Title: | Package Dependency Resolution and Downloads |
---|---|
Description: | Find recursive dependencies of 'R' packages from various sources. Solve the dependencies to obtain a consistent set of packages to install. Download packages, and install them. It supports packages on 'CRAN', 'Bioconductor' and other 'CRAN-like' repositories, 'GitHub', package 'URLs', and local package trees and files. It caches metadata and package files via the 'pkgcache' package, and performs all 'HTTP' requests, downloads, builds and installations in parallel. 'pkgdepends' is the workhorse of the 'pak' package. |
Authors: | Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd] |
Maintainer: | Gábor Csárdi <[email protected]> |
License: | MIT + file LICENSE |
Version: | 0.8.0.9000 |
Built: | 2024-11-05 11:14:33 UTC |
Source: | https://github.com/r-lib/pkgdepends |
pkgdepends is a toolkit for package dependencies, downloads and installations, to be used in other packages. If you are looking for a package manager, see pak.
Look up package dependencies recursively.
Visualize package dependencies.
Download packages and their dependencies.
Install downloaded packages.
Includes a dependency solver to find a consistent set of dependencies.
Supports CRAN and Bioconductor packages automatically.
Supports packages on GitHub and GitLab.
Supports packages in git repositories.
Supports package bundles or files on the web.
Supports local package file and trees.
Supports the Remotes
entry in the DESCRIPTION
file.
Caches metadata and downloaded packages via pkgcache
Performs all downloads and HTTP queries concurrently.
Builds and installs packages in parallel.
Install the package with:
install.packages("pkgdepends")
If you need the development version, install it with
pak::pak("r-lib/pkgdepends")
library(pkgdepends)
A package reference (ref) specifies a location from which an R package can be obtained from. Examples:
devtools cran::devtools bioc::Biobase r-lib/pkgdepends https://github.com/r-lib/pkgdepends local::~/works/shiny
See “Package references” for details.
Dependencies of the development version of the cli package:
pd <- new_pkg_deps("r-lib/pkgcache") pd$solve() pd$draw()
## ✔ Loading metadata database ... done ## r-lib/pkgcache 2.1.0.9000 ✨👷🏽🔧 ## ├─callr 3.7.3 ✨ ⬇ (431.00 kB) ## │ ├─processx 3.8.1 ✨ ⬇ (316.20 kB) ## │ │ ├─ps 1.7.5 ✨ ⬇ (313.92 kB) ## │ │ └─R6 2.5.1 ✨ ## │ └─R6 ## ├─cli 3.6.1 ✨ ⬇ (1.38 MB) ## ├─curl 5.0.0 ✨ ⬇ (777.64 kB) ## ├─filelock 1.0.2 ✨ ⬇ (29.58 kB) ## ├─jsonlite 1.8.4 ✨ ⬇ (1.13 MB) ## ├─prettyunits 1.1.1 ✨ ⬇ (35.23 kB) ## ├─processx ## ├─R6 ## └─rappdirs 0.3.3 ✨ ⬇ (47.50 kB) ## ## Key: ✨ new | ⬇ download | 👷🏽 build | 🔧 compile
See the pkg_deps
class for details.
Downloading all dependencies of a package:
pdl <- new_pkg_download_proposal("r-lib/cli") pdl$resolve() pdl$download()
## ℹ No downloads are needed, 1 pkg is cached
##
See the pkg_download_proposal
class for
details.
Installing or updating a set of package:
lib <- tempfile() dir.create(lib) pdi <- new_pkg_installation_proposal( "r-lib/cli", config = list(library = lib) ) pdi$solve() pdi$download() pdi$install()
## ℹ No downloads are needed, 1 pkg is cached ## ✔ Installed cli 3.6.1.9000 (github::r-lib/cli@c37f34b) (36ms) ## ✔ Summary: ✨ 1 new in 36ms
pkg_deps
,
pkg_download_proposal
and
pkg_installation_proposal
all resolve
their dependencies recursively, to obtain information about all packages
needed for the specified package references. See
“Dependency resolution” for details.
The dependency solver takes the resolution information, and works out the exact versions of each package that must be installed, such that version and other requirements are satisfied. See “The dependency solver” for details.
pkg_installation_proposal
can create
installation plans, and then also install them. It is also possible to
import installation plans that were created by other tools. See
“Installation plans” for details.
The details of pkg_deps
,
pkg_download_proposal
and
pkg_installation_proposal
can be tuned
with a list of configuration options. See
“Configuration” for details.
pak – R package manager
pkgcache – Metadata and package cache
devtools – Tools for R package developers
Please note that the pkgdepends project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
MIT (c) RStudio
Maintainer: Gábor Csárdi [email protected]
Other contributors:
Posit Software, PBC [copyright holder, funder]
Useful links:
Report bugs at https://github.com/r-lib/pkgdepends/issues
Shorthands for dependency specifications
as_pkg_dependencies(deps)
as_pkg_dependencies(deps)
deps |
See below. |
R packages may have various types of dependencies, see Writing R Extensions.
pkgdepends groups dependencies into three groups:
hard dependencies: "Depends", "Imports", and "LinkingTo",
soft dependencies: "Suggests" and "Enhances",
extra dependencies, see below.
pkgdepends supports concise ways of specifying which types of
dependencies of a package should be installed.
It is similar to how 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.
If you need more flexibility, the full description of possible values for
the deps
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.
See pkg_dep_types_hard()
.
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.
If "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.
pkgdepends 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:
Config/Needs/website: r-lib/pkgdown
To use these dependency types, you need to specify them in the
deps
argument to
pkgdepends 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.
A named list with two character vectors: direct
, indirect
,
the dependency types to use for direct installations and dependent
packages.
Other package dependency utilities:
pkg_dep_types_hard()
default_platfoms()
returns the default platforms for the current R
session. These typically consist of the detected platform of the current
R session, and "source"
, for source packages.
current_r_platform() default_platforms()
current_r_platform() default_platforms()
current_r_platform()
detects the platform of the current R version.
By default pkgdepends works with source packages and binary packages for the current platform. You can change this, see 'Configuration'.
The following platform names can be configured and returned by
current_r_platform()
and default_platforms()
:
"source"
for source packages,
A platform string like R.version$platform
, but on Linux the name
and version of the distribution are also included. Examples:
x86_64-apple-darwin17.0
: macOS High Sierra.
aarch64-apple-darwin20
: macOS Big Sur on arm64.
x86_64-w64-mingw32
: 64 bit Windows.
i386-w64-mingw32
: 32 bit Windows.
i386+x86_64-w64-mingw32
: 64 bit + 32 bit Windows.
i386-pc-solaris2.10
: 32 bit Solaris. (Some broken 64 Solaris
builds might have the same platform string, unfortunately.)
x86_64-pc-linux-gnu-debian-10
: Debian Linux 10 on x86_64.
x86_64-pc-linux-musl-alpine-3.14.1
: Alpine Linux.
x86_64-pc-linux-gnu-unknown
: Unknown Linux Distribution on x86_64.
s390x-ibm-linux-gnu-ubuntu-20.04
: Ubuntu Linux 20.04 on S390x.
amd64-portbld-freebsd12.1
: FreeBSD 12.1 on x86_64.
In addition, the following platform names can be used to configure pkgdepends:
"macos"
for macOS binaries that are appropriate for the R versions
pkgdepends is working with (defaulting to the version of the current
session), as defined by CRAN binaries. E.g. on R 3.5.0 macOS binaries
are built for macOS El Capitan.
