v0.3.3

.Rbuildignore

@@ -13,3 +13,4 @@
 ^codecov\.yml$
 ^cran-comments\.md$
 ^data-raw
+^sql

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CohortConstructor
 Title: Build and Manipulate Study Cohorts Using a Common Data Model
-Version: 0.3.2.900
+Version: 0.3.3
 Authors@R: c(
     person("Edward", "Burn", , "[email protected]", 
     role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9286-1128")),

cran-comments.md

@@ -1,3 +1,3 @@
 ## R CMD check results
 
-This is a new release.
+This is a patch release due to a breaking change in a dependency.

tests/testthat/test-addIndex.R

@@ -1,6 +1,6 @@
 
 test_that("local tibble and duckdb test - will do nothing for these", {
-
+  skip_on_cran()
   cdm <- omock::mockCdmReference() |>
     omock::mockCdmFromTables(tables = list("cohort" = dplyr::tibble(
       "cohort_definition_id" = 1,

tests/testthat/test-collapseCohorts.R

@@ -1,4 +1,5 @@
 test_that("simple example", {
+  skip_on_cran()
   cdm <- omock::mockCdmReference() |>
     omock::mockCdmFromTables(tables = list("cohort" = dplyr::tibble(
       "cohort_definition_id" = 1L,

tests/testthat/test-conceptCohort.R

@@ -1,4 +1,5 @@
 test_that("expected errors and messages", {
+  skip_on_cran()
   cdm <- omock::mockCdmReference() |>
     omock::mockPerson() |>
     omock::mockObservationPeriod()

tests/testthat/test-intersectCohorts.R

@@ -1,4 +1,5 @@
 test_that("intersect example - two cohorts", {
+  skip_on_cran()
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 2)
   cdm_local <- omopgenerics::insertTable(

tests/testthat/test-matchCohorts.R

@@ -1,4 +1,5 @@
 test_that("matchCohorts runs without errors", {
+  skip_on_cran()
   cdm <- mockCohortConstructor(nPerson = 1000)
 
   cdm$cohort1 <- cdm$cohort1 |>

tests/testthat/test-requireCohortIntersect.R

@@ -1,4 +1,5 @@
 test_that("requiring presence in another cohort", {
+  skip_on_cran()
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 4, seed = 1) |>
     omock::mockObservationPeriod(seed = 1) |>

tests/testthat/test-requireConceptIntersect.R

@@ -1,4 +1,5 @@
 test_that("require flag in concept", {
+  skip_on_cran()
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 4, seed = 1) |>
     omock::mockObservationPeriod(seed = 1) |>

tests/testthat/test-sampleCohorts.R

@@ -1,4 +1,5 @@
 test_that("sampleCohort subsetting one cohort", {
+  skip_on_cran()
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 4, seed = 1) |>
     omock::mockObservationPeriod(seed = 1) |>
@@ -28,6 +29,7 @@ test_that("sampleCohort subsetting one cohort", {
 })
 
 test_that("sampleCohort subsetting multiple cohorts", {
+  skip_on_cran()
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 10,seed = 1) |>
     omock::mockObservationPeriod(seed = 1) |>
@@ -57,6 +59,7 @@ test_that("sampleCohort subsetting multiple cohorts", {
 })
 
 test_that("sampleCohort subsetting all cohorts", {
+  skip_on_cran()
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 4,seed = 1) |>
     omock::mockObservationPeriod(seed = 1) |>
@@ -76,7 +79,8 @@ test_that("sampleCohort subsetting all cohorts", {
 })
 
 test_that("expected errors", {
-  cdm_local <- omock::mockCdmReference() |>
+  skip_on_cran()
+   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 4) |>
     omock::mockObservationPeriod() |>
     omock::mockCohort(name = c("cohort1"), numberCohorts = 3, seed = 2)
@@ -97,9 +101,8 @@ test_that("expected errors", {
   PatientProfiles::mockDisconnect(cdm)
 })
 
-
 test_that("original cohort attributes unchanged", {
-
+  skip_on_cran()
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(nPerson = 20) |>
     omock::mockObservationPeriod()

tests/testthat/test-stratifyCohorts.R

@@ -1,4 +1,5 @@
 test_that("simple stratification", {
+  skip_on_cran()
   cdm <- omopgenerics::cdmFromTables(
     tables = list(
       "person" = dplyr::tibble(

tests/testthat/test-subsetCohorts.R

@@ -1,4 +1,5 @@
 test_that("subsetCohort works", {
+  skip_on_cran()
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 4, seed = 1) |>
     omock::mockObservationPeriod(seed = 1) |>

tests/testthat/test-unionCohorts.R

@@ -1,4 +1,5 @@
 test_that("unionCohorts works", {
+  skip_on_cran()
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 4, seed = 1) |>
     omock::mockObservationPeriod(seed = 1) |>