A convenient tool to install and update Bioconductor packages.
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
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it prints a report of out-of-date and/or too new packages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
USER VISIBLE CHANGES
o install() '...' arguments must be named.
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.
NEW FEATURES
o biocLite() supports full URLs, e.g., to archived Bioconductor
packages.
o Support MRAN (Microsoft R) archives.
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out-of-date, but does not try (and fail) to update them.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.
BUG FIXES
o biocLite() uses lib.loc when calling update.packages
NEW FEATURES
o biocLite() supports github repositories (implicitly, 'packages'
following the 'maintainer/package' convention)
NEW FEATURES
o biocUpdatePackages updates installed packages and their
dependencies.
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.