Vcf sanity check

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

@@ -0,0 +1,139 @@
+name: Build & Push Docker image on package version change
+
+on:
+  push:
+    branches: [ main, vcf_sanity_check ]
+    paths:
+      - .github/workflows/dockerhub-on-version.yml
+      - Dockerfile
+      - DESCRIPTION
+  workflow_dispatch:
+
+concurrency:
+  group: docker-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  IMAGE: docker.io/breedinginsight/bigapp
+  IMAGE_DEPS: docker.io/breedinginsight/bigapp-deps
+  DEPS_TAG: r4.5-bioc3.21-2025-08
+
+jobs:
+  check-version:
+    runs-on: ubuntu-latest
+    outputs:
+      changed: ${{ steps.ver.outputs.changed }}
+      version: ${{ steps.ver.outputs.version }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - id: ver
+        shell: bash
+        run: |
+          set -euo pipefail
+          cur_ver=$(sed -n 's/^Version:[[:space:]]*//p' DESCRIPTION | tr -d '[:space:]')
+          prev_sha="${{ github.event.before }}"
+          if git show "${prev_sha}:DESCRIPTION" >/dev/null 2>&1; then
+            prev_ver=$(git show "${prev_sha}:DESCRIPTION" | sed -n 's/^Version:[[:space:]]*//p' | tr -d '[:space:]')
+          else
+            prev_ver=""
+          fi
+          changed=false
+          if [[ -z "${prev_ver}" || "${cur_ver}" != "${prev_ver}" ]]; then changed=true; fi
+          echo "version=${cur_ver}" >> "$GITHUB_OUTPUT"
+          echo "changed=${changed}" >> "$GITHUB_OUTPUT"
+
+  build-amd64:
+    needs: check-version
+    if: needs['check-version'].outputs.changed == 'true'
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    steps:
+      - uses: actions/checkout@v4
+      - uses: docker/setup-qemu-action@v3
+      - uses: docker/setup-buildx-action@v3
+      - uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.IMAGE }}
+          tags: |
+            type=raw,value=v${{ needs['check-version'].outputs.version }}-amd64
+            type=raw,value=sha-${{ github.sha }}-amd64
+      - name: Build & push app (amd64)
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: Dockerfile
+          platforms: linux/amd64
+          push: true
+          build-args: |
+            BASE_IMAGE=${{ env.IMAGE_DEPS }}:${{ env.DEPS_TAG }}
+          tags: ${{ steps.meta.outputs.tags }}
+          cache-from: |
+            type=registry,ref=${{ env.IMAGE }}:buildcache-amd64
+          cache-to: type=registry,ref=${{ env.IMAGE }}:buildcache-amd64,mode=max,compression=zstd
+
+  build-arm64:
+    needs: check-version
+    if: needs['check-version'].outputs.changed == 'true' 
+    continue-on-error: true
+    runs-on: ubuntu-latest
+    timeout-minutes: 350
+    steps:
+      - uses: actions/checkout@v4
+      - uses: docker/setup-qemu-action@v3
+      - uses: docker/setup-buildx-action@v3
+      - uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.IMAGE }}
+          tags: |
+            type=raw,value=v${{ needs['check-version'].outputs.version }}-arm64
+            type=raw,value=sha-${{ github.sha }}-arm64
+      - name: Build & push app (arm64)
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: Dockerfile
+          platforms: linux/arm64
+          push: true
+          build-args: |
+            BASE_IMAGE=${{ env.IMAGE_DEPS }}:${{ env.DEPS_TAG }}
+          tags: ${{ steps.meta.outputs.tags }}
+          cache-from: |
+            type=registry,ref=${{ env.IMAGE }}:buildcache-arm64
+          cache-to: type=registry,ref=${{ env.IMAGE }}:buildcache-arm64,mode=max,compression=zstd
+
+  manifest:
+    needs: [check-version, build-amd64, build-arm64]
+    if: >
+      needs['check-version'].outputs.changed == 'true' &&
+      needs['build-amd64'].result == 'success' &&
+      needs['build-arm64'].result == 'success'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+      - name: Create multi-arch manifest
+        env:
+          IMAGE: ${{ env.IMAGE }}
+          PKG_VERSION: ${{ needs['check-version'].outputs.version }}
+        run: |
+          set -euo pipefail
+          docker buildx imagetools create \
+            -t "$IMAGE:v${PKG_VERSION}" \
+            -t "$IMAGE:latest" \
+            "$IMAGE:v${PKG_VERSION}-amd64" \
+            "$IMAGE:v${PKG_VERSION}-arm64"

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BIGapp
 Title: Breeding Insight Genomics Shiny Application
-Version: 1.4.0
+Version: 1.5.1
 Authors@R: 
     c(
               person(c("Alexander", "M."), "Sandercock",
@@ -73,7 +73,6 @@ Imports:
     methods
 Remotes:
     github::jendelman/GWASpoly,
-    github::Breeding-Insight/BIGr,
     bioc::Rsamtools
 Suggests:
     testthat

