use rlang::check_installed instead of ensure_installed

OHDSI · Dec 17, 2024 · 4c2d18c · 4c2d18c
1 parent fbea755
commit 4c2d18c
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Showing 14 changed files with 18 additions and 68 deletions.
diff --git a/R/CyclopsSettings.R b/R/CyclopsSettings.R
@@ -195,8 +195,7 @@ setIterativeHardThresholding <- function(
   threshold = 1e-06, 
   delta = 0
   ) {
-
-  ensure_installed("IterativeHardThresholding")
+  rlang::check_installed("IterativeHardThresholding") 
 
   if (K < 1)
     stop("Invalid maximum number of predictors")

diff --git a/R/DatabaseMigration.R b/R/DatabaseMigration.R
@@ -56,7 +56,7 @@ migrateDataModel <- function(connectionDetails, databaseSchema, tablePrefix = ""
 
 
 getDataMigrator <- function(connectionDetails, databaseSchema, tablePrefix = "") {
-  ensure_installed("ResultModelManager")
+  rlang::check_installed("ResultModelManager")
 
   ResultModelManager::DataMigrationManager$new(
     connectionDetails = connectionDetails,
@@ -65,4 +65,4 @@ getDataMigrator <- function(connectionDetails, databaseSchema, tablePrefix = "")
     migrationPath = "migrations",
     packageName = utils::packageName()
   )
-}
+}
diff --git a/R/FeatureImportance.R b/R/FeatureImportance.R
@@ -99,7 +99,7 @@ pfi <- function(plpResult, population, plpData, repeats = 1,
   savePlpData(plpData, file = plpDataLocation)
 
   if(is.null(cores)){
-    ensure_installed('parallel')
+    rlang::check_installed("parallel")
     ParallelLogger::logInfo(paste0('Number of cores not specified'))
     cores <- parallel::detectCores()
     ParallelLogger::logInfo(paste0('Using all ', cores))

diff --git a/R/GradientBoostingMachine.R b/R/GradientBoostingMachine.R
@@ -39,7 +39,7 @@ setGradientBoostingMachine <- function(ntrees=c(100, 300), nthread=20, earlyStop
                                   scalePosWeight=1, lambda=1, alpha=0,
                                   seed= sample(10000000,1)){
 
-  ensure_installed("xgboost")
+  rlang::check_installed("xgboost")
 
   checkIsClass(seed, c('numeric', 'integer'))
 

diff --git a/R/HelperFunctions.R b/R/HelperFunctions.R
@@ -7,42 +7,6 @@ removeInvalidString <- function(string){
 }
 
 
-# Borrowed from devtools: https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L44
-is_installed <- function (pkg) {
-  installed_version <- tryCatch(utils::packageVersion(pkg), 
-                                error = function(e) NA)
-  !is.na(installed_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', "IterativeHardThresholding", "ShinyAppBuilder", "ResultModelManager")){
-
-          # add code to check for devtools...
-          dvtCheck <- tryCatch(utils::packageVersion('devtools'), 
-                      error = function(e) NA)
-          if(is.na(dvtCheck)){
-            utils::install.packages('devtools')
-          }
-
-          devtools::install_github(paste0('OHDSI/',pkg))
-        }else{
-          utils::install.packages(pkg)
-        }
-      } else {
-        stop(msg, call. = FALSE)
-      }
-    } else {
-      stop(msg, call. = FALSE)
-    }
-  }
-}
-
 #' Create a temporary model location
 #' 
 #' @export

diff --git a/R/ImportFromCsv.R b/R/ImportFromCsv.R
@@ -23,7 +23,7 @@ insertCsvToDatabase <- function(
   csvTableAppend = ''
 ){
 
-  ensure_installed('readr')
+  rlang::check_installed("readr")
 
