From 6d37e1b7041603b143a0425fb5878a861b9faa40 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Patricie=20Skal=C3=A1kov=C3=A1?=
 <158295213+Patricie34@users.noreply.github.com>
Date: Thu, 1 Aug 2024 10:35:10 +0200
Subject: [PATCH] Update Dockerfile

---
 rdocker/Dockerfile | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/rdocker/Dockerfile b/rdocker/Dockerfile
index c8d09fe..43a69bf 100644
--- a/rdocker/Dockerfile
+++ b/rdocker/Dockerfile
@@ -1,7 +1,7 @@
 # Use the official Ubuntu image as the base
 FROM ubuntu:20.04
 
-# Install system dependencies and R
+# Install system dependencies
 RUN apt-get update && apt-get install -y \
     libcurl4-openssl-dev \
     libxml2-dev \
@@ -12,12 +12,22 @@ RUN apt-get update && apt-get install -y \
     libgmp-dev \
     libgit2-dev \
     gfortran \
-    && apt-get install -y --no-install-recommends r-base \
+    software-properties-common \
     && rm -rf /var/lib/apt/lists/*
 
-# Install R packages from CRAN and Bioconductor
-RUN R -e "install.packages(c('ggplot2', 'scales', 'gtable', 'grid'), repos='http://cran.rstudio.com/')" \
-    && R -e "if (!require('BiocManager', quietly = TRUE)) install.packages('BiocManager'); BiocManager::install('DNAcopy', update = TRUE, ask = FALSE)"
+# Add CRAN repository and install R base version 4.4.0
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 \
+    && add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends r-base=4.4.0-1.2004.0 \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install R packages from CRAN
+RUN R -e "install.packages(c('ggplot2', 'scales', 'gtable', 'grid'), repos='http://cran.rstudio.com/')"
+
+# Install Bioconductor and DNAcopy package
+RUN R -e "install.packages('BiocManager', repos='http://cran.rstudio.com/')" \
+    && R -e "BiocManager::install('DNAcopy', update = TRUE, ask = FALSE)"
 
 # Set the working directory (optional)
 WORKDIR /app