skip tests if missing suggested package ncdf4

cran-comments.md

@@ -4,4 +4,5 @@
 * local windows
 
 ## Comment
-* removed geoknife as suggested package
+* removed geoknife as suggested package
+* avoid ncdf4 tests if not installed

tests/testthat/helper-functions.R

@@ -1,5 +1,4 @@
-testthat::skip_if_not(require(ncdf4))
-
+require(ncdf4)
 library(RNetCDF)
 library(sf)
 

tests/testthat/test_check_ncdf.R

@@ -28,6 +28,7 @@ test_that("line", {
 })
 
 test_that("multi polygon holes", {
+  testthat::skip_if_not(require("ncdf4"))
   polygonData <- get_fixture_data("multipolygons_holes")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = polygonData)
   nc<-nc_open(nc_file)
@@ -41,6 +42,7 @@ test_that("multi polygon holes", {
 })
 
 test_that("polygon", {
+  testthat::skip_if_not(require("ncdf4"))
   polygonData <- get_fixture_data("polygon")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = polygonData)
   nc<-nc_open(nc_file)
@@ -54,6 +56,7 @@ test_that("polygon", {
 })
 
 test_that("basic point works", {
+  testthat::skip_if_not(require("ncdf4"))
   pointData <- get_fixture_data("point")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = pointData)
   nc<-nc_open(nc_file)
@@ -64,6 +67,7 @@ test_that("basic point works", {
 })
 
 test_that("a crs gets found correctly", {
+  testthat::skip_if_not(require("ncdf4"))
   polygonData <- sf::read_sf("data/Yahara_alb/Yahara_River_HRUs_alb_eq.shp")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = polygonData)
   nc<-nc_open(nc_file)
@@ -82,6 +86,7 @@ test_that("a crs gets found correctly", {
 })
 
 test_that("errors", {
+  testthat::skip_if_not(require("ncdf4"))
   pointData <- get_fixture_data("point")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = pointData)
   nc <- nc_open(nc_file, write = TRUE)

tests/testthat/test_line.R

@@ -1,6 +1,7 @@
 context("line")
 
 test_that("linedata works", {
+  testthat::skip_if_not(require("ncdf4"))
   lineData <- get_fixture_data("linestring")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = lineData)
   nc<-nc_open(nc_file)
@@ -16,6 +17,7 @@ test_that("linedata works", {
 })
 
 test_that("multiLine data works", {
+  testthat::skip_if_not(require("ncdf4"))
   lineData <- get_fixture_data("multilinestring")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = lineData)
   nc<-nc_open(nc_file)
@@ -34,6 +36,7 @@ test_that("multiLine data works", {
 })
 
 test_that("multiline data frame works", {
+  testthat::skip_if_not(require("ncdf4"))
   lineData <- get_fixture_data("multilinestring")
   testdata<-as.data.frame(list("name"=c("test_name"), "id"=c(1)), stringsAsFactors = FALSE)
   lineData <- sf::st_sf(dplyr::bind_cols(lineData, testdata))
@@ -46,6 +49,7 @@ test_that("multiline data frame works", {
 })
 
 test_that("shapefile line data works", {
+  testthat::skip_if_not(require("ncdf4"))
   lineData <- sf::st_zm(sf::read_sf("data/NHDLine/NHDLine.shp"))
   nc_file <- write_geometry(nc_file=tempfile(), 
                       geom_data = lineData)

tests/testthat/test_point.R

@@ -2,7 +2,7 @@
 context("point")
 
 test_that("Point_timeSeries", {
-
+  testthat::skip_if_not(require("ncdf4"))
   pointData <- get_fixture_data("point")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = pointData)
   nc<-nc_open(nc_file)
@@ -44,6 +44,7 @@ test_that("multiPoint_timeSeries", {
 })
 
 test_that("shapefile_point", {
+  testthat::skip_if_not(require("ncdf4"))
   pointData <- sf::read_sf("data/se_sites/se_sitest.shp")
   nc_file <- write_geometry(nc_file = tempfile(), geom_data = pointData)
   nc <- nc_open(nc_file)
@@ -65,6 +66,7 @@ test_that("shapefile_point", {
 })
 
