NEWS

BiocCheck 1.40.0

NEW FEATURES

Check for duplicate chunk labels in vignettes and produce an error when present (@hpages, #199)
Warn when Rnw vignettes are present (@jwokaty, #190)
Add error when maintainer email not parse-able in DESCRIPTION
Check for Bioconductor dependencies in the Imports and Depends fields; if none, produce a warning (@vjcitn).
Remove redundant 'DESCRIPTION' and 'NAMESPACE' consistency checks; these are already included in 'R CMD check'

BUG FIXES AND MINOR IMPROVEMENTS

Produce 'NOTE' instead of 'WARNING' for infrastructure packages without Bioconductor dependencies
'% \VignetteEngine' tags with spaces were not recognized; this has been fixed
Skip '\value' checks for package and class documentation; '\formats' checked for data documentation
Delegate system calls to 'devtools::build' to build packages
Update 'checkRbuildignore' to flag 'test' and 'longtests' entries appropriately (@hpages, #197)
Fix issue where BiocCheck would fail when errors caused by duplicate chunk labels were present (@hpages, #199)
Avoid format checks e.g., length, indentation, and tabs for Rd files that use roxygen2
Use the 'tools:::analyze_licenses' function to check for restrictive license use (@hpages, #119)
Use httr2 over httr for http requests
Clarify 'NOTE' and 'WARNING' messages for 'CITATION' file inclusion (#209).

BiocCheck 1.38.0

BUG FIXES AND MINOR IMPROVEMENTS

Exclude data docs with ‘\\format' tags in addition to ’package' docs when checking for '\\value' / '@return' in documentation.
Resolve unknown macro warnings when using Rdpack (@LiNK-NY, #196)
Improve the 'read.dcf' operation that looks for any deprecated packages in both Bioconductor release and devel versions.
Remove overwrite prompt when updating cached resources in deprecated packages check.

BiocCheck 1.36.0

NEW FEATURES

Include size limit checks for data files in 'data', 'inst/extdata', and 'data-raw' folders (@lshep, @const-ae, #167, #67)
Source package directories that include an 'inst/doc' folder with files are now flagged with an error. 'doc' folders are generated during 'R CMD build'.
The error for packages already hosted on CRAN has been converted to a warning (@lshep, #177). Any such incoming packages must be removed from CRAN before the following Bioconductor release.

BUG FIXES AND MINOR IMPROVEMENTS

Filter out 'package' docTypes from '\value' documentaiton checks (@grimbough, #189)
Obtain a more complete list of deprecated packages for 'checkDeprecatedPkgs'
Fix issue with path seperators on Windows ('\\' vs '/') causing the unit test for 'getBiocCheckDir' to report erroneous mismatches (@grimbough, #175)
Fix bug where the wrong number of functions with length greater than 50 was reported (@grimbough, #182)
biocViews term suggestions should be a scalar character (@lcolladotor, #184)
Update email in bioc-devel subscription check (@lshep, #185)
Handle function length checks when there is no R code (@lshep, #186)
Edit warning text when empty or missing 'value' sections are found in a package (@vjcitn)
'checkForValueSection' re-implemented for clarity; filters out comments in 'value' sections (@LiNk-NY)
Correctly identify 'Rd' comments by updating the regular expression to identify them (@LiNk-NY)

BiocCheck 1.34

NEW FEATURES

Redundant package dependencies checks between 'DESCRIPTION' and 'NAMESPACE' have been removed. These are already present in 'R CMD check' as "checking package dependencies".
Use 'callr' to run 'BiocCheck' in a separate process, this avoids interference with loaded packages (@vjcitn, #158)

BUG FIXES AND MINOR IMPROVEMENTS

Update 'checkVigInstalls' and 'checkVigBiocInst' to avoid false positives (@almeidasilvaf, #170).
Only count non evaluated chunks when there are any present in the vignette
Fix false positive WARNING "Import {pkg} in NAMESPACE as well as DESCRIPTION." where pkg was not in NAMESPACE but it was used using double colons pkg::function inside an S4 method. (@zeehio, #166)
Fix bug where inputs to 'getDirFile' were vectors in 'checkForValueSection' (@zeehio, #163)
Allow lookback for matching T/F and exclude list elements, e.g., 'list$F' (@lshep, #161)
Fix indentation count by excluding yaml front matter from vignettes (@harpomaxx, #100)
Update internal documentation of the 'BiocCheck-class'
Fix bug where line numbers were off due to removal of empty lines at parsing (@lshep, #159)
Slightly improve sentence counter for Description field check (@lshep, #160)
Update documentation links to point to contributions.bioconductor.org (@LiNk-NY, #157)

BiocCheck 1.32

NEW FEATURES

Add package metadata to main report for easier diagnostics
'pkgname.BiocCheck' folder, created above the package folder, includes the full report and NAMESPACE suggestions, if available.
Add check to find any stray 'pkgname.BiocCheck' folders
Update doc links and recommendations for additional information in report
Update 'BiocCheck' report to be more brief by only noting the conditions; details are included in the full report

