Package 'piamenv'

piamenv: Package environment support for PIAM

Description

Enables easier management of package environments, based on renv and conda.

Author(s)

Maintainer: Pascal Sauer [email protected]

Authors:

• Tonn Rüter [email protected]

See Also

Useful links:

• https://github.com/pik-piam/piamenv

---

archiveRenv

Description

Writes a new <timestamp>_renv.lock based on the current package environment into renv::project()/renv/archive.

Usage

archiveRenv()

Value

Invisibly, the absolute path to the created lockfile.

Author(s)

Pascal Sauer

---

Check Dependencies

Description

Check if package requirements specified in the given DESCRIPTION are met.

Usage

checkDeps(
  descriptionFile = ".",
  dependencyTypes = c("Depends", "Imports", "LinkingTo"),
  action = "stop"
)

Arguments

descriptionFile	Path to a DESCRIPTION file or a path that belongs to a source package project. If /DEPENDENCIES exists that will be used instead.
dependencyTypes	The types of dependencies to check. Must be a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances").
action	Action to take on unmet dependencies: "stop": Issue an error with the unmet dependencies. (Default.) "warn": Issue a warning with the unmet dependencies. "note": Issue a message with the unmet dependencies. "pass": Do nothing, just return invisibly. "ask": Ask the user whether to auto-fix missing dependencies. Requires an active renv. Will also write renv.lock. If no active renv is found, stops instead.

Value

Invisibly, a named list of strings indicating whether each package requirement is met ("TRUE") or not, in which case the reason is stated.

Author(s)

Pascal Sauer, Michaja Pehl

Examples

checkDeps(system.file("DESCRIPTION", package = "piamenv"))

---

condaInit

Description

Determine initialization commands to make conda available

Usage

condaInit(how = "", log = NULL, verbose = 0)

Arguments

how	Method to activate conda if not found (e.g., "pik-cluster")
log	Path to log file or NULL to use stdout
verbose	Verbosity level (0 for silent, higher for more verbose)

Value

List containing 'setup' and 'teardown' commands, and environment variables ('env').

---

condaRun

Description

Run a command in a specified conda environment with given environment variables.

Usage

condaRun(
  cmd,
  path,
  env = c(),
  init = list(setup = "", teardown = ""),
  log = NULL,
  verbose = 0
)

Arguments

cmd	Command to run in the conda environment
path	Path to the conda environment
env	Named vector of environment variables to set, i.e., c("VAR0" = "value0", "VAR1" = "value1")
init	List containing 'setup' and 'teardown' commands to run before and after the command
log	Path to log file or NULL to use stdout
verbose	Verbosity level (0 for silent, higher for more verbose).

Value

Invisible NULL

---

Fix Dependencies

Description

Automatically install package versions as suggested by piamenv::checkDeps into an renv.

Usage

fixDeps(
  ask = FALSE,
  requirementMet = checkDeps(action = if (ask) "note" else "pass")
)

Arguments

ask	Whether to ask before fixing dependencies.
requirementMet	The output of piamenv::checkDeps.

Value

Invisibly, the return value of renv::install.

Author(s)

Pascal Sauer

---

installDeps

Description

Install dependencies, identified by renv::dependencies for a given path, into the current renv.

Usage

installDeps(path)

Arguments

path	The path to scan for dependencies.

Author(s)

Pascal Sauer

---

restoreRenv

Description

Restores the current renv to the state described in the given lockfile. If multiple lockfiles are given, ask the user which one to restore.

Usage

restoreRenv(
  lockfile = Sys.glob(c("output/*/*renv.lock", "renv/archive/*renv.lock"))
)

Arguments

lockfile

One or more paths to lockfiles. The default value assumes an output folder with run folders containing renv.lock files, and/or an renv/archive folder with renv.lock files.

Value

Invisibly, the return value of renv::restore.

Author(s)

Pascal Sauer

---

Revert Development Versions of Packages

Description

All PIK-PIAM packages in the current renv that are development versions, i.e. that have a non-zero fourth version number component (e.g. ⁠0.4.3.9001⁠), are reverted to the highest version lower than the development versions (e.g. ⁠0.4.3⁠).

Usage

revertDevelopmentVersions()

Value

Invisibly the return value of renv::install().

---

showUpdates

Description

Print available updates of the given packages.

Usage

showUpdates(packages = piamPackages())

Arguments

packages

A character vector of package names.

Value

Invisibly, a data.frame as returned by utils::old.packages

---

stopIfLoaded

Description

Throw an error if any of the given packages is loaded.

Usage

stopIfLoaded(updatedPackage)

Arguments

updatedPackage

One or more names of packages that were just updated.

Details

This is useful after updating packages. If any of the updated packages was loaded before the update R might crash when trying to lazy load a function from the updated package.

Author(s)

Pascal Sauer

Examples

## Not run: 
updates <- piamenv::fixDeps()
piamenv::stopIfLoaded(names(updates))

updates <- piamenv::updateRenv()
piamenv::stopIfLoaded(names(updates))

## End(Not run)

---

updateRenv

Description

Update all PIK-PIAM packages in the current renv, write renv.lock into archive.

Usage

updateRenv(exclude = NULL)

Arguments

exclude

vector of packages not to be updated

Value

Invisibly, the return value of renv::update.

Author(s)

Pascal Sauer

---