R/50-tidymass_install.R

In tidymass/tidymass: R packages for mass spectrometry data processing and analysis

#' ##------------------------------------------------------------------------------
#' #' @title tidymass_install
#' #' @description Install all packages in tidymass.
#' #' @author Xiaotao Shen
#' #' \email{shenxt1990@@outlook.com}
#' #' @param force Force installation, even if the remote state has not changed since the previous install.
#' #' @param upgrade One of "default", "ask", "always", or "never".
#' #' "default" respects the value of the R_REMOTES_UPGRADE environment variable if set,
#' #' and falls back to "ask" if unset. "ask" prompts the user for which out of date
#' #' packages to upgrade. For non-interactive sessions "ask" is equivalent to "always".
#' #' TRUE and FALSE are also accepted and correspond to "always" and "never" respectively.
#' #' @param dependencies Which dependencies do you want to check? Can be a character vector
#' #' (selecting from "Depends", "Imports", "LinkingTo", "Suggests", or "Enhances"),
#' #' or a logical vector.TRUE is shorthand for "Depends", "Imports", "LinkingTo"
#' #' and "Suggests". NA is shorthand for "Depends", "Imports" and "LinkingTo"
#' #' and is the default. FALSE is shorthand for no dependencies
#' #' (i.e. just check this package, not its dependencies).
#' #' The value "soft" means the same as TRUE, "hard" means the same as NA.
#' #' @param demo_data Install demo_data package or not.
#' #' @param which_package What packages you want to install? Default is all.
#' #' You can set it as a character vector.
#' #' @param ... Other parameters from devtools::install_github() or devtools::install_git()
#' #' @importFrom devtools install_github
#' #' @importFrom devtools install_git
#' #' @export
#' 
#' tidymass_install <-
#'   function(force = FALSE,
#'            upgrade = "never",
#'            dependencies = NA,
#'            demo_data = TRUE,
#'            which_package = c(
#'              "all",
#'              "massdataset",
#'              "massprocesser",
#'              "masscleaner",
#'              "massqc",
#'              "metid",
#'              "massstat",
#'              "metpath",
#'              "masstools"
#'              # "demodata"
#'            ),
#'            ...) {
#'     which_package = match.arg(which_package)
#'     which_package = stringr::str_to_lower(which_package)
#'     
#'     ##detach packages
#'     
#'     if ("massdataset" %in% search()) {
#'       detach("package:massdataset")
#'     }
#'     
#'     if ("massprocesser" %in% search()) {
#'       detach("package:massprocesser")
#'     }
#'     
#'     if ("masscleaner" %in% search()) {
#'       detach("package:masscleaner")
#'     }
#'     
#'     if ("massqc" %in% search()) {
#'       detach("package:massqc")
#'     }
#'     
#'     if ("metid" %in% search()) {
#'       detach("package:metid")
#'     }
#'     
#'     if ("massstat" %in% search()) {
#'       detach("package:massstat")
#'     }
#'     
#'     if ("metpath" %in% search()) {
#'       detach("package:metpath")
#'     }
#'     
#'     if ("masstools" %in% search()) {
#'       detach("package:masstools")
#'     }
#'     
#'     ##masstools
#'     if (any(which_package == "all") |
#'         any(which_package == "masstools")) {
#'       devtools::install_github(
#'         repo = "tidymass/masstools",
#'         force = force,
#'         upgrade = upgrade,
#'         dependencies = TRUE,
#'         ...
#'       )
#'     }
#'     
#'     ##massdataset
#'     if (any(which_package == "all") |
#'         any(which_package == "massdataset")) {
#'       devtools::install_github(
#'         repo = "tidymass/massdataset",
#'         force = force,
#'         upgrade = upgrade,
#'         dependencies = TRUE,
#'         ...
#'       )
#'     }
#'     
#'     ##massdataset
#'     # if (any(which_package == "all") |
#'     #     any(which_package == "demodata")) {
#'     #   devtools::install_github(
#'     #     repo = "tidymass/demodata",
#'     #     force = force,
#'     #     upgrade = upgrade,
#'     #     dependencies = TRUE,
#'     #     ...
#'     #   )
#'     # }
#'     
#'     ##massprocesser
#'     if (any(which_package == "all") |
#'         any(which_package == "massprocesser")) {
#'       devtools::install_github(
#'         repo = "tidymass/massprocesser",
#'         force = force,
#'         upgrade = upgrade,
#'         dependencies = TRUE,
#'         ...
#'       )
#'     }
#'     
#'     ##masscleaner
#'     if (any(which_package == "all") |
#'         any(which_package == "masscleaner")) {
#'       devtools::install_github(
#'         repo = "tidymass/masscleaner",
#'         force = force,
#'         upgrade = upgrade,
#'         dependencies = TRUE,
#'         ...
#'       )
#'     }
#'     
#'     ##massqc
#'     if (any(which_package == "all") |
#'         any(which_package == "massqc")) {
#'       devtools::install_github(
#'         repo = "tidymass/massqc",
#'         force = force,
#'         upgrade = upgrade,
#'         dependencies = TRUE,
#'         ...
#'       )
#'     }
#'     
#'     ##metid
#'     if (any(which_package == "all") |
#'         any(which_package == "metid")) {
#'       devtools::install_github(
#'         repo = "tidymass/metid",
#'         force = force,
#'         upgrade = upgrade,
#'         dependencies = TRUE,
#'         ...
#'       )
#'     }
#'     
#'     ##massstat
#'     if (any(which_package == "all") |
#'         any(which_package == "massstat")) {
#'       devtools::install_github(
#'         repo = "tidymass/massstat",
#'         force = force,
#'         upgrade = upgrade,
#'         dependencies = TRUE,
#'         ...
#'       )
#'     }
#'     
#'     ##metpath
#'     if (any(which_package == "all") |
#'         any(which_package == "metpath")) {
#'       devtools::install_github(
#'         repo = "tidymass/metpath",
#'         force = force,
#'         upgrade = upgrade,
#'         dependencies = TRUE,
#'         ...
#'       )
#'     }
#'   }