Access the Bioconductor Project Package Repository

A convenient tool to install and update Bioconductor packages.


News

CHANGES IN VERSION 1.31.3

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 1.31.2

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it prints a report of out-of-date and/or too new packages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 1.31.0

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.

Reference manual

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install.packages("BiocManager")

1.30.4 by Marcel Ramos, a month ago


Report a bug at https://github.com/Bioconductor/BiocManager/issues


Browse source code at https://github.com/cran/BiocManager


Authors: Martin Morgan [aut] , Marcel Ramos [ctb, cre]


Documentation:   PDF Manual  


Artistic-2.0 license


Imports utils

Suggests BiocStyle, BiocVersion, remotes, testthat, knitr, withr


Imported by CNVScope, anyLib.

Suggested by available, devtools, pacman, pkggraph.


See at CRAN