cran fixes

Author: cebarboza

.github/workflows/test-coverage.yaml

@@ -14,6 +14,8 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      # Use the CI library for coverage and its test subprocesses.
+      RENV_CONFIG_AUTOLOADER_ENABLED: "false"
 
     steps:
       - uses: actions/checkout@v6

NAMESPACE

@@ -59,7 +59,7 @@ importFrom(stringr,
   str_replace_all,
   str_to_lower
 )
-importFrom(usethis,proj_set)
+importFrom(usethis,proj_get)
 importFrom(zip,
   unzip,
   zip

R/pullConceptsAtlas.R

@@ -65,7 +65,7 @@ pullConceptsAtlas <- function(
   checkmate::assertLogical(deletePrevious)
   checkmate::assertCharacter(patternToRemove)
   for (package in c("httr", "RJSONIO", "lubridate", "rlang")) {
-    studyGenerics:::requireInstall(package)
+    requireInstall(package)
   }
   checkmate::assertString(authHeader)
 
@@ -215,7 +215,7 @@ pullConceptsAtlas <- function(
 getConceptSetDefinition <- function(conceptSetId, baseUrl,
                                     authHeader = Sys.getenv("ATLAS_TOKEN")) {
   for (package in c("httr", "RJSONIO", "lubridate", "rlang")) {
-    studyGenerics:::requireInstall(package)
+    requireInstall(package)
   }
   checkmate::assertInt(conceptSetId, lower = 1)
   checkmate::assertString(baseUrl, min.chars = 1)
@@ -301,8 +301,8 @@ getWebApiVersion <- function(baseUrl, authHeader = "") {
 }
 
 .request <- function(url, method, authHeader = "") {
-  studyGenerics:::requireInstall("httr")
-  studyGenerics:::requireInstall("rlang")
+  requireInstall("httr")
+  requireInstall("rlang")
   checkmate::assertChoice(method, "GET")
   headers <- httr::accept_json()
   if (nzchar(authHeader)) {
@@ -347,7 +347,7 @@ getWebApiVersion <- function(baseUrl, authHeader = "") {
 }
 
 .convertToDateTime <- function(x) {
-  studyGenerics:::requireInstall("lubridate")
+  requireInstall("lubridate")
   if (is.numeric(x)) {
     x <- .millisecondsToDate(x)
   } else if (is.character(x)) {

cran-comments.md

@@ -1,11 +1,11 @@
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
+0 errors | 0 warnings | 0 notes
 
-* This is a new release.
+* This is a new submission.
 
-* Concept-set retrieval helpers from ROhdsiWebApi are bundled under
-  Apache-2.0, with upstream copyright notices, source revision, and changes
-  documented in R/pullConceptsAtlas.R and inst/COPYRIGHTS. The package no
-  longer depends on ROhdsiWebApi. The replacement optional dependencies
-  (httr, RJSONIO, lubridate, and rlang) are available on CRAN.
+* The package includes adapted concept-set retrieval helpers from
+  ROhdsiWebApi, licensed under Apache License 2.0. Upstream copyright,
+  source revision, and modifications are documented in `inst/COPYRIGHTS`.
+  studyGenerics does not depend on ROhdsiWebApi; the optional dependencies
+  used by these helpers (httr, RJSONIO, lubridate, and rlang) are on CRAN.