Package 'renv'

Description

Project-local environments for R.

Details

You can use renv to construct isolated, project-local R libraries. Each project using renv will share package installations from a global cache of packages, helping to avoid wasting disk space on multiple installations of a package that might otherwise be shared across projects.

Author(s)

Maintainer: Kevin Ushey [email protected] (ORCID)

Authors:

• Hadley Wickham [email protected] (ORCID)

Other contributors:

• Posit Software, PBC [copyright holder, funder]

See Also

Useful links:

• https://rstudio.github.io/renv/

• https://github.com/rstudio/renv

• Report bugs at https://github.com/rstudio/renv/issues

Description

activate() enables renv for a project in both the current session and in all future sessions. You should not generally need to call activate() yourself as it's called automatically by init(), which is the best way to start using renv in a new project.

activate() first calls scaffold() to set up the project infrastructure. Most importantly, this creates a project library and adds a an auto-loader to .Rprofile to ensure that the project library is automatically used for all future instances of the project. It then restarts the session to use that auto-loader.

deactivate() removes the infrastructure added by activate(), and restarts the session. By default it will remove the auto-loader from the .Rprofile; use clean = TRUE to also delete the lockfile and the project library.

Usage

activate(project = NULL, profile = NULL)

deactivate(project = NULL, clean = FALSE)

Arguments

Value

The project directory, invisibly. Note that this function is normally called for its side effects.

Temporary deactivation

If you need to temporarily disable autoload activation you can set the RENV_CONFIG_AUTOLOADER_ENABLED envvar, e.g. Sys.setenv(RENV_CONFIG_AUTOLOADER_ENABLED = "false").

Examples

## Not run: 

# activate the current project
renv::activate()

# activate a separate project
renv::activate(project = "~/projects/analysis")

# deactivate the currently-activated project
renv::deactivate()


## End(Not run)

Description

Automatically load the renv project associated with a particular directory. renv will search parent directories for the renv project root; if found, that project will be loaded via load().

Usage

autoload()

Details

To enable the renv auto-loader, you can place:

renv::autoload()

into your site-wide or user .Rprofile to ensure that renv projects are automatically loaded for any newly-launched R sessions, even if those R sessions are launched within the sub-directory of an renv project.

If you'd like to launch R within the sub-directory of an renv project without auto-loading renv, you can set the environment variable:

RENV_AUTOLOAD_ENABLED = FALSE

before starting R.

Note that renv::autoload() is only compatible with projects using ⁠renv 0.15.3⁠ or newer, as it relies on features within the renv/activate.R script that are only generated with newer versions of renv.

Description

renv::checkout() can be used to retrieve the latest-availabe packages from a (set of) package repositories.

Usage

checkout(
  repos = NULL,
  ...,
  packages = NULL,
  date = NULL,
  clean = FALSE,
  actions = "restore",
  project = NULL
)

Arguments

Details

renv::checkout() is most useful with services like the Posit's Package Manager, as it can be used to switch between different repository snapshots within an renv project. In this way, you can upgrade (or downgrade) all of the packages used in a particular renv project to the package versions provided by a particular snapshot.

If your library contains packages installed from other remote sources (e.g. GitHub), but a version of a package of the same name is provided by the repositories being checked out, then please be aware that the package will be replaced with the version provided by the requested repositories. This could be a concern if your project uses R packages from GitHub whose name matches that of an existing CRAN package, but is otherwise unrelated to the package on CRAN.

Examples

## Not run: 

# check out packages from PPM using the date '2023-01-02'
renv::checkout(date = "2023-01-02")

# alternatively, supply the full repository path
renv::checkout(repos = "https://packagemanager.rstudio.com/cran/2023-01-02")

# only check out some subset of packages (and their recursive dependencies)
renv::checkout(packages = "dplyr", date = "2023-01-02")


## End(Not run)

Description

Clean up a project and its associated R libraries.

Usage

clean(project = NULL, ..., actions = NULL, prompt = interactive())

Arguments

Value

The project directory, invisibly. Note that this function is normally called for its side effects.

Actions

The following clean actions are available:

package.locks

During package installation, R will create package locks in the library path, typically named ⁠00LOCK-<package>⁠. On occasion, if package installation fails or R is terminated while installing a package, these locks can be left behind and will inhibit future attempts to reinstall that package. Use this action to remove such left-over package locks.

library.tempdirs

During package installation, R may create temporary directories with names of the form ⁠file\w{12}⁠, and on occasion those files can be left behind even after they are no longer in use. Use this action to remove such left-over directories.

system.library

In general, it is recommended that only packages distributed with R are installed into the default library (the library path referred to by .Library). Use this action to remove any user-installed packages that have been installed to the system library.

Because this action is destructive, it is by default never run – it must be explicitly requested by the user.

unused.packages

Remove packages that are installed in the project library, but no longer appear to be used in the project sources.

Because this action is destructive, it is by default only run in interactive sessions when prompting is enabled.

Examples

## Not run: 

# clean the current project
renv::clean()


## End(Not run)

Description

Configure different behaviors of renv.

Usage

config

Details

For a given configuration option:

1. If an R option of the form ⁠renv.config.<name>⁠ is available, then that option's value will be used;

2. If an environment variable of the form ⁠RENV_CONFIG_<NAME>⁠ is available, then that option's value will be used;

3. Otherwise, the default for that particular configuration value is used.

Any periods (.)s in the option name are transformed into underscores (⁠_⁠) in the environment variable name, and vice versa. For example, the configuration option auto.snapshot could be configured as:

• ⁠options(renv.config.auto.snapshot = <...>)⁠

• ⁠Sys.setenv(RENV_CONFIG_AUTO_SNAPSHOT = <...>)⁠

Note that if both the R option and the environment variable are defined, the R option will be used instead. Environment variables can be more useful when you want a particular configuration to be automatically inherited by child processes; if that behavior is not desired, then the R option may be preferred.

If you want to set and persist these options across multiple projects, it is recommended that you set them in a a startup .Renviron file; e.g. in your own ⁠~/.Renviron⁠, or in the R installation's etc/Rprofile.site file. See Startup for more details.

Configuration options can also be set within the project .Rprofile, but be aware the options should be set before source("renv/activate.R") is called.

Configuration

The following renv configuration options are available:

renv.config.activate.prompt

Automatically prompt the user to activate the current project, if it does not appear to already be activated? This is mainly useful to help ensure that calls to renv::snapshot() and renv::restore() use the project library. See ?renv::activate for more details. Defaults to TRUE.

renv.config.autoloader.enabled

Enable the renv auto-loader? When FALSE, renv will not automatically load a project containing an renv autoloader within its .Rprofile. In addition, renv will not write out the project auto-loader in calls to renv::init(). Defaults to TRUE.

renv.config.auto.snapshot

Automatically snapshot changes to the project library when the project dependencies change? Defaults to FALSE.

renv.config.bitbucket.host

The default Bitbucket host to be used during package retrieval. Defaults to "api.bitbucket.org/2.0".

renv.config.copy.method

The method to use when attempting to copy directories. See Copy Methods for more information. Defaults to "auto".

renv.config.connect.timeout

The amount of time to spend (in seconds) when attempting to download a file. Only applicable when the curl downloader is used. Defaults to 20L.

renv.config.connect.retry

The number of times to attempt re-downloading a file, when transient download errors occur. Only applicable when the curl downloader is used. Defaults to 3L.

renv.config.cache.enabled

Enable the global renv package cache? When active, renv will install packages into a global cache, and link or copy packages from the cache into your R library as appropriate. This can greatly save on disk space and install time when R packages are shared across multiple projects in the same environment. Defaults to TRUE.

