CHANGES IN VERSION 1.44.0
-----------------------
NEW FEATURES
o Add `lifeCycle`, `deprecate_warn`, and `deprecate_stop` to the list of
functions for the `.Deprecated` / `.Defunct` check.
o Support checking `\()` syntax as anonymous R functions.
o Exclude comment-only lines in function lengths check (@hpages, #220)
o Add `checkFndPerson()` to validate Authors@R / Authors fields in the
`DESCRIPTION` file. A corresponding `NOTE` is shown in the vignette (#215)
o Refactor function length check to count only coding lines and not comment
lines (@hpages, #220)
BUG FIXES AND MINOR IMPROVEMENTS
o Check file sizes only for source directories and in `BiocCheckGitClone`
(@hpages, #219)
o Use R version from `BiocManager:::.version_map` for
`checkRVersionDependency` (@helenalc, #223)
o Use `checkInstalled()` to verify packages listed in `Suggests:`
o Suppress warning in `.hasPkg()` when the package is not installed
o Use `INFO` messages instead of bullet points in output
CHANGES IN VERSION 1.42.0
-----------------------
NEW FEATURES
o Use the `cli` R package to update the aesthetics of the output.
BUG FIXES AND MINOR IMPROVEMENTS
o Fix issue in `checkVigSuggests` internal function to only extract
packages that should be in the `Suggests` field.
o Fix issue where the lookbacks in static code searches were not
iterating over all of the indices. This affects all functions that
searched through code in R and vignette files.
o Non-interactive sessions default to old output syntax.
o Use full names e.g., 'WARNING' in report output for `grep`ping by
dependent software, i.e., Single Package Builder (SPB)
CHANGES IN VERSION 1.40.0
-----------------------
NEW FEATURES
o Check for duplicate chunk labels in vignettes and produce an error when
present (@hpages, #199)
o Warn when Rnw vignettes are present (@jwokaty, #190)
o Add error when maintainer email not parse-able in DESCRIPTION
o Check for Bioconductor dependencies in the Imports and Depends fields;
if none, produce a warning (@vjcitn).
o Remove redundant `DESCRIPTION` and `NAMESPACE` consistency checks; these
are already included in `R CMD check`
BUG FIXES AND MINOR IMPROVEMENTS
o Produce `NOTE` instead of `WARNING` for infrastructure packages without
Bioconductor dependencies
o `% \VignetteEngine` tags with spaces were not recognized; this has been
fixed
o Skip `\value` checks for package and class documentation; `\formats`
checked for data documentation
o Delegate system calls to `devtools::build` to build packages
o Update `checkRbuildignore` to flag `test` and `longtests` entries
appropriately (@hpages, #197)
o Fix issue where BiocCheck would fail when errors caused by duplicate chunk
labels were present (@hpages, #199)
o Avoid format checks e.g., length, indentation, and tabs for Rd files
that use roxygen2
o Use the `tools:::analyze_licenses` function to check for restrictive
license use (@hpages, #119)
o Use httr2 over httr for http requests
o Clarify `NOTE` and `WARNING` messages for `CITATION` file inclusion
(#209).
CHANGES IN VERSION 1.38.0
-----------------------
BUG FIXES AND MINOR IMPROVEMENTS
o Exclude data docs with `\\format` tags in addition to 'package' docs when
checking for `\\value` / `@return` in documentation.
o Resolve unknown macro warnings when using Rdpack (@LiNK-NY, #196)
o Improve the `read.dcf` operation that looks for any deprecated packages
in both Bioconductor release and devel versions.
o Remove overwrite prompt when updating cached resources in deprecated
packages check.
