fix #21, fix compatibility issues, fix broken urls + badges (PR #19)

- Fix aliasing for package manual entry (#21). - Fix compatibility with updates to _ggplot2_ package. - Fix compatibility with updates to package citation format. - Fix broken URLs in package documentation. - Fix broken badges in README.
prioritizr · May 26, 2024 · dbe2eca · dbe2eca
1 parent abc9a6a
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diff --git a/.github/workflows/R-CMD-check-macos.yaml b/.github/workflows/R-CMD-check-macos.yaml
@@ -37,41 +37,32 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          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: Cache R packages
-        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'
+          cache-version: 1
+          extra-packages: |
+            cran/XML
+            any::remotes
+            any::covr
+            any::rcmdcheck
+            gurobi=?ignore
+            Rsymphony=?ignore
+            lpsymphony=?ignore
+            ggtree=?ignore
+
+      - name: Install additional packages
         run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          options("install.packages.compile.from.source" = "never")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
+          options(repos = "https://cloud.r-project.org/")
+          remotes::install_cran("Rsymphony")
+          remotes::install_bioc("lpsymphony")
+          remotes::install_bioc("ggtree")
         shell: Rscript {0}
 
       - name: Session information
@@ -81,19 +72,11 @@ jobs:
           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}
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
 
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
diff --git a/.github/workflows/R-CMD-check-ubuntu.yaml b/.github/workflows/R-CMD-check-ubuntu.yaml
@@ -25,8 +25,8 @@ jobs:
       matrix:
         config:
           - {os: ubuntu-20.04, r: 'release', pkgs: 'all'}
-          - {os: ubuntu-20.04, r: 'devel', pkgs: 'all'}
-          - {os: ubuntu-20.04, r: 'devel', pkgs: 'depends only'}
+          # - {os: ubuntu-20.04, r: 'devel', pkgs: 'all'}
+          # - {os: ubuntu-20.04, r: 'devel', pkgs: 'depends only'}
 
     env:
       _R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true
@@ -39,40 +39,36 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-cache-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-cache-
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
       - name: Install system dependencies
         run: |
-          sudo apt-get -y install libcurl4-openssl-dev
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          sudo apt-get install libxml2 coinor-libsymphony-dev
 
-      - name: Install dependencies
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 4
+          extra-packages: |
+            cran/XML
+            any::remotes
+            any::covr
+            any::rcmdcheck
+            gurobi=?ignore
+            Rsymphony=?ignore
+            lpsymphony=?ignore
+            ggtree=?ignore
+
+      - name: Install additional packages
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
+          options(repos = "https://cloud.r-project.org/")
+          remotes::install_cran("Rsymphony")
+          remotes::install_bioc("lpsymphony")
+          remotes::install_bioc("ggtree")
         shell: Rscript {0}
 
       - name: Session information
@@ -87,17 +83,9 @@ jobs:
         run: |
           echo "_R_CHECK_DEPENDS_ONLY_=true" >> $GITHUB_ENV
 
-      - name: Check
-        run: |
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - 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
 
       - name: Show testthat output
         if: always()
@@ -106,5 +94,20 @@ jobs:
 
       - name: Test coverage
         if: runner.os == 'Linux' && matrix.config.r == 'release'
-        run: covr::codecov()
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        if: runner.os == 'Linux' && matrix.config.r == 'release'
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/R-CMD-check-windows.yaml b/.github/workflows/R-CMD-check-windows.yaml
@@ -35,27 +35,40 @@ jobs:
       CI: true
 
     steps:
+      # configure git to prevent it from automatically converting line-endings
+      # this is important to avoid WARNINGS during CRAN checks
+      # that are false-positives, see:
+      # https://msmith.de/2020/03/12/r-cmd-check-github-actions.html
+      - name: Configure git
+        run: git config --global core.autocrlf false
+
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          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}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 1
+          extra-packages: |
+            cran/XML
+            any::remotes
+            any::rcmdcheck
+            gurobi=?ignore
+            Rsymphony=?ignore
+            lpsymphony=?ignore
+            ggtree=?ignore
 
-      - name: Install dependencies
+      - name: Install additional packages
         run: |
-          options("install.packages.compile.from.source" = "never", pkgType = "binary")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
+          options(repos = "https://cloud.r-project.org/")
+          remotes::install_cran("Rsymphony")
+          remotes::install_bioc("lpsymphony")
+          remotes::install_bioc("ggtree")
         shell: Rscript {0}
 
       - name: Session information
@@ -65,19 +78,11 @@ jobs:
           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}
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
 
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: oppr
 Type: Package
-Version: 1.0.4
+Version: 1.0.4.1
 Title: Optimal Project Prioritization
 Description: A decision support tool for prioritizing conservation projects.
     Prioritizations can be developed by maximizing expected feature richness,
@@ -41,10 +41,11 @@ Imports:
     tibble (>= 2.0.0),
     ape (>= 5.2),
     tidytree (>= 0.3.3),
-    ggplot2 (>= 3.0.0),
+    ggplot2 (>= 3.5.0),
     viridisLite (>= 0.3.0),
     lpSolveAPI (>= 5.5.2.0.17),
     withr (>= 2.4.1),
+    rlang (>= 1.1.3)
 Suggests:
     testthat (>= 2.0.0),
     knitr (>= 1.20),
@@ -65,11 +66,10 @@ LinkingTo:
     RcppProgress (>= 0.4.1)
 License: GPL-3
 LazyData: true
-SystemRequirements: C++11
 URL: https://prioritizr.github.io/oppr/
 BugReports: https://github.com/prioritizr/oppr/issues
 VignetteBuilder: knitr
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 Language: en-US
 Collate:

diff --git a/NAMESPACE b/NAMESPACE
@@ -16,7 +16,6 @@ S3method(print,ScalarParameter)
 S3method(print,Solver)
 export("%>%")
 export("%T>%")
-export()
 export(ArrayParameter)
 export(Collection)
 export(Constraint)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# oppr 1.0.4.1
+
+- Fix aliasing for package manual entry (#21).
+- Fix compatibility with updates to _ggplot2_ package.
+- Fix compatibility with updates to package citation format.
+- Fix broken URLs in package documentation.
+- Fix broken badges in README.
+
 # oppr 1.0.4
 
