Update Dockerfile

Dockerfile

@@ -1,14 +1,78 @@
-FROM rocker/r-base:latest
-
+# syntax=docker/dockerfile:1
+FROM rocker/r2u:22.04
 WORKDIR /code
 
-RUN install2.r --error \
-    shiny \
-    dplyr \
-    ggplot2 \
-    readr \
-    ggExtra
-    
+ARG DEBIAN_FRONTEND=noninteractive
+
+# ------------------------------------------------------------------------------
+# System deps
+# ------------------------------------------------------------------------------
+RUN apt-get update -y && apt-get install -y --no-install-recommends \
+    wget bzip2 git unzip ca-certificates locales tzdata \
+    build-essential gfortran \
+    libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev \
+    libopenblas-dev liblapack-dev \
+    libjpeg-dev libpng-dev libtiff5-dev \
+  && rm -rf /var/lib/apt/lists/*
+
+ENV LC_ALL=C.UTF-8 LANG=C.UTF-8 HF_HUB_DISABLE_TELEMETRY=1 PIP_NO_CACHE_DIR=1
+
+# ------------------------------------------------------------------------------
+# Fast-install R packages via Debian, when available
+# ------------------------------------------------------------------------------
+ARG APT_R_PKGS="\
+  r-cran-shiny r-cran-dplyr r-cran-ggplot2 r-cran-readr r-cran-ggextra \
+  r-cran-dt r-cran-shinydashboard r-cran-reticulate \
+  r-cran-remotes r-cran-data.table r-cran-stringdist r-cran-fastmatch \
+  r-cran-stringr r-cran-rfast r-cran-foreach r-cran-doparallel r-cran-digest \
+  r-cran-scales r-cran-tidyr"
+RUN set -eux; \
+    apt-get update -y; \
+    for pkg in $APT_R_PKGS; do \
+      if apt-cache show "$pkg" >/dev/null 2>&1; then \
+        echo "Installing $pkg via apt ..."; \
+        if ! apt-get install -y --no-install-recommends "$pkg"; then \
+          echo "WARN: apt install failed for $pkg; will try R fallback."; \
+        fi; \
+      else \
+        echo "INFO: $pkg not found in apt; will try R fallback."; \
+      fi; \
+    done; \
+    rm -rf /var/lib/apt/lists/*
+
+# ------------------------------------------------------------------------------
+# R fallback (pak) for anything missing
+# ------------------------------------------------------------------------------
+RUN Rscript - <<'RSCRIPT'
+options(Ncpus = parallel::detectCores())
+cran <- "https://cloud.r-project.org"
+
+req <- c(
+  "shiny","dplyr","ggplot2","readr","ggExtra","DT","shinydashboard",
+  "reticulate","remotes","data.table","stringdist","fastmatch",
+  "stringr","Rfast","foreach","doParallel","digest",
+  # app-specific
+  "bslib","shinyWidgets","bsplus","magrittr","tidyr","scales","shinycssloaders"
+)
+installed <- rownames(installed.packages())
+need <- setdiff(req, installed)
+
+if (length(need)) {
+  if (!requireNamespace("pak", quietly = TRUE)) {
+    install.packages("pak", repos = "https://r-lib.github.io/p/pak/stable")
+  }
+  ok <- tryCatch({ pak::pak(need); TRUE }, error = function(e) FALSE)
+  if (!ok) install.packages(need, repos = cran)
+}
+RSCRIPT
+
+# ------------------------------------------------------------------------------
+# App code + data
+# ------------------------------------------------------------------------------
 COPY . .
 
-CMD ["R", "--quiet", "-e", "shiny::runApp(host='0.0.0.0', port=7860)"]
+# ------------------------------------------------------------------------------
+# Shiny entry point (honor $PORT; default 7860)
+# ------------------------------------------------------------------------------
+EXPOSE 7860
+CMD ["R", "--quiet", "-e", "port <- as.integer(Sys.getenv('PORT', '7860')); shiny::runApp('/code', host='0.0.0.0', port=port)"]