Package 'BiocCheck'

Title: Bioconductor-specific package checks
Description: BiocCheck guides maintainers through Bioconductor best practicies. It runs Bioconductor-specific package checks by searching through package code, examples, and vignettes. Maintainers are required to address all errors, warnings, and most notes produced.
Authors: Bioconductor Package Maintainer [aut], Lori Shepherd [aut], Daniel von Twisk [ctb], Kevin Rue [ctb], Marcel Ramos [aut, cre] , Leonardo Collado-Torres [ctb], Federico Marini [ctb]
Maintainer: Marcel Ramos <[email protected]>
License: Artistic-2.0
Version: 1.41.7
Built: 2024-07-24 02:42:41 UTC
Source: https://github.com/bioc/BiocCheck

Help Index

Check a package's adherence with the Bioconductor Package Guidelines

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

package

The path to an R package directory or tarball (.tar.gz). The BiocCheck function is intended to be run from the package directory; therefore, the current working directory (given by getwd()) is the default.
checkDir

The directory where the BiocCheck output directory will be stored. By default, it will be placed in the same directory as the package directory i.e., dirname(pkg_dir).
debug

Whether to append the names of functions that correspond to each condition raised by BiocCheck in the written log (i.e., in the '<package_name>.BiocCheck' folder). This option is only relevant to developers and contributors to BiocCheck.
callr

logical(1) Whether to use the callr package to run BiocCheck in an isolated R session to prevent namespace collisions.
...

See the details section for available options. When running BiocCheck, options can be specified as: 

 BiocCheck(package, `no-check-vignettes`=TRUE)

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.

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

  • new-package: enable checks specific to new packages

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

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

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

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

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

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

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

  • no-check-bioc-views: disable biocViews-specific checks (for non-BioC packages)

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

  • no-check-description: disable DESCRIPTION file checks

  • no-check-vignettes: disable vignette checks

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

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

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

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

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

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

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

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

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

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

  • no-check-bioc-help: disable check for registration on Bioconductor mailing list and support site

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

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

Author(s)

Dan Tenenbaum, Lori Shepherd, and Marcel Ramos

References

https://contributions.bioconductor.org

See Also

BiocCheck-class, Message-class

Examples

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

A list of methods for the BiocCheck reference class

Description

A list of methods for the BiocCheck reference class

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.
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.

Value

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

methods

  • 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

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

  • 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

Checks specific to a Git clone of a package repository

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

package

A directory containing an R source package. Not a package tar ball.
...

Currently, only quit-with-status is available. See BiocCheck

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-class

Examples

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

Report context of events to user with a data.frame of events and locations

Description

Report context of events to user with a data.frame of events and locations

Usage

Context(file = "", lines = character(), idx = logical(), offset = 0L)

Arguments

file

character(1) full path (including package name) of file being summarized.
lines

character() vector of text lines in file
idx

logical() same length as lines indicating lines in which event occurs
offset

integer(1) The number of lines to add to the 'Line' column calculation. It is mainly used to account for the number of lines that the YAML header occupies.

Value

Context: a data.frame() with columns File, Line, and Context

A lower level Message helper class for BiocCheck

Description

A lower level Message helper class for BiocCheck

Value

A Message class instance

Fields

msg

list() A list of character messages usually grown with append with conditions raised by a check

condition

character(1) One of the three conditions handled: error, warning, or note

See Also

BiocCheck-class

A list of methods for the Message reference class

Description

A list of methods for the Message reference class

Arguments

condition

character(1) One of the three conditions handled: error, warning, or note
verbose

logical(1) Whether to output the full text in the check or only the check name itself in the report
...

list() A nested list with the check name as the top level layer. Second level lists include any help_text and messages that are part of the check.

Value

An internal R5 Reference Class to handle messages and their conditions, e.g., for errors, warnings, or notes.