CHANGES IN VERSION 1.36.0
-----------------------
NEW FEATURES
o Include size limit checks for data files in `data`, `inst/extdata`, and
`data-raw` folders (@lshep, @const-ae, #167, #67)
o 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`.
o 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
o Filter out 'package' docTypes from '\value' documentaiton checks
(@grimbough, #189)
o Obtain a more complete list of deprecated packages for
`checkDeprecatedPkgs`
o Fix issue with path seperators on Windows ('\\' vs '/') causing the unit
test for `getBiocCheckDir` to report erroneous mismatches (@grimbough, #175)
o Fix bug where the wrong number of functions with length greater than 50
was reported (@grimbough, #182)
o biocViews term suggestions should be a scalar character (@lcolladotor,
#184)
o Update email in bioc-devel subscription check (@lshep, #185)
o Handle function length checks when there is no R code (@lshep, #186)
o Edit warning text when empty or missing `value` sections are found in
a package (@vjcitn)
o `checkForValueSection` re-implemented for clarity; filters out comments
in `value` sections (@LiNk-NY)
o Correctly identify `Rd` comments by updating the regular expression to
identify them (@LiNk-NY)
CHANGES IN VERSION 1.34
-----------------------
NEW FEATURES
o Redundant package dependencies checks between `DESCRIPTION` and
`NAMESPACE` have been removed. These are already present in `R CMD check`
as "checking package dependencies".
o Use `callr` to run `BiocCheck` in a separate process, this avoids
interference with loaded packages (@vjcitn, #158)
BUG FIXES AND MINOR IMPROVEMENTS
o Update `checkVigInstalls` and `checkVigBiocInst` to avoid false positives
(@almeidasilvaf, #170).
o Only count non evaluated chunks when there are any present in the
vignette
o 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)
o Fix bug where inputs to `getDirFile` were vectors in
`checkForValueSection` (@zeehio, #163)
o Allow lookback for matching T/F and exclude list elements, e.g., `list$F`
(@lshep, #161)
o Fix indentation count by excluding yaml front matter from vignettes
(@harpomaxx, #100)
o Update internal documentation of the `BiocCheck-class`
o Fix bug where line numbers were off due to removal of empty lines at
parsing (@lshep, #159)
o Slightly improve sentence counter for Description field check
(@lshep, #160)
o Update documentation links to point to contributions.bioconductor.org
(@LiNk-NY, #157)
CHANGES IN VERSION 1.32
-----------------------
NEW FEATURES
o Add package metadata to main report for easier diagnostics
o `<pkgname>.BiocCheck` folder, created above the package folder, includes
the full report and NAMESPACE suggestions, if available.
o Add check to find any stray `<pkgname>.BiocCheck` folders
o Update doc links and recommendations for additional information in report
o Update `BiocCheck` report to be more brief by only noting the conditions;
details are included in the full report
BUG FIXES AND MINOR IMPROVEMENTS
o Initialize default verbose value (FALSE) for internal reference object
o Flag only hidden '.RData' files as bad files and allow 'myData.RData'
(@hpages, #155)
o Improve internal handling of condition messages with unified mechanism
o Internal improvements to `BiocCheck` mechanism: export `.BiocCheck` object
which contains all conditions, log list, and method for writing to JSON
o Update to changes in R 4.2 `--no-echo` flag
o Make use of `lib.loc` to helper functions that install and load the
checked package
o (1.31.36) Reduce function length count slightly by removing empty lines.
o (1.31.35) Restricted files in `inst` will be flagged with a `WARNING`
instead of an `ERROR`
o (1.31.32) Account for S3 print methods when checking for `cat` usage
o (1.31.31) Single package imports in the NAMESPACE were breaking the code
to get all package imports.
o (1.31.29) Include other import fields from NAMESPACE file when checking
consistency between imports in DESCRIPTION/NAMESPACE.
o (1.31.27) Update and clean up unit tests.
o (1.31.26) Improve load test for the package being checked.
o (1.31.25) Exclude GitHub URLs that end in HTML from external data check.
o (1.31.23) Internal updates to the `require` and `library` check.
o (1.31.22) Remove old code related to running `BiocCheck` on the command
line and update `BiocCheck` documentation.
o (1.31.21) Remove redundant `=` from message to avoid `=` assignment.
o (1.31.20) Add line feed to "Checking function lengths..." message
o (1.31.18) Packages should not download files when loaded or attached.
