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Install packages required by camtrapReport

Source: R/install_all.R
install-all.Rd

Install packages in camtrapReport's module inventory and additional packages requested through pkgs.

Usage

install_all(pkgs = NULL, update = FALSE, github = TRUE,
  gitlab = FALSE, ...)

# S4 method for class 'ANY'
install_all(pkgs = NULL, update = FALSE, github = TRUE, gitlab = FALSE, ...)

Arguments

pkgs

An optional character vector of additional package names. The default is NULL.

update

A logical value. If TRUE, optional packages are force-reinstalled. The default is FALSE.

github

A logical value (default TRUE) specifying whether packages configured in GitHub repositories are included.

gitlab

A logical value (default FALSE) specifying whether packages configured in GitLab repositories are included.

...

Additional named arguments passed to pak::pkg_install(), such as lib, ask, dependencies, or upgrade.

Value

Called for its side effects. The function returns NULL invisibly.

Details

The function checks the package list used by camtrapReport and installs packages that are not currently available. Packages configured as GitHub or GitLab dependencies are installed from their corresponding repositories. All package installation is handled by pak::pkg_install().

Unlike a direct call to pak, install_all() discovers package declarations in the installed report-module pool and any packaged configuration inventory. It does not inspect a project's copied module registry or an object's selected profile. Supply custom-module and other optional analytical requirements explicitly through pkgs; these are added to, not substituted for, the discovered inventory. It then delegates resolution and installation to pak. The function is opt-in and is never called when the package is loaded or a report is rendered.

install_All() is retained as a deprecated compatibility alias. New code should use install_all().

To inspect optional packages without installing anything, examine module YAML #| packages: declarations (see the module guide). Use pkgs[!vapply(pkgs, requireNamespace, logical(1), quietly = TRUE)] to check a character vector of package names. There is currently no dry_run argument; passing that name through ... is not a supported inspection API.

When update = TRUE, the requested optional packages are force-reinstalled from their configured sources using the pak reinstall parameter. Dependencies are upgraded only when required by the requested packages, unless upgrade = TRUE is supplied through ....

See also

camData(), report(), status()

Examples

# Inspect one module's optional packages without installing anything.
module_file <- system.file(
  "reportSections", "sampling.yml", package = "camtrapReport"
)
declaration <- grep(
  "#| packages:", readLines(module_file, warn = FALSE),
  value = TRUE, fixed = TRUE
)
pkgs <- trimws(strsplit(
  sub("#| packages:", "", declaration, fixed = TRUE), ","
)[[1]])
pkgs[!vapply(pkgs, requireNamespace, logical(1), quietly = TRUE)]
#> [1] "gt"

# Package installation changes the user's R library, so these examples are
# enabled only by a deliberate environment-variable opt-in.
if (interactive() && identical(Sys.getenv("CAMTRAPREPORT_INSTALL_EXAMPLE"), "true")) {
install_all()
install_all(pkgs = "readr")
install_all(update = TRUE)

# Reinstall the requested packages and also update their dependencies.
install_all(update = TRUE, upgrade = TRUE)
}