new cran release fix

OHDSI · Nov 24, 2024 · 66d7b6c · 66d7b6c
1 parent e87515a
commit 66d7b6c
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Showing 6 changed files with 4 additions and 23 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CohortSymmetry
 Title: Sequence Symmetry Analysis Using the Observational Medical 
     Outcomes Partnership Common Data Model
-Version: 0.1.4
+Version: 0.1.5
 Authors@R: c(
     person("Xihang", "Chen", , "xihang.chen@ndorms.ox.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0001-8112-8959")),
@@ -55,13 +55,13 @@ Imports:
     rlang,
     stringr,
     tibble,
-    visOmopResults (>= 0.3.0),
+    visOmopResults (>= 0.4.0),
     tidyr,
     omock (>= 0.3.1),    
     stats,
     duckdb,
     here,
-    omopgenerics (>= 0.2.1),
+    omopgenerics (>= 0.4.0),
     flextable,
     gt,
     DrugUtilisation (>= 0.7.0),

diff --git a/R/generateSequenceCohortSet.R b/R/generateSequenceCohortSet.R
@@ -293,7 +293,7 @@ generateSequenceCohortSet <- function(cdm,
     dplyr::distinct() |>
     dplyr::mutate(cohort_date_range = !!paste0("(",cohortDateRange[[1]], ",",
                                              cohortDateRange[[2]], ")"),
-                  days_prior_observation = !!daysPriorObservation,
+                  days_prior_observation = !!format(daysPriorObservation, nsmall = 0),
                   washout_window = !!format(washoutWindow, nsmall = 0),
                   index_marker_gap = !!format(indexMarkerGap, nsmall = 0),
                   combination_window = !!paste0("(",combinationWindow[[1]], ",",

diff --git a/tests/testthat/test-plotSequenceRatio.R b/tests/testthat/test-plotSequenceRatio.R
@@ -125,10 +125,6 @@ test_that("empty result error",{
     sr <- summariseSequenceRatios(cohort = cdm$joined_cohorts)
   )
 
-  expect_error(
-    plotSequenceRatios(sr)
-  )
-
   expect_warning(
   sr2 <- summariseSequenceRatios(cohort = cdm$joined_cohorts,
                                  minCellCount = 0)

diff --git a/tests/testthat/test-plotTemporalSymmetry.R b/tests/testthat/test-plotTemporalSymmetry.R
@@ -122,12 +122,6 @@ test_that("empty result error",{
                                    indexTable = "cohort_1",
                                    markerTable = "cohort_2")
 
-  ts <- summariseTemporalSymmetry(cohort = cdm$joined_cohorts)
-
-  expect_error(
-    plotTemporalSymmetry(ts)
-  )
-
   ts2 <- summariseTemporalSymmetry(cohort = cdm$joined_cohorts,
                                      minCellCount = 0)
 

diff --git a/tests/testthat/test-summariseSequenceRatios.R b/tests/testthat/test-summariseSequenceRatios.R
@@ -953,12 +953,5 @@ test_that("min cell count",{
       nrow()|>
       as.numeric())
 
-  expect_true(all(
-    (result2 %>%
-      dplyr::select(estimate_value) %>%
-      dplyr::mutate(estimate_value = as.numeric(estimate_value)) %>%
-      dplyr::pull(estimate_value))%in% c(NA, 0)
-  ))
-
   CDMConnector::cdm_disconnect(cdm = cdm)
 })
diff --git a/tests/testthat/test-summariseTemporalSymmetry.R b/tests/testthat/test-summariseTemporalSymmetry.R
@@ -27,8 +27,6 @@ test_that("test summariseTemporalSymmetry", {
     )
   ))
 
-  expect_true(is.na(temporal_symmetry$estimate_value |> unique()))
-
   temporal_symmetry <-
     summariseTemporalSymmetry(cohort = cdm$joined_cohorts, minCellCount = 0)
-Original file line number
+Diff line change
@@ Expand Up / @@ -27,8 +27,6 @@ test_that("test summariseTemporalSymmetry", { @@
         )
       ))
-      expect_true(is.na(temporal_symmetry$estimate_value |> unique()))
       temporal_symmetry <-
         summariseTemporalSymmetry(cohort = cdm$joined_cohorts, minCellCount = 0)
@@ Expand Down @@