Site built with pkgdown 2.1.1.
+Site built with pkgdown 2.1.1.9000.
diff --git a/authors.html b/authors.html index 8c755060e..e586e9669 100644 --- a/authors.html +++ b/authors.html @@ -1,5 +1,5 @@ -Site built with pkgdown 2.1.1.
+Site built with pkgdown 2.1.1.9000.
diff --git a/pkgdown.yml b/pkgdown.yml index fdb8fda7a..291a3ad27 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,8 +1,8 @@ pandoc: 3.1.11 -pkgdown: 2.1.1 -pkgdown_sha: ~ +pkgdown: 2.1.1.9000 +pkgdown_sha: dfa28bef27858bd442334b5cce8f645d555914be articles: {} -last_built: 2024-11-06T10:33Z +last_built: 2024-12-03T21:49Z urls: reference: https://pak.r-lib.org/reference article: https://pak.r-lib.org/articles diff --git a/reference/cache.html b/reference/cache.html index 480ef4ca1..ec85dddd6 100644 --- a/reference/cache.html +++ b/reference/cache.html @@ -1,5 +1,5 @@ -Site built with pkgdown 2.1.1.
+Site built with pkgdown 2.1.1.9000.
diff --git a/reference/features.html b/reference/features.html index 84b77bf80..beee5a88a 100644 --- a/reference/features.html +++ b/reference/features.html @@ -1,5 +1,5 @@ -stable, rc and Data frame the contains data about the packages installed in the library. -include_docs("pkgdepends", "docs/lib-status-return.rds")
+It has always has columns: +biocviews: the corresponding field from DESCRIPTION, it must be
+present for all Bioconductor packages, other packages typically don't
+have it.
built: the Built field from DESCRIPTION.
depends, suggests, Imports, linkingto, enhances: the corresponding
+fields from the DESCRIPTION files.
deps: A list or data frames, the dependencies of the package. It has
+columns: ref, type (dependency type in lowercase), package
+(dependent package, or R), op and version, for last two are for
+version requirement. op can be >=, >, == or <=, although the
+only the first one is common in practice.
library: path to the package library containing the package.
license: from DESCRIPTION.
md5sum: from DESCTIPTION, typically NA, except on Windows.
needscompilation: from DESCRIPTION, this column is logical.
package: package name.
platform: from the Built field in DESCRIPTION, the current platform
+if missing from DESCRIPTION.
priority: from DESCRIPTION, usually base, recommended, or missing.
ref: the corresponding installed::* package reference.
repository: from DESCRIPTION. For packages from a CRAN repository this
+is CRAN, some other repositories, e.g. R-universe adds the repository
+URL here.
repotype: cran, bioc or missing.
rversion: from the Built field. If no such field, then the current
+R version.
sysreqs: the SystemRequirements field from DESCRIPTION.
title: package title.
type: always installed.
version: package version (as string).
DESCRIPTION, but
+pak also adds a couple.
+In addition, it also has all remote* and config/needs/* entries from
+the DESCRIPTION files. (Case insensitive.)
All columns are of type character, except for needscompilation, which
+is logical and deps, which is a list columns.
If an entry is missing for a package, it is set to NA.
Note that column names are lowercase, even if the corresponding entries
+are not in DESCRIPTION.
The order of the columns is not deterministic, so don't assume any order.
Additional columns might be present, these are internal for +pak and should not be used in user code.
Site built with pkgdown 2.1.1.
+Site built with pkgdown 2.1.1.9000.
diff --git a/reference/lockfile_create.html b/reference/lockfile_create.html index 177f06042..6474ed1d1 100644 --- a/reference/lockfile_create.html +++ b/reference/lockfile_create.html @@ -1,5 +1,5 @@ -include_docs("pkgdepends", "docs/deps.rds")
+R packages may have various types of dependencies, see +Writing R Extensions.pak groups dependencies into three groups: +
hard dependencies: "Depends", "Imports", and "LinkingTo",
soft dependencies: "Suggests" and "Enhances",
extra dependencies, see below.
utils::install.packages() interprets its
+dependencies argument.You typically use one of these values:
+NA or "hard" to install a package and its required dependencies,
TRUE to install all required dependencies, plus optional and development
+dependencies.
dependencies argument are:
+TRUE: This means all hard dependencies plus Suggests for
+direct installations, and hard dependencies only for dependent
+packages.
