lazyRepo: lazyRepo

In switchr: Installing, Managing, and Switching Between Distinct Sets of Installed Packages

lazyRepo

Description

Create a lazy repository for installing directly from a package manifest. Most users will want to call Install directly, which will call this as needed behind the scenes.

Usage

lazyRepo(
  pkgs,
  pkg_manifest,
  versions = rep(NA, times = length(pkgs)),
  dir = tempdir(),
  rep_path = file.path(dir, "repo"),
  get_suggests = FALSE,
  verbose = FALSE,
  scm_auths = list(bioconductor = c("readonly", "readonly")),
  param = SwitchrParam(),
  force_refresh = FALSE
)

## S4 method for signature 'SessionManifest,ANY'
lazyRepo(
  pkgs,
  pkg_manifest,
  versions = rep(NA, times = length(pkgs)),
  dir = tempdir(),
  rep_path = file.path(dir, "repo"),
  get_suggests = FALSE,
  verbose = FALSE,
  scm_auths = list(bioconductor = c("readonly", "readonly")),
  param = SwitchrParam(),
  force_refresh = FALSE
)

## S4 method for signature 'PkgManifest,ANY'
lazyRepo(
  pkgs,
  pkg_manifest,
  versions = rep(NA, times = length(pkgs)),
  dir = tempdir(),
  rep_path = file.path(dir, "repo"),
  get_suggests = FALSE,
  verbose = FALSE,
  scm_auths = list(bioconductor = c("readonly", "readonly")),
  param = SwitchrParam(),
  force_refresh = FALSE
)

## S4 method for signature 'character,SessionManifest'
lazyRepo(
  pkgs,
  pkg_manifest,
  versions = rep(NA, times = length(pkgs)),
  dir = tempdir(),
  rep_path = file.path(dir, "repo"),
  get_suggests = FALSE,
  verbose = FALSE,
  scm_auths = list(bioconductor = c("readonly", "readonly")),
  param = SwitchrParam(),
  force_refresh = FALSE
)

## S4 method for signature 'character,PkgManifest'
lazyRepo(
  pkgs,
  pkg_manifest,
  versions = rep(NA, times = length(pkgs)),
  dir = tempdir(),
  rep_path = file.path(dir, "repo"),
  get_suggests = FALSE,
  verbose = FALSE,
  scm_auths = list(bioconductor = c("readonly", "readonly")),
  param = SwitchrParam(),
  force_refresh = FALSE
)

Arguments

pkgs	The packages to install
pkg_manifest	The manifest to use
versions	Specific versions of the packages to install. Should be a vector of the same length as pkgs (and in the same order). Defaults to NA (any version) for all packages.
dir	The directory packages should be downloaded/checkedout/built into
rep_path	The path of the final repository
get_suggests	Whether suggested packages should be included in the lazy repository. Defaults to FALSE
verbose	Should extra information be printed to the user during the construction process
scm_auths	Named list of username/password credentials for checking out package sources from one or more sources listed in manifest Defaults to readonly access to Bioconductor SVN
param	A SwitchrParam object
force_refresh	If a package already appears in the lazy repo area, it be updated (e.g. from SCM) and built again? Defaults to FALSE

Details

When checking building from SVN or git checkouts, this function will first look for existing checkouts for the relevant packages in dir. If found, these will be updated (in the case of conflicts, the behavior is undefined and will likely fail if they are not resolvable). This allows the user to have an existing, checkout directory where he or she works on development versions of multiple, interrelated packages, as local changes WILL be reflected in the packages built into the lazy repository.

Value

A path to the populated lazy repository, suitable for 'coercing' to a url and installing from.

Author(s)

Gabriel Becker

References

Becker G, Barr C, Gentleman R, Lawrence M; Enhancing Reproducibility and Collaboration via Management of R Package Cohorts. Journal of Statistical Software, 81(1). 2017. doi: 10.18637/jss.v082.i01

switchr documentation built on March 31, 2023, 5:13 p.m.