BUG FIXES AND MINOR IMPROVEMENTS

Initialize default verbose value (FALSE) for internal reference object
Flag only hidden '.RData' files as bad files and allow 'myData.RData' (@hpages, #155)
Improve internal handling of condition messages with unified mechanism
Internal improvements to 'BiocCheck' mechanism: export '.BiocCheck' object which contains all conditions, log list, and method for writing to JSON
Update to changes in R 4.2 '--no-echo' flag
Make use of 'lib.loc' to helper functions that install and load the checked package
(1.31.36) Reduce function length count slightly by removing empty lines.
(1.31.35) Restricted files in 'inst' will be flagged with a 'WARNING' instead of an 'ERROR'
(1.31.32) Account for S3 print methods when checking for 'cat' usage
(1.31.31) Single package imports in the NAMESPACE were breaking the code to get all package imports.
(1.31.29) Include other import fields from NAMESPACE file when checking consistency between imports in DESCRIPTION/NAMESPACE.
(1.31.27) Update and clean up unit tests.
(1.31.26) Improve load test for the package being checked.
(1.31.25) Exclude GitHub URLs that end in HTML from external data check.
(1.31.23) Internal updates to the 'require' and 'library' check.
(1.31.22) Remove old code related to running 'BiocCheck' on the command line and update 'BiocCheck' documentation.
(1.31.21) Remove redundant '=' from message to avoid '=' assignment.
(1.31.20) Add line feed to "Checking function lengths..." message
(1.31.18) Packages should not download files when loaded or attached.
(1.31.17) Using '=' for assignment should be avoided and '<-' should be used instead for clarity and legibility.
(1.31.16) Note the use of 'cat' and 'print' outside of show methods.
(1.31.15) Check for pinned package versions in the 'DESCRIPTION' file denoted by the use of '=='.
(1.31.14) Enhancements to internal helper functions and 'BiocCheckGitClone'
(1.31.13) Revert move to new package checks. Update Bioc-devel mailing list check to fail early when not in BBS environment.
(1.31.12) Move Bioc-devel mailing list and support site registration checks to new package checks.
(1.31.10) Various internal improvements to 'BiocCheck' and the identification of the package directory and name.
(1.31.6) Use a more reliable approach to identify package name from the 'DESCRIPTION' file.
(1.31.5) Fixed bug in the case where the ‘VignetteBuilder' field in the a package’s 'DESCRIPTION' has more than one listed.
(1.31.3) Add 'BioCbooks' repository url to 'checkIsPackageNameAlreadyInUse', 'VIEWS' file is pending.
(1.31.2) Fix logical length > 1 error in 'checkImportSuggestions' (@vjcitn, #141)
(1.31.1) Simplify check for function lengths; remove excessive dots.

BiocCheck 1.30

NEW FEATURES

(1.29.10) Check for 'Sys.setenv' and 'suppressWarnings'/'suppressMessages'
(1.29.8) Check for 'sessionInfo' / 'session_info' in vignette code.
(1.29.5) Check for installation calls in vignette code.
(1.29.1) Check for 'install()' function calls in R code.

BUG FIXES

(1.29.14) Various internal improvements to the codebase.
(1.29.12) Checks on class membership code now include 'is() ==' grammar.
(1.29.6) Use appropriate input ('pkgdir') to internal checking functions.
(1.29.3) Add unit tests for legacy function searches.
(1.29.2) rename internal function from checkIsPackageAlreadyInRepo to checkIsPackageNameAlreadyInUse

BiocCheck 1.27

BUG FIX

(1.27.17) Update support site watched tags. tags are case insensitive
(1.27.15) Reporting checking of vignette despite package type (@lshep, #136)
(1.27.9) Allow portability of child Rmd documents via parseFile
(1.27.3) Correct check for if package already exists in CRAN/Bioc
(1.27.3) Correct check for single colon use
(1.27.2) Correct path to R license database file by calling R.home('share').

NEW FEATURES

(1.27.16) Check vignettes for all package types (@lshep, #136)
(1.27.12) Check for 'LazyData: TRUE' in the DESCRIPTION (@lshep, #128)
(1.27.11) R version dependency check in the 'DESCRIPTION' is now a 'NOTE' (@lshep, #126)
(1.27.10) Check for 'error' and other keywords in signaler functions, 'message', 'warning', and 'stop' etc. (@hpages, #125)
(1.27.8) Check for 'tests' entry in '.Rbuildignore'
(1.27.7) Removed BiocCheck and BiocCheckGitClone installation scripts; recommended usage is 'BiocCheck()'
(1.27.6) Check that a user has the package name in watched tags of support site
(1.27.5) Check for 'paste' / 'paste0' in signaler functions, 'message', 'warning', and 'stop' (@LiNk-NY, #64)
(1.27.4) Check for downloads from external resources (github, gitlab, bitbucket, dropbox; @LiNk-NY, #75)
(1.27.1) Check that licenses do not exclude classes of users, e.g., non-academic users.