o (1.31.17) Using '=' for assignment should be avoided and '<-' should be
used instead for clarity and legibility.
o (1.31.16) Note the use of `cat` and `print` outside of show methods.
o (1.31.15) Check for pinned package versions in the `DESCRIPTION` file
denoted by the use of `==`.
o (1.31.14) Enhancements to internal helper functions and
`BiocCheckGitClone`
o (1.31.13) Revert move to new package checks. Update Bioc-devel mailing
list check to fail early when not in BBS environment.
o (1.31.12) Move Bioc-devel mailing list and support site registration
checks to new package checks.
o (1.31.10) Various internal improvements to `BiocCheck` and the
identification of the package directory and name.
o (1.31.6) Use a more reliable approach to identify package name from the
`DESCRIPTION` file.
o (1.31.5) Fixed bug in the case where the `VignetteBuilder` field in the
a package's `DESCRIPTION` has more than one listed.
o (1.31.3) Add `BioCbooks` repository url to
`checkIsPackageNameAlreadyInUse`, `VIEWS` file is pending.
o (1.31.2) Fix logical length > 1 error in `checkImportSuggestions`
(@vjcitn, #141)
o (1.31.1) Simplify check for function lengths; remove excessive dots.
CHANGES IN VERSION 1.30
-----------------------
NEW FEATURES
o (1.29.10) Check for `Sys.setenv` and `suppressWarnings`/`suppressMessages`
o (1.29.8) Check for `sessionInfo` / `session_info` in vignette code.
o (1.29.5) Check for installation calls in vignette code.
o (1.29.1) Check for `install()` function calls in R code.
BUG FIXES
o (1.29.14) Various internal improvements to the codebase.
o (1.29.12) Checks on class membership code now include `is() ==` grammar.
o (1.29.6) Use appropriate input (`pkgdir`) to internal checking functions.
o (1.29.3) Add unit tests for legacy function searches.
o (1.29.2) rename internal function from checkIsPackageAlreadyInRepo to
checkIsPackageNameAlreadyInUse
CHANGES IN VERSION 1.27
-----------------------
BUG FIX
o (1.27.17) Update support site watched tags. tags are case insensitive
o (1.27.15) Reporting checking of vignette despite package type
(@lshep, #136)
o (1.27.9) Allow portability of child Rmd documents via parseFile
o (1.27.3) Correct check for if package already exists in CRAN/Bioc
o (1.27.3) Correct check for single colon use
o (1.27.2) Correct path to R license database file by calling
R.home('share').
NEW FEATURES
o (1.27.16) Check vignettes for all package types (@lshep, #136)
o (1.27.12) Check for `LazyData: TRUE` in the DESCRIPTION (@lshep, #128)
o (1.27.11) R version dependency check in the 'DESCRIPTION' is now a
'NOTE' (@lshep, #126)
o (1.27.10) Check for 'error' and other keywords in signaler functions,
'message', 'warning', and 'stop' etc. (@hpages, #125)
o (1.27.8) Check for 'tests' entry in '.Rbuildignore'
o (1.27.7) Removed BiocCheck and BiocCheckGitClone installation scripts;
recommended usage is `BiocCheck()`
o (1.27.6) Check that a user has the package name in watched tags of
support site
o (1.27.5) Check for 'paste' / 'paste0' in signaler functions, 'message',
'warning', and 'stop' (@LiNk-NY, #64)
o (1.27.4) Check for downloads from external resources (github, gitlab,
bitbucket, dropbox; @LiNk-NY, #75)
o (1.27.1) Check that licenses do not exclude classes of users,
e.g., non-academic users.
CHANGES IN VERSION 1.25
-----------------------
DEPRECATION ANNOUNCEMENT
o (1.25.11) R CMD BiocCheck and R CMD BiocCheckGitClone are deprecated. The
recommended way to run the functions is within R.
