Fix test errors

- Added linter
- Removed mac-arm64
- Missing directory separator in Windows runner

.github/workflows/check-standard.yaml

@@ -19,7 +19,7 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
-          - {os: macos-13-xlarge,   r: 'release'}
+          #- {os: macos-13-xlarge,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}

.github/workflows/lint.yaml

@@ -0,0 +1,32 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/test-coverage.yaml

@@ -16,7 +16,7 @@ jobs:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} # Add this line
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

tests/testthat/test-download_functions.R

@@ -91,8 +91,8 @@ testthat::test_that("EPA AQS download URLs have HTTP status 200.", {
   year_end <- 2022
   resolution_temporal <- "daily"
   parameter_code <- 88101
-  directory_to_download <- testthat::test_path("..", "testdata/")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_download <- testthat::test_path("..", "testdata/", "")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   # run download function
   download_data(dataset_name = "aqs",
                 year_start = year_start,
@@ -134,8 +134,8 @@ testthat::test_that("Ecoregion download URLs have HTTP status 200.", {
   withr::local_package("httr")
   withr::local_package("stringr")
   # function parameters
-  directory_to_download <- testthat::test_path("..", "testdata/")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_download <- testthat::test_path("..", "testdata/", "")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   certificate <- system.file("extdata/cacert_gaftp_epa.pem",
                              package = "amadeus")
   # run download function
@@ -179,7 +179,7 @@ testthat::test_that("GEOS-CF download URLs have HTTP status 200.", {
   date_end <- "2019-09-21"
   collections <- c("aqc_tavg_1hr_g1440x721_v1",
                    "chm_inst_1hr_g1440x721_p23")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   for (c in seq_along(collections)) {
     # run download function
     download_data(dataset_name = "geos",
@@ -221,8 +221,8 @@ testthat::test_that("GMTED download URLs have HTTP status 200.", {
                   # "Mean Statistic", "Maximum Statistic",
                   "Standard Deviation Statistic")
   resolution <- "7.5 arc-seconds"
-  directory_to_download <- testthat::test_path("..", "testdata/")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_download <- testthat::test_path("..", "testdata/", "")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   for (s in seq_along(statistics)) {
     # run download function
     download_data(dataset_name = "gmted",
@@ -265,7 +265,7 @@ testthat::test_that("MERRA2 download URLs have HTTP status 200.", {
   date_start <- "2022-02-14"
   date_end <- "2022-03-08"
   collections <- c("inst1_2d_asm_Nx", "inst3_3d_asm_Np")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   for (c in seq_along(collections)) {
     # run download function
     download_data(dataset_name = "merra2",
@@ -301,7 +301,7 @@ testthat::test_that("MERRA2 download URLs have HTTP status 200.", {
 testthat::test_that("MERRA2 returns message with unrecognized collection.", {
   # function parameters
   collections <- "uNrEcOgNiZeD"
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   testthat::expect_error(
     download_data(
       dataset_name = "merra",
@@ -319,7 +319,7 @@ testthat::test_that("NARR monolevel download URLs have HTTP status 200.", {
   year_start <- 2018
   year_end <- 2018
   variables <- c("weasd", "air.2m")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   # run download function
   download_data(dataset_name = "narr_monolevel",
                 year_start = year_start,
@@ -354,7 +354,7 @@ testthat::test_that("NARR p-levels download URLs have HTTP status 200.", {
   year_start <- 2020
   year_end <- 2021
   variables <- c("shum", "omega")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   # run download function
   download_data(dataset_name = "narr_p_levels",
                 year_start = year_start,
@@ -388,8 +388,8 @@ testthat::test_that("NOAA HMS Smoke download URLs have HTTP status 200.", {
   # function parameters
   date_start <- "2022-08-12"
   date_end <- "2022-09-21"
-  directory_to_download <- testthat::test_path("..", "testdata/")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_download <- testthat::test_path("..", "testdata/", "")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   # run download function
   download_data(dataset_name = "smoke",
                 date_start = date_start,
@@ -429,8 +429,8 @@ testthat::test_that("NLCD download URLs have HTTP status 200.", {
   years <- c(2021, 2019, 2016)
   collections <- c(rep("Coterminous United States", 2), "Alaska")
   collection_codes <- c(rep("l48", 2), "ak")
-  directory_to_download <- testthat::test_path("..", "testdata/")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_download <- testthat::test_path("..", "testdata/", "")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   # run download function
   for (y in seq_along(years)) {
     download_data(dataset_name = "nlcd",
@@ -487,8 +487,8 @@ testthat::test_that("SEDAC groads download URLs have HTTP status 200.", {
   # function parameters
   data_regions <- c("Americas", "Global")
   data_formats <- c("Geodatabase", "Shapefile")
-  directory_to_download <- testthat::test_path("..", "testdata/")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_download <- testthat::test_path("..", "testdata/", "")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   # run download function
   for (r in seq_along(data_regions)) {
     data_region <- data_regions[r]
@@ -548,8 +548,8 @@ testthat::test_that("SEDAC population download URLs have HTTP status 200.", {
   data_formats <- c("GeoTIFF")
   data_resolutions <- cbind(c("30 second"),
                             c("30_sec"))
-  directory_to_download <- testthat::test_path("..", "testdata/")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_download <- testthat::test_path("..", "testdata/", "")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   for (f in seq_along(data_formats)) {
     data_format <- data_formats[f]
     for (y in seq_along(years)) {
@@ -655,8 +655,8 @@ testthat::test_that("Koppen Geiger download URLs have HTTP status 200.", {
   # function parameters
   time_periods <- c("Present", "Future")
   data_resolutions <- c("0.0083")
-  directory_to_download <- testthat::test_path("..", "testdata/")
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_download <- testthat::test_path("..", "testdata/", "")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   # run download function
   for (p in seq_along(time_periods)) {
     time_period <- time_periods[p]
@@ -709,7 +709,7 @@ testthat::test_that("MODIS-MOD09GA download URLs have HTTP status 200.", {
   horizontal_tiles <- c(12, 13)
   vertical_tiles <- c(5, 6)
   nasa_earth_data_token <- "tOkEnPlAcEhOlDeR"
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   for (y in seq_along(years)) {
     date_start <- paste0(years[y], "-06-20")
     date_end <- paste0(years[y], "-06-24")
@@ -763,7 +763,7 @@ testthat::test_that("MODIS-MOD06L2 download URLs have HTTP status 200.", {
   nasa_earth_data_token <- "tOkEnPlAcEhOlDeR"
   horizontal_tiles <- c(8, 10)
   vertical_tiles <- c(4, 5)
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
 
