Merge branch 'master' into update/dependencies-renv

dependencies.Rmd

@@ -14,10 +14,19 @@ 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.
+-   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.
+
+1. Install the R compilation tool chain https://mac.thecoatlessprofessor.com/macrtools/. If any issues with FORTRAN, follow instructions for downloading FORTRAN compiler here for Apple silicon Macs: <https://mac.r-project.org/tools/>
+
+2. Install gcc `brew install gcc`. This requires having brew set up. 
+
+3. Make sure homebrew is in terminal path. Add it by `export PATH=$PATH:/opt/homebrew/bin`.
+
+4. Create `~/.R/Makevars` and insert the following. This will need to be updated depending on gcc version. 
 
 ```
 CXX14FLAGS += -O3 -arch arm64 -ftemplate-depth-256
@@ -26,5 +35,13 @@ F77 = /opt/homebrew/Cellar/gcc/13.2.0/bin/gfortran
 FLIBS = -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/13
 ```
 
+5. RStudio may have a bug in accessing the correct terminal path. The workaround is to copy your terminal path (`echo $PATH`) into `.Renviron` per instructions here: <https://community.rstudio.com/t/how-to-get-rstudio-ide-to-use-the-correct-terminal-path-in-mac-os-x/131528/6>
+
+6. Some packages may need additional help for R to find the correct paths. For `units`:
+`remotes::install_version(package = "units", 
+                         version = "0.8-5", 
+                         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 These systems have been superceded by `renv`.