"windows"
for Windows binaries for the default CRAN architecture.
This is currently Windows Vista for all supported R versions, but it
might change in the future. The actual binary packages in the
repository might support both 32 bit and 64 builds, or only one of
them. In practice 32-bit only packages are very rare. CRAN builds
before and including R 4.1 have both architectures, from R 4.2 they
are 64 bit only. "windows"
is an alias to i386+x86_64-w64-mingw32
currently.
current_r_platform()
returns a string, the name of the current
platform.
default_platforms()
returns a character vector of platform names.
current_r_platform() default_platforms()
current_r_platform() default_platforms()
See 'Installation plans' for the details and the format.
install_package_plan( plan, lib = .libPaths()[[1]], num_workers = 1, cache = NULL )
install_package_plan( plan, lib = .libPaths()[[1]], num_workers = 1, cache = NULL )
plan |
Package plan object, a data frame, see 'Installation plans' for the format. |
lib |
Library directory to install to. |
num_workers |
Number of worker processes to use. |
cache |
Package cache to use, or |
Information about the installation process.
An installation plan contains all data that is needed to install a set of package files. It is usually created from an installation proposal with solving the dependencies and downloading the package files.
It is also possible to create an installation plan a different way. An installation plan object must be a data frame, with at least the following columns:
package
: The name of the package.
type
: The type of the package reference.
binary
: Whether the package is a binary package.
file
: Full path to the package file or directory.
dependencies
: A list column that lists the names of the dependent
packages for each package.
needscompilation
: Whether the package needs compilation. This should
be FALSE
for binary packages.
For installation plans created via pkg_installation_proposal, the plan
contains all columns from pkg_download_result
objects, and some additional ones:
library
: the library the package is supposed to be installed to.
direct
: whether the package was directly requested or it is
installed as a dependency.
vignettes: whether the vignettes need to be (re)built.
packaged
: whether R CMD build
was already called for the package.
pkg_installation_proposal to create install plans,
install_package_plan()
to install plans from any source.
## Not run: pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$download() pdi$get_install_plan() ## End(Not run)
## Not run: pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$download() pdi$get_install_plan() ## End(Not run)
Check whether a package name is valid
is_valid_package_name(nm)
is_valid_package_name(nm)
nm |
Potential package name, string of length 1. |
Logical flag. If FALSE
, then the reason
attribute
contains a character string, the explanation why the package name
is invalid. See examples below.
is_valid_package_name("pak") is_valid_package_name("pkg") is_valid_package_name("pak\u00e1ge") is_valid_package_name("good-package") is_valid_package_name("x") is_valid_package_name("1stpackage") is_valid_package_name("dots.")
is_valid_package_name("pak") is_valid_package_name("pkg") is_valid_package_name("pak\u00e1ge") is_valid_package_name("good-package") is_valid_package_name("x") is_valid_package_name("1stpackage") is_valid_package_name("dots.")
Query data of all packages in a package library.
lib_status(library = .libPaths()[1], packages = NULL)
lib_status(library = .libPaths()[1], packages = NULL)
library |
Path to library. |
packages |
If not |
Data frame that contains data about the packages installed in the library.
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).
Most of these columns are unchanged from DESCRIPTION
, but
pkgdepends 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 pkgdepends and should not be used in user code.
Look up dependencies of R packages from various sources.
new_pkg_deps(refs, ...)
new_pkg_deps(refs, ...)
refs |
Package names or references. See 'Package references' for the syntax. |
... |
Additional arguments, passed to
|
new_pkg_deps()
creates a new object from the pkg_deps
class.
The advantage of new_pkg_deps()
compared to using the pkg_deps
constructor directly is that it avoids making pkgdepends a build time
dependency.
The usual steps to query package dependencies are:
Create a pkg_deps
object with new_pkg_deps()
.
Resolve all possible dependencies with
pkg_deps$resolve()
.
Solve the dependencies, to obtain a subset of all possible
dependencies that can be installed together, with
pkg_deps$solve()
.
Call pkg_deps$get_solution()
to list the
result of the dependency solver.
new_pkg_deps()
returns a new pkg_deps
object.
new()
Create a new pkg_deps
object. Consider using new_pkg_deps()
instead of calling the constructor directly.
The returned object can be used to look up (recursive) dependencies
of R packages from various sources. To perform the actual lookup,
you'll need to call the resolve()
method.
pkg_deps$new( refs, config = list(), policy = c("lazy", "upgrade"), remote_types = NULL )
refs
Package names or references. See 'Package references' for the syntax.
config
Configuration options, a named list. See 'Configuration'.
policy
Solution policy. See 'The dependency solver'.
remote_types
Custom remote ref types, this is for advanced use, and experimental currently.
A new pkg_deps
object.
get_refs()
The package refs that were used to create the pkg_deps
object.
pkg_deps$get_refs()
A character vector of package refs that were used to create the
pkg_deps
object.
get_config()
Configuration options for the pkg_deps
object. See
'Configuration' for details.
pkg_deps$get_config()
See 'Configuration' for the configuration entries.
resolve()
Resolve the dependencies of the specified package references. This usually means downloading metadata from CRAN and Bioconductor, unless already cached, and also from GitHub if GitHub refs were included, either directly or indirectly. See 'Dependency resolution' for details.
pkg_deps$resolve()
The pkg_deps
object itself, invisibly.
async_resolve()
The same as resolve()
, but asynchronous.
This method is for advanced use.
pkg_deps$async_resolve()
A deferred value.
get_resolution()
Query the result of the dependency resolution. This method can be
called after resolve()
has completed.
pkg_deps$get_resolution()
A pkg_resolution_result object, which is also a data frame. See 'Dependency resolution' for its columns.
get_solve_policy()
Returns the current policy of the dependency solver. See 'The dependency solver' for details.
pkg_deps$get_solve_policy()
A character vector of length one.
set_solve_policy()
Set the current policy of the dependency solver. If the object already contains a solution and the new policy is different than the old policy, then the solution is deleted. See 'The dependency solver' for details.
pkg_deps$set_solve_policy(policy = c("lazy", "upgrade"))
policy
Policy to set.
solve()
Solve the package dependencies. Out of the resolved dependencies, it works out a set of packages, that can be installed together to create a functional installation. The set includes all directly specified packages, and all required (or suggested, depending on the configuration) packages as well. It includes every package at most once. See 'The dependency solver' for details.
solve()
calls resolve()
automatically, if it
hasn't been called yet.
pkg_deps$solve()
The pkg_deps
object itself, invisibly.
get_solution()
Returns the solution of the package dependencies.
pkg_deps$get_solution()
A pkg_solution_result object, which is a list. See pkg_solution_result for details.
stop_for_solution_error()
Error if the dependency solver failed to find a consistent set of packages that can be installed together.
pkg_deps$stop_for_solution_error()
draw()
Draw a tree of package dependencies. It returns a tree
object, see
cli::tree()
. Printing this object prints the dependency tree to the
screen.
pkg_deps$draw()
A tree
object from the cli package, see cli::tree()
.
format()
Format a pkg_deps
object, typically for printing.
pkg_deps$format(...)
...
Not used currently.
A character vector, each element should be a line in the printout.
print()
Prints a pkg_deps
object to the screen. The printout includes:
The package refs.
Whether the object has the resolved dependencies.
Whether the resolution had errors.
Whether the object has the solved dependencies.
Whether the solution had errors.
Advice on which methods to call next.
See the example below.
pkg_deps$print(...)