renv.config.cache.symlinks

Symlink packages from the global renv package cache into your project library? When TRUE, renv will use symlinks (or, on Windows, junction points) to reference packages installed in the cache. Set this to FALSE if you'd prefer to copy packages from the cache into your project library. Enabled by default, except on Windows where this feature is only enabled if the project library and global package cache are on the same volume. Defaults to NULL.

renv.config.dependency.errors

Many renv APIs require the enumeration of your project's R package dependencies. This option controls how errors that occur during this enumeration are handled. By default, errors are reported but are non-fatal. Set this to "fatal" to force errors to be fatal, and "ignored" to ignore errors altogether. See dependencies() for more details. Defaults to "reported".

renv.config.dependencies.limit

By default, renv reports if it discovers more than this many files when looking for dependencies, as that may indicate you are running dependencies() in the wrong place. Set to Inf to disable this warning. Defaults to 1000L.

renv.config.exported.functions

When library(renv) is called, should its exports be placed on the search path? Set this to FALSE to avoid issues that can arise with, for example, renv::load() masking base::load(). In general, we recommend referencing renv functions from its namespace explicitly; e.g. prefer renv::snapshot() over snapshot(). By default, all exported renv functions are attached and placed on the search path, for backwards compatibility with existing scripts using renv. Defaults to "*".

renv.config.external.libraries

A character vector of external libraries, to be used in tandem with your projects. Be careful when using external libraries: it's possible that things can break within a project if the version(s) of packages used in your project library happen to be incompatible with packages in your external libraries; for example, if your project required ⁠xyz 1.0⁠ but ⁠xyz 1.1⁠ was present and loaded from an external library. Can also be an R function that provides the paths to external libraries. Library paths will be expanded via .expand_R_libs_env_var() as necessary. Defaults to NULL.

renv.config.filebacked.cache

Enable the renv file-backed cache? When enabled, renv will cache the contents of files that are read (e.g. DESCRIPTION files) in memory, thereby avoiding re-reading the file contents from the filesystem if the file has not changed. renv uses the file mtime to determine if the file has changed; consider disabling this if mtime is unreliable on your system. Defaults to TRUE.

renv.config.github.host

The default GitHub host to be used during package retrieval. Defaults to "api.github.com".

renv.config.gitlab.host

The default GitLab host to be used during package retrieval. Defaults to "gitlab.com".

renv.config.hydrate.libpaths

A character vector of library paths, to be used by hydrate() when attempting to hydrate projects. When empty, the default set of library paths (as documented in ?renv::hydrate) are used instead. See hydrate() for more details. Defaults to NULL.

renv.config.install.build

Should downloaded package archives be built (via ⁠R CMD build⁠) before installation? When TRUE, package vignettes will also be built as part of package installation. Because building packages before installation may require packages within 'Suggests' to be available, this option is not enabled by default. Defaults to FALSE.

renv.config.install.remotes

Should renv read a package's ⁠Remotes:⁠ field when determining how package dependencies should be installed? Defaults to TRUE.

renv.config.install.shortcuts

Allow for a set of 'shortcuts' when installing packages with renv? When enabled, if renv discovers that a package to be installed is already available within the user or site libraries, then it will install a local copy of that package. Defaults to TRUE.

renv.config.install.staged

DEPRECATED: Please use renv.config.install.transactional instead. Defaults to TRUE.

renv.config.install.transactional

Perform a transactional install of packages during install and restore? When enabled, renv will first install packages into a temporary library, and later copy or move those packages back into the project library only if all packages were successfully downloaded and installed. This can be useful if you'd like to avoid mutating your project library if installation of one or more packages fails. Defaults to TRUE.

renv.config.install.verbose

Be verbose when installing R packages from sources? When TRUE, renv will stream any output generated during package build + installation to the console. Defaults to FALSE.

renv.config.locking.enabled

Use interprocess locks when invoking methods which might mutate the project library? Enable this to allow multiple processes to use the same renv project, while minimizing risks relating to concurrent access to the project library. Disable this if you encounter locking issues. Locks are stored as files within the project at renv/lock; if you need to manually remove a stale lock you can do so via unlink("renv/lock", recursive = TRUE). Defaults to FALSE.

renv.config.mran.enabled

DEPRECATED: MRAN is no longer maintained by Microsoft. Defaults to FALSE.

renv.config.pak.enabled

Use the pak package to install packages? Defaults to FALSE.

renv.config.ppm.enabled

Boolean; enable Posit Package Manager integration in renv projects? When TRUE, renv will attempt to transform repository URLs used by PPM into binary URLs as appropriate for the current Linux platform. Set this to FALSE if you'd like to continue using source-only PPM URLs, or if you find that renv is improperly transforming your repository URLs. You can still set and use PPM repositories with this option disabled; it only controls whether renv tries to transform source repository URLs into binary URLs on your behalf. Defaults to TRUE.

renv.config.ppm.default

Boolean; should new projects use the Posit Public Package Manager instance by default? When TRUE (the default), projects initialized with renv::init() will use the P3M instance if the repos R option has not already been set by some other means (for example, in a startup .Rprofile). Defaults to TRUE.

renv.config.ppm.url

The default PPM URL to be used for new renv projects. Defaults to the CRAN mirror maintained by Posit at https://packagemanager.posit.co/. This option can be changed if you'd like renv to use an alternate package manager instance. Defaults to "https://packagemanager.posit.co/cran/latest".

renv.config.repos.override

Override the R package repositories used during restore()? Primarily useful for deployment / continuous integration, where you might want to enforce the usage of some set of repositories over what is defined in renv.lock or otherwise set by the R session. Defaults to NULL.

renv.config.rspm.enabled

DEPRECATED: Please use renv.config.ppm.enabled instead. Defaults to TRUE.

renv.config.sandbox.enabled

Enable sandboxing for renv projects? When active, renv will attempt to sandbox the system library, preventing non-system packages installed in the system library from becoming available in renv projects. (That is, only packages with priority "base" or "recommended", as reported by installed.packages(), are made available.) Sandboxing is done by linking or copying system packages into a separate library path, and then instructing R to use that library path as the system library path. In some environments, this action can take a large amount of time – in such a case, you may want to disable the renv sandbox. Defaults to TRUE.

renv.config.shims.enabled

Should renv shims be installed on package load? When enabled, renv will install its own shims over the functions install.packages(), update.packages() and remove.packages(), delegating these functions to install(), update() and remove() as appropriate. Defaults to TRUE.

renv.config.snapshot.inference

For packages which were installed from local sources, should renv try to infer the package's remote from its DESCRIPTION file? When TRUE, renv will check and prompt you to update the package's DESCRIPTION file if the remote source can be ascertained. Currently, this is only implemented for packages hosted on GitHub. Note that this check is only performed in interactive R sessions. Defaults to TRUE.

renv.config.snapshot.validate

Validate R package dependencies when calling snapshot? When TRUE, renv will attempt to diagnose potential issues in the project library before creating renv.lock – for example, if a package installed in the project library depends on a package which is not currently installed. Defaults to TRUE.

renv.config.startup.quiet

Be quiet during startup? When set, renv will not display the typical ⁠Project <path> loaded. [renv <version>]⁠ banner on startup. Defaults to NULL.

renv.config.synchronized.check

Check that the project library is synchronized with the lockfile on load? Defaults to TRUE.

renv.config.updates.check

Check for package updates when the session is initialized? This can be useful if you'd like to ensure that your project lockfile remains up-to-date with packages as they are released on CRAN. Defaults to FALSE.

renv.config.updates.parallel

Check for package updates in parallel? This can be useful when a large number of packages installed from non-CRAN remotes are installed, as these packages can then be checked for updates in parallel. Defaults to 2L.

renv.config.user.environ

Load the user R environ (typically located at ⁠~/.Renviron⁠) when renv is loaded? Defaults to TRUE.

renv.config.user.library

Include the system library on the library paths for your projects? Note that this risks breaking project encapsulation and is not recommended for projects which you intend to share or collaborate on with other users. See also the caveats for the renv.config.external.libraries option. Defaults to FALSE.

renv.config.user.profile

Load the user R profile (typically located at ⁠~/.Rprofile⁠) when renv is loaded? This is disabled by default, as running arbitrary code from the the user ⁠~/.Rprofile⁠ could risk breaking project encapsulation. If your goal is to set environment variables that are visible within all renv projects, then placing those in ⁠~/.Renviron⁠ is often a better choice. Defaults to FALSE.

