pkgSnapshot: Take a snapshot of all the packages and version numbers

In Require: Installing and Loading R Packages for Reproducible Workflows

Take a snapshot of all the packages and version numbers

Description

This can be used later by Require to install or re-install the correct versions. See examples.

Usage

pkgSnapshot(
  packageVersionFile = getOption("Require.packageVersionFile"),
  libPaths = .libPaths(),
  standAlone = FALSE,
  purge = getOption("Require.purge", FALSE),
  exact = TRUE,
  includeBase = FALSE,
  verbose = getOption("Require.verbose")
)

pkgSnapshot2(
  packageVersionFile = getOption("Require.packageVersionFile"),
  libPaths,
  standAlone = FALSE,
  purge = getOption("Require.purge", FALSE),
  exact = TRUE,
  includeBase = FALSE,
  verbose = getOption("Require.verbose")
)

Arguments

packageVersionFile	A filename to save the packages and their currently installed version numbers. Defaults to "packageVersions.txt". If this is specified to be NULL, the function will return the exact Require call needed to install all the packages at their current versions. This can be useful to add to a script to allow for reproducibility of a script.
libPaths	The path to the local library where packages are installed. Defaults to the .libPaths()[1].
standAlone	Logical. If TRUE, all packages will be installed to and loaded from the libPaths only. NOTE: If TRUE, THIS WILL CHANGE THE USER'S .libPaths(), similar to e.g., the checkpoint package. If FALSE, then libPath will be prepended to .libPaths() during the Require call, resulting in shared packages, i.e., it will include the user's default package folder(s). This can be create dramatically faster installs if the user has a substantial number of the packages already in their personal library. Default FALSE to minimize package installing.
purge	Logical. Should all caches be purged? Default is getOption("Require.purge", FALSE). There is a lot of internal caching of results throughout the Require package. These help with speed and reduce calls to internet sources. However, sometimes these caches must be purged. The cached values are renewed when found to be too old, with the age limit. This maximum age can be set in seconds with the environment variable R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE, or if unset, defaults to 3600 (one hour – see utils::available.packages). Internally, there are calls to available.packages.
exact	Logical. If TRUE, the default, then for GitHub packages, it will install the exact SHA, rather than the head of the account/repo@branch. For CRAN packages, it will install the exact version. If FALSE, then GitHub packages will identify their branch if that had been specified upon installation, not a SHA. If the package had been installed with reference to a SHA, then it will return the SHA as it does not know what branch it came from. Similarly, CRAN packages will report their version and specify with a >=, allowing a subsequent user to install with a minimum version number, as opposed to an exact version number.
includeBase	Logical. Should R base packages be included, specifically, those in tail(.libPath(), 1)
verbose	Numeric or logical indicating how verbose should the function be. If -1 or -2, then as little verbosity as possible. If 0 or FALSE, then minimal outputs; if 1 or TRUE, more outputs; 2 even more. NOTE: in Require function, when verbose >= 2, the return object will have an attribute: attr(.., "Require") which has lots of information about the processes of the installs.

Details

A file is written with the package names and versions of all packages within libPaths. This can later be passed to Require.

pkgSnapshot2 returns a vector of package names and versions, with no file output. See examples.

Value

Will both write a file, and (invisibly) return a vector of packages with the version numbers. This vector can be used directly in Require, though it should likely be used with require = FALSE to prevent attaching all the packages.

Examples

## Not run: 
if (Require:::.runLongExamples()) {
  opts <- Require:::.setupExample()
  # install one archived version so that below does something interesting

  libForThisEx <- tempdir2("Example")
  Require("crayon (==1.5.1)", libPaths = libForThisEx, require = FALSE)
  # Normal use -- using the libForThisEx for example;
  #    normally libPaths would be omitted to get all
  #    packages in user or project library
  tf <- tempfile()

  # writes to getOption("Require.packageVersionFile")
  # within project; also returns a vector
  # of packages with version
  pkgs <- pkgSnapshot(
    packageVersionFile = tf,
    libPaths = libForThisEx
  )

  # Now move this file to another computer e.g. by committing in git,
  #   emailing, googledrive
  #   on next computer/project
  Require(packageVersionFile = tf, libPaths = libForThisEx)

  # Using pkgSnapshot2 to get the vector of packages and versions

  tf <- tempfile()
  pkgs <- pkgSnapshot2(
    packageVersionFile = tf,
    libPaths = libForThisEx
  )
  Require(pkgs, require = FALSE) # will install packages from previous line
  # (likely want require = FALSE
  #  and not load them all)

  Require:::.cleanup(opts)
  unlink(getOption("Require.packageVersionFile"))
}

## End(Not run)

Require documentation built on May 31, 2023, 7:06 p.m.