From b7fde2c723ee5006a2f1f0198df682fa20fcf857 Mon Sep 17 00:00:00 2001
From: Collin Schwantes <schwantes@ecohealthalliance.org>
Date: Tue, 9 Jan 2024 12:05:08 -0600
Subject: [PATCH 1/2] adding system dependencies

---
 .github/workflows/bookdown_action.yml | 4 ++++
 sys_deps/sys_deps.sh                  | 9 +++++++++
 2 files changed, 13 insertions(+)
 create mode 100644 sys_deps/sys_deps.sh

diff --git a/.github/workflows/bookdown_action.yml b/.github/workflows/bookdown_action.yml
index 0ee28fc..483aabc 100644
--- a/.github/workflows/bookdown_action.yml
+++ b/.github/workflows/bookdown_action.yml
@@ -31,6 +31,10 @@ jobs:
       - name: Install libgit2
         run: sudo apt install libgit2-dev
         
+      - name: Install system dependencies
+        run: |
+          sh sys_deps/sys_deps.sh
+        
       - name: Cache bookdown results
         uses: actions/cache@v2
         with:
diff --git a/sys_deps/sys_deps.sh b/sys_deps/sys_deps.sh
new file mode 100644
index 0000000..2cacd21
--- /dev/null
+++ b/sys_deps/sys_deps.sh
@@ -0,0 +1,9 @@
+apt-get update && apt-get install -y --no-install-recommends \
+          libcurl4-openssl-dev \
+          libssl-dev \
+          git-crypt \
+          libudunits2-dev \
+          libgdal-dev \
+          libgeos-dev \
+          libproj-dev \
+          libglpk-dev
\ No newline at end of file

From bf61279611089edf75882f2817e9de24d833fb81 Mon Sep 17 00:00:00 2001
From: Collin Schwantes <schwantes@ecohealthalliance.org>
Date: Tue, 9 Jan 2024 12:09:29 -0600
Subject: [PATCH 2/2] added section on gcc

---
 dependencies.Rmd | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/dependencies.Rmd b/dependencies.Rmd
index 07bb1c2..5046363 100644
--- a/dependencies.Rmd
+++ b/dependencies.Rmd
@@ -14,5 +14,17 @@ project](http://ropenscilabs.github.io/r-docker-tutorial/)
 
 -   R packages can be a useful project output. We have some in-house R packages to provide access to internal data and generate reports, and may be developing more for external audiences. Hadley Wickham's [R Packages Book](http://r-pkgs.had.co.nz/) provides guidance for these, and we expect our packages to be up to [rOpenSci standards](https://github.com/ropensci/onboarding).
 
+##  GCC and mac silicon
 
+For some reason mac computers with mac silicon (e.g. M2 chip) have issues with 
+c compilers. Use the following to ensure your mac knows which c compiler to use.
+
+```
+CXX14FLAGS += -O3 -arch arm64 -ftemplate-depth-256
+FC = /opt/homebrew/Cellar/gcc/13.2.0/bin/gfortran
+F77 = /opt/homebrew/Cellar/gcc/13.2.0/bin/gfortran
+FLIBS = -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/13
+```
+
+##
 Historically some projects used [Packrat](https://rstudio.github.io/packrat/) or [checkpoint](https://CRAN.R-project.org/package=checkpoint) to fix R package versions. These systems have been superceded by `renv`.
\ No newline at end of file