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it prints a report of out-of-date and/or too new packages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

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("BiocManager")

1.30.10 by Marcel Ramos, 20 days 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, withr, curl, knitr


Imported by CNVScope, MetaIntegrator, RAMClustR, STRAH, anyLib, librarian, maGUI, rvcheck.

Suggested by PCMBase, TcGSA, available, bbl, devtools, metacoder, pacman, pkggraph.


See at CRAN