NEWS

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BiocManager 1.30.25 (2024-08-28)

MINOR CHANGES

• Maintainer email change.

BiocManager 1.30.24 (2024-08-20)

NEW FEATURES

• Force BiocManager to use unsupported version of R with 'R_BIOC_VERSION' environment variable (@mtmorgan, #193)

BiocManager 1.30.23 (2024-05-04)

NEW FEATURES

• Ensure compatibility with 'package_version' changes in R 4.4.0 (@kurthornik)

MINOR CHANGES

• Added "Updating old packages" and "Archived CRAN packages" sections in the vignette
• Use 'BiocStyle' formatting in the vignette
• Update Posit links in the vignette

BiocManager 1.30.22 (2023-08-08)

NEW FEATURES

• Enable site_repository environment variable or option for install, valid

MINOR CHANGES

• Ensure character input to package_version function (@kurthornik)

BiocManager 1.30.21 (2023-06-09)

NEW FEATURES

• Enable the use of the Bioc-devel branch on R-devel during the 'summer' release cycle (@mtmorgan, #166)
• Allow 'BIOCMANAGER_SITE_REPOSITORY' environment variable and 'BiocManager.site_repository' option as a more permanent option for 'site_repository' users (@LiNk-NY).
• Support for "time machine" CRAN installations has moved to BiocArchive and has been removed from the package (#151, @LiNk-NY)

MINOR CHANGES

• Correct links on help pages. See <https://github.com/Bioconductor/BiocManager/pull/160>; thanks @aitap
• Additional documentation provided for offline use of BiocManager in '?install' and in the main vignette (#165, @mtmorgan).

BiocManager 1.30.20 (2023-02-24)

NEW FEATURES

• Add 'BIOCMANAGER_CHECK_REPOSITORIES' environment variable for non-interactive sessions as an alternative to the 'BiocManager.check_repositories' option (#144, @HenrikBengtsson)

MINOR CHANGES

• Re-use and translate 'update' and 'ask' arguments when installing via 'install_github' (#126, @Jiefei-Wang)
• Allow 'type' argument during package installation to opt out of binary installations (#103, @lshep)
• Check 'BiocVersion' installation with 'system.file' rather than with 'packageVersion' (K. Hornik)

BiocManager 1.30.19 (2022-10-25)

MINOR CHANGES

• Updated warning message for clarity when packages are installed of the same version or greater.
• The 'ask' argument is passed through to the 'remotes::install_github'
• Update unit tests which did not include the full scenario of options
• Catch zero length outputs when timeouts occur (#140, @hpages)

BiocManager 1.30.18 (2022-05-18)

MINOR CHANGES

• Increase robustness of code when loading and working with the version map
• Add internal checks to version tags in map and update unit tests
• Include a 'troubleshooting' section in the vignette

BiocManager 1.30.17 (2022-04-21)

NEW FEATURES

• 'containerRepository' reports the location of binary packages for containerized images of Bioconductor, if available.

BUG FIXES

• 'install' appropriately returns a warning from 'install.packages' instead of a character vector (#112, @mtmorgan).

BiocManager 1.30.16 (2021-06-15)

BUG FIXES

• Ensure that the 'force' argument is passed along after installation of 'BiocVersion' (#105, @lshep, @jwokaty)
• Fix typo in '.VERSION_MAP_SENTINEL' ('RSPM' column name).

BiocManager 1.30.15 (2021-05-11)

BUG FIXES

• '.skip_if_misconfigured' function should work with '_R_CHECK_DEPENDS_ONLY=true'
• Switch to 'interactive()' only examples for 'available()'

BiocManager 1.30.14 (2021-05-10)

BUG FIXES

• 'install' now passes the 'force' argument to 'install_github' (#101, @lgeistlinger)
• Treat warnings as warnings internally in 'install.packages()' (#100, @biobenkj)
• Check version validity '.onAttach' rather than '.onLoad'

BiocManager 1.30.13 (2021-05-07)

NEW FEATURES

• Downloading the same version of a remote package already installed will be avoided unless the user supplies 'force=TRUE' to 'install'.

USER VISIBLE CHANGES

• Devel users on a newer version of R will not get an error when the minor version of R is +1 of the recommended

BUG FIXES

• Added a warning and informative message when a package is 'not available' (#85, @LTLA).
• 'BIOCONDUCTOR_CONFIG_FILE' now included in the documentation for 'install' (#93, @glin).

BiocManager 1.30.12 (2021-03-28)

NEW FEATURES

• 'BIOCONDUCTOR_CONFIG_FILE' option allows users to provide an offline and local configuration file (config.yaml) for version validation.
• Bioconductor 'BioCbooks' repository now available in Bioconductor versions >= "3.12"

USER VISIBLE CHANGES

• Enable use of historical snapshots ('MRAN' or 'RSPM' via 'options(BiocManager.snapshots=)') to install CRAN packages for out-of-date Bioconductor versions.
• Respect 'options(repos = c(CRAN = "..."))'. See https://github.com/Bioconductor/BiocManager/issues/69

BUG FIXES

• Increase timeout from 1 to 5 minutes (300 seconds) to make download of large packages more robust.

