Package 'patRoonInst'

Manage patRoon installations

Description

Installs and updates patRoon and its dependencies.

Package options

The following package options (see options()) can be set:

• patRoonInst.repos.patRoonDeps The URL to the patRoonDeps R package repository.

• patRoonInst.repos.runiverse The URL to the r-universe R package repository.

• patRoonInst.path.legacy The directory where legacy files were installed.

See Also

Useful links:

• https://github.com/rickhelmus/patRoonInst

• https://rickhelmus.github.io/patRoonInst/

• Report bugs at https://github.com/rickhelmus/patRoon/issues

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Installation data for patRoon and its direct dependencies

Description

Returns information for patRoon and its direct R package dependencies.

Usage

getDirectDeps()

Details

The information returned by this function may change over time, and is downloaded from the internet.

Value

A list with miscellaneous package information.

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Managing patRoon installations

Description

Functions to install, update and synchronize patRoon and its dependencies from various repositories.

Usage

install(
  pkgs = NULL,
  ignorePkgs = NULL,
  origin = NULL,
  lib.loc = NULL,
  ask = TRUE,
  force = FALSE,
  quiet = TRUE
)

update(
  pkgs = NULL,
  ignorePkgs = NULL,
  origin = NULL,
  lib.loc = NULL,
  ask = TRUE,
  quiet = TRUE
)

sync(
  pkgs = NULL,
  ignorePkgs = NULL,
  origin = NULL,
  lib.loc = NULL,
  allDeps = FALSE,
  ask = TRUE,
  quiet = TRUE
)

Arguments

pkgs, ignorePkgs	A character vector with packages to consider/ignore. Execute names(getDirectDeps()) to obtain valid package options. If NULL then all packages are considered/none are ignored. The ignorePkgs argument can also include "big" to exclude large packages (e.g. patRoonDeps), and will override pkgs in case of conflicts.
origin	Where patRoon and its R dependencies are installed from. Valid values are: "patRoonDeps", "runiverse", "regular". If NULL then the default on Windows is "patRoonDeps" and "runiverse" otherwise. See below for more details.
lib.loc	The path to the R library where packages will be installed. Set to NULL for the default R library.
ask	Set to TRUE to ask before proceeding package installations. No effect on non-interactive R sessions.
force	If TRUE then packages will always be installed, even if already present and with the correct version.
quiet	If TRUE the installations are performed more quietly (sets the quiet option to install.packages().
allDeps	Consider all dependencies when synchronizing, including recursive dependencies. This is currently only supported for origin="patRoonDeps". Note that handling of recursive dependencies currently are not influenced by the pkgs and ignorePkgs arguments.

Details

The installation of patRoon involves installing several dependencies, including R packages not available from common repositories (CRAN, BioConductor) and software outside the R environment. The following three functions automate this process and are used to install and maintain patRoon and its dependencies:

• install() Installs patRoon and any missing dependencies.

• update() Like install() and updates outdated packages.

• sync() Like update() but may also downgrade packages to fully synchronize package versions with the repository.

The R packages are currently sourced from the following repositories (set by the origin argument):

• "patRoonDeps": a specialized miniCRAN repository contains binary R packages with versions that are automatically tested with patRoon. Currently this is only supported for Windows.

• "runiverse": an r-universe repository containing the latest versions of patRoon and its dependencies.

• "regular": the last versions are sourced from regular CRAN/BioConductor repositories and GitHub. The latter means that suitable build tools (e.g. Rtools on windows).

Note that some large R packages, currently patRoonDeps, patRoonExt and MetaCleanData, are always sourced directly from GitHub.

Synchronization with sync() was mainly designed to be used in combination with the patRoonDeps repository, since it contains package versions already tested with patRoon. Doing a synchronization is most commonly used with patRoon bundle installations or when patRoon is installed in a separate R library (i.e. using the lib.loc argument). Furthermore, the allDeps argument should be set to TRUE to ensure all dependencies are synchronized.

Packages that originate from GitHub (even when obtained via patRoonDeps/runiverse) will also be synchronized with update(), since these packages typically involve 'snapshots' with unreliable version information.

Value

All functions return NULL invisibly.

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Manage legacy patRoon installations

Description

Toggles or removes installations of patRoon that were installed by the legacy installation script (install_patRoon.R).

Usage

toggleLegacy(enable = NULL, ask = TRUE)

removeLegacy(restoreRProfile = FALSE, ask = TRUE)

Arguments

enable	Enables (enable=TRUE), disables (enable=FALSE) or toggles (enable=NULL) a legacy patRoon installation.
ask	Set to TRUE to ask before proceeding. No effect on non-interactive R sessions.
restoreRProfile	If TRUE then the modifications to the user's .Rprofile file will be removed that were automatically performed by the legacy installation script.

Details

Previous versions of patRoon (⁠<2.3⁠) could be installed via a (now legacy) installation R script (install_patRoon.R). The functions documented here can (temporarily) undo the changes by this script, so that the installation functions in this package can be used to manage patRoon installations.

The toggleLegacy() function is used to enable or disable legacy installations temporarily.

The removeLegacy() function is used to undo legacy installations.

Value

All functions return NULL invisibly.

Background

This section is purely informative, but may be of use when you want to manually manage legacy installations.

The legacy installation script typically results in the following changes:

1. ⁠~/patRoon-install⁠: a directory with external dependencies (MetFrag, SIRIUS, ...) and may contain R packages from the patRoonDeps repository depending on user input during the installation.

2. ⁠~/.Rprofile-patRoon.R⁠: An R script that should be loaded during R startup, and initializes the configuration needed to use the files (1).

3. Code in ⁠~/.Rprofile⁠ to actually load (2) on R startup (only if it exists)

When toggleLegacy() is used to disable legacy installations the function simply renames the initialization script (2) so it won't be loaded on R startup. The removeLegacy() function removes the files from (1-2) and optionally the changes from (3).

Note

The R session should be restarted to make the changes effective.

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