Dockerfile

@@ -1,47 +1,25 @@
-FROM rocker/r-ver:4.4.2
-RUN apt-get update && apt-get install -y  cmake libz-dev libcurl4-openssl-dev libssl-dev
-RUN R -e 'install.packages("remotes")'
-RUN Rscript -e 'remotes::install_version("adegenet",upgrade="never", version = "2.1.10")'
-RUN Rscript -e 'remotes::install_version("curl",upgrade="never", version = "6.0.1")'
-RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.33")'
-RUN Rscript -e 'remotes::install_version("dplyr",upgrade="never", version = "1.1.4")'
-RUN Rscript -e 'remotes::install_version("vcfR",upgrade="never", version = "1.15.0")'
-RUN Rscript -e 'remotes::install_version("ggplot2",upgrade="never", version = "3.5.1")'
-RUN Rscript -e 'remotes::install_version("tidyr",upgrade="never", version = "1.3.1")'
-RUN Rscript -e 'remotes::install_version("curl",upgrade="never", version = "6.0.1")'
-RUN Rscript -e 'remotes::install_version("shiny",upgrade="never", version = "1.9.1")'
-RUN Rscript -e 'remotes::install_version("config",upgrade="never", version = "0.3.2")'
-RUN Rscript -e 'remotes::install_version("bs4Dash",upgrade="never", version = "2.3.4")'
-RUN Rscript -e 'remotes::install_version("golem",upgrade="never", version = "0.5.1")'
-RUN Rscript -e 'remotes::install_version("purrr",upgrade="never", version = "1.0.2")'
-RUN Rscript -e 'remotes::install_version("markdown",upgrade="never", version = "1.13")'
-RUN Rscript -e 'remotes::install_version("scales",upgrade="never", version = "1.3.0")'
-RUN Rscript -e 'remotes::install_version("plotly",upgrade="never", version = "4.10.4")'
-RUN Rscript -e 'remotes::install_version("shinyWidgets",upgrade="never", version = "0.8.7")'
-RUN Rscript -e 'remotes::install_version("shinyjs",upgrade="never", version = "2.1.0")'
-RUN Rscript -e 'remotes::install_version("shinydisconnect",upgrade="never", version = "0.1.1")'
-RUN Rscript -e 'remotes::install_version("shinyalert",upgrade="never", version = "3.1.0")'
-RUN Rscript -e 'remotes::install_version("stringr",upgrade="never", version = "1.5.1")'
-RUN Rscript -e 'remotes::install_version("updog",upgrade="never", version = "2.1.5")'
-RUN Rscript -e 'remotes::install_version("AGHmatrix",upgrade="never", version = "2.1.4")'
-RUN Rscript -e 'remotes::install_version("factoextra",upgrade="never", version = "1.0.7")'
-RUN Rscript -e 'remotes::install_version("httr",upgrade="never", version = "1.4.7")'
-RUN Rscript -e 'remotes::install_version("future",upgrade="never", version = "1.34.0")'
-RUN Rscript -e 'remotes::install_version("shinycssloaders",upgrade="never", version = "1.1.0")'
-RUN Rscript -e 'remotes::install_version("RColorBrewer",upgrade="never", version = "1.1.3")'
-RUN Rscript -e 'remotes::install_version("tibble",upgrade="never", version = "3.2.1")'
-RUN Rscript -e 'remotes::install_version("rrBLUP",upgrade="never", version = "4.6.3")'
-RUN Rscript -e 'remotes::install_version("MASS",upgrade="never", version = "7.3.60.2")'
-RUN Rscript -e 'remotes::install_version("Matrix",upgrade="never", version = "1.7.0")'
-RUN Rscript -e 'remotes::install_version("matrixcalc",upgrade="never", version = "1.0.6")'
-RUN Rscript -e 'remotes::install_github("Breeding-Insight/BIGr",upgrade="never")'
-RUN Rscript -e 'remotes::install_github("jendelman/GWASpoly",upgrade="never")'
+# 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
+FROM ${BASE_IMAGE}
 
-RUN mkdir /build_zone
-ADD . /build_zone
-WORKDIR /build_zone
-RUN R -e 'remotes::install_local(upgrade="never")'
-RUN rm -rf /build_zone
-EXPOSE 80
-CMD R -e "options('shiny.port'=80,shiny.host='0.0.0.0');BIGapp::run_app()"
+SHELL ["/bin/bash","-eo","pipefail","-c"]
+ENV DEBIAN_FRONTEND=noninteractive TZ=UTC
+ENV MAKEFLAGS="-j2" R_PKG_INSTALL_ARGS="--no-build-vignettes --no-manual"
+
+# App install (only your code changes should rebuild this layer)
+WORKDIR /app
+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'))"
 
+# Runtime
+RUN useradd -m appuser
+USER appuser
+WORKDIR /app
+EXPOSE 80
+HEALTHCHECK --interval=30s --timeout=5s --retries=5 \
+  CMD wget -qO- http://localhost:${PORT:-80}/ || exit 1
+CMD ["R","-q","-e","options(shiny.port=as.integer(Sys.getenv('PORT','80')), shiny.host='0.0.0.0'); BIGapp::run_app()"]

