A Using the ‘Devel’ Version of Bioconductor | Bioconductor Packages: Development, Maintenance, and Peer Review (original) (raw)

Which version of R?

Package authors should develop against the version of R that will be available to users when the Bioconductor devel branch becomes the_Bioconductor_ release branch.

R has a ‘.y’ release in x.y.z every year (typically mid-April), but_Bioconductor_ has a .y release (where current devel becomes release) every 6 months (mid-April and mid-October).

This means that, from mid-October through mid-April, _Bioconductor_developers should be developing against R-devel. From mid-April to mid-October, developers should use R-release (actually, the R snapshot from the R-x-y-branch) for Bioconductor development.

See the BiocManager vignette for instructions on using multiple versions of Bioconductor.

Using ‘bioc-devel’ during mid-April to mid-October

In order to use the ‘bioc-devel’ version of Bioconductor during the mid-April to mid-October release cycle, use the release version of _R_and invoke the function install(version="devel") (from theBiocManager package):

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "devel")
BiocManager::valid()              # checks for out of date packages

After doing this, all packages will be installed from the ‘bioc-devel’ repository.

Using ‘bioc-devel’ during mid-October to mid-April

In order to use the ‘bioc-devel’ version of Bioconductor during the mid-October to mid-April release cycle, you must install the devel version of R.

• Source
• macOS
• Windows

Then, make sure that your version of BiocManager is current and your packages up-to-date.

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(version="devel")
BiocManager::valid()

"Bioconductor Packages: Development, Maintenance, and Peer Review" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2025-04-09.

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