BiocCheck-class: An internal class for composing BiocCheck reports
In Bioconductor/BiocCheck: Bioconductor-specific package checks

BiocCheck-class

R Documentation

An internal 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).

Arguments

`...`	`character()` A vector that makes up the `BiocCheck` exception message (e.g., 'Vignette must be built by R CMD build'). The character vector is handled with `paste0` and made into a list and appended with `help_text` and `messages`.
`help_text`	`character(1)` Additional text prompting a list of files (e.g,. "Found in files:")
`condition`	`character(1)` One of the three conditions handled: `error`, `warning`, or `note`
`messages`	`character()` Often a vector of file names where the check was triggered.
`debug`	`logical(1)` Whether to append the name of the originating check name into for trace-ability
`checkName`	`character(1)` The title of the current group of checks. It can be set with `handleCheck`, e.g., `handleCheck("Checking for version number mismatch...")`. Internally, it ' is saved with `setCheck` and obtained with `getLastCheck`.
`isOnBBS`	`logical(1)` Indicates whether the checks are being run on the Bioconductor Build System (BBS). This is helpful for avoiding the creation of folders in the BBS.
`file`	`character(1)` A path to a JSON file for writing or reading as created by `toJSON` and `fromJSON` `BiocCheck` methods.

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