optimize dep installation

scripts/references/Dockerfile

@@ -1,19 +1,31 @@
 FROM rstudio/r-base:4.0-bullseye
 
+# Set working directory
 WORKDIR /usr/local/src/myscripts
 
+# Set environment variable for renv version
 ENV RENV_VERSION 0.14.0
-# RUN rm /etc/apt/apt.conf.d/default
-RUN apt-get update -y && apt-get install -y dpkg-dev zlib1g-dev libssl-dev libffi-dev curl libcurl4-openssl-dev procps
 
+# Update apt-get and install system dependencies
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+    dpkg-dev zlib1g-dev libssl-dev libffi-dev \
+    libcurl4-openssl-dev curl procps && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
-RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
-RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
+# Install R packages including remotes and renv
+RUN R -e "install.packages('remotes', repos = 'https://cloud.r-project.org')" && \
+    R -e "remotes::install_github('rstudio/renv', ref = '${RENV_VERSION}')" || true
+
+# Install synapser with specific version
 RUN R -e "remotes::install_version('synapser', version = '0.11.7', repos = c('http://ran.synapse.org', 'http://cran.fhcrc.org'))"
 
+# Set Python environment variable for R
 ENV PYTHON /usr/local/lib/R/site-library/PythonEmbedInR/bin/python3.6
 
-
+# Copy the local project files into the container
 COPY . .
 
-RUN R -e "renv::restore()"
+# Restore R environment with renv
+RUN R -e "renv::restore()"