From d8b6199dda22dda268a9f1445cd37e09d39b1621 Mon Sep 17 00:00:00 2001
From: Bill Denney <wdenney@humanpredictions.com>
Date: Mon, 7 Nov 2022 17:00:34 -0500
Subject: [PATCH] Update workflows to match working main branch R CMD check

---
 .github/workflows/R-CMD-check.yaml   | 9 +++++----
 .github/workflows/pkgdown.yaml       | 6 ++++++
 .github/workflows/test-coverage.yaml | 4 +++-
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 32370a423..91a360496 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -20,13 +20,14 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
 
     env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_KEEP_PKG_SOURCE: yes
+      _R_CHECK_FORCE_SUGGESTS_: false
 
     steps:
       - name: Install deps on MacOS
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index b79eed2e0..70e92cf10 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -20,7 +20,11 @@ jobs:
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      _R_CHECK_FORCE_SUGGESTS_: false
+
     steps:
       - uses: actions/checkout@v3
 
@@ -28,6 +32,8 @@ jobs:
 
       - 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-r-dependencies@v2
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 1deec7e31..108bae410 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -12,7 +12,10 @@ jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      _R_CHECK_FORCE_SUGGESTS_: false
 
     steps:
       - uses: actions/checkout@v3
@@ -30,7 +33,6 @@ jobs:
             nlmixr2/rxode2parse
             nlmixr2/rxode2random
             nlmixr2/rxode2et
-            nlmixr2/rxode2
           needs: coverage
 
       - name: Test coverage