## DONT FORGET MCMC ENGINS
* JAGS  ()
* STAN  (See SetupNewInstall.r )


## CHANGE HOME DIRECTORY, USE: 
usermod -d /path/to/new/homedir/ username

software to install on the linux side: 
* screen
* libcurl
* libxml 
* git 
* symlinks
* Java 1.7


## These need to be pointed to correctly
#    libcurl 
#    curl-config 


## MAKE SURE X11 is installed
sudo yum -y groupinstall "X Window System" "Desktop" "Fonts" "General Purpose Desktop"
sudo yum install -y xorg-x11-apps.x86_64 xorg-x11-server-utils.x86_64 xorg-x11-utils.x86_64 xorg-x11-xauth.x86_64 xorg-x11-xdm.x86_64 xorg-x11-xinit.x86_64 xorg-x11-xkb-utils.x86_64 xorg-x11-xkb-utils-devel.x86_64

## RELATED TO GTK2+
sudo yum -y install glibc-common.x86_64 glib2.x86_64 glib2-devel.x86_64
sudo yum -y install pango.x86_64 pango-devel.x86_64

## RGtk2  (And maybe others)
sudo yum groupinstall -y "Development Tools"

## CURL and XML
sudo yum -y install libcurl libcurl-devel
sudo yum -y install libxml2-devel

## Postgress installs
sudo yum -y install postgresql-libs
sudo yum -y install unixODBC-devel

## JAVA for R
R CMD javareconf

## 
sudo yum -y install JAGS
http://rpm.pbone.net/index.php3/stat/4/idpl/21879958/dir/centos_7
ftp://ftp.pbone.net/mirror/ftp5.gwdg.de/pub/opensuse/repositories/home:/cornell_vrdc/CentOS_CentOS-6/x86_64/jags-1.0.4-7.3.x86_64.rpm


## I COPIED THESE FROM SOME WEBSITE, re RevoR Install
sudo yum -y install libicuuc.so.42
sudo yum -y install libtiff.so.3
sudo yum -y install libtk8.5.so

## IF anything was left over from the yum install s, run complete transaction
sudo yum-complete-transaction



## RSYNC
http://www.thegeekstuff.com/2010/09/rsync-command-examples/
http://www.jveweb.net/en/archives/2010/11/synchronizing-folders-with-rsync.html
rsync -rtvuh $OLD $NEW
-------------------------------------

# create a user group
groupadd RUsers

adduser rstudio
adduser revor
adduser neo
adduser rsaporta

usermod -a -G RUsers rsaporta
usermod -a -G wheel rsaporta

usermod -a -G RUsers rstudio
usermod -a -G RUsers revor
usermod -a -G RUsers neo

chown -R rsaporta:RUsers ~rsaporta/
chown -R rstudio:RUsers ~rstudio/
chown -R revor:RUsers ~revor/
chown -R neo:RUsers ~neo/

#### Make Home Directory on external drive
#### And point the home directory to there
mkdir -p /mnt/data/home/rsaporta/
usermod -d /mnt/data/home/rsaporta/ rsaporta

mkdir -p /mnt/data/home/rstudio/
usermod -d /mnt/data/home/rstudio/ rstudio

mkdir -p /mnt/data/home/revor/
usermod -d /mnt/data/home/revor/ revor

mkdir -p /mnt/data/home/neo/
usermod -d /mnt/data/home/neo/ neo

### Copy over personal files
#  rsync -a ....

### Symlink the rprofile

### Add the following to the .bashrc file per user
# add this: #  # Source global definitions
# add this: #  if [ -f /etc/bashrc ]; then
# add this: #          . /etc/bashrc
# add this: #  fi
# add this: #  
# add this: #  # Ricks .bashrc file
# add this: #  if [ -f /etc/ricks.bashrc ]; then
# add this: #          . /etc/ricks.bashrc
# add this: #  fi


-------------------------------------

## Add the following line to ~/.ssh/config keep the ssh connection alive
## Alternatively, it can be added to /etc/ssh/config
ServerAliveInterval 60

touch ~/.ssh/config
subl ~/.ssh/config


-------------------------------------

ssh -X ubuntu@107.20.192.2
screen -S Proj_name  # or screen -r
  # press space
sux rstudio
{password}
bash
cd {workingdir}  # cd ~/git/orch
R 
## DO NOT EXIT THE NORMAL WAY
<to disconnect from ssh, without closing R, ctrl+a, d>



cat(rep("\n", 11))
tmpDir <- "~/R_StillRunning.tmpdir"
dir.create(tmpDir)
for (i in seq(7)) {
  cmd <- sprintf("touch %s/tmpfile_%04d.txt", tmpDir, i)
  system(cmd)
  print(sprintf( "%04d  -- %s", i, 
    format(Sys.time(), format="%l:%m:%S %p", tz = "America/New_York")))
  Sys.sleep(4)
}

{
  x <- data.frame(A=LETTERS)
  Sys.sleep(25)
  newVar <- "I have survived!"
  newFile <- paste("~/R_connection_text.txt")
  write.csv(x, file=newFile)
}



if (x)
 repeat(why)

## Install Sublime 
install package installer

install enhanced-R
Sublime-Text Pref > Package Settings > Enhanced-R > User

  "default_pkgs":
  [
    "data.table",
    "reshape2",
    "ggplot2"
  ]

##  Setup your .Rprofile

  
on the RBOX run: 
sudo ln ./firstScreen.sh /usr/bin/RR


chmod 755 all of the scripts
 # --------------------------------- #
# FOR COLOR OUTPUT
## IMPORTANT -- Make sure it is installed for all users.  eg in /usr/local/lib/R/site-library
## Possibly requires a sudo sudo mv /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.0/colorout/ /usr/local/lib/R/site-library/
download.file("http://www.lepem.ufc.br/jaa/colorout_1.0-1.tar.gz", destfile = "colorout_1.0-1.tar.gz")
install.packages("colorout_1.0-1.tar.gz", type = "source", repos = NULL)

 # --------------------------------- #