From c565b60841f1c6144914fd5bc9541fc84b01514b Mon Sep 17 00:00:00 2001
From: edward-burn <9583964+edward-burn@users.noreply.github.com>
Date: Tue, 26 Nov 2024 17:17:44 +0000
Subject: [PATCH] v0.3.3

---
 .Rbuildignore                                 | 1 +
 DESCRIPTION                                   | 2 +-
 cran-comments.md                              | 2 +-
 tests/testthat/test-addIndex.R                | 2 +-
 tests/testthat/test-collapseCohorts.R         | 1 +
 tests/testthat/test-conceptCohort.R           | 1 +
 tests/testthat/test-intersectCohorts.R        | 1 +
 tests/testthat/test-matchCohorts.R            | 1 +
 tests/testthat/test-requireCohortIntersect.R  | 1 +
 tests/testthat/test-requireConceptIntersect.R | 1 +
 tests/testthat/test-sampleCohorts.R           | 9 ++++++---
 tests/testthat/test-stratifyCohorts.R         | 1 +
 tests/testthat/test-subsetCohorts.R           | 1 +
 tests/testthat/test-unionCohorts.R            | 1 +
 14 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index dcf62e42..50cc86aa 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -13,3 +13,4 @@
 ^codecov\.yml$
 ^cran-comments\.md$
 ^data-raw
+^sql
diff --git a/DESCRIPTION b/DESCRIPTION
index caa818fb..51d348fb 100644
--- a/DESCRIPTION
+++ b/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", , "edward.burn@ndorms.ox.ac.uk", 
     role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9286-1128")),
diff --git a/cran-comments.md b/cran-comments.md
index e7ab6ec5..c74776b2 100644
--- a/cran-comments.md
+++ b/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.
diff --git a/tests/testthat/test-addIndex.R b/tests/testthat/test-addIndex.R
index 00811c20..415954a9 100644
--- a/tests/testthat/test-addIndex.R
+++ b/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,
diff --git a/tests/testthat/test-collapseCohorts.R b/tests/testthat/test-collapseCohorts.R
index 53db286f..ae7a09fe 100644
--- a/tests/testthat/test-collapseCohorts.R
+++ b/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,
diff --git a/tests/testthat/test-conceptCohort.R b/tests/testthat/test-conceptCohort.R
index 49ce7f2a..bdbfd210 100644
--- a/tests/testthat/test-conceptCohort.R
+++ b/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()
diff --git a/tests/testthat/test-intersectCohorts.R b/tests/testthat/test-intersectCohorts.R
index 8d6519ef..2fb016f9 100644
--- a/tests/testthat/test-intersectCohorts.R
+++ b/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(
diff --git a/tests/testthat/test-matchCohorts.R b/tests/testthat/test-matchCohorts.R
index 7d690950..7edf3bee 100644
--- a/tests/testthat/test-matchCohorts.R
+++ b/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 |>
diff --git a/tests/testthat/test-requireCohortIntersect.R b/tests/testthat/test-requireCohortIntersect.R
index b23a52e5..3857b4e7 100644
--- a/tests/testthat/test-requireCohortIntersect.R
+++ b/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) |>
diff --git a/tests/testthat/test-requireConceptIntersect.R b/tests/testthat/test-requireConceptIntersect.R
index a98073e7..391f1613 100644
--- a/tests/testthat/test-requireConceptIntersect.R
+++ b/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) |>
diff --git a/tests/testthat/test-sampleCohorts.R b/tests/testthat/test-sampleCohorts.R
index c89f6375..0177e247 100644
--- a/tests/testthat/test-sampleCohorts.R
+++ b/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()
diff --git a/tests/testthat/test-stratifyCohorts.R b/tests/testthat/test-stratifyCohorts.R
index b55c405e..e14a3de6 100644
--- a/tests/testthat/test-stratifyCohorts.R
+++ b/tests/testthat/test-stratifyCohorts.R
@@ -1,4 +1,5 @@
 test_that("simple stratification", {
+  skip_on_cran()
   cdm <- omopgenerics::cdmFromTables(
     tables = list(
       "person" = dplyr::tibble(
diff --git a/tests/testthat/test-subsetCohorts.R b/tests/testthat/test-subsetCohorts.R
index 321b58f9..c918f587 100644
--- a/tests/testthat/test-subsetCohorts.R
+++ b/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) |>
diff --git a/tests/testthat/test-unionCohorts.R b/tests/testthat/test-unionCohorts.R
index a5f456f8..864bfbc0 100644
--- a/tests/testthat/test-unionCohorts.R
+++ b/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) |>