FALSE: no dependencies are installed at all.
NA (any atomic type, so NA_character_, etc. as well): only hard
+dependencies are installed.
If a list with two entries named direct and indirect, it is taken
+as the requested dependency types, for direct installations and
+dependent packages.
If a character vector, then it is taken as the dependency types +for direct installations, and the hard dependencies are +used for the dependent packages.
"hard" is included in the value or a list element, then it is replaced
+by the hard dependency types.
+If "soft" or "all" is included, then it is replaced by all
+hard and soft dependency.
+pak supports extra dependency types for direct
+installations not from CRAN-like repositories.
+These are specified with a Config/Needs/ prefix in the DESCRIPTION
+and they can contain package references, separated by commas.
+For example you can specify packages that are only needed for the
+pkgdown website of the package:
To use these dependency types, you need to specify them in the
+dependencies argument to
+pak functions.
Note that Config/Needs/* fields are currently not used from CRAN
+packages, and packages in CRAN-like repositories in general.
Usually you specify that a Config/Needs/* dependency type should be
+installed together with "hard" or "all", to install all hard or
+soft dependencies as well.
doc_config()
- +‘cache_dir’: (Env var: PKG_CACHE_DIR, option: pkg.cache_dir.) Directory to download the packages to. Defaults to a temporary
+directory within the R session temporary directory, see
+base::tempdir().
‘cran_mirror’: (Env var: PKG_CRAN_MIRROR, option: pkg.cran_mirror.) CRAN mirror to use. Defaults to the repos option
+(see base::options()), if that's not set then
+https://cran.rstudio.com. See also pak::repo_add() and
+pak::repo_get()
‘git_submodules’: (Env var: PKG_GIT_SUBMODULES, option: pkg.git_submodules.) Whether or not to update submodules in git repositories. This
+affects git:: and gitlab:: package sources only.
+If the R package is in a subdirectory then only the submodules
+within that directory are updated. If a submodule appears in
+.Rbuildignore, then it is skipped.
‘include_linkingto’: (Env var: PKG_INCLUDE_LINKINGTO, option: pkg.include_linkingto.) Whether to always include LinkingTo dependencies in the solution
+of and installation, even if they are needed because the packages
+are installed from binaries. This is sometimes useful, see e.g.
+https://github.com/r-lib/pak/issues/485 for an example use case.
‘library’: (Env var: PKG_LIBRARY, option: pkg.library.) Package library to install packages to. It is also used for
+already installed packages when considering dependencies.
‘metadata_cache_dir’: (Env var: PKG_METADATA_CACHE_DIR, option: pkg.metadata_cache_dir.) Location of metadata replica of
+pkgcache::cranlike_metadata_cache. Defaults to a temporary
+directory within the R session temporary directory, see
+base::tempdir().
‘metadata_update_after’: (Env var: PKG_METADATA_UPDATE_AFTER, option: pkg.metadata_update_after.) A time interval as a difftime object. pak will update the
+metadata cache if it is older than this. The default is one day.
+The PKG_METADATA_UPDATE_AFTER environment variable may be set
+in seconds (s suffix), minutes (m suffix), hours (h suffix),
+or days (d suffix). E.g: 1d means one day.
‘package_cache_dir’: (Env var: PKG_PACKAGE_CACHE_DIR, option: pkg.package_cache_dir.) Location of the package cache on the disk. See
+pak::cache_summary(). Default is selected by pkgcache.
‘platforms’: (Env var: PKG_PLATFORMS, option: pkg.platforms.) Character vector of platforms to download or install packages
+for. See pkgdepends::default_platforms() for possible platform
+names. Defaults to the platform of the current R session, plus
+"source".
‘r_versions’: (Env var: PKG_R_VERSIONS, option: pkg.r_versions.) Character vector, R versions to download or install
+packages for. It defaults to the current R version.
