Package 'animovement'

Conflicts between the animovement and other packages

Description

This function lists all the conflicts among animovement packages and between animovement packages and other attached packages. It can also be used to check conflicts for any other attached packages.

Usage

animovement_conflicts(pkg = animovement_packages())

Arguments

pkg	character. A vector of packages to check conflicts for. The default is all animovement packages.

Value

An object of class 'animovement_conflicts': A named list of character vectors where the names are the conflicted objects, and the content are the names of the package namespaces containing the object, in the order they appear on the search path.

See Also

animovement

Examples

# Check conflicts between animovement packages and all attached packages
animovement_conflicts()

# Check conflicts among all attached packages
animovement_conflicts(sub("package:", "", search()[-1]))

---

List all animovement dependencies

Description

Lists all animovement dependencies and the local and CRAN versions of packages and dependencies.

Usage

animovement_deps(
  pkg = animovement_packages(),
  recursive = FALSE,
  repos = animovement_repos(),
  include.self = FALSE,
  check.deps = TRUE
)

Arguments

pkg	character vector of packages to check dependencies and versions of. The default is all animovement packages.
recursive	logical. TRUE recursively determines all packages required to operate these packages. FALSE will only list the packages and their direct dependencies.
repos	the repositories to use to check for updates. Defaults to animovement_repos(), which is getOption("repos") plus the R-universe the animovement packages are published on.
include.self	logical. TRUE also includes the animovement package and checks against the CRAN version.
check.deps	logical. FALSE will not determine dependencies but only display the update status of packages in pkg.

Value

A data frame giving the package names, the CRAN and local version, and a logical variable stating whether the local version is behind the CRAN version.

See Also

animovement_sitrep, animovement

Examples

# The packages the suite depends on, and their versions
head(animovement_deps())

# Including their dependencies in turn
nrow(animovement_deps(recursive = TRUE))

---

Detach animovement packages

Description

Detaches animovement packages, removing them from the search path.

Usage

animovement_detach(
  ...,
  unload = FALSE,
  force = FALSE,
  include.self = TRUE,
  session = FALSE
)

Arguments

...	comma-separated package names, quoted or unquoted, or vectors of package names. If left empty, all packages returned by animovement_packages are detached.
unload	logical. TRUE also unloads the packages using detach(name, unload = TRUE).
force	logical. should a animovement package be detached / unloaded even though other attached packages depend on it?
include.self	logical. TRUE also includes the animovement package - only applicable if ... is left empty.
session	logical. TRUE also removes the packages from options("animovement.extend"), so they will not be attached again with library(animovement) in the current session. If ... is left empty and include.self = TRUE, this will clear all animovement options set for the session.

Value

animovement_detach returns NULL invisibly.

See Also

animovement_extend, animovement

Examples

# Detach one package
animovement_detach(aniread)

# Detach the whole suite, and forget any session extensions
animovement_detach(session = TRUE)

---

Extend the animovement

Description

Loads additional packages as part of the animovement.

Usage

animovement_extend(
  ...,
  install = FALSE,
  check.conflicts = !isTRUE(getOption("animovement.quiet"))
)

Arguments

...	comma-separated package names, quoted or unquoted, or vectors of package names.
install	logical. Install packages not available?
check.conflicts	logical. Should conflicts between extension packages and attached packages be checked?

Details

When the animovement is extended calling animovement_extend(...), the packages that are not attached are attached, but conflicts are checked for all specified packages. An options("animovement.extend") is set which stores these extension packages, regardless of whether they were already attached or not. When calling animovement_packages, animovement_deps, animovement_conflicts, animovement_update, animovement_sitrep or animovement_detach, these packages are included as part of the animovement. To extend the animovement for the current session when it is not yet loaded, users can also set options(animovement.extend = c(...)), where c(...) is a character vector of package names, before calling library(animovement).

Value

animovement_extend returns NULL invisibly.

See Also

animovement_detach, animovement

Examples

# Add packages to your animovement for this session. They are attached, and
# their conflicts reported alongside the core packages.
animovement_extend(ggplot2, tidyr)

# Set the option before library(animovement) to extend on attach instead
options(animovement.extend = c("ggplot2", "tidyr"))

---

Install (missing) animovement packages

Description

This function (by default) checks if any animovement package is missing and installs the missing package(s).

Usage

animovement_install(
  ...,
  only.missing = TRUE,
  install = TRUE,
  repos = animovement_repos()
)

Arguments

...	comma-separated package names, quoted or unquoted, or vectors of package names. If left empty, all packages returned by animovement_packages are checked.
only.missing	logical. TRUE only installs packages that are unavailable. FALSE installs all packages, even if they are available.
install	logical. TRUE will proceed to install packages, whereas FALSE (recommended) will print the installation command asking you to run it in a clean R session.
repos	the repositories to install from. Defaults to animovement_repos(), which adds the animovement R-universe to getOption("repos").

