deb dependencies. Fix GITHUB_PAT.

Dockerfile

@@ -14,7 +14,23 @@ ENV PATH=/usr/lib/rstudio-server/bin:$PATH
 # Install OpenJDK
 RUN apt-get update && apt-get install -y openjdk-8-jdk-headless openjdk-8-jre-headless
 
-# Install a lot of R packages
+# 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
+
+# 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
 
@@ -28,6 +44,8 @@ RUN for l in `cat /tmp/r_non_cran_pkgs.txt` ; do \
 
 # From github
 ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_github_pkgs.txt /tmp
+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