BiocCheck-class: A class for composing BiocCheck reports.
In Bioconductor/BiocCheck: Bioconductor-specific package checks

BiocCheck-class

R Documentation

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.