Merge pull request #113 from ecohealthalliance/update/dependencies-renv

adding system dependencies

.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:

dependencies.Rmd

@@ -14,6 +14,9 @@ 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
+
 -   R package installation can be especially tricky on Mac computers with [Apple Silicon](https://support.apple.com/en-us/HT211814). Below are some steps to get 
     package install set ups.
 
@@ -40,4 +43,5 @@ FLIBS = -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/13
                          configure.args = "--with-udunits2-lib=/opt/homebrew/Cellar/udunits/2.2.28/lib --with-udunits2-include=/opt/homebrew/Cellar/udunits/2.2.28/include")`
 
 
+##
 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 These systems have been superceded by `renv`.

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