...
not used currently.
The pkg_deps
object itself, invisibly.
clone()
The objects of this class are cloneable with this method.
pkg_deps$clone(deep = FALSE)
deep
Whether to make a deep clone.
# Method initialize() pd <- pkg_deps$new("r-lib/pkgdepends") pd # Method get_refs() pd <- new_pkg_deps(c("pak", "jsonlite")) pd$get_refs() # Method get_config() pd <- new_pkg_deps("pak") pd$get_config() # Method resolve() pd <- new_pkg_deps("pak") pd$resolve() pd$get_resolution() # Method get_resolution() pd <- new_pkg_deps("r-lib/pkgdepends") pd$resolve() pd$get_resolution() # Method get_solve_policy() pdi <- new_pkg_deps("r-lib/pkgdepends") pdi$get_solve_policy() pdi$set_solve_policy("upgrade") pdi$get_solve_policy() # Method set_solve_policy() pdi <- new_pkg_deps("r-lib/pkgdepends") pdi$get_solve_policy() pdi$set_solve_policy("upgrade") pdi$get_solve_policy() # Method solve() pd <- new_pkg_deps("r-lib/pkgdepends") pd$resolve() pd$solve() pd$get_solution() # Method get_solution() pd <- new_pkg_deps("pkgload") pd$resolve() pd$solve() pd$get_solution() # Method stop_for_solution_error() # This is an error, because the packages conflict: pd <- new_pkg_deps( c("r-lib/pak", "cran::pak"), config = list(library = tempfile()) ) pd$resolve() pd$solve() pd # This fails: # pd$stop_for_solution_error() # Method draw() pd <- new_pkg_deps("pkgload") pd$solve() pd$draw() # Method print() pd <- new_pkg_deps("r-lib/pkgdepends") pd pd$resolve() pd pd$solve() pd
# Method initialize() pd <- pkg_deps$new("r-lib/pkgdepends") pd # Method get_refs() pd <- new_pkg_deps(c("pak", "jsonlite")) pd$get_refs() # Method get_config() pd <- new_pkg_deps("pak") pd$get_config() # Method resolve() pd <- new_pkg_deps("pak") pd$resolve() pd$get_resolution() # Method get_resolution() pd <- new_pkg_deps("r-lib/pkgdepends") pd$resolve() pd$get_resolution() # Method get_solve_policy() pdi <- new_pkg_deps("r-lib/pkgdepends") pdi$get_solve_policy() pdi$set_solve_policy("upgrade") pdi$get_solve_policy() # Method set_solve_policy() pdi <- new_pkg_deps("r-lib/pkgdepends") pdi$get_solve_policy() pdi$set_solve_policy("upgrade") pdi$get_solve_policy() # Method solve() pd <- new_pkg_deps("r-lib/pkgdepends") pd$resolve() pd$solve() pd$get_solution() # Method get_solution() pd <- new_pkg_deps("pkgload") pd$resolve() pd$solve() pd$get_solution() # Method stop_for_solution_error() # This is an error, because the packages conflict: pd <- new_pkg_deps( c("r-lib/pak", "cran::pak"), config = list(library = tempfile()) ) pd$resolve() pd$solve() pd # This fails: # pd$stop_for_solution_error() # Method draw() pd <- new_pkg_deps("pkgload") pd$solve() pd$draw() # Method print() pd <- new_pkg_deps("r-lib/pkgdepends") pd pd$resolve() pd pd$solve() pd
Download packages with their dependencies, from various sources.
new_pkg_download_proposal(refs, ...)
new_pkg_download_proposal(refs, ...)
refs |
Package names or references. See 'Package references' for the syntax. |
... |
Additional arguments, passed to
|
new_pkg_download_proposal()
creates a new object from the
pkg_download_proposal
class, that can be used to look up and download
R packages and their dependencies. The advantage of
new_pkg_download_proposal()
compared to using the
pkg_download_proposal constructor directly is that it avoids making
pkgdepends a build time dependency.
Typical workflow to download a set of packages:
Create a pkg_download_proposal
object with
new_pkg_download_proposal()
.
Resolve all possible dependencies with
pkg_download_proposal$resolve()
.
Download all files with
pkg_download_proposal$download()
.
Get the data about the packages and downloads with
pkg_download_proposal$get_downloads()
.
new_pkg_download_proposal()
returns a new
pkg_download_proposal
object.
new()
Create a new pkg_download_proposal
object. Consider using
new_pkg_download_proposal()
instead of calling the constructor
directly.
The returned object can be used to look up (recursive) dependencies of R packages from various sources, and then to download the package files.
pkg_download_proposal$new(refs, config = list(), remote_types = NULL)
refs
Package names or references. See 'Package references' for the syntax.
config
Configuration options, a named list. See 'Configuration'.
remote_types
Custom remote ref types, this is for advanced use, and experimental currently.
pdl <- pkg_download_proposal$new("r-lib/pkgdepends") pdl
get_refs()
The package refs that were used to create the
pkg_download_proposal
object.
pkg_download_proposal$get_refs()
A character vector of package refs that were used to create the
pkg_download_proposal
object.
get_config()
Configuration options for the pkg_download_proposal
object. See
'Configuration' for details.
pkg_download_proposal$get_config()
Named list. See 'Configuration' for the configuration options.
resolve()
Resolve the dependencies of the specified package references. This usually means downloading metadata from CRAN and Bioconductor, unless already cached, and also from GitHub if GitHub refs were included, either directly or indirectly. See 'Dependency resolution' for details.
pkg_download_proposal$resolve()
The pkg_download_proposal
object itself, invisibly.
async_resolve()
The same as resolve()
, but asynchronous.
This method is for advanced use.
pkg_download_proposal$async_resolve()
A deferred value.
get_resolution()
Query the result of the dependency resolution. This method can be
called after resolve()
has completed.
pkg_download_proposal$get_resolution()
A pkg_resolution_result object, which is also a data frame. See 'Dependency resolution' for its columns.
download()
Download all resolved packages. It uses the package cache in the pkgcache package by default, to avoid downloads if possible.
pkg_download_proposal$download()
The pkg_download_proposal
object, invisibly.
async_download()
The same as download()
, but asynchronous.
This method is for advanced use.
pkg_download_proposal$async_download()
A deferred value.
get_downloads()
Returns the summary of the package downloads.
pkg_download_proposal$get_downloads()
A pkg_download_result object, which is a list. See pkg_download_result for details.
stop_for_download_error()
Throw and error if the some of the downloads have failed for the
most recent
pkg_download_proposal$download()
call.
pkg_download_proposal$stop_for_download_error()
format()
Format a pkg_download_proposal
object, typically for printing.
pkg_download_proposal$format(...)
...
not used currently.
Nothing. A character vector, each element should be a line in the printout.
print()
Prints a pkg_download_proposal
object to the screen. The printout
includes:
The package refs.
Whether the object has the resolved dependencies.
Whether the resolution had errors.
Whether the downloads were completed.
Whether the downloads had errors.
Advice on which methods to call next.
See the example below.
pkg_download_proposal$print(...)
...
not used currently.
The pkg_download_proposal
object itself, invisibly.
clone()
The objects of this class are cloneable with this method.
pkg_download_proposal$clone(deep = FALSE)
deep
Whether to make a deep clone.