Value

animovement_install returns NULL invisibly.

Note

There is also the possibility to set options(animovement.install = TRUE) before library(animovement), which will call animovement_install() before loading any packages to make sure all packages are available. If you are using a .animovement configuration file inside a project (see vignette), you can also place _opt_animovement.install = TRUE before the list of packages in that file.

See Also

animovement_update, animovement

Examples

# Install any ecosystem packages that are missing
animovement_install()

---

Download all suggested packages

Description

In animovement, we have a minimal dependency policy to keep the package light and fast to install. However, we rely on several packages for testing and specific features. These "soft dependencies" can be downloaded at once using this function, allowing you to fully utilize all of animovement's functionalities without errors.

Usage

animovement_install_suggested(package = "animovement")

animovement_show_suggested(package = "animovement")

Arguments

package

Character string specifying the package name. Currently only "animovement" is supported.

Details

To reduce the dependency load, animovement by default will not download all internally needed packages. It will ask the user to download them only if they are needed. The current function can help install all packages that animovement and its ecosystem packages might need. animovement_show_suggested() is a convenient helper to show the current list of suggested packages.

This function will check the Suggests field of animovement and all its imported packages (anicore, anispace, aniread, aniprocess, animetric, anicheck, anivis), excluding packages only needed for development or documentation workflows (knitr, rmarkdown, testthat, pak, here, covr, pkgdown, withr, ragg, curl, readxl, tibble, tinytable), and packages already required by an ecosystem package, which are installed regardless.

Under WebR, packages are installed with webr::install(), since utils::install.packages() cannot build Emscripten packages in the browser. Otherwise, if {pak} is installed then pak::pkg_install() is used, and failing that utils::install.packages(). Repositories searched are CRAN, the animovement R-universe and the Bioconductor R-universe – the last of which is where rhdf5 comes from.

Value

Invisible NULL. Used for side-effect of installing packages.

Examples

# listing all soft/weak dependencies
animovement_show_suggested()


# download all suggested packages
animovement_install_suggested("animovement")

---

List all packages in the animovement

Description

Core packages are first fetched from a project-level configuration file (named .animovement, if found), otherwise the standard set of core packages is returned. In addition, if extensions = TRUE, any packages used to extend the animovement for the current session are also returned.

Usage

animovement_packages(extensions = TRUE, include.self = TRUE)

Arguments

extensions	logical. TRUE appends the set of core packages with all packages found in options("animovement.extend").
include.self	logical. Include the animovement package in the list?

Value

A character vector of package names.

See Also

animovement_extend, animovement

Examples

animovement_packages()

---

Repositories to find animovement packages in

Description

The animovement packages are published on R-universe rather than CRAN, so getOption("repos") alone will not find them. This adds the R-universe to a repository vector unless it is already present, and is the default for animovement_deps, animovement_update and animovement_install.

Usage

animovement_repos(repos = getOption("repos"))

Arguments

repos

a repository vector to extend. Defaults to getOption("repos").

Details

A fresh R installation leaves CRAN set to the "@CRAN@" placeholder, which available.packages refuses to resolve. Any such entry is replaced with the CRAN cloud mirror. The CRAN entry is kept rather than dropped because the animovement dependencies live there.

Value

A named character vector of repository URLs.

See Also

animovement_update, animovement

Examples

animovement_repos()


# Make it apply to install.packages() and friends for the whole session
old <- options(repos = animovement_repos())
getOption("repos")
options(old)

---

Get a situation report on the animovement

Description

This function gives a quick overview of the version of R and all animovement packages (including availability updates for packages) and indicates whether any project-level configuration files are used.

Usage

animovement_sitrep(...)

Arguments

...	arguments other than pkg passed to animovement_deps.

Value

animovement_sitrep returns NULL invisibly.

See Also

animovement_deps, animovement

Examples

# Versions of every animovement package, and whether any are behind
animovement_sitrep()

---

Update animovement packages

Description

This will check all animovement packages (and their dependencies) for updates and (optionally) install those updates.

Usage

animovement_update(..., install = FALSE, repos = animovement_repos())

Arguments

...	arguments passed to animovement_deps.
install	logical. TRUE will proceed to install outdated packages, whereas FALSE (recommended) will print the installation command asking you to run it in a clean R session.
repos	the repositories to check against and install from. Defaults to animovement_repos(), which adds the animovement R-universe to getOption("repos").

Value

animovement_update returns NULL invisibly.

See Also

animovement_deps, animovement

Examples

# Report which packages are behind, without changing anything
animovement_update()

# Pass install = TRUE to actually install what is out of date
animovement_update(install = TRUE)

---