pkg_refs: Package references

In pkgdepends: Package Dependency Resolution and Downloads

Package references

Description

A package reference (ref) specifies a location from which an R package can be obtained from. The full syntax of a reference is type::ref, but type can be often omitted, the common ref types have shortcuts.

Package references

Many pkgdepends and pak functions take package names as arguments. E.g. pak::pkg_install() takes the names of the packages to install, pak::pkg_deps_tree() takes the names of the packages to draw dependency trees for.

Most of these function can also take a more generic package reference instead of a package name. A package reference also tells pkgdepends where to find the package, the package source.

To specify a package source, use its name as a prefix, with a :: separator. E.g. cran::mypkg means the mypkg package from CRAN.

A package name is a special package reference, that implicitly specifies the configured CRAN(-like) repositories as the package source. (We call this the standard package source.) So mypkg is equivalent to standard::mypkg and pak look for mypkg in any of the configured CRAN-like repositories. If you did not explicitly specify any CRAN-like repositories (e.g. with options("repos")), then pak uses the CRAN and Bioconductor repositories by default.

This is the list of the currently supported package sources. We will discuss each in detail below.

• cran: a CRAN package.

• bioc: a Bioconductor package.

• standard: a package from a configured CRAN-like repository.

• github: a package from GitHub.

• gitlab: a package from GitLab.

• git: a package in a git repository.

• local: a local package file or directory.

• url: an URL that points to a package archive.

• installed an installed package.

• deps the dependencies of a local package file or directory.

• any a special reference type that accepts a package from any source. See below.

• param a special reference to change how other references are downloaded or installed. See "Parameters" below.

Shorthands

To save typing, you do not always need to fully specify the package source in a package reference. You have seen before that a package name implicitly has a standard package source. Here are the complete rules for such shorthands, in the order they are applied:

• If the ref is a valid package name, or a package name with a @ version specification, the standard package source is used. E.g. pkg is equivalent to standard::pkg and ⁠pkg@1.0⁠ is equivalent to ⁠standard::pkg@1.0⁠.

• If the ref is a valid github ref type without the ⁠github::⁠ prefix, then github is used. E.g. user/repo is equivalent to github::user/repo and user/repo@tag is equivalent to github::user/repo@tag, etc.

• If the ref is a GitHub URL (see below) without the ⁠github::⁠ prefix, then github is used.

• If the ref is a path that starts with . or / or ⁠\⁠ or ~ then local is used. (pkgdepends does not check if the path exists.)

• If a package reference if of the form ⁠<package-name>=?<parameters>⁠, then it will be the special param type. See "Parameters" below.

If the package reference does not have an explicit package source, and the package source cannot be determined from these rules, then pkgdepends throws an error.

Package names

When pkgdepends is looking up the dependencies of a package, it needs to be able to determine the name of the dependency from the package reference. This is sometimes not easy for dependencies in Remotes (or similar) fields.

• For ⁠github::⁠ and ⁠gitlab::⁠ dependencies pkgdepends assumes that the package name is the same as the name of the repository. If this does not hold, then you need to specify the package name explicitly, using a ⁠<package>=⁠ prefix. E.g. pins=rstudio/pins-r. If you specify both the package source type and the package name, the package name comes first: pins=github::rstudio/pins-r.

• For ⁠git::⁠ dependencies, pkgdepends assumes that the package name is the same as the last component of the repository. If this does not hold, then you need to specify the package name explicitly, using a ⁠<package>=⁠ prefix. E.g. ⁠pins=git::https://github.com/rstudio/pins-r⁠.

• For ⁠local::⁠ dependencies, you always need to specify the package name explicitly. E.g. ⁠pins=local::~/works/pins⁠.

• For ⁠url::⁠ dependencies, you always need to specify the package name explicitly. E.g. ⁠ggplot2=url::https://cloud.r-project.org/src/contrib/...⁠.

Parameters

Package references may have optional parameters, added after a question mark. Different parameters are separated by an ampersand (&) character. (This is very similar to how HTTP URLs take query parameters.)

Parameters may be flags that turn on some behavior, or they can have a string value, assigned with an equal sign (=). If no value is assigned, then we assume the true value. For example these two package refs are equivalent:

cran::testthat?source&nocache
cran::testthat?source=true&nocache=true

Parameters for downstream packages

pkgdepends allows specifying parameters for downstream packages, using the ⁠<package>=?<params>⁠ special package reference, where package is the name of the package, and ⁠<params>⁠ are the parameters, as above. This is useful if you want to add a parameter to a downstream dependency.

For example, to install ggplot2, and always reinstall its cli package dependency you could use the ggplot2 and cli=?reinstall package references. The latter tells pkgdepends to always reinstall cli, even if it is already installed.

Currently supported parameters

• ignore is a flag parameter. If specified, the package is ignored. This usually makes sense in the packagename=?ignore form, to ignore a downstream soft dependency. If all versions of a hard dependency are ignored that will lead to a solution error.

