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BiocCheck.R
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BiocCheck.R
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#' Check a package's adherence with the Bioconductor Package Guidelines
#'
#' Analyzes an R package for adherence with Bioconductor package guidelines and
#' best practices. The check outputs are categorized into ERROR, WARNING, and
#' NOTE. See the vignette for more details. `BiocCheck` is complementary
#' to `R CMD check`, which should always be run first.
#'
#' `BiocCheck()` reviews R packages for adherence with Bioconductor
#' package guidelines and best practices. See
#' \url{https://contributions.bioconductor.org} for the latest guidance for
#' writing Bioconductor software. Some rationale behind these best practices
#' can be seen in the vignette and pages in the `references` section. The
#' vignette also provides detailed explanations of all the checks performed by
#' `BiocCheck`.
#'
#' `BiocCheck` is called within R with \preformatted{ BiocCheck(<package>)
#' } where `package` points to the source directory or the `.tar.gz`
#' tarball that was created using `R CMD build`.
#'
#' \emph{Note} that `BiocCheck` is complementary to `R CMD check`.
#' `R CMD check` should always be run first for best results.
#'
#' @section dot-options:
#'
#' * `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-coding-practices`: disable check for some common best coding
#' practices
#' * `no-check-function-len`: disable check for function length
#' * `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-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
#' * `quit-with-status`: enable exit code option when performing check
#'
#' @param package The path to an R package directory or tarball (`.tar.gz`).
#' The `BiocCheck` function is intended to be run from the package
#' directory; therefore, the current working directory (given by `getwd()`)
#' is the default.
#'
#' @param checkDir The directory where the `BiocCheck` output directory will be
#' stored. By default, it will be placed in the same directory as the package
#' directory i.e., `dirname(pkg_dir)`.
#'
#' @param debug Whether to append the names of functions that correspond to
#' each condition raised by `BiocCheck` in the written log (i.e., in the
#' `'<package_name>.BiocCheck'` folder). This option is only relevant to
#' developers and contributors to `BiocCheck`.
#'
#' @param callr logical(1) Whether to use the `callr` package to run `BiocCheck`
#' in an isolated R session to prevent namespace collisions.
#'
#' @param \dots See the details section for available options. When running
#' `BiocCheck`, options can be specified as:
#' \preformatted{ BiocCheck(package, `no-check-vignettes`=TRUE) }
#'
#' @return `BiocCheck()` is chiefly called for the side effect of the check
#' reporting. The function also creates a `<package_name>.BiocCheck` folder
#' and returns a `BiocCheck` reference class with three main list elements:
#'
#' * **error**: Items to address before the package can be accepted
#'
#' * **warning**: Strongly suggested items that may require attention
#'
#' * **note**: Items to consider, though not required, before acceptance
#'
#' @author Dan Tenenbaum, Lori Shepherd, and Marcel Ramos
#'
#' @references \url{https://contributions.bioconductor.org}
#' @seealso \link{BiocCheck-class}, \link{Message-class}
#'
#' @examples
#'
#' packageDir <- system.file("testpackages", "testpkg0", package="BiocCheck")
#' BiocCheck(packageDir, `quit-with-status`=FALSE)
#'
#' @export BiocCheck
BiocCheck <- function(
package = getwd(),
checkDir = dirname(package),
debug = FALSE,
callr = FALSE,
...
) {
if (callr) {
callr::r(
function(...) { BiocCheck:::BiocCheckRun(...) },
args = list(
package = package, checkDir = checkDir, debug = debug, ...
),
cmdargs = c("--no-echo", "--no-save", "--no-restore"),
show = TRUE
)
} else {
BiocCheckRun(
package = package, checkDir = checkDir, debug = debug, ...
)
}
}
#' @importFrom BiocBaseUtils isScalarCharacter
BiocCheckRun <-
function(package, checkDir, debug, ...)
{
.BiocCheck$zero()
package <- normalizePath(package)
if (!file.exists(package) || !isScalarCharacter(package))
.stop("Package directory or tarball provided does not exist.")
