extras/packageDeps.R

In ohdsi-studies/DistributedLMM: Predicting Length of Hopsital Stay for COVID-19

# code to set up package dependancies
packages <- c('DatabaseConnector', 'SqlRender', 'Cyclops', 'FeatureExtraction', 
              'PatientLevelPrediction','OhdsiSharing', 'ParallelLogger',
              'ggplot2','ff','ffbase','zip','magrittr','dplyr','officer',
              'gridExtra','rvg','jsonlite','shiny','shinycssloaders',
              'shinydashboard', 'R.utils', 'DT')


# Borrowed from devtools: https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L44
is_installed <- function (pkg, version = 0) {
  installed_version <- tryCatch(utils::packageVersion(pkg), 
                                error = function(e) NA)
  !is.na(installed_version) && installed_version >= version
}

# Borrowed and adapted from devtools: https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L74
ensure_installed <- function(pkg) {
  if (!is_installed(pkg)) {
    msg <- paste0(sQuote(pkg), " must be installed for this functionality.")
    if (interactive()) {
      message(msg, "\nWould you like to install it?")
      if (utils::menu(c("Yes", "No")) == 1) {
        if(pkg%in%c('BigKnn','DatabaseConnector', 'SqlRender', 'Cyclops', 'FeatureExtraction', 'PatientLevelPrediction','OhdsiSharing', 'ParallelLogger')){
          devtools::install_github(paste0('OHDSI/',pkg))
        }else{
          utils::install.packages(pkg)
        }
      } else {
        stop(msg, call. = FALSE)
      }
    } else {
      stop(msg, call. = FALSE)
    }
  }
}


sapply(packages, ensure_installed)