• ignore-before-r is a version number parameter. The package will be ignored on R versions that are older than the specified one. E.g. ⁠Matrix=?ignore-before-r=4.1.2⁠ will ignore the Matrix package on R versions that are older than 4.1.2. This parameter really only makes sense in the packgename=?ignore form.

• source is a flag parameter. If specified, then a source R package is requested from a CRAN-like repository. For package installations source always triggers a re-install. In other words, source implies the reinstall parameter. This parameter is supported for ⁠bioc::⁠, ⁠cran::⁠ and ⁠standard::⁠ remote types, and it is ignored for others.

• reinstall requests a re-install for package installations. It is supported by the ⁠bioc::⁠, ⁠cran::⁠, ⁠git::⁠, ⁠github::⁠, ⁠gitlab::⁠, ⁠local::⁠, ⁠standard::⁠, and ⁠url::⁠ remote types.

• nocache will ignore the package cache. It will always download the package file, and it will not add the downloaded (and built) package(s) to the package cache. It is supported by the ⁠bioc::⁠, ⁠cran::⁠, ⁠git::⁠, ⁠github::⁠, ⁠gitlab::⁠, ⁠standard::⁠ and ⁠url::⁠ remote types.

Package source details

CRAN packages (⁠cran::⁠)

A package from CRAN. Full syntax:

[cran::]<package>[@[>=]<version> | @current | @last]

• ⁠<package>⁠ is a valid package name.

• ⁠<version>⁠ is a version or a version requirement.

Examples:

forecast
forecast@8.8
forecast@>=8.8
cran::forecast
forecast@last
forecast@current

Note: pkgdepends currently parses the version specification part (everything after @), but does not use it.

Bioconductor packages (⁠bioc::⁠)

A package from Bioconductor. The syntax is the same as for CRAN packages, except for the prefix.

[bioc::]<package>[@[>=]<version> | @current | @last]

Standard packages (⁠standard::⁠)

These are packages either from CRAN or Bioconductor, the full syntax is the same as for CRAN packages, except for the prefix:

[standard::]<package>[@[>=]<version> | current | last]

GitHub packages (⁠github::⁠)

Packages from a GitHub repository. Full syntax:

[<package>=][github::]<username>/<repository>[/<subdir>][<detail>]

• ⁠<package>⁠ is the name of the package. If this is missing, then the name of the repository is used.

• ⁠<username>⁠ is a GitHub username or organization name.

• ⁠<repository>⁠ is the name of the repository.

• ⁠<subdir>⁠ optional subdirectory, if the package is within a subdirectory in the repository.

• ⁠<detail>⁠ specifies a certain version of the package, see below.

⁠<detail>⁠ may specify:

• a git branch, tag or (prefix of) a commit hash: ⁠@<commitish>⁠;

• a pull request: ⁠#<pull-request>⁠; or

• the latest release: ⁠@*release⁠.

If ⁠<detail>⁠ is missing, then the latest commit of the default branch is used.

Examples:

r-lib/crayon
github::r-lib/crayon
r-lib/crayon@84be6207
r-lib/crayon@branch
r-lib/crayon#41
r-lib/crayon@release

For convenience GitHub HTTP URLs can also be used to specify a package from GitHub. Examples:

https://github.com/r-lib/withr
# A branch:
https://github.com/r-lib/withr/tree/ghactions
# A tag:
https://github.com/r-lib/withr/tree/v2.1.1
# A commit:
https://github.com/r-lib/withr/commit/8fbcb548e316
# A pull request:
https://github.com/r-lib/withr/pull/76
# A release:
https://github.com/r-lib/withr/releases/tag/v2.1.0

A GitHub remote string can also be used instead of an URL, for example: [e-mail]:r-lib/pak.git

GitLab packages (⁠gitlab::⁠)

Packages from a GitLab repository. Full syntax:

[<package>=][github::]<username>/<repository>[/<subdir>][<detail>]

• ⁠<package>⁠ is the name of the package. If this is missing, then the name of the repository is used.

• ⁠<username>⁠ is a GitLab username or group name.

• ⁠<repository>⁠ is the name of the repository.

• ⁠<subdir>⁠ optional subdirectory, if the package is within a subdirectory in the repository.

• ⁠<detail>⁠ may specify a git branch, tag or (prefix of) a commit hash.

If ⁠<detail>⁠ is missing, then the latest commit of the default branch is used.

Examples:

gitlab::gaborcsardi/cli
gitlab::r-hub/filelock@main

Packages in git repositories (⁠git::⁠)

Full syntax:

[<package>=]git::https?://<host>[<detail>]

• ⁠<package>⁠ is the name of the package. If this is missing, then the last component of the ⁠<host>⁠ is used.

• ⁠<host>⁠ host name and path of the git repository. Some git repositories need the .git suffix here, others are more forgiving.

