Merge pull request #652 from OHDSI/develop

Develop

Author: katy-sadowski

.github/workflows/R_CMD_check_Hades.yml

@@ -90,6 +90,14 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
 
+      - name: Configure Java for R (macOS)
+        if: runner.os == 'macOS'
+        shell: bash
+        run: |
+          export JAVA_HOME=$(/usr/libexec/java_home)
+          echo "JAVA_HOME=$JAVA_HOME" >> $GITHUB_ENV
+          R CMD javareconf
+
       - uses: r-lib/actions/setup-tinytex@v2
 
       - uses: r-lib/actions/setup-pandoc@v2

.github/workflows/R_CMD_check_main_weekly.yaml

@@ -64,6 +64,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Setup Java
+        if: runner.os != 'Linux'
         uses: actions/setup-java@v4
         with:
           distribution: 'corretto'
@@ -73,6 +74,14 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
 
+      - name: Configure Java for R (macOS)
+        if: runner.os == 'macOS'
+        shell: bash
+        run: |
+          export JAVA_HOME=$(/usr/libexec/java_home)
+          echo "JAVA_HOME=$JAVA_HOME" >> $GITHUB_ENV
+          R CMD javareconf
+
       - uses: r-lib/actions/setup-tinytex@v2
 
       - uses: r-lib/actions/setup-pandoc@v2

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: DataQualityDashboard
 Type: Package
 Title: Execute and View Data Quality Checks on OMOP CDM Database
-Version: 2.8.5
-Date: 2026-01-17
+Version: 2.8.6
+Date: 2026-01-22
 Authors@R: c(
   person("Katy", "Sadowski", email = "sadowski@ohdsi.org", role = c("aut", "cre")),
   person("Clair", "Blacketer", role = c("aut")),
@@ -15,7 +15,7 @@ Authors@R: c(
   )
 Author: Katy Sadowski [aut, cre], Clair Blacketer [aut], Maxim Moinat [aut], Ajit Londhe [aut], Anthony Sena [aut], Anthony Molinaro [aut], Frank DeFalco [aut], Pavel Grafkin [aut]
 Maintainer: Katy Sadowski <sadowski@ohdsi.org>
-Description: An R package for assessing data quality in Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) databases.  Executes data quality checks and provides an R Shiny application to view the results.
+Description: Assesses data quality in Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) databases. Executes data quality checks and provides an R `shiny` application to view the results.
 License: Apache License 2.0
 Config/build/clean-inst-doc: FALSE
 VignetteBuilder: knitr

NAMESPACE

@@ -28,7 +28,5 @@ importFrom(stringr,regex)
 importFrom(stringr,str_detect)
 importFrom(tidyselect,all_of)
 importFrom(tools,file_path_sans_ext)
-importFrom(utils,install.packages)
-importFrom(utils,menu)
 importFrom(utils,packageVersion)
 importFrom(utils,write.table)

NEWS.md

@@ -1,3 +1,7 @@
+DataQualityDashboard 2.8.6
+==========================
+This release contains minor changes needed to support CRAN submission.
+
 DataQualityDashboard 2.8.5
 ==========================
 This release contains updates to the GitHub Actions workflow files to resolve some issues with workflow errors.

R/view.R

@@ -24,12 +24,13 @@
 #'
 #' @return NULL (launches Shiny application)
 #'
-#' @importFrom utils menu install.packages
 #' @importFrom jsonlite toJSON parse_json
 #'
 #' @export
 viewDqDashboard <- function(jsonPath, launch.browser = NULL, display.mode = NULL, ...) {
-  ensure_installed("shiny")
+  if (!requireNamespace("shiny", quietly = TRUE)) {
+    stop("The 'shiny' package must be installed to use this function. Please install it with: install.packages(\"shiny\")", call. = FALSE)
+  }
 
   Sys.setenv(jsonPath = jsonPath)
   appDir <- system.file("shinyApps", package = "DataQualityDashboard")
@@ -44,40 +45,3 @@ viewDqDashboard <- function(jsonPath, launch.browser = NULL, display.mode = NULL
 
   shiny::runApp(appDir = appDir, launch.browser = launch.browser, display.mode = display.mode, ...)
 }
-
-
-# Borrowed from devtools:
-# https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L44
-#' @return A logical value indicating whether the package is installed
-#' @keywords internal
-is_installed <- function(pkg, version = "0") {
-  installed_version <-
-    tryCatch(
-      utils::packageVersion(pkg),
-      error = function(e) {
-        NA
-      }
-    )
-  return(!is.na(installed_version) && installed_version >= version)
-}
-
-# Borrowed and adapted from devtools:
-# https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L74
-#' @return NULL (installs package if needed or stops with error)
-#' @keywords internal
-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 (menu(c("Yes", "No")) == 1) {
-        install.packages(pkg)
-      } else {
-        stop(msg, call. = FALSE)
-      }
-    } else {
-      stop(msg, call. = FALSE)
-    }
-  }
-}