BiocCheck-methods: A list of methods for the BiocCheck reference class
In Bioconductor/BiocCheck: Bioconductor-specific package checks

BiocCheck-methods

R Documentation

A list of methods for the BiocCheck reference class

A list of methods for the BiocCheck reference class

`...`	`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.
`verbose`	`logical(1)` Whether or not to output both the `help_text` and `messages` as part of the report
`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.

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

add: Include a condition to the BiocCheck report
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