anchor.diff:  
   #Supervisord
   RUN DEBIAN_FRONTEND=noninteractive apt-get install -y supervisor && \
  -	mkdir -p /var/log/supervisor
  +   mkdir -p /var/log/supervisor
   CMD ["/usr/bin/supervisord", "-n"]
   
  -#Config files
  +#SSHD
  +#RUN DEBIAN_FRONTEND=noninteractive apt-get install -y openssh-server && \
  +#	mkdir /var/run/sshd && \
  +#	echo 'root:root' |chpasswd
  +
  +# Config files
   RUN cd /r-studio && \
       cp supervisord-RStudio.conf /etc/supervisor/conf.d/supervisord-RStudio.conf
   RUN rm /r-studio/*
  
positive.code: FROM   ubuntu:12.04
  MAINTAINER Mark McCahill "mark.mccahill@duke.edu"
  
  # no Upstart or DBus
  # https://github.com/dotcloud/docker/issues/1724#issuecomment-26294856
  RUN apt-mark hold initscripts udev plymouth mountall
  RUN dpkg-divert --local --rename --add /sbin/initctl && ln -sf /bin/true /sbin/initctl
  RUN apt-get update \
      && apt-get upgrade -y
  
  #Utilities
  RUN DEBIAN_FRONTEND=noninteractive apt-get install -y vim less net-tools inetutils-ping curl git telnet nmap socat python-software-properties
  
  # need wget and the curl dev libraries to install and run R-Studio and associated packages
  RUN DEBIAN_FRONTEND=noninteractive apt-get install -y wget sudo libcurl4-openssl-dev 
  
  # we need TeX for the rmarkdown package in RStudio - this backport seems to work
  RUN apt-add-repository ppa:texlive-backports/ppa
  RUN apt-get update
  RUN DEBIAN_FRONTEND=noninteractive apt-get install -y texlive texlive-base texlive-latex-extra texlive-pstricks
  
  # get R from the CRAN archive at http://cran.cnr.Berkeley.edu 
  RUN DEBIAN_FRONTEND=noninteractive apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 
  RUN echo "deb http://cran.cnr.Berkeley.edu/bin/linux/ubuntu precise/" >> /etc/apt/sources.list 
  RUN apt-get update
  RUN DEBIAN_FRONTEND=noninteractive apt-get install -y r-base r-base-dev
  
  # R-Studio
  RUN DEBIAN_FRONTEND=noninteractive apt-get install -y gdebi-core
  RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libapparmor1
  RUN DEBIAN_FRONTEND=noninteractive wget http://download2.rstudio.org/rstudio-server-0.98.1028-amd64.deb
  RUN DEBIAN_FRONTEND=noninteractive gdebi -n rstudio-server-0.98.1028-amd64.deb
  RUN rm rstudio-server-0.98.1028-amd64.deb
  
  # update the R packages we will need for knitr
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/knitr_1.8.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/yaml_2.1.13.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/htmltools_0.2.6.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/caTools_1.17.1.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/bitops_1.0-6.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/digest_0.6.4.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/stringr_0.6.2.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/markdown_0.7.4.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/highr_0.4.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/formatR_1.0.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/evaluate_0.5.5.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/mime_0.2.tar.gz
  
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL bitops_1.0-6.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL caTools_1.17.1.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL digest_0.6.4.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL htmltools_0.2.6.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL yaml_2.1.13.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL stringr_0.6.2.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL highr_0.4.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL formatR_1.0.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL evaluate_0.5.5.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL mime_0.2.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL markdown_0.7.4.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL knitr_1.8.tar.gz
  RUN rm evaluate_0.5.5.tar.gz
  RUN rm formatR_1.0.tar.gz
  RUN rm highr_0.4.tar.gz
  RUN rm markdown_0.7.4.tar.gz
  RUN rm stringr_0.6.2.tar.gz
  RUN rm knitr_1.8.tar.gz
  RUN rm yaml_2.1.13.tar.gz
  RUN rm htmltools_0.2.6.tar.gz
  RUN rm caTools_1.17.1.tar.gz
  RUN rm bitops_1.0-6.tar.gz
  RUN rm digest_0.6.4.tar.gz
  RUN rm mime_0.2.tar.gz
  
  # R packages we need for devtools - and we need devtools to be able to update the rmarkdown package
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/rstudioapi_0.1.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/devtools_1.6.1.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/httr_0.5.tar.gz 
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/RCurl_1.95-4.3.tar.gz 
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/memoise_0.2.1.tar.gz 
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/whisker_0.3-2.tar.gz 
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/jsonlite_0.9.13.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL jsonlite_0.9.13.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL memoise_0.2.1.tar.gz 
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL whisker_0.3-2.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL RCurl_1.95-4.3.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL httr_0.5.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL rstudioapi_0.1.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL devtools_1.6.1.tar.gz
  RUN rm jsonlite_0.9.13.tar.gz
  RUN rm whisker_0.3-2.tar.gz
  RUN rm memoise_0.2.1.tar.gz
  RUN rm RCurl_1.95-4.3.tar.gz
  RUN rm httr_0.5.tar.gz
  RUN rm devtools_1.6.1.tar.gz
  RUN rm rstudioapi_0.1.tar.gz
  
  # downloader
  RUN DEBIAN_FRONTEND=noninteractive wget http://cran.r-project.org/src/contrib/downloader_0.3.tar.gz
  RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL downloader_0.3.tar.gz
  RUN rm downloader_0.3.tar.gz
  
  # install rmarkdown
  ADD ./conf /r-studio
  
negative.code: 
  EXPOSE 8787 
  
  CMD ["/usr/bin/supervisord"]