From 8113fa3b385aabb6145c0d4b84622a0d68b6a496 Mon Sep 17 00:00:00 2001
From: wlandau-lilly <will.landau@lilly.com>
Date: Tue, 9 Jan 2024 10:49:14 -0500
Subject: [PATCH] Try installing cmdstanr another way

---
 .github/workflows/check-fixed.yaml    | 14 +++++++-------
 .github/workflows/check-implicit.yaml | 13 ++++++-------
 .github/workflows/cover.yaml          | 14 +++++++-------
 .github/workflows/pkgdown.yaml        | 14 +++++++-------
 4 files changed, 27 insertions(+), 28 deletions(-)

diff --git a/.github/workflows/check-fixed.yaml b/.github/workflows/check-fixed.yaml
index 671666f..9dbd747 100644
--- a/.github/workflows/check-fixed.yaml
+++ b/.github/workflows/check-fixed.yaml
@@ -32,21 +32,21 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::rcmdcheck, local::.
-          needs: check
-          cache-version: 2
-    
       - name: Repos
         run: |
           cat("\noptions(repos=c(stan='https://mc-stan.org/r-packages/',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
         shell: Rscript {0}
 
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, local::., any::cmdstanr
+          needs: check
+          cache-version: 2
+
       - name: Install CmdStan
         shell: Rscript {0}
         run: |
-          install.packages("cmdstanr")
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
           cmdstanr::install_cmdstan()
           cmdstan <- file.path(Sys.getenv("RUNNER_TEMP"), "cmdstan")
           file.rename(cmdstanr::cmdstan_path(), cmdstan)
diff --git a/.github/workflows/check-implicit.yaml b/.github/workflows/check-implicit.yaml
index a381ee6..db75552 100644
--- a/.github/workflows/check-implicit.yaml
+++ b/.github/workflows/check-implicit.yaml
@@ -37,21 +37,20 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::rcmdcheck, local::.
-          needs: check
-          cache-version: 2
-
       - name: Repos
         run: |
           cat("\noptions(repos=c(stan='https://mc-stan.org/r-packages/',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
         shell: Rscript {0}
 
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, local::., any::cmdstanr
+          needs: check
+          cache-version: 2
+
       - name: Install CmdStan
         shell: Rscript {0}
         run: |
-          install.packages("cmdstanr")
           cmdstanr::check_cmdstan_toolchain(fix = TRUE)
           cmdstanr::install_cmdstan()
     
diff --git a/.github/workflows/cover.yaml b/.github/workflows/cover.yaml
index bd77b19..bf928c0 100644
--- a/.github/workflows/cover.yaml
+++ b/.github/workflows/cover.yaml
@@ -20,21 +20,21 @@ jobs:
           use-public-rspm: true
           extra-repositories: 'https://mc-stan.org/r-packages/'
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::covr, local::.
-          needs: coverage
-          cache-version: 2
-
       - name: Repos
         run: |
           cat("\noptions(repos=c(stan='https://mc-stan.org/r-packages/',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
         shell: Rscript {0}
 
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, local::., any::cmdstanr
+          needs: coverage
+          cache-version: 2
+
       - name: Install CmdStan
         shell: Rscript {0}
         run: |
-          install.packages("cmdstanr")
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
           cmdstanr::install_cmdstan()
 
       - name: Test coverage
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index e9640cd..2757644 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -27,21 +27,21 @@ jobs:
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::pkgdown, local::.
-          needs: website
-          cache-version: 2
-
       - name: Repos
         run: |
           cat("\noptions(repos=c(stan='https://mc-stan.org/r-packages/',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
         shell: Rscript {0}
 
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::., any::cmdstanr
+          needs: website
+          cache-version: 2
+
       - name: Install CmdStan
         shell: Rscript {0}
         run: |
-          install.packages("cmdstanr")
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
           cmdstanr::install_cmdstan()
 
       - name: Build site