updates, cleanup, R CMD check

.github/workflows/R-CMD-check.yaml

@@ -3,7 +3,6 @@ on:
     branches:
       - master
       - development
-      - LandWeb
   pull_request:
     branches:
       - master
@@ -13,6 +12,7 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
+    if: "!contains(github.event.commits[0].message, '[skip-ci]')"
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -21,81 +21,35 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'devel'}
-          - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6'}
-          - {os: ubuntu-18.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: macOS-latest,   nosuggests: false, r: 'release'}
+          - {os: windows-latest, nosuggests: false, r: 'devel'}
+          - {os: windows-latest, nosuggests: false, r: 'release'}
+          - {os: ubuntu-20.04,   nosuggests: false, r: 'devel'}
+          - {os: ubuntu-20.04,   nosuggests: false, r: 'release'}
+          - {os: ubuntu-20.04,   nosuggests: true,  r: 'release'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      _R_CHECK_DEPENDS_ONLY_: ${{ matrix.config.nosuggests }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
 
     steps:
       - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
-
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+          use-public-rspm: true
 
-      - name: Install additional dependencies
-        run: |
-          remotes::install_github('PredictiveEcology/Require@development')
-          remotes::install_github('PredictiveEcology/reproducible@development')
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "18.04"), sep = "\n")')
-          sudo apt-get install -y hunspell-en-ca
-
-      - name: Install dependencies
-        run: |
-          if (R.version$major < 4) {
-            remotes::install_cran("versions")
-            versions::install.versions("XML", "3.99-0.3")
-          }
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
+          extra-packages: |
+            any::rcmdcheck
+            any::XML
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v2
 
       - name: Show testthat output
         if: always()

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: usefulFuns
 Type: Package
 Title: Useful functions for my modules and packages
-Version: 0.1.0
+Version: 0.1.1
 Author: Tati Micheletti
 Maintainer: Tati Micheletti <[email protected]>
 Description: A few functions and wrappers around useful code.
@@ -10,7 +10,7 @@ Encoding: UTF-8
 Language: en-CA
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Depends:
     R (>= 3.6)
 Imports:
@@ -33,8 +33,8 @@ Imports:
     raster,
     rasterVis,
     RColorBrewer,
-    remotes,
     reproducible,
+    Require,
     sp,
     sf,
     showtext,
@@ -45,6 +45,7 @@ Imports:
 Suggests:
     covr,
     lintr,
+    remotes,
     spelling
 Remotes:
     achubaty/amc@development,

NAMESPACE

@@ -44,6 +44,7 @@ importFrom(LandR,prepInputsLCC)
 importFrom(LandR,sppColors)
 importFrom(LandR,vegTypeMapGenerator)
 importFrom(RColorBrewer,brewer.pal)
+importFrom(Require,Require)
 importFrom(SpaDES.core,paddedFloatToChar)
 importFrom(SpaDES.tools,randomPolygon)
 importFrom(SpaDES.tools,rasterizeReduced)
@@ -108,7 +109,6 @@ importFrom(raster,writeRaster)
 importFrom(raster,xyFromCell)
 importFrom(rasterVis,gplot)
 importFrom(reproducible,Cache)
-importFrom(reproducible,Require)
 importFrom(reproducible,asPath)
 importFrom(reproducible,assessDataType)
 importFrom(reproducible,basename2)

R/bootstrapPercentChanges.R

@@ -10,7 +10,7 @@
 #' @param n numeric. Default is 100. How many iterations (random selection of `sampleSize` pixels) should be done?
 #' @param species character. Default is NULL. Which species should this function be ran ?
 #' @param useFuture logical. Should use \pkg{future} to parallelize?
-#'                  Requires `future` and `future_apply`` packages.
+#'                  Requires `future` and `future_apply` packages.
 #'
 #' @return list of significant species or scenarios with indication of increasing or decreasing
 #'
@@ -38,7 +38,7 @@ bootstrapPercentChanges <- function(dataPath,
                                     n = 100,
                                     shp = NULL,
                                     species = NULL, useFuture = FALSE) {
-  if (class(shp) == "character") {
+  if (inherits(shp, "character")) {
     studyArea <- Cache(.prepStudyAreaForBirds,
       studyArea = shp,
       dataPath = reproducible::checkPath(file.path(dataPath, "birdRTMEdehzhieRAS"),

