BiocCheck {BiocCheck} | R Documentation

## Check a package for compliance with Bioconductor package guidelines

### 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

    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

    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

[Package BiocCheck version 1.22.0 Index]