fix cran issues (#47)

- fix cran issues
- update readme
- fix Matrix update compatibility issues

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

@@ -0,0 +1,96 @@
+# 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
+on:
+  schedule:
+    - cron: 0 0 * * 1 # schedule to run at midnight on Monday each week
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: Fedora
+
+jobs:
+  R-CMD-check:
+    name: Fedora (devel)
+
+    runs-on: ubuntu-latest
+
+    container:
+      image: docker://rhub/fedora-clang-devel:latest
+      options: --user root
+      env:
+        _R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true
+        _R_CHECK_FORCE_SUGGESTS_: false
+        _R_CHECK_TIMINGS_: 10
+        _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        _R_CHECK_LIMIT_CORES_: true
+        _R_CHECK_LICENSE_: true
+        OMP_THREAD_LIMIT: 2
+        KMP_DEVICE_THREAD_LIMIT: 2
+        KMP_TEAMS_THREAD_LIMIT: 2
+        KMP_ALL_THREADS: 2
+        NOT_CRAN: true
+        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        CI: true
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup path
+        run: |
+          echo "/opt/R-devel/bin" >> $GITHUB_PATH
+
+      - name: Install system dependencies
+        run: |
+          echo $PATH
+          dnf install -y \
+            mpfr-devel \
+            automake \
+            fftw-devel \
+            gmp-devel \
+            openssl-devel \
+            zlib-devel \
+            pandoc \
+            pandoc-citeproc \
+            geos-devel \
+            make \
+            gdal \
+            libxml2-devel \
+            cmake \
+            proj-devel \
+            sqlite-devel \
+            gdal-devel \
+            libicu-devel \
+            udunits2-devel \
+            coin-or-SYMPHONY-devel \
+            git-all
+
+      - name: Install dependencies
+        run: |
+          options(repos = "https://cloud.r-project.org/")
+          install.packages("remotes")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session information
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        run: |
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash

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

@@ -31,6 +31,8 @@ jobs:
       _R_CHECK_FORCE_SUGGESTS_: false
       _R_CHECK_TIMINGS_: 10
       _R_CHECK_CRAN_INCOMING_REMOTE_: false
+      _R_CHECK_LIMIT_CORES_: true
+      OMP_THREAD_LIMIT: 2
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       CI: true
 

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

@@ -32,6 +32,8 @@ jobs:
       _R_CHECK_FORCE_SUGGESTS_: false
       _R_CHECK_TIMINGS_: 10
       _R_CHECK_CRAN_INCOMING_REMOTE_: false
+      _R_CHECK_LIMIT_CORES_: true
+      OMP_THREAD_LIMIT: 2
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       CI: true
 

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

@@ -31,6 +31,8 @@ jobs:
       _R_CHECK_FORCE_SUGGESTS_: false
       _R_CHECK_TIMINGS_: 10
       _R_CHECK_CRAN_INCOMING_REMOTE_: false
+      _R_CHECK_LIMIT_CORES_: true
+      OMP_THREAD_LIMIT: 2
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       CI: true
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: surveyvoi
 Type: Package
-Version: 1.0.4
+Version: 1.0.5
 Title: Survey Value of Information
 Description: Decision support tool for prioritizing sites for ecological
     surveys based on their potential to improve plans for conserving
@@ -13,7 +13,7 @@ Description: Decision support tool for prioritizing sites for ecological
     algorithms. After generating such survey plans, they can be evaluated using
     conditions) and maximizing value of information. Please note that several
     functions depend on the 'Gurobi' optimization software (available from
-    <https://www.gurobi.com>). Additionally, the JAGS software (available from
+    <https://www.gurobi.com>). Additionally, the 'JAGS' software (available from
     <https://mcmc-jags.sourceforge.io/>) is required to fit hierarchical
     generalized linear models.
 Authors@R: c(person(c('Jeffrey', 'O'), 'Hanson',
@@ -114,4 +114,5 @@ Collate:
     'simulate_site_data.R'
     'validate.R'
     'weighted_survey_scheme.R'
+    'zzz.R'
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,3 +1,12 @@
+# surveyvoi 1.0.5
+
+- CRAN release.
+- Skip tests on Fedora systems because unable to reproduce error on CRAN.
+- Fix compiler warning thrown during installation.
+- Fix compatibility issues with upcoming _Matrix_ package (version >= 1.4-2) .
+- Fix issues unloading package properly.
+- Update citation information in README.
+
 # surveyvoi 1.0.4
 