Copy methods

If you find that renv is unable to copy some directories in your environment, you may want to try setting the copy.method option. By default, renv will try to choose a system tool that is likely to succeed in copying files on your system – robocopy on Windows, and cp on Unix. renv will also instruct these tools to preserve timestamps and attributes when copying files. However, you can select a different method as appropriate.

The following methods are supported:

You can also provide a custom copy method if required; e.g.

options(renv.config.copy.method = function(src, dst) {
  # copy a file from 'src' to 'dst'
})

Note that renv will always first attempt to copy a directory first to a temporary path within the target folder, and then rename that temporary path to the final target destination. This helps avoid issues where a failed attempt to copy a directory could leave a half-copied directory behind in the final location.

Project-local settings

For settings that should persist alongside a particular project, the various settings available in settings can be used.

Examples

# disable automatic snapshots
options(renv.config.auto.snapshot = FALSE)

# disable with environment variable
Sys.setenv(RENV_CONFIG_AUTO_SNAPSHOT = FALSE)

Description

Provide consent to renv, allowing it to write and update certain files on your filesystem.

Usage

consent(provided = FALSE)

Arguments

Details

As part of its normal operation, renv will write and update some files in your project directory, as well as an application-specific cache directory. These paths are documented within paths.

In accordance with the CRAN Repository Policy, renv must first obtain consent from you, the user, before these actions can be taken. Please call renv::consent() first to provide this consent.

You can also set the R option:

options(renv.consent = TRUE)

to implicitly provide consent for e.g. non-interactive R sessions.

Value

TRUE if consent is provided, or an R error otherwise.

Description

dependencies() will crawl files within your project, looking for R files and the packages used within those R files. This is done primarily by parsing the code and looking for calls of the form library(package), require(package), requireNamespace("package"), and package::method(). renv also supports package loading with box (box::use(...)) and pacman (pacman::p_load(...)) .

For R package projects, dependencies expressed in the DESCRIPTION file will also be discovered.

Note that the rmarkdown package is required in order to crawl dependencies in R Markdown files.

Usage

dependencies(
  path = getwd(),
  root = NULL,
  ...,
  quiet = NULL,
  progress = TRUE,
  errors = c("reported", "fatal", "ignored"),
  dev = FALSE
)

Arguments

Value

An R data.frame of discovered dependencies, mapping inferred package names to the files in which they were discovered. Note that the Package field might name a package remote, rather than just a plain package name.

Missing dependencies

dependencies() uses static analysis to determine which packages are used by your project. This means that it inspects, but doesn't run, your source. Static analysis generally works well, but is not 100% reliable in detecting the packages required by your project. For example, renv is unable to detect this kind of usage:

for (package in c("dplyr", "ggplot2")) {
  library(package, character.only = TRUE)
}

It also can't generally tell if one of the packages you use, uses one of its suggested packages. For example, tidyr::separate_wider_delim() uses the stringr package which is only suggested, not required by tidyr.

If you find that renv's dependency discovery misses one or more packages that you actually use in your project, one escape hatch is to include a file called ⁠_dependencies.R⁠ that includes straightforward library calls:

library(dplyr)
library(ggplot2)
library(stringr)

Explicit dependencies

Alternatively, you can suppress dependency discover and instead rely on an explicit set of packages recorded by you in a project DESCRIPTION file. Call renv::settings$snapshot.type("explicit") to enable "explicit" mode, then enumerate your dependencies in a project DESCRIPTION file.

In that case, your DESCRIPTION might look something like this:

Type: project
Description: My project.
Depends:
    tidyverse,
    devtools,
    shiny,
    data.table

Ignoring files

By default, renv will read your project's .gitignores (if present) to determine whether certain files or folders should be included when traversing directories. If preferred, you can also create a .renvignore file (with entries of the same format as a standard .gitignore file) to tell renv which files to ignore within a directory. If both .renvignore and .gitignore exist within a folder, the .renvignore will be used in lieu of the .gitignore.

See https://git-scm.com/docs/gitignore for documentation on the .gitignore format. Some simple examples here:

# ignore all R Markdown files
*.Rmd

# ignore all data folders
data/

# ignore only data folders from the root of the project
/data/

Using ignore files is important if your project contains a large number of files; for example, if you have a ⁠data/⁠ directory containing many text files.

Errors

renv's attempts to enumerate package dependencies in your project can fail – most commonly, because of failures when attempting to parse your R code. You can use the errors argument to suppress these problems, but a more robust solution is tell renv not to look at the problematic code. As well as using .renvignore, as described above, you can also suppress errors discovered within individual .Rmd chunks by including renv.ignore=TRUE in the chunk header. For example:

```{r chunk-label, renv.ignore=TRUE}
# code in this chunk will be ignored by renv
```

Similarly, if you'd like renv to parse a chunk that is otherwise ignored (e.g. because it has eval=FALSE as a chunk header), you can set:

```{r chunk-label, eval=FALSE, renv.ignore=FALSE}
# code in this chunk will _not_ be ignored
```

Development dependencies

renv has some support for distinguishing between development and run-time dependencies. For example, your Shiny app might rely on ggplot2 (a run-time dependency) but while you use usethis during development, your app doesn't need it to run (i.e. it's only a development dependency).

You can record development dependencies by listing them in the Suggests field of your project's DESCRIPTION file. Development dependencies will be installed by install() (when called without arguments) but will not be tracked in the project snapshot. If you need greater control, you can also try project profiles as discussed in vignette("profiles").

Examples

## Not run: 

# find R package dependencies in the current directory
renv::dependencies()


## End(Not run)

Description

Print a diagnostics report, summarizing the state of a project using renv. This report can occasionally be useful when diagnosing issues with renv.

Usage

diagnostics(project = NULL)

Arguments

Value

This function is normally called for its side effects.

Description

Together, embed() and use() provide a lightweight way to specify and restore package versions within a file. use() is a lightweight lockfile specification that embed() can automatically generate and insert into a script or document.

Calling embed() inspects the dependencies of the specified document then generates and inserts a call to use() that looks something like this:

renv::use(
  "[email protected]",
  "[email protected]"
)

Then, when you next run your R script or render your .Rmd, use() will:

1. Create a temporary library path.

2. Install the requested packages and their recursive dependencies into that library.

3. Activate the library, so it's used for the rest of the script.

Manual usage

You can also create calls to use() yourself, either specifying the packages needed by hand, or by supplying the path to a lockfile, renv::use(lockfile = "/path/to/renv.lock").

This can be useful in projects where you'd like to associate different lockfiles with different documents, as in a blog where you want each post to capture the dependencies at the time of writing. Once you've finished writing each, the post, you can use renv::snapshot(lockfile = "/path/to/renv.lock") to "save" the state that was active while authoring that bost, and then use renv::use(lockfile = "/path/to/renv.lock") in that document to ensure the blog post always uses those dependencies onfuture renders.

renv::use() is inspired in part by the groundhog package, which also allows one to specify a script's R package requirements within that same R script.

