From 22a4d36e57955e2c7770e4aaa587ee41387a39c1 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>
Date: Wed, 30 Mar 2022 17:19:14 +0200
Subject: [PATCH] First commit.

---
 Dockerfile | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
 README.md  |  3 +++
 2 files changed, 53 insertions(+)
 create mode 100644 Dockerfile
 create mode 100644 README.md

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..49fea3c
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,50 @@
+FROM rocker/r-ver:4.1.3
+
+LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
+      org.opencontainers.image.source="https://github.com/rocker-org/rocker-versioned2" \
+      org.opencontainers.image.vendor="Rocker Project" \
+      org.opencontainers.image.authors="Carl Boettiger <cboettig@ropensci.org>"
+
+# Some R dependencies
+RUN apt-get update && apt-get install -y \
+    libxml2 \
+    git \
+    gdal-bin \
+    netcdf-bin \
+    sshpass \
+    p7zip-full \
+    sox \
+    imagemagick \
+    proj-bin \
+    proj-data \
+    libgsl23 \
+    postgresql-server-dev-all \
+    libsecret-1-0
+
+# Install the R packages we need, using the binary distribution
+# at https://packagemanager.rstudio.com/client/#/repos/1/overview
+ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/install2r-packages.txt /tmp
+RUN for f in `cat /tmp/install2r-packages.txt` ; do install2.r --error --skipinstalled --ncpus -1 $f ; done
+
+# Non CRAN repositories
+ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_non_cran_pkgs.txt /tmp
+RUN for l in `cat /tmp/r_non_cran_pkgs.txt` ; do \
+    pkg=`echo $l | cut -d : -f 1` ; \
+    mirror=`echo $l | cut -d : -f 2-` ; \
+    Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
+    -e "install.packages(pkgs='$pkg', repos=c('$mirror/'));" ; done
+
+# From github
+ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_github_pkgs.txt /tmp
+RUN mkdir -p /etc/R
+RUN echo "GITHUB_PAT=$GITHUB_PAT" >> /etc/R/Renviron.site
+#RUN for g in `cat /tmp/r_github_pkgs.txt` ; do \
+#    Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
+#    -e " require(devtools); devtools::install_github('$g')" ; done
+#RUN for g in `cat /tmp/r_github_pkgs.txt` ; do installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest $g ; done
+#RUN grep -v "GITHUB_PATH" /etc/R/Renviron.site > /etc/R/Renviron.site.1
+#RUN mv -f /etc/R/Renviron.site.1 /etc/R/Renviron.site
+RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest DanOvando/sraplus
+
+# Ensure that we remove the source packages
+RUN rm -fr /tmp/downloaded_packages/*
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..d7872e9
--- /dev/null
+++ b/README.md
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+# R image with plenty of packages installed
+
+The image starts from `rocker/r-ver:4.1.3` and installs a (long) list of R packages commonly used in the D4Science environment.