[SAT-218] fix docker build

.github/workflows/dockerhub-on-version.yml

@@ -2,7 +2,7 @@ name: Build & Push Docker image on package version change
 
 on:
   push:
-    branches: [ main, vcf_sanity_check ]
+    branches: [ main, docker_fix ]
     paths:
       - .github/workflows/dockerhub-on-version.yml
       - Dockerfile
@@ -16,7 +16,7 @@ concurrency:
 env:
   IMAGE: docker.io/breedinginsight/bigapp
   IMAGE_DEPS: docker.io/breedinginsight/bigapp-deps
-  DEPS_TAG: r4.5-bioc3.21-2025-08
+  DEPS_TAG: latest
 
 jobs:
   check-version:
@@ -71,6 +71,7 @@ jobs:
           file: Dockerfile
           platforms: linux/amd64
           push: true
+          pull: true
           build-args: |
             BASE_IMAGE=${{ env.IMAGE_DEPS }}:${{ env.DEPS_TAG }}
           tags: ${{ steps.meta.outputs.tags }}
@@ -106,6 +107,7 @@ jobs:
           file: Dockerfile
           platforms: linux/arm64
           push: true
+          pull: true
           build-args: |
             BASE_IMAGE=${{ env.IMAGE_DEPS }}:${{ env.DEPS_TAG }}
           tags: ${{ steps.meta.outputs.tags }}

Dockerfile

@@ -1,6 +1,6 @@
 # syntax=docker/dockerfile:1.7
 # Buildx/Actions will pass BASE_IMAGE as a manifest tag that covers both arches
-ARG BASE_IMAGE=docker.io/breedinginsight/bigapp-deps:r4.5-bioc3.21-2025-08
+ARG BASE_IMAGE=docker.io/breedinginsight/bigapp-deps:latest
 FROM ${BASE_IMAGE}
 
 SHELL ["/bin/bash","-eo","pipefail","-c"]
@@ -13,7 +13,9 @@ COPY DESCRIPTION /app/
 # COPY NAMESPACE /app/  # if present, include for better cache hits
 COPY . /app
 RUN R -q -e "remotes::install_local('.', upgrade='never', dependencies=TRUE, \
-                                    INSTALL_opts=c('--no-build-vignettes','--no-manual'))"
+                                    INSTALL_opts=c('--no-build-vignettes','--no-manual')); \
+             library(BIGapp)" \
+    || (echo 'ERROR: BIGapp or one of its dependencies failed to install' >&2; exit 1)
 
 # Runtime
 RUN useradd -m appuser

inst/Dockerfile.deps

@@ -20,9 +20,10 @@ RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
       r-cran-remotes r-cran-pak r-cran-biocmanager \
     && rm -rf /var/lib/apt/lists/*
 
-# ccache
+# ccache (scoped to this R/Bioc combo so a base-image bump can't reuse stale, ABI-incompatible objects)
+ARG DEPS_TAG=r4.5-bioc3.21-2025-08
 ENV CCACHE_DIR=/root/.cache/ccache
-RUN --mount=type=cache,target=/root/.cache/ccache ccache -M 2G && \
+RUN --mount=type=cache,target=/root/.cache/ccache,id=ccache-${DEPS_TAG} ccache -M 2G && \
     { echo 'CC=ccache gcc'; echo 'CXX=ccache g++'; echo 'FC=ccache gfortran'; } >> /usr/lib/R/etc/Makevars.site
 
 # ---- CRAN via r2u binaries first (fast) ----
@@ -33,12 +34,12 @@ shinyWidgets shinyjs shinydisconnect shinyalert \
 stringr updog AGHmatrix factoextra \
 httr future shinycssloaders RColorBrewer \
 tibble rrBLUP MASS Matrix matrixcalc BIGr"
-RUN install2.r --skipinstalled --ncpus 1 $CRAN_PKGS || true
+RUN install2.r --skipinstalled --ncpus 1 $CRAN_PKGS
 
-# ---- Bioconductor from source (R 4.5 -> Bioc 3.21) ----
-RUN --mount=type=cache,target=/root/.cache/R/src Rscript - <<'RS'
+# ---- Bioconductor from source (version auto-matched to whatever R the base image ships) ----
+RUN --mount=type=cache,target=/root/.cache/R/src,id=rsrc-${DEPS_TAG} Rscript - <<'RS'
 options(Ncpus = 2)
-repos <- BiocManager::repositories(version = "3.21")
+repos <- BiocManager::repositories()
 options(repos = repos)
 bioc_pkgs <- c("Rsamtools","Biostrings","pwalign","VariantAnnotation")
 for (p in bioc_pkgs) {
@@ -47,11 +48,12 @@ for (p in bioc_pkgs) {
     install.packages(p, dependencies = TRUE, type = "source",
                      INSTALL_opts = c("--no-build-vignettes","--no-manual"))
   }
+  library(p, character.only = TRUE)
 }
 RS
 