• ⁠<detail>⁠ specifies a certain version of the package: a git branch, tag or (prefix of) a commit hash: ⁠@<commitish>⁠.

If ⁠<detail>⁠ is missing, then the latest commit of the default branch is used.

Examples:

git::https://github.com/r-lib/crayon
git::https://github.com/r-lib/crayon.git
git::https://github.com/r-lib/crayon.git@84be6207
git::https://github.com/r-lib/crayon.git@branch
git::https://gitlab.com/gaborcsardi/cli.git

Note that pkgdepends has a built-in git client, and does not require a system git installation.

If the system has git installed, then pkgdepends will use the credentials stored in the configured git credential store, automatically, via the gitcreds package.

Local packages (⁠local::⁠)

A path that refers to a package file built with ⁠R CMD build⁠, or a directory that contains a package. Full syntax:

local::<path>

For brevity, you can omit the ⁠local::⁠ prefix, if you specify an absolute path, a path from the user's home directory, starting with ~, or a relative path starting with ⁠./⁠ or ⁠.\\⁠.

A single dot (".") is considered to be a local package in the current working directory.

Examples:

local::/foo/bar/package_1.0.0.tar.gz
local::/foo/bar/pkg
local::.
/absolute/path/package_1.0.0.tar.gz
~/path/from/home
./relative/path
.

If you specify a local package in a dependency (i.e. in DESCRIPTION), then you also need to specify the name of the package, see "Package names" above.

URLs (⁠url::⁠)

You can use ⁠url::⁠ to refer to URLs that hold R package archives (i.e. properly built with ⁠R CMD build⁠), or compressed directories of package trees (i.e. not built with ⁠R CMD build⁠). pkgdepends will figure out if it needs to run ⁠R CMD build⁠ on the package first.

This remote type supports .tar.gz and .zip files.

Note that URLs are not ideal remote types, because pkgdepends needs to download the package file to resolve its dependencies. When this happens, it puts the package file in the cache, so no further downloads are needed when installing the package later.

Examples:

url::https://cloud.r-project.org/src/contrib/Archive/cli/cli_1.0.0.tar.gz
url::https://github.com/tidyverse/stringr/archive/HEAD.zip

If you specify a package from an URL in a dependency (i.e. in DESCRIPTION), then you also need to specify the name of the package, see "Package names" above.

Installed packages (⁠installed::⁠)

This is usually used internally, but can also be used directly. Full syntax:

installed::<path>/<package>

• ⁠<path>⁠ is the library the package is installed to.

• ⁠<package>⁠ is the package name.

Example:

installed::~/R/3.6/crayon

Package dependencies (⁠deps::⁠)

Usually used internally, it specifies the dependencies of a local package. It can be used to download or install the dependencies of a package, without downloading or installing the package itself. Full syntax:

deps::<path>

Examples:

deps::/foo/bar/package_1.0.0.tar.gz
deps::/foo/bar/pkg
deps::.

⁠any::⁠ packages

Sometimes you need to install additional packages, but you don't mind where they are installed from. Here is an example. You want to install cli from GitHub, from r-lib/cli. You also want to install glue, and you don't mind which version of glue is installed, as long as it is compatible with the requested cli version. If cli specifies the development version of glue, then that is fine. If cli is fine with the CRAN version of glue, that's OK, too. If a future version of cli does not depend on glue, you still want glue installed, from CRAN. The ⁠any::⁠ reference type does exactly this.

In our example you might write

pak::pkg_install(c("glue", "r-lib/cli"))

first, but this will fail if rlib/cli requests (say) tidyverse/glue, because in pkg_install() "glue" is interpreted as "standard::glue", creating a conflict with tidyverse/glue. On the other hand

pak::pkg_install(c("any::glue", "r-lib/cli"))

works, independently of which glue version is requested by cli.

Parameter refs (⁠param::⁠)

See "Parameters" above.

The Remotes field

In the DESCRIPTION file of an R package you can mark any regular dependency defined in the Depends, Imports, Suggests or Enhances fields as being installed from a non-standard package source by adding a package reference to a Remotes entry. pkgdepends will download and install the package from the from the specified location, instead of a CRAN-like repository.

The remote dependencies specified in Remotes is a comma separated list of package sources:

Remotes: <pkg-source-1>, <pkg-source-2>, [ ... ]

Note that you will still need add the package to one of the regular dependency fields, i.e. Imports, Suggests, etc. Here is a concrete example that specifies the r-lib/glue package:

Imports: glue
Remotes: r-lib/glue,
  r-lib/httr@v0.4,
  klutometis/roxygen#142,
  r-lib/testthat@c67018fa4970

The CRAN and Bioconductor repositories do not support the Remotes field, so you need to remove this field, before submitting your package to either of them.

pkgdepends documentation built on Nov. 10, 2023, 5:06 p.m.