BiocCheckGitClone {BiocCheck} | R Documentation

## Additional checks for 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 BiocCheckGitClone`). Not meant to replace `R CMD check` or `R CMD BiocCheck`, which should always be run first.

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

`R CMD BiocCheckGitClone package`

where `package` is a directory containing an `R` source package.

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

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

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)

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

[Package BiocCheck version 1.22.0 Index]