data-science-courses

for coursera johns hopkins data science courses

Useful git repos

Notes are at: https://github.com/DataScienceSpecialization/courses

But apparently each of the instructors has their own fork: https://github.com/bcaffo/courses https://github.com/rdpeng/courses

Swirl: https://github.com/swirldev/swirl/wiki/Installing-swirl-on-Linux

Setup r-studio server

On an aws ubuntu instance, I tried to follow instructions at http://www.rstudio.com/products/rstudio/download-server/.

Those instructions say you need at least R version 2.11.1 or higher and it recommends adding the CRAN repository to your system before getting R so you get the most up to date version. http://cran.rstudio.com/bin/linux/ubuntu/README.html But when I did that, I continually ran into problems installing r-base and r-base-core, it was not able to install all the dependencies. So I undid it and just stuck with the default version, which was version 3.0.2 anyway.

  $ sudo apt-get install r-base
  $ sudo apt-get install gdebi-core
  $ sudo apt-get install libapparmor1 # Required only for Ubuntu, not Debian
  $ wget http://download2.rstudio.org/rstudio-server-0.98.1091-i386.deb
  $ sudo gdebi rstudio-server-0.98.1091-i386.deb

As soon as it is installed, it starts running, and if the machine is bounced it will restart when the machine is restarted. To verify that things are working, and to restart rstudio-server run this:

  $ sudo rstudio-server verify-installation
  rstudio-server stop/waiting
  rstudio-server start/running, process 734

Add port 8787 to the AWS security key's incoming access.

Access the server at http://my-ip:8787/

The server uses the system's usernames and passwords. By default, an aws ubuntu server only has user ubuntu and I don't know the password. So we need to set up a new user for rstudio

  $ sudo adduser <username>

This will prompt you for a password (and some other stuff that doesn't matter) It will also create the home directory.

adduser is a perl wrapper around the lower level command 'useradd'. If you use useradd directly, you'll need to set the password with passwd, and you'll need to create the home directory yourself. In short, don't use useradd directly, always use adduser. Similarly, remove users with deluser, not userdel.

http://askubuntu.com/questions/345974/what-is-the-difference-between-adduser-and-useradd

Actually, I see that the course recommends R version 3.1.1. To upgrade to that, I ran

  $ sudo add-apt-repository ppa:marutter/rrutter
  $ sudo apt-get update
  $ sudo apt-get upgrade

Then I restarted rstudio-server with verify-installation (not sure if this is necessary). Then, from inside rstudio, I quit rstudio and started a new session, and that new session had the new version of R.

In one lecture, they give an example and say that you may need the library "UsingR". I tried installing this from inside RStudio:

> install.packages("UsingR")

The first time I tried it, I got a lot of errors like:

Warning in install.packages :
  system call failed: Cannot allocate memory
Warning in install.packages :
  installation of package 'UsingR' had non-zero exit status

From http://stackoverflow.com/questions/21785616/ubuntu-12-04-r-install-packages-does-not-work-no-warning-no-install, I decided to try setting up swaps by following the directions at https://www.digitalocean.com/community/tutorials/how-to-add-swap-on-ubuntu-12-04

 # check to see if there is an existing swap
 $ sudo swapon -s

 # make sure we have enough disk space free, need at least 256k
 $ df -h

 # make the swap.  this will only last until the machine is rebooted
 $ sudo /bin/dd if=/dev/zero of=/swapfile bs=1024 count=256k
 $ sudo /sbin/mkswap /swapfile

 # results in:
 # Setting up swapspace version 1, size = 262140 KiB
 # no label, UUID=2193e5eb-0482-420c-9a7d-53558084fd06

 $ sudo /sbin/swapon /swapfile

 # confirm that you can see it:
 $ swapon -s

 # To turn off the swap, run:
 $ sudo /sbin/swapoff /swapfile

 # To make it use this swap every time the machine is started
 # Add this to /etc/fstab:
 /swapfile swap swap defaults 0 0

This wasn't enough to install knitr, so I increased it to 1G of swap, then it worked.

 # To resize the swap to 1G instead of 256Mb
 $ sudo /sbin/swapoff /swapfile
 $ sudo rm /swapfile
 $ sudo /bin/dd if=/dev/zero of=/swapfile bs=1M count=1024
 1024+0 records in
 1024+0 records out
 1073741824 bytes (1.1 GB) copied, 29.6197 s, 36.3 MB/s
 $ sudo /sbin/mkswap /swapfile
 Setting up swapspace version 1, size = 1048572 KiB
 no label, UUID=17f490d4-4188-4eaa-84aa-3ea0fd62bfe4
 $ sudo swapon /swapfile

After that, the install.packages command worked.

Aside from 'UsingR', I also installed 'ggplot2', 'dplyr', and 'reshape'

an intro for programmers

http://www.johndcook.com/blog/r_language_for_programmers/

Here's what I tried to do to add CRAN (but this failed)

  # Add CRAN
  deb http://cran.cnr.Berkeley.edu/bin/linux/ubuntu utopic/

to /etc/apt/sources.list. Go to SECURE APT on that page to find the command to download the gpg key

   sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9

Then run

   sudo apt-get update
   sudo apt-get upgrade
   sudo apt-get install r-base

Now I know why this failed. In the first command "utopic" refers to the name of the Ubuntu release. You have to put the right value for your release. My release is actually "trusty", not "utopic". You can get the name of your release like this:

# Grabs your version of Ubuntu as a BASH variable
CODENAME=`grep CODENAME /etc/lsb-release | cut -c 18-`

wcyuan / data-science-courses Goto Github PK