# Method get_refs() pdl <- new_pkg_download_proposal(c("pak", "jsonlite")) pdl$get_refs() # Method get_config() pdl <- new_pkg_download_proposal("pak") pdl$get_config() # Method resolve() pdl <- new_pkg_download_proposal("pak") pdl$resolve() pdl$get_resolution() # Method get_resolution() pdl <- new_pkg_download_proposal("r-lib/pkgdepends") pdl$resolve() pdl$get_resolution() # Method download() pdl <- new_pkg_download_proposal("r-lib/pkgdepends") pdl$resolve() pdl$download() pdl$get_downloads() # Method get_downloads() pdl <- new_pkg_download_proposal("pkgload") pdl$resolve() pdl$download() pdl$get_downloads() # Method print() pdl <- new_pkg_download_proposal("r-lib/pkgdepends") pdl pdl$resolve() pdl pdl$download() pdl
# Method get_refs() pdl <- new_pkg_download_proposal(c("pak", "jsonlite")) pdl$get_refs() # Method get_config() pdl <- new_pkg_download_proposal("pak") pdl$get_config() # Method resolve() pdl <- new_pkg_download_proposal("pak") pdl$resolve() pdl$get_resolution() # Method get_resolution() pdl <- new_pkg_download_proposal("r-lib/pkgdepends") pdl$resolve() pdl$get_resolution() # Method download() pdl <- new_pkg_download_proposal("r-lib/pkgdepends") pdl$resolve() pdl$download() pdl$get_downloads() # Method get_downloads() pdl <- new_pkg_download_proposal("pkgload") pdl$resolve() pdl$download() pdl$get_downloads() # Method print() pdl <- new_pkg_download_proposal("r-lib/pkgdepends") pdl pdl$resolve() pdl pdl$download() pdl
An installation plan is similar to an installation proposal (i.e. pkg_installation_proposal), but it already contains the solved dependencies, complete with download URLs.
new_pkg_installation_plan(lockfile = "pkg.lock", config = list(), ...)
new_pkg_installation_plan(lockfile = "pkg.lock", config = list(), ...)
lockfile |
Path to the lock file to use. |
config |
Configuration options, a named list. See
'Configuration'. If it does not include |
... |
Additional arguments, passed to
|
Typically you create a pkg_installation_plan
object with
new_pkg_installation_plan()
and then call its $download()
method
to download the packages and then its $install()
method to install
them.
new_pkg_installation_plan()
returns a pkg_installation_plan
object.
pkgdepends::pkg_installation_proposal
-> pkg_installation_plan
pkgdepends::pkg_installation_proposal$async_download()
pkgdepends::pkg_installation_proposal$create_lockfile()
pkgdepends::pkg_installation_proposal$download()
pkgdepends::pkg_installation_proposal$draw()
pkgdepends::pkg_installation_proposal$get_config()
pkgdepends::pkg_installation_proposal$get_downloads()
pkgdepends::pkg_installation_proposal$get_install_plan()
pkgdepends::pkg_installation_proposal$get_refs()
pkgdepends::pkg_installation_proposal$get_resolution()
pkgdepends::pkg_installation_proposal$get_solution()
pkgdepends::pkg_installation_proposal$get_sysreqs()
pkgdepends::pkg_installation_proposal$install()
pkgdepends::pkg_installation_proposal$install_sysreqs()
pkgdepends::pkg_installation_proposal$print()
pkgdepends::pkg_installation_proposal$show_solution()
pkgdepends::pkg_installation_proposal$show_sysreqs()
pkgdepends::pkg_installation_proposal$stop_for_download_error()
pkgdepends::pkg_installation_proposal$stop_for_solution_error()
new()
Create a new pkg_installation_plan
object. Consider using
new_pkg_installation_plan()
instead of calling the constructor
directly.
The returned object can be used to download and install packages, according to the plan.
pkg_installation_plan$new( lockfile = "pkg.lock", config = list(), remote_types = NULL )
lockfile
Path to the lock file to use.
config
Configuration options. See
'Configuration'. It needs to include the package
library to install to, in library
.
remote_types
Custom remote ref types, this is for advanced use, and experimental currently.
resolve()
This function is implemented for installation plans, and will error.
pkg_installation_plan$resolve()
async_resolve()
This function is implemented for installation plans, and will error.
pkg_installation_plan$async_resolve()
get_solve_policy()
Installation plans are already solved, and this method will return
NA_character_
, always.
pkg_installation_plan$get_solve_policy()
set_solve_policy()
This function is implemented for installation plans, and will error.
pkg_installation_plan$set_solve_policy()
solve()
This function is implemented for installation plans, and will error.
pkg_installation_plan$solve()
update()
Update the plan to the current state of the library. If the library has not changed since the plan was created, then it does nothing. If new packages have been installed, then it might not be necessary to download and install all packages in the plan.
pkg_installation_plan$update()
This operation is different than creating a new proposal with the
updated library, because it uses the the packages and package
versions of the original plan. E.g. if the library has a newer
version of a package, then $update()
will downgrade it to the
version in the plan.
update_sysreqs()
Update information about installed and missing system requirements.
pkg_installation_plan$update_sysreqs()
format()
Format a pkg_installation_plan
object, typically for printing.
pkg_installation_plan$format(...)
...
not used currently.
A character vector, each element should be a line in the printout.
clone()
The objects of this class are cloneable with this method.
pkg_installation_plan$clone(deep = FALSE)
deep
Whether to make a deep clone.
Download and install R packages, with their dependencies, from various sources.
new_pkg_installation_proposal(refs, config = list(), ...)
new_pkg_installation_proposal(refs, config = list(), ...)
refs |
Package names or references. See 'Package references' for the syntax. |
config |
Configuration options, a named list. See
'Configuration'. If it does not include |
... |
Additional arguments, passed to
|
new_pkg_installation_proposal()
creates a new object from the
pkg_installation_proposal
class. The advantage of
new_pkg_installation_proposal()
compared to using the
pkg_installation_proposal constructor directly is that it avoids
making pkgdepends a build time dependency.
Typical workflow to install a set of packages:
Create a pkg_installation_proposal
object with
new_pkg_installation_proposal()
.
Resolve all possible dependencies with
pkg_installation_proposal$resolve()
.
Solve the package dependencies, to get an installation plan, with
pkg_installation_proposal$solve()
.
Download all files with
pkg_installation_proposal$download()
.
Install the downloaded files with
pkg_installation_proposal$install()
.
new_pkg_installation_proposal()
returns a new
pkg_installation_proposal
object.
new()
Create a new pkg_installation_proposal
object. Consider using
new_pkg_installation_proposal()
instead of calling the constructor
directly.