# be careful here:
if (identical(.Platform$OS.type, "windows"))
package <- gsub("\\\\", "/", package)
dots <- list(...)
if (length(dots) == 1L && is.list(dots[[1]]))
dots <- dots[[1]] # command line args come as list
oldwarn <- getOption("warn")
oldwidth <- getOption("cli.width")
on.exit({
options(warn = oldwarn, cli.width = oldwidth)
})
options(warn = 1, cli.width = 80)
.BiocPackage <- .BiocPackage$initialize(
packageDir = package, checkDir = checkDir
)
## consider merging these operations into one
cli::cli_div(theme = list(.pkg = list(color = "orange")))
cli::cli_rule("Installing {.pkg { .BiocPackage$packageName }}")
package_install_dir <- installAndLoad(.BiocPackage)
cli::cli_alert_success("Package installed successfully")
libloc <- file.path(package_install_dir, "lib")
isBBS <- Sys.getenv("IS_BIOC_BUILD_MACHINE")
onBBS <- nzchar(isBBS) && identical(tolower(isBBS), "true")
hasAdmin <- nzchar(Sys.getenv("BIOC_DEVEL_PASSWORD"))
.BiocCheck$addMetadata(
BiocPackage = .BiocPackage, installDir = package_install_dir
)
cli::cli_rule("{.pkg { .BiocPackage$packageName }} session metadata")
.BiocCheck$show_meta()
cli::cli_rule("Running BiocCheck on {.pkg { .BiocPackage$packageName }}")
# BiocCheck checks --------------------------------------------------------
if (is.null(dots[["no-check-deprecated"]])) {
handleCheck("Checking for deprecated package usage...")
checkDeprecatedPackages(.BiocPackage)
}
if (is.null(dots[["no-check-remotes"]])){
handleCheck("Checking for remote package usage...")
checkRemotesUsage(.BiocPackage)
}
handleCheck("Checking for 'LazyData: true' usage...")
checkLazyDataUsage(.BiocPackage)
if (is.null(dots[["no-check-version-num"]])){
handleCheck("Checking version number...")
if (!.BiocPackage$isSourceDir) {
handleCheck("Checking for version number mismatch...")
checkForVersionNumberMismatch(.BiocPackage)
}
if (!is.null(dots[["new-package"]])) {
handleCheck("Checking new package version number...")
checkNewPackageVersionNumber(.BiocPackage)
} else {
handleCheck("Checking version number validity...")
checkVersionNumber(.BiocPackage)
}
}
if (is.null(dots[["no-check-R-ver"]])) {
handleCheck("Checking R version dependency...")
checkRVersionDependency(.BiocPackage)
}
if (is.null(dots[["no-check-pkg-size"]])){
handleCheck("Checking package size...")
if (.BiocPackage$isTar){
checkPackageSize(.BiocPackage, size=5)
} else {
handleMessage("Skipped... only checked on source tarball", indent=4)
}
}
if (is.null(dots[["no-check-file-size"]])){
handleCheck("Checking individual file sizes...")
checkIndivFileSizes(.BiocPackage)
checkDataFileSizes(.BiocPackage)
}
if (is.null(dots[["no-check-bioc-views"]]))
{
handleCheck("Checking biocViews...")
result <- checkBiocViews(.BiocPackage)
if(result)
{
cli::cli_alert_info(
"Search 'biocViews' at https://contributions.bioconductor.org"
)
}
}
if (is.null(dots[["no-check-bbs"]])){
handleCheck("Checking build system compatibility...")
checkBBScompatibility(.BiocPackage)
}
if (is.null(dots[["no-check-description"]])) {
checkDESCRIPTIONFile(.BiocPackage)
}
handleCheck("Checking .Rbuildignore...")
checkRbuildignore(.BiocPackage)
handleCheck("Checking for stray BiocCheck output folders...")
checkBiocCheckOutputFolder(.BiocPackage)
if (!.BiocPackage$isTar) {
handleCheck("Checking for inst/doc folders...")
checkInstDocFolder(.BiocPackage)
}
if (is.null(dots[["no-check-vignettes"]])) {
handleCheck("Checking vignette directory...")
checkVignetteDir(.BiocPackage)
if ("build-output-file" %in% names(dots)) {
handleCheck(
"Checking whether vignette is built with 'R CMD build'..."