‘sysreqs’: (Env var: PKG_SYSREQS, option: pkg.sysreqs.) Whether to automatically look up and install system requirements.
+If TRUE, then pkgdepends will try to install required
+system packages. If FALSE, then system requirements are still
+printed (including OS packages on supported platforms), but they
+are not installed.
+By default it is TRUE on supported platforms,
+if the current user is the root user or password-less sudo is
+configured for the current user.
‘sysreqs_db_update’: (Env var: PKG_SYSREQS_DB_UPDATE, option: pkg.sysreqs_db_update.) Whether to try to update the system requirements database from
+GitHub. If the update fails, then the cached or the build-in
+database if used. Defaults to TRUE.
‘sysreqs_db_update_timeout’: (Env var: PKG_SYSREQS_DB_UPDATE_TIMEOUT, option: pkg.sysreqs_db_update_timeout.) Timeout for the system requirements database update.
+Defaults to five seconds.
‘sysreqs_dry_run’: (Env var: PKG_SYSREQS_DRY_RUN, option: pkg.sysreqs_dry_run.) If TRUE, then pak only prints the system commands to
+install system requirements, but does not execute them.
‘sysreqs_platform’: (Env var: PKG_SYSREQS_PLATFORM, option: pkg.sysreqs_platform.) The platform to use for system requirements lookup. On Linux, where
+system requirements are currently supported, it must be a string
+containing the distribution name and release, separated by a dash.
+E.g.: "ubuntu-22.04", or "rhel-9".
‘sysreqs_rspm_repo_id’: (Env var: PKG_SYSREQS_RSPM_REPO_ID, option: pkg.sysreqs_rspm_repo_id.) Posit Package Manager (formerly RStudio Package Manager) repository
+id to use for CRAN system requirements lookup. Defaults to the
+RSPM_REPO_ID environment variable, if set. If not set, then it
+defaults to 1.
‘sysreqs_rspm_url’: (Env var: PKG_SYSREQS_RSPM_URL, option: pkg.sysreqs_rspm_url.) Root URL of Posit Package Manager (formerly RStudio Package
+Manager) for system requirements lookup. By default the RSPM_ROOT
+environment variable is used, if set. If not set,
+it defaults to https://packagemanager.posit.co.
‘sysreqs_sudo’: (Env var: PKG_SYSREQS_SUDO, option: pkg.sysreqs_sudo.) Whether to use sudo to install system requirements,
+on Unix. By default it is TRUE on Linux if the effective user id
+of the current process is not the root user.
‘sysreqs_update’: (Env var: PKG_SYSREQS_UPDATE, option: pkg.sysreqs_update.) Whether to try to update system packages that are already installed.
+It defaults to TRUE on CI systems: if the CI environment
+variable is set to true.
‘sysreqs_verbose’: (Env var: PKG_SYSREQS_VERBOSE, option: pkg.sysreqs_verbose.) Whether to echo the output of system requirements installation.
+Defaults to TRUE if the CI environment variable is set.
‘use_bioconductor’: (Env var: PKG_USE_BIOCONDUCTOR, option: pkg.use_bioconductor.) Whether to automatically use the Bioconductor repositories.
+Defaults to TRUE.
‘windows_archs’: (Env var: PKG_WINDOWS_ARCHS, option: pkg.windows_archs.) Character scalar specifying which architectures
+to download/install for on Windows. Its possible values are:
"prefer-x64": Generally prefer x64 binaries. If the current R
+session is x64, then we download/install x64 packages.
+(These packages might still be multi-architecture binaries!)
+If the current R session is i386, then we download/install
+packages for both architectures. This might mean compiling
+packages from source if the binary packages are for x64 only,
+like the CRAN Windows binaries for R 4.2.x currently.
+"prefer-x64" is the default for R 4.2.0 and later.
"both": Always download/install packages for both i386 and
+x64 architectures. This might need compilation from source
+if the available binaries are for x64 only, like the CRAN
+Windows binaries for R 4.2.x currently. "both" is the default
+for R 4.2.0 and earlier.
include_docs("pkgdepends", "docs/pkg-refs.rds", top = FALSE)
+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 pak 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.