The returned object can be used to look up (recursive) dependencies of R packages from various sources, and then download and install the package files.
pkg_installation_proposal$new( refs, config = list(), policy = c("lazy", "upgrade"), remote_types = NULL )
refs
Package names or references. See 'Package references' for the syntax.
config
Configuration options, a named list. See
'Configuration'. It needs to include the package
library to install to, in library
.
policy
Solution policy. See 'The dependency solver'.
remote_types
Custom remote ref types, this is for advanced use, and experimental currently.
get_refs()
The package refs that were used to create the
pkg_installation_proposal
object.
pkg_installation_proposal$get_refs()
A character vector of package refs that were used to create the
pkg_installation_proposal
object.
get_config()
Configuration options for the pkg_installation_proposal
object. See
'Configuration' for details.
pkg_installation_proposal$get_config()
Named list. See 'Configuration' for the configuration options.
resolve()
Resolve the dependencies of the specified package references. This usually means downloading metadata from CRAN and Bioconductor, unless already cached, and also from GitHub if GitHub refs were included, either directly or indirectly. See 'Dependency resolution' for details.
pkg_installation_proposal$resolve()
The pkg_installation_proposal
object, invisibly.
async_resolve()
The same as resolve()
, but asynchronous. This
method is for advanced use.
pkg_installation_proposal$async_resolve()
A deferred value.
get_resolution()
Query the result of the dependency resolution. This method can be
called after resolve()
has completed.
pkg_installation_proposal$get_resolution()
A pkg_resolution_result object, which is also a data frame. See 'Dependency resolution' for its columns.
get_solve_policy()
Returns the current policy of the dependency solver. See 'The dependency solver' for details.
pkg_installation_proposal$get_solve_policy()
A character vector of length one.
set_solve_policy()
Set the current policy of the dependency solver. If the object already contains a solution and the new policy is different than the old policy, then the solution is deleted. See 'The dependency solver' for details.
pkg_installation_proposal$set_solve_policy(policy = c("lazy", "upgrade"))
policy
Policy to set.
solve()
Solve the package dependencies. Out of the resolved dependencies, it works out a set of packages, that can be installed together to create a functional installation. The set includes all directly specified packages, and all required (or suggested, depending on the configuration) packages as well. It includes every package at most once. See 'The dependency solver' for details.
pkg_installation_proposal$solve()
The pkg_installation_proposal
object itself, invisibly.
get_solution()
Returns the solution of the package dependencies.
pkg_installation_proposal$get_solution()
A pkg_solution_result object, which is a list. See pkg_solution_result for details.
show_solution()
Show the solution on the screen.
pkg_installation_proposal$show_solution(key = FALSE)
key
Whether to show the key to the package list annotation.
A pkg_solution_result object, which is a list. See pkg_solution_result for details.
get_sysreqs()
Query and categorize system requirements.
pkg_installation_proposal$get_sysreqs()
show_sysreqs()
Show system requirements for the packages in the solution.
pkg_installation_proposal$show_sysreqs()
stop_for_solution_error()
Error if the dependency solver failed to find a consistent set of packages that can be installed together.
pkg_installation_proposal$stop_for_solution_error()
create_lockfile()
Create a lock file that contains the information to perform the installation later, possibly in another R session.
pkg_installation_proposal$create_lockfile(path = "pkg.lock", version = 1)
path
Name of the lock file. The default is pkg.lock
in the
current working directory.
version
Only version 1 is supported currently.
Note, since the URLs of CRAN and most CRAN-like repositories change over time, in practice you cannot perform the plan of the lock file much later. For example, binary packages of older package version are removed, and won't be found.
Similarly, for url::
remote types, the URL might hold an updated
version of the package, compared to when the lock file was created.
Should this happen, pkgdepends prints a warning, but it will try
to continue the installation. The installation might fail if the
updated package has different (e.g. new) dependencies.
Currently the intended use case of lock files in on CI systems, to facilitate caching. The (hash of the) lock file provides a good key for caching systems.
draw()
Draw a tree of package dependencies. It returns a tree
object, see
cli::tree()
. Printing this object prints the dependency tree to the
screen.
pkg_installation_proposal$draw()
A tree
object from the cli package, see cli::tree()
.
download()
Download all packages that are part of the solution. It uses the package cache in the pkgcache package by default, to avoid downloads if possible.
pkg_installation_proposal$download()
The pkg_installation_proposal
object itself, invisibly.
async_download()
The same as download()
, but asynchronous.
This method is for advanced use.
pkg_installation_proposal$async_download()
A deferred value.
get_downloads()
Returns the summary of the package downloads.
pkg_installation_proposal$get_downloads()
A pkg_download_result object, which is a list. See pkg_download_result for details.
stop_for_download_error()
Throw and error if the some of the downloads have failed for the
most recent
pkg_installation_proposal$download()
call.
pkg_installation_proposal$stop_for_download_error()
install()
Install the downloaded packages. It calls install_package_plan()
.
pkg_installation_proposal$install()
The return value of install_package_plan()
.
install_sysreqs()
Install system requirements. It does nothing if system requirements are turned off. Create an installation plan for the downloaded packages.
pkg_installation_proposal$install_sysreqs()
get_install_plan()
pkg_installation_proposal$get_install_plan()
An installation plan, see 'Installation plans' for the format.
format()
Format a pkg_installation_proposal
object, typically for printing.
pkg_installation_proposal$format(...)
...
not used currently.
A character vector, each element should be a line in the printout.
print()
Prints a pkg_installation_proposal
object to the screen.
The printout includes:
The package refs.
The policy of the dependency solver.
Whether the object has the solved dependencies.
Whether the solution had errors.
Whether the object has downloads.
Whether the downloads had errors.
Advice on which methods to call next.
See the example below.
pkg_installation_proposal$print(...)
...
not used currently.
The pkg_installation_proposal
object itself, invisibly.
clone()
The objects of this class are cloneable with this method.
pkg_installation_proposal$clone(deep = FALSE)
deep
Whether to make a deep clone.
## Not run: pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi pdi$resolve() pdi pdi$solve() pdi pdi$download() pdi ## End(Not run) pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile())) pdi pdi <- new_pkg_installation_proposal("r-lib/pkgdepends") pdi$get_refs() pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi$get_config() ## Not run: pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi$resolve() pdi$get_resolution() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$resolve() pdi$get_resolution() ## End(Not run) pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$get_solve_policy() pdi$set_solve_policy("upgrade") pdi$get_solve_policy() pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$get_solve_policy() pdi$set_solve_policy("upgrade") pdi$get_solve_policy() ## Not run: pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$get_solution() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$get_solution() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$get_solution() pdi$show_solution() ## End(Not run) ## Not run: # This is an error, because the packages conflict: pdi <- new_pkg_installation_proposal( c("r-lib/pak", "cran::pak"), config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi # This fails: # pdi$stop_for_solution_error() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$draw() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( c("r-lib/pak", "cran::pak"), config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$download() pdi$get_downloads() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( c("r-lib/pak", "cran::pak"), config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$download() pdi$get_downloads() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$download() pdi$get_install_plan() ## End(Not run) # Method print pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi pdi$resolve() pdi pdi$solve() pdi pdi$download() pdi
## Not run: pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi pdi$resolve() pdi pdi$solve() pdi pdi$download() pdi ## End(Not run) pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile())) pdi pdi <- new_pkg_installation_proposal("r-lib/pkgdepends") pdi$get_refs() pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi$get_config() ## Not run: pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi$resolve() pdi$get_resolution() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$resolve() pdi$get_resolution() ## End(Not run) pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$get_solve_policy() pdi$set_solve_policy("upgrade") pdi$get_solve_policy() pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$get_solve_policy() pdi$set_solve_policy("upgrade") pdi$get_solve_policy() ## Not run: pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$get_solution() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$get_solution() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( "r-lib/pkgdepends", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$get_solution() pdi$show_solution() ## End(Not run) ## Not run: # This is an error, because the packages conflict: pdi <- new_pkg_installation_proposal( c("r-lib/pak", "cran::pak"), config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi # This fails: # pdi$stop_for_solution_error() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$draw() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( c("r-lib/pak", "cran::pak"), config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$download() pdi$get_downloads() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( c("r-lib/pak", "cran::pak"), config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$download() pdi$get_downloads() ## End(Not run) ## Not run: pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi$resolve() pdi$solve() pdi$download() pdi$get_install_plan() ## End(Not run) # Method print pdi <- new_pkg_installation_proposal( "pak", config = list(library = tempfile()) ) pdi pdi$resolve() pdi pdi$solve() pdi pdi$download() pdi
See pkg_refs for more about supported package references.
parse_pkg_refs(refs, remote_types = NULL, ...) parse_pkg_ref(ref, remote_types = NULL, ...)
parse_pkg_refs(refs, remote_types = NULL, ...) parse_pkg_ref(ref, remote_types = NULL, ...)
refs |
Character vector of references. |
remote_types |
Custom remote types can be added here, this is for advanced use, and experimental currently. |
... |
Additional arguments are passed to the individual parser functions. |
ref |
A package reference, like |
parse_pkg_refs()
returns a list of parsed references.
parse_pkg_ref()
returns one parsed reference. A parsed reference is
a list, with at least elements:
ref
: The original reference string.
type
: The reference type.
package
: The package name.
