From d9483beabdfb28ecc27741f19693fe00c07028eb Mon Sep 17 00:00:00 2001
From: Jack Leary <j.leary@ufl.edu>
Date: Fri, 24 Nov 2023 00:07:42 -0500
Subject: [PATCH] changed R CMD check workflow etc

---
 .DS_Store                            | Bin 10244 -> 10244 bytes
 .github/workflows/R-CMD-check.yaml   |  12 ++++--------
 .github/workflows/render-README.yaml |   9 ++++++++-
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/.DS_Store b/.DS_Store
index 9ec15cac60aa1d0cd4a45a5e368a36e55cba0979..412ed02b166f258bab4560771829b84b56019b65 100644
GIT binary patch
delta 179
zcmZn(XbG6$FDS&oz`)4BAi$85ZWx@LpIfl8a2or>2Eonj94s95AXyd$J%)6KOokGe
z3ZNJR<K7%6WVzgY7nh`*{3M_lM@2(=4P(bqM^yO~yz&JZ5Zi%z7#P1U08uOqnVW?K
RYWX*_EBs>F+$qA$3;^weD)RsU

delta 57
zcmZn(XbG6$FUrTjz`)4BAi$7RUR;orlb;0S@7$QUn0+%l2MY%y-{uy9X8wr<6`R==
Mez9z>6lG=x0J5?V+5i9m

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 08d75f8..fb568d2 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -26,20 +26,16 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-
       - name: Checkout repo
         uses: actions/checkout@v3
-
       - name: Setup Pandoc
         uses: r-lib/actions/setup-pandoc@v2
-
       - name: Setup R
         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
-
       - name: Setup dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -50,7 +46,10 @@ jobs:
         run: |
           install.packages("Matrix", type = "source", force = TRUE)
           install.packages("irlba", type = "source", force = TRUE)
-
+          install.packages("TMB", type = "source", force = TRUE)
+          install.packages("glmmTMB", type = "source", force = TRUE)
+        shell: Rscript {0}
+        working-directory: '.'
       - name: Check
         id: rcmdcheck
         run: |
@@ -60,7 +59,6 @@ jobs:
           check_results <- rcmdcheck::rcmdcheck(args = c("--no-vignettes", "--no-manual", "--as-cran"), build_args = c("--no-build-vignettes", "--no-manual"), check_dir = "check", error_on = "error")
         shell: Rscript {0}
         working-directory: '.'
-
       - name: Show testthat output
         if: always()
         run: |
@@ -70,14 +68,12 @@ jobs:
           echo ::endgroup::
         shell: bash
         working-directory: '.'
-
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@v3
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: ${{ steps.rcmdcheck.outputs.check-dir-path }}
-
       - name: Upload snapshots
         uses: actions/upload-artifact@v3
         with:
diff --git a/.github/workflows/render-README.yaml b/.github/workflows/render-README.yaml
index 9d46354..cf80b1b 100644
--- a/.github/workflows/render-README.yaml
+++ b/.github/workflows/render-README.yaml
@@ -20,9 +20,16 @@ jobs:
           use-public-rspm: true
       - uses: r-lib/actions/setup-r-dependencies@v2
       - uses: r-lib/actions/setup-pandoc@v2
-
       - name: install CRAN packages
         run: Rscript -e 'install.packages(c("rmarkdown","ggplot2", "dplyr", "purrr", "remotes", "devtools", "BiocManager", "Seurat"), force = TRUE)'
+      - name: Extra dependencies
+        id: extra-deps
+        run: |
+          install.packages("Matrix", type = "source", force = TRUE)
+          install.packages("irlba", type = "source", force = TRUE)
+          install.packages("TMB", type = "source", force = TRUE)
+          install.packages("glmmTMB", type = "source", force = TRUE)
+        shell: Rscript {0}
       - name: install BioConductor packages
         run: Rscript -e 'BiocManager::install(c("SingleCellExperiment", "scater", "scran", "scuttle", "bluster"), force = TRUE)'
       - name: install GitHub packages