BiocCheck: Check a package for compliance with Bioconductor package...

In BiocCheck: Bioconductor-specific package checks

Description

Analyzes R packages for compliance with Bioconductor package guidelines and best practices. Divides output into three categories: ERROR, WARNING, and NOTE. See the vignette for more details. Not meant to replace R CMD check, which should always be run first.

Usage

BiocCheck(package = ".", ...)
usage()

Arguments

package	A directory or tarball (.tar.gz file) containing an R source package.
...	Run usage() to see the available options. When running BiocCheck interactively, options can be passed like so: BiocCheck(package, `no-check-vignettes`=TRUE)

Details

BiocCheck() analyzes R packages for compliance with Bioconductor package guidelines and best practices. For the rationale behind these guidelines and best practices, see the vignette and pages in the references section. usage() displays the options that can be passed to BiocCheck().

BiocCheck is called within R with

BiocCheck(<package>)

where package is a directory or .tar.gz file containing an R source package.

BiocCheck is not meant as a replacement for R CMD check, which should always be run first for best results.

See the vignette for detailed explanations of all the checks performed by BiocCheck.

Value

Mostly called for the side effect of the information displayed. When called interactively, returns a list with three components:

ERROR	Items that must be fixed before the package can be accepted into Bioconductor.
WARNING	We strongly suggest fixing these items.
NOTE	Fixing these items is not required, there is no expectation that considerations will escalate in severity.

Author(s)

Dan Tenenbaum and Lori Shepherd

References

http://www.bioconductor.org/developers/how-to/coding-style/ http://www.bioconductor.org/developers/package-guidelines/ http://www.bioconductor.org/developers/how-to/version-numbering/ http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/

Examples

packageDir <- system.file("testpackages", "testpkg0", package="BiocCheck")
BiocCheck(packageDir, `quit-with-status`=FALSE)

BiocCheck documentation built on Nov. 8, 2020, 5:38 p.m.