da625747480093d5faacdb9d055f591c3908c67d
max
  Wed Jan 13 11:33:05 2016 -0800
reducing R's footprint a bit in the GBiB, refs #16616

diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
index d7a91f1..e60f4ec 100755
--- src/browserbox/root/updateBrowser.sh
+++ src/browserbox/root/updateBrowser.sh
@@ -192,50 +192,54 @@
    echo 'Unattended-Upgrade::Automatic-Reboot "true";' >> /etc/apt/apt.conf.d/20auto-upgrades
    # remove packages not used anymore
    echo 'Unattended-Upgrade::Remove-Unused-Dependencies "true";' >> /etc/apt/apt.conf.d/20auto-upgrades
    # and remove the downloaded tarballs at the end
    echo 'APT::Periodic::AutocleanInterval "1";' >> /etc/apt/apt.conf.d/20auto-upgrades
    /etc/init.d/unattended-upgrades restart
 fi
    
 # unattended security upgrades take a while to start, better to force one right now and show the progress
 # this may lead to an auto-reboot, so let's skip the auto-update of this script for this reboot
 touch /root/gbibSkipNextUpdate
 echo - Applying Ubuntu security updates
 unattended-upgrade -v
 rm -f /root/gbibSkipNextUpdate
 
-# The original GBiB image did not use the Ubuntu Virtualbox guest utils
-# fix this now and switch to these
+# The original GBiB image did not use the Ubuntu Virtualbox guest utils but the
+# ones from VirtualBox in /opt. Fix this now and switch to the Ubuntu guest
+# utilities, so they are updated automatically by the Ubuntu tools
 if apt-cache policy virtualbox-guest-dkms | grep "Installed: .none." > /dev/null; then
+    echo - Updating VirtualBox Guest utilities
     apt-get install -y linux-headers-generic 
     apt-get install -y virtualbox-guest-dkms
     apt-get -y autoremove
     /etc/init.d/vboxadd start
+
     # during 2015, a directory /home/browser/bin got created in the official image and filled with a copy of the user tools
     # remove this directory now to avoid confusion
+    # this is unrelated to the virtualbox tools, but doing this now will make sure it is executed only once
     shred -fzu -n1 /home/browser/bin/blat/*
     rm -rf /home/browser/bin/blat
     shred -fzu -n1 /home/browser/bin/*
     rm -rf /home/browser/bin
 fi
 
 # install R for the gtex tracks
 if apt-cache policy r-base | grep "Installed: .none." > /dev/null; then
    echo - Installing R
    apt-get update
-   apt-get install -y r-base
+   apt-get --no-install-recommends install -y r-base-core
    apt-get -y autoremove
 fi
 
 echo
 echo - Updating the genome browser software via rsync:
 
 # CGI-BIN and HTDOCS:
 # the parameter "hgwdev" copies over only the beta/alpha CGIs from hgwdev
 if [ "$1" == "hgwdev" ] ; then
     # note the missing -u option to RSYNC: in hgwdev mode, we want to overwrite everything.
     # On a development machine, the developer might have touched a file
     # for testing. We want to make sure that all local files are overwritten by the 
     # files on hgwdev
     RSYNCOPTS="-ltrzvh"
     user=$2