)
checkIsVignetteBuilt(dots[["build-output-file"]])
}
}
if (is.null(dots[["no-check-library-calls"]])){
handleCheck("Checking package installation calls in R code...")
checkPkgInstallCalls(.BiocPackage)
}
package_dir <- .BiocPackage$sourceDir
package_name <- .BiocPackage$packageName
parsedCode <- parseFiles(.BiocPackage)
if (is.null(dots[["no-check-install-self"]])){
handleCheck(sprintf("Checking for library/require of %s...",
package_name))
checkForLibraryRequire(.BiocPackage)
}
if (is.null(dots[["no-check-coding-practices"]])){
handleCheck("Checking coding practice...")
checkCodingPractice(.BiocPackage, parsedCode)
}
if (is.null(dots[["no-check-function-len"]])){
handleCheck("Checking function lengths...")
checkFunctionLengths(parsedCode, package_name)
}
if (is.null(dots[["no-check-man-doc"]])){
handleCheck("Checking man page documentation...")
checkManDocumentation(.BiocPackage, libloc)
}
if (is.null(dots[["no-check-news"]])){
handleCheck("Checking package NEWS...")
checkNEWS(package_dir)
}
if (is.null(dots[["no-check-unit-tests"]])){
handleCheck("Checking unit tests...")
checkUnitTests(package_dir)
}
if (is.null(dots[["no-check-skip-bioc-tests"]])){
handleCheck("Checking skip_on_bioc() in tests...")
checkSkipOnBioc(package_dir)
}
if (is.null(dots[["no-check-formatting"]])){
handleCheck(
"Checking formatting of DESCRIPTION, NAMESPACE, ",
"man pages, R source, and vignette source...")
checkFormatting(.BiocPackage)
}
if (is.null(dots[["no-check-CRAN"]]))
{
handleCheck("Checking if package already exists in CRAN...")
checkIsPackageNameAlreadyInUse(package_name, "CRAN")
}
if (!is.null(dots[["new-package"]]))
{
handleCheck("Checking if new package already exists in Bioconductor...")
checkIsPackageNameAlreadyInUse(package_name, "BioCsoft")
checkIsPackageNameAlreadyInUse(package_name, "BioCann")
checkIsPackageNameAlreadyInUse(package_name, "BioCexp")
checkIsPackageNameAlreadyInUse(package_name, "BioCworkflows")
# TODO: add VIEWS files for books
# checkIsPackageNameAlreadyInUse(package_name, "BioCbooks")
}
if (is.null(dots[["no-check-bioc-help"]])) {
handleCheck("Checking for bioc-devel mailing list subscription...")
if (hasAdmin) {
checkForBiocDevelSubscription(.BiocPackage)
} else {
handleNote(
"Cannot determine whether maintainer is subscribed to the ",
"Bioc-Devel mailing list (requires admin credentials). ",
"Subscribe here: ",
"https://stat.ethz.ch/mailman/listinfo/bioc-devel"
)
}
handleCheck("Checking for support site registration...")
checkForSupportSiteRegistration(.BiocPackage)
}
cli::cli_rule(
left = paste0("BiocCheck v", packageVersion("BiocCheck"), " results")
)
cli::cli_text(
paste0(
"{symbol$cross} { .BiocCheck$getNum('error') } ERRORS | ",
"{symbol$warning} { .BiocCheck$getNum('warning') } WARNINGS | ",
"{symbol$bullet} { .BiocCheck$getNum('note') } NOTES\n"
)
)
cli::cli_alert_info(
paste0(
"\nSee the { .BiocPackage$packageName }.BiocCheck folder and run\n",
" browseVignettes(package = 'BiocCheck')\n",
" for details."
)
)
.BiocCheck$report(debug, onBBS)
if (isTRUE(dots[["quit-with-status"]])) {
errcode <- as.integer(.BiocCheck$getNum("error") > 0)
q("no", errcode)
}
return(.BiocCheck)
}