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Bioconductor Packages: Development, Maintenance, and Peer Review

A Using the ‘Devel’ Version of Bioconductor

A.1 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.

A.2 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 the BiocManager 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BiocManager::valid()              # checks for out of date packages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.

A.3 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.

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()