assorted updates (#18)

- fix cran issues
- fix compatibility with Matrix pkg updates
- fix typos in documentation
- rename macosx to macos
- update cran comments

.Rbuildignore

@@ -16,10 +16,12 @@ check.log
 test.log
 gp.log
 spell.log
+examples.log
 README.Rmd
 inst/extdata/dictionary.txt
 ^_pkgdown\.yml$
 ^CONTRIBUTING\.md$
 ^CONTRIBUTING\.Rmd$
 ^CRAN-RELEASE$
 ^\.github$
+inst/WORDLIST

.github/workflows/R-CMD-check-mac-osx.yaml → .github/workflows/R-CMD-check-macos.yaml

@@ -12,7 +12,7 @@ on:
       - main
       - master
 
-name: Mac OSX
+name: macOS
 
 jobs:
   R-CMD-check:

.gitignore

@@ -15,6 +15,7 @@ test.log
 check.log
 spell.log
 gp.log
+examples.log
 # system files
 .directory
 # do not ignore the following files

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: oppr
 Type: Package
-Version: 1.0.3
+Version: 1.0.4
 Title: Optimal Project Prioritization
 Description: A decision support tool for prioritizing conservation projects.
     Prioritizations can be developed by maximizing expected feature richness,
@@ -51,8 +51,8 @@ Suggests:
     roxygen2 (>= 6.1.0),
     rmarkdown (>= 1.10),
     gurobi (>= 8.0.0),
-    ggtree (>= 2.4.2),
     Rsymphony (>= 0.1.28),
+    ggtree (>= 2.4.2),
     lpsymphony (>= 1.10.0),
     shiny (>= 1.2.0),
     rhandsontable (>= 0.3.7),
@@ -69,8 +69,9 @@ SystemRequirements: C++11
 URL: https://prioritizr.github.io/oppr/
 BugReports: https://github.com/prioritizr/oppr/issues
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.1
 Encoding: UTF-8
+Language: en-US
 Collate:
     'internal.R'
     'pproto.R'

Makefile

@@ -43,7 +43,7 @@ quickcheck:
 
 check:
 	echo "\n===== R CMD CHECK =====\n" > check.log 2>&1
-	R --slave -e "devtools::check(build_args = '--no-build-vignettes', args = '--no-build-vignettes', run_dont_test = TRUE, vignettes = FALSE)" >> check.log 2>&1
+	R --slave -e "devtools::check(remote = TRUE, build_args = '--no-build-vignettes', args = '--no-build-vignettes', run_dont_test = TRUE, vignettes = FALSE)" >> check.log 2>&1
 	cp -Rf doc inst/
 	touch inst/doc/.gitkeep
 
@@ -66,7 +66,17 @@ quickbuild:
 	R --slave -e "devtools::build(vignettes = FALSE)"
 	cp -Rf doc inst/
 
+urlcheck:
+	R --slave -e "devtools::document();urlchecker::url_check()"
+
+spellcheck:
+	R --slave -e "devtools::document();devtools::spell_check()"
+
+examples:
+	R --slave -e "devtools::run_examples(run_donttest = TRUE, run_dontrun = TRUE);warnings()" > examples.log 2>&1
+	rm -f Rplots.pdf
+
 install:
-	R --slave -e "devtools::install_local('../oppr', force = TRUE, upgrade = 'never')"
+	R --slave -e "devtools::install_local('.', force = TRUE, upgrade = 'never')"
 
 .PHONY: initc data docs readme site test check checkwb build install man

NEWS.md

@@ -1,4 +1,14 @@
-# oppr 1.0.3 (released)
+# oppr 1.0.4
+
+- CRAN release.
+- Fix compiler warnings raised by CRAN checks.
+- Remove references to the *ggtree* package in documentation.
+- Fix memory issues encountered during installation on CRAN Windows server.
+- Fix compatibility issues with upcoming version of the *Matrix* package
+  (version 1.4-2).
+- Fix broken URLs in package documentation.
+
+# oppr 1.0.3
 
 - CRAN release.
 - Fix URLs for CRAN.
@@ -46,23 +56,23 @@
 - Fix "Non-file package-anchored link(s) in documentation object" warnings in
   R-devel checks.
 
-# oppr 1.0.2 (released)
+# oppr 1.0.2
 
 - CRAN release.
 
 # oppr 1.0.1.1
 
 - Replace `tibble::as.tibble` with `tibble::as_tibble` to avoid warnings.
 
-# oppr 1.0.1 (released)
+# oppr 1.0.1
 
 - CRAN release.
 
 # oppr 1.0.0.1
 
 - Fix compatibility issues with upcoming _tibble_ (3.0.0) R package.
 
-# oppr 1.0.0 (released)
+# oppr 1.0.0
 
 - CRAN release.
 
@@ -71,7 +81,7 @@
 - Fix warnings in R-devel CRAN checks related to documentation.
 - Add citation for the research article that accompanies this package.
 
