In a previous blog post I showed how you can install and get started with using RStudio on a server by using RStudio Server. My previous post showed how you could do that on the Oracle BigDataLite VM. On this VM everything was nicely scripted and set up for you. But when it comes to installing it on a different server, well things can be a bit different.
The purpose of this blog post is to go through the install steps you need to follow on your own server or Oracle Database server. The following is based on a server that is setup with Oracle Linux. (I’m actually using the Oracle DB Developer VM).
1. Download the latest version of RStudio Server.
Use the following link to download RStudio Server. But do a quick check on the RStudio server to get the current version number.
The following shows you what you will see when you run this command.
--2016-03-16 06:22:30-- https://download2.rstudio.org/rstudio-server-rhel-0.99.892-x86_64.rpm Resolving download2.rstudio.org (download2.rstudio.org)... 126.96.36.199, 188.8.131.52, 184.108.40.206, ... Connecting to download2.rstudio.org (download2.rstudio.org)|220.127.116.11|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 38814908 (37M) [application/x-redhat-package-manager] Saving to: ‘rstudio-server-rhel-0.99.892-x86_64.rpm’ 100%[============================================================>] 38,814,908 6.54MB/s in 6.0s 2016-03-16 06:22:37 (6.17 MB/s) - ‘rstudio-server-rhel-0.99.892-x86_64.rpm’ saved [38814908/38814908]
2. Install RStudio Server
sudo yum install --nogpgcheck rstudio-server-rhel-0.99.892-x86_64.rpm
when prompted if it is OK to install, enter y (highlighted in bold below)
Loaded plugins: langpacks Examining rstudio-server-rhel-0.99.892-x86_64.rpm: rstudio-server-0.99.892-1.x86_64 Marking rstudio-server-rhel-0.99.892-x86_64.rpm to be installed Resolving Dependencies --> Running transaction check ---> Package rstudio-server.x86_64 0:0.99.892-1 will be installed --> Finished Dependency Resolution ol7_UEKR3/x86_64 | 1.2 kB 00:00:00 ol7_addons/x86_64 | 1.2 kB 00:00:00 ol7_latest/x86_64 | 1.4 kB 00:00:00 ol7_optional_latest/x86_64 | 1.2 kB 00:00:00 Dependencies Resolved =========================================================================================================== Package Arch Version Repository Size =========================================================================================================== Installing: rstudio-server x86_64 0.99.892-1 /rstudio-server-rhel-0.99.892-x86_64 280 M Transaction Summary =========================================================================================================== Install 1 Package Total size: 280 M Installed size: 280 M Is this ok [y/d/N]: y Downloading packages: Running transaction check Running transaction test Transaction test succeeded Running transaction Installing : rstudio-server-0.99.892-1.x86_64 1/1 groupadd: group 'rstudio-server' already exists rsession: no process found ln -s '/etc/systemd/system/rstudio-server.service' '/etc/systemd/system/multi-user.target.wants/rstudio-server.service' rstudio-server.service - RStudio Server Loaded: loaded (/etc/systemd/system/rstudio-server.service; enabled) Active: active (running) since Wed 2016-03-16 10:46:00 PDT; 1s ago Process: 3191 ExecStart=/usr/lib/rstudio-server/bin/rserver (code=exited, status=0/SUCCESS) Main PID: 3192 (rserver) CGroup: /system.slice/rstudio-server.service ├─3192 /usr/lib/rstudio-server/bin/rserver └─3205 /usr/lib64/R/bin/exec/R --slave --vanilla -e cat(R.Version()$major,R.Version()$minor,~+~sep=".") Mar 16 10:46:00 localhost.localdomain systemd: Started RStudio Server. Verifying : rstudio-server-0.99.892-1.x86_64 1/1 Installed: rstudio-server.x86_64 0:0.99.892-1 Complete!
3. Open RStudio using a web browser.
Open your favourite web browser and put in the host name or the IP address of your server. In my example I’m using the Oracle DB Developer VM to demonstrate the install, so I can use localhost, followed by the port number for RStudio Server.
