fix cran issues

Author: ablack3

R/Eunomia.R

@@ -187,7 +187,7 @@ download_eunomia_data <- function(dataset_name = "GiBleed",
 #' to a folder on your computer where the datasets will be downloaded to. This file can
 #' be opened by calling `usethis::edit_r_environ()`.
 #'
-#' @param datasetName One of "GiBleed" (default),
+#' @param datasetName,dataset_name One of "GiBleed" (default),
 #' "synthea-allergies-10k",
 #' "synthea-anemia-10k",
 #' "synthea-breast_cancer-10k",

R/cdm.R

@@ -18,26 +18,26 @@
 #'
 #' @param con A DBI database connection to a database where an OMOP CDM v5.4 or
 #'   v5.3 instance is located.
-#' @param cdmSchema The schema where the OMOP CDM tables are located. Defaults
+#' @param cdmSchema,cdm_schema The schema where the OMOP CDM tables are located. Defaults
 #'   to NULL.
-#' @param writeSchema An optional schema in the CDM database that the user has
+#' @param writeSchema,write_schema An optional schema in the CDM database that the user has
 #'   write access to.
-#' @param cohortTables A character vector listing the cohort table names to be
+#' @param cohortTables,cohort_tables A character vector listing the cohort table names to be
 #'   included in the CDM object.
-#' @param cdmVersion The version of the OMOP CDM. Cam be "5.3", "5.4", or NULL (default).
+#' @param cdmVersion,cdm_version The version of the OMOP CDM. Cam be "5.3", "5.4", or NULL (default).
 #' If NULL we will attempt to automatically determine the cdm version using
 #' the cdm_source table and heuristics.
-#' @param cdmName The name of the CDM. If NULL (default) the cdm_source_name
+#' @param cdmName,cdm_name The name of the CDM. If NULL (default) the cdm_source_name
 #'.  field in the CDM_SOURCE table will be used.
-#' @param achillesSchema An optional schema in the CDM database
+#' @param achillesSchema,achilles_schema An optional schema in the CDM database
 #' that contains achilles tables.
-#' @param .softValidation Normally the observation period table should not
+#' @param .softValidation,.soft_validation Normally the observation period table should not
 #' have overlapping observation periods for a single person. If `.softValidation` is `TRUE` the
 #' validation check that looks for overlapping observation periods will be skipped.
 #' Other analytic packages may break or produce incorrect results if `softValidation` is `TRUE` and
 #' the observation period table contains overlapping observation periods.
 #'
-#' @param writePrefix A prefix that will be added to all tables created in the write_schema. This
+#' @param writePrefix,write_prefix A prefix that will be added to all tables created in the write_schema. This
 #' can be used to create namespace in your database write_schema for your tables.
 #'
 #' @return A list of dplyr database table references pointing to CDM tables

R/utils.R

@@ -304,8 +304,8 @@ ensureInstalled <- function(pkg) {
     msg <- paste0(sQuote(pkg), " must be installed for this functionality.")
     if (interactive()) {
       rlang::inform(paste(msg, "Would you like to install it?", sep = "\n"))
-      if (menu(c("Yes", "No")) == 1) {
-        install.packages(pkg)
+      if (utils::menu(c("Yes", "No")) == 1) {
+        utils::install.packages(pkg)
       } else {
         stop(msg, call. = FALSE)
       }

man/cdmFromCon.Rd

@@ -246,6 +246,7 @@ test_that("no error is given if attrition table already exists and overwrite = T
 
 test_that("readCohortSet works from working directory", {
   skip("manual test") # seems to work as a standalone test but fails when running testtat
+  skip_if_not_installed("fs")
   fs::dir_copy(system.file("cohorts1", package = "CDMConnector", mustWork = TRUE),
                file.path(tempdir(), "cohorts1"),
                overwrite = TRUE)