Installing R shiny server on OCI compute instance (always free tier)

Introduction

Oracle Compute Infrastructure (OCI) is the next generation cloud platform run by Oracle. Like some of its competitors, Oracle offers an always free tier where you can access a range of cloud products and services without having to pay anything ever. And while you will need to provide credit card information to prove that you are not a bot, it will not going to be charged unless you explicitly upgrade to a paid account.

For us database folks OCI is mainly interesting because you can run a database in there, but OCI has much more stuff: storage, application server, Zeppellin notebooks etc. In this post I will describe how you can set up an R shiny server on an OCI compute instance and connect it to an autonomous database running in the same cloud.

High level overview

This guide assumes that you already have an account on OCI and have created an autonomous database. Both steps are extremely simple (creating a database in OCI hardly requires more than pressing a button on a web console), but if you need any help with that you can refer to OCI hands-on labs.

The high level outline of the remaining steps are as follows:

  • Create a Virtual Cloud Network (VCN)
  • Create a compute instance
  • Install R
  • Install R packages
  • Configure firewall to open the port 3838 for R shiny
  • Add ingress rule in the Security List for the same port on VCN
  • Install Oracle client
  • Install ROracle with paths pointing to Oracle client
  • Set up Oracle Wallet to connect to your database from the Shiny server

While it’s not too complicated, I found that some of the dependencies may fail to install automatically — maybe because I didn’t add some yum repositories properly or something like that. So I just installed them manually.

All in all, the entire installation process should take about 40-45 minutes of your time.

Detailed instructions

1. Log in to your OCI account

2. Create VNC network for the shiny server

Main page, left-hand side menu:

Networking -> Virtual Cloud Networks -> Start VCN Wizard, accept all default options

3. Create a compute instance

Same menu:
Compute -> Instances -> Create Instance

You will need to provide a public ssh key to connect to the instance.

4. Note the public IP address for later
5. Log on to the instance via ssh

ssh -i  opc@ip_address_from_prev_step

6. Install R

sudo yum install R

7. Install R shiny (not the server)

sudo su - -c "R -e \"install.packages('shiny',repos='https://cran.rstudio.com/')\""

8. Use the commands specified on rstudio.com:


wget https://download3.rstudio.org/centos6.3/x86_64/shiny-server-1.5.14.948-x86_64.rpm

9. and then
 install it

sudo rpm -i shiny-server-1.5.14.948-x86_64.rpm

10. Make the shiny server start automatically starting from the next reboot

sudo systemctl enable shiny-server

11. Start the shiny server manually

sudo systemctl start shiny-server

12. Open 3838 port in the firewall


sudo firewall-cmd --permanent --add-port=3838/tcp

sudo firewall-cmd --permanent --add-port=3838/udp

sudo firewall-cmd --reload

13. Add ingress rule for Security List for Rshiny-network with 0.0.0.0/0 as CIDR block, TCP protocol, port=3838
14. Install package cairo-devel which somehow fails to install automatically

sudo yum install cairo-devel

15. Install Cairo R package

sudo su - -c "R -e \"install.packages('Cairo', repos='https://cran.rstudio.com/')\""

16. Download Oracle instant client

wget https://download.oracle.com/otn_software/linux/instantclient/19600/oracle-instantclient19.6-basic-19.6.0.0.0-1.x86_64.rpm

wget https://download.oracle.com/otn_software/linux/instantclient/19600/oracle-instantclient19.6-sqlplus-19.6.0.0.0-1.x86_64.rpm

wget https://download.oracle.com/otn_software/linux/instantclient/19600/oracle-instantclient19.6-devel-19.6.0.0.0-1.x86_64.rpm

17. Install the Oracle instant client rpms downloaded in the previous step

sudo rpm -i oracle-instantclient19.6-basic-19.6.0.0.0-1.x86_64.rpm

sudo rpm -i oracle-instantclient19.6-sqlplus-19.6.0.0.0-1.x86_64.rpm

sudo rpm -i oracle-instantclient19.6-devel-19.6.0.0.0-1.x86_64.rpm

18. Download ROracle package

wget https://cran.r-project.org/src/contrib/ROracle_1.3-1.tar.gz

19. Install DBI R package

sudo su - -c "R -e \"install.packages('DBI', repos='https://cran.rstudio.com/')\""

20. Install ROracle

sudo su - -c "R CMD INSTALL --configure-args='--with-oci-lib=/usr/lib/oracle/19.6/client64/lib --with-oci-inc=/usr/include/oracle/19.6/client64' path_to_the_file/ROracle_1.3-1.tar.gz"

where path_to_the_file should obviously be replaced with the actual path.
21. Download the wallet from the “DB connection” tab, unpack and edit sqlnet.ora to set DIRECTORY to the actual path where wallet contents are located
22. Create a wallet directory for the shiny user

sudo mkdir -p /etc/ORACLE/WALLETS/shiny/

and copy contents of the wallet zip archive there

That’s it. You can now create a simple database web application to make sure everything works together.

sudo mkdir -p /srv/shiny-server/sample-apps/dbhello
chown shiny /srv/shiny-server/sample-apps/dbhello
sudo su shiny -
cd /srv/shiny-server/sample-apps/dbhello

And then create two files, ui.R:

library(shiny)

shinyUI(pageWithSidebar(

  headerPanel("It's Alive!"),

  sidebarPanel(
    textInput("txtUselessInput",
                  "Enter useless text:"
                  )
  ),

  mainPanel(
    textOutput("mytext")
  )
))

and server.R:

library(shiny)
library(ROracle)

shinyServer(function(input, output) {

  output$mytext <- renderText({
    con <- dbConnect(drv=dbDriver("Oracle"), user="username", pass="password", dbname='(description= (retry_count=20)(retry_delay=3)(address=(protocol=tcps)(port=1522)(host=adb.uk-london-1.oraclecloud.com))(connect_data=(service_name=mvrzyguheaz9w3v_myatp_high.atp.oraclecloud.com))(security=(ssl_server_cert_dn="CN=adwc.eucom-central-1.oraclecloud.com,OU=Oracle BMCS FRANKFURT,O=Oracle Corporation,L=Redwood City,ST=California,C=US")))')
    dbGetQuery(con, "select * from global_name")$GLOBAL_NAME
  })
})

with the actual username, password and database connect string (from tnsnames.ora in your wallet zip archive) instead of the placeholders.

At this point, your application should be accessible from the browser at your_public_