3 General Bioconductor Package Development
3.1 Version of Bioconductor and
Package developers should always use the devel version of Bioconductor and Bioconductor packages when developing and testing packages to be contributed.
Depending on the release cycle, using Bioconductor devel may or may not involve also using the devel version of . See the how-to on using devel version of Bioconductor for up-to-date information.
3.2 Correctness, Space and Time
3.2.1 R CMD build
Bioconductor packages must minimally pass
R CMD build (or
R CMD INSTALL --build) and pass
R CMD check with no errors and no warnings using a recent
R-devel. Authors should also try to address all errors, warnings, and notes that
arise during build or check.
Packages must also pass
BiocCheck::BiocCheck('new-package'=TRUE) with no errors and no warnings. The
BiocCheck package is a set of tests that encompass
Bioconductor Best Practices. Every effort should be made to address any
errors, warnings, and notes that arise during this build or check.
3.2.3 ERROR, WARNGING, and NOTES
The Bioconductor team member assigned to review the package during the submission process will expect all ERROR, WARNINGS, and NOTES to be addressed from both R CMD build, R CMD check, and BiocCheck. If there are any remaining, a justification of why they are not corrected will be expected.
3.2.4 File names
Do not use filenames that differ only in case, as not all file systems are case-sensitive.
3.2.5 Package size
The source package resulting from running
R CMD build should occupy less than 5 MB on disk.
3.2.6 Check duration
The package should require less than 10 minutes to run
R CMD check --no-build-vignettes.
--no-build-vignettes option ensures that the vignette is built only once.
Vignette and man page examples should not use more than 3 GB of memory since cannot allocate more than this on 32-bit Windows.
3.2.8 Individual file size
For software packages, individual files must be <= 5MB. This restriction exists even after the package is accepted and added to the Bioconductor repository. See data section for advice on packages using large data files.
3.2.9 Undesirable files
The raw package directory should not contain unnecessary files, system files, or
hidden files such as
.git, cache files, log files,
*.so, etc. These files may be present in your local directory but should not be commited to
.gitignore). Any files or directories for other
applications (Github Actions, devtool, etc) should ideally be in a different
branch and not submitted to the Bioconductor version of the package.
3.3 R CMD check environment
It is possible to activate or deactivate a number of options in
R CMD build and
R CMD check.
Options can be set as individual environment variables or they can be listed in a file.
Descriptions of all the different options available can be found here.
Bioconductor has chosen to customize some of these options for incoming submission during
R CMD check.
The file of utilized flags can be downloaded from GitHub.
The file can either be placed in a default directory as directed here or can be set through environment variable
R_CHECK_ENVIRON with a command similar to:
export R_CHECK_ENVIRON = <path to downloaded file>