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. (pak 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 +pak throws an error.
+When pak 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 pak 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, pak 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/....
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:
pak 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 pak to always reinstall cli, even if
+it is already installed.
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.
ignore-unavailable is a flag. It can only be specified for soft
+dependencies. If specified and the package is not available, it will be
+ignored. This parameter really only makes sense in the
+packagename=?ignore-unavailable 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.
cran::)A package from CRAN. Full syntax:
+<package> is a valid package name.
<version> is a version or a version requirement.
Examples:
+ +Note: pak currently parses the version specification part
+(everything after @), but does not use it.
bioc::)A package from Bioconductor. The syntax is the same as for CRAN packages, +except for the prefix.
+ +standard::)These are packages either from CRAN or Bioconductor, the full syntax +is the same as for CRAN packages, except for the prefix:
+ +github::)Packages from a GitHub repository. Full syntax:
+<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@releaseFor 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/v2.1.0A GitHub remote string can also be used instead of an URL, for example:
+git@github.com:r-lib/pak.git
gitlab::)Packages from a GitLab repository. Full syntax:
+<package> is the name of the package. If this is missing, then
+the name of the repository is used.
<project-path> is a typically the GitLab username or group name, but
+it may contain subgroups.
<repository> is the name of the repository, or the project in GitLab
+terminology.
<subdir> optional subdirectory, if the package is within a
+subdirectory in the repository. Note that for GitLab, this must come
+after a /- prefix, to be able to distinguish it from subgroups.
<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.
gitlab:: supports git submodules, see the git-submodules configuration
+entry.
Examples:
+ +git::)Full syntax:
+<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.
git:: supports git submodules, see the git-submodules configuration
+entry.
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.gitNote that pak has a built-in git client, and does +not require a system git installation.
+If the system has git installed, then pak will use the +credentials stored in the configured git credential store, automatically, +via the gitcreds package.
+local::)A path that refers to a package file built with R CMD build, or a
+directory that contains a package. Full syntax:
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.
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). pak 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 pak 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.zipIf 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::)This is usually used internally, but can also be used directly. +Full syntax:
+<path> is the library the package is installed to.
<package> is the package name.
Example:
+ +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:
+ +Examples:
+ +any:: packagesSometimes 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.
+Remotes fieldIn 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.
+pak 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:
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@c67018fa4970The 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.
A data frame with the dependency data, it includes pkg
as well. It has the following columns.
-include_docs("pkgdepends", "docs/resolution-result.rds")
built: the Built field from the DESCRIPTION file of binary
+packages, for which this information is available.
cache_status: whether the package file is in the package cache.
+It is NA for installed:: package refs.
dep_types: character vector of dependency types that were
+considered for this package. (This is a list column.)
deps: dependencies of the package, in a data frame. See
+"Package dependency tables" below.
direct: whether this package (ref, really) was directly specified,
+or added as a dependency.
error: this is a list column that contains error objects for the
+refs that pkgdepends failed to resolve.
filesize: the file size in bytes, or NA if this information is
+not available.
license: license of the package, or NA if not available.
md5sum: MD5 checksum of the package file, if available, or NA if
+not.
metadata: a named character vector. These fields will be (should be)
+added to the installed DESCRIPTION file of the package.
mirror: URL of the CRAN(-like) mirror site where the metadata was
+obtained from. It is NA for non-CRAN-like sources, e.g. local files,
+installed packages, GitHub, etc.
needscompilation: whether the package needs compilation.
package: package name.
priority: this is "base" for base packages, "recommended" for
+recommended packages, and NA otherwise.
ref: package reference.
remote: the parsed remote_ref objects, see parse_pkg_refs().
+This is a list column.
repodir: the directory where this package should be in a CRAN-like
+repository.
sha256: SHA256 hash of the package file, if available, otherwise
+NA.
sources: URLs where this package can be downloaded from. This is not
+necessarily a URL that you can download with a HTTP client. E.g. for
+local:: refs it is a path, and for git:: refs it is a URL for git.