 - CRAN release.

diff --git a/R/add_gurobi_solver.R b/R/add_gurobi_solver.R
@@ -71,16 +71,12 @@ NULL
 #'
 #'   To install the \pkg{gurobi} package, the
 #'   [Gurobi](https://www.gurobi.com) optimization suite will first need to
-#'   be installed (see instructions for [Linux](https://www.gurobi.com/documentation/8.1/quickstart_linux/software_installation_guid.html),
-#'   [Mac OSX](https://www.gurobi.com/documentation/8.1/quickstart_mac/software_installation_guid.html), and
-#'   [Windows](https://www.gurobi.com/documentation/8.1/quickstart_windows/software_installation_guid.html) operating systems). Although
+#'   be installed (see <https://support.gurobi.com/hc/en-us/articles/4534161999889-How-do-I-install-Gurobi-Optimizer> for instructions). Although
 #'   [Gurobi](https://www.gurobi.com) is a commercial software, academics
 #'   can obtain a
 #'   [special license for no cost](https://www.gurobi.com/downloads/end-user-license-agreement-academic/). After installing the
 #'   [Gurobi](https://www.gurobi.com) optimization suite, the \pkg{gurobi}
-#'   package can then be installed (see instructions for [Linux](https://www.gurobi.com/documentation/8.1/quickstart_linux/r_installing_the_r_package.html),
-#'   [Mac OSX](https://www.gurobi.com/documentation/8.1/quickstart_mac/r_installing_the_r_package.html), and
-#'   [Windows](https://www.gurobi.com/documentation/8.1/quickstart_windows/r_installing_the_r_package.html) operating systems).
+#'   package can then be installed (see <https://www.gurobi.com/documentation/current/refman/r_ins_the_r_package.html> for instructions).
 #'
 #' @return [ProjectProblem-class] object with the solver added
 #'   to it.

diff --git a/R/add_lpsolveapi_solver.R b/R/add_lpsolveapi_solver.R
@@ -14,7 +14,7 @@ NULL
 #'
 #' @inheritParams add_gurobi_solver
 #'
-#' @details [*lp_solve*](http://lpsolve.sourceforge.net/5.5/) is an
+#' @details [*lp_solve*](https://lpsolve.sourceforge.net/5.5/) is an
 #'   open-source integer programming solver.
 #'   Although this solver is the slowest currently supported solver,
 #'   it is also the only exact algorithm solver that can be installed on all

diff --git a/R/package.R b/R/package.R
@@ -37,23 +37,17 @@ NULL
 #' If the installation process fails, please consult the
 #' [package's online documentation](https://bioconductor.org/packages/release/bioc/html/ggtree.html). To install the \pkg{gurobi} package, the
 #' [Gurobi](https://www.gurobi.com) optimization suite will first need to
-#' be installed (see instructions for [Linux](https://www.gurobi.com/documentation/8.1/quickstart_linux/software_installation_guid.html),
-#'   [Mac OSX](https://www.gurobi.com/documentation/8.1/quickstart_mac/software_installation_guid.html), and
-#'   [Windows](https://www.gurobi.com/documentation/8.1/quickstart_windows/software_installation_guid.html) operating systems). Although
+#' be installed (see <https://support.gurobi.com/hc/en-us/articles/4534161999889-How-do-I-install-Gurobi-Optimizer> for instructions). Although
 #' [Gurobi](https://www.gurobi.com) is a commercial software, academics
 #' can obtain a
 #' [special license for no cost](https://www.gurobi.com/downloads/end-user-license-agreement-academic/). After installing the
 #' [Gurobi](https://www.gurobi.com) optimization suite, the \pkg{gurobi}
-#'  package can then be installed (see instructions for [Linux](https://www.gurobi.com/documentation/8.1/quickstart_linux/r_installing_the_r_package.html),
-#'   [Mac OSX](https://www.gurobi.com/documentation/8.1/quickstart_mac/r_installing_the_r_package.html), and
-#'   [Windows](https://www.gurobi.com/documentation/8.1/quickstart_windows/r_installing_the_r_package.html) operating systems).
+#'  package can then be installed (see <https://www.gurobi.com/documentation/current/refman/r_ins_the_r_package.html> for instructions).
 #'
 #' @seealso Please refer to the package vignette for more information and worked
 #'   examples. This can be accessed using the code
 #'   `vignette("oppr")`.
 #'
-#' @name oppr
-#'
 #' @examples
 #' # load data
 #' data(sim_projects, sim_features, sim_actions)
@@ -94,5 +88,8 @@ NULL
 #' # visualize solution
 #' plot(p, s)
 #' }
+#'
+#' @name oppr
 #' @docType package
-NULL
+#' @aliases oppr-package
+"_PACKAGE"