From c9007aeb5daa5ccb1d87b19d89b5f55efe39bc1e Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toniher@cau.cat>
Date: Sat, 12 Oct 2024 17:10:05 +0200
Subject: [PATCH] updated Dockerfile for R

---
 docker/Rscript/Dockerfile | 22 ++++++++++++----------
 docker/Rscript/deps.R     |  8 --------
 2 files changed, 12 insertions(+), 18 deletions(-)
 delete mode 100644 docker/Rscript/deps.R

diff --git a/docker/Rscript/Dockerfile b/docker/Rscript/Dockerfile
index 0ca646c..206bf74 100644
--- a/docker/Rscript/Dockerfile
+++ b/docker/Rscript/Dockerfile
@@ -1,16 +1,18 @@
-FROM rocker/r-ver:4
+FROM rocker/r-ver:4.4.1
 
 RUN apt-get -y update && apt-get install -y libnlopt-dev zlib1g-dev \
   libzmq3-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev \
-  libtiff5-dev libjpeg-dev build-essential libcurl4-openssl-dev libxml2-dev \ 
-  libssl-dev libfontconfig1-dev \
+  libtiff5-dev libjpeg-dev build-essential libcurl4-gnutls-dev libxml2-dev \ 
+  libssl-dev libfontconfig1-dev cmake \
   && rm -rf /var/lib/apt/lists/*
 
-RUN install2.r --error devtools 
-COPY deps.R /tmp
-RUN Rscript /tmp/deps.R > /tmp/deps.log
-RUN install2.r --error igraph ggplot2 nplotr 
-# RUN Rscript -e "install.packages(c('pbkrtest', 'lme4', 'pbkrtest', 'lme4'), repos='http://cran.us.r-project.org');"
-# RUN Rscript -e "install.packages(c('ggpubr', 'cowplot', 'rshape2'), repos='http://cran.us.r-project.org');"
-# devtools::install_github('nathan-russell/hashmap')
+ARG REPO=http://cran.us.r-project.org
 
+RUN install2.r -s -e -r ${REPO} remotes
+RUN Rscript -e "remotes::install_github('nathan-russell/hashmap')"
+RUN install2.r -s -e -r ${REPO} igraph ggplot2
+RUN install2.r -s -e -r ${REPO} pbkrtest lme4 pbkrtest lme4
+RUN install2.r -s -e -r ${REPO} ggpubr cowplot reshape2 nloptr
+
+RUN rm -rf /tmp/downloaded_packages \
+  && strip /usr/local/lib/R/site-library/*/libs/*.so
diff --git a/docker/Rscript/deps.R b/docker/Rscript/deps.R
deleted file mode 100644
index c6fd5d7..0000000
--- a/docker/Rscript/deps.R
+++ /dev/null
@@ -1,8 +0,0 @@
-# install.packages('devtools', dependencies=TRUE, repos='cran.rstudio.com/');
-# require(devtools)
-# install.packages(c('igraph'), repos='http://cran.us.r-project.org');
-# install.packages(c('ggplot2'), repos='http://cran.us.r-project.org');
-# install.packages(c('nloptr'), repos='http://cran.us.r-project.org');
-# install.packages(c('pbkrtest', 'lme4', 'pbkrtest', 'lme4'), repos='http://cran.us.r-project.org');
-# install.packages(c('ggpubr', 'cowplot', 'rshape2'), repos='http://cran.us.r-project.org');
-devtools::install_github('nathan-russell/hashmap')