Merge pull request #234 from jemus42/actions-fix

Update GitHub Actions

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

@@ -1,14 +1,10 @@
-# 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
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -22,64 +18,32 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {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", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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-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
+      - uses: r-lib/actions/setup-r-dependencies@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}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -1,55 +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
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    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@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - 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}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@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-
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("pkgdown")
-          # Vignette dependencies
-          remotes::install_cran("TBFmultinomial")
-          remotes::install_cran("etm")
-          remotes::install_cran("scam")
-          remotes::install_cran("coxme")
-          remotes::install_cran("eha")
-          remotes::install_cran("timereg")
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -1,48 +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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
-      - name: Query dependencies
+      - name: Test coverage
         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")
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         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
+      - name: Show testthat output
+        if: always()
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov(type = "all", line_exclusions = "R/zzz.R")
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -35,6 +35,12 @@ Imports:
     vctrs (>= 0.3.0)
 Suggests:
     testthat
+Config/Needs/website: 
+  coxme,
+  eha,
+  etm,
+  scam,
+  TBFmultinomial
 License: MIT + file LICENSE
 LazyData: true
 URL: https://adibender.github.io/pammtools/

R/viz-elra.R

@@ -40,7 +40,7 @@ gg_partial <- function(data, model, term, ..., reference = NULL, ci = TRUE) {
       geom_line(aes(y = .data[["fit"]]))
   } else {
     # if (n_vars == 2) {
-      gg_out <- gg_base + aes(y = vars[2], z = .data[["fit"]]) +
+      gg_out <- gg_base + aes(y = .data[[vars[2]]], z = .data[["fit"]]) +
         geom_tile(aes(fill = .data[["fit"]])) +
         geom_contour(col = "grey30") +
         scale_y_continuous(expand = c(0, 0)) +

README.Rmd

@@ -9,13 +9,12 @@ opts_chunk$set(warning = FALSE)
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/adibender/pammtools/workflows/R-CMD-check/badge.svg)](https://github.com/adibender/pammtools/actions)
+[![R-CMD-check](https://github.com/adibender/pammtools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/adibender/pammtools/actions/workflows/R-CMD-check.yaml)
 [![cran
 checks](https://cranchecks.info/badges/worst/pammtools)](https://cran.r-project.org/web/checks/check_results_pammtools.html)
 [![lifecycle](https://lifecycle.r-lib.org/articles/figures/lifecycle-stable.svg)](https://lifecycle.r-lib.org/articles/stages.html)
 [![Build
 Status](https://travis-ci.org/adibender/pammtools.svg?branch=master)](https://travis-ci.org/adibender/pammtools)
-[![Build
 Status](https://ci.appveyor.com/api/projects/status/github/adibender/pammtools?branch=master&svg=true)](https://ci.appveyor.com/project/adibender/pammtools/branch/master)
 [![codecov.io](https://codecov.io/github/adibender/pammtools/coverage.svg?branch=master)](https://codecov.io/github/adibender/pammtools/branch/master)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version-ago/pammtools)](https://cran.r-project.org/package=pammtools)

vignettes/baseline.Rmd

@@ -3,7 +3,7 @@ title: "Baseline Hazard"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
- %\VignetteIndexEntry{baseline}
+ %\VignetteIndexEntry{Baseline Hazard}
  %\VignetteEngine{knitr::rmarkdown}
 ---
 

vignettes/competing-risks.Rmd

@@ -4,7 +4,7 @@ author: "Andreas Bender"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{competing-risks}
+  %\VignetteIndexEntry{Competing Risks}
   %\VignetteEngine{knitr::rmarkdown}
 ---
 

vignettes/convenience.Rmd

@@ -3,7 +3,7 @@ title: "Workflow and convenience functions"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{convenience}
+  %\VignetteIndexEntry{Workflow and convenience functions}
   %\VignetteEngine{knitr::rmarkdown}
 bibliography: Remote.bib
 link-citations: yes

vignettes/cumulative-effects.Rmd

@@ -3,7 +3,7 @@ title: "Cumulative Effects"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{cumulative-effects}
+  %\VignetteIndexEntry{Cumulative Effects}
   %\VignetteEngine{knitr::rmarkdown}
 bibliography: Remote.bib
 link-citations: yes

vignettes/data-transformation.Rmd

@@ -3,7 +3,7 @@ title: "Data Transformation"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{data-transformation}
+  %\VignetteIndexEntry{Data Transformation}
   %\VignetteEngine{knitr::rmarkdown}
 bibliography: Remote.bib
 ---

vignettes/frailty.Rmd

@@ -3,7 +3,7 @@ title: "Frailty and random effects"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{frailty}
+  %\VignetteIndexEntry{Frailty and random effects}
   %\VignetteEngine{knitr::rmarkdown}
 bibliography: Remote.bib
 ---

vignettes/left-truncation.Rmd

@@ -3,7 +3,7 @@ title: "Left Truncation"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{left-truncation}
+  %\VignetteIndexEntry{Left Truncation}
   %\VignetteEngine{knitr::rmarkdown}
 bibliography: Remote.bib
 link-citations: yes

vignettes/model-evaluation.Rmd

@@ -3,7 +3,7 @@ title: "Model evaluation"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{model-evaluation}
+  %\VignetteIndexEntry{Model evaluation}
   %\VignetteEngine{knitr::rmarkdown}
 bibliography: Remote.bib
 link-citations: yes

vignettes/recurrent-events.Rmd

@@ -5,7 +5,7 @@ date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 number_sections: true
 vignette: >
-  %\VignetteIndexEntry{recurrent-events}
+  %\VignetteIndexEntry{Recurrent Events}
   %\VignetteEngine{knitr::rmarkdown}
 bibliography: Remote.bib
 link-citations: yes

vignettes/smj-tutorial.Rmd

@@ -3,7 +3,7 @@ title: "Paper: A generalized additive model approach to time-to-event analysis"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{smj-tutorial}
+  %\VignetteIndexEntry{Paper: A generalized additive model approach to time-to-event analysis}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---