lazyRepo: 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 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 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 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 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
)

Value

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

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

Author

Gabriel Becker

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.

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