Defines functions RepoBuildParam

Documented in RepoBuildParam

#' RepoBuildParam
#' Parameters for building a GRAN repository. Most behavior during the
#' GRAN building process is specified via this object/constructor.
#' @param basedir The base directory. By default the temporary repository,
#' temporary install library, and package staging area will be located in
#' <basedir>/<subrepoName>/, while the  temporary source checkout will be in t
#' he basedir itself.
#' @param repo_name The name of the repository, e.g. stable or devel
#' @param temp_repo Location to create the temporary repository
#' @param temp_checkout Location to create temporary checkouts/copies of package
#'   source code
#' @param errlog The file to append error output to during the building and
#'   testing processes
#' @param logfile The file to append summary log information to during building
#'   and testing
#' @param check_note_ok logical. Whether packages that raise notes during
#'   R CMD check should be considered to have passed
#' @param check_warn_ok logical. Whether packages that raise warnings during
#'   R CMD check should be considered to have passed
#' @param tempLibLoc Location to create the temporary installed package library
#'   for use during the testing process
#' @param extra_fun currently ignored
#' @param destination Base location (not including repository name) of the
#'   final repository to be built. NOTE: GRANBase:::buildReportURL() expects
#'   this argument to have a trailing slash.
#' @param auth character. Authentication information required to add packages
#'   to the manifest.
#' @param dest_url The base URL the destination directory corresponds to. The
#' subrepository name will be appended to this to generate the URL used when
#' installing from the repository.
#' @param shell_init An optional shell script to source before invoking system
#' commands, e.g. a bashrc file. Ignored if "" or not specified.
#' @param loginnerfun The function to use to write log messages during the repository
#' build process. It will be passed pkg, ..., errfile, logfile, and pkglog based on
#' the other arguments to this function. Defaults to writeGRANLog
#' specified as the full and error log locations, respectively.
#' @param install_test logical. Should the install test be performed? Required
#' to build packages with vignettes, and for the check test
#' @param check_test logical. Should R CMD check be run on the packages as a
#' cohort. Requires install test.
#' @param use_cran_granbase logical. Currently ignored.
#' @param archive_timing numeric. Number of seconds to wait between attempts to
#' pull a package from the CRAN archive
#' @param archive_retries numeric. Number of times to retry pulling a package
#' from the CRAN archive.
#' @param build_timeout numeric. Number of seconds before timeout during
#' the build step for a single package. Defaults to 10 minutes.
#' @param check_timeout numeric. Number of seconds before timeout during
#' the check step for a single package. Defaults to 15 minutes.
#' @param email_notifications logical. Should email notifications be sent
#' regarding packages that fail to build on GRAN? Defaults to FALSE
#' @param email_opts List. Email options for sending emails regarding packages
#' that fail to build on GRAN. The list contains 4 elements: \code{smtp_server}:
#' the SMTP server - defaults to "localhost", \code{smtp_port}: SMTP port
#' number - defaults to 25, \code{sender_email}: Whom should the emails
#' be sent as? Defaults to "gran<repo_name>@localhost", \code{unsubscribers}:
#' Vector of Perl-style regexes for unsubscribers - defaults to NULL.
#' @param repo_archive Archive directory where older package sources will be saved
#' @param repo_metadata_dir Directory containing metadata files
#' @param make_windows_bins Whether to make Windows binary packages
#' @param platform Name of platform this GRANRepository is being build on
#' @param r_version R version for this GRANRepository
#' @param bioc_version Bioconductor version for this GRANRepository
#' @rdname repobuildparam
#' @examples
#' rbp = RepoBuildParam(basedir = tempdir(), repo_name = "myrepo")
#' @export

RepoBuildParam <- function(
    repo_name = "current",
    temp_repo = file.path(basedir, repo_name, "tmprepo"),
    temp_checkout = file.path(basedir, "tmpcheckout"),
    errlog = file.path(basedir, repo_name,
                       paste0("GRAN", repo_name, "-error.log")),
    logfile = file.path(basedir, repo_name,
                        paste0("GRAN", repo_name, "-full.log")),
    check_note_ok = TRUE,
    check_warn_ok = TRUE,
    tempLibLoc = file.path(basedir, repo_name, "LibLoc"),
    extra_fun = function(...) NULL,
    destination = basedir,
    auth = "",
    dest_url = makeFileURL(normalizePath2(destination)),
    shell_init = character(),
    loginnerfun = writeGRANLog,
    install_test = TRUE,
    check_test = TRUE,
    use_cran_granbase = TRUE,
    archive_timing = 2,
    archive_retries = 2,
    build_timeout = 10*60,
    check_timeout = 15*60,
    email_notifications = FALSE,
    email_opts = list(smtp_server = "localhost",
                      smtp_port = 25,
                      sender_email = paste0("gran", repo_name, "@localhost"),
                      unsubscribers = NULL),
    repo_archive = file.path(destination, repo_name,
                             "src", "contrib", "Archive"),
    repo_metadata_dir = file.path(destination, repo_name,
                                  "src", "contrib", "Meta"),
    make_windows_bins = TRUE,
    platform = "",
    r_version = "",
    bioc_version = "") {
        dir.create(basedir, recursive = TRUE)

    basedir <- normalizePath2(basedir)

    prepDirStructure(basedir, repo_name, temp_repo, temp_checkout, tempLibLoc,
                     destination, logfile, errlog)

    if(check_test && !install_test)
        stop("Cannot run check test without install test")

    repo <- new("RepoBuildParam",
                base_dir = basedir,
                repo_name = repo_name,
                temp_repo = normalizePath2(temp_repo),
                temp_checkout = normalizePath2(temp_checkout),
                errlog = errlog,
                logfile = logfile,
                check_note_ok = check_note_ok,
                check_warn_ok = check_warn_ok,
                tempLibLoc = normalizePath2(tempLibLoc),
                extra_fun = extra_fun,
                dest_base= normalizePath2(destination),
                auth = auth,
                dest_url = dest_url,
                shell_init = shell_init,
                logfun = function(x) NULL, #this is replaced below
                install_test = install_test,
                check_test = check_test,
                use_cran_granbase = use_cran_granbase,
                archive_timing = archive_timing,
                archive_retries = archive_retries,
                build_timeout = build_timeout,
                check_timeout = check_timeout,
                email_notifications = email_notifications,
                email_opts = email_opts,
                repo_archive = repo_archive,
                repo_metadata_dir = repo_metadata_dir,
                make_windows_bins = make_windows_bins,
		platform = platform,
		r_version = r_version,
		bioc_version = bioc_version)

    logfun(repo) <- function(pkg, ...) {
      loginnerfun(pkg, ..., errfile = errlogfile(repo),
                  logfile = logfile(repo),
                  pkglog = pkg_log_file(pkg, repo))

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GRANCore documentation built on Feb. 4, 2020, 5:06 p.m.