From 8cfef6a161fdda90fcae9b753891d6a96cb4d574 Mon Sep 17 00:00:00 2001
From: "Lisa N. Cao" <20377512+lisancao@users.noreply.github.com>
Date: Sat, 17 Jul 2021 12:05:58 -0700
Subject: [PATCH 1/5] add install-checks.yml

---
 .github/workflows/install-checks.yml | 37 ++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 .github/workflows/install-checks.yml

diff --git a/.github/workflows/install-checks.yml b/.github/workflows/install-checks.yml
new file mode 100644
index 0000000..a41fb40
--- /dev/null
+++ b/.github/workflows/install-checks.yml
@@ -0,0 +1,37 @@
+# This is a basic workflow to help you get started with Actions
+
+name: install-checks
+
+# Controls when the action will run. 
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest, ubuntu-latest]
+        R: [ '3.5.3', '3.6.3', '4.1.0' ]
+    name: Environment Setup
+    steps:
+    - uses: actions/checkout@v2
+    - name: Get Directory
+      run: ls ${{ github.workspace }}
+    - name: Setup BiocSwirl Dev using ${{ matrix.R }} on ${{ matrix.os }}
+      uses: r-lib/actions/setup-r@v1
+      with: 
+        r-version: ${{ matrix.R }}
+    - run: Rscript -e 'install.packages("remotes")'
+    - run: Rscript -e 'remotes::install_github("biocswirl-dev-team/BiocSwirl")'
+    - run: Rscript -e 'library(BiocSwirl)'
+
+        

From bec541d728a710bd4c9b4007374234fbb8e890bc Mon Sep 17 00:00:00 2001
From: "Lisa N. Cao" <20377512+lisancao@users.noreply.github.com>
Date: Sat, 17 Jul 2021 12:13:07 -0700
Subject: [PATCH 2/5] add swirl dependency and list course

---
 .github/workflows/install-checks.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/install-checks.yml b/.github/workflows/install-checks.yml
index a41fb40..ccee194 100644
--- a/.github/workflows/install-checks.yml
+++ b/.github/workflows/install-checks.yml
@@ -30,8 +30,10 @@ jobs:
       uses: r-lib/actions/setup-r@v1
       with: 
         r-version: ${{ matrix.R }}
-    - run: Rscript -e 'install.packages("remotes")'
+    - run: Rscript -e 'install.packages(c("remotes", "swirl"))'
     - run: Rscript -e 'remotes::install_github("biocswirl-dev-team/BiocSwirl")'
+    - run: Rscript -e 'library(swirl)'
     - run: Rscript -e 'library(BiocSwirl)'
+    - run: Rscript -e 'list_courses()'
 
         

From aff5325be2ffa7758ad98c9408690eaa6895bae8 Mon Sep 17 00:00:00 2001
From: "Lisa N. Cao" <20377512+lisancao@users.noreply.github.com>
Date: Sat, 17 Jul 2021 12:36:52 -0700
Subject: [PATCH 3/5] add windows

---
 .github/workflows/install-checks.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/install-checks.yml b/.github/workflows/install-checks.yml
index ccee194..e382570 100644
--- a/.github/workflows/install-checks.yml
+++ b/.github/workflows/install-checks.yml
@@ -19,7 +19,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest, ubuntu-latest]
+        os: [macos-latest, ubuntu-latest, windows-latest]
         R: [ '3.5.3', '3.6.3', '4.1.0' ]
     name: Environment Setup
     steps:

From 25ae2cb084622f75ab53d5eff385b1c524a27b66 Mon Sep 17 00:00:00 2001
From: "Lisa N. Cao" <20377512+lisancao@users.noreply.github.com>
Date: Sat, 17 Jul 2021 12:46:47 -0700
Subject: [PATCH 4/5] comment out r script lines for debug

---
 .github/workflows/install-checks.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/install-checks.yml b/.github/workflows/install-checks.yml
index e382570..6733931 100644
--- a/.github/workflows/install-checks.yml
+++ b/.github/workflows/install-checks.yml
@@ -31,9 +31,9 @@ jobs:
       with: 
         r-version: ${{ matrix.R }}
     - run: Rscript -e 'install.packages(c("remotes", "swirl"))'
-    - run: Rscript -e 'remotes::install_github("biocswirl-dev-team/BiocSwirl")'
-    - run: Rscript -e 'library(swirl)'
-    - run: Rscript -e 'library(BiocSwirl)'
-    - run: Rscript -e 'list_courses()'
+    #- run: Rscript -e 'remotes::install_github("biocswirl-dev-team/BiocSwirl")'
+    #- run: Rscript -e 'library(swirl)'
+    #- run: Rscript -e 'library(BiocSwirl)'
+   # - run: Rscript -e 'list_courses()'
 
         

From d35723cd6b459c5d27a8615f8e46774590e07359 Mon Sep 17 00:00:00 2001
From: "Lisa N. Cao" <20377512+lisancao@users.noreply.github.com>
Date: Sat, 17 Jul 2021 13:11:47 -0700
Subject: [PATCH 5/5] split install lines - debug

help us see if its all package installs or just remotes
---
 .github/workflows/install-checks.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/install-checks.yml b/.github/workflows/install-checks.yml
index 6733931..e904c93 100644
--- a/.github/workflows/install-checks.yml
+++ b/.github/workflows/install-checks.yml
@@ -30,7 +30,9 @@ jobs:
       uses: r-lib/actions/setup-r@v1
       with: 
         r-version: ${{ matrix.R }}
-    - run: Rscript -e 'install.packages(c("remotes", "swirl"))'
+    - run: Rscript -e 'install.packages("swirl")'
+    - run: Rscript -e 'install.packages("remotes")'
+
     #- run: Rscript -e 'remotes::install_github("biocswirl-dev-team/BiocSwirl")'
     #- run: Rscript -e 'library(swirl)'
     #- run: Rscript -e 'library(BiocSwirl)'