Merge pull request #358 from DrylandEcology/bugfix357_masterCIs_failing

- closes #357 by requiring a fixed version of rSOILWAT2 v2.3.5
- fixed DayMet unit tests
- fixed netCDF unit tests

.travis.yml

@@ -61,11 +61,16 @@ install:
 script:
   - R CMD build --no-build-vignettes --no-manual .
   # The extended unit test project
-  # (commit db3948e6aa746d012dbc4f25b0e9bb2a4186305f) takes about 16 min which
-  # is too long for the default settings of 10-min and times out
-  # On failure, display file 'testthat.Rout.fail' for more information and fail
-#  - travis_wait 30 R CMD check *tar.gz --as-cran --ignore-vignettes --no-manual || { cat rSFSW2.Rcheck/tests/testthat.Rout* && 1; }
-  - travis_wait 30 R CMD check *tar.gz --as-cran --ignore-vignettes --no-manual && cat rSFSW2.Rcheck/tests/testthat.Rout*
+  #   (commit db3948e6aa746d012dbc4f25b0e9bb2a4186305f) takes about 16 min which
+  #   is too long for the default settings of 10-min and times out --> use `travis_wait`
+  - travis_wait 30 R CMD check *tar.gz --as-cran --ignore-vignettes --no-manual
 
 after_success:
+  # Display testthat log file for more information if it exists and has content
+  - fname="rSFSW2.Rcheck/tests/testthat.Rout" && [ -s $fname ] && cat $fname
+  # Perform code cover estimate
   - travis_wait 30 Rscript -e 'covr::codecov()'
+
+after_failure:
+  # Display failed testthat log file for more information if it exists and has content
+  - fname="rSFSW2.Rcheck/tests/testthat.Rout.fail" && [ -s $fname ] && cat $fname

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rSFSW2
 Title: Simulation Framework for SOILWAT2
-Version: 3.1.2
-Date: 2018-10-27
+Version: 3.1.3
+Date: 2019-03-01
 Authors@R: c(
   person("Daniel", "Schlaepfer", email = "daniel.schlaepfer@yale.edu",
     comment = c(ORCID = "0000-0001-9973-2065"), role = c("aut", "cre")),
@@ -12,9 +12,9 @@ Authors@R: c(
 Description: Setting up, carrying out, and analyzing ecosystem water balance
     simulation experiments with SOILWAT2.
 Depends:
-    R (>= 3.3.0)
+    R (>= 3.4.0)
 Imports:
-    rSOILWAT2 (>= 2.3.2),
+    rSOILWAT2 (>= 2.3.5),
     RSQLite (>= 2.1.1),
     DBI (>= 1.0),
     Rcpp (>= 0.12.12),
@@ -45,7 +45,8 @@ Suggests:
     spelling (>= 1.1),
     hunspell (>= 2.9),
     covr,
-    lintr
+    lintr (>= 1.0.3),
+    goodpractice
 Remotes:
     github::dschlaep/weathergen
 LinkingTo:

README.md

@@ -61,7 +61,7 @@ There are several options:
 'rSFSW2' will compile some c code via 'Rcpp'. Your computer must be set up
 adequately.
 - If you use a Windows OS, then you need the
-  [Rtools](http://cran.us.r-project.org/bin/windows/Rtools/)
+  [Rtools](https://cran.r-project.org/bin/windows/Rtools/)
   installed that match your R version; please find further information for
   instance [here](https://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html).
 - If you use a macOS, then you need [Xcode](https://developer.apple.com/xcode/)
@@ -88,7 +88,7 @@ someone without development tools) for a platform to which you do not have
 access, then you may consider using one of the cloud services (no endorsements):
 - [r-hub](https://builder.r-hub.io) offers different Linux, Windows, and mac OS
   flavors as targets
-- [win-builder](http://win-builder.r-project.org/) offers Windows OS as target
+- [win-builder](https://win-builder.r-project.org/) offers Windows OS as target
 
 Alternatively, you may access the previous binary package version for Windows
 OS from our CI appveyor service if the build was successful and an artifact was
@@ -193,7 +193,7 @@ You can contribute to this project in different ways:
 - __Code documentation__
   * Read the section 'Object documentation' in
     [Wickham's book 'R packages'](http://r-pkgs.had.co.nz/man.html)
-  * Use [roxygen2](https://cran.r-project.org/web/packages/roxygen2/vignettes/formatting.html)
+  * Use [roxygen2](https://CRAN.R-project.org/package=roxygen2/vignettes/formatting.html)
     to write inline code documentation
   * Update help pages and NAMESPACE with the command `devtools::document()`
   * Ideally, add examples to function documentation and check these examples

tests/testthat/test_WeatherDB_DayMet.R

@@ -41,11 +41,11 @@ if (!any(do_skip) && is_online) {
     repeat {
       # Make sure that `avail_end_year` is indeed available
       # (e.g., during first days of a new year)
-      testavail <- get_DayMet_NorthAmerica(dir_data = dm_path,
+      testavail <- try(get_DayMet_NorthAmerica(dir_data = dm_path,
         cellID = "daymet_pixel_+002083_+000426",
         Xdm_WGS84 = -105.5934, Ydm_WGS84 = 41.31557,
         start_year = avail_end_year, end_year = avail_end_year,
-        dbW_digits = 2L)
+        dbW_digits = 2L), silent = TRUE)
 
       if (inherits(testavail, "try-error") && avail_end_year > 1980) {
         avail_end_year <- avail_end_year - 1L

tests/testthat/test_netCDF_functions.R

@@ -77,20 +77,35 @@ if (!any(do_skip) && is_online) {
   )
 