Log in using your Server username and password. This is oracle/oracle on the VM.
4. Use and Enjoy
If you get logged into RStudio Server then you will see a screen something like the following!
Job Done and Enjoy!
5. An Extra Step is using the Oracle DB Developer VM
If you want to use RStudio on the Oracle DB Developer VM from your local OS, then you will need to open the port 8787 on the VM. To do this power down the VM, if you have it open. The open the Network section of the VM settings. I’m using VirtualBox. And then click on the Port Forwarding.
Click on OK to save your Port Forwarding setting and then click on the OK button again to close the Network settings for the VM.
Now start up the VM. When it has loaded and you have the desktop displayed in the VM window, you should now be able to connect to RStudio in the VM, from your local machine.
To do this open your web browser on your local machine and type in
You should now get the RStudio login in screen that is shown in point 3 above. Go ahead, login and enjoy.
6. A little warning
Make sure to log out of RStudio when you are finished using it. If you don’t then your R environment may not have been saved and you will get a message when you log in next. Now we don’t want that happenings, so just log out of RStudio. You can do that by looking at the top right hand corner of the RStudio Server application.
I will have one more blog post on how you can configure RStudion Server to work with an Oracle Database server that has Oracle R Enterprise installed.
A very popular tool for data scientists is RStudio. This tool allows you to interactively work with your R code, view the R console, the graphs and charts you create, manage the various objects and data frames you create, as well shaving easy access to the R help documentation. Basically it is a core everyday tool.
The typical approach is to have RStudio installed on your desktop or laptop. What this really means is that the data is pulled to your desktop or laptop and all analytics is performed there. In most cases this is fine but as your data volumes goes does does the limitations of using R on your local machine.
An alternative is to install a version called RStudio Server on an analytics server or on the database server. You can now use the computing capabilities of this server to overcome some of the limitations of using R or RStudio locally. Now you will use your web browser to access RStudio Server on your database server.
In this blog post I will walk you through how to install and get connected to RStudio Server on the Oracle BigDataLite VM.
After starting up the Oracle BigDataLite VM and logging into the Oracle user (password=welcome1) you will see the Start Here icon on the desktop. You will need to double click on this.
This will open a webpage on the VM that contains details of all the various tools that are installed on the VM or are ready for you to install and configure. This information contains all the http addresses and ports you need to access each of these tools via a web browser or some other way, along with the usernames and passwords you need to use them.
One of the tools lists is for RStudio Server. This product is not installed on the VM but Oracle has provided a script that you can run to perform the install in an automated way. This script is located in:
[oracle@bigdatalite ~]$ cd /home/oracle/scripts/
Use the following command to run the RStudio Server install script.
[oracle@bigdatalite scripts]$ ./install_rstudio.sh
The following is the output from running this script and it will be displayed in your terminal window. You can use this to monitor the progress of the installation.