Usage

embed(path = NULL, ..., lockfile = NULL, project = NULL)

use(
  ...,
  lockfile = NULL,
  library = NULL,
  isolate = sandbox,
  sandbox = TRUE,
  attach = FALSE,
  verbose = TRUE
)

Arguments

Value

This function is normally called for its side effects.

Description

history() uses your version control system to show prior versions of the lockfile and revert() allows you to restore one of them.

These functions are currently only implemented for projects that use git.

Usage

history(project = NULL)

revert(commit = "HEAD", ..., project = NULL)

Arguments

Value

history() returns a data.frame summarizing the commits in which renv.lock has been changed. revert() is usually called for its side-effect but also invisibly returns the commit used.

Examples

## Not run: 

# get history of previous versions of renv.lock in VCS
db <- renv::history()

# choose an older commit
commit <- db$commit[5]

# revert to that version of the lockfile
renv::revert(commit = commit)


## End(Not run)

Description

Imbue an renv installation into a project, thereby making the requested version of renv available within.

Usage

imbue(project = NULL, version = NULL, quiet = FALSE)

Arguments

Details

Normally, this function does not need to be called directly by the user; it will be invoked as required by init() and activate().

Value

The project directory, invisibly. Note that this function is normally called for its side effects.

Description

Call renv::init() to start using renv in the current project. This will:

1. Set up project infrastructure (as described in scaffold()) including the project library and the .Rprofile that ensures renv will be used in all future sessions,

2. Discover the packages that are currently being used in your project (via dependencies()), and install them into the project library (as described in hydrate()),

3. Create a lockfile that records the state of the project library so it can be restored by others (as described in snapshot()),

4. Restart R (if running inside RStudio).

If you call renv::init() with a project that is already using renv, it will attempt to do the right thing: it will restore the project library if it's missing, or otherwise ask you what to do.

Usage

init(
  project = NULL,
  ...,
  profile = NULL,
  settings = NULL,
  bare = FALSE,
  force = FALSE,
  repos = NULL,
  bioconductor = NULL,
  load = TRUE,
  restart = interactive()
)

Arguments

Value

The project directory, invisibly. Note that this function is normally called for its side effects.

Repositories

If the default R repositories have not already been set, renv will use the Posit Public Package Manager CRAN mirror for package installation. The primary benefit to using this mirror is that it can provide pre-built binaries for R packages on a variety of commonly-used Linux distributions. This behavior can be configured or disabled if desired – see the options in config() for more details.

Examples

## Not run: 

# disable automatic snapshots
auto.snapshot <- getOption("renv.config.auto.snapshot")
options(renv.config.auto.snapshot = FALSE)

# initialize a new project (with an empty R library)
renv::init(bare = TRUE)

# install digest 0.6.19
renv::install("[email protected]")

# save library state to lockfile
renv::snapshot()

# remove digest from library
renv::remove("digest")

# check library status
renv::status()

# restore lockfile, thereby reinstalling digest 0.6.19
renv::restore()

# restore automatic snapshots
options(renv.config.auto.snapshot = auto.snapshot)


## End(Not run)

Description

Install one or more R packages, from a variety of remote sources. install() uses the same machinery as restore() (i.e. it uses cached packages where possible) but it does not respect the lockfile, instead installing the latest versions available from CRAN.

See vignette("package-install") for more details.

Usage

install(
  packages = NULL,
  ...,
  exclude = NULL,
  library = NULL,
  type = NULL,
  rebuild = FALSE,
  repos = NULL,
  prompt = interactive(),
  dependencies = NULL,
  verbose = NULL,
  lock = FALSE,
  project = NULL
)

Arguments

Value

A named list of package records which were installed by renv.

Remotes

install() (called without arguments) will respect the Remotes field of the DESCRIPTION file (if present). This allows you to specify places to install a package other than the latest version from CRAN. See https://remotes.r-lib.org/articles/dependencies.html for details.

Bioconductor

Packages from Bioconductor can be installed by using the ⁠bioc::⁠ prefix. For example,

renv::install("bioc::Biobase")

will install the latest-available version of Biobase from Bioconductor.

renv depends on BiocManager (or, for older versions of R, BiocInstaller) for the installation of packages from Bioconductor. If these packages are not available, renv will attempt to automatically install them before fulfilling the installation request.

Examples

## Not run: 

# install the latest version of 'digest'
renv::install("digest")

# install an old version of 'digest' (using archives)
renv::install("[email protected]")

# install 'digest' from GitHub (latest dev. version)
renv::install("eddelbuettel/digest")

# install a package from GitHub, using specific commit
renv::install("eddelbuettel/digest@df55b00bff33e945246eff2586717452e635032f")

# install a package from Bioconductor
# (note: requires the BiocManager package)
renv::install("bioc::Biobase")

# install a package, specifying path explicitly
renv::install("~/path/to/package")

# install packages as declared in the project DESCRIPTION file
renv::install()


## End(Not run)

Description

Copy packages from the renv cache directly into the project library, so that the project can continue to function independently of the renv cache.

Usage

isolate(project = NULL)

Arguments

Details

After calling isolate(), renv will still be able to use the cache on future install()s and restore()s. If you'd prefer that renv copy packages from the cache, rather than use symlinks, you can set the renv configuration option:

options(renv.config.cache.symlinks = FALSE)

to force renv to copy packages from the cache, as opposed to symlinking them. If you'd like to disable the cache altogether for a project, you can use:

settings$use.cache(FALSE)

to explicitly disable the cache for the project.

Value

The project directory, invisibly. Note that this function is normally called for its side effects.

Examples

## Not run: 

# isolate a project
renv::isolate()


## End(Not run)

Description

renv::load() sets the library paths to use a project-local library, sets up the system library sandbox, if needed, and creates shims for install.packages(), update.packages(), and remove.packages().

You should not generally need to call renv::load() yourself, as it's called automatically by the project auto-loader created by init()/ activate(). However, if needed, you can use renv::load("<project>") to explicitly load an renv project located at a particular path.

Usage

load(project = NULL, quiet = FALSE, profile = NULL, ...)

Arguments

Value

The project directory, invisibly. Note that this function is normally called for its side effects.

Shims

To help you take advantage of the package cache, renv places a couple of shims on the search path:

• install.packages() instead calls renv::install().

• remove.packages() instead calls renv::remove().

• update.packages() instead calls renv::update().

This allows you to keep using your existing muscle memory for installing, updating, and remove packages, while taking advantage of renv features like the package cache.

If you'd like to bypass these shims within an R session, you can explicitly call the version of these functions from the utils package, e.g. with ⁠utils::install.packages(<...>)⁠.

If you'd prefer not to use the renv shims at all, they can be disabled by setting the R option options(renv.config.shims.enabled = FALSE) or by setting the environment variable RENV_CONFIG_SHIMS_ENABLED = FALSE. See ?config for more details.

Examples

## Not run: 

# load a project -- note that this is normally done automatically
# by the project's auto-loader, but calling this explicitly to
# load a particular project may be useful in some circumstances
renv::load()


## End(Not run)

Description

A lockfile records the state of a project at some point in time.

Usage

lockfile_create(
  type = settings$snapshot.type(project = project),
  libpaths = .libPaths(),
  packages = NULL,
  exclude = NULL,
  prompt = interactive(),
  force = FALSE,
  ...,
  project = NULL
)

lockfile_read(file = NULL, ..., project = NULL)

lockfile_write(lockfile, file = NULL, ..., project = NULL)

lockfile_modify(
  lockfile = NULL,
  ...,
  remotes = NULL,
  repos = NULL,
  project = NULL
)

Arguments

Details

A lockfile captures the state of a project's library at some point in time. In particular, the package names, their versions, and their sources (when known) are recorded in the lockfile.