 - CRAN release.
@@ -9,19 +18,19 @@
 
 # surveyvoi 1.0.3.11
 
-- Update `simulate_site_data()` function to remove RandomFields package
+- Update `simulate_site_data()` function to remove _RandomFields_ package
   as a dependency.
 
 # surveyvoi 1.0.3.10
 
-- Fix CRAN note about utils package dependency.
-- Skip unit tests that require RandomFields package on Windows to avoid
+- Fix CRAN note about _utils_ package dependency.
+- Skip unit tests that require _RandomFields_ package on Windows to avoid
   spurious failures.
 
 # surveyvoi 1.0.3.9
 
 - Update documentation for new code repository location.
-- Add remote for RandomFields package to facilitate installation.
+- Add remote for _RandomFields_ package to facilitate installation.
 
 # surveyvoi 1.0.3.8
 
@@ -30,11 +39,11 @@
 # surveyvoi 1.0.3.7
 
 - Tweak package documentation.
-- The RandomFields package is now an optional dependency.
+- The _RandomFields_ package is now an optional dependency.
 
 # surveyvoi 1.0.3.6
 
-- Update README with system requirements for PoissonBinomial package (#42).
+- Update README with system requirements for _PoissonBinomial_ package (#42).
 
 # surveyvoi 1.0.3.5
 
@@ -54,11 +63,11 @@
 
 # surveyvoi 1.0.3.2
 
-- Fix compatibility issues with updates to the xgboost package (version 1.5.0).
-- Fix parallel processing tests given updates to the testthat package
+- Fix compatibility issues with updated _xgboost_ package (version 1.5.0).
+- Fix parallel processing tests given updates to the _testthat_ package
   (version 3.1.2).
 - Fix tests for environmental and geographic survey schemes given updates to
-  the gurobi package (version 9.5.0).
+  the _gurobi_ package (version 9.5.0).
 
 # surveyvoi 1.0.3.1
 
@@ -100,7 +109,7 @@
 # surveyvoi 1.0.0
 
 - Refactor for official release.
-- Add support for generating surveys with the Rsymphony package.
+- Add support for generating surveys with the _Rsymphony_ package.
 
 # surveyvoi 0.0.76
 

R/feasible_survey_schemes.R

@@ -178,7 +178,7 @@ gurobi_feasible_survey_schemes <- function(cost, budget, locked_in,
                   nrow = 2, ncol = length(cost), byrow = TRUE)
   m <- list(
     obj = rep(1, length(costs)),
-    A = methods::as(rcpp_feasible_actions_ilp_matrix(costs), "dgCMatrix"),
+    A = as_Matrix(rcpp_feasible_actions_ilp_matrix(costs), "dgCMatrix"),
     sense = c(rep("=", ncol(costs)), "<="),
     rhs = c(rep(1, ncol(costs)), budget),
     lb = rep(0, length(costs)),

R/ilp.R

@@ -203,7 +203,7 @@ weight_based_prioritizations <- function(
   ## create objective function
   obj <- c(x)
   ## create constraints
-  A <- methods::as(matrix(costs, nrow = 1, ncol = length(x)), "dgCMatrix")
+  A <- as_Matrix(matrix(costs, nrow = 1, ncol = length(x)), "dgCMatrix")
   ## create RHS vector
   rhs <- c(NA_real_)
   ## create sense vector

R/internal.R

@@ -145,3 +145,63 @@ is_jags_installed <- function() {
   if (!file.exists(x)) return(FALSE)
   TRUE
 }
+
+#' 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
+  # nocov start
+  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)
+  }
+  # nocov end
+  # return result
+  out
+}

R/zzz.R

@@ -0,0 +1,3 @@
+.onUnload <- function(libpath) {
+  library.dynam.unload("surveyvoi", libpath)
+}