Merge pull request #562 from imbs-hl/gh_actions

Add GH actions standard workflow

.Rbuildignore

@@ -4,6 +4,6 @@
 ^NEWS\.md$
 ^README\.md$
 ^.*\.tar.gz$
-^\.travis.yml$
 ^cpp\_version$
-^appveyor\.yml$
+^\.github$
+^codecov\.yml$

.github/.gitignore

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

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

@@ -0,0 +1,87 @@
+# 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:
+  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: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    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}
+
+      - name: Restore R package cache
+        if: runner.os != 'Windows'
+        uses: actions/cache@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'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/test-coverage.yaml

@@ -0,0 +1,48 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@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 dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

DESCRIPTION

@@ -2,7 +2,7 @@ Package: ranger
 Type: Package
 Title: A Fast Implementation of Random Forests
 Version: 0.12.4
-Date: 2020-07-24
+Date: 2021-05-03
 Author: Marvin N. Wright [aut, cre], Stefan Wager [ctb], Philipp Probst [ctb]
 Maintainer: Marvin N. Wright <cran@wrig.de>
 Description: A fast implementation of Random Forests, particularly suited for high
@@ -15,7 +15,10 @@ License: GPL-3
 Imports: Rcpp (>= 0.11.2), Matrix
 LinkingTo: Rcpp, RcppEigen
 Depends: R (>= 3.1)
-Suggests: survival, testthat
+Suggests: 
+    covr,
+    survival,
+    testthat
 Encoding: UTF-8
 RoxygenNote: 7.1.0
 URL: https://github.com/imbs-hl/ranger

README.md

@@ -1,6 +1,5 @@
-[![Travis Build Status](https://travis-ci.org/imbs-hl/ranger.svg?branch=master)](https://travis-ci.org/imbs-hl/ranger)
-[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/imbs-hl/ranger?branch=master&svg=true)](https://ci.appveyor.com/project/mnwright/ranger)
-[![Coverage Status](https://coveralls.io/repos/github/imbs-hl/ranger/badge.svg?branch=master)](https://coveralls.io/github/imbs-hl/ranger?branch=master)
+[![R-CMD-check](https://github.com/imbs-hl/ranger/workflows/R-CMD-check/badge.svg)](https://github.com/imbs-hl/ranger/actions)
+[![Codecov test coverage](https://codecov.io/gh/imbs-hl/ranger/branch/master/graph/badge.svg)](https://codecov.io/gh/imbs-hl/ranger?branch=master)
 ![CRAN Downloads month](http://cranlogs.r-pkg.org/badges/ranger?color=brightgreen)
 ![CRAN Downloads overall](http://cranlogs.r-pkg.org/badges/grand-total/ranger?color=brightgreen)
 ## ranger: A Fast Implementation of Random Forests

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

src/Forest.cpp

@@ -144,7 +144,6 @@ void Forest::initR(std::unique_ptr<Data> input_data, uint mtry, uint num_trees,
     uint num_random_splits, bool order_snps, uint max_depth, const std::vector<double>& regularization_factor,
     bool regularization_usedepth) {
 
-  this->memory_mode = memory_mode;
   this->verbose_out = verbose_out;
 
   // Call other init function