+It is a zero length vector for installed:: refs.
status: status of the dependency resolution, "OK" or "FAILED".
target: path where this package should be saved in a CRAN-repository.
type: ref type.
version: package version.
direct (logical),
+needscompilation (logical), filesize (integer), deps (list column, see
+"Package dependency tables" below), sources (list of character vectors),
+remote (list), error (list), metadata (list), dep_types (list).
+A package dependency tables in the deps list column have five columns
+currently:
ref: the package ref of the dependency.
type: the dependency type, in all lowercase. I.e. imports,
+suggests, etc.
package: package name of the dependency.
op: operator for version requirements, e.g. >=.
version: version number, for version requirements.
Data frame with information about the downloaded packages, invisibly. Columns: -include_docs("pkgdepends", "docs/download-result.rds")
+built: the Built field from the DESCRIPTION file of binary
+packages, for which this information is available.
cache_status: whether the package file is in the package cache.
+It is NA for installed:: package refs.
dep_types: character vector of dependency types that were
+considered for this package. (This is a list column.)
deps: dependencies of the package, in a data frame. See
+"Package dependency tables" below.
direct: whether this package (ref, really) was directly specified,
+or added as a dependency.
error: this is a list column that contains error objects for the
+refs that pkgdepends failed to resolve.
filesize: the file size in bytes, or NA if this information is
+not available.
license: license of the package, or NA if not available.
md5sum: MD5 checksum of the package file, if available, or NA if
+not.
metadata: a named character vector. These fields will be (should be)
+added to the installed DESCRIPTION file of the package.
mirror: URL of the CRAN(-like) mirror site where the metadata was
+obtained from. It is NA for non-CRAN-like sources, e.g. local files,
+installed packages, GitHub, etc.
needscompilation: whether the package needs compilation.
package: package name.
priority: this is "base" for base packages, "recommended" for
+recommended packages, and NA otherwise.
ref: package reference.
remote: the parsed remote_ref objects, see parse_pkg_refs().
+This is a list column.
repodir: the directory where this package should be in a CRAN-like
+repository.
sha256: SHA256 hash of the package file, if available, otherwise
+NA.
sources: URLs where this package can be downloaded from. This is not
+necessarily a URL that you can download with a HTTP client. E.g. for
+local:: refs it is a path, and for git:: refs it is a URL for git.
+It is a zero length vector for installed:: refs.
status: status of the dependency resolution, "OK" or "FAILED".
target: path where this package should be saved in a CRAN-repository.
type: ref type.
version: package version.
fulltarget: absolute path to the downloaded file. At most one of
+fulltarget and fulltarget_tree must exist on the disk.
fulltarget_tree: absolute path to a package tree directory. At most
+one of fulltarget and fulltarget_tree must exist on the disk.
download_status: "Had" or "Got", depending on whether the file
+was obtained from the cache.
download_error: error object for failed downloads.
file_size: Size of the file, or NA. For installed:: refs, it is
+NA, and it is also NA for refs that created fulltarget_tree
+instead of fulltarget.
fulltarget, if it exists, contains a packaged (via R CMD build)
+source R package. If fulltarget_tree exists, it is a package tree
+directory, that still needs an R CMD build call.Additional columns might be present. They are either used internally or
+they are experimental. They might be removed or changed at any time.All columns are of type character, except for direct (logical),
+needscompilation (logical), filesize (integer), deps (list column, see
+"Package dependency tables" below), sources (list of character vectors),
+remote (list), error (list), metadata (list), dep_types (list).
+A package dependency tables in the deps list column have five columns
+currently:
ref: the package ref of the dependency.
type: the dependency type, in all lowercase. I.e. imports,
+suggests, etc.
package: package name of the dependency.
op: operator for version requirements, e.g. >=.
version: version number, for version requirements.
Data frame with data about installations of pkg.
