Update Dockerfile

Dockerfile

@@ -1,34 +1,62 @@
-# Use the Miniconda3 base image
-FROM continuumio/miniconda3
+# Use the R base image
+FROM rocker/r-base:latest
 
-# Set the working directory to /code
+# Switch to /code as our working directory
 WORKDIR /code
 
-# Install system dependencies
+# ------------------------------------------------------------------------------
+# 1) Install system dependencies + Miniconda
+# ------------------------------------------------------------------------------
 RUN apt-get update -y && \
     apt-get install -y --no-install-recommends \
         wget \
         bzip2 \
     && rm -rf /var/lib/apt/lists/*
 
-# Install R using conda
-RUN conda install -y r-base && \
-    conda clean -afy
-
-# Install required R packages from CRAN
-RUN Rscript -e "install.packages(c('shiny', 'dplyr', 'parallel', 'ggplot2', 'readr', 'ggExtra', 'DT', 'shinydashboard', 'reticulate', 'remotes'), repos='https://cloud.r-project.org/')"
+# Install Miniconda to /opt/conda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh \
+    && /bin/bash /tmp/miniconda.sh -b -p /opt/conda \
+    && rm /tmp/miniconda.sh \
+    && /opt/conda/bin/conda clean -afy
+
+# Make sure conda is on PATH
+ENV PATH=/opt/conda/bin:$PATH
+
+# ------------------------------------------------------------------------------
+# 2) Install required R packages
+#    (We add reticulate + a few extras such as DT and shinydashboard
+#     since your app uses them.)
+# ------------------------------------------------------------------------------
+RUN install2.r --error \
+    shiny \
+    dplyr \
+    ggplot2 \
+    readr \
+    ggExtra \
+    DT \
+    parallel \
+    shinydashboard \
+    reticulate \
+    remotes
+
+# ------------------------------------------------------------------------------
+# 3) Copy your local code (including app.R and CODEBASE) into the container
+# ------------------------------------------------------------------------------
+COPY . .
 
-# Install the fastrerandomize package from GitHub
+# If your fastrerandomize package is on GitHub and not installed yet,
+# uncomment and adjust the GitHub URL as appropriate:
 RUN Rscript -e "remotes::install_github('cjerzak/fastrerandomize-software/fastrerandomize')"
 
-# Copy local code into the container
-COPY . .
-
-# Pre-build the conda environment for Python dependencies
+# ------------------------------------------------------------------------------
+# 4) (Optional) Pre-build the conda environment inside the Docker image
+#    by calling your 'build_backend()' function. 
+#    This ensures that JAX/numpy are already installed.
+# ------------------------------------------------------------------------------
 RUN Rscript -e "library(fastrerandomize); fastrerandomize::build_backend(conda='auto')"
 
-# Expose the Shiny app port
+# ------------------------------------------------------------------------------
+# 5) Expose the Shiny port and set default command to run the Shiny app
+# ------------------------------------------------------------------------------
 EXPOSE 7860
-
-# Set the command to run the Shiny app
 CMD ["R", "--quiet", "-e", "shiny::runApp('/code', host='0.0.0.0', port=7860)"]