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NEWS
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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
<https://github.com/Bioconductor/BiocManager/pull/160>; 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.