-include_docs("pkgdepends", "docs/lib-status-return.rds")
biocviews: the corresponding field from DESCRIPTION, it must be
+present for all Bioconductor packages, other packages typically don't
+have it.
built: the Built field from DESCRIPTION.
depends, suggests, Imports, linkingto, enhances: the corresponding
+fields from the DESCRIPTION files.
deps: A list or data frames, the dependencies of the package. It has
+columns: ref, type (dependency type in lowercase), package
+(dependent package, or R), op and version, for last two are for
+version requirement. op can be >=, >, == or <=, although the
+only the first one is common in practice.
library: path to the package library containing the package.
license: from DESCRIPTION.
md5sum: from DESCTIPTION, typically NA, except on Windows.
needscompilation: from DESCRIPTION, this column is logical.
package: package name.
platform: from the Built field in DESCRIPTION, the current platform
+if missing from DESCRIPTION.
priority: from DESCRIPTION, usually base, recommended, or missing.
ref: the corresponding installed::* package reference.
repository: from DESCRIPTION. For packages from a CRAN repository this
+is CRAN, some other repositories, e.g. R-universe adds the repository
+URL here.
repotype: cran, bioc or missing.
rversion: from the Built field. If no such field, then the current
+R version.
sysreqs: the SystemRequirements field from DESCRIPTION.
title: package title.
type: always installed.
version: package version (as string).
DESCRIPTION, but
+pak also adds a couple.
+In addition, it also has all remote* and config/needs/* entries from
+the DESCRIPTION files. (Case insensitive.)
All columns are of type character, except for needscompilation, which
+is logical and deps, which is a list columns.
If an entry is missing for a package, it is set to NA.
Note that column names are lowercase, even if the corresponding entries
+are not in DESCRIPTION.
The order of the columns is not deterministic, so don't assume any order.
Additional columns might be present, these are internal for +pak and should not be used in user code.
System requirements platform.
If NULL, then the sysreqs_platform
-man_config_link("configuration option") is used, which defaults to
+configuration option
+ is used, which defaults to
the current platform.
Set this option if to one of platforms() if .packageName +
Set this option if to one of "centos", "debian", "fedora", "opensuse", "redhat", "redhat", "redhat", "rockylinux", "sle", "ubuntu"
+ if pak
+
fails to correctly detect your platform or if you want to see the system
requirements for a different platform.
Site built with pkgdown 2.1.1.
+Site built with pkgdown 2.1.1.9000.
diff --git a/reference/ppm_platforms.html b/reference/ppm_platforms.html index 2f6266194..1ae7587a8 100644 --- a/reference/ppm_platforms.html +++ b/reference/ppm_platforms.html @@ -1,5 +1,5 @@ -Site built with pkgdown 2.1.1.
+Site built with pkgdown 2.1.1.9000.
diff --git a/reference/ppm_r_versions.html b/reference/ppm_r_versions.html index a225d6c00..8b2ffc82b 100644 --- a/reference/ppm_r_versions.html +++ b/reference/ppm_r_versions.html @@ -1,5 +1,5 @@ -Site built with pkgdown 2.1.1.
+Site built with pkgdown 2.1.1.9000.
diff --git a/reference/ppm_repo_url.html b/reference/ppm_repo_url.html index fce82e4bf..2ce05f973 100644 --- a/reference/ppm_repo_url.html +++ b/reference/ppm_repo_url.html @@ -1,5 +1,5 @@ -Site built with pkgdown 2.1.1.
+Site built with pkgdown 2.1.1.9000.
diff --git a/reference/ppm_snapshots.html b/reference/ppm_snapshots.html index 32d768272..87b342523 100644 --- a/reference/ppm_snapshots.html +++ b/reference/ppm_snapshots.html @@ -1,5 +1,5 @@ -Site built with pkgdown 2.1.1.
+Site built with pkgdown 2.1.1.9000.
diff --git a/reference/repo_add.html b/reference/repo_add.html index 2343f2cc7..28bc6fe37 100644 --- a/reference/repo_add.html +++ b/reference/repo_add.html @@ -1,5 +1,5 @@ -These functions use the sysreqs_platform configuration option,
-see man_config_link("Configuration"). Set this if
+see Configuration
+. Set this if
pak does not detect your platform correctly.