Further refinements

CONTRIBUTING.md

@@ -75,6 +75,11 @@ To support CI/CD, in terms of reducing setup time, a Docker images has been crea
 
 This image is automatically re-built once a month to contain the latest version of R and its packages. The code to create this images can be found in `misc/docker`.
 
+To build the image locally run the following from the project root directory:
+```
+docker build -f misc/docker/Dockerfile  -t rbmi:latest .
+```
+
 
 ### Reproducibility, Print Tests & Snaps
 

misc/docker/Dockerfile

@@ -42,8 +42,8 @@ RUN apt-get update -y --fix-missing && \
     apt-get upgrade -y && \
     apt-get install -y $REQD_PKGS
 
-ADD install_packages.R /
-ADD ../../DESCRIPTION /
+ADD misc/docker/install_packages.R /
+ADD DESCRIPTION /
 
 RUN Rscript  /install_packages.R
 

misc/docker/install_packages.R

@@ -30,13 +30,29 @@ if (!requireNamespace("desc", quietly = TRUE)) {
     install.packages("desc")
 }
 
+
+# Get a list of all packages that we claim we depend on in the DESCRIPTION file
 pkgs <- desc::desc("DESCRIPTION")$get_deps()$package |> unique()
 
 # Add on additional packages that might be needed in the future
 pkgs <- c(pkgs, "tidyverse")
 
+
+# R will error if you try to update the base packages so remove them
+# if they are in any of the imports / suggests / depends list
+base_pkgs <- c(
+    "KernSmooth", "class", "foreign", "methods", "rpart", "survival",
+    "MASS", "cluster", "grDevices", "mgcv", "spatial", "tcltk",
+    "Matrix", "codetools", "graphics", "nlme", "splines", "tools",
+    "base", "compiler", "grid", "nnet", "stats", "translations",
+    "boot", "datasets", "lattice", "parallel", "stats4", "utils",
+    "R"
+)
+pkgs <- pkgs[!pkgs %in% base_pkgs]
+
 install.packages(pkgs, dependencies = TRUE)
 
+# Install cmdstanr (not available from CRAN)
 install.packages(
     "cmdstanr",
     repos = c("https://stan-dev.r-universe.dev", getOption("repos"))