From 15a6ff3492caccf5b4025d5efaab6ef3b4c18739 Mon Sep 17 00:00:00 2001
From: karissawhiting <whitingk@mskcc.org>
Date: Tue, 14 May 2024 15:35:46 -0400
Subject: [PATCH] try updating actions

---
 .github/workflows/R-CMD-check.yaml | 28 +++++++++++++---------------
 README.Rmd                         |  1 +
 2 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index d1ab8bb..0f2fe08 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,9 +1,5 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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
-#
-# NOTE: This workflow is overkill for most R packages and
-# check-standard.yaml is likely a better choice.
-# usethis::use_github_action("check-standard") will install it.
 on:
   push:
     branches: [main, master]
@@ -12,6 +8,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -22,22 +20,18 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          # Use older ubuntu to maximise backward compatibility
-          - {os: ubuntu-18.04,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-18.04,   r: 'release'}
-          - {os: ubuntu-18.04,   r: 'oldrel-1'}
-          # - {os: ubuntu-18.04,   r: 'oldrel-2'}
-          # - {os: ubuntu-18.04,   r: 'oldrel-3'}
-          # - {os: ubuntu-18.04,   r: 'oldrel-4'}
+          - {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@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -49,6 +43,10 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          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")'
diff --git a/README.Rmd b/README.Rmd
index 0086ba6..28da9c3 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -18,6 +18,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/MSKCC-Epi-Bio/bstfun/workflows/R-CMD-check/badge.svg)](https://github.com/MSKCC-Epi-Bio/bstfun/actions)
 [![Codecov test coverage](https://codecov.io/gh/MSKCC-Epi-Bio/bstfun/branch/main/graph/badge.svg)](https://app.codecov.io/gh/MSKCC-Epi-Bio/bstfun?branch=main)
+[![R-CMD-check](https://github.com/MSKCC-Epi-Bio/bstfun/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/MSKCC-Epi-Bio/bstfun/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 A miscellaneous collection of functions to used by members of the Biostatistics Department at MSKCC. Functions in the {bstfun} package do not fall within the well-defined packages with more narrow scope used by the department.