Merge branch 'master' into xgboost-event-level

Author: topepo

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

@@ -1,9 +1,17 @@
+# NOTE: This workflow is overkill for most R packages
+# check-standard.yaml is likely a better choice
+# usethis::use_github_action("check-standard") will install it.
+#
+# 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
@@ -21,58 +29,53 @@ jobs:
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: windows-latest, r: '3.6'}
-          - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-18.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/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@master
+      - uses: r-lib/actions/setup-r@v1
+        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v1
 
-      - name: Query dependencies
+      - name: Install pak and 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")
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - 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-
+          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
 
       - name: Install system dependencies
         if: runner.os == 'Linux'
         run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "16.04"), sep = "\n")')
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
+        shell: Rscript {0}
 
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("rcmdcheck")
         shell: Rscript {0}
 
       - name: Install Miniconda
         run: |
-          Rscript -e "remotes::install_github('rstudio/reticulate')"
+          Rscript -e "pak::pkg_install('rstudio/reticulate')"
           Rscript -e "reticulate::install_miniconda()"
 
       - name: Find Miniconda on macOS
@@ -83,7 +86,7 @@ jobs:
         run: |
           reticulate::conda_create('r-reticulate', packages = c('python==3.6.9'))
           tensorflow::install_tensorflow(version='1.14.0')
-        shell: Rscript {0}        
+        shell: Rscript {0}
 
       - name: Session info
         run: |
@@ -95,7 +98,9 @@ jobs:
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
       - name: Show testthat output
@@ -107,5 +112,5 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@main
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
           path: check

.github/workflows/check-pak.yaml

@@ -0,0 +1,30 @@
+name: 'Lock Threads'
+
+on:
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  lock:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: dessant/lock-threads@v2
+        with:
+          github-token: ${{ github.token }}
+          issue-lock-inactive-days: '14'
+#          issue-exclude-labels: ''
+#          issue-lock-labels: 'outdated'
+          issue-lock-comment: >
+            This issue has been automatically locked. If you believe you have
+            found a related problem, please file a new issue (with a reprex:
+            <https://reprex.tidyverse.org>) and link to this issue.
+          issue-lock-reason: ''
+          pr-lock-inactive-days: '14'
+#          pr-exclude-labels: 'wip'
+          pr-lock-labels: ''
+          pr-lock-comment: >
+            This pull request has been automatically locked. If you believe you
+            have found a related problem, please file a new issue (with a reprex:
+            <https://reprex.tidyverse.org>) and link to this issue.
+          pr-lock-reason: ''
+#          process-only: 'issues'

.github/workflows/lock.yaml

@@ -1,64 +1,63 @@
 on:
   push:
     branches:
-      - master
       - main
-  pull_request:
-    branches:
       - master
-      - main
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-18.04
     env:
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/bionic/latest
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v1
+        id: install-r
 
       - uses: r-lib/actions/setup-pandoc@v1
 
       - name: System dependencies
         run: brew install harfbuzz fribidi
 
-      - name: Query dependencies
+      - name: Install pak and 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")
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
         shell: Rscript {0}
 
-      - name: Cache R packages
+      - 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-
+          key: ubuntu-18.04-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ubuntu-18.04-${{ steps.install-r.outputs.installed-r-version }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("pkgdown", execute = TRUE)
+        shell: Rscript {0}
 
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_github("tidyverse/tidytemplate")
-          remotes::install_cran("tidymodels")
-          remotes::install_cran("C50")
-          install.packages("pkgdown", type = "binary")
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("pkgdown")
+          pak::pkg_install("tidyverse/tidytemplate")
+          pak::pkg_install("tidymodels")
+          pak::pkg_install("C50")
         shell: Rscript {0}
 
       - name: Install package
         run: R CMD INSTALL .
 
-      - name: Build site
-        if: github.event_name == 'pull_request'
-        run: |
-          Rscript -e 'pkgdown::build_site()'
-
-      - name: Deploy package
-        if: github.event_name == 'push'
+      - name: Build and deploy pkgdown site
         run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
           Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'