 test_that("Point data can be written", {
+  testthat::skip_if_not(require("ncdf4"))
   dataFrame <- read.csv(system.file("extdata/yahara_alb_attributes.csv", package = "ncdfgeom"))
   nc_file <- ncdfgeom:::write_point_dsg(nc_file=tempfile(), lats = dataFrame$YCOORD, lons = dataFrame$XCOORD, 
                              alts = rep(0, length(dataFrame$XCOORD)), times = as.POSIXct("1970-01-01 00:00:00 UTC", tz = "UTC"),

tests/testthat/test_poly.R

@@ -2,6 +2,7 @@
 context("polygon")
 
 test_that("data for basic polygon", {
+  testthat::skip_if_not(require("ncdf4"))
   polygonData <- get_fixture_data("polygon")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = polygonData)
   nc<-nc_open(nc_file)
@@ -42,6 +43,7 @@ test_that("data for basic polygon", {
 })
 
 test_that("polygon with a hole.", {
+  testthat::skip_if_not(require("ncdf4"))
   polygonData <- get_fixture_data("polygon_hole")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = polygonData)
   nc<-nc_open(nc_file)
@@ -69,6 +71,7 @@ test_that("polygon with a hole.", {
 })
 
 test_that("multipolygon.", {
+  testthat::skip_if_not(require("ncdf4"))
   polygonData <- get_fixture_data("multipolygon")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = polygonData)
   nc<-nc_open(nc_file)
@@ -86,6 +89,7 @@ test_that("multipolygon.", {
 })
 
 test_that("multipolygon with a hole.", {
+  testthat::skip_if_not(require("ncdf4"))
   polygonData <-get_fixture_data("multipolygon_hole")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = polygonData)
   nc<-nc_open(nc_file)
@@ -118,6 +122,7 @@ test_that("multipolygon with a hole.", {
 })
 
 test_that("multipolygons with holes.", {
+  testthat::skip_if_not(require("ncdf4"))
   polygonData <- get_fixture_data("multipolygons_holes")
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = polygonData)
   nc<-nc_open(nc_file)
@@ -141,6 +146,7 @@ test_that("multipolygons with holes.", {
 })
 
 test_that("A whole shapefile can be written", {
+  testthat::skip_if_not(require("ncdf4"))
   polygonData <- read_sf("data/Yahara_alb/Yahara_River_HRUs_alb_eq.shp", check_ring_dir = TRUE)
   nc_file <- write_geometry(nc_file=tempfile(), geom_data = polygonData)
   nc<-nc_open(nc_file)

tests/testthat/test_read-write_attribute_data.R

@@ -2,6 +2,7 @@
 context("instance attributes")
 
 test_that("A dataframe can be round tripped to netCDF.", {
+  testthat::skip_if_not(require("ncdf4"))
   dataFrame <- sf::st_set_geometry(sf::read_sf("data/NHDLine/NHDLine.shp"), NULL)
   units<-c("unitless","date","unitless","unitless","unitless","km","unitless","unitless","unknown")
   nc_file <- write_attribute_data(nc_file=tempfile(), att_data = dataFrame, instance_dim_name = "instance", units = units)
@@ -23,6 +24,7 @@ test_that("A dataframe can be round tripped to netCDF.", {
   })
 
 test_that("instance data can be added to an existing netcdf file.", {
+  testthat::skip_if_not(require("ncdf4"))
 	hucPolygons <- read_sf(system.file('extdata','example_huc_eta.json', package = 'ncdfgeom'))
 	hucPolygons <- st_set_geometry(hucPolygons, NULL)
 	outFile <- tempfile()

tests/testthat/test_read-write_timeseries_dsg.R

@@ -1,7 +1,7 @@
 context("orthogonal netcdf timeseries")
 
 test_that("Create basic DSG file", {
-
+  testthat::skip_if_not(require("ncdf4"))
   # NOTE: this code has been moved to helper files but was left here to not mess with it.
   nc_file<-tempfile(fileext = ".nc")
   nc_summary<-'test summary'
@@ -342,6 +342,7 @@ test_that("Create basic DSG file", {
 })
 
 test_that('soilmoisturetools data writes as expected', {
+  testthat::skip_if_not(require("ncdf4"))
   ok<-readRDS("data/soilmoisturetools/ok.rds")
   ok_meta<-readRDS("data/soilmoisturetools/ok_meta.rds")
   attributes <- list(