Projects can be restored from a lockfile using the restore() function. This implies reinstalling packages into the project's private library, as encoded within the lockfile.

While lockfiles are normally generated and used with snapshot() / restore(), they can also be edited by hand if so desired. Lockfiles are written as .json, to allow for easy consumption by other tools.

An example lockfile follows:

{
  "R": {
    "Version": "3.6.1",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cloud.r-project.org"
      }
    ]
  },
  "Packages": {
    "markdown": {
      "Package": "markdown",
      "Version": "1.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "4584a57f565dd7987d59dda3a02cfb41"
    },
    "mime": {
      "Package": "mime",
      "Version": "0.7",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "908d95ccbfd1dd274073ef07a7c93934"
    }
  }
}

The sections used within a lockfile are described next.

renv

Information about the version of renv used to manage this project.

R

Properties related to the version of R associated with this project.

Packages

R package records, capturing the packages used or required by a project at the time when the lockfile was generated.

Additional remote fields, further describing how the package can be retrieved from its corresponding source, will also be included as appropriate (e.g. for packages installed from GitHub).

Python

Metadata related to the version of Python used with this project (if any).

Note that the Name field may be empty. In that case, a project-local Python environment will be used instead (when not directly using a system copy of Python).

Caveats

These functions are primarily intended for expert users – in most cases, snapshot() and restore() are the primariy tools you will need when creating and using lockfiles.

See Also

Other reproducibility: restore(), snapshot()

Description

Migrate a project's infrastructure from packrat to renv.

Usage

migrate(
  project = NULL,
  packrat = c("lockfile", "sources", "library", "options", "cache")
)

Arguments

Value

The project directory, invisibly. Note that this function is normally called for its side effects.

Migration

When migrating Packrat projects to renv, the set of components migrated can be customized using the packrat argument. The set of components that can be migrated are as follows:

Examples

## Not run: 

# migrate Packrat project infrastructure to renv
renv::migrate()


## End(Not run)

Description

Modify a project's lockfile, either interactively or non-interactively.

Usage

modify(project = NULL, changes = NULL)

Arguments

Details

After edit, if the lockfile edited is associated with the active project, any state-related changes (e.g. to R repositories) will be updated in the current session.

Value

The project directory, invisibly. Note that this function is normally called for its side effects.

Examples

## Not run: 

# modify an existing lockfile
if (interactive())
  renv::modify()


## End(Not run)

Description

By default, renv stores global state in the following OS-specific folders:

If desired, this path can be customized by setting the RENV_PATHS_ROOT environment variable. This can be useful if you'd like, for example, multiple users to be able to share a single global cache.

Usage

paths

Customising individual paths

The various state sub-directories can also be individually adjusted, if so desired (e.g. you'd prefer to keep the cache of package installations on a separate volume). The various environment variables that can be set are enumerated below:

(If you want these settings to persist in your project, it is recommended that you add these to an appropriate R startup file. For example, these could be set in: a project-local .Renviron, the user-level .Renviron, or a site-wide file at file.path(R.home("etc"), "Renviron.site"). See Startup for more details).

Note that renv will append platform-specific and version-specific entries to the set paths as appropriate. For example, if you have set:

Sys.setenv(RENV_PATHS_CACHE = "/mnt/shared/renv/cache")

then the directory used for the cache will still depend on the renv cache version (e.g. v2), the R version (e.g. 3.5) and the platform (e.g. x86_64-pc-linux-gnu). For example:

/mnt/shared/renv/cache/v2/R-3.5/x86_64-pc-linux-gnu

This ensures that you can set a single RENV_PATHS_CACHE environment variable globally without worry that it may cause collisions or errors if multiple versions of R needed to interact with the same cache.

If reproducibility of a project is desired on a particular machine, it is highly recommended that the renv cache of installed packages + binary packages is backed up and persisted, so that packages can be easily restored in the future – installation of packages from source can often be arduous.

Sharing state across operating systems

If you need to share the same cache with multiple different Linux operating systems, you may want to set the RENV_PATHS_PREFIX environment variable to help disambiguate the paths used on Linux. For example, setting RENV_PATHS_PREFIX = "ubuntu-bionic" would instruct renv to construct a cache path like:

/mnt/shared/renv/cache/v2/ubuntu-bionic/R-3.5/x86_64-pc-linux-gnu

If this is required, it's strongly recommended that this environment variable is set in your R installation's Renviron.site file, typically located at file.path(R.home("etc"), "Renviron.site"), so that it can be active for any R sessions launched on that machine.

Starting from ⁠renv 0.13.0⁠, you can also instruct renv to auto-generate an OS-specific component to include as part of library and cache paths, by setting the environment variable:

RENV_PATHS_PREFIX_AUTO = TRUE

The prefix will be constructed based on fields within the system's ⁠/etc/os-release⁠ file. Note that this is the default behavior with ⁠renv 1.0.6⁠ when using R 4.4.0 or later.

Package cellar

If your project depends on one or R packages that are not available in any remote location, you can still provide a locally-available tarball for renv to use during restore. By default, these packages should be made available in the folder as specified by the RENV_PATHS_CELLAR environment variable. The package sources should be placed in a file at one of these locations:

• ⁠${RENV_PATHS_CELLAR}/<package>_<version>.<ext>⁠

• ⁠${RENV_PATHS_CELLAR}/<package>/<package>_<version>.<ext>⁠

• ⁠<project>/renv/cellar/<package>_<version>.<ext>⁠

• ⁠<project>/renv/cellar/<package>/<package>_<version>.<ext>⁠

where ⁠.<ext>⁠ is .tar.gz for source packages, or .tgz for binaries on macOS and .zip for binaries on Windows. During restore(), renv will search the cellar for a compatible package, and prefer installation with that copy of the package if appropriate.

Older versions

Older version of renv used a different default cache location. Those cache locations are:

If an renv root directory has already been created in one of the old locations, that will still be used. This change was made to comply with the CRAN policy requirements of R packages.

Examples

# get the path to the project library
path <- renv::paths$library()

Description

Retrieve the path to the active project (if any).

Usage

project(default = NULL)

Arguments

Value

The active project directory, as a length-one character vector.

Examples

## Not run: 

# get the currently-active renv project
renv::project()


## End(Not run)

Description

Purge packages from the cache. This can be useful if a package which had previously been installed in the cache has become corrupted or unusable, and needs to be reinstalled.

Usage

purge(package, ..., version = NULL, hash = NULL, prompt = interactive())

Arguments

Details

purge() is an inherently destructive option. It removes packages from the cache, and so any project which had symlinked that package into its own project library would find that package now unavailable. These projects would hence need to reinstall any purged packages. Take heed of this in case you're looking to purge the cache of a package which is difficult to install, or if the original sources for that package are no longer available!

Value

The set of packages removed from the renv global cache, as a character vector of file paths.

Examples

## Not run: 

# remove all versions of 'digest' from the cache
renv::purge("digest")

# remove only a particular version of 'digest' from the cache
renv::purge("digest", version = "0.6.19")


## End(Not run)

Description

Rebuild and reinstall packages in your library. This can be useful as a diagnostic tool – for example, if you find that one or more of your packages fail to load, and you want to ensure that you are starting from a clean slate.

Usage

rebuild(
  packages = NULL,
  recursive = TRUE,
  ...,
  type = NULL,
  prompt = interactive(),
  library = NULL,
  project = NULL
)

Arguments

Value

A named list of package records which were installed by renv.

