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https://github.com/datasnakes/renv
Creating virtual environments for R.
https://github.com/datasnakes/renv
biohackathon cli hackathon package-management project-environment python r renv reproducible-research virtual-environment
Last synced: about 1 month ago
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Creating virtual environments for R.
- Host: GitHub
- URL: https://github.com/datasnakes/renv
- Owner: datasnakes
- License: mit
- Created: 2018-05-24T18:15:34.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2019-10-24T19:09:30.000Z (over 4 years ago)
- Last Synced: 2024-05-03T01:28:06.735Z (2 months ago)
- Topics: biohackathon, cli, hackathon, package-management, project-environment, python, r, renv, reproducible-research, virtual-environment
- Language: Python
- Homepage:
- Size: 245 KB
- Stars: 17
- Watchers: 6
- Forks: 0
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Lists
- jimsghstars - datasnakes/renv - Creating virtual environments for R. (Python)
README
[](https://badge.fury.io/py/renv)
[](https://travis-ci.com/datasnakes/renv)
# 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](https://github.com/python/cpython/blob/3.6/Lib/venv/__init__.py)
virtual environment manager for creating virtual environments for R.
## Installation
This package is being managed with [`poetry`](https://github.com/sdispater/poetry) and is also available on PyPi.
```bash
pip install renv
```
## 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](https://github.com/datasnakes/renv/issues)
or [PR](https://github.com/datasnakes/renv/pulls). 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 need to initialize renv to set up the `.beRi/.renv` folder in your `$HOME` directory:
```bash
renv init
```
Now, you can easily create an environment:
```bash
renv -e myenv -r /path/to/R/folder # Find your current R folder is using `which R` on Linux.
```
An environment folder named `myenv` will be created in `$HOME/.beRi/.renv`.
To activate the environment:
```
cd $HOME/.beRi/.renv/myenv/bin
. ./activate
```
To deactivate the R environment:
```bash
deactivate
```
Use `--help` to see the other command-line options.
```console
user@host:~$ renv --help
Usage: renv [OPTIONS] COMMAND [ARGS]...
Options:
-r, --r_home TEXT Provide the root of the directory tree where
R is installed ($R_HOME). This would be R's
installation directory when using
./configure --prefix=. [required]
-e, --env_name TEXT Name of the environment. [required]
-p, --path TEXT An absolute installation path for renv.
[default: ~/.beRi]
-n, --name TEXT A directory name for renv. [default: .renv]
-b, --bindir TEXT Provide the bin directory if R was installed
when using ./configure --bindir=.
-l, --libdir TEXT Provide the lib directory if R was installed
when using ./configure --libdir=.
-i, --includedir TEXT Provide the include directory if R was
installed when using ./configure
--includedir=.
-rp, --recommended_packages BOOLEAN
This determines wheather or not the
recommended packages are installed in theR
environment along with the base packages.
In most cases it's best to keep thedefault
value.
--clear BOOLEAN Deletes the contents of the environment
directory if it already exists, before
environment creation.
-u, --upgrade BOOLEAN Upgrades the environment directory to use
this version of R.
-p, --prompt TEXT Provide an alternative prompt prefix for
this environment.
-v, --verbose Show verbose cli output.
--help Show this message and exit.
Commands:
init Initialize renv using the /.
Show this message and exit.
```
### Creating an R Environment
```console
user@host:~$ renv -e ~/projects/rna-brain -r /usr/local/apps/R/R-3.4.4/
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
1. Creates a default R virtual environment using default config settings
or a YAML file in the pre-existing environment directory.
2. 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.
```yaml
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](https://rstudio.github.io/packrat/), which allows you to
create isolated package libraries, and python's
[venv](https://docs.python.org/3/library/venv.html) 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](https://github.com/grabear) | [✉](mailto:[email protected])
Santina Lin | [@santina](https://github.com/santina) | [✉](mailto:[email protected])
Shaurita Hutchins | [@sdhutchins](https://github.com/sdhutchins) | [✉](mailto:[email protected])