CHANGES IN VERSION 1.29 ----------------------- 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