The renv package is a CLI tool for creating environments for the R statistical programming language. It takes advantage of the python venv module and its modular EnvBuilder class.
Project description
renv (beta)
Creating virtual environments for R. (currently a Linux-only implementation)
Description
One of the problems with using R for data analysis can be dependency issues especially for
scientists who use multiple versions of R or R packages and have a large number of
projects that they are developing with R. Dependency issues are especially prevalent among those individuals or groups
that are developing R packages. renv is a Python style
virtual environment manager for creating virtual environments for R.
Installation
This package is being managed with poetry.
# Clone the repository
git clone https://github.com/datasnakes/renv.git
cd renv
# Make sure you have activated an environment of Python >= 3.6
# Get poetry and build the project using it
curl -sSL https://raw.githubusercontent.com/sdispater/poetry/master/get-poetry.py | python
poetry install
poetry build
pip install dist/renv-0.2.0-py2.py3-none-any.whl
Usage
Renv is currently in beta and is only supported in Linux so there may be some issues if your R has been installed in a way other than the default. There are probably plenty of unforeseen bugs, misspellings, and general use cases where the code could be more efficient. Please submit an issue or PR. We'd love to get community feedback.
The default .Rprofile also prompts you to install some commonly used packages. The functionality of this is useful, but will change for the actual release of this package.
Commands
Once you have renv installed, you can create an R environment by a simple command:
renv -n myenv
An environment folder myenv will be created under $HOME/.renv.
To activate the environment
cd $HOME\.renv\myenv\bin
. ./activate
To deactivate the R environment:
deactivate
Use --help to see the other command-line options.
user@host:~$ renv --help
Usage: renv [OPTIONS]
Options:
-r, --r_home TEXT Provide the root of the directory tree where
R is installed. This would be R's
installation directory when using
./configure --prefix=<r_home>.
-n, --env_name TEXT Name of the environment.
-d, --env_home TEXT A directory for creating the environment in.
-b, --binpath TEXT Provide the bin directory if R was installed
when using ./configure --bindir=<binpath>.
-l, --libpath TEXT Provide the lib directory if R was installed
when using ./configure --libdir=<libpath>.
-i, --includepath TEXT Provide the include directory if R was
installed when using ./configure
--includedir=<includepath>.
-sp, --system_site_packages BOOLEAN
This determines whether or not the
R_LIBS_USER environment variable utilizes
the original R's package library as a
secondary source for loading packages.
-rp, --recommended_packages BOOLEAN
This determines wheather or not the
recommended packages are installed in theR
environment along with the base packages.
In most cases it's best to keep thedefault
value.
--clear BOOLEAN Deletes the contents of the environment
directory if it already exists, before
environment creation.
-u, --upgrade BOOLEAN Upgrades the environment directory to use
this version of R.
-p, --prompt TEXT Provide an alternative prompt prefix for
this environment.
-v, --verbose Show verbose cli output.
-V, --version Show the version of renv and exit.
--help Show this message and exit.
Creating an R Environment
user@host:~$ renv -r /usr/local/R -d ~/projects/rna-brain
user@host:~$ source projects/rna-brain/bin/activate
(rna-brain) user@host:~$ R
R version x.y.z (YYY-MM-DD) -- "Dist"
Copyright (C) YYY The R Foundation for Statistical Computing
Platform: Renv is working for some linux distrubutions
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
..................Attempting to Load Bioconductor...................
Warning: Prompting for Bioconductor Installation...
Do you want to install Bioconductor??? [Y/N]
n
..................Attempting to Load Devtools...................
Warning: Prompting for Devtools Installation...
Do you want to install Devtools??? [Y/N]
n
..................Attempting to Load Tidyverse...................
Warning: Prompting for Tidyverse Installation...
Do you want to install Tidyverse??? [Y/N]
n
Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘BiocInstaller’
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘devtools’
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘tidyverse’
>
Features
- Creates a default R virtual environment using default config settings or a YAML file in the pre-existing environment directory.
- Manages the user's and the environment's .Rprofile and .Renviron files.
Below is an example of the YAML config file (there may be mistakes or missing keys). Try to use absolute paths.
R_ABS_HOME: "/home/grabear/R-installs/R-3.4.3/lib64/R"
R_ENV_HOME: "/home/grabear/rna-brain"
R_LIBS_USER: "/home/grabear/rna-brain/lib64/R/library"
R_INCLUDE_DIR: "/home/grabear/rna-brain/lib64/R/include"
R_VERSION: "3.4.3"
# LIST OF DEFAULT variables for .Rprofile
CRAN_MIRROR: "https://cran.rstudio.com/"
CRANEXTRA_MIRROR: "https://mirrors.nics.utk.edu/cran/"
# Determine how to format this for .Rprofile
STANDARD_PKG_LIST:
BiocInstaller: "Bioconductor"
devtools: "Devtools"
tidyverse: "Tidyverse"
REPRODUCIBLE_WORKFLOW_PKG_LIST:
packrat: "Packrat"
miniCRAN: "MiniCRAN"
Questions
Why renv?
Tools for creating reproducible workflows with R have been needed for a long time. Renv gets its inspiration from packrat, which allows you to create isolated package libraries, and python's venv module, which creates an environment with its own package library AND python binaries. Renv, therefore, helps user better manage a system with multiple installations of R by creating a virtual environments for specific versions of R that have their own R binaries (R and Rscript) as well as their own isolated package libraries.
Why click and poetry?
Click is used over argparse for speed of development. It requires an extra dependency, but it's easy to use and what we know. Poetry is used for similar reasons. It's a developing project, so we may have regrets later down the road, but for now it's proven to be a very useful tool.
Why not develop everything in R?
Again, we are going with what we know. We aren't unfamiliar with programming or making packages with R, but we are way better at developing and maintaining python code. Virtual environments are already widely used for the python language, which means we don't have to recreate the .whl.
Maintainers
Rob Gilmore | @grabear | ✉
Santina Lin | @santina | ✉
Shaurita Hutchins | @sdhutchins | ✉
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