430 lines
11 KiB
Plaintext
430 lines
11 KiB
Plaintext
CHANGES IN VERSION 1.30.25
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-------------------------
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MINOR CHANGES
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o Maintainer email change.
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CHANGES IN VERSION 1.30.24
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-------------------------
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NEW FEATURES
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o Force BiocManager to use unsupported version of R with `R_BIOC_VERSION`
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environment variable (@mtmorgan, #193)
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CHANGES IN VERSION 1.30.23
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-------------------------
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NEW FEATURES
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o Ensure compatibility with `package_version` changes in R 4.4.0
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(@kurthornik)
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MINOR CHANGES
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o Added "Updating old packages" and "Archived CRAN packages" sections in
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the vignette
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o Use `BiocStyle` formatting in the vignette
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o Update Posit links in the vignette
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CHANGES IN VERSION 1.30.22
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-------------------------
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NEW FEATURES
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o Enable site_repository environment variable or option for install, valid
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MINOR CHANGES
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o Ensure character input to package_version function (@kurthornik)
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CHANGES IN VERSION 1.30.21
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-------------------------
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NEW FEATURES
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o Enable the use of the Bioc-devel branch on R-devel during the 'summer'
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release cycle (@mtmorgan, #166)
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o Allow `BIOCMANAGER_SITE_REPOSITORY` environment variable and
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`BiocManager.site_repository` option as a more permanent option for
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`site_repository` users (@LiNk-NY).
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o Support for "time machine" CRAN installations has moved to BiocArchive
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and has been removed from the package (#151, @LiNk-NY)
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MINOR CHANGES
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o Correct links on help pages. See
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<https://github.com/Bioconductor/BiocManager/pull/160>; thanks
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@aitap
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o Additional documentation provided for offline use of BiocManager in
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`?install` and in the main vignette (#165, @mtmorgan).
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CHANGES IN VERSION 1.30.20
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-------------------------
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NEW FEATURES
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o Add `BIOCMANAGER_CHECK_REPOSITORIES` environment variable for
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non-interactive sessions as an alternative to the
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`BiocManager.check_repositories` option (#144, @HenrikBengtsson)
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MINOR CHANGES
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o Re-use and translate `update` and `ask` arguments when installing via
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`install_github` (#126, @Jiefei-Wang)
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o Allow `type` argument during package installation to opt out of binary
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installations (#103, @lshep)
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o Check `BiocVersion` installation with `system.file` rather than with
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`packageVersion` (K. Hornik)
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CHANGES IN VERSION 1.30.19
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-------------------------
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MINOR CHANGES
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o Updated warning message for clarity when packages are installed of the
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same version or greater.
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o The `ask` argument is passed through to the `remotes::install_github`
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o Update unit tests which did not include the full scenario of options
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o Catch zero length outputs when timeouts occur (#140, @hpages)
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CHANGES IN VERSION 1.30.18
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-------------------------
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MINOR CHANGES
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o Increase robustness of code when loading and working with the
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version map
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o Add internal checks to version tags in map and update unit tests
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o Include a 'troubleshooting' section in the vignette
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CHANGES IN VERSION 1.30.17
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-------------------------
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NEW FEATURES
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o `containerRepository` reports the location of binary packages for
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containerized images of Bioconductor, if available.
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BUG FIXES
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o `install` appropriately returns a warning from `install.packages` instead
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of a character vector (#112, @mtmorgan).
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CHANGES IN VERSION 1.30.16
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-------------------------
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BUG FIXES
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o Ensure that the `force` argument is passed along after installation of
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`BiocVersion` (#105, @lshep, @jwokaty)
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o Fix typo in `.VERSION_MAP_SENTINEL` (`RSPM` column name).
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CHANGES IN VERSION 1.30.15
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-------------------------
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BUG FIXES
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o `.skip_if_misconfigured` function should work with
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`_R_CHECK_DEPENDS_ONLY=true`
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o Switch to `interactive()` only examples for `available()`
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CHANGES IN VERSION 1.30.14
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-------------------------
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BUG FIXES
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o `install` now passes the `force` argument to `install_github`
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(#101, @lgeistlinger)
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o Treat warnings as warnings internally in `install.packages()`
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(#100, @biobenkj)
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o Check version validity `.onAttach` rather than `.onLoad`
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CHANGES IN VERSION 1.30.13
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-------------------------
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NEW FEATURES
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o Downloading the same version of a remote package already installed will
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be avoided unless the user supplies `force=TRUE` to `install`.
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USER VISIBLE CHANGES
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o Devel users on a newer version of R will not get an error when the minor
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version of R is +1 of the recommended
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BUG FIXES
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o Added a warning and informative message when a package is 'not available'
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(#85, @LTLA).
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o `BIOCONDUCTOR_CONFIG_FILE` now included in the documentation for
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`install` (#93, @glin).
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CHANGES IN VERSION 1.30.12
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-------------------------
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NEW FEATURES
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o 'BIOCONDUCTOR_CONFIG_FILE' option allows users to provide an offline
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and local configuration file (config.yaml) for version validation.
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o Bioconductor 'BioCbooks' repository now available in Bioconductor
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versions >= "3.12"
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USER VISIBLE CHANGES
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o Enable use of historical snapshots ('MRAN' or 'RSPM' via
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`options(BiocManager.snapshots=)`) to install CRAN packages for
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out-of-date Bioconductor versions.
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o Respect `options(repos = c(CRAN = "..."))`. See
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https://github.com/Bioconductor/BiocManager/issues/69
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BUG FIXES
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o Increase timeout from 1 to 5 minutes (300 seconds) to make
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download of large packages more robust.
