use_bioconductor configuration option in meta_*() and
repo_*() functions (#295, #726, @meztez).pkg_deps() now accepts a vector of package names.
The metadata cache now does not use source URLs for packages in Archive
on Posit Package Manager repositories. This URLs may serve a different
package, even a source package when the main URL for the same package
serves a binary package. The alternative URLs are not needed on PPM,
anyway, because PPM is in a consistent state w.r.t. metadata and
package files (#623).
pak now supports gitlab:: package sources better, by adding
explicit syntax to specify subdirectories (https://github.com/r-lib/pkgdepends/issues/353, @dgkf).
gitlab:: and git:: package sources now support git submodules if
the git-submodules configuration option is set to TRUE. See
?"pak-config" (https://github.com/r-lib/pkgdepends/issues/354).
The new ?ignore-unavailable parameter makes it easy to ignore soft
dependencies that are unavailable (#606).
pak now automatically ignores soft dependencies that have an
incompatible OS type (OS_type entry in DESCRIPTION) when installing
packages.
repo_add() and the ppm_*() functions, e.g. ppm_snapshots(), now
work again after the PPM API changes
(https://github.com/r-lib/pkgcache/issues/110,
https://github.com/r-lib/pkgcache/issues/115).
pak now supports using parameters for all packages with the
*=?<param> form. E.g. *=?source installs all packages from source.
pak now supports R 4.4.0 again, and also Rtools44.
pak can now handle the case when Config/Needs/* dependencies
are requested for package from a repository.
pak uses safer *printf() format strings now.
pak now correctly handles the latest GitHub release with
the @*release notation (@pawelru,
https://github.com/r-lib/pkgdepends/pull/321)
pak now correctly handles having multiple instances of the same package in the metadata, with different R version requirements (#534, #538, https://github.com/r-lib/pkgdepends/pull/331).
git:: package references work better now for Azure DevOps
(@jameslairdsmith, https://github.com/r-lib/pkgdepends/pull/333,
https://github.com/r-lib/pkgdepends/pull/342).
pak now does a better job at accepting installed packages, and avoids reinstalling more packages than needed when using a lock file (https://github.com/r-lib/actions/issues/759, https://github.com/r-lib/pkgdepends/pull/338).
pak now requires R >= 3.5.0.
Many improvements in system requirements support:
pkg_sysreqs(): calculate system requirements of packages.sysreqs_db_list(), sysreqs_db_match(), sysreqs_db_update():
query the system requirements database.sysreqs_list_system_packages(), sysreqs_check_installed(),
sysreqs_fix_installed(): query and install missing system packages.sysreqs_platforms(): list supported platforms.sysreqs_platform configuration option to override the auto-detected
platform.sysreqs_update configuration option.)New gitlab:: package source to install packages from GitLab
(https://github.com/r-lib/pkgdepends/pull/315).
pak now correctly parses multiple git:: packages at once
(https://github.com/r-lib/pkgdepends/issues/318).
git:: package sources now support version 1 of the git protocol.
E.g. the Bioconductor git repositories now work:
git::https://git.bioconductor.org/packages/limma
(https://github.com/r-lib/pkgdepends/issues/314).
The platforms config parameter now works correctly with deps::
package sources (#522).
New include_linkingto config parameter to always include LinkingTo
packages in the solution, even for binaries
(https://github.com/r-lib/pkgdepends/issues/485).
pkg_name_check() now does not include Acromine results, because the web
site was unstable.
In repo_add() and repo_resolve() the MRAN@ prefix is now deprecated
and resolves to PPM, because MRAN will be retired soon. See more at
https://posit.co/blog/migrating-from-mran-to-posit-package-manager/.
The metadata cache now has SystemRequirements information for Bioconductor
packages.
The meta_*() functions now consider the platforms, cran_mirror and
r_versions config entries, see ?"pak-config".
Better Posit Package Manager (PPM) support. New +ppm_has_binaries(),
ppm_r_versions(), ppm_repo_url(), ppm_snapshots() and ppm_platforms()
functions to help interacting with PPM. See the new 'pkgcache and Posit
Package Manager on Linux' article at https://r-lib.github.io/pkgcache.
(r-lib/pkgcache#47 and r-lib/pkgdepends#186).
New system_r_platform() and system_r_platform_data() functions to query
the current platform.
pak now support git repositories as package references. E.g.
git::https://github.com/r-lib/pak.git.
pak now supports versioned CRAN packages, e.g. [email protected] will
always install dplyr 1.1.1. Note that only CRAN packages are supported,
Bioconductor packages are not (yet).
pak now has an alternative system requirements lookup
implementation. It supports Fedora and Debian systems as well, in
addition to Debian, Ubuntu, SUSE and RedHat derivatives.
