rm cstdlib include statements from heap.cpp files to fix #260

.github/workflows/check-standard.yaml

@@ -1,10 +1,13 @@
+# 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
+    branches: [main, master]
   pull_request:
-    branches: main
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -20,10 +23,9 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-            # - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
@@ -46,3 +48,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -1,13 +1,16 @@
+# 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
+    branches: [main, master]
   pull_request:
-    branches: main
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -39,7 +42,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -1,21 +1,18 @@
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
 
-name: test-coverage
+name: test-coverage.yaml
 
-jobs:
+permissions: read-all
 
+jobs:
   test-coverage:
-
     runs-on: ubuntu-latest
-
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
@@ -27,29 +24,39 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package"),
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
             line_exclusions = list('src/heaps/bheap.cpp','src/heaps/bheap.h','src/heaps/fheap.h','src/heaps/fheap.cpp','src/heaps/heap23.h','src/heaps/heap23.cpp','src/heaps/heap23_2.h','src/heaps/heap.h','src/heaps/heap_lib.h','src/heaps/triheap.h','src/heaps/triheap.cpp','src/heaps/triheap_ext.h','src/heaps/triheap_ext.cpp','src/dgraph.cpp')
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dodgr
 Title: Distances on Directed Graphs
-Version: 0.4.1.040
+Version: 0.4.1.042
 Authors@R: c(
     person("Mark", "Padgham", , "[email protected]", role = c("aut", "cre")),
     person("Andreas", "Petutschnig", role = "aut"),

codemeta.json

@@ -11,7 +11,7 @@
   "codeRepository": "https://github.com/UrbanAnalyst/dodgr",
   "issueTracker": "https://github.com/UrbanAnalyst/dodgr/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.4.1.040",
+  "version": "0.4.1.042",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",

src/heaps/bheap.cpp

@@ -2,7 +2,6 @@
  * ----------------------------------------------------------------------------
  *  Mark Padgham, adapted from code by Shane Saunders
  */
-#include <cstdlib>
 #include "bheap.h"
 
 /* This implementation stores the binary heap in a 1 dimensional array. */

src/heaps/fheap.cpp

@@ -2,7 +2,6 @@
  * ----------------------------------------------------------------------------
  * Mark Padgham, adapted from code by Shane Saunders
  */
-#include <cstdlib>
 #include <cmath>
 #if defined(FHEAP_DUMP) && FHEAP_DUMP > 0
 #include <cstdio>

src/heaps/heap23.cpp

@@ -9,7 +9,6 @@
  * nodes.  In this implementation, the child pointer points to the highest
  * dimension child node.
  */
-#include <cstdlib>
 #include <cmath>
 #include <cstdio>
 #if defined(TTHEAP_DUMP) && TTHEAP_DUMP > 0

src/heaps/triheap.cpp

@@ -10,7 +10,6 @@
  */
 
 #include "triheap.h"
-#include <cstdlib>
 #include <cmath>
 #if SHOW_trih
 #include <cstdio>

src/heaps/triheap_ext.cpp

@@ -10,7 +10,6 @@
  */
 
 #include "triheap_ext.h"
-#include <cstdlib>
 #include <cmath>
 //#if SHOW_trih_ext
 #include <cstdio>