R/createDynamicLayersRSF.R

@@ -22,7 +22,8 @@
 #' @export
 #' @importFrom data.table data.table setkey
 #' @importFrom raster raster projectRaster extract dropLayer stack nlayers extent
-#' @importFrom reproducible prepInputs postProcess Require
+#' @importFrom reproducible prepInputs postProcess
+#' @importFrom Require Require
 #' @importFrom SpaDES.tools rasterizeReduced
 #' @include burnFromAge.R
 #' @include nameAndBringOn.R

R/createModObject.R

@@ -41,7 +41,7 @@ createModObject <- function(data, sim = NULL, pathInput, currentTime, fun = read
     )) == 0) {
       stop(paste0("Please place the data in the input folder ", pathInput))
     }
-    if (class(currentTime) != "numeric") {
+    if (inherits(currentTime, "numeric")) {
       stop("Current time needs to be numeric!")
     }
     dataName <- grepMulti(

R/createShrubHerbLayers.R

@@ -14,7 +14,8 @@ utils::globalVariables(c("classesECCC", "ECCC_Description"))
 #' @export
 #' @importFrom data.table data.table setkey
 #' @importFrom raster raster setValues
-#' @importFrom reproducible prepInputs postProcess Require
+#' @importFrom reproducible prepInputs postProcess
+#' @importFrom Require Require
 #'
 #' @rdname createShrubHerbLayers
 createShrubHerbLayers <- function(landCoverECCC, reclassLCC05, layerName, includeCrops = FALSE) {

R/createStaticLayersRSF.R

@@ -20,7 +20,8 @@
 #' @export
 #' @importFrom data.table data.table setkey
 #' @importFrom raster dropLayer extent extract nlayers projectRaster raster reclassify stack
-#' @importFrom reproducible prepInputs postProcess Require
+#' @importFrom reproducible prepInputs postProcess
+#' @importFrom Require Require
 #' @importFrom SpaDES.tools rasterizeReduced
 #' @include createShrubHerbLayers.R
 #' @include nameAndBringOn.R

R/defineStudyArea.R

@@ -22,12 +22,13 @@ utils::globalVariables(c("PRENAME"))
 #' @rdname defineStudyArea
 #'
 #' @examples
+#' \donttest{
 #' ## rp is the whole North American boreal region
 #' rp <- defineStudyArea(testArea = TRUE, specificTestArea = "boreal", mapSubset = NULL)
 #'
 #' ## Alberta
 #' rp <- defineStudyArea(testArea = TRUE, specificTestArea = "Alberta", mapSubset = NULL)
-#' \dontrun{
+#'
 #' ## Alberta inside boreal extension
 #' rp <- defineStudyArea(testArea = TRUE, specificTestArea = "boreal", mapSubset = "Alberta")
 #' }
@@ -57,7 +58,7 @@ defineStudyArea <- function(testArea = NULL, specificTestArea = NULL, mapSubset
         if (is.null(mapSubset)) {
           message(crayon::yellow("Test area is TRUE, specificTestArea is 'boreal', and mapSubset is NULL. Cropping and masking to the whole Boreal."))
           rP <- reproducible::prepInputs(
-            url = "http://206.167.182.7/BAM/dataset/EnvironmentCanada/Brandt_boreal.zip",
+            url = "http://206.167.182.7/BAM/dataset/EnvironmentCanada/Brandt_boreal.zip", ## TODO: invalid URL
             destinationPath = destinationFolder
           )
         }

usefulFuns.Rproj

@@ -20,3 +20,6 @@ PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace,vignette
+
+QuitChildProcessesOnExit: Yes
+DisableExecuteRprofile: Yes