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CHANGES IN VERSION 1.30.10
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-------------------------
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MINOR CHANGES
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o Restore startup message with recommended version
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o Update mis-configuration skip in tests
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CHANGES IN VERSION 1.30.9
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-------------------------
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MINOR CHANGES
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o Use `packageStartupMessage()` in .onLoad
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o Tests are robust to missing Suggests: BiocVersion
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CHANGES IN VERSION 1.30.8
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-------------------------
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MINOR CHANGES
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o Tests are skipped if is there is a misconfiguration or the CRAN
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builder has no internet access.
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CHANGES IN VERSION 1.30.7
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-------------------------
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NEW FEATURES
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o Support R-4.0
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MINOR CHANGES
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o Conform to CRAN policy to fail with messages rather than
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warnings or errors when internet access fails; internet access
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failures continue to generate warnings or errors during regular
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use.
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CHANGES IN VERSION 1.30.6
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-------------------------
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MINOR CHANGES
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o Improve unit tests under Bioconductor versions 3.8, 3.9, 3.10.
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o Improve error message when non-interactive version update fails.
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BUG FIXES
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o BiocManager loads when off-line.
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CHANGES IN VERSION 1.30.5
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-------------------------
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NEW FEATURES
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o Allow users to specify `checkBuilt` when invoking `valid()` or
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`install()`. Set default `FALSE`.
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MINOR CHANGES
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o Allow use of BiocInstaller for R < 3.5, pointing to biocLite()
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when appropriate.
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o Improve performance of version checking (issue #42 @HenrikBengtsson).
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o Document off-line installation best practices.
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o Warn about out-of-date packages on load (in addition to on
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attach) (issue #29)
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CHANGES IN VERSION 1.30.4
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-------------------------
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NEW FEATURES
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o Provide an 'http' fallback when 'https' fails for accessing the version
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map hosted on Bioconductor.org
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MINOR CHANGES
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o Conform tests to devel and release R versions
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o Add tests for the 'http' fallback scenarios
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BUG FIXES
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o Fixed issue with multiple error version messages for Bioc version `3.9`
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'devel' and 'future'
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o Return a warning message instead of an error when unable to validate
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a given version
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CHANGES IN VERSION 1.30.3
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-------------------------
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NEW FEATURES
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o 'BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS' option allows users to skip
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online version map validation. Local installation of 'BiocVersion' will be
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used when this option is enabled.
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MINOR CHANGES
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o Removed extra prompts when switching versions and updating packages
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o Clarified 'See Also' documentation (@lwaldron #16)
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o Added several unit tests to increase robustness (@mtmorgan)
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BUG FIXES
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o Obtain CRAN 'repos' option independent of name (@kasperdanielhansen #17)
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o Fixed a bug when switching to 'devel' version of Bioconductor
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(@kasperdanielhansen #25)
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o When installation is valid, return zero invalid packages rather than
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accessing non-existent list structure
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CHANGES IN VERSION 1.30.2
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-------------------------
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USER VISIBLE CHANGES
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o install() only allows Bioconductor version upgrades and downgrades with
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an empty 'pkgs' argument. Otherwise, it gives the user an informative error.
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o 'ask' argument is respected when in non-interactive mode (@lshep #9)
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o valid() returns TRUE for valid Bioconductor installations otherwise,
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it prints a report of out-of-date and/or too new packages
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MINOR CHANGES
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o updated unit tests for install()
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o when changing versions via 'install(version = "x.x")', Bioconductor
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packages to be up or down-graded are now enumerated
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BUG FIXES
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o Remove tests that were dependent on system configuration rather
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than the package itself
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CHANGES IN VERSION 1.30.1
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-------------------------
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USER VISIBLE CHANGES
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o install() '...' arguments must be named.
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CHANGES IN VERSION 1.30.0
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-------------------------
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NEW FEATURES
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o package renamed to BiocManager
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o install() supports github repositories using the remotes
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package, rather than devtools. This change should be transparent
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to end users. (@PeteHaitch, #4)
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o functions renamed to the following: biocLite > install;
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biocInstallRepos > repositories; biocValid > valid;
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biocVersion > version
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o functions removed: biocases_group, biocUpdatePackages, isDevel,
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useDevel, *_group
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o available() enables package discovery via grep()
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o Removed support for MRAN (Microsoft R) archives.
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CHANGES IN VERSION 1.28.0
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-------------------------
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NEW FEATURES
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o biocLite() supports full URLs, e.g., to archived Bioconductor
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packages.
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o Support MRAN (Microsoft R) archives.
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CHANGES IN VERSION 1.24.0
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-------------------------
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NEW FEATURES
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o biocLite() uses lib.loc= to find devtools, reports more
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informatively why devtools fails to load
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o biocLite() only offers to update non-masked packages
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o biocLite() reports when packages in unwriteable directories are
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out-of-date, but does not try (and fail) to update them.
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o isDevel() returns TRUE if the version of BiocInstaller
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corresponds to the development version of Bioconductor.
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CHANGES IN VERSION 1.20.0
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-------------------------
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BUG FIXES
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o biocLite() uses lib.loc when calling update.packages
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CHANGES IN VERSION 1.18.0
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-------------------------
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NEW FEATURES
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o biocLite() supports github repositories (implicitly, 'packages'
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following the 'maintainer/package' convention)
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CHANGES IN VERSION 1.14.0
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-------------------------
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NEW FEATURES
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o biocUpdatePackages updates installed packages and their
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dependencies.
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CHANGES IN VERSION 1.10.0
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-------------------------
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NEW FEATURES
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o biocValid() checks that installed packages are consistent with
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those available via biocLite().
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o biocVersion() returns the version of Bioconductor expected with
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this version of the BiocInstaller package.
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USER-VISIBLE CHANGES
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o biocLite() invoked with no arguments updates currently installed
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packages to their most-recent version.
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