BiocCheckGitClone: Checks specific to a Git clone of a package repository

In Bioconductor/BiocCheck: Bioconductor-specific package checks

Checks specific to a Git clone of a package repository

Description

Analyzes an R package for adherence with Bioconductor package guidelines and best practices. The check outputs are categorized into ERROR, WARNING, and NOTE. This function is typically used in the Bioconductor Build System (BBS) and not intended for general use.

Usage

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

Arguments

package	A directory containing an R source package. Not a package tar ball.
...	Currently, only quit-with-status is available. See BiocCheck

Details

BiocCheckGitClone() reviews R packages for adherence with Bioconductor package guidelines and best practices. See https://contributions.bioconductor.org for the latest guidance for writing Bioconductor software. This function should only be run on a source directory and not on a tarball.

BiocCheckGitClone is called within R with, as

BiocCheckGitClone(<package>) 

where package is the source directory containing the R package.

Value

BiocCheckGitClone() is chiefly called for the side effect of the check reporting. The function returns a BiocCheck reference class with three main list elements:

• error: Items to address before the package can be accepted

• warning: Strongly suggested items that may require attention

• note: Items to consider, though not required, before acceptance

Author(s)

Lori Shepherd

References

https://contributions.bioconductor.org

See Also

BiocCheck-class

Examples

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

Bioconductor/BiocCheck documentation built on Nov. 11, 2024, 4:27 p.m.