diff --git a/NEWS b/NEWS index 10c9705..3ab47ec 100644 --- a/NEWS +++ b/NEWS @@ -18,6 +18,8 @@ BUG FIXES AND MINOR IMPROVEMENTS checks o Chunks in Rnw vignettes with no labels are now correctly identified o `sessionInfo` checks in vignettes occur only when code chunks are present + o BiocCheck() options are now ordered alphabetically in documentation to + make it easier to find specific options (@Bisaloo, #229). CHANGES IN VERSION 1.44.0 ----------------------- diff --git a/R/BiocCheck.R b/R/BiocCheck.R index b1078d2..b129b15 100644 --- a/R/BiocCheck.R +++ b/R/BiocCheck.R @@ -22,39 +22,39 @@ #' #' @section dot-options: #' +#' * `build-output-file`: file containing R CMD build output, for +#' additional analysis #' * `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-bioc-help`: disable check for registration on Bioconductor +#' * `no-check-bioc-views`: disable biocViews-specific checks (for non-BioC +#' packages) +#' mailing list and support site #' * `no-check-coding-practices`: disable check for some common best coding #' practices +#' * `no-check-CRAN`: disable check for if package exists in CRAN +#' * `no-check-dependencies`: disable check for bad dependencies +#' * `no-check-deprecated`: disable check for usage of deprecated packages +#' * `no-check-description`: disable DESCRIPTION file checks +#' * `no-check-file-size`: disable check for individual file size +#' * `no-check-formatting`: disable checks for file formatting #' * `no-check-function-len`: disable check for function length +#' * `no-check-install-self`: disable check for require or library of +#' itself +#' * `no-check-library-calls`: disable check usage of functions that +#' install or update packages #' * `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-pkg-size`: disable check for package tarball size +#' * `no-check-R-ver`: disable check for valid R version +#' * `no-check-remotes`: disable check for usage of remote packages other +#' than those hosted on CRAN or Bioconductor #' * `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 +#' * `no-check-unit-tests`: disable checks for unit tests +#' * `no-check-version-num`: disable check for valid version number +#' * `no-check-vignettes`: disable vignette checks #' * `quit-with-status`: enable exit code option when performing check #' #' @param package The path to an R package directory or tarball (`.tar.gz`). diff --git a/man/BiocCheck.Rd b/man/BiocCheck.Rd index 6fe125b..b829d08 100644 --- a/man/BiocCheck.Rd +++ b/man/BiocCheck.Rd @@ -69,39 +69,39 @@ tarball that was created using \verb{R CMD build}. \section{dot-options}{ \itemize{ +\item \code{build-output-file}: file containing R CMD build output, for +additional analysis \item \code{new-package}: enable checks specific to new packages -\item \code{no-check-dependencies}: disable check for bad dependencies -\item \code{no-check-deprecated}: disable check for usage of deprecated packages -\item \code{no-check-remotes}: disable check for usage of remote packages other -than those hosted on CRAN or Bioconductor -\item \code{no-check-version-num}: disable check for valid version number -\item \code{no-check-R-ver}: disable check for valid R version -\item \code{no-check-pkg-size}: disable check for package tarball size -\item \code{no-check-file-size}: disable check for individual file size -\item \code{no-check-bioc-views}: disable biocViews-specific checks (for non-BioC -packages) \item \code{no-check-bbs}: disable BBS-specific checks (for non-BioC packages). Valid DESCRIPTION -\item \code{no-check-description}: disable DESCRIPTION file checks -\item \code{no-check-vignettes}: disable vignette checks -\item \code{no-check-library-calls}: disable check usage of functions that -install or update packages -\item \code{no-check-install-self}: disable check for require or library of -itself +\item \code{no-check-bioc-help}: disable check for registration on Bioconductor +\item \code{no-check-bioc-views}: disable biocViews-specific checks (for non-BioC +packages) +mailing list and support site \item \code{no-check-coding-practices}: disable check for some common best coding practices +\item \code{no-check-CRAN}: disable check for if package exists in CRAN +\item \code{no-check-dependencies}: disable check for bad dependencies +\item \code{no-check-deprecated}: disable check for usage of deprecated packages +\item \code{no-check-description}: disable DESCRIPTION file checks +\item \code{no-check-file-size}: disable check for individual file size +\item \code{no-check-formatting}: disable checks for file formatting \item \verb{no-check-function-len}: disable check for function length +\item \code{no-check-install-self}: disable check for require or library of +itself +\item \code{no-check-library-calls}: disable check usage of functions that +install or update packages \item \code{no-check-man-doc}: disable checks for man page documentation \item \code{no-check-news}: disable checks for NEWS file -\item \code{no-check-unit-tests}: disable checks for unit tests +\item \code{no-check-pkg-size}: disable check for package tarball size +\item \code{no-check-R-ver}: disable check for valid R version +\item \code{no-check-remotes}: disable check for usage of remote packages other +than those hosted on CRAN or Bioconductor \item \code{no-check-skip-bioc-tests}: disable check for tests that skip when on bioc -\item \code{no-check-formatting}: disable checks for file formatting -\item \code{no-check-CRAN}: disable check for if package exists in CRAN -\item \code{no-check-bioc-help}: disable check for registration on Bioconductor -mailing list and support site -\item \code{build-output-file}: file containing R CMD build output, for -additional analysis +\item \code{no-check-unit-tests}: disable checks for unit tests +\item \code{no-check-version-num}: disable check for valid version number +\item \code{no-check-vignettes}: disable vignette checks \item \code{quit-with-status}: enable exit code option when performing check } }