pierreroudier · pierreroudier · May 30, 2025 · Apr 30, 2025 · Apr 30, 2025 · Apr 30, 2025
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,17 +1,14 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -22,72 +19,33 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - 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}
-
-      - name: Restore R package cache
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - 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 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: "[Custom block] [macOS] Install spatial libraries"
-        if: runner.os == 'macOS'
-        run: |
-          # conflicts with gfortran from r-lib/actions when linking gcc
-          # rm '/usr/local/bin/gfortran'
-          brew install pkg-config gdal proj geos
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,16 @@
 Package: clhs
 Type: Package
 Title: Conditioned Latin Hypercube Sampling
-Version: 0.9.0
-Date: 2021-10-14
+Version: 0.9.1
+Date: 2025-05-29
 Authors@R: c(
     person("Pierre", "Roudier", email = "roudierp@landcareresearch.co.nz", role = c("aut", "cre")),
     person("Colby", "Brugnard", email = "cbrung@ad.nmsu.edu", role = "ctb"),
     person("Dylan", "Beaudette", email = "dylan.beaudette@ca.usda.gov", role = "ctb"),
     person("Benjamin", "Louis", email = "contact@benjaminlouis-stat.fr", role = "ctb"),
     person("Kiri", "Daust", email = "Kiri.Daust@gov.bc.ca", role = "ctb"),
-    person("David", "Clifford", email = "david.clifford@gmail.com", role = "ctb"))
+    person("David", "Clifford", email = "david.clifford@gmail.com", role = "ctb"),
+    person("Andrew", "Brown", email = "andrew.g.brown@usda.gov", role = "ctb", comment = c(ORCID="0000-0002-4565-533X")))
 Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
 URL: https://github.com/pierreroudier/clhs/
 BugReports: https://github.com/pierreroudier/clhs/issues
@@ -19,7 +20,6 @@ Imports: utils,
     methods, 
     grid, 
     ggplot2, 
-    sp,
     sf,
     raster, 
     reshape2, 
@@ -30,11 +30,12 @@ LinkingTo: RcppArmadillo, Rcpp
 License: GPL (>= 2)
 Encoding: UTF-8
 LazyLoad: yes
-Suggests: knitr,
+Suggests: sp,
+    knitr,
     rmarkdown,
     testthat
 VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 Collate: 
     'RcppExports.R'
     'clhs-internal.R'

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,7 @@
 <!-- NEWS.md is maintained by https://cynkra.github.io/fledge, do not edit -->
 
 - Fixed slow example in the plot docs
-- fixed the way RcppAramadillo dependecny is handled so to pass CRAN tests
+- fixed the way RcppArmadillo dependency is handled so to pass CRAN tests
 - added Rcpp and RcppArmadillo dependencies
 - Added C++ implementation (much faster!)
 
@@ -24,37 +24,37 @@
 - Implemented an improved logic to drop worse sample (thanks to David Clifford)
 - Various minor bug fixes to support R > 4.0
 
-# clhs_0.7-2 
+# clhs 0.7-2 
 - Maintenance version fixing new RNG sampler call.
 
-# clhs_0.7-0 
+# clhs 0.7-0 
 - New DLHS method contributed by Benjamin Louis
 - Included possibility to include compulsory/existing samples in the set (thanks to Benjamin Louis)
 - Added more tests
 
-# clhs_0.6-0
+# clhs 0.6-0
 - Added Gower similarity tool (thanks to Colby Brugnard)
 - Switched documentation to Roxygen
 - Implemented the first few tests
 
-# clhs_0.5-7
+# clhs 0.5-7
 - fixed sneaky bug that produced duplicated sampling points (thanks Ankur Gupta for the pointers)
 
-# clhs_0.5-6
+# clhs 0.5-6
 - fixed bug when passing a single raster layer (Github issue #1, thanks Github user GreatEmerald)
 - Raster* clhs method now returns SpatialPointsDataFrame
 
-# clhs_0.5-3
+# clhs 0.5-3
 - corrected dependencies - now depend on R >= 2.14 (due to ggplot2)
 
-# clhs_0.5-2
+# clhs 0.5-2
 - version ready for release when ggplot2_0.9.2.1 is rolled out
 
-# clhs_0.5-1
+# clhs 0.5-1
 - minor bugfix version fixing compatibility issues with ggplot2 >= 0.9.2
 - added ggplot2 in Suggests temporary to fix bug in ggplot2_0.9.2
 
-# clhs_0.5-0 
+# clhs 0.5-0 
 - introduced cost and cost tracking modes
 - general code cleaning
 - improved plot function:
@@ -64,40 +64,40 @@
   - new boxplot mode
 - cleaner NAMESPACE
 
-# clhs_0.4-3
+# clhs 0.4-3
 - Dummy version increment to solve CRAN upload problems
 
-# clhs_0.4-2
+# clhs 0.4-2
 - Added the choice between histogram and density plots in
 the plot method
 
-# clhs_0.4-1 
+# clhs 0.4-1 
 - Improved doc
 - Complete plot.cLHS_result method using ggplot2
 - new reshape2 dependency
 - various buxfixes, esp. for spatial classes
 
-# clhs_0.4-0
+# clhs 0.4-0
 - Introduced cLHS_result S3 class with associated plot method
 - Introduced simple = ... option to the clhs() method. If set to true, returns only the indices of the selected samples, if set to FALSE, returns a cLHS_result object (eg if you want to plot the objective function behaviour).
 - added a plot() method. For the moment, it just plots the objective function.
 
