R/repository.R

In PRL-PRG/dynalyzer: Dynamic Analysis Data Analysis Pipeline

#' @export
setup_repository <- function(object, ...) UseMethod("setup_repository")


#' @export
setup_repository.dynalyzer.settings.repository <- function(settings) {

    if(settings$setup_cran) {
        setup_cran(settings)
    }

    if(settings$setup_bioc) {
        setup_bioc(settings)
    }
}


setup_cran <- function(settings) {
    options(repos = settings$cran_mirror_url)

    dir_create(settings$cran_src_dirpath)
    dir_create(settings$cran_lib_dirpath)

    packages <- setdiff(available.packages()[,1],
                        installed.packages()[,1])

    cat("Installing", length(packages), "packages.\n")

    install.packages(packages,
                     lib = settings$cran_lib_dirpath,
                     dependencies = TRUE,
                     destdir = settings$cran_src_dirpath,
                     INSTALL_opts = c('--example',
                                      '--install-tests',
                                      '--with-keep.source',
                                      '--no-multiarch'),
                     Ncpus = settings$ncpus,
                     keep_outputs = settings$cran_log_dirpath)
}


setup_bioc <- function(settings) {
    options(repos = settings$cran_mirror_url)

    dir_create(settings$bioc_src_dirpath)
    dir_create(settings$bioc_lib_dirpath)

    packages <- setdiff(BiocManager::available(),
                        installed.packages()[,1])

    cat("Installing", length(packages), "packages.\n")

    BiocManager::install(packages,
                         lib = settings$bioc_lib_dirpath,
                         dependencies = TRUE,
                         destdir = settings$bioc_src_dirpath,
                         INSTALL_opts = c('--example',
                                          '--install-tests',
                                          '--with-keep.source',
                                          '--no-multiarch'),
                         Ncpus = settings$ncpus,
                         update = TRUE,
                         ask = FALSE,
                         keep_outputs = settings$bioc_log_dirpath)
}


#' @export
create_repository_settings <- function(ncpus,
                                       setup_cran,
                                       setup_bioc,
                                       cran_mirror_url,
                                       cran_lib_dirpath,
                                       cran_src_dirpath,
                                       cran_log_dirpath,
                                       bioc_lib_dirpath,
                                       bioc_src_dirpath,
                                       bioc_log_dirpath) {
    structure(list(ncpus = ncpus,
                   setup_cran = setup_cran,
                   setup_bioc = setup_bioc,
                   cran_mirror_url = cran_mirror_url,
                   cran_lib_dirpath = cran_lib_dirpath,
                   cran_src_dirpath = cran_src_dirpath,
                   cran_log_dirpath = cran_log_dirpath,
                   bioc_lib_dirpath = bioc_lib_dirpath,
                   bioc_src_dirpath = bioc_src_dirpath,
                   bioc_log_dirpath = bioc_log_dirpath),
              class = "dynalyzer.settings.repository")
}


#' @export
parse_repository_settings <- function(args = commandArgs(trailingOnly = TRUE)) {
    usage <- "%prog [OPTIONS] ..."
    description <- ""

    option_list <- list(
        make_option(c("--ncpus"),
                    action = "store",
                    type = "integer",
                    default = 8,
                    help = "number of CPUs to use for installing packages",
                    metavar = "ncpus"),

        make_option(c("--setup-cran"),
                    action = "store_true",
                    default = FALSE,
                    help = "setup CRAN packages",
                    metavar = "setup_cran"),

        make_option(c("--setup-bioc"),
                    action = "store_true",
                    default = FALSE,
                    help = "setup BIOC packages",
                    metavar = "setup_bioc"),

        make_option(c("--cran-mirror-url"),
                    action = "store",
                    type = "character",
                    help = "CRAN mirror URL",
                    metavar = "cran_mirror_url"),

        make_option(c("--cran-lib-dirpath"),
                    action = "store",
                    type = "character",
                    help = "directory in which to store the CRAN package libraries",
                    metavar = "cran_lib_dirpath"),

        make_option(c("--cran-src-dirpath"),
                    action = "store",
                    type = "character",
                    help = "directory in which to store the CRAN package sources",
                    metavar = "cran_src_dirpath"),

        make_option(c("--cran-log-dirpath"),
                    action = "store",
                    type = "character",
                    help = "directory in which to store the CRAN package installation logs",
                    metavar = "cran_log_dirpath"),

        make_option(c("--bioc-lib-dirpath"),
                    action = "store",
                    type = "character",
                    help = "directory in which to store the BIOC package libraries",
                    metavar = "bioc_lib_dirpath"),

        make_option(c("--bioc-src-dirpath"),
                    action = "store",
                    type = "character",
                    help = "directory in which to store the BIOC package sources",
                    metavar = "bioc_src_dirpath"),

        make_option(c("--bioc-log-dirpath"),
                    action = "store",
                    type = "character",
                    help = "directory in which to store the BIOC package installation logs",
                    metavar = "bioc_log_dirpath")

    )


    option_parser <- OptionParser(usage = usage,
                                  description = description,
                                  add_help_option = TRUE,
                                  option_list = option_list)

    arguments <- parse_args2(option_parser, args)

    create_repository_settings(ncpus = arguments$options$ncpus,
                               setup_cran = arguments$options$setup_cran,
                               setup_bioc = arguments$options$setup_bioc,
                               cran_mirror_url = arguments$options$cran_mirror_url,
                               cran_lib_dirpath = arguments$options$cran_lib_dirpath,
                               cran_src_dirpath = arguments$options$cran_src_dirpath,
                               cran_log_dirpath = arguments$options$cran_log_dirpath,
                               bioc_lib_dirpath = arguments$options$bioc_lib_dirpath,
                               bioc_src_dirpath = arguments$options$bioc_src_dirpath,
                               bioc_log_dirpath = arguments$options$bioc_log_dirpath)
}