-# oppr 0.0.4 (released)
+# oppr 0.0.4
 
 - CRAN release.
 
@@ -80,15 +90,15 @@
 - Fix typo.
 - Fix broken links to Gurobi academic licenses.
 
-# oppr 0.0.3 (released)
+# oppr 0.0.3
 
 - CRAN release.
 
 # oppr 0.0.2.1
 
 - Retain debugging symbols to conform with CRAN policies.
 
-# oppr 0.0.2 (released)
+# oppr 0.0.2
 
 - CRAN release.
 
@@ -97,7 +107,7 @@
 - Fix address sanitizer issues causing CRAN checks to fail.
 - Tests successfully complete when the _shiny_ R package is not installed.
 
-# oppr 0.0.1 (released)
+# oppr 0.0.1
 
 - CRAN release.
 

R/ProjectProblem-proto.R

@@ -400,7 +400,7 @@ ProjectProblem <- pproto(
              self$project_names())
   },
   pf_matrix = function(self) {
-    m <- methods::as(as.matrix(
+    m <- as_Matrix(as.matrix(
       self$data$projects[, self$data$features[[self$data$feature_name_column]],
                          drop = FALSE]), "dgCMatrix")
     m@x[is.na(m@x)] <- 0
@@ -410,11 +410,13 @@ ProjectProblem <- pproto(
   },
   epf_matrix = function(self) {
     # extract persistence probabilities, but not accounting for baseline
-    m <- as(self$pf_matrix() * matrix(self$project_success_probabilities(),
-                                      ncol = self$number_of_features(),
-                                      nrow = self$number_of_projects()),
-                                      "dgCMatrix")
-    m <- as(m, "dgCMatrix")
+    m <- as_Matrix(
+    self$pf_matrix() *
+      matrix(self$project_success_probabilities(),
+             ncol = self$number_of_features(),
+             nrow = self$number_of_projects()),
+     "dgCMatrix")
+    m <- as_Matrix(m, "dgCMatrix")
     m <- Matrix::drop0(m)
     # if include baseline probabilities, then account for probabilities of
     # each project persisting and the baseline project not failing
@@ -430,15 +432,15 @@ ProjectProblem <- pproto(
       ## overwrite baseline data
       m[bp, ] <- bpp
       ## coerce data type
-      m <- as(m, "dgCMatrix")
+      m <- as_Matrix(m, "dgCMatrix")
       m <- Matrix::drop0(m)
     }
     rownames(m) <- self$project_names()
     colnames(m) <- self$feature_names()
     m
   },
   pa_matrix = function(self) {
-    m <- methods::as(as.matrix(
+    m <- as_Matrix(as.matrix(
       self$data$projects[, self$data$actions[[self$data$action_name_column]],
                          drop = FALSE]), "dgCMatrix")
     rownames(m) <- self$data$projects[[self$data$project_name_column]]

R/add_lpsolveapi_solver.R

@@ -85,7 +85,7 @@ add_lpsolveapi_solver <- function(x, gap = 0, presolve = FALSE,
       # extract parameters
       p <- as.list(self$parameters)
       # extract constraints
-      m <- methods::as(x$A(), "dgTMatrix")
+      m <- as_Matrix(x$A(), "dgTMatrix")
       mrhs <- x$rhs()
       msense <- x$sense()
       # manually add in locked constraints

R/add_lpsymphony_solver.R

@@ -10,7 +10,7 @@ NULL
 #'
 #' @inheritParams add_gurobi_solver
 #'
-#' @details [*SYMPHONY*](https://projects.coin-or.org/SYMPHONY) is an
+#' @details [*SYMPHONY*](https://github.com/coin-or/SYMPHONY) is an
 #'   open-source integer programming solver that is part of the Computational
 #'   Infrastructure for Operations Research (COIN-OR) project, an initiative
 #'   to promote development of open-source tools for operations research (a

R/add_max_phylo_div_objective.R

@@ -252,7 +252,7 @@ add_max_phylo_div_objective <- function(x, budget, tree) {
         bm[, bo, drop = FALSE], fp$edge.length[bo],
         rep(0, y$number_of_features()),
         y$feature_weights()[fp$tip.label],
-        methods::as(as.matrix(solution), "dgCMatrix"))
+        as_Matrix(as.matrix(solution), "dgCMatrix"))
     },
     apply = function(self, x, y) {
       assertthat::assert_that(inherits(x, "OptimizationProblem"),

R/add_max_richness_objective.R

@@ -200,7 +200,7 @@ add_max_richness_objective <- function(x, budget) {
         y$epf_matrix()[, y$feature_phylogeny()$tip.label, drop = FALSE],
         bm[, bo, drop = FALSE], rep(0, ncol(bm)),
         rep(0, y$number_of_features()), w,
-        methods::as(as.matrix(solution), "dgCMatrix"))
+        as_Matrix(as.matrix(solution), "dgCMatrix"))
     },
     apply = function(self, x, y) {
       assertthat::assert_that(inherits(x, "OptimizationProblem"),