Retrieving RStudio --2016-03-12 02:06:15-- https://download2.rstudio.org/rstudio-server-rhel-0.99.489-x86_64.rpm Resolving download2.rstudio.org... 18.104.22.168, 22.214.171.124, 126.96.36.199, ... Connecting to download2.rstudio.org|188.8.131.52|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 34993428 (33M) [application/x-redhat-package-manager] Saving to: `rstudio-server-rhel-0.99.489-x86_64.rpm' 100%[======================================>] 34,993,428 5.24M/s in 10s 2016-03-12 02:06:26 (3.35 MB/s) - `rstudio-server-rhel-0.99.489-x86_64.rpm' saved [34993428/34993428] Installing RStudio Loaded plugins: refresh-packagekit, security, ulninfo Setting up Install Process Examining rstudio-server-rhel-0.99.489-x86_64.rpm: rstudio-server-0.99.489-1.x86_64 Marking rstudio-server-rhel-0.99.489-x86_64.rpm to be installed public_ol6_UEKR3_latest | 1.2 kB 00:00 public_ol6_UEKR3_latest/primary | 22 MB 00:03 public_ol6_UEKR3_latest 568/568 public_ol6_latest | 1.4 kB 00:00 public_ol6_latest/primary | 55 MB 00:12 public_ol6_latest 33328/33328 Resolving Dependencies --> Running transaction check ---> Package rstudio-server.x86_64 0:0.99.489-1 will be installed --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: rstudio-server x86_64 0.99.489-1 /rstudio-server-rhel-0.99.489-x86_64 251 M Transaction Summary ================================================================================ Install 1 Package(s) Total size: 251 M Installed size: 251 M Downloading Packages: Running rpm_check_debug Running Transaction Test Transaction Test Succeeded Running Transaction Installing : rstudio-server-0.99.489-1.x86_64 1/1 useradd: user 'rstudio-server' already exists groupadd: group 'rstudio-server' already exists rsession: no process killed rstudio-server start/running, process 5037 Verifying : rstudio-server-0.99.489-1.x86_64 1/1 Installed: rstudio-server.x86_64 0:0.99.489-1 Complete! Restarting RStudio rstudio-server stop/waiting rsession: no process killed rstudio-server start/running, process 5066
When the installation is finished you are now ready to connect to the RStudio Server. So open your web browser and enter the following into the address bar.
The initial screen you are presented with is a login screen. Enter your Linux username and password. In the case of the BigDataLite VM this will be oracle/welcome1.
Then you will be presented with the RStudio Server application in your web browser, as shown below. As you can see it is very similar to using RStudio on your desktop. Happy Days! You are now setup and able to run RStudio on the database server.
Make sure to log out of RStudio Server before closing down the window.
If you don’t log out of RStudio Server then the next time you open RStudio Server your session will automatically open. Perhaps this is not the best for security, so try to remember to log out each time.
By now using RStudio Server on the Oracle Database server I can not get some of the benefits of computing capabilities of this server. Although there are still the typical limitations with of using R. But now I access RStudio on the database server and process the data on the database server, all from my local PC or laptop.
Everything is nicely setup and ready for you to install on the BigDataLite VM (thank you Oracle). But what about when we want to install RStudion Server on a different server. What are the steps necessary to install, configure and log in. Yes they should be similar but I will give a complete list of steps in my next blog post.
Recently I ran out of space on one of my Windows virtual machines. I needed to increase the size of the disk to allow me to install some new software. When creating the VM I had created the disks as VMDK. Yes I know now that is not the best format to use 😦 VMDK disks/files do not allow you to dynamically change their size 😦 So what can you do? Is it possible in any way? If so how? Well this is what I did (after a bit of research using the google and StackOverFlow.
- Make a copy of the vmdk file on the OS. Just in case anything happens! (always have a backup)
- Clone the vmdk disk file into vdi format. To do this you need to use the VBoxManage command/app to clone the file into a vdi formatted file. For example this is what I ran.
VBoxManage clonehd “Win7-184.108.40.206-ORE-03-Jan-14-disk1.vmdk” “cloned.vdi” –format vdi
- There was some suggestions that you could then clone the vdi file back into vmdk format. This did not work for me. It kept on giving me errors when the cloning process was nearly finished. After a bit of time researching this I wasn’t able to find a solution to fix this. Instead I did the following
- Replace the vodka disk/file with the vdi disk/file in my VirtualBox VM. Open VirtualBox, select the VM and then click on the Storage section. In this I was able to add the new vdi disk/file and then removed the old vodka disk/file.
- Start up the VM. The VM starts up as normal and everything works OK.
- To allocate and make the extract space useable you need to allocated the new space to the c:\ drive. To do this I did the following:
- Click on Start Button, then right click on Computer and select Manage from the drop down menu.
- In the Computer Management console select Disk Management. A screen something like the following appears shows the amount of allocated and unallocated disk.
- Right click on the area for the c:\ drive and select Extend Volume from the drop down menu.
- Select all the defaults are you go through the Wizard to Extend the Volume. When you are finished the c:\ drive will be extended with all the extra space, as shown below.
- All done. You now have a larger disk/drive for your Windows VM.