NEW FEATURES
o (1.25.1) Check for warning/notes on too-brief a Description: field
(@federicomarini, #65)
o (1.25.4) Check for single colon typos when using qualified imports
pkg::foo()
o (1.25.8) Validate ORCID iDs (if any) in the DESCRIPTION file
(@LiNk-NY, #97)
o (1.25.10) Add check for properly formatted CITATION file
o (1.25.12) Add NOTE to change dontrun to donttest
BUG FIXES
o (1.25.14) The ORCID iD check now accepts IDs with a X at the end.
o (1.25.9) All packages including infrastructure require a vignette
o Usage of donttest and dontrun in manual pages tagged with the keyword
'internal' will no longer trigger a NOTE (@grimbough, #59)
o (1.25.7) Adding the sessionInfo at the end of the vignette (@llrs)
USER SIGNIFICANT CHANGES
o (1.25.3) Require Aurhors@R format over Author/Maintainer fields in the
DESCRIPTION file. This has been upgraded to an ERROR.
o (1.25.2) Suggest styler over formatR for automatic code re-formatting
(@lcolladotor, #57).
o (1.25.5) Add warning to new package versions with non-zero x version
(@mtmorgan, #101)
CHANGES IN VERSION 1.23
-----------------------
BUG FIX
o (1.23.4) Update locations for NEWS
o (1.23.1) Fix False Positive class == check
CHANGES IN VERSION 1.19
-----------------------
NEW FEATURES
o (1.19.33) Add Authors@R vs Author/Maintainer check
o (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}.
o (1.19.28) Check that vignette metadata set correctly
o (1.19.27) Check for Author@R or Author/Maintainer but not both
o (1.19.25) Check for use of remotes: in Description
o (1.19.18) Check for use of dontrun/donttest
o (1.19.15) Check vignetteEngine/vignetteBuilder minimially declared in
Suggests
o (1.19.9) Check usage of donttest and dontrun in man page documentation
o (1.19.9) Update deprecated check to check for Bioconductor release and
devel deprecated packages as specified in biocViews
o (1.19.7) More helpful ERROR when using a non valid command line option.
o (1.19.4) All checks module. Ability to turn on/off with flag options. See
'R CMD BiocCheck --help'
o (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
o (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.
o (1.19.3) Remove Native Routine Registrations (use flag in R CMD check
instead _R_CHECK_NATIVE_ROUTINE_REGISTRATION_)
o (1.19.2) Match CRAN standards of package size <= 5MB (updated from 4MB)
BUG FIXES
o (1.19.26) Fix NEWS check to recognize NEWS.md
o (1.19.26) Check all repos for existing package not just software
o (1.19.23) Informative message if no biocViews term found
o (1.19.22) Fix output of system2 usage check
o (1.19.19) Test only closures for T/F
o (1.19.14) Fix ERROR when more than one VignetteEngine found
o (1.19.10) Add suggestion of FormatR package to formatting notes
o (1.19.10) Fix function lengths to be a NOTE and only display if functions
are greater than 50 lines long.
o (1.19.6) Replace use of devtools::create with usethis::create_package as
function was deprecated.
o (1.19.5) Fix length > 1 logical comparison in if statement
CHANGES IN VERSION 1.17
-----------------------
NEW FEATURES
o (1.17.21) Added quit-with-status option to both BiocCheck and
BiocCheckGitClone for compatibility with travis
o (1.17.18) Update devel to use BiocManager instructions instead of
BiocInstaller
o (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
o (1.17.17) BiocCheck addition: Checks vignette directory for intermediate
and end files that should not be included.
o (1.17.16) Checks for Bioconductor package size requirement if checking
tarball
BUG FIXES
o (1.17.19) Updated internal functions to use BiocManger instead of
BiocInstaller
CHANGES IN VERSION 1.16
-----------------------
BUG FIXES
o handle interactive BiocCheck() arguments correctly
CHANGES IN VERSION 1.14
-----------------------
NEW FEATURES
o NOTE when maintainer subscription to bioc-devel mailing list
cannot be checked (checking requires mailing list admin
password).
BUG FIXES
o Use shell quotes to allow spaces in package paths