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insightsengineering · Sep 26, 2024 · 8dc5fc9 · 8dc5fc9
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commit 8dc5fc9
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Showing 4 changed files with 39 additions and 124 deletions.
diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
@@ -1,9 +1,11 @@
-name: Build fixed version Docker images
+name: Build latest version Docker images
 
 env:
   REGISTRY: ghcr.io
 
 on:
+  schedule:
+    - cron: '0 5 1 * *'
   workflow_dispatch:
 
 
@@ -18,16 +20,7 @@ jobs:
       matrix:
         config:
           - {
-              src_image: "rocker/r-ver:4.0.4", 
-              cran_url: "https://packagemanager.rstudio.com/cran/2021-04-20",
-              tag: "rbmi:r404",
-              mmrm_version : "v0.1.5"
-            }
-          - {
-              src_image: "rocker/r-ver:4.1.0", 
-              cran_url: "https://packagemanager.rstudio.com/cran/2021-08-04",
-              tag: "rbmi:r410",
-              mmrm_version : "v0.1.5"
+              tag: "rbmi:latest"
             }
 
     # Token permissions
@@ -37,8 +30,8 @@ jobs:
 
     # Build steps
     steps:
-      - name: Checkout repository 
-        uses: actions/checkout@v3
+      - name: Check out the repo
+        uses: actions/checkout@v4
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
@@ -64,9 +57,6 @@ jobs:
         run: |
           echo push = ${{ github.event_name == 'push' }}
           echo tag = ${{ env.REGISTRY }}/${{ github.repository_owner }}/${{ matrix.config.tag }}
-          echo IMAGE=${{ matrix.config.src_image }}
-          echo CRANURL=${{ matrix.config.cran_url }}
-          echo MMRM_VERSION=${{ matrix.config.mmrm_version }}
 
       - name: Build and push image 
         uses: docker/build-push-action@v3
@@ -75,9 +65,6 @@ jobs:
           push: true
           tags: ${{ env.REGISTRY }}/${{ github.repository_owner }}/${{ matrix.config.tag }}
           build-args: |
-            IMAGE=${{ matrix.config.src_image }}
-            CRANURL=${{ matrix.config.cran_url }}
-            MMRM_VERSION=${{ matrix.config.mmrm_version }}
           cache-from: type=local,src=/tmp/.buildx-cache
           cache-to: type=local,dest=/tmp/.buildx-cache-new
 

diff --git a/.github/workflows/build_docker_latest.yaml b/.github/workflows/build_docker_latest.yaml
diff --git a/misc/docker/Dockerfile b/misc/docker/Dockerfile
@@ -1,9 +1,5 @@
-ARG IMAGE
 
-FROM ${IMAGE}
-
-ARG CRANURL
-ARG MMRM_VERSION
+FROM rocker/r-ver:latest
 
 ENV REQD_PKGS="\
     libicu-dev \

diff --git a/misc/docker/install_packages.R b/misc/docker/install_packages.R
@@ -1,32 +1,42 @@
 
 
+OS_CODENAME <- system(
+    'cat /etc/os-release | grep "VERSION_CODENAME" | sed -e "s/VERSION_CODENAME=//"',
+    intern = TRUE
+)
 
-options(warn = 2)
+CRANURL <- sprintf(
+    "https://packagemanager.posit.co/cran/__linux__/%s/latest",
+    OS_CODENAME
+)
 
-install.packages("remotes", repos = Sys.getenv("CRANURL"))
+options(
+    "repos" = list("CRAN" = CRANURL),
+    "HTTPUserAgent" = sprintf(
+        "R/%s R (%s)",
+        getRversion(),
+        paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"])
+    )
+)
 
-# mmrm wasn't available when in-house servers locked their package versions
-# and instead had v0.13 of mmrm patched in after the fact
-# here we allow the build to specify "latest" to grab the latest version of mmrm
-# or a specific named version from github
-mmrm_version <- Sys.getenv("MMRM_VERSION")
-if (mmrm_version == "latest") {
-    install.packages("mmrm", repos = Sys.getenv("CRANURL"), dependencies = TRUE)
-} else {
-    remotes::install_git("https://github.com/openpharma/mmrm.git", ref = mmrm_version, upgrade = FALSE)
-}
+options(warn = 2)
 
 pkgs <- c(
-    "tidyverse",
-    "glmmTMB",
+    "dplyr",
+    "purrr",
+    "tibble",
+    "lubridate",
+    "purrr",
     "mvtnorm",
     "devtools",
     "rstan",
     "rstantools",
     "RcppParallel",
     "Rcpp",
+    "knitr",
     "R6",
     "assertthat",
+    "rmarkdown",
     "emmeans",
     "covr",
     "testthat",
@@ -38,4 +48,11 @@ pkgs <- c(
     "R.rsp"
 )
 
-install.packages(pkgs, repos = Sys.getenv("CRANURL"), dependencies = TRUE)
+install.packages(pkgs, dependencies = TRUE)
+
+install.packages(
+    "cmdstanr",
+    repos = c("https://stan-dev.r-universe.dev", getOption("repos"))
+)
+
+cmdstanr::install_cmdstan(cores = 2)