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

Description Usage Arguments Details Value Author(s) References Examples

View source: R/BiocCheck.R

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 mostly meant to be called from the operating system's command line (via R CMD BiocCheck; see the vignette). Not meant to replace R CMD check, which should always be run first.

Usage

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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 typically called from the operating system's command line, as

R CMD 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.

Installing BiocCheck will attempt to install the BiocCheck script, which could fail; details in the vignette.

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

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

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

## or from the operating system's command line as:
## R CMD BiocCheck myPackage

BiocCheck documentation built on Oct. 31, 2019, 4:24 a.m.