-# clhs_0.3-2
+# clhs 0.3-2
 - slight improvement on the Raster method using rasterToPoints(...)
 - added plotting option for the objective function
 
-# clhs_0.3-1
+# clhs 0.3-1
 - Corrected bug on Raster* methods. Now returns a SpatialPointsDataFrame object.
 
-# clhs_0.3-0
+# clhs 0.3-0
 - Switch to S4 methods
 - Introduced methods for Raster* and SpatialP*DataFrame classes
 
-# clhs_0.2-1
+# clhs 0.2-1
 - changed examples
 
-# clhs_0.2-0
+# clhs 0.2-0
 - Fixed important bugs in the annealing process.
 
-# clhs_0.1-0
+# clhs 0.1-0
 - Initial release of the package.
diff --git a/R/clhs-data.frame.R b/R/clhs-data.frame.R
@@ -113,11 +113,11 @@ clhs.data.frame <- function(
 
     if(is.null(include)){
       dat <- data
-      inc <- dat[0,]
+      inc <- dat[0, , drop = FALSE] # keep as matrix if just one column
       ssize <- size
     } else{
       dat <- data[-include,]
-      inc <- data[include,,drop = FALSE] ##keep as matrix if just one row
+      inc <- data[include, , drop = FALSE] # keep as matrix if just one row
       ssize <- size - length(include)
       can.include <- 1:nrow(dat)
     }

diff --git a/R/clhs-package.R b/R/clhs-package.R
@@ -45,7 +45,7 @@
 #' @import Rcpp 
 #' @useDynLib clhs
 #' 
-NULL
+"_PACKAGE"
 
 #' Conditioned Latin Hypercube Sampling result
 #' 

diff --git a/R/clhs-sf.R b/R/clhs-sf.R
@@ -17,7 +17,7 @@ clhs.sf <- function(
     # When coords are used only points/multipoints are supported
     if (! st_geometry_type(x, by_geometry = FALSE) %in% c("POINT", "MULTIPOINT")) {
       stop(
-        "When use.coords` is set to TRUE, only POINT/MULTIPOINT geometries are supported.",
+        "When `use.coords` is set to TRUE, only POINT/MULTIPOINT geometries are supported.",
         call. = FALSE
       )
     }

diff --git a/R/similarity.R b/R/similarity.R
@@ -24,13 +24,13 @@
 #' 
 #' @export
 #' 
-#' @examples 
+#' @examplesIf requireNamespace("sp") 
 #' library(raster)
 #' library(sp)
 #' 
 #' data(meuse.grid)
 #' coordinates(meuse.grid) = ~x+y
-#' proj4string(meuse.grid) <- CRS("+init=epsg:28992")
+#' proj4string(meuse.grid) <- CRS("EPSG:28992")
 #' gridded(meuse.grid) = TRUE
 #' ms <- stack(meuse.grid)
 #' 
@@ -100,4 +100,4 @@ similarity_buffer <- function(covs, pts, buffer, fac = NA, metric = "gower", sta
   names(res_s) <- paste0('similarity_point_', 1:nlayers(res_s))
 
   res_s
-} 
+} 
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-[![R build status](https://github.com/pierreroudier/clhs/workflows/R-CMD-check/badge.svg)](https://github.com/pierreroudier/clhs/actions)
+[![R-CMD-check](https://github.com/pierreroudier/clhs/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pierreroudier/clhs/actions/workflows/R-CMD-check.yaml)
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/clhs)](https://cran.r-project.org/package=clhs)
 [![Total_Downloads](http://cranlogs.r-pkg.org/badges/grand-total/clhs)](https://cran.r-project.org/package=clhs)
 

diff --git a/man/similarity_buffer.Rd b/man/similarity_buffer.Rd
diff --git a/src/Makevars b/src/Makevars
@@ -8,7 +8,7 @@
 ##
 ## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
 ## support within Armadillo prefers / requires it
-CXX_STD = CXX11
+# CXX_STD = CXX11
 
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/src/Makevars.win b/src/Makevars.win
@@ -8,7 +8,7 @@
 ##
 ## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
 ## support within Armadillo prefers / requires it
-CXX_STD = CXX11
+# CXX_STD = CXX11
 
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/tests/testthat/test-clhs-gower.R b/tests/testthat/test-clhs-gower.R
@@ -1,7 +1,9 @@
 context("clhs-gower")
 
 test_that("Gower similarity works", {
-
+
+  skip_if_not_installed("sp")
+
   library(raster)
   library(sp)
 

diff --git a/tests/testthat/test-spdf.R b/tests/testthat/test-spdf.R
@@ -2,6 +2,8 @@ context("clhs-sp")
 
 test_that("clhs on a SpatialPointsDataFrame works", {
 
+  skip_if_not_installed("sp")
+
   suppressWarnings(RNGversion("3.5.0"))
   set.seed(1)
 
@@ -16,7 +18,7 @@ test_that("clhs on a SpatialPointsDataFrame works", {
   spdf <- sp::SpatialPointsDataFrame(
     coords = df[, c("x", "y")],
     data = df[, c("a", "b", "c")],
-    proj4string = sp::CRS("+init=epsg:4326")
+    proj4string = sp::CRS("EPSG:4326")
   )
 
   res1 <- clhs(spdf, size = 5, iter = 100, progress = FALSE, simple = TRUE)