You can switch to this implementation by setting the
R_PKG_SYSREQS2 environment variable to true.
pak now does a better job looking up dependencies for
hand-selected dependency types. E.g. dependencies = "LinkingTo".
pak now removes ?ignore-d packages from dependencies, and
uses the correct version comparison for ?ignore-before.r
(https://github.com/r-lib/actions/issues/708).
pak now does not fail for circular soft dependencies (#306).
pak now reports dependency solver failures better in some cases (#305, https://github.com/r-lib/pak/issues/474).
pak now uses locally built CRAN binaries from the cache. Use the
?nocache parameter to opt out from this, or
cache_delete(package = ...) to remove a package from the cache.
pak has much improved and more informative error messages now. This work is not yet finished, so if you find an unclear error message, please open an issue. Thank you!
The solver is now more robust for non-canonical input (e.g. DESCRIPTION
files) (https://github.com/r-lib/pak/issues/423).
Better installation output. Standard output and error are now collected together (https://github.com/r-lib/pkgdepends/commit/0669f0f8c).
The solver is now doing a better job when multiple versions of the same package are present in the same repository (https://github.com/r-lib/actions/issues/559).
pkg_name_check() now works again, it needed a fix after changes at
https://crandb.r-pkg.org.
Explicit package names in local and URL package sources, as in
package=local::... or package=url::... are now parsed correctly in
dependencies.
pak is now more robust to Archs fields missing from the CRAN
metadata for packages with compiled code
(https://github.com/r-lib/pak/issues/448).
url:: packages now always work correctly, even if the digest package is
not installed (https://github.com/r-lib/pak/issues/433).
pak is now more robust when installing packages from subdirectories of GitHub repositories (https://github.com/r-lib/pak/issues/431, @paleolimbot).
Parameters ?reinstall, ?source and ?ignore now work correctly when
specified in the package=?parameter format (#294).
The ?ignore parameter works correctly now.
Dependency resolution now does not fail if a package is not found.
pak can now install url:: remotes from GitHub.
pak now does not fail when the package of a .tar.gz GitHub
snapshot is in a subdirectory, or in a subdirectory of a subdirectory.
pak now errors early if it cannot deduce the name of the package
from a Remotes or Config/Needs/* entry.
Solver failures now include details in some cases where previously they did not.
pak can now update packages in Docker containers where the old version was installed in the different Docker later (https://github.com/r-lib/pak/issues/251)
Update R version -> Bioconductor version mapping. R 4.2.x now maps to Bioconductor 3.16.
The ?ignore parameter works correctly now.
Dependency resolution now does not fail if a package is not found.
pak can now install url:: remotes from GitHub.
pak now does not fail when the package of a .tar.gz GitHub
snapshot is in a subdirectory, or in a subdirectory of a subdirectory.
pak now errors early if it cannot deduce the name of the package
from a Remotes or Config/Needs/* entry.
Solver failures now include details in some cases where previously they did not.
pak can now update packages in Docker containers where the old version was installed in the different Docker later (#251)
pak errors are now user friendlier and better formatted.
pak now does not load tibble and its dependencies in the pak subprocess, so their dlls are not locked by the pak subprocess on Windows.
pak now does not fail when installing a package that uses a non-UTF-8 encoding on R 4.3.x and later (#404).
pak functions that used to return tibbles return data frames now.
While data frames and tibbles are very similar, they are not completely
compatible. To convert the outputs of pak functions to tibbles call the
tibble::as_tibble() function on them. If the pillar package is loaded,
it improves the printing of the returned data frames.
Relatedly, pak::pak_install_extra() installs pillar now, instead of tibble.
pak now supports file:// repositories.
pak now uses HTTP 1.1 to download packages on Linux, in addition to macOS. This fixes HTTP issues with some servers (#358).
New ?ignore-before-r parameter to ignore optional dependencies that
need a newer R version (https://github.com/r-lib/pkgdepends/issues/243).
New ?ignore parameter to ignore an optional dependency.
Allow specifying downstream package parameters with the package=?param
syntax.
lockfile_install() now works better for any:: refs, and pak always
install the version it has planned for.
System requirement installation is now more robust and works for Unix shell expressions (#347).
CRAN-like resolution is more robust now if a repository is missing the usual metadata.
The lock file is pretty JSON now.
pak now handles all version requirement types properly:
'<', '<=', ==, >=, >.
The dependency solver now uses better heuristics and does not (effectively) freeze if multiple repositories have multiple versions of the same packages (e.g. RSPM and CRAN) (https://github.com/r-lib/pkgdepends/pull/277)
No user visible changes.
Lots of news, too much to list. This is a completely new package now.
First version on CRAN.