diff --git a/.Rbuildignore b/.Rbuildignore index dcf62e4..50cc86a 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -13,3 +13,4 @@ ^codecov\.yml$ ^cran-comments\.md$ ^data-raw +^sql diff --git a/DESCRIPTION b/DESCRIPTION index caa818f..51d348f 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 e7ab6ec..c74776b 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 00811c2..415954a 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 53db286..ae7a09f 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 49ce7f2..bdbfd21 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 8d6519e..2fb016f 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 7d69095..7edf3be 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 b23a52e..3857b4e 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 a98073e..391f161 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 c89f637..0177e24 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 b55c405..e14a3de 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 321b58f..c918f58 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 a5f456f..864bfbc 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) |>