It typically contains additional data, specific to the various
reference types. See pkg_refs for details.
The parsed reference always has class remote_ref_<type>
and
remote_ref
.
Configuration entries for several pkgdepends classes.
current_config()
current_config()
pkgdepends configuration is set from several source. They are, in the order of preference:
Function arguments, e.g. the config
argument of
new_pkg_installation_proposal()
.
Global options, set via options()
. The name of the global option
is the pkg.
prefix plus the name of the pkgdepends configuration
entry. E.g. pkg.platforms
.
Environment variables. The name of the environment variable is the
PKG_
prefix, plus the name of the pkgdepends configuration entry, in
uppercase. E.g. PKG_PLATFORMS
.
Default values.
Not all classes use all entries. E.g. a pkg_download_proposal
is not
concerned about package libraries, so it'll ignore the library
configuration entry.
Call current_config()
to print the current configuration.
build_vignettes
: Whether to build vignettes for package trees.
This is only used if the package is obtained from a package tree,
and not from a source (or binary) package archive. By default
vignettes are not built in this case. If you set this to TRUE
,
then you need to make sure that the vignette builder packages are
available, as these are not installed by default currently.
cache_dir
: Directory to download the packages to. Defaults to a temporary
directory within the R session temporary directory, see
base::tempdir()
.
cran_mirror
: CRAN mirror to use. Defaults to the repos
option
(see base::options()
), if that's not set then
https://cran.rstudio.com
.
dependencies
: Dependencies to consider or download or install.
Defaults to the hard dependencies, see
pkg_dep_types_hard()
. The following values are
supported in the PKG_DEPENDENCIES
environment variable:
"TRUE"
, "FALSE"
, "NA"
, or a semicolon separated list of
dependency types. See as_pkg_dependencies()
for
details.
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
: 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
: Package library to install packages to. It is also used for
already installed packages when considering dependencies in
dependency lookup or
package installation. Defaults to the
first path in .libPaths()
.
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
: A time interval as a difftime object. pkgdepends 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
: Package cache location of pkgcache::package_cache
. The default
is the pkgcache default.
platforms
: Character vector of platforms to download or install packages
for. See default_platforms()
for possible platform
names. Defaults to the platform of the current R session, plus
"source"
.
r_versions
: Character vector, R versions to download or install
packages for. It defaults to the current R version.
sysreqs
: Whether to automatically look up and install system requirements.
If TRUE
, then r pak_or_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
: 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
: Timeout for the system requirements database update.
Defaults to five seconds.
sysreqs_dry_run
: If TRUE
, then pkgdepends only prints the system commands to
install system requirements, but does not execute them.
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
: 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
: 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
: 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
: 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
: Whether to echo the output of system requirements installation.
Defaults to TRUE
if the CI
environment variable is set.
use_bioconductor
: Whether to automatically use the Bioconductor repositories.
Defaults to TRUE
.
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.
Hard dependencies are needed for a package to load, soft dependencies are optional.
pkg_dep_types_hard() pkg_dep_types_soft() pkg_dep_types()
pkg_dep_types_hard() pkg_dep_types_soft() pkg_dep_types()
A string vector of dependency types, capitalized.
Other package dependency utilities:
as_pkg_dependencies()
The pkg_download_proposal
and pkg_installation_proposal
classes
both have download methods, to downloads package files into a
configured directory (see 'Configuration').
They return a pkg_download_result
object, which is a data frame,
that adds extra columns to pkg_resolution_result
(for
pkg_download_proposal
) or pkg_solution_result
(for pkg_installation_proposal
):
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.
Additionally, look up the candidate name in a number of dictionaries, to make sure that it does not have a negative meaning.
pkg_name_check(name, dictionaries = NULL)
pkg_name_check(name, dictionaries = NULL)
name |
Package name candidate. |
dictionaries |
Character vector, the dictionaries to query.
Available dictionaries:
* |
Check the validity of name
as a package name. See 'Writing R
Extensions' for the allowed package names. Also checked against a list
of names that are known to cause problems.
Check name
against the names of all past and current packages on
CRAN, including base and recommended packages.
Check name
against all past and current Bioconductor packages.
Check name
with https://www.purgomalum.com/service/containsprofanity
to make sure it is not a profanity.
See the dictionaries
argument.
pkg_name_check
object with a custom print method.
pkg_name_check("cli")
pkg_name_check("cli")
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.
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.
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 [email protected]
is equivalent to
standard::[email protected]
.
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.
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/...
.
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
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.
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:
[cran::]<package>[@[>=]<version> | @current | @last]
<package>
is a valid package name.
<version>
is a version or a version requirement.
Examples:
forecast [email protected] forecast@>=8.8 cran::forecast forecast@last forecast@current
Note: pkgdepends 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.
[bioc::]<package>[@[>=]<version> | @current | @last]
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 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:
[email protected]:r-lib/pak.git
gitlab::
)Packages from a GitLab repository. Full syntax:
[<package>=][github::]<project-path>/<repository>[/-/<subdir>][<detail>]
<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:
gitlab::gaborcsardi/cli gitlab::r-hub/filelock@main gitlab::group/subgroup/subsubgroup/project/-/subdir@ref
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.
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.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::
)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.
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::
)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
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::
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.
param::
)See "Parameters" above.
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.
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/[email protected], 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.
Collect information about dependencies of R packages, recursively.
pkg_deps
, pkg_download_proposal
and pkg_installation_proposal
all resolve their dependencies recursively, to obtain information about
all packages needed for the specified package references.
Resolution currently start by downloading the CRAN and Bioconductor metadata, if it is out of date. For CRAN, we also download additional metadata, that includes file sizes, SHA hashes, system requirements, and "built" (for binary packages) and "packaged" time stamps. The extra meta information is updated daily currently, so for some packages it might be incorrect or missing.
For GitHub packages, we query their download URL to be able to
download the package later, and also download their DESCRIPTION
file, to learn about their dependencies.
From local package files we extract the DESCRIPTION
file, to learn
about their dependencies.
remotes
field in DESCRIPTION
We support the non-standard Remotes
field in the package DESCRIPTION
file. This field may contain a list of package references for any of the
dependencies that are specified in one of the Depends
, Includes
,
Suggests
or Enhances
fields. The syntax is a comma separated list of
package references.
The result of the resolution is a data frame with information about the packages and their dependencies.
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.
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.
The resolution process does not stop on error. Instead, failed
resolutions return and error object in the error
column of the result
data frame.
