From ea309623e48a9364ba00905c63e72c59d790b81a Mon Sep 17 00:00:00 2001
From: edward-burn <9583964+edward-burn@users.noreply.github.com>
Date: Tue, 12 Nov 2024 20:24:48 +0000
Subject: [PATCH] v0.3.2

---
 DESCRIPTION                             |  2 +-
 cran-comments.md                        |  2 +-
 tests/testthat/test-collapseCohorts.R   |  2 ++
 tests/testthat/test-conceptCohort.R     |  6 ++++--
 tests/testthat/test-intersectCohorts.R  | 16 ++++++++++++++++
 tests/testthat/test-matchCohorts.R      |  6 ++++++
 tests/testthat/test-measurementCohort.R |  2 ++
 tests/testthat/test-padCohortDate.R     |  6 ++++++
 tests/testthat/test-unionCohorts.R      |  6 ++++++
 9 files changed, 44 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 97bc8344..06898dea 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: CohortConstructor
 Title: Build and Manipulate Study Cohorts Using a Common Data Model
-Version: 0.3.1.900
+Version: 0.3.2
 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 f12cc45b..e7ab6ec5 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,3 +1,3 @@
 ## R CMD check results
 
-This is a patch releasing, fixing a small issue from the previous release.
+This is a new release.
diff --git a/tests/testthat/test-collapseCohorts.R b/tests/testthat/test-collapseCohorts.R
index 257603d7..53db286f 100644
--- a/tests/testthat/test-collapseCohorts.R
+++ b/tests/testthat/test-collapseCohorts.R
@@ -192,6 +192,7 @@ test_that("out of observation", {
 })
 
 test_that("infitine", {
+  skip_on_cran()
 
   cdm <- omock::mockCdmFromTables()
   cdm$person <- dplyr::tibble(
@@ -249,6 +250,7 @@ test_that("infitine", {
 
 test_that("multiple observation periods", {
 # collapse should respect observation end dates
+  skip_on_cran()
 
   cdm <- omock::mockCdmReference() |>
     omock::mockCdmFromTables(tables = list("cohort" = dplyr::tibble(
diff --git a/tests/testthat/test-conceptCohort.R b/tests/testthat/test-conceptCohort.R
index 07c9375f..49ce7f2a 100644
--- a/tests/testthat/test-conceptCohort.R
+++ b/tests/testthat/test-conceptCohort.R
@@ -554,7 +554,8 @@ test_that("table not present in the cdm", {
 })
 
 test_that("cohort exit as event start date", {
-  cdm <- omock::mockCdmReference() |>
+  skip_on_cran()
+   cdm <- omock::mockCdmReference() |>
     omock::mockCdmFromTables(tables = list("cohort" = dplyr::tibble(
       "cohort_definition_id" = 1L,
       "subject_id" = c(1L, 2L, 3L),
@@ -625,7 +626,8 @@ test_that("cohort exit as event start date", {
 })
 
 test_that("use source field concepts", {
-  cdm <- omock::mockCdmReference() |>
+  skip_on_cran()
+   cdm <- omock::mockCdmReference() |>
     omock::mockCdmFromTables(tables = list("cohort" = dplyr::tibble(
       "cohort_definition_id" = 1L,
       "subject_id" = c(1L, 2L, 3L),
diff --git a/tests/testthat/test-intersectCohorts.R b/tests/testthat/test-intersectCohorts.R
index 3228513d..8d6519ef 100644
--- a/tests/testthat/test-intersectCohorts.R
+++ b/tests/testthat/test-intersectCohorts.R
@@ -46,6 +46,8 @@ test_that("intersect example - two cohorts", {
 })
 
 test_that("intersect example - three cohorts", {
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 2)
   cdm_local <- omopgenerics::insertTable(
@@ -95,6 +97,8 @@ test_that("intersect example - three cohorts", {
 })
 
 test_that("intersect example - nobody with intersection", {
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 2)
   cdm_local <- omopgenerics::insertTable(
@@ -140,6 +144,8 @@ test_that("intersect example - nobody with intersection", {
 })
 
 test_that("intersect with gap", {
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 1)
   cdm_local <- omopgenerics::insertTable(
@@ -195,6 +201,8 @@ test_that("intersect with gap", {
 })
 
 test_that("keepOriginalCohorts", {
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 2)
   cdm_local <- omopgenerics::insertTable(
@@ -274,6 +282,8 @@ test_that("keepOriginalCohorts", {
 })
 
 test_that("returnNonOverlappingCohorts - two cohorts", {
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 2)
   cdm_local <- omopgenerics::insertTable(
@@ -323,6 +333,8 @@ test_that("returnNonOverlappingCohorts - two cohorts", {
 })
 