BiocCheck 1.25

DEPRECATION ANNOUNCEMENT

(1.25.11) R CMD BiocCheck and R CMD BiocCheckGitClone are deprecated. The recommended way to run the functions is within R.

NEW FEATURES

(1.25.1) Check for warning/notes on too-brief a Description: field (@federicomarini, #65)
(1.25.4) Check for single colon typos when using qualified imports pkg::foo()
(1.25.8) Validate ORCID iDs (if any) in the DESCRIPTION file (@LiNk-NY, #97)
(1.25.10) Add check for properly formatted CITATION file
(1.25.12) Add NOTE to change dontrun to donttest

BUG FIXES

(1.25.14) The ORCID iD check now accepts IDs with a X at the end.
(1.25.9) All packages including infrastructure require a vignette
Usage of donttest and dontrun in manual pages tagged with the keyword 'internal' will no longer trigger a NOTE (@grimbough, #59)
(1.25.7) Adding the sessionInfo at the end of the vignette (@llrs)

USER SIGNIFICANT CHANGES

(1.25.3) Require Aurhors@R format over Author/Maintainer fields in the DESCRIPTION file. This has been upgraded to an ERROR.
(1.25.2) Suggest styler over formatR for automatic code re-formatting (@lcolladotor, #57).
(1.25.5) Add warning to new package versions with non-zero x version (@mtmorgan, #101)

BiocCheck 1.23

BUG FIX

(1.23.4) Update locations for NEWS
(1.23.1) Fix False Positive class == check

BiocCheck 1.19

NEW FEATURES

(1.19.33) Add Authors@R vs Author/Maintainer check
(1.19.29) Add non evaluated code chunks that have not been executed because of invalid syntax (“', “'R, “'r). Valid syntax for an evaluated code chunk takes the form “'{r} or “'{R}.
(1.19.28) Check that vignette metadata set correctly
(1.19.27) Check for Author@R or Author/Maintainer but not both
(1.19.25) Check for use of remotes: in Description
(1.19.18) Check for use of dontrun/donttest
(1.19.15) Check vignetteEngine/vignetteBuilder minimially declared in Suggests
(1.19.9) Check usage of donttest and dontrun in man page documentation
(1.19.9) Update deprecated check to check for Bioconductor release and devel deprecated packages as specified in biocViews
(1.19.7) More helpful ERROR when using a non valid command line option.
(1.19.4) All checks module. Ability to turn on/off with flag options. See 'R CMD BiocCheck --help'
(1.19.1) New Check options to turn off if in CRAN (--no-check-CRAN) and Bioconductor mailing list and support site (--no-check-bioc-help)

USER SIGNIFICANT CHANGES

(1.19.8) Updated Documentation in vignette for flag/option controls and reorganization of code/checks. Grouped similar checks together and changed order of checks.
(1.19.3) Remove Native Routine Registrations (use flag in R CMD check instead _R_CHECK_NATIVE_ROUTINE_REGISTRATION_)
(1.19.2) Match CRAN standards of package size <= 5MB (updated from 4MB)

BUG FIXES

(1.19.26) Fix NEWS check to recognize NEWS.md
(1.19.26) Check all repos for existing package not just software
(1.19.23) Informative message if no biocViews term found
(1.19.22) Fix output of system2 usage check
(1.19.19) Test only closures for T/F
(1.19.14) Fix ERROR when more than one VignetteEngine found
(1.19.10) Add suggestion of FormatR package to formatting notes
(1.19.10) Fix function lengths to be a NOTE and only display if functions are greater than 50 lines long.
(1.19.6) Replace use of devtools::create with usethis::create_package as function was deprecated.
(1.19.5) Fix length > 1 logical comparison in if statement

BiocCheck 1.17

NEW FEATURES

(1.17.21) Added quit-with-status option to both BiocCheck and BiocCheckGitClone for compatibility with travis
(1.17.18) Update devel to use BiocManager instructions instead of BiocInstaller
(1.17.17) Add a new function that can be run interactive or command line BiocCheckGitClone which is only run on a source directory not a tarball. This will check for bad system files
(1.17.17) BiocCheck addition: Checks vignette directory for intermediate and end files that should not be included.
(1.17.16) Checks for Bioconductor package size requirement if checking tarball

BUG FIXES

(1.17.19) Updated internal functions to use BiocManger instead of BiocInstaller

BiocCheck 1.16

BUG FIXES

handle interactive BiocCheck() arguments correctly

BiocCheck 1.14

NEW FEATURES

NOTE when maintainer subscription to bioc-devel mailing list cannot be checked (checking requires mailing list admin password).

BUG FIXES

Use shell quotes to allow spaces in package paths