From d8da4a49b2d208882297e9126934cd2412bc66be Mon Sep 17 00:00:00 2001 From: Frank DeFalco Date: Mon, 22 Apr 2024 16:38:34 -0400 Subject: [PATCH] resolve cran feedback --- .Rbuildignore | 1 + CRAN-SUBMISSION | 3 +++ DESCRIPTION | 7 +++---- R/Connection.R | 2 +- R/EunomiaData.R | 3 +++ cran-comments.md | 1 + man/Eunomia-package.Rd | 4 ++-- man/exportDataFiles.Rd | 3 +++ man/extractLoadData.Rd | 3 +++ man/loadDataFiles.Rd | 3 +++ 10 files changed, 23 insertions(+), 7 deletions(-) create mode 100644 CRAN-SUBMISSION diff --git a/.Rbuildignore b/.Rbuildignore index f2ecccc..46bbf0c 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -10,3 +10,4 @@ _pkgdown.yml cran-comments.md ^CRAN-RELEASE$ work/* +^CRAN-SUBMISSION$ diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 0000000..311ff14 --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 2.0.0 +Date: 2024-04-16 20:03:15 UTC +SHA: 53f57cba7a55b79e60ec84baea9399f4ae19743c diff --git a/DESCRIPTION b/DESCRIPTION index ccc6e55..2a21e10 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: Eunomia Type: Package -Title: Standard Dataset Manager for OMOP CDM Sample Datasets +Title: Standard Dataset Manager for Observational Medical Outcomes Partnership Common Data Model Sample Datasets Version: 2.0.0 -Date: 2024-04-16 +Date: 2024-04-22 Authors@R: c( person("Frank", "DeFalco", , "fdefalco@ohdsi.org", role = c("aut", "cre")), person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut")), @@ -13,7 +13,7 @@ Authors@R: c( person("Observational Health Data Science and Informatics", role = c("cph")) ) Maintainer: Frank DeFalco -Description: Facilitates access to sample datasets from the EunomiaDatasets repository (). +Description: Facilitates access to sample datasets from the 'EunomiaDatasets' repository (). License: Apache License 2.0 URL: https://github.com/OHDSI/Eunomia BugReports: https://github.com/OHDSI/Eunomia/issues @@ -29,7 +29,6 @@ Suggests: withr, duckdb, DatabaseConnector -Remotes: OHDSI/CommonDataModel Encoding: UTF-8 LazyData: true RoxygenNote: 7.3.1 diff --git a/R/Connection.R b/R/Connection.R index 59597b5..074ddfd 100644 --- a/R/Connection.R +++ b/R/Connection.R @@ -139,7 +139,7 @@ getDatabaseFile <- function(datasetName, } if (!datasetAvailable && !archiveAvailable) { - writeLines(paste("attempting to download", datasetName)) + message(paste("attempting to download", datasetName)) downloadedData <- downloadEunomiaData(datasetName = datasetName, cdmVersion = cdmVersion, pathToData = pathToData, verbose=verbose) if (verbose) { message("downloaded: ",downloadedData,appendLF = TRUE) diff --git a/R/EunomiaData.R b/R/EunomiaData.R index 9f9856a..528b0e5 100644 --- a/R/EunomiaData.R +++ b/R/EunomiaData.R @@ -70,6 +70,7 @@ downloadEunomiaData <- function(datasetName, #' @param cdmVersion The version of the OMOP CDM that are represented in the archive files. #' @param inputFormat The format of the files expected in the archive. (csv or parquet) #' @param verbose Provide additional logging details during execution. +#' @returns No return value, called to load archive into a database file. #' @importFrom tools file_ext #' @examples #' \dontrun{ @@ -111,6 +112,7 @@ extractLoadData <- function(from, to, dbms = "sqlite",cdmVersion="5.3", inputFor #' @param cdmDatabaseSchema The schema in which to create the CDM tables. Default is main. #' @param verbose Provide additional logging details during execution. #' @param overwrite Remove and replace an existing data set. +#' @returns No return value, loads data into database file. #' @export loadDataFiles <- function(dataPath, dbPath, @@ -239,6 +241,7 @@ loadDataFiles <- function(dataPath, #' @param dbms The file-based database system to use: 'sqlite' (default) or 'duckdb' #' @param outputFormat The output format for the files. Supported formats include csv, parquet. #' @param verbose Boolean argument controlling verbose debugging output +#' @returns No return value, called to export to outputFolder. #' @export exportDataFiles <- function(dbPath, outputFolder, outputFormat="csv", dbms = "sqlite", verbose=FALSE) { stopifnot(outputFormat %in% c("csv","parquet")) diff --git a/cran-comments.md b/cran-comments.md index fe4402b..a9e0d43 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,4 +1,5 @@ Release of 2.0 version of package. +Resolved CRAN feedback issues --- diff --git a/man/Eunomia-package.Rd b/man/Eunomia-package.Rd index f4f24fd..64065e9 100644 --- a/man/Eunomia-package.Rd +++ b/man/Eunomia-package.Rd @@ -4,9 +4,9 @@ \name{Eunomia-package} \alias{Eunomia} \alias{Eunomia-package} -\title{Eunomia: Standard Dataset Manager for OMOP CDM Sample Datasets} +\title{Eunomia: Standard Dataset Manager for Observational Medical Outcomes Partnership Common Data Model Sample Datasets} \description{ -Facilitates access to sample datasets from the EunomiaDatasets repository (\url{https://github.com/ohdsi/EunomiaDatasets}). +Facilitates access to sample datasets from the 'EunomiaDatasets' repository (\url{https://github.com/ohdsi/EunomiaDatasets}). } \seealso{ Useful links: diff --git a/man/exportDataFiles.Rd b/man/exportDataFiles.Rd index 8319b0e..a14c9fb 100644 --- a/man/exportDataFiles.Rd +++ b/man/exportDataFiles.Rd @@ -23,6 +23,9 @@ exportDataFiles( \item{verbose}{Boolean argument controlling verbose debugging output} } +\value{ +No return value, called to export to outputFolder. +} \description{ Helper function to export data to csv or parquet files from a database file (sqlite or duckdb). } diff --git a/man/extractLoadData.Rd b/man/extractLoadData.Rd index 67eb982..f2ef734 100644 --- a/man/extractLoadData.Rd +++ b/man/extractLoadData.Rd @@ -28,6 +28,9 @@ extractLoadData( \item{verbose}{Provide additional logging details during execution.} } +\value{ +No return value, called to load archive into a database file. +} \description{ Extract the Eunomia data files and load into a database Extract files from a .ZIP file and creates a OMOP CDM database that is then stored in the diff --git a/man/loadDataFiles.Rd b/man/loadDataFiles.Rd index af48e61..a578ca5 100644 --- a/man/loadDataFiles.Rd +++ b/man/loadDataFiles.Rd @@ -32,6 +32,9 @@ loadDataFiles( \item{overwrite}{Remove and replace an existing data set.} } +\value{ +No return value, loads data into database file. +} \description{ Load data from csv or parquet files into a database file (sqlite or duckdb). }