Prepare 2.19.2

.github/workflows/check.yml

@@ -0,0 +1,161 @@
+
+on:
+  push:
+    branches: [master, devel]
+  pull_request:
+    branches: [master, devel]
+  schedule:
+    - cron: '33 4 * * *'  # work 4:33 in the morning
+name: check
+
+env:
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+  R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+  WARNINGS_ARE_ERRORS: 1
+  _R_CHECK_CRAN_INCOMING_REMOTE_: false
+  _R_CHECK_TESTS_NLINES_: 0  # disable limiting of output lines
+  _R_CHECK_CRAN_INCOMING_: false
+
+jobs:
+  check:
+    defaults:
+      run:
+        shell: bash
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false  # continue runs even when a parallel run failed
+      matrix:
+        # run on ubuntu, macos, windows. 20.04 is more recent than ubuntu-latest, currently.
+        os: [macos-latest, windows-latest, ubuntu-latest]
+        action: [check]
+        r: [release]
+        include:
+          # additionally run r-devel, but only on ubuntu, and an old R version on an old ubuntu
+          - os: ubuntu-latest
+            action: check
+            r: devel
+          - os: ubuntu-20.04
+            action: check
+            r: '4.1'
+          - os: ubuntu-latest
+            action: coverage
+            r: release
+          - os: ubuntu-latest
+            action: githubversions
+            r: release
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: r-lib/actions/setup-r@v2
+        id: install-r
+        with:
+          r-version: ${{ matrix.r }}
+      - if: runner.os == 'Linux'
+        name: apt-get update
+        run: sudo apt-get update
+      - name: Install curl for Ubuntu  
+        # necessary for pkgdown & covr, so we do that on ubuntu-latest / R release only
+        if: ${{ matrix.r == 'release' && matrix.os == 'ubuntu-latest' }}
+        run: sudo apt-get install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-tinytex@v2-branch
+      - name: Create Cache Key
+        shell: Rscript {0}
+        run: |
+          if (!require("remotes", quietly = TRUE)) install.packages("remotes")
+          writeLines(capture.output(print(remotes::dev_package_deps())), ".github/deps.txt")
+      - uses: actions/cache@v4
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ matrix.os }}-${{ steps.install-r.outputs.installed-r-version }}-${{ hashFiles('.github/deps.txt') }}
+      - shell: Rscript {0}
+        name: install necessary build env packages
+        run: for (req in c("remotes", "roxygen2", "covr", "pkgdown")) if (!require(req, quietly = TRUE)) install.packages(req)
+      - if: runner.os == 'Linux'
+        name: install system requirements
+        run: |
+          while read -r depinst ; do
+            echo "> $depinst"
+            eval sudo $depinst
+          done < <( Rscript -e "writeLines(remotes::system_requirements('ubuntu', '$( . /etc/os-release ; echo $VERSION_ID )'))")
+      - shell: Rscript {0}
+        name: install package dependencies
+        run: | 
+          remotes::install_deps(dependencies = TRUE)
+      - name: install github versions
+        if: ${{ matrix.action == 'githubversions' }}
+        shell: Rscript {0}
+        run: |
+          system("sudo apt-get install libhiredis-dev")
+          remotes::install_github("mlr-org/paradox")
+          remotes::install_github("mlr-org/bbotk")
+          remotes::install_github("mlr-org/mlr3tuning")
+      - name: Session Info
+        shell: Rscript {0}
+        run: |
+          options(width = 200)
+          installed.packages()[, c("Package", "Version", "Built")]
+          sessionInfo() 
+      - name: Document
+        shell: Rscript {0}
+        run: |
+          roxygen2::roxygenise()
+          system("attic/clean_man.sh")
+      - if: runner.os == 'windows'
+        name: Remove hypertarget from Latex for Windows
+        run: "sed -i 's/\\\\hypertarget{[^}]*}//g' man/*"
+      - if: runner.os == 'windows'
+        name: Install tinytex packages
+        shell: Rscript {0}
+        run: |
+          library(tinytex)
+          tlmgr_version()
+          tlmgr_update()
+          tlmgr_install('collection-latexrecommended')
+          tlmgr_install('collection-fontsrecommended')
+          tlmgr(c('list', '--only-installed'))
+      - name: Build
+        if: ${{ matrix.action != 'coverage' }}
+        working-directory: ..
+        run: 'R CMD build */'
+      - name: Check
+        if: ${{ matrix.action != 'coverage' }}
+        working-directory: ..
+        run: 'R CMD check --as-cran --run-donttest *.tar.gz'
+      - name: Coverage
+        if: ${{ matrix.action == 'coverage' }}
+        shell: Rscript {0}
+        run: covr::codecov(quiet = FALSE, type = "tests")
+      - name: install
+        if: ${{ matrix.action != 'coverage' && matrix.os == 'ubuntu-20.04' && matrix.r == 'release' }}
+        working-directory: ..
+        run: 'R CMD INSTALL *.tar.gz'
+      - name: Build Docs
+        if: ${{ matrix.action != 'coverage' && matrix.os == 'ubuntu-20.04' && matrix.r == 'release' }}
+        shell: Rscript {0}
+        run: |
+          pkgdown::build_site()
+          roxygen2::roxygenise()
+          tools::buildVignettes(dir = ".")
+      - name: Deploy Docs
+        if: ${{ matrix.action != 'coverage' && matrix.os == 'ubuntu-20.04' && matrix.r == 'release' && github.ref == 'refs/heads/master' }}
+        run: |
+          git config --local user.name "github-actions[bot]"
+          git config --local user.email "[email protected]"
+          git checkout --orphan gh-pages
+          git --work-tree=docs add --all
+          git --work-tree=docs commit -m "gh-pages"
+          git push origin HEAD:gh-pages --force
+      - name: Install Log
+        if: ${{ failure() }}
+        working-directory: ..
+        run: 'cat *.Rcheck/00install.out'
+      - name: Check Log
+        if: ${{ failure() }}
+        working-directory: ..
+        run: 'cat *.Rcheck/00check.log'
+      - name: Latex Log
+        if: ${{ failure() }}
+        working-directory: ..
+        run: 'cat *.Rcheck/Rdlatex.log'
+

DESCRIPTION

@@ -129,7 +129,6 @@ Suggests:
     mlbench,
     mldr,
     mlrMBO,
-    mmpf,
     modeltools,
     mRMRe,
     neuralnet,
@@ -148,6 +147,7 @@ Suggests:
     rappdirs,
     refund,
     rex,
+    mmpf,
     rFerns,
     rgenoud,
     rmarkdown,
@@ -167,7 +167,6 @@ Suggests:
     stepPlr,
     survAUC,
     svglite,
-    SwarmSVM,
     testthat,
     tgp,
     TH.data,
@@ -176,6 +175,9 @@ Suggests:
     vdiffr,
     wavelets,
     xgboost (>= 0.7)
+Remote:
+    zmjones/mmpf/pkg,
+    mb706/SwarmSVM@patch-1
 VignetteBuilder:
     knitr
 ByteCompile: yes