Merge pull request #363 from DrylandEcology/bugfix_external_API_changes

Addressing changes in interfaces of dependencies:
- roxygen2 v6.1.1
- devtools v2.0.1
- R-devel (upcoming v3.6.0)
- lintr (incompatible with R-devel)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rSFSW2
 Title: Simulation Framework for SOILWAT2
-Version: 3.1.4
+Version: 3.1.5
 Date: 2019-03-14
 Authors@R: c(
   person("Daniel", "Schlaepfer", email = "daniel.schlaepfer@yale.edu",
@@ -57,6 +57,7 @@ NeedsCompilation: yes
 License: GPL-3 + file LICENSE
 URL: https://github.com/DrylandEcology/rSFSW2
 BugReports: https://github.com/DrylandEcology/rSFSW2/issues
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
 VignetteBuilder: knitr
 Language: en-US
+Encoding: UTF-8

R/ExtractData_ClimateDownscaling.R

@@ -1175,7 +1175,7 @@ doQmapQUANT.default_drs <- function(x, fobj, type = NULL, lin_extrapol = NULL,
       }
     } else if (identical(type, "tricub")) {
       sfun <- stats::splinefun(x = fobj[["par"]]$modq[, 1], y = fobj[["par"]]$fitq[, 1],
-        method = spline_method)
+        method = spline_method, ties = mean)
       temp <- sfun(x[wet])
 
       if (!is.null(monthly_extremes) && !identical(fix_spline, "none")) {
@@ -1188,7 +1188,8 @@ doQmapQUANT.default_drs <- function(x, fobj, type = NULL, lin_extrapol = NULL,
             stop("Out-of-range splinefun values and 'fix_spline' set to fail")
           }
           sfun <- stats::splinefun(x = jitter(fobj[["par"]]$modq[, 1]),
-            y = jitter(fobj[["par"]]$fitq[, 1]), method = spline_method)
+            y = jitter(fobj[["par"]]$fitq[, 1]), method = spline_method,
+            ties = mean)
           temp <- sfun(x[wet])
           icount <- icount + 1
         }

R/Mathematical_Functions.R

@@ -253,8 +253,8 @@ whereNearest <- function(val, matrix) {
 #' @return A logical value.
 is.natural <- function(x) {
   typeof(x) %in% c("integer", "double", "complex") &&
-  !is.null(x) && length(x) > 0 && !is.na(x) &&
-  isTRUE(all.equal(x, round(x))) && x > 0
+  !is.null(x) && length(x) > 0 && !anyNA(x) &&
+  isTRUE(all.equal(x, round(x))) && all(x > 0)
 }
 
 #' The intersection on any number of vectors
@@ -382,9 +382,8 @@ check_monotonic_increase <- function(x, MARGIN = 1, increase = TRUE,
     }
 
   ord <- !match.fun(mfun)(x[, -1, drop = FALSE], x[, -ncol(x), drop = FALSE])
-  has_na <- is.na(x)
 
-  if (any(ord, na.rm = TRUE) || (has_na && !na.rm && strictly)) {
+  if ((!na.rm && strictly && anyNA(x)) || any(ord, na.rm = TRUE)) {
     if (fail) {
       stop(paste0("'check_monotonic_increase': data are not ",
         if (strictly) "strictly ", "monotonically ",

README.md

@@ -195,9 +195,14 @@ You can contribute to this project in different ways:
     [Wickham's book 'R packages'](http://r-pkgs.had.co.nz/man.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()`
+  * Update help pages and NAMESPACE with the command `devtools::document()`;
+    note: you may need to compile dynamic libraries first with
+    `pkgbuild::compile_dll()`.
   * Ideally, add examples to function documentation and check these examples
-    with the command `devtools::run_examples()`
+    with the command `devtools::run_examples()`.
+    Note: "devtools" v2.0.1 mixed up the logic for "dontrun" examples (see
+    https://github.com/r-lib/devtools/issues/2003); until this is fixed,
+    use `devtools::run_examples(run = FALSE)`.
   * Ideally, expand and/or add vignettes.
 
 
@@ -268,13 +273,17 @@ You can contribute to this project in different ways:
 
     1. Make sure that the documentation is up-to-date with:
        ```{r}
+       pkgbuild::compile_dll()
        devtools::document()
        ```
 
     1. Run and check the code from the examples and vignettes:
        ```{r}
        devtools::run_examples()
        ```
+       Note: "devtools" v2.0.1 mixed up the logic for "dontrun" examples (see
+       https://github.com/r-lib/devtools/issues/2003); until this is fixed,
+       use `devtools::run_examples(run = FALSE)`.
 
     1. Run tests as if not on CRAN, in an interactive R session,
        and with a sequential schedule.

tests/testthat/test_Mathematical_Functions.R

@@ -42,10 +42,15 @@ test_that("Monotonicity:", {
       x
     }
   good_strict_matrices[["x4"]] <- {
-      x <- test_matrices[["x4"]]
-      x[2, 3] <- replacement
-      x
-    }
+    x <- test_matrices[["x4"]]
+    x[2, 3] <- replacement
+    x
+  }
+  good_strict_matrices[["x5"]] <- {
+    x <- test_matrices[["x5"]]
+    x[2, 2:3] <- replacement
+    x
+  }
   good_strict_matrices[["x6"]] <- {
       x <- test_matrices[["x6"]]
       x[2, 3] <- replacement

tests/testthat/test_rSFSW2_CodeStylePractices.R

@@ -17,6 +17,11 @@ test_that("Package code style", {
     skip("Installed version of lintr is insufficient.")
   }
 
+  # as of 2019-03-11 `lintr` fails R-devel `_R_CHECK_LENGTH_1_LOGIC2_`, see
+  # https://github.com/jimhester/lintr/issues/377 (undo once this is fixed)
+  rctemp <- Sys.getenv("_R_CHECK_LENGTH_1_LOGIC2_")
+  Sys.setenv(`_R_CHECK_LENGTH_1_LOGIC2_` = "false")
+
   # Files that are not checked for lints
   files_not_tolint <- c(
     "ExtractData_ClimateDownscaling.R", # needs linting
@@ -57,6 +62,9 @@ test_that("Package code style", {
       expect_identical(length(badstyle), 0L, info = print(badstyle))
     }
   }
+
+  # reset
+  Sys.setenv(`_R_CHECK_LENGTH_1_LOGIC2_` = rctemp)
 })