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
R CMD check, which should always be run first.
A directory or tarball (.tar.gz file) containing an R source package.
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
usage() displays the options that can be passed
BiocCheck is typically called from the operating system's
command line, as
R CMD BiocCheck package
package is a directory or .tar.gz file containing
R source package.
BiocCheck is not meant as a replacement for
R CMD check, which should always be run first
for best results.
BiocCheck will attempt to install
BiocCheck script, which could fail; details
in the vignette.
See the vignette for detailed explanations of all
the checks performed by
Mostly called for the side effect of the information displayed. When called interactively, returns a list with three components:
Items that must be fixed before the package can be accepted into Bioconductor.
We strongly suggest fixing these items.
Fixing these items is not required, there is no expectation that considerations will escalate in severity.
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/
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