V1.6 cran release (#514)

darwin-eu · Nov 13, 2024 · af064fc · af064fc
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -18,3 +18,4 @@ LICENSE
 ^vignettes2/*
 ^a/*
 ^work/*
+^revdep/*
diff --git a/.gitignore b/.gitignore
@@ -47,3 +47,4 @@ inst/doc
 /work/
 errorReportSql.txt
 *.DS_Store*
+/revdep/
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,4 +1,3 @@
-Version: 1.5.0
-Date: 2024-07-16 07:51:33 UTC
-SHA:
-    2e0187639dd1357d328c06898715e3b4fa081174
+Version: 1.6.0
+Date: 2024-11-13 09:13:28 UTC
+SHA: f875fad89f0d4f83ea2fee1bf830870d103da77b
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -55,7 +55,6 @@ Suggests:
     odbc,
     ggplot2,
     bigrquery,
-    DatabaseConnector,
     lubridate,
     clock,
     tibble,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# CDMConnector 1.6.0
+
+- fix bug in copyCdmTo where attribute tables were not being copied #231 @catalamarti
+- check that overwrite argument works in compute when using temp tables #222 @ablack3
+- added synpuf1k with achilles tables to example datasets #230 @ablack3
+
 # CDMConnector 1.5.0
 
 - Get all tests passing on Databricks/Spark using odbc driver

diff --git a/R/Eunomia.R b/R/Eunomia.R
@@ -172,11 +172,11 @@ download_eunomia_data <- function(dataset_name = "GiBleed",
 #' This is useful for creating test data for studies or analytic packages.
 #' The empty CDM includes the vocabulary tables and all OMOP CDM tables but
 #' the clinical tables are empty and need to be populated with data. For additional information on
-#' creating small test CDM datasets see \url{https://ohdsi.github.io/omock} and
+#' creating small test CDM datasets see \url{https://ohdsi.github.io/omock/} and
 #' \url{https://darwin-eu.github.io/TestGenerator/}.
 #'
 #' To contribute synthetic observational health data to the Eunomia project please
-#' open an issue at \url{https://github.com/OHDSI/Eunomia/issues}
+#' open an issue at \url{https://github.com/OHDSI/Eunomia/issues/}
 #'
 #'
 #' @param datasetName,dataset_name One of "GiBleed" (default),
@@ -277,7 +277,7 @@ eunomiaDir <- function(datasetName = "GiBleed",
     on.exit(unlink(tempFileLocation), add = TRUE)
 
     specs <- omopgenerics::omopTableFields(cdmVersion) %>%
-      dplyr::filter(type %in% c("cdm_table", "achilles")) %>%
+      dplyr::filter(.data$type %in% c("cdm_table", "achilles")) %>%
       dplyr::mutate(cdm_datatype = dplyr::if_else(.data$cdm_datatype == "varchar(max)", "varchar(2000)", .data$cdm_datatype)) %>%
       dplyr::mutate(cdm_field_name = dplyr::if_else(.data$cdm_field_name == '"offset"', "offset", .data$cdm_field_name)) %>%
       tidyr::nest(col = -"cdm_table_name") %>%

diff --git a/R/generateCohortSet.R b/R/generateCohortSet.R
@@ -481,8 +481,8 @@ generateCohortSet <- function(cdm,
   # Create the object. Let the constructor handle getting the counts.----
 
   cohortSetRef <- dplyr::transmute(cohortSet,
-    cohort_definition_id = as.integer(cohort_definition_id),
-    cohort_name = as.character(cohort_name))
+    cohort_definition_id = as.integer(.data$cohort_definition_id),
+    cohort_name = as.character(.data$cohort_name))
 
   cdm[[name]] <- omopgenerics::newCohortTable(
     table = cdm[[name]],

diff --git a/R/generateConceptCohortSet.R b/R/generateConceptCohortSet.R
@@ -411,7 +411,7 @@ generateConceptCohortSet <- function(cdm,
 
