add actions to CMD-checks, coverage and lint

.Rbuildignore

@@ -12,3 +12,4 @@
 ^LICENSE\.md$
 ^CODE_OF_CONDUCT\.md$
 ^\.github$
+^README\.Rmd$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,50 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {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'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/lint.yaml

@@ -0,0 +1,32 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.lintr

@@ -0,0 +1,2 @@
+linters: linters_with_defaults() # see vignette("lintr")
+encoding: "UTF-8"

CrossClustering.Rproj

@@ -19,3 +19,5 @@ BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageRoxygenize: rd,collate,namespace,vignette
+
+QuitChildProcessesOnExit: Yes

README.md

@@ -1,16 +1,18 @@
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # CrossClustering
 
-[![Travis Build
-Status](https://travis-ci.org/CorradoLanera/CrossClustering.svg?branch=develop)](https://travis-ci.org/CorradoLanera/CrossClustering)
-[![AppVeyor Build
-Status](https://ci.appveyor.com/api/projects/status/github/CorradoLanera/CrossClustering?branch=develop&svg=true)](https://ci.appveyor.com/project/CorradoLanera/CrossClustering)
+<!-- badges: start -->
+
+[![R-CMD-check](https://github.com/CorradoLanera/CrossClustering/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/CorradoLanera/CrossClustering/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/CorradoLanera/CrossClustering/branch/master/graph/badge.svg)](https://app.codecov.io/gh/CorradoLanera/CrossClustering?branch=master)
+[![lint](https://github.com/CorradoLanera/CrossClustering/actions/workflows/lint.yaml/badge.svg)](https://github.com/CorradoLanera/CrossClustering/actions/workflows/lint.yaml)
 [![CRAN Status
 Badge](http://www.r-pkg.org/badges/version/CrossClustering)](https://CRAN.R-project.org/package=CrossClustering)
-[![Coverage
-Status](https://codecov.io/gh/CorradoLanera/CrossClustering/branch/develop/graph/badge.svg)](https://codecov.io/gh/CorradoLanera/CrossClustering?branch=develop)
 [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
+<!-- badges: end -->
 
 CrossClustering is a partial clustering algorithm that combines the
 Ward’s minimum variance and Complete Linkage algorithms, providing

README.rmd

@@ -1,7 +1,5 @@
 ---
-output:
-  md_document:
-    variant: gfm
+output: github_document
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -16,11 +14,13 @@ knitr::opts_chunk$set(
 
 # CrossClustering
 
-[![Travis Build Status](https://travis-ci.org/CorradoLanera/CrossClustering.svg?branch=develop)](https://travis-ci.org/CorradoLanera/CrossClustering)
-[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/CorradoLanera/CrossClustering?branch=develop&svg=true)](https://ci.appveyor.com/project/CorradoLanera/CrossClustering)
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/CorradoLanera/CrossClustering/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/CorradoLanera/CrossClustering/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/CorradoLanera/CrossClustering/branch/master/graph/badge.svg)](https://app.codecov.io/gh/CorradoLanera/CrossClustering?branch=master)
+[![lint](https://github.com/CorradoLanera/CrossClustering/actions/workflows/lint.yaml/badge.svg)](https://github.com/CorradoLanera/CrossClustering/actions/workflows/lint.yaml)
 [![CRAN Status Badge](http://www.r-pkg.org/badges/version/CrossClustering)](https://CRAN.R-project.org/package=CrossClustering)
-[![Coverage Status](https://codecov.io/gh/CorradoLanera/CrossClustering/branch/develop/graph/badge.svg)](https://codecov.io/gh/CorradoLanera/CrossClustering?branch=develop)
 [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
+<!-- badges: end -->
 
 CrossClustering is a partial clustering algorithm that combines the Ward's
 minimum variance and Complete Linkage algorithms, providing automatic

codecov.yml

@@ -6,7 +6,9 @@ coverage:
       default:
         target: auto
         threshold: 1%
+        informational: true
     patch:
       default:
         target: auto
         threshold: 1%
+        informational: true

cran-comments.md

@@ -1,5 +1,5 @@
 ## Test environments
-* local win 10 pro, R 3.5.1
+* local win 11 edu, R 4.4.0
 
 * ubuntu 14.04.5 LTS, and macOS Sierra 10.12.6 (on travis-ci);
     both on R 3.4.4, R 3.5.0, and R under development (2018-06-20 r74923)
@@ -17,12 +17,14 @@ R CMD check results
 
 R CMD check succeeded.
 
-
-## Downstream dependencies
-* devtools::revdep_check() results in no errors
-
-
-## Resubmission
-This is a resubmission. In this version I have:
-
-* Removed the package name from the title.
+## Re-submission
+This is a re-submission, after the package has been removed from CRAN.
+In this version I have:
+
+* Replace all `{assertive}`'s functions calls to `{checkmate}`'s ones.
+* Replace `{magrittr}`'s pipe instances with native pipe (updating 
+  Dependencies)
+* Overall general lint of source code
+* Update the documentation format
+* Switch from Travis and AppVeyor to GH-actions for CMD-checks, lint, 
+  and coverage.

revdep/.gitignore

@@ -2,5 +2,6 @@ checks
 library
 checks.noindex
 library.noindex
+cloud.noindex
 data.sqlite
 *.html