diff --git a/.Rbuildignore b/.Rbuildignore index fa0908bc..903f32a5 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -18,3 +18,4 @@ LICENSE ^vignettes2/* ^a/* ^work/* +^revdep/* diff --git a/.gitignore b/.gitignore index 626bd841..8cc010bc 100644 --- a/.gitignore +++ b/.gitignore @@ -47,3 +47,4 @@ inst/doc /work/ errorReportSql.txt *.DS_Store* +/revdep/ diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 2a242a7a..0489aa83 100644 --- 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 index 95b434b4..86d1d946 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -55,7 +55,6 @@ Suggests: odbc, ggplot2, bigrquery, - DatabaseConnector, lubridate, clock, tibble, diff --git a/NEWS.md b/NEWS.md index d60b1dca..e9fe0d76 100644 --- 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 index 2323adea..48dc5431 100644 --- 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$cdm_field_name)) %>% tidyr::nest(col = -"cdm_table_name") %>% diff --git a/R/generateCohortSet.R b/R/generateCohortSet.R index c64c8e10..404f3a3a 100644 --- a/R/generateCohortSet.R +++ b/R/generateCohortSet.R @@ -481,8 +481,8 @@ generateCohortSet <- function(cdm, # Create the object. Let the constructor handle getting the counts.---- cohortSetRef <- dplyr::transmute(cohortSet, - cohort_definition_id = as.integer(cohort_definition_id), - cohort_name = as.character(cohort_name)) + cohort_definition_id = as.integer(.data$cohort_definition_id), + cohort_name = as.character(.data$cohort_name)) cdm[[name]] <- omopgenerics::newCohortTable( table = cdm[[name]], diff --git a/R/generateConceptCohortSet.R b/R/generateConceptCohortSet.R index a06fd85c..084957f3 100644 --- a/R/generateConceptCohortSet.R +++ b/R/generateConceptCohortSet.R @@ -411,7 +411,7 @@ generateConceptCohortSet <- function(cdm, cohortCodelistRef <- df %>% dplyr::mutate(type = "index event", - concept_id = as.integer(concept_id)) %>% + concept_id = as.integer(.data$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 index dfaaa367..9a143a8d 100644 --- 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 index b9c29fa2..e97d150a 100644 --- a/README.md +++ b/README.md @@ -124,7 +124,7 @@ cdm$person %>% ``` ## # Source: SQL [1 x 1] - ## # Database: DuckDB v1.1.2 [root@Darwin 23.1.0:R 4.3.3//private/var/folders/2j/8z0yfn1j69q8sxjc7vj9yhz40000gp/T/Rtmpo91CdK/file62e371c580a2.duckdb] + ## # Database: DuckDB v1.1.2 [root@Darwin 23.1.0:R 4.3.3//private/var/folders/2j/8z0yfn1j69q8sxjc7vj9yhz40000gp/T/RtmpDw9JTb/fileeea2255bd10b.duckdb] ## n ## ## 1 2694 @@ -138,7 +138,7 @@ cdm$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 ## @@ -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, ## . ## @@ -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 index 693dec44..500502e7 100644 --- 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 index 31f41de9..753b8c7c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -8,70 +8,57 @@ Page not found (404) • CDMConnector - - - - + + + Skip to contents - -