Fix broken docker build (#427)

Closes #410
insightsengineering · Sep 26, 2024 · 25e71ba · 25e71ba
1 parent 84df256
commit 25e71ba
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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/.github/workflows/check_for_cran.yaml b/.github/workflows/check_for_cran.yaml
diff --git a/.github/workflows/on_biweekly.yaml b/.github/workflows/on_biweekly.yaml
@@ -13,8 +13,6 @@ jobs:
       fail-fast: true
       matrix:
        config:
-        # - { image: "ghcr.io/${{ github.repository_owner }}/rbmi:r404"}
-        # - { image: "ghcr.io/${{ github.repository_owner }}/rbmi:r410"}
          - { image: "ghcr.io/${{ github.repository_owner }}/rbmi:latest"}
 
     runs-on: ubuntu-latest

diff --git a/.github/workflows/on_pr_main.yaml b/.github/workflows/on_pr_main.yaml
@@ -12,13 +12,10 @@ name: On Pull Request
 jobs:
 
   rcmdcheck:
-
     strategy:
       fail-fast: true
       matrix:
        config:
-        # - { image: "ghcr.io/${{ github.repository_owner }}/rbmi:r404"}
-        # - { image: "ghcr.io/${{ github.repository_owner }}/rbmi:r410"}
         - { image: "ghcr.io/${{ github.repository_owner }}/rbmi:latest"}
     runs-on: ubuntu-latest
     container:
@@ -44,8 +41,6 @@ jobs:
       fail-fast: true
       matrix:
        config:
-        # - { image: "ghcr.io/${{ github.repository_owner }}/rbmi:r404"}
-        # - { image: "ghcr.io/${{ github.repository_owner }}/rbmi:r410"}
         - { image: "ghcr.io/${{ github.repository_owner }}/rbmi:latest"}
     runs-on: ubuntu-latest
     container:

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -60,24 +60,20 @@ test_that("some unit test", {
 
 The scheduled tests can also be manually activated by going to "https://github.com/insightsengineering/rbmi" -> "Actions" -> "Bi-Weekly" -> "Run Workflow". It is advisable to do this before releasing to CRAN.
 
-### CRAN Releases
-
-In order to release a package to CRAN it needs to be tested across multiple different OS's and versions of R. This has been implemented in this project via a GitHub Action Workflow titled "Check for CRAN" which needs to be manually activated. To do this go to "https://github.com/insightsengineering/rbmi" -> "Actions" -> "Check for CRAN" -> "Run Workflow".
-
-If all these tests pass then the package can be safely released to CRAN (after updating the relevant `cran-comments.md` file)
 
 
 ### Docker Images
 
-To support CI/CD in terms of reducing installation time, several Docker images have been pre-built which contain all the packages and system dependencies that this project needs. The current relevant images can be found at:
+To support CI/CD, in terms of reducing setup time, a Docker images has been created which contains all the packages and system dependencies required for this project. The image can be found at:
 
-- ghcr.io/insightsengineering/rbmi:r404
-- ghcr.io/insightsengineering/rbmi:r410
 - ghcr.io/insightsengineering/rbmi:latest
 
-The `latest` image is automatically re-built once a month to contain the latest version of R and its packages. The other versions are built with older versions of R (as indicated by the tag number) and contain package versions as they were when that version of R was released. This is important to ensure that the package works with older versions of R which many companies typically run due to delays in their validation processes.
+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`.
 
-The code to create these images can be found in `misc/docker`. The legacy images (i.e. everything excluding the "latest" image) are only built on manual request by running the corresponding GitHub Actions Workflow. 
+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

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 \
@@ -39,13 +35,15 @@ ENV REQD_PKGS="\
     qpdf \
     devscripts \
     cmake \
+    libpq-dev \
     "
 
 RUN apt-get update -y --fix-missing && \
     apt-get upgrade -y && \
     apt-get install -y $REQD_PKGS
 
-ADD install_packages.R /
+ADD misc/docker/install_packages.R /
+ADD DESCRIPTION /
 
 RUN Rscript  /install_packages.R
 

diff --git a/misc/docker/install_packages.R b/misc/docker/install_packages.R
@@ -1,41 +1,59 @@
 
 
+# Determine which OS we are on
+# Rocker images are Ubuntu based so should be jammy / focal / etc
+OS_CODENAME <- system(
+    'cat /etc/os-release | grep "VERSION_CODENAME" | sed -e "s/VERSION_CODENAME=//"',
+    intern = TRUE
+)
+
+# Configure PPM URL for binary package installation
+CRANURL <- sprintf(
+    "https://packagemanager.posit.co/cran/__linux__/%s/latest",
+    OS_CODENAME
+)
 
+# Configure useragent to enable binary package installation from PPM
+options(
+    "repos" = list("CRAN" = CRANURL),
+    "HTTPUserAgent" = sprintf(
+        "R/%s R (%s)",
+        getRversion(),
+        paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"])
+    )
+)
+
+# Throw errors if any warnings arise
 options(warn = 2)
 
-install.packages("remotes", repos = Sys.getenv("CRANURL"))
-
-# 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)
+if (!requireNamespace("desc", quietly = TRUE)) {
+    install.packages("desc")
 }
 
-pkgs <- c(
-    "tidyverse",
-    "glmmTMB",
-    "mvtnorm",
-    "devtools",
-    "rstan",
-    "rstantools",
-    "RcppParallel",
-    "Rcpp",
-    "R6",
-    "assertthat",
-    "emmeans",
-    "covr",
-    "testthat",
-    "nlme",
-    "roxygen2",
-    "tinytex",
-    "bookdown",
-    "RhpcBLASctl",
-    "R.rsp"
+
+# 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", "devtools")
+
+
+# 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, repos = Sys.getenv("CRANURL"), dependencies = TRUE)
+install.packages(pkgs, dependencies = TRUE)
+
+# Install cmdstanr (not available from CRAN)
+install.packages(
+    "cmdstanr",
+    repos = c("https://stan-dev.r-universe.dev", getOption("repos"))
+)