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). BUG FIXES AND MINOR IMPROVEMENTS 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 `.BiocCheck` folder, created above the package folder, includes the full report and NAMESPACE suggestions, if available. o Add check to find any stray `.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