   # Download test files
-  has_test_ncs <- lapply(test_ncs, function(x) {
+  is_nc <- function(filename) {
+    .local <- function() {
+      stopifnot(requireNamespace("ncdf4"))
+
+      nc <- ncdf4::nc_open(filename = filename, write = FALSE, readunlim = TRUE,
+        verbose = FALSE)
+      ncdf4::nc_close(nc)
+    }
+
+    try(.local(), silent = TRUE)
+  }
+
+  # suppress warnings if a download fails (e.g., "cannot open URL",
+  #   "NetCDF: Unknown file format")
+  has_test_ncs <- suppressWarnings(lapply(test_ncs, function(x) {
     if (is.na(x[["url"]]) || is.na(x[["expect"]])) {
       FALSE
     } else {
       has <- try(utils::download.file(url = x[["url"]],
         destfile = x[["filename"]], quiet = TRUE), silent = TRUE)
-      if (isTRUE(has == 0)) {
+
+      if (isTRUE(has == 0) && isTRUE(is_nc(x[["filename"]]))) {
         TRUE
       } else {
         unlink(x[["filename"]])
         FALSE
       }
     }
-  })
+  }))
 
   #--- Tests
   test_that("read_time_netCDF:", {

tests/testthat/test_rSFSW2_CodeStylePractices.R

@@ -10,10 +10,12 @@ test_that("Package code style", {
   skip_if_not(identical(tolower(Sys.getenv("RSFSW2_ALLTESTS")), "true"))
   skip_on_cran()
   skip_on_appveyor()
-  # minimum version of lintr required for:
+  # as of 2019-03-01 development is minimum version of lintr required for:
   #  - empty commas in multi-dimensional array subsetting, e.g., x[, , 1:3]
-  skip_if_not_installed("lintr", minimum_version = "1.0.2.9000")
-
+  lintr_v <- unlist(utils::packageVersion("lintr"))
+  if (length(lintr_v) < 4 || isTRUE(lintr_v[4L] < 9000)) {
+    skip("Installed version of lintr is insufficient.")
+  }
 
   # Files that are not checked for lints
   files_not_tolint <- c(
@@ -48,7 +50,10 @@ test_that("Package code style", {
     files_tolint <- pkg_code_files[ids]
 
     for (k in seq_along(files_tolint)) {
-      badstyle <- lintr::lint(files_tolint[k])
+      # 2019 Feb 27: this call to `lint` generates a number of warnings
+      # "argument is not a function" --> ignore for now because we include
+      # with `pkg_code_files` code that includes scripts etc.
+      suppressWarnings(badstyle <- lintr::lint(files_tolint[k]))
       expect_identical(length(badstyle), 0L, info = print(badstyle))
     }
   }

tests/testthat/test_rSFSW2_Spelling.R

@@ -11,35 +11,12 @@ test_that("Package spell checks", {
   skip_if_not(identical(tolower(Sys.getenv("RSFSW2_ALLTESTS")), "true"))
   skip_on_cran()
   skip_on_appveyor()
-
-  # Check which package is available for spell-checking
-  do_spelling <- requireNamespace("spelling", quietly = TRUE) &&
-    utils::packageVersion("spelling") >= "1.1.0"
-  has_old_devtools <- if (do_spelling) FALSE else {
-      requireNamespace("devtools", quietly = TRUE) &&
-      utils::packageVersion("devtools") < "2.0.0"
-  }
+  skip_if_not_installed("spelling", minimum_version = "1.1.0")
 
   # Spell check with `hunspell` as backend:
-  if (do_spelling) {
-    # TODO: turn spell-checking on for vignettes
-    temp <- spelling::spell_check_package(pkg_path, vignettes = FALSE)
-    misspelled <- temp[["word"]]
-
-  } else if (has_old_devtools) {
-    # old devtools version with `ignore` argument
-    #   ignores text in roxygen2 content directives, e.g., \url{}, \var{},
-    #   but checks text in roxygen2 formatting directives, e.g., \sQuote{}
-
-    # ignore additional words (keep as short as possible)
-    spell_ignores <- scan(file.path(pkg_path, "inst", "WORDLIST"),
-      what = "character", comment.char = "#", quiet = TRUE)
-
-    misspelled <- devtools::spell_check(pkg = pkg_path, ignore = spell_ignores)
-
-  } else {
-    skip("No spell-checker found.")
-  }
+  # TODO: turn spell-checking on for vignettes
+  temp <- spelling::spell_check_package(pkg_path, vignettes = FALSE)
+  misspelled <- temp[["word"]]
 
   expect_identical(length(misspelled), 0L, info = print(misspelled))
 })