BiocCheck-class: A class for composing BiocCheck reports.

In Bioconductor/BiocCheck: Bioconductor-specific package checks

A class for composing BiocCheck reports.

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).

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

A BiocCheck instance

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.

verbose

logical(1) Whether to show the full information pertaining to the checks. A FALSE value will only show the condition messages and not any relevant files or additional information. The defaults are FALSE and TRUE for BiocCheck and BiocCheckGitClone, respectively.

See Also

Message-class

Examples

bc <- BiocCheck:::.BiocCheck

bc$verbose

Bioconductor/BiocCheck documentation built on April 28, 2024, 9:24 p.m.