Examples

## Not run: 

# rebuild the 'dplyr' package + all of its dependencies
renv::rebuild("dplyr", recursive = TRUE)

# rebuild only 'dplyr'
renv::rebuild("dplyr", recursive = FALSE)


## End(Not run)

Description

Use record() to record a new entry within an existing renv lockfile.

Usage

record(records, lockfile = NULL, project = NULL)

Arguments

Details

This function can be useful when you need to change one or more of the package records within an renv lockfile – for example, because a recorded package cannot be restored in a particular environment, and you know of a suitable alternative.

Records

Records can be provided either using the remotes short-hand syntax, or by using an R list of entries to record within the lockfile. See ?lockfiles for more information on the structure of a package record.

Examples

## Not run: 

# use digest 0.6.22 from package repositories -- different ways
# of specifying the remote. use whichever is most natural
renv::record("[email protected]")
renv::record(list(digest = "0.6.22"))
renv::record(list(digest = "[email protected]"))

# alternatively, provide a full record as a list
digest_record <- list(
  Package = "digest",
  Version = "0.6.22",
  Source  = "Repository",
  Repository = "CRAN"
)

renv::record(list(digest = digest_record))


## End(Not run)

Description

Query the active R package repositories for available packages, and update the in-memory cache of those packages.

Usage

refresh()

Details

Note that R also maintains its own on-disk cache of available packages, which is used by available.packages(). Calling refresh() will force an update of both types of caches. renv prefers using an in-memory cache as on occasion the temporary directory can be slow to access (e.g. when it is a mounted network filesystem).

Value

A list of package databases, invisibly – one for each repository currently active in the R session. Note that this function is normally called for its side effects.

Examples

## Not run: 

# check available packages
db <- available.packages()

# wait some time (suppose packages are uploaded / changed in this time)
Sys.sleep(5)

# refresh the local available packages database
# (the old locally cached db will be removed)
db <- renv::refresh()


## End(Not run)

Description

Re-hash packages in the renv cache, ensuring that any previously-cached packages are copied to a new cache location appropriate for this version of renv. This can be useful if the cache scheme has changed in a new version of renv, but you'd like to preserve your previously-cached packages.

Usage

rehash(prompt = interactive(), ...)

Arguments

Details

Any packages which are re-hashed will retain links to the location of the newly-hashed package, ensuring that prior installations of renv can still function as expected.

Description

Given a remote specification, resolve it into an renv package record that can be used for download and installation (e.g. with install).

Usage

remote(spec)

Arguments

Description

Remove (uninstall) R packages.

Usage

remove(packages, ..., library = NULL, project = NULL)

Arguments

Value

A vector of package records, describing the packages (if any) which were successfully removed.

Examples

## Not run: 

# disable automatic snapshots
auto.snapshot <- getOption("renv.config.auto.snapshot")
options(renv.config.auto.snapshot = FALSE)

# initialize a new project (with an empty R library)
renv::init(bare = TRUE)

# install digest 0.6.19
renv::install("[email protected]")

# save library state to lockfile
renv::snapshot()

# remove digest from library
renv::remove("digest")

# check library status
renv::status()

# restore lockfile, thereby reinstalling digest 0.6.19
renv::restore()

# restore automatic snapshots
options(renv.config.auto.snapshot = auto.snapshot)


## End(Not run)

Description

Use repair() to recover from some common issues that can occur with a project. Currently, two operations are performed:

Usage

repair(library = NULL, lockfile = NULL, project = NULL)

Arguments

Details

1. Packages with broken symlinks into the cache will be re-installed.

2. Packages that were installed from sources, but appear to be from an remote source (e.g. GitHub), will have their DESCRIPTION files updated to record that remote source explicitly.

Description

Restore a project's dependencies from a lockfile, as previously generated by snapshot(). renv::restore() compares packages recorded in the lockfile to the packages installed in the project library. Where there are differences it resolves them by installing the lockfile-recorded package into the project library. If clean = TRUE, restore() will additionally delete any packages in the project library that don't appear in the lockfile.

Usage

restore(
  project = NULL,
  ...,
  library = NULL,
  lockfile = NULL,
  packages = NULL,
  exclude = NULL,
  rebuild = FALSE,
  repos = NULL,
  clean = FALSE,
  prompt = interactive()
)

Arguments

Value

A named list of package records which were installed by renv.

See Also

Other reproducibility: lockfiles, snapshot()

Examples

## Not run: 

# disable automatic snapshots
auto.snapshot <- getOption("renv.config.auto.snapshot")
options(renv.config.auto.snapshot = FALSE)

# initialize a new project (with an empty R library)
renv::init(bare = TRUE)

# install digest 0.6.19
renv::install("[email protected]")

# save library state to lockfile
renv::snapshot()

# remove digest from library
renv::remove("digest")

# check library status
renv::status()

# restore lockfile, thereby reinstalling digest 0.6.19
renv::restore()

# restore automatic snapshots
options(renv.config.auto.snapshot = auto.snapshot)


## End(Not run)

Description

Run an R script, in the context of a project using renv. The script will be run within an R sub-process.

Usage

run(script, ..., job = NULL, name = NULL, project = NULL)

Arguments

Value

The project directory, invisibly. Note that this function is normally called for its side effects.

Description

An R installation can have up to three types of library paths available to the user:

• The user library, where R packages downloaded and installed by the current user are installed. This library path is only visible to that specific user.

• The site library, where R packages maintained by administrators of a system are installed. This library path, if it exists, is visible to all users on the system.

• The default library, where R packages distributed with R itself are installed. This library path is visible to all users on the system.

Normally, only so-called "base" and "recommended" packages should be installed in the default library. (You can get a list of these packages with installed.packages(priority = c("base", "recommended"))). However, it is possible for users and administrators to install packages into the default library, if the filesystem permissions permit them to do so. (This, for example, is the default behavior on macOS.)

Because the site and default libraries are visible to all users, having those accessible in renv projects can potentially break isolation – that is, if a package were updated in the default library, that update would be visible to all R projects on the system.

To help defend against this, renv uses something called the "sandbox" to isolate renv projects from non-"base" packages that are installed into the default library. When an renv project is loaded, renv will:

• Create a new, empty library path (called the "sandbox"),

• Link only the "base" and "recommended" packages from the default library into the sandbox,

• Mark the sandbox as read-only, so that users are unable to install packages into this library,

• Instruct the R session to use the "sandbox" as the default library.

This process is mostly transparent to the user. However, because the sandbox is read-only, if you later need to remove the sandbox, you'll need to reset file permissions manually; for example, with renv::sandbox$unlock().

If you'd prefer to keep the sandbox unlocked, you can also set:

RENV_SANDBOX_LOCKING_ENABLED = FALSE

in an appropriate startup .Renviron or Renviron.site file.

The sandbox can also be disabled entirely with:

RENV_CONFIG_SANDBOX_ENABLED = FALSE

The sandbox library path can also be configured using the RENV_PATHS_SANDBOX environment variable: see paths for more details.

Usage

sandbox

Description

Create the renv project infrastructure. This will:

• Create a project library, renv/library.

• Install renv into the project library.

• Update the project .Rprofile to call source("renv/activate.R") so that renv is automatically loaded for new R sessions launched in this project.

• Create renv/.gitignore, which tells git to ignore the project library.

• Create .Rbuildignore, if the project is also a package. This tells ⁠R CMD build⁠ to ignore the renv infrastructure,

• Write a (bare) lockfile, renv.lock.

