From 958bd51d8070435c73a840d08a70631d03393425 Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Tue, 15 Oct 2024 15:55:48 -0400
Subject: [PATCH 1/5] CI: Update build versions

Remove deprecated actions, build on supported ubuntu
---
 .github/workflows/R-CMD-check.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 22c64ab66c..961bf2c0aa 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -20,20 +20,20 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -73,7 +73,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

From 43efad9d930c1635900e035036dfb997c277b7fc Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Fri, 18 Oct 2024 10:16:02 -0400
Subject: [PATCH 2/5] CI: See if we can do without rhub on modern Ubuntu

---
 .github/workflows/R-CMD-check.yaml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 961bf2c0aa..4dd89e90ff 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -54,10 +54,6 @@ jobs:
         if: runner.os == 'Linux'
         env:
           RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
 
       - name: Install dependencies
         run: |

From 2c672295522b80192ede52bfa90a08422fc92318 Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Sat, 19 Oct 2024 15:57:09 -0400
Subject: [PATCH 3/5] CI: workflow dispatch

---
 .github/workflows/R-CMD-check.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 4dd89e90ff..467176b845 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -5,6 +5,7 @@ on:
   pull_request:
     branches:
       - master
+  workflow_dispatch:
 
 name: R-CMD-check
 

From 872eccd53da4b9ba9f88babbae193ed3044a3abe Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Sat, 19 Oct 2024 16:02:20 -0400
Subject: [PATCH 4/5] CI: linux setup

---
 .github/workflows/R-CMD-check.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 467176b845..a9e4813b01 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -53,6 +53,9 @@ jobs:
 
       - name: Install system dependencies
         if: runner.os == 'Linux'
+        run: |
+          # Add the appropriate commands to install system dependencies here
+          echo "Linux setup"
         env:
           RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
 

From d1254507b565f4397ee4efefbb4f8b86dc0a887b Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Sun, 20 Oct 2024 17:36:48 -0400
Subject: [PATCH 5/5] COMP: Update Windows to c++17

---
 configure.win | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configure.win b/configure.win
index a1398504ef..e4cf9874bb 100755
--- a/configure.win
+++ b/configure.win
@@ -1,5 +1,5 @@
 #!/bin/bash
-CXX_STD=CXX14
+CXX_STD=CXX17
 CC=`${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD config CC`
 CXX=`${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD config CXX`
 JTHREADS=1