CHANGES IN VERSION 1.30.25 ------------------------- MINOR CHANGES o Maintainer email change. CHANGES IN VERSION 1.30.24 ------------------------- NEW FEATURES o Force BiocManager to use unsupported version of R with `R_BIOC_VERSION` environment variable (@mtmorgan, #193) CHANGES IN VERSION 1.30.23 ------------------------- NEW FEATURES o Ensure compatibility with `package_version` changes in R 4.4.0 (@kurthornik) MINOR CHANGES o Added "Updating old packages" and "Archived CRAN packages" sections in the vignette o Use `BiocStyle` formatting in the vignette o Update Posit links in the vignette CHANGES IN VERSION 1.30.22 ------------------------- NEW FEATURES o Enable site_repository environment variable or option for install, valid MINOR CHANGES o Ensure character input to package_version function (@kurthornik) CHANGES IN VERSION 1.30.21 ------------------------- NEW FEATURES o Enable the use of the Bioc-devel branch on R-devel during the 'summer' release cycle (@mtmorgan, #166) o Allow `BIOCMANAGER_SITE_REPOSITORY` environment variable and `BiocManager.site_repository` option as a more permanent option for `site_repository` users (@LiNk-NY). o Support for "time machine" CRAN installations has moved to BiocArchive and has been removed from the package (#151, @LiNk-NY) MINOR CHANGES o Correct links on help pages. See ; thanks @aitap o Additional documentation provided for offline use of BiocManager in `?install` and in the main vignette (#165, @mtmorgan). CHANGES IN VERSION 1.30.20 ------------------------- NEW FEATURES o Add `BIOCMANAGER_CHECK_REPOSITORIES` environment variable for non-interactive sessions as an alternative to the `BiocManager.check_repositories` option (#144, @HenrikBengtsson) MINOR CHANGES o Re-use and translate `update` and `ask` arguments when installing via `install_github` (#126, @Jiefei-Wang) o Allow `type` argument during package installation to opt out of binary installations (#103, @lshep) o Check `BiocVersion` installation with `system.file` rather than with `packageVersion` (K. Hornik) CHANGES IN VERSION 1.30.19 ------------------------- MINOR CHANGES o Updated warning message for clarity when packages are installed of the same version or greater. o The `ask` argument is passed through to the `remotes::install_github` o Update unit tests which did not include the full scenario of options o Catch zero length outputs when timeouts occur (#140, @hpages) CHANGES IN VERSION 1.30.18 ------------------------- MINOR CHANGES o Increase robustness of code when loading and working with the version map o Add internal checks to version tags in map and update unit tests o Include a 'troubleshooting' section in the vignette CHANGES IN VERSION 1.30.17 ------------------------- NEW FEATURES o `containerRepository` reports the location of binary packages for containerized images of Bioconductor, if available. BUG FIXES o `install` appropriately returns a warning from `install.packages` instead of a character vector (#112, @mtmorgan). CHANGES IN VERSION 1.30.16 ------------------------- BUG FIXES o Ensure that the `force` argument is passed along after installation of `BiocVersion` (#105, @lshep, @jwokaty) o Fix typo in `.VERSION_MAP_SENTINEL` (`RSPM` column name). CHANGES IN VERSION 1.30.15 ------------------------- BUG FIXES o `.skip_if_misconfigured` function should work with `_R_CHECK_DEPENDS_ONLY=true` o Switch to `interactive()` only examples for `available()` CHANGES IN VERSION 1.30.14 ------------------------- BUG FIXES o `install` now passes the `force` argument to `install_github` (#101, @lgeistlinger) o Treat warnings as warnings internally in `install.packages()` (#100, @biobenkj) o Check version validity `.onAttach` rather than `.onLoad` CHANGES IN VERSION 1.30.13 ------------------------- NEW FEATURES o Downloading the same version of a remote package already installed will be avoided unless the user supplies `force=TRUE` to `install`. USER VISIBLE CHANGES o 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 o Added a warning and informative message when a package is 'not available' (#85, @LTLA). o `BIOCONDUCTOR_CONFIG_FILE` now included in the documentation for `install` (#93, @glin). CHANGES IN VERSION 1.30.12 ------------------------- NEW FEATURES o 'BIOCONDUCTOR_CONFIG_FILE' option allows users to provide an offline and local configuration file (config.yaml) for version validation. o Bioconductor 'BioCbooks' repository now available in Bioconductor versions >= "3.12" USER VISIBLE CHANGES o Enable use of historical snapshots ('MRAN' or 'RSPM' via `options(BiocManager.snapshots=)`) to install CRAN packages for out-of-date Bioconductor versions. o Respect `options(repos = c(CRAN = "..."))