Usage

scaffold(
  project = NULL,
  version = NULL,
  repos = getOption("repos"),
  settings = NULL
)

Arguments

Examples

## Not run: 
# create scaffolding with 'devtools' ignored
renv::scaffold(settings = list(ignored.packages = "devtools"))

## End(Not run)

Description

Define project-local settings that can be used to adjust the behavior of renv with your particular project.

• Get the current value of a setting with (e.g.) settings$snapshot.type()

• Set current value of a setting with (e.g.) settings$snapshot.type("explicit").

Settings are automatically persisted across project sessions by writing to renv/settings.json. You can also edit this file by hand, but you'll need to restart the session for those changes to take effect.

bioconductor.version

The Bioconductor version to be used with this project. Use this if you'd like to lock the version of Bioconductor used on a per-project basis. When unset, renv will try to infer the appropriate Bioconductor release using the BiocVersion package if installed; if not, renv uses BiocManager::version() to infer the appropriate Bioconductor version.

external.libraries

A vector of library paths, to be used in addition to the project's own private library. This can be useful if you have a package available for use in some system library, but for some reason renv is not able to install that package (e.g. sources or binaries for that package are not publicly available, or you have been unable to orchestrate the pre-requisites for installing some packages from source on your machine).

ignored.packages

A vector of packages, which should be ignored when attempting to snapshot the project's private library. Note that if a package has already been added to the lockfile, that entry in the lockfile will not be ignored.

package.dependency.fields

When explicitly installing a package with install(), what fields should be used to determine that packages dependencies? The default uses Imports, Depends and LinkingTo fields, but you also want to install Suggests dependencies for a package, you can set this to c("Imports", "Depends", "LinkingTo", "Suggests").

ppm.enabled

Enable Posit Package Manager integration in this project? When TRUE, renv will attempt to transform repository URLs used by PPM into binary URLs as appropriate for the current Linux platform. Set this to FALSE if you'd like to continue using source-only PPM URLs, or if you find that renv is improperly transforming your repository URLs. You can still set and use PPM repositories with this option disabled; it only controls whether renv tries to transform source repository URLs into binary URLs on your behalf.

ppm.ignored.urls

When Posit Package Manager integration is enabled, renv will attempt to transform source repository URLs into binary repository URLs. This setting can be used if you'd like to avoid this transformation with some subset of repository URLs.

r.version

The version of R to encode within the lockfile. This can be set as a project-specific option if you'd like to allow multiple users to use the same renv project with different versions of R. renv will still warn the user if the major + minor version of R used in a project does not match what is encoded in the lockfile.

snapshot.type

The type of snapshot to perform by default. See snapshot for more details.

use.cache

Enable the renv package cache with this project. When active, renv will install packages into a global cache, and link packages from the cache into your renv projects as appropriate. This can greatly save on disk space and install time when for R packages which are used across multiple projects in the same environment.

vcs.manage.ignores

Should renv attempt to manage the version control system's ignore files (e.g. .gitignore) within this project? Set this to FALSE if you'd prefer to take control. Note that if this setting is enabled, you will need to manually ensure internal data in the project's ⁠renv/⁠ folder is explicitly ignored.

vcs.ignore.cellar

Set whether packages within a project-local package cellar are excluded from version control. See vignette("cellar", package = "renv") for more information.

vcs.ignore.library

Set whether the renv project library is excluded from version control.

vcs.ignore.local

Set whether renv project-specific local sources are excluded from version control.

Usage

settings

Value

A named list of renv settings.

Defaults

You can change the default values of these settings for newly-created renv projects by setting R options for renv.settings or ⁠renv.settings.<name>⁠. For example:

options(renv.settings = list(snapshot.type = "all"))
options(renv.settings.snapshot.type = "all")

If both of the renv.settings and ⁠renv.settings.<name>⁠ options are set for a particular key, the option associated with ⁠renv.settings.<name>⁠ is used instead. We recommend setting these in an appropriate startup profile, e.g. ⁠~/.Rprofile⁠ or similar.

Examples

## Not run: 

# view currently-ignored packaged
renv::settings$ignored.packages()

# ignore a set of packages
renv::settings$ignored.packages("devtools", persist = FALSE)


## End(Not run)

Description

Call renv::snapshot() to update a lockfile with the current state of dependencies in the project library. The lockfile can be used to later restore these dependencies as required.

It's also possible to call renv::snapshot() with a non-renv project, in which case it will record the current state of dependencies in the current library paths. This makes it possible to restore the current packages, providing lightweight portability and reproducibility without isolation.

If you want to automatically snapshot after each change, you can set config$config$auto.snapshot(TRUE), see ?config for more details.

Usage

snapshot(
  project = NULL,
  ...,
  library = NULL,
  lockfile = paths$lockfile(project = project),
  type = settings$snapshot.type(project = project),
  dev = FALSE,
  repos = getOption("repos"),
  packages = NULL,
  exclude = NULL,
  prompt = interactive(),
  update = FALSE,
  force = FALSE,
  reprex = FALSE
)

Arguments

Value

The generated lockfile, as an R object (invisibly). Note that this function is normally called for its side effects.

Snapshot types

Depending on how you prefer to manage dependencies, you might prefer selecting a different snapshot mode. The modes available are as follows:

"implicit"

(The default) Capture only packages which appear to be used in your project, as determined by renv::dependencies(). This ensures that only the packages actually required by your project will enter the lockfile; the downside if it might be slow if your project contains a large number of files. If speed becomes an issue, you might consider using .renvignore files to limit which files renv uses for dependency discovery, or switching to explicit mode, as described next.

"explicit"

Only capture packages which are explicitly listed in the project DESCRIPTION file. This workflow is recommended for users who wish to manage their project's R package dependencies directly.

"all"

Capture all packages within the active R libraries in the lockfile. This is the quickest and simplest method, but may lead to undesired packages (e.g. development dependencies) entering the lockfile.

"custom"

Like "implicit", but use a custom user-defined filter instead. The filter should be specified by the R option renv.snapshot.filter, and should either be a character vector naming a function (e.g. "package::method"), or be a function itself. The function should only accept one argument (the project directory), and should return a vector of package names to include in the lockfile.

You can change the snapshot type for the current project with settings(). For example, the following code will switch to using "explicit" snapshots:

renv::settings$snapshot.type("explicit")

When the packages argument is set, type is ignored, and instead only the requested set of packages, and their recursive dependencies, will be written to the lockfile.

See Also

More on handling package dependencies()

Other reproducibility: lockfiles, restore()

Examples

## Not run: 

# disable automatic snapshots
auto.snapshot <- getOption("renv.config.auto.snapshot")
options(renv.config.auto.snapshot = FALSE)

# initialize a new project (with an empty R library)
renv::init(bare = TRUE)

# install digest 0.6.19
renv::install("[email protected]")

# save library state to lockfile
renv::snapshot()

# remove digest from library
renv::remove("digest")

# check library status
renv::status()

# restore lockfile, thereby reinstalling digest 0.6.19
renv::restore()

# restore automatic snapshots
options(renv.config.auto.snapshot = auto.snapshot)


## End(Not run)

Description

renv::status() reports issues caused by inconsistencies across the project lockfile, library, and dependencies(). In general, you should strive to ensure that status() reports no issues, as this maximizes your chances of successfully restore()ing the project in the future or on another machine.

renv::load() will report if any issues are detected when starting an renv project; we recommend resolving these issues before doing any further work on your project.

See the headings below for specific advice on resolving any issues revealed by status().

Usage

status(
  project = NULL,
  ...,
  library = NULL,
  lockfile = NULL,
  sources = TRUE,
  cache = FALSE,
  dev = FALSE
)

Arguments

Value

This function is normally called for its side effects, but it invisibly returns a list containing the following components:

• library: packages in your library.