If you use these in R, make sure you specify perl = TRUE
, see
base::grep()
.
pkg_rx()
pkg_rx()
Currently included:
pkg_name
: A valid package name.
type_cran
: A cran::
package reference.
type_bioc
: A bioc::
package reference.
type_standard
: A standard::
package reference.
type_github
: A github::
package reference.
type_git
: A git::
package reference.
type_local
: A local::
package reference.
type_deps
: A deps::
package reference.
type_installed
: An installed::
package reference.
github_username
: A GitHub username.
github_repo
: A GitHub repository name.
github_url
: A GitHub URL.
A named list of strings.
pkg_rx()
pkg_rx()
The dependency solver takes the resolution information, and works out the exact versions of each package that must be installed, such that version and other requirements are satisfied.
The dependency solver currently supports two policies: lazy
and
upgrade
. The lazy
policy prefers to minimize installation time,
and it does not perform package upgrades, unless version requirements
require them. The upgrade
policy prefers to update all package to
their latest possible versions, but it still considers that version
requirements.
Solving the package dependencies requires solving an integer linear problem (ILP). This subsection briefly describes how the problem is represented as an integer problem, and what the solution policies exactly mean.
Every row of the package resolution is a candidate for the dependency solver. In the integer problem, every candidate corresponds to a binary variable. This is 1 if that candidate is selected as part of the solution, and 0 otherwise.
The objective of the ILP minimization is defined differently for different solution policies. The ILP conditions are the same.
For the lazy
policy, installed::
packaged get 0 points, binary
packages 1 point, sources packages 5 points.
For the 'upgrade' policy, we rank all candidates for a given package according to their version numbers, and assign more points to older versions. Points are assigned by 100 and candidates with equal versions get equal points. We still prefer installed packages to binaries to source packages, so also add 0 point for already installed candidates, 1 extra points for binaries and 5 points for source packages.
For directly specified refs, we aim to install each package exactly once. So for these we require that the variables corresponding to the same package sum up to 1.
For non-direct refs (i.e. dependencies), we require that the variables corresponding to the same package sum up to at most one. Since every candidate has at least 1 point in the objective function of the minimization problem, non-needed dependencies will be omitted.
For direct refs, we require that their candidates satisfy their references. What this means exactly depends on the ref types. E.g. for CRAN packages, it means that a CRAN candidate must be selected. For a standard ref, a GitHub candidate is OK as well.
We rule out candidates for which the dependency resolution failed.
We go over all the dependency requirements and rule out packages
that do not meet them. For every package A
, that requires
package B
, we select the B(i, i=1..k)
candidates of B
that
satisfy A
's requirements and add a A - B(1) - ... - B(k) <= 0
rule. To satisfy this rule, either we cannot install A
, or if A
is installed, then one of the good B
candidates must be installed
as well.
We rule out non-installed CRAN and Bioconductor candidates for packages that have an already installed candidate with the same exact version.
We also rule out source CRAN and Bioconductor candidates for packages that have a binary candidate with the same exact version.
To be able to explain why a solution attempt failed, we also add a dummy variable for each directly required package. This dummy variable has a very large objective value, and it is only selected if there is no way to install the directly required package.
After a failed solution, we look the dummy variables that were selected, to see which directly required package failed to solve. Then we check which rule(s) ruled out the installation of these packages, and their dependencies, recursively.
The result of the solution is a pkg_solution_result
object. It is a
named list with entries:
status
: Status of the solution attempt, "OK"
or "FAILED"
.
data
: The selected candidates. This is very similar to a
pkg_resolution_result object, but it has two extra columns:
lib_status
: status of the package in the library, after the
installation. Possible values: new
(will be newly installed),
current
(up to date, not installed), update
(will be updated),
no-update
(could update, but will not).
old_version
: The old (current) version of the package in the
library, or NA
if the package is currently not installed.
problem
: The ILP problem. The exact representation is an
implementation detail, but it does have an informative print method.
solution
: The return value of the internal solver.
Scan all R files of a project or directory for packages used within
them. It parses R code to find library(package)
, package::func()
,
and similar calls that imply package dependencies. See details below.
scan_deps(path = ".")
scan_deps(path = ".")
path |
Path to the directory of the project. |
Data frame with columns:
path
: Path to the file in which the dependencies was found.
package
: Detected package dependency. Typically a package name,
but it can also be a package reference, e.g. a package from GitHub.
type
: Dependency type. It is "prod"
, "test"
or "dev"
. See
'Dependency types' below.
code
: The piece of code the dependency was extracted from.
start_row
: Start row of the code the dependency was extracted
from.
start_column
: Start column of the code the dependency was
extracted from.
start_byte
: Start byte of the code the dependency was extracted
from.
Note the data frame may contain the same package multiple times, if it
was detected multiple times, e.g. multiple library()
calls load the
same package.
scan_deps()
detects package dependencies from these R expressions:
library()
, require()
, loadNamespace()
and requireNamespace
calls.
::
and :::
operators.
Any of the calls in this list in R code from R markdown or quarto
R
and Rscript
(case insensitive) code blocks or inline R code.
A dependency on the methods package is inferred from finding
setClass()
and/or setGeneric()
calls.
xfun::pkg_attach()
and xfun::pkg_attach2()
calls.
pacman::p_load()
calls.
modules::import()
and modules::module()
calls.
import::from()
, import::here()
and import::into()
calls.
box::use()
calls.
targets::tar_option_set(packages = ...)
calls.
Any of the calls in this list in R code from glue::glue()
strings.
A dependency on the svglite package is inferred from
ggplot2::ggsave()
calls saving .svg
files.
Dependencies from parsnip::set_engine()
calls, the default engine
to package mapping is:
"glm"
-> stats,
"glmnet"
-> glmnet,
"keras"
-> keras,
"kknn"
-> kknn,
"nnet"
-> nnet,
"rpart"
-> rpart,
"spark"
-> sparklyr,
"stan"
-> rstanarm.
You can override the default mapping by setting the
renv.parsnip.engines
option to a named list.
A dependency on the xml2 package is inferred from using the
"Junit" reporter (JunitReporter
) from the testthat package.
A dependency on the ragg package is inferred from setting the default
knitr device (dev
option) to "ragg_png"
.
A dependency on the hexbin package is inferred from using
ggplot2::geom_hex()
.
A custom symbol name to package name mapping can be defined in the
renv.dependencies.database
option. This must be a named list of
named lists, where the outer names are package names, the inner names
are function or object names, and the values are package names. E.g.
options(renv.dependencies.database = list( ggplot2 = list(geom_hex = "hexbin"), testthat = list(JunitReporter = "xml2") ))
scan_deps()
classifies package dependencies into three groups, based
on which files they were found:
Production dependencies: "prod"
.
Test dependencies: "test"
.
Development dependencies: "dev"
.
sysreqs_check_installed()
checks if the system requirements of all
packages (or a subset of packages) are installed.
sysreqs_fix_installed()
installs the missing system packages.
sysreqs_check_installed(packages = NULL, library = .libPaths()[1]) sysreqs_fix_installed(packages = NULL, library = .libPaths()[1])
sysreqs_check_installed(packages = NULL, library = .libPaths()[1]) sysreqs_fix_installed(packages = NULL, library = .libPaths()[1])
packages |
If not |
library |
Library or libraries to check. |
These functions use the sysreqs_platform
configuration option,
see Configuration. Set this if
pkgdepends does not detect your platform correctly.