`. See https://github.com/Bioconductor/BiocManager/issues/69 BUG FIXES o Increase timeout from 1 to 5 minutes (300 seconds) to make download of large packages more robust. CHANGES IN VERSION 1.30.10 ------------------------- MINOR CHANGES o Restore startup message with recommended version o Update mis-configuration skip in tests CHANGES IN VERSION 1.30.9 ------------------------- MINOR CHANGES o Use `packageStartupMessage()` in .onLoad o Tests are robust to missing Suggests: BiocVersion CHANGES IN VERSION 1.30.8 ------------------------- MINOR CHANGES o Tests are skipped if is there is a misconfiguration or the CRAN builder has no internet access. CHANGES IN VERSION 1.30.7 ------------------------- NEW FEATURES o Support R-4.0 MINOR CHANGES o 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. CHANGES IN VERSION 1.30.6 ------------------------- MINOR CHANGES o Improve unit tests under Bioconductor versions 3.8, 3.9, 3.10. o Improve error message when non-interactive version update fails. BUG FIXES o BiocManager loads when off-line. CHANGES IN VERSION 1.30.5 ------------------------- NEW FEATURES o Allow users to specify `checkBuilt` when invoking `valid()` or `install()`. Set default `FALSE`. MINOR CHANGES o Allow use of BiocInstaller for R < 3.5, pointing to biocLite() when appropriate. o Improve performance of version checking (issue #42 @HenrikBengtsson). o Document off-line installation best practices. o Warn about out-of-date packages on load (in addition to on attach) (issue #29) CHANGES IN VERSION 1.30.4 ------------------------- NEW FEATURES o Provide an 'http' fallback when 'https' fails for accessing the version map hosted on Bioconductor.org MINOR CHANGES o Conform tests to devel and release R versions o Add tests for the 'http' fallback scenarios BUG FIXES o Fixed issue with multiple error version messages for Bioc version `3.9` 'devel' and 'future' o Return a warning message instead of an error when unable to validate a given version CHANGES IN VERSION 1.30.3 ------------------------- NEW FEATURES o '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 o Removed extra prompts when switching versions and updating packages o Clarified 'See Also' documentation (@lwaldron #16) o Added several unit tests to increase robustness (@mtmorgan) BUG FIXES o Obtain CRAN 'repos' option independent of name (@kasperdanielhansen #17) o Fixed a bug when switching to 'devel' version of Bioconductor (@kasperdanielhansen #25) o When installation is valid, return zero invalid packages rather than accessing non-existent list structure CHANGES IN VERSION 1.30.2 ------------------------- USER VISIBLE CHANGES o install() only allows Bioconductor version upgrades and downgrades with an empty 'pkgs' argument. Otherwise, it gives the user an informative error. o 'ask' argument is respected when in non-interactive mode (@lshep #9) o valid() returns TRUE for valid Bioconductor installations otherwise, it prints a report of out-of-date and/or too new packages MINOR CHANGES o updated unit tests for install() o when changing versions via 'install(version = "x.x")', Bioconductor packages to be up or down-graded are now enumerated BUG FIXES o Remove tests that were dependent on system configuration rather than the package itself CHANGES IN VERSION 1.30.1 ------------------------- USER VISIBLE CHANGES o install() '...' arguments must be named. CHANGES IN VERSION 1.30.0 ------------------------- NEW FEATURES o package renamed to BiocManager o install() supports github repositories using the remotes package, rather than devtools. This change should be transparent to end users. (@PeteHaitch, #4) o functions renamed to the following: biocLite > install; biocInstallRepos > repositories; biocValid > valid; biocVersion > version o functions removed: biocases_group, biocUpdatePackages, isDevel, useDevel, *_group o available() enables package discovery via grep() o Removed support for MRAN (Microsoft R) archives. CHANGES IN VERSION 1.28.0 ------------------------- NEW FEATURES o biocLite() supports full URLs, e.g., to archived Bioconductor packages. o Support MRAN (Microsoft R) archives. CHANGES IN VERSION 1.24.0 ------------------------- NEW FEATURES o biocLite() uses lib.loc= to find devtools, reports more informatively why devtools fails to load o biocLite() only offers to update non-masked packages o biocLite() reports when packages in unwriteable directories are out-of-date, but does not try (and fail) to update them. o isDevel() returns TRUE if the version of BiocInstaller corresponds to the development version of Bioconductor. CHANGES IN VERSION 1.20.0 ------------------------- BUG FIXES o biocLite() uses lib.loc when calling update.packages CHANGES IN VERSION 1.18.0 ------------------------- NEW FEATURES o biocLite() supports github repositories (implicitly, 'packages' following the 'maintainer/package' convention) CHANGES IN VERSION 1.14.0 ------------------------- NEW FEATURES o biocUpdatePackages updates installed packages and their dependencies. CHANGES IN VERSION 1.10.0 ------------------------- NEW FEATURES o biocValid() checks that installed packages are consistent with those available via biocLite(). o biocVersion() returns the version of Bioconductor expected with this version of the BiocInstaller package. USER-VISIBLE CHANGES o biocLite() invoked with no arguments updates currently installed packages to their most-recent version.