Dockerfile.deps

@@ -0,0 +1,78 @@
+# syntax=docker/dockerfile:1.7
+FROM rocker/r2u:noble
+
+SHELL ["/bin/bash","-eo","pipefail","-c"]
+ENV DEBIAN_FRONTEND=noninteractive TZ=UTC
+# keep compiles gentle for CI/QEMU
+ENV MAKEFLAGS="-j2"
+ENV R_PKG_INSTALL_ARGS="--no-build-vignettes --no-manual"
+
+# System libs (no Bioc via apt to avoid ABI/arch mismatches)
+RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
+    --mount=type=cache,target=/var/lib/apt/lists,sharing=locked \
+    apt-get update && apt-get install -y --no-install-recommends \
+      build-essential gfortran cmake git wget pkg-config \
+      ccache \
+      libhts-dev \
+      libcurl4-gnutls-dev libssl-dev libxml2-dev \
+      libpng-dev libjpeg-dev libfreetype6-dev libfontconfig1-dev \
+      libbz2-dev liblzma-dev zlib1g-dev \
+      r-cran-remotes r-cran-pak r-cran-biocmanager \
+    && rm -rf /var/lib/apt/lists/*
+
+# ccache
+ENV CCACHE_DIR=/root/.cache/ccache
+RUN --mount=type=cache,target=/root/.cache/ccache 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) ----
+ENV CRAN_PKGS="adegenet curl DT dplyr vcfR \
+ggplot2 tidyr shiny config bs4Dash \
+golem purrr markdown scales plotly \
+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
+
+# ---- Bioconductor from source (R 4.5 -> Bioc 3.21) ----
+RUN --mount=type=cache,target=/root/.cache/R/src Rscript - <<'RS'
+options(Ncpus = 2)
+repos <- BiocManager::repositories(version = "3.21")
+options(repos = repos)
+bioc_pkgs <- c("Rsamtools","Biostrings","pwalign","VariantAnnotation")
+for (p in bioc_pkgs) {
+  if (!requireNamespace(p, quietly = TRUE)) {
+    message("Installing Bioconductor (source): ", p)
+    install.packages(p, dependencies = TRUE, type = "source",
+                     INSTALL_opts = c("--no-build-vignettes","--no-manual"))
+  }
+}
+RS
+
+# ---- Fallback for any missing CRAN pkgs (source, sequential) ----
+RUN --mount=type=cache,target=/root/.cache/R/src Rscript - <<'RS'
+pkgs <- strsplit(Sys.getenv("CRAN_PKGS"), " +")[[1]]
+miss <- setdiff(pkgs, rownames(installed.packages()))
+if (length(miss)) {
+  message("Installing remaining CRAN from source: ", paste(miss, collapse=", "))
+  for (p in miss) {
+    install.packages(p, repos="https://cloud.r-project.org", type="source",
+                     INSTALL_opts=c("--no-build-vignettes","--no-manual"))
+  }
+}
+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'))"
+
+# Version snapshot (handy for audits)
+RUN R -q -e "pkgs <- c('adegenet','curl','DT','dplyr','vcfR','ggplot2','tidyr','shiny','config','bs4Dash', \
+                       'golem','purrr','markdown','scales','plotly','shinyWidgets','shinyjs','shinydisconnect','shinyalert', \
+                       'stringr','updog','AGHmatrix','factoextra','httr','future','shinycssloaders','RColorBrewer', \
+                       'tibble','rrBLUP','MASS','Matrix','matrixcalc','BIGr', \
+                       'Rsamtools','VariantAnnotation','Biostrings','pwalign'); \
+                 ip <- installed.packages(); dir.create('/opt/pins', recursive=TRUE, showWarnings=FALSE); \
+                 write.table(data.frame(Package=pkgs, Version=ip[pkgs,'Version']), \
+                             file='/opt/pins/deps_versions.tsv', sep='\t', row.names=FALSE, quote=FALSE)"

R/app_ui.R

@@ -103,8 +103,9 @@ app_ui <- function(request) {
           )
         ),
         left = div(
-          style = "display: flex; align-items: center; height: 100%;",  # Center the version text vertically
-          "v1.4.0 development")
+          style = "display: flex; align-items: center; height: 100%;",  
+          sprintf("v%s", as.character(utils::packageVersion("BIGapp")))
+        )
       ),
       dashboardBody(
         disconnectMessage(), #Adds generic error message for any error if not already accounted for

R/mod_DosageCall.R

@@ -397,13 +397,14 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
 
         error_if_false <- c(
           "VCF_header", "VCF_columns", "unique_FORMAT", 
-          "samples",  "max_markers", "chrom_info", "pos_info", "allele_counts"
+          "samples", "chrom_info", "pos_info", "allele_counts", "VCF_compressed"
         )
 
         error_if_true <- c(
           "duplicated_samples", "duplicated_markers"
         )
-        warning_if_false <- "ref_alt"
+        warning_if_false <- c("ref_alt","max_markers")
+
         checks_result <- vcf_sanity_messages(checks, 
                                              error_if_false, 
                                              error_if_true,