VerR

VerR offers tools to run expression or scripts inside custom R environments. These environments are created with the help of the renv package. Using these environments, it is therefore possible to easily compare the behavior of different versions of a package.

Installation

Get the package:

# Check if remotes is installed. Otherwise install it.
if (!require("remotes", quietly = TRUE)){
    install.packages("remotes")
}
# Install the package
remotes::install_github("leopoldguyot/VerR",
    build_manual = TRUE,
    build_vignettes = TRUE
)
# Load the package
library(VerR)

Usage

Create Environments

When a new environment is initialized, a new directory is created inside the .envs/ directory. This new directory will contain all the installed packages specific to this environment. The creation of a new environment goes like this:

envCreate(envName = "env_name",
          packages = c("jsonlite", # CRAN
                       "jsonlite@1.9.1", # CRAN with specific ver.
                       "bioc::BioBase", # BioConductor
                       "leopoldguyot/VerR" # GitHub
                       )    
)

To specify the packages you want to install within the environment you can use different syntax:

• pkg: install latest version of pkg from CRAN.

• pkg@version: install specified version of pkg from CRAN.

• username/repo: install package from GitHub. You can also specify the commit with username/repo@commitId

• bioc::pkg: install pkg from Bioconductor.

Note that to install a specific version of a Bioconductor package it is recommended to install it via GitHub.

You can find more information on package installation within the renv documentation:

?renv::install

Manage your environments

# get the names of your environments
envList()

# remove an environment
envDelete(envName = "env_name")

# remove all your environments
envDelete()

# copy a file/dir from your working directory to environments
envCopyTo(sourcePath = "path",
           envName = envList(),
           targetPath = "" # Where in the env should the file/dir be copied 
)

# remove a file/dir from your environments
envRemoveFrom(targetPath = "path",
               envName = envList()
)

Run expression within environments

To run an expression within an environment you can directly pass your expression to the runInEnv function. Note that you need to call library() within your expression if you want to use packages installed in your environment.

runInEnv(expr = {
        packageVersion("jsonlite")
    },
    envName = "env_name"
)

If you run this expression within the environment created earlier you should get:

"0.6.18"

You can also use runInEnv to evaluate your expression within multiple environments.

runInEnv(expr = {
        packageVersion("jsonlite")
    },
    envName = envList()
)

This will return a named list with the return value for each environment.