fix: solving cran issues

- wrapped long runtime examples into donttest - merged latest changes from patch-branch
miracum · Jul 20, 2023 · b1344f3 · b1344f3
2 parents dbb16cb + 13d53e1
commit b1344f3
Show file tree

Hide file tree

Showing 17 changed files with 53 additions and 9 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -9,11 +9,13 @@
 
 #### Other changes
 
+-   updated news.md
+    ([dbb16cb](https://gitlab.miracum.org/miracum/dqa/dqastats/tree/dbb16cb29c084281ebc73494792ca51eb4dff095))
 -   updated dev-version
     ([91a749c](https://gitlab.miracum.org/miracum/dqa/dqastats/tree/91a749cf1232b86af3d499c60b3cbb06dfe68618))
 
 Full set of changes:
-[`v0.3.2...482ea46`](https://gitlab.miracum.org/miracum/dqa/dqastats/compare/v0.3.2...482ea46)
+[`v0.3.2...dbb16cb`](https://gitlab.miracum.org/miracum/dqa/dqastats/compare/v0.3.2...dbb16cb)
 
 ## v0.3.2 (2023-01-23)
 

diff --git a/R/completeness.R b/R/completeness.R
@@ -27,6 +27,7 @@
 #'   data system and the target data system.
 #'
 #' @examples
+#' \donttest{# runtime ~ 5 sec.
 #' utils_path <- system.file(
 #'   "demo_data/utilities/",
 #'   package = "DQAstats"
@@ -125,6 +126,7 @@
 #'   headless = rv$headless,
 #'   logfile_dir = rv$log$logfile_dir
 #' )
+#' }
 #'
 #' @export
 #'

diff --git a/R/conformance.R b/R/conformance.R
@@ -37,6 +37,7 @@
 #'   }
 #'
 #' @examples
+#' \donttest{# runtime ~ 5 sec.
 #' utils_path <- system.file(
 #'   "demo_data/utilities/",
 #'   package = "DQAstats"
@@ -154,6 +155,7 @@
 #'   headless = rv$headless,
 #'   logfile_dir = rv$log$logfile_dir
 #' )
+#' }
 #'
 #' @export
 #'

diff --git a/R/dataloading.R b/R/dataloading.R
@@ -387,6 +387,11 @@ load_database <- function(rv,
         sql <- sql_statements[[i]]
       }
 
+      # replace not-allowed AS for aliasing r_interediate in case of oracle statements
+      if (db_type == "oracle") {
+        sql <- gsub("AS r_intermediate", "r_intermediate", sql)
+      }
+
       ## The `sql_extended` is the same like the normal `sql` but extened with
       ## additional information needed to run the SQL, e.g. the commands
       ## to create a view which the `sql` utilizes:

diff --git a/R/descriptive_results.R b/R/descriptive_results.R
@@ -36,6 +36,7 @@
 #'   }
 #'
 #' @examples
+#' \donttest{# runtime ~ 5 sec.
 #' utils_path <- system.file(
 #'   "demo_data/utilities/",
 #'   package = "DQAstats"
@@ -129,6 +130,7 @@
 #'   rv = rv,
 #'   headless = rv$headless
 #' )
+#' }
 #'
 #' @export
 #'

diff --git a/R/etl.R b/R/etl.R
@@ -28,6 +28,7 @@
 #'   data system.
 #'
 #' @examples
+#' \donttest{# runtime ~ 5 sec.
 #' utils_path <- system.file(
 #'   "demo_data/utilities/",
 #'   package = "DQAstats"
@@ -123,6 +124,7 @@
 #' )
 #'
 #' etl_checks(results = rv$results_descriptive)
+#' }
 #'
 #' @export
 #'

diff --git a/R/format_value_conformance_results.R b/R/format_value_conformance_results.R
@@ -31,6 +31,7 @@
 #'   results for one data element.
 #'
 #' @examples
+#' \donttest{# runtime ~ 5 sec.
 #' utils_path <- system.file(
 #'   "demo_data/utilities/",
 #'   package = "DQAstats"
@@ -165,6 +166,8 @@
 #'     }
 #'   }
 #' )
+#' }
+#'
 #' @export
 
 format_value_conformance_results <- function(results, # nolint

diff --git a/R/plausibility_results.R b/R/plausibility_results.R
@@ -40,6 +40,7 @@
 #'   }
 #'
 #' @examples
+#' \donttest{# runtime ~ 5 sec.
 #' utils_path <- system.file(
 #'   "demo_data/utilities/",
 #'   package = "DQAstats"
@@ -141,6 +142,7 @@
 #'   mdr = rv$mdr,
 #'   headless = rv$headless
 #' )
+#' }
 #'
 #' @export
 #'

diff --git a/R/reduce_cat.R b/R/reduce_cat.R
@@ -31,6 +31,7 @@
 #'   with `levellimit`.
 #'
 #' @examples
+#' \donttest{# runtime ~ 5 sec.
 #' utils_path <- system.file(
 #'   "demo_data/utilities/",
 #'   package = "DQAstats"
@@ -129,6 +130,7 @@
 #'   data = rv$results_descriptive,
 #'   levellimit = 25
 #' )
+#' }
 #'
 #' @export
 #'

diff --git a/man/atemp_plausi_results.Rd b/man/atemp_plausi_results.Rd
diff --git a/man/completeness.Rd b/man/completeness.Rd
diff --git a/man/descriptive_results.Rd b/man/descriptive_results.Rd
diff --git a/man/etl_checks.Rd b/man/etl_checks.Rd
diff --git a/man/format_value_conformance_results.Rd b/man/format_value_conformance_results.Rd
diff --git a/man/reduce_cat.Rd b/man/reduce_cat.Rd
diff --git a/man/value_conformance.Rd b/man/value_conformance.Rd
diff --git a/vignettes/DQAstats2SHIPdataset.Rmd b/vignettes/DQAstats2SHIPdataset.Rmd
@@ -49,13 +49,15 @@ For further information on `dataquieR`, please refer to [https://dataquality.shi
 # ) %>%
 #   data.table::data.table()
 ship_fn <- file.path(tempdir(), "ship.RDS")
+ship_url <- paste0(
+  "https://raw.githubusercontent.com/cran/dataquieR/",
+  "master/inst/extdata/ship.RDS"
+)
 download.file(
-  url = paste0(
-    "https://github.com/cran/",
-    "dataquieR/raw/master/inst/extdata/ship.RDS"
-  ),
+  url = ship_url,
   destfile = ship_fn
 )
+Sys.sleep(1)
 ship_data <- readRDS(ship_fn) %>%
   data.table::data.table()
 
@@ -65,20 +67,25 @@ data.table::fwrite(
   x = ship_data,
   file = file.path(tempdir(), ship_data_export_fn)
 )
+```
+
 
+```{r}
 # load the ship metadata
 # ship_meta <- readRDS(
 #   system.file("extdata/ship_meta.RDS", package = "dataquieR")
 # ) %>%
 #   data.table::data.table()
 ship_meta_fn <- file.path(tempdir(), "ship_meta.RDS")
+ship_meta_url <- paste0(
+  "https://raw.githubusercontent.com/cran/dataquieR/",
+  "master/inst/extdata/ship_meta.RDS"
+)
 download.file(
-  url = paste0(
-    "https://github.com/cran/",
-    "dataquieR/raw/master/inst/extdata/ship_meta.RDS"
-  ),
+  url = ship_meta_url,
   destfile = ship_meta_fn
 )
+Sys.sleep(1)
 ship_meta <- readRDS(ship_meta_fn) %>%
   data.table::data.table()
 ```