 # ---- Fallback for any missing CRAN pkgs (source, sequential) ----
-RUN --mount=type=cache,target=/root/.cache/R/src Rscript - <<'RS'
+RUN --mount=type=cache,target=/root/.cache/R/src,id=rsrc-${DEPS_TAG} Rscript - <<'RS'
 pkgs <- strsplit(Sys.getenv("CRAN_PKGS"), " +")[[1]]
 miss <- setdiff(pkgs, rownames(installed.packages()))
 if (length(miss)) {
@@ -61,11 +63,14 @@ if (length(miss)) {
                      INSTALL_opts=c("--no-build-vignettes","--no-manual"))
   }
 }
+# Hard-fail the build if any package is installed but fails to actually load (e.g. ABI mismatch)
+for (p in pkgs) library(p, character.only = TRUE)
 RS
 
 # ---- GitHub dep (pak-free to avoid QEMU helper issues) ----
 RUN R -q -e "remotes::install_github('jendelman/GWASpoly', upgrade='never', dependencies=TRUE, \
-                                     INSTALL_opts=c('--no-build-vignettes','--no-manual'))"
+                                     INSTALL_opts=c('--no-build-vignettes','--no-manual')); \
+             library(GWASpoly)"
 
 # Version snapshot (handy for audits)
 RUN R -q -e "pkgs <- c('adegenet','curl','DT','dplyr','vcfR','ggplot2','tidyr','shiny','config','bs4Dash', \

inst/update_dep_image.sh

@@ -1,3 +1,6 @@
+#!/bin/bash
+set -euo pipefail
+
 # The arm64 image is too large to load with Github actions
 # So we build and push locally with the following commands
 
@@ -6,27 +9,42 @@
 
 # Make sure to login with BI user
 IMAGE_DEPS=docker.io/breedinginsight/bigapp-deps
-DEPS_TAG=r4.5-bioc3.21-2025-08 # Update version here
+BUILD_ID=build-$(date +%s) # throwaway tag used only to inspect the freshly built image
 
-# amd64 (load locally instead of pushing)
+# amd64 (load locally so we can inspect it before deciding the real tag)
 docker buildx build \
   -f Dockerfile.deps \
   --platform linux/amd64 \
-  -t $IMAGE_DEPS:$DEPS_TAG-amd64 \
+  -t $IMAGE_DEPS:$BUILD_ID-amd64 \
   --progress=plain \
   --load \
   .
 
+# Derive DEPS_TAG from what's actually inside the image (R version, Bioc version, build date)
+# instead of hardcoding it, so the tag can never drift from reality.
+R_VER=$(docker run --rm $IMAGE_DEPS:$BUILD_ID-amd64 Rscript -e 'cat(R.version$major, sub("\\..*", "", R.version$minor), sep=".")')
+BIOC_VER=$(docker run --rm $IMAGE_DEPS:$BUILD_ID-amd64 Rscript -e 'cat(as.character(BiocManager::version()))')
+DEPS_TAG="r${R_VER}-bioc${BIOC_VER}-$(date +%Y-%m)"
+echo "Resolved DEPS_TAG=$DEPS_TAG"
+
+docker tag $IMAGE_DEPS:$BUILD_ID-amd64 $IMAGE_DEPS:$DEPS_TAG-amd64
+docker rmi $IMAGE_DEPS:$BUILD_ID-amd64
+docker push $IMAGE_DEPS:$DEPS_TAG-amd64
+
 # arm64 (push or save to a tar; cannot load multi-arch to local daemon)
 docker buildx build \
   -f Dockerfile.deps \
   --platform linux/arm64 \
+  --build-arg DEPS_TAG=$DEPS_TAG \
   -t $IMAGE_DEPS:$DEPS_TAG-arm64 \
   --progress=plain \
   --push \
   .
-  
+
 docker buildx imagetools create \
   -t $IMAGE_DEPS:$DEPS_TAG \
+  -t $IMAGE_DEPS:latest \
   $IMAGE_DEPS:$DEPS_TAG-amd64 \
-  $IMAGE_DEPS:$DEPS_TAG-arm64
+  $IMAGE_DEPS:$DEPS_TAG-arm64
+
+echo "Pushed $IMAGE_DEPS:$DEPS_TAG and $IMAGE_DEPS:latest"