BiocManager 1.30.10 (2019-11-16)

MINOR CHANGES

• Restore startup message with recommended version
• Update mis-configuration skip in tests

BiocManager 1.30.9 (2019-10-23)

MINOR CHANGES

• Use 'packageStartupMessage()' in .onLoad
• Tests are robust to missing Suggests: BiocVersion

BiocManager 1.30.8 (2019-10-16)

MINOR CHANGES

• Tests are skipped if is there is a misconfiguration or the CRAN builder has no internet access.

BiocManager 1.30.7 (2019-10-07)

NEW FEATURES

• Support R-4.0

MINOR CHANGES

• Conform to CRAN policy to fail with messages rather than warnings or errors when internet access fails; internet access failures continue to generate warnings or errors during regular use.

BiocManager 1.30.6

MINOR CHANGES

• Improve unit tests under Bioconductor versions 3.8, 3.9, 3.10.
• Improve error message when non-interactive version update fails.

BUG FIXES

• BiocManager loads when off-line.

BiocManager 1.30.5

NEW FEATURES

• Allow users to specify 'checkBuilt' when invoking 'valid()' or 'install()'. Set default 'FALSE'.

MINOR CHANGES

• Allow use of BiocInstaller for R < 3.5, pointing to biocLite() when appropriate.
• Improve performance of version checking (issue #42 @HenrikBengtsson).
• Document off-line installation best practices.
• Warn about out-of-date packages on load (in addition to on attach) (issue #29)

BiocManager 1.30.4 (2018-11-13)

NEW FEATURES

• Provide an 'http' fallback when 'https' fails for accessing the version map hosted on Bioconductor.org

MINOR CHANGES

• Conform tests to devel and release R versions
• Add tests for the 'http' fallback scenarios

BUG FIXES

• Fixed issue with multiple error version messages for Bioc version ‘3.9' ’devel' and 'future'
• Return a warning message instead of an error when unable to validate a given version

BiocManager 1.30.3 (2018-10-10)

NEW FEATURES

• 'BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS' option allows users to skip online version map validation. Local installation of 'BiocVersion' will be used when this option is enabled.

MINOR CHANGES

• Removed extra prompts when switching versions and updating packages
• Clarified 'See Also' documentation (@lwaldron #16)
• Added several unit tests to increase robustness (@mtmorgan)

BUG FIXES

• Obtain CRAN 'repos' option independent of name (@kasperdanielhansen #17)
• Fixed a bug when switching to 'devel' version of Bioconductor (@kasperdanielhansen #25)
• When installation is valid, return zero invalid packages rather than accessing non-existent list structure

BiocManager 1.30.2 (2018-08-24)

USER VISIBLE CHANGES

• install() only allows Bioconductor version upgrades and downgrades with an empty 'pkgs' argument. Otherwise, it gives the user an informative error.
• 'ask' argument is respected when in non-interactive mode (@lshep #9)
• valid() returns TRUE for valid Bioconductor installations otherwise, it prints a report of out-of-date and/or too new packages

MINOR CHANGES

• updated unit tests for install()
• when changing versions via 'install(version = "x.x")', Bioconductor packages to be up or down-graded are now enumerated

BUG FIXES

• Remove tests that were dependent on system configuration rather than the package itself

BiocManager 1.30.1 (2018-06-15)

USER VISIBLE CHANGES

• install() '...' arguments must be named.

BiocManager 1.30.0

NEW FEATURES

• package renamed to BiocManager
• install() supports github repositories using the remotes package, rather than devtools. This change should be transparent to end users. (@PeteHaitch, #4)
• functions renamed to the following: biocLite > install; biocInstallRepos > repositories; biocValid > valid; biocVersion > version
• functions removed: biocases_group, biocUpdatePackages, isDevel, useDevel, *_group
• available() enables package discovery via grep()
• Removed support for MRAN (Microsoft R) archives.

BiocManager 1.28.0

NEW FEATURES

• biocLite() supports full URLs, e.g., to archived Bioconductor packages.
• Support MRAN (Microsoft R) archives.

BiocManager 1.24.0

NEW FEATURES

• biocLite() uses lib.loc= to find devtools, reports more informatively why devtools fails to load
• biocLite() only offers to update non-masked packages
• biocLite() reports when packages in unwriteable directories are out-of-date, but does not try (and fail) to update them.
• isDevel() returns TRUE if the version of BiocInstaller corresponds to the development version of Bioconductor.

BiocManager 1.20.0

BUG FIXES

• biocLite() uses lib.loc when calling update.packages

BiocManager 1.18.0

NEW FEATURES

• biocLite() supports github repositories (implicitly, 'packages' following the 'maintainer/package' convention)

BiocManager 1.14.0

NEW FEATURES

• biocUpdatePackages updates installed packages and their dependencies.

BiocManager 1.10.0

NEW FEATURES

• biocValid() checks that installed packages are consistent with those available via biocLite().
• biocVersion() returns the version of Bioconductor expected with this version of the BiocInstaller package.

USER-VISIBLE CHANGES

• biocLite() invoked with no arguments updates currently installed packages to their most-recent version.