Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of BiocManager

BiocManager - CRAN Release v1.30.26

CHANGES IN VERSION 1.30.26

MINOR CHANGES

o Remove mention of biocLite script and remove `.LEGACY_INSTALL_CMD`
(@sneumann, #195)
o Explain management of multiple Bioconductor versions when using the same
R version in the vignette
o Use `BIOCONDUCTOR_NAME` environment variable for binary URL resolution
(@almahmoud, #199)
o Use `download.file` to obtain the `config.yaml` file before running
`readLines` (@glin, #198)

Full Changelog: https://github.com/Bioconductor/BiocManager/compare/v1.30.25...v1.30.26

- R
Published by LiNk-NY 9 months ago

BiocManager - CRAN Release 1.30.25

CHANGES IN VERSION 1.30.25

MINOR CHANGES

o Maintainer email change.

Full Changelog: https://github.com/Bioconductor/BiocManager/compare/v1.30.24...v1.30.25

- R
Published by LiNk-NY over 1 year ago

BiocManager - CRAN Release v1.30.24

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)

Full Changelog: https://github.com/Bioconductor/BiocManager/compare/v1.30.23...v1.30.24

- R
Published by LiNk-NY over 1 year ago

BiocManager - CRAN Release v1.30.23

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

- R
Published by LiNk-NY almost 2 years ago

BiocManager - CRAN Release v1.30.22

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)

- R
Published by LiNk-NY almost 2 years ago

BiocManager - CRAN Release v1.30.21

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).

- R
Published by LiNk-NY over 2 years ago

BiocManager - CRAN Release v1.30.20

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)

- R
Published by LiNk-NY about 3 years ago

BiocManager - CRAN Release 1.30.19

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)

- R
Published by LiNk-NY over 3 years ago

BiocManager - CRAN Release v1.30.18

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

- R
Published by LiNk-NY over 3 years ago

BiocManager - CRAN Release v1.30.17

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).

- R
Published by LiNk-NY almost 4 years ago

BiocManager - CRAN Release v1.30.16

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).

- R
Published by LiNk-NY over 4 years ago

BiocManager - CRAN Release v1.30.14

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`

- R
Published by LiNk-NY almost 5 years ago

BiocManager - CRAN Release v1.30.13

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).

Do Not Use

- R
Published by LiNk-NY almost 5 years ago

BiocManager - CRAN Release v1.30.15

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()`

- R
Published by LiNk-NY almost 5 years ago

BiocManager - CRAN Release v1.30.12

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.

- R
Published by LiNk-NY almost 5 years ago

BiocManager - CRAN Release v1.30.10

CHANGES IN VERSION 1.30.10

MINOR CHANGES

o Restore startup message with recommended version

o Update mis-configuration skip in tests

- R
Published by LiNk-NY over 6 years ago

BiocManager - CRAN Release v1.30.9

CHANGES IN VERISON 1.30.9

MINOR CHANGES

o Use `packageStartupMessage()` in .onLoad

o Tests are robust to missing Suggests: BiocVersion

- R
Published by LiNk-NY over 6 years ago

BiocManager - CRAN Release v1.30.8

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.

- R
Published by LiNk-NY over 6 years ago

BiocManager - CRAN Release v1.30.7

CHANGES IN VERSION 1.30.7

NEW FEATURES

* Support R-4.0

MINOR CHANGES

* 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

* Improve unit tests under Bioconductor versions 3.8, 3.9, 3.10.

* Improve error message when non-interactive version update fails.

BUG FIXES

* BiocManager loads when off-line.

- R
Published by LiNk-NY over 6 years ago

BiocManager - CRAN Release v1.30.5

CHANGES IN VERSION 1.30.5

NEW FEATURES

  • Allow users to specify checkBuilt when invoking valid() or install(). Set default FALSE.

MINOR CHANGES

  • Allow use of BiocInstaller for R < 3.5, pointing to biocLite() when appropriate.
  • Improve performance of version checking (#42 @HenrikBengtsson).
  • Document off-line installation best practices.
  • Warn about out-of-date packages on load (in addition to on attach) (#29)

- R
Published by LiNk-NY over 6 years ago

BiocManager - CRAN Release v1.30.4

CHANGES IN VERSION 1.30.4

NEW FEATURES

  • Provide an 'http' fallback when 'https' fails for accessing the version map hosted on Bioconductor.org

MINOR CHANGES

  • Conform tests to devel and release R versions
  • Add tests for the 'http' fallback scenarios

BUG FIXES

  • Fixed issue with multiple error version messages for Bioc version 3.9 'devel' and 'future'
  • Return a warning message instead of an error when unable to validate a given version

- R
Published by LiNk-NY over 7 years ago

BiocManager - CRAN Release v1.30.3

CHANGES IN VERSION 1.30.3

NEW FEATURES

  • 'BIOCONDUCTORONLINEVERSION_DIAGNOSIS' option allows users to skip online version map validation. Local installation of 'BiocVersion' will be used when this option is enabled.

MINOR CHANGES

  • Removed extra prompts when switching versions and updating packages

  • Clarified 'See Also' documentation (@lwaldron #16)

  • Added several unit tests to increase robustness (@mtmorgan)

BUG FIXES

  • Obtain CRAN 'repos' option independent of name (@kasperdanielhansen #17)

  • Fixed a bug when switching to 'devel' version of Bioconductor (@kasperdanielhansen #25)

  • When installation is valid, return zero invalid packages rather than accessing non-existent list structure

- R
Published by LiNk-NY over 7 years ago

BiocManager - CRAN Release v1.30.2

CHANGES IN VERSION 1.30.2

USER VISIBLE CHANGES

  • install() only allows Bioconductor version upgrades and downgrades with an empty 'pkgs' argument. Otherwise, it gives the user an informative error.

  • 'ask' argument is respected when in non-interactive mode (@lshep #9)

  • valid() returns TRUE for valid Bioconductor installations otherwise, it prints a report of out-of-date and/or too new packages

MINOR CHANGES

  • updated unit tests for install()

  • when changing versions via 'install(version = "x.x")', Bioconductor packages to be up or down-graded are now enumerated

BUG FIXES

  • Remove tests that were dependent on system configuration rather than the package itself

- R
Published by LiNk-NY over 7 years ago

BiocManager - CRAN Release v1.30.1

CHANGES IN VERSION 1.30.1

BiocManager (formerly BiocInstaller) is now part of CRAN :tada:

USER VISIBLE CHANGES

  • install() '...' arguments must be named.

NEW FEATURES

  • install() supports github repositories using the remotes package, rather than devtools. This change should be transparent to end users. (From Peter Hickey @PeteHaitch, https://github.com/Bioconductor/BiocInstaller/issues/4)

  • functions renamed to the following: biocLite > install; biocInstallRepos > repositories; biocValid > valid; biocVersion > version

  • functions removed: biocasesgroup, biocUpdatePackages, isDevel, useDevel, *group

  • available() enables package discovery via grep()

- R
Published by LiNk-NY over 7 years ago