   ParallelLogger::logInfo('Starting input checks')
 

diff --git a/R/KNN.R b/R/KNN.R
@@ -28,7 +28,7 @@
 #' }
 #' @export
 setKNN <- function(k=1000, indexFolder=file.path(getwd(),'knn'), threads = 1  ){
-  ensure_installed("BigKnn")
+  rlang::check_installed("BigKnn")
 
   checkIsClass(indexFolder, c('character'))
 

diff --git a/R/LearningCurve.R b/R/LearningCurve.R
@@ -133,7 +133,7 @@ createLearningCurve <- function(
   ExecutionDateTime <- Sys.time()
 
   if(parallel){
-    ensure_installed('parallel')
+    rlang::check_installed("parallel")
     if(is.null(cores)){
       ParallelLogger::logInfo(paste0('Number of cores not specified'))
       cores <- parallel::detectCores()

diff --git a/R/LightGBM.R b/R/LightGBM.R
@@ -49,7 +49,7 @@ setLightGBM <- function(nthread = 20,
                         scalePosWeight = 1,
                         isUnbalance = FALSE,
                         seed = sample(10000000, 1)) {
-  ensure_installed("lightgbm")
+  rlang::check_installed("lightgbm")
   checkIsClass(seed, c("numeric", "integer"))
 
   if (length(nthread) > 1) {

diff --git a/R/Plotting.R b/R/Plotting.R
@@ -54,8 +54,7 @@ outcomeSurvivalPlot <- function(
   yLabel = 'Fraction of those who are outcome free in target population'
 )
 {
-
-  ensure_installed("survminer")
+  rlang::check_installed("survminer") 
   if(missing(plpData)){
     stop('plpData missing')
   }

diff --git a/R/SaveLoadPlp.R b/R/SaveLoadPlp.R
@@ -291,10 +291,10 @@ loadPlpModel <- function(dirPath) {
 
 
   if(attr(plpModel, 'saveType') == "xgboost"){
-    ensure_installed("xgboost")
+    rlang::check_installed("xgboost")
     plpModel$model <- xgboost::xgb.load(file.path(dirPath, "model.json"))
   } else if(attr(plpModel, 'saveType') == "lightgbm"){
-    ensure_installed("lightgbm")
+    rlang::check_installed("lightgbm")
     plpModel$model <- lightgbm::lgb.load(file.path(dirPath, "model.json"))
   } else if(attr(plpModel, 'saveType') %in% c("RtoJson")){
     plpModel$model <- ParallelLogger::loadSettingsFromJson(file.path(dirPath, "model.json"))
@@ -579,7 +579,7 @@ extractDatabaseToCsv <- function(
   fileAppend = NULL
   ){
 
-  ensure_installed('readr')
+  rlang::check_installed("readr")
 
   # check inputs
   if(!is.null(fileAppend)){

diff --git a/R/ViewShinyPlp.R b/R/ViewShinyPlp.R
@@ -126,9 +126,8 @@ viewDatabaseResultPlp <- function(
 # one shiny app 
 
 viewPlps <- function(databaseSettings){
-  ensure_installed("ShinyAppBuilder") 
-  ensure_installed("ResultModelManager")
-
+  rlang::check_installed("ShinyAppBuilder")
+  rlang::check_installed("ResultModelManager")
   connectionDetails <- do.call(
     DatabaseConnector::createConnectionDetails, 
     databaseSettings$connectionDetailSettings
@@ -177,4 +176,4 @@ viewPlps <- function(databaseSettings){
   }
 
 
-}
+}
diff --git a/R/uploadToDatabase.R b/R/uploadToDatabase.R
@@ -24,7 +24,7 @@ insertRunPlpToSqlite <- function(
 
   sqliteLocation <- tempdir()
 
-  ensure_installed('RSQLite')
+  rlang::check_installed("RSQLite")
 
   # create sqlite database
   connectionDetails <- DatabaseConnector::createConnectionDetails(
@@ -121,9 +121,7 @@ insertResultsToSqlite <- function(
   if(!dir.exists(sqliteLocation)){
     dir.create(sqliteLocation, recursive = T)
   }
-
-  ensure_installed('RSQLite')
-
+  rlang::check_installed("RSQLite")
   # create sqlite database
   connectionDetails <- DatabaseConnector::createConnectionDetails(
     dbms = 'sqlite',

diff --git a/tests/testthat/test-helperfunctions.R b/tests/testthat/test-helperfunctions.R
@@ -17,15 +17,6 @@
 library("testthat")
 context("HelperFunctions")
 
-test_that("is_installed", {
-  testthat::expect_equal(PatientLevelPrediction:::is_installed('FeatureExtraction'), T)
-  testthat::expect_equal(PatientLevelPrediction:::is_installed('MadeUp4u834t3f'), F)
-})
-
-test_that("ensure_installed", {
-  testthat::expect_equal(PatientLevelPrediction:::ensure_installed('FeatureExtraction'), NULL)
-})
-
 # how to test checkPlpInstallation?