| BiocCheckGitClone {BiocCheck} | R Documentation |
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.
BiocCheckGitClone(package=".", ...) usage2()
package |
A directory containing an R source package. Not a package tar ball. |
... |
Only available option currently is quit-with-status.
See |
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.
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. |
Lori Shepherd
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/
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