Data frame with a custom print and format method, and a
pkg_sysreqs_check_result
class. Its columns are:
system_package
: string, name of the required system package.
installed
: logical, whether the system package is correctly
installed.
packages
: list column of character vectors. The names of the
installed R packages that need this system package.
pre_install
: list column of character vectors. Commands to run
before the installation of the the system package.
post_install
: list column of character vectors. Commands to run
after the installation of the system package.
The data frame also have two attributes with additional data:
sysreqs_records
: the raw system requirements records, and
system_packages
: the list of the installed system packages.
sysreqs_fix_packages()
returns the same value, but invisibly.
Other system requirements functions:
sysreqs_db_list()
,
sysreqs_db_match()
,
sysreqs_db_update()
,
sysreqs_install_plan()
,
sysreqs_is_supported()
,
sysreqs_list_system_packages()
,
sysreqs_platforms()
# This only works on supported platforms sysreqs_check_installed()
# This only works on supported platforms sysreqs_check_installed()
It also tries to update the system dependency database, if it is
outdated. (I.e. older than allowed in the metadata_update_after
configuration option.
sysreqs_db_list(sysreqs_platform = NULL)
sysreqs_db_list(sysreqs_platform = NULL)
sysreqs_platform |
System requirements platform. If |
Data frame with columns:
name
: cross platform system dependency name in the database.
patterns
: one or more regular expressions to match to
SystemRequirements
fields.
packages
: one or more system package names to install.
pre_install
: command(s) to run before installing the packages.
post_install
:: command(s) to run after installing the packages.
Other system requirements functions:
sysreqs_check_installed()
,
sysreqs_db_match()
,
sysreqs_db_update()
,
sysreqs_install_plan()
,
sysreqs_is_supported()
,
sysreqs_list_system_packages()
,
sysreqs_platforms()
sysreqs_db_list(sysreqs_platform = "ubuntu-22.04")
sysreqs_db_list(sysreqs_platform = "ubuntu-22.04")
In the usual workflow pkgdepends matches the
SystemRequirements
fields of the DESCRIPTION
files to the database.
sysreqs_db_match(specs, sysreqs_platform = NULL)
sysreqs_db_match(specs, sysreqs_platform = NULL)
specs |
Character vector of system requirements descriptions. |
sysreqs_platform |
System requirements platform. If |
The sysreqs_db_match()
function lets you match any string, and it is
mainly useful for debugging.
Data frame with columns:
spec
: the input specs
.
sysreq
: name of the system library or tool.
packages
: system packages, list column of character vectors.
Rarely it can be an empty string, e.g. if a pre_install
script
performs the installation.
pre_install
: list column of character vectors. Shell script(s) to
run before the installation.
post_install
: list column of character vectors. Shell script(s) to
run after the installation.
Other system requirements functions:
sysreqs_check_installed()
,
sysreqs_db_list()
,
sysreqs_db_update()
,
sysreqs_install_plan()
,
sysreqs_is_supported()
,
sysreqs_list_system_packages()
,
sysreqs_platforms()
sysreqs_db_match( c("Needs libcurl", "Java, libssl"), sysreqs_platform = "ubuntu-22.04" )
sysreqs_db_match( c("Needs libcurl", "Java, libssl"), sysreqs_platform = "ubuntu-22.04" )
Update the cached copy of the system requirements database
sysreqs_db_update()
sysreqs_db_update()
If the the cached copy is recent, then no update is attempted. See the
metadata_update_after
configuration option.
Other system requirements functions:
sysreqs_check_installed()
,
sysreqs_db_list()
,
sysreqs_db_match()
,
sysreqs_install_plan()
,
sysreqs_is_supported()
,
sysreqs_list_system_packages()
,
sysreqs_platforms()
This function uses new_pkg_installation_proposal()
and its methods
to create an installation plan for one or more packages, and then print
their system requirements.
sysreqs_install_plan(refs, upgrade = TRUE, config = list())
sysreqs_install_plan(refs, upgrade = TRUE, config = list())
refs |
Packages to install. |
upgrade |
If |
config |
Configuration options. See
'Configuration'. If it does not include
|
List with entries:
os
: character string. Operating system.
distribution
: character string. Linux distribution, NA
if the
OS is not Linux.
version
: character string. Distribution version, NA
is the OS
is not Linux.
pre_install
: character vector. Commands to run before the
installation of system packages.
install_scripts
: character vector. Commands to run to install the
system packages.
post_install
: character vector. Commands to run after the
installation of system packages.
packages
: data frame. Information about the system packages that
are needed. It has columns:
sysreq
: string, cross-platform name of the system requirement.
packages
: list column of character vectors. The names of the R
packages that have this system requirement.
pre_install
: list column of character vectors. Commands run
before the package installation for this system requirement.
system_packages
: list column of character vectors. Names of
system packages to install.
post_install
: list column of character vectors. Commands run
after the package installation for this system requirement.
new_pkg_installation_proposal()
to actually install
packages, and potentially system requirements.
Other system requirements functions:
sysreqs_check_installed()
,
sysreqs_db_list()
,
sysreqs_db_match()
,
sysreqs_db_update()
,
sysreqs_is_supported()
,
sysreqs_list_system_packages()
,
sysreqs_platforms()
sysreqs_install_plan( "tidyverse", config = list(sysreqs_platform = "ubuntu-22.04") )
sysreqs_install_plan( "tidyverse", config = list(sysreqs_platform = "ubuntu-22.04") )
Check if a platform has system requirements support
sysreqs_is_supported(sysreqs_platform = NULL)
sysreqs_is_supported(sysreqs_platform = NULL)
sysreqs_platform |
System requirements platform. If |
Logical scalar.
The sysreqs_platform
configuration option.
Other system requirements functions:
sysreqs_check_installed()
,
sysreqs_db_list()
,
sysreqs_db_match()
,
sysreqs_db_update()
,
sysreqs_install_plan()
,
sysreqs_list_system_packages()
,
sysreqs_platforms()
sysreqs_is_supported()
sysreqs_is_supported()
List installed system packages
sysreqs_list_system_packages()
sysreqs_list_system_packages()
This function uses the sysreqs_platform
configuration option,
see Configuration. Set this if
pkgdepends does not detect your platform correctly.
Data frame with columns:
status
. two or three characters, the notation of dpkg
on Debian
based systems. "ii"
means the package is correctly installed.
On RPM
based systems it is always "ii"
currently.
package
: name of the system package.
version
: installed version of the system package.
capabilities
: list column of character vectors, the capabilities
provided by the package.
Other system requirements functions:
sysreqs_check_installed()
,
sysreqs_db_list()
,
sysreqs_db_match()
,
sysreqs_db_update()
,
sysreqs_install_plan()
,
sysreqs_is_supported()
,
sysreqs_platforms()
sysreqs_list_system_packages()[1:10,]
sysreqs_list_system_packages()[1:10,]
List platforms with system requirements support
sysreqs_platforms()
sysreqs_platforms()
Data frame with columns:
name
: human readable OS name.
os
: OS name, e.g. linux
.
distribution
: OS id, e.g. ubuntu
or redhat
.
version
: distribution version. A star means that all versions are
supported, that are also supported by the vendor.
update_command
: command to run to update the system package metadata.
install_command
: command to run to install packages.
query_command
: name of the tool to use to query system package
information.
Other system requirements functions:
sysreqs_check_installed()
,
sysreqs_db_list()
,
sysreqs_db_match()
,
sysreqs_db_update()
,
sysreqs_install_plan()
,
sysreqs_is_supported()
,
sysreqs_list_system_packages()
sysreqs_platforms()
sysreqs_platforms()