R/add_max_targets_met_objective.R

@@ -233,7 +233,7 @@ add_max_targets_met_objective <- function(x, budget) {
         y$action_costs(), y$pa_matrix(), y$epf_matrix(),
         bm[, bo, drop = FALSE], fp$edge.length[bo],
         y$targets$output()$value, w,
-        methods::as(as.matrix(solution), "dgCMatrix"))
+        as_Matrix(as.matrix(solution), "dgCMatrix"))
     },
     apply = function(self, x, y) {
       assertthat::assert_that(inherits(x, "OptimizationProblem"),

R/add_min_set_objective.R

@@ -175,7 +175,7 @@ add_min_set_objective <- function(x) {
         y$epf_matrix()[, y$feature_phylogeny()$tip.label, drop = FALSE],
         bm[, bo, drop = FALSE], fp$edge.length[bo],
         rep(0, y$number_of_features()), rep(0, y$number_of_features()),
-        methods::as(as.matrix(solution), "dgCMatrix"))
+        as_Matrix(as.matrix(solution), "dgCMatrix"))
     },
     apply = function(self, x, y) {
       assertthat::assert_that(inherits(x, "OptimizationProblem"),

R/add_rsymphony_solver.R

@@ -10,7 +10,7 @@ NULL
 #'
 #' @inheritParams add_gurobi_solver
 #'
-#' @details [*SYMPHONY*](https://projects.coin-or.org/SYMPHONY) is an
+#' @details [*SYMPHONY*](https://github.com/coin-or/SYMPHONY) is an
 #'   open-source integer programming solver that is part of the Computational
 #'   Infrastructure for Operations Research (COIN-OR) project, an initiative
 #'   to promote development of open-source tools for operations research (a

R/data.R

@@ -3,7 +3,7 @@ NULL
 
 #' Simulated data
 #'
-#' Simulated data for prioritizing conservations projects.
+#' Simulated data for prioritizing conservation projects.
 #'
 #' @usage data(sim_actions)
 #' @usage data(sim_projects)

R/internal.R

@@ -300,3 +300,61 @@ lp_solve_status <- function(x) {
     warning("solver returned unrecognized code")
   as.character(x)
 }
+
+#' Convert to Matrix
+#'
+#' Convert an object to a matrix class provided by the \pkg{Matrix} package.
+#'
+#' @param object object.
+#'
+#' @param class `character` name of new classes.
+#'
+#' @details
+#' This function is a wrapper that is designed to provide
+#' compatibility with older and newer versions of the \pkg{Matrix} package.
+#'
+#' @return `Matrix` object.
+#'
+#' @noRd
+as_Matrix <- function(object, class) {
+  # assert valid argument
+  assertthat::assert_that(
+    assertthat::is.string(class),
+    assertthat::noNA(class)
+  )
+  # if we just want to convert to generic Matrix class then do that...
+  if (identical(class, "Matrix")) {
+    return(methods::as(object, class))
+  }
+  # convert matrix
+  if (utils::packageVersion("Matrix") >= as.package_version("1.4-2")) {
+    if (identical(class, "dgCMatrix")) {
+      c1 <- "dMatrix"
+      c2 <- "generalMatrix"
+      c3 <- "CsparseMatrix"
+    } else if (identical(class, "dgTMatrix")) {
+      c1 <- "dMatrix"
+      c2 <- "generalMatrix"
+      c3 <- "TsparseMatrix"
+    } else if (identical(class, "dsCMatrix")) {
+      c1 <- "dMatrix"
+      c2 <- "symmetricMatrix"
+      c3 <- "CsparseMatrix"
+    } else if (identical(class, "dsTMatrix")) {
+      c1 <- "dMatrix"
+      c2 <- "symmetricMatrix"
+      c3 <- "TsparseMatrix"
+    } else if (identical(class, "lgCMatrix")) {
+      c1 <- "lMatrix"
+      c2 <- "generalMatrix"
+      c3 <- "CsparseMatrix"
+    } else {
+      stop("argument to \"class\" not recognized")
+    }
+    out <- methods::as(methods::as(methods::as(object, c1), c2), c3)
+  } else {
+    out <- methods::as(object, class)
+  }
+  # return result
+  out
+}

R/plot_feature_persistence.R

@@ -132,8 +132,8 @@ plot_feature_persistence <- function(x, solution, n = 1, symbol_hjust = 0.007,
   feature_probs <- rcpp_expected_persistences(
     x$pa_matrix(),
     x$epf_matrix()[, x$feature_names(), drop = FALSE],
-    methods::as(diag(x$number_of_features()), "dgCMatrix"),
-    methods::as(as.matrix(solution), "dgCMatrix"))[1, ]
+    as_Matrix(diag(x$number_of_features()), "dgCMatrix"),
+    as_Matrix(as.matrix(solution), "dgCMatrix"))[1, ]
 
   ## create plotting data
   d <- tibble::tibble(name = x$feature_names(),