   testthat::expect_error(
     kax <- download_data(dataset_name = "modis",
@@ -842,7 +842,7 @@ testthat::test_that("MODIS download error cases.", {
   horizontal_tiles <- c(12, 13)
   vertical_tiles <- c(5, 6)
   nasa_earth_data_token <- "tOkEnPlAcEhOlDeR"
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   date_start <- paste0(years, "-06-25")
   date_end <- paste0(years, "-06-30")
 
@@ -973,7 +973,7 @@ testthat::test_that("EPA TRI download URLs have HTTP status 200.", {
   withr::local_package("httr")
   withr::local_package("stringr")
   # function parameters
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   # run download function
   download_data(dataset_name = "tri",
                 directory_to_save = directory_to_save,
@@ -1012,7 +1012,7 @@ testthat::test_that("EPA NEI (AADT) download URLs have HTTP status 200.", {
   withr::local_package("httr")
   withr::local_package("stringr")
   # function parameters
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   certificate <- system.file("extdata/cacert_gaftp_epa.pem",
                              package = "amadeus")
   # run download function
@@ -1056,7 +1056,7 @@ testthat::test_that("Test error cases in EPA gaftp sources 1", {
   withr::local_package("stringr")
   # function parameters
   tdir <- tempdir()
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   certificate <- file.path(tdir, "cacert_gaftp_epa.pem")
   # run download function
   year_target <- c(2017L)
@@ -1082,16 +1082,14 @@ testthat::test_that("Test error cases in EPA gaftp sources 1", {
   # remove file with commands after test
   testthat::expect_true(file.exists(commands_path))
   file.remove(commands_path)
-  file.remove(certificate)
-  file.remove(sub("pem", "crt", certificate))
 })
 
 testthat::test_that("Test error cases in EPA gaftp sources 2", {
   withr::local_package("httr")
   withr::local_package("stringr")
   # function parameters
   tdir <- tempdir(check = TRUE)
-  directory_to_save <- testthat::test_path("..", "testdata/")
+  directory_to_save <- testthat::test_path("..", "testdata/", "")
   certificate <- file.path(tdir, "cacert_gaftp_epa.pem")
   # run download function
 
@@ -1117,6 +1115,4 @@ testthat::test_that("Test error cases in EPA gaftp sources 2", {
   # remove file with commands after test
   testthat::expect_true(file.exists(commands_path))
   file.remove(commands_path)
-  file.remove(certificate)
-  file.remove(sub("pem", "crt", certificate))
 })