BiocCheckGitClone: Additional checks for a package for compliance with...

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. This function is not meant to replace R CMD check or BiocCheck.

Usage

BiocCheckGitClone(package=".", ...)
usage2()

Arguments

package	A directory containing an R source package. Not a package tar ball.
...	Only available option currently is quit-with-status. See BiocCheck

Details

BiocCheckGitClone() analyzes R packages for compliance with Bioconductor package guidelines and best practices. This function should only be run on a open source directory not a tarball.

BiocCheckGitClone is called within R with, as

BiocCheckGitClone(<package>)

where package is a directory containing an R source package.

BiocCheckGitClone is not meant as a replacement for R CMD check or BiocCheck.

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

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)

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")
BiocCheckGitClone(packageDir, `quit-with-status`=FALSE)

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