     cohortCodelistRef <- df  %>%
       dplyr::mutate(type = "index event",
-                    concept_id = as.integer(concept_id)) %>%
+                    concept_id = as.integer(.data$concept_id)) %>%
       dplyr::select("cohort_definition_id",
                     "codelist_name" = "cohort_name",
                     "concept_id",

diff --git a/R/reexports-omopgenerics.R b/R/reexports-omopgenerics.R
@@ -63,10 +63,10 @@ omopgenerics::cohortCodelist
 #' @export
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' library(CDMConnector)
 #'
-#' person <- tibble(
+#' person <- dplyr::tibble(
 #'   person_id = 1, gender_concept_id = 0, year_of_birth = 1990,
 #'   race_concept_id = 0, ethnicity_concept_id = 0
 #' )

diff --git a/README.md b/README.md
@@ -124,7 +124,7 @@ cdm$person %>%
 ```
 
     ## # Source:   SQL [1 x 1]
-    ## # Database: DuckDB v1.1.2 [root@Darwin 23.1.0:R 4.3.3//private/var/folders/2j/8z0yfn1j69q8sxjc7vj9yhz40000gp/T/Rtmpo91CdK/file62e371c580a2.duckdb]
+    ## # Database: DuckDB v1.1.2 [root@Darwin 23.1.0:R 4.3.3//private/var/folders/2j/8z0yfn1j69q8sxjc7vj9yhz40000gp/T/RtmpDw9JTb/fileeea2255bd10b.duckdb]
     ##       n
     ##   <dbl>
     ## 1  2694
@@ -138,7 +138,7 @@ cdm$condition_era %>%
 ```
 
     ## # Source:     SQL [?? x 2]
-    ## # Database:   DuckDB v1.1.2 [root@Darwin 23.1.0:R 4.3.3//private/var/folders/2j/8z0yfn1j69q8sxjc7vj9yhz40000gp/T/Rtmpo91CdK/file62e371c580a2.duckdb]
+    ## # Database:   DuckDB v1.1.2 [root@Darwin 23.1.0:R 4.3.3//private/var/folders/2j/8z0yfn1j69q8sxjc7vj9yhz40000gp/T/RtmpDw9JTb/fileeea2255bd10b.duckdb]
     ## # Ordered by: desc(n)
     ##    top_conditions                               n
     ##    <chr>                                    <dbl>
@@ -169,7 +169,7 @@ If you encounter a clear bug, please file an issue with a minimal
     ## To cite package 'CDMConnector' in publications use:
     ## 
     ##   Black A, Gorbachev A, Burn E, Catala Sabate M (????). _CDMConnector:
-    ##   Connect to an OMOP Common Data Model_. R package version 1.5.0,
+    ##   Connect to an OMOP Common Data Model_. R package version 1.6.0,
     ##   https://github.com/darwin-eu/CDMConnector,
     ##   <https://darwin-eu.github.io/CDMConnector/>.
     ## 
@@ -178,7 +178,7 @@ If you encounter a clear bug, please file an issue with a minimal
     ##   @Manual{,
     ##     title = {CDMConnector: Connect to an OMOP Common Data Model},
     ##     author = {Adam Black and Artem Gorbachev and Edward Burn and Marti {Catala Sabate}},
-    ##     note = {R package version 1.5.0, https://github.com/darwin-eu/CDMConnector},
+    ##     note = {R package version 1.6.0, https://github.com/darwin-eu/CDMConnector},
     ##     url = {https://darwin-eu.github.io/CDMConnector/},
     ##   }
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,9 +1,8 @@
 ## R CMD check results
 
-This is a new minor release that fixes issues on Databricks/Spark
-
-One NOTE is expected:
-Suggests or Enhances not in mainstream repositories: Capr
+This is a resubmission of a new minor release. 
+I removed the revdep folder that does not need to be included.
+I also fixed errors identified in incoming cran checks.
 
 RCMD check passed on the following platforms with 0 errors, 0 warnings, and 0 notes 
 

diff --git a/docs/404.html b/docs/404.html
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,3 +18,4 @@ LICENSE @@
     ^vignettes2/*
     ^a/*
     ^work/*
+    ^revdep/*