• lockfile: packages in the lockfile.

• synchronized: are the library and lockfile in sync?

Missing packages

status() first checks that all packages used by the project are installed. This must be done first because if any packages are missing we can't tell for sure that a package isn't used; it might be a dependency that we don't know about. Once you have resolve any installation issues, you'll need to run status() again to reveal the next set of potential problems.

There are four possibilities for an uninstalled package:

• If it's used and recorded, call renv::restore() to install the version specified in the lockfile.

• If it's used and not recorded, call renv::install() to install it from CRAN or elsewhere.

• If it's not used and recorded, call renv::snapshot() to remove it from the lockfile.

• If it's not used and not recorded, there's nothing to do. This the most common state because you only use a small fraction of all available packages in any one project.

If you have multiple packages in an inconsistent state, we recommend renv::restore(), then renv::install(), then renv::snapshot(), but that also suggests you should be running status more frequently.

Lockfile vs dependencies()

Next we need to ensure that packages are recorded in the lockfile if and only if they are used by the project. Fixing issues of this nature only requires calling snapshot() because there are four possibilities for a package:

• If it's used and recorded, it's ok.

• If it's used and not recorded, call renv::snapshot() to add it to the lockfile.

• If it's not used but is recorded, call renv::snapshot() to remove it from the lockfile.

• If it's not used and not recorded, it's also ok, as it may be a development dependency.

Out-of-sync sources

The final issue to resolve is any inconsistencies between the version of the package recorded in the lockfile and the version installed in your library. To fix these issues you'll need to either call renv::restore() or renv::snapshot():

• Call renv::snapshot() if your project code is working. This implies that the library is correct and you need to update your lockfile.

• Call renv::restore() if your project code isn't working. This probably implies that you have the wrong package versions installed and you need to restore from known good state in the lockfile.

If you're not sure which case applies, it's generally safer to call renv::snapshot(). If you want to rollback to an earlier known good status, see history() and revert().

Different R Version

renv will also notify you if the version of R used when the lockfile was generated, and the version of R currently in use, do not match. In this scenario, you'll need to consider:

• Is the version of R recorded in the lockfile correct? If so, you'll want to ensure that version of R is installed and used when working in this project.

• Otherwise, you can call renv::snapshot() to update the version of R recorded in the lockfile, to match the version of R currently in use.

If you'd like to set the version of R recorded in a lockfile independently of the version of R currently in use, you can set the r.version project setting – see settings for more details.

Examples

## Not run: 

# disable automatic snapshots
auto.snapshot <- getOption("renv.config.auto.snapshot")
options(renv.config.auto.snapshot = FALSE)

# initialize a new project (with an empty R library)
renv::init(bare = TRUE)

# install digest 0.6.19
renv::install("[email protected]")

# save library state to lockfile
renv::snapshot()

# remove digest from library
renv::remove("digest")

# check library status
renv::status()

# restore lockfile, thereby reinstalling digest 0.6.19
renv::restore()

# restore automatic snapshots
options(renv.config.auto.snapshot = auto.snapshot)


## End(Not run)

Description

Update packages which are currently out-of-date. Currently supports CRAN, Bioconductor, other CRAN-like repositories, GitHub, GitLab, Git, and BitBucket.

Updates will only be checked from the same source – for example, if a package was installed from GitHub, but a newer version is available on CRAN, that updated version will not be seen.

Usage

update(
  packages = NULL,
  ...,
  exclude = NULL,
  library = NULL,
  rebuild = FALSE,
  check = FALSE,
  prompt = interactive(),
  lock = FALSE,
  project = NULL
)

Arguments

Value

A named list of package records which were installed by renv.

Examples

## Not run: 

# update the 'dplyr' package
renv::update("dplyr")


## End(Not run)

Description

Upgrade the version of renv associated with a project, including using a development version from GitHub. Automatically snapshots the update renv, updates the activate script, and restarts R.

If you want to update all packages (including renv) to their latest CRAN versions, use update().

Usage

upgrade(project = NULL, version = NULL, reload = NULL, prompt = interactive())

Arguments

Value

A boolean value, indicating whether the requested version of renv was successfully installed. Note that this function is normally called for its side effects.

Examples

## Not run: 

# upgrade to the latest version of renv
renv::upgrade()

# upgrade to the latest version of renv on GitHub (development version)
renv::upgrade(version = "main")


## End(Not run)

Description

Associate a version of Python with your project.

Usage

use_python(
  python = NULL,
  ...,
  type = c("auto", "virtualenv", "conda", "system"),
  name = NULL,
  project = NULL
)

Arguments

Details

When Python integration is active, renv will:

• Save metadata about the requested version of Python in renv.lock – in particular, the Python version, and the Python type ("virtualenv", "conda", "system"),

• Capture the set of installed Python packages during renv::snapshot(),

• Re-install the set of recorded Python packages during renv::restore().

In addition, when the project is loaded, the following actions will be taken:

• The RENV_PYTHON environment variable will be set, indicating the version of Python currently active for this sessions,

• The RETICULATE_PYTHON environment variable will be set, so that the reticulate package can automatically use the requested copy of Python as appropriate,

• The requested version of Python will be placed on the PATH, so that attempts to invoke Python will resolve to the expected version of Python.

You can override the version of Python used in a particular project by setting the RENV_PYTHON environment variable; e.g. as part of the project's .Renviron file. This can be useful if you find that renv is unable to automatically discover a compatible version of Python to be used in the project.

Value

TRUE, indicating that the requested version of Python has been successfully activated. Note that this function is normally called for its side effects.

Finding Python

In interactive sessions, when python = NULL, renv will prompt for an appropriate version of Python. renv will search a pre-defined set of locations when attempting to find Python installations on the system:

• getOption("renv.python.root"),

• ⁠/opt/python⁠,

• ⁠/opt/local/python⁠,

• ⁠~/opt/python⁠,

• ⁠/usr/local/opt⁠ (for macOS Homebrew-installed copies of Python),

• ⁠/opt/homebrew/opt⁠ (for M1 macOS Homebrew-installed copies of Python),

• ⁠~/.pyenv/versions⁠,

• Python instances available on the PATH.

In non-interactive sessions, renv will first check the RETICULATE_PYTHON environment variable; if that is unset, renv will look for Python on the PATH. It is recommended that the version of Python to be used is explicitly supplied for non-interactive usages of use_python().

Warning

We strongly recommend using Python virtual environments, for a few reasons:

1. If something goes wrong with a local virtual environment, you can safely delete that virtual environment, and then re-initialize it later, without worry that doing so might impact other software on your system.

2. If you choose to use a "system" installation of Python, then any packages you install or upgrade will be visible to any other application that wants to use that same Python installation. Using a virtual environment ensures that any changes made are isolated to that environment only.

3. Choosing to use Anaconda will likely invite extra frustration in the future, as you may be required to upgrade and manage your Anaconda installation as new versions of Anaconda are released. In addition, Anaconda installations tend to work poorly with software not specifically installed as part of that same Anaconda installation.

In other words, we recommend selecting "system" or "conda" only if you are an expert Python user who is already accustomed to managing Python / Anaconda installations on your own.

Examples

## Not run: 

# use python with a project
renv::use_python()

# use python with a project; create the environment
# within the project directory in the '.venv' folder
renv::use_python(name = ".venv")

# use python with a pre-existing virtual environment located elsewhere
renv::use_python(name = "~/.virtualenvs/env")

# use virtualenv python with a project
renv::use_python(type = "virtualenv")

# use conda python with a project
renv::use_python(type = "conda")


## End(Not run)