Package 'BiocCheck'

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

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.

To skip installation of the package during the check, set the install option to FALSE or NULL:

BiocCheck(package, install=FALSE)
## OR
BiocCheck(package, install=NULL)

To re-use an existing installation log file, set the install option to the name of the installation log file. For example, the following will put the install_out.txt log file in the ⁠<package_name>.BiocCheck⁠ directory: BiocCheck(package, install="check:install_out.txt")

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

To use the dot-options, BiocCheck can be called with named arguments corresponding to the options below. Typically, these options are set to TRUE to disable specific checks, e.g., BiocCheck(package, 'no-check-vignettes'=TRUE). Unless otherwise stated, these options can be left unset (i.e., NULL) to enable checks but FALSE can also be used to explicitly enable them. The available options are:

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

• new-package: enable checks specific to new packages

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

• no-check-bioc-help: disable check for registration on Bioconductor

• no-check-bioc-views: disable biocViews-specific checks (for non-BioC packages) mailing list and support site

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

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

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

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

• no-check-description: disable DESCRIPTION file checks

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

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

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

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

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

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

• no-check-namespace: disable NAMESPACE file checks

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

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

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

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

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

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

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

• no-check-vignettes: disable vignette checks

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

• install: if FALSE, the package is not installed; otherwise, if not specified, the package is installed by default. Optionally, a ⁠check:<file>⁠ key-value pair is provided to identify the name of the installation output file which will be copied to the ⁠<package_name>.BiocCheck⁠ directory.

• libloc: when install is specified, the library location where the package is installed. By default, this is .libPaths()[1].

Author(s)

Dan Tenenbaum, Lori Shepherd, and Marcel Ramos

References

https://contributions.bioconductor.org

See Also

BiocCheck, Message

Examples

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

Description

The BiocCheck class provides a framework for reporting checks based on Bioconductor guidelines. The class has several methods for working with the provided checks that handle and display messages and the display of the metadata. These methods also record the output of the BiocCheck() report in both plain text and JSON formats.

Note that currently, multiple BiocCheck runs will interfere with each other given that they are implemented via a reference class semantic. When running multiple checks in the same session, you can separate these instances by running them in separate processes (e.g., via BiocParallel).

Arguments

Details

The metadata includes a number of standard fields to allow easier troubleshooting and display of potentially relevant information. Currently, the fields included are:

• BiocCheckVersion: The version of the BiocCheck package

• BiocVersion: The version of Bioconductor

• Package: The name of the package in check

• PackageVersion: The version of the package in check

• sourceDir: The directory of the package source or tarball in check

• installDir: The directory where the package is installed for testing, a temporary location by default

• BiocCheckDir: The directory where the ⁠<package>.BiocCheck⁠ folder is saved. Usually the same folder as the package in check

• platform: The platform/OS where the check is taking place

• isTarBall: Whether the package in check is a source directory or a tarball

Value

An internal BiocCheck R5 Reference Class used to document conditions such as errors, warnings, and notes

Fields

log

list() A running list of all conditions raised (i.e., notes, warnings, errors)

check

character(1) The title of the last check used for logging purposes.

error,warning,note

list() Finer extraction of each condition type

metadata

list() A list of additional information relevant to the package and its state. See details.

methods

• add: Include a condition to the BiocCheck report

• addMetadata: Add metadata to the BiocCheck object from a BiocPackage object

• getLastCheck: Obtain the name of the last check run

• setCheck: Create a new element in the internal list for a check

• get: Extract the list of conditions raised by BiocCheck

• getNum: Tally the number of condition provided by the input

• zero: Reset the internal log of the condition provided

• getBiocCheckDir: Report and create the ⁠<package>.BiocCheck⁠ directory as obtained from the metadata

• composeReport: Simplify the list structure from the log and provide a character vector of conditions raised

• report: Write the ⁠00BiocCheck.log⁠ report into the BiocCheck folder

• toJSON: Write a JSON file to the location indicated with the conditions raised

• fromJSON: Read a JSON file from the location indicated with the output of previous conditions raised in the check

• show: Display the information in the class. Currently empty.

• show_meta: Display the metadata information stored in the metadata field

See Also

Message, BiocPackage

Examples

bc <- BiocCheck:::.BiocCheck

Description

Analyzes an R package for adherence with Bioconductor package guidelines and best practices. The check outputs are categorized into ERROR, WARNING, and NOTE. This function is typically used in the Bioconductor Build System (BBS) and not intended for general use.

Usage

BiocCheckGitClone(package = ".", ...)

Arguments

Details

BiocCheckGitClone() 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. This function should only be run on a source directory and not on a tarball.

BiocCheckGitClone is called within R with, as BiocCheckGitClone("package") where package is the source directory containing the R package.

Value

BiocCheckGitClone() is chiefly called for the side effect of the check reporting. The function 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

Author(s)

Lori Shepherd

References

https://contributions.bioconductor.org

See Also

BiocCheck

Examples

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