BiocCheck: Check a package's adherence with the Bioconductor Package...

In Bioconductor/BiocCheck: Bioconductor-specific package checks

Check a package's adherence with the Bioconductor Package Guidelines

Description

Analyzes an R package for adherence with Bioconductor package guidelines and best practices. The check outputs are categorized into ERROR, WARNING, and NOTE. See the vignette for more details. BiocCheck is complementary to ⁠R CMD check⁠, which should always be run first.

Usage

BiocCheck(
  package = getwd(),
  checkDir = dirname(package),
  debug = FALSE,
  callr = FALSE,
  ...
)

Arguments

package	The path to an R package directory or tarball (.tar.gz). The BiocCheck function is intended to be run from the package directory; therefore, the current working directory (given by getwd()) is the default.
checkDir	The directory where the BiocCheck output directory will be stored. By default, it will be placed in the same directory as the package directory i.e., dirname(pkg_dir).
debug	Whether to append the names of functions that correspond to each condition raised by BiocCheck in the written log (i.e., in the '<package_name>.BiocCheck' folder). This option is only relevant to developers and contributors to BiocCheck.
callr	logical(1) Whether to use the callr package to run BiocCheck in an isolated R session to prevent namespace collisions.
...	See the details section for available options. When running BiocCheck, options can be specified as: BiocCheck(package, `no-check-vignettes`=TRUE)

Details

BiocCheck() reviews R packages for adherence with Bioconductor package guidelines and best practices. See https://contributions.bioconductor.org for the latest guidance for writing Bioconductor software. Some rationale behind these best practices can be seen in the vignette and pages in the references section. The vignette also provides detailed explanations of all the checks performed by BiocCheck.

BiocCheck is called within R with

 BiocCheck(<package>)

where package points to the source directory or the .tar.gz tarball that was created using ⁠R CMD build⁠.

Note that BiocCheck is complementary to ⁠R CMD check⁠. ⁠R CMD check⁠ should always be run first for best results.

Value

BiocCheck() is chiefly called for the side effect of the check reporting. The function also creates a ⁠<package_name>.BiocCheck⁠ folder and returns a BiocCheck reference class with three main list elements:

• error: Items to address before the package can be accepted

• warning: Strongly suggested items that may require attention

• note: Items to consider, though not required, before acceptance

dot-options

• new-package: enable checks specific to new packages

• no-check-dependencies: disable check for bad dependencies

• no-check-deprecated: disable check for usage of deprecated packages

• no-check-remotes: disable check for usage of remote packages other than those hosted on CRAN or Bioconductor

• no-check-version-num: disable check for valid version number

• no-check-R-ver: disable check for valid R version

• no-check-pkg-size: disable check for package tarball size

• no-check-file-size: disable check for individual file size

• no-check-bioc-views: disable biocViews-specific checks (for non-BioC packages)

• no-check-bbs: disable BBS-specific checks (for non-BioC packages). Valid DESCRIPTION

• no-check-description: disable DESCRIPTION file checks

• no-check-vignettes: disable vignette checks

• no-check-library-calls: disable check usage of functions that install or update packages

• no-check-install-self: disable check for require or library of itself

• no-check-coding-practices: disable check for some common best coding practices

• ⁠no-check-function-len⁠: disable check for function length

• no-check-man-doc: disable checks for man page documentation

• no-check-news: disable checks for NEWS file

• no-check-unit-tests: disable checks for unit tests

• no-check-skip-bioc-tests: disable check for tests that skip when on bioc

• no-check-formatting: disable checks for file formatting

• no-check-CRAN: disable check for if package exists in CRAN

• no-check-bioc-help: disable check for registration on Bioconductor mailing list and support site

• build-output-file: file containing R CMD build output, for additional analysis

• quit-with-status: enable exit code option when performing check

Author(s)

Dan Tenenbaum, Lori Shepherd, and Marcel Ramos

References

https://contributions.bioconductor.org

See Also

BiocCheck-class, Message-class

Examples

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

Bioconductor/BiocCheck documentation built on Aug. 16, 2024, 5:39 a.m.