lazyRepo {switchr}

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