc.org/]
  -v, --verbose         be verbose when installing packages