 test_that("returnNonOverlappingCohorts - three cohorts", {
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 2)
   cdm_local <- omopgenerics::insertTable(
@@ -532,6 +544,8 @@ test_that("codelist", {
 })
 
 test_that("records combined for gap must be in the same observation period", {
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 2)
   cdm_local <- omopgenerics::insertTable(
@@ -586,6 +600,8 @@ test_that("records combined for gap must be in the same observation period", {
 })
 
 test_that("multiple observation periods", {
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 4, seed = 1)
   cdm_local$observation_period <- dplyr::tibble(
diff --git a/tests/testthat/test-matchCohorts.R b/tests/testthat/test-matchCohorts.R
index a33cdbcb..7d690950 100644
--- a/tests/testthat/test-matchCohorts.R
+++ b/tests/testthat/test-matchCohorts.R
@@ -77,6 +77,8 @@ test_that("matchCohorts runs without errors", {
 })
 
 test_that("matchCohorts, no duplicated people within a cohort", {
+  skip_on_cran()
+
   cdm <- mockCohortConstructor(nPerson = 1000)
   cdm$cohort1 <- cdm$cohort1 |>
     dplyr::group_by(subject_id) |>
@@ -120,6 +122,7 @@ test_that("matchCohorts, no duplicated people within a cohort", {
 })
 
 test_that("check that we obtain expected result when ratio is 1", {
+  skip_on_cran()
 
   cdm <- mockCohortConstructor(nPerson = 1000)
 
@@ -179,6 +182,7 @@ test_that("check that we obtain expected result when ratio is 1", {
 })
 
 test_that("test exactMatchingCohort with a ratio bigger than 1", {
+  skip_on_cran()
 
   cdm <- omock::emptyCdmReference(cdmName = "mock")
   cdm$person <- cdm$person |>
@@ -278,6 +282,8 @@ test_that("test exactMatchingCohort with a ratio bigger than 1", {
 })
 
 test_that("keepOriginalCohorts works" , {
+  skip_on_cran()
+
   cdm <- mockCohortConstructor()
   cohort <- cdm$cohort2 |> matchCohorts(cohortId = 1, keepOriginalCohorts = TRUE, name = "new_cohort")
   expect_identical(settings(cohort), dplyr::tibble(
diff --git a/tests/testthat/test-measurementCohort.R b/tests/testthat/test-measurementCohort.R
index 2b01e28e..fb75091c 100644
--- a/tests/testthat/test-measurementCohort.R
+++ b/tests/testthat/test-measurementCohort.R
@@ -1,4 +1,6 @@
 test_that("mearurementCohorts works", {
+  skip_on_cran()
+
   cdm <- mockCohortConstructor(con = NULL, seed = 1)
   cdm$concept <- cdm$concept |>
     dplyr::union_all(
diff --git a/tests/testthat/test-padCohortDate.R b/tests/testthat/test-padCohortDate.R
index 9d32be84..79c1217c 100644
--- a/tests/testthat/test-padCohortDate.R
+++ b/tests/testthat/test-padCohortDate.R
@@ -1,4 +1,5 @@
 test_that("simple example", {
+  skip_on_cran()
 
   cdm <-  omock::mockCdmFromTables(tables = list(
     cohort =
@@ -53,6 +54,7 @@ test_that("simple example", {
 })
 
 test_that("overlapping entries", {
+  skip_on_cran()
 
   cdm <-  omock::mockCdmFromTables(tables = list(
     cohort =
@@ -162,6 +164,8 @@ test_that("test indexes - postgres", {
 })
 
 test_that("adding days to cohort start", {
+  skip_on_cran()
+
   cdm <- omock::mockCdmFromTables(tables = list(
     cohort =
       data.frame(
@@ -348,6 +352,8 @@ test_that("test indexes - postgres", {
 })
 
 test_that("test padCohortDate", {
+  skip_on_cran()
+
   cdm <- omock::mockCdmFromTables(tables = list(
     cohort = dplyr::tibble(
       cohort_definition_id = 1L,
diff --git a/tests/testthat/test-unionCohorts.R b/tests/testthat/test-unionCohorts.R
index fbb2c8e7..a5f456f8 100644
--- a/tests/testthat/test-unionCohorts.R
+++ b/tests/testthat/test-unionCohorts.R
@@ -72,6 +72,8 @@ test_that("unionCohorts works", {
 })
 
 test_that("gap and name works", {
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 4, seed = 1) |>
     omock::mockObservationPeriod(seed = 1) |>
@@ -277,6 +279,8 @@ test_that("test codelist", {
 })
 
 test_that("keep original cohorts", {
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 4, seed = 1) |>
     omock::mockObservationPeriod(seed = 1) |>
@@ -299,6 +303,8 @@ test_that("keep original cohorts", {
 })
 
 test_that("multiple observation periods", {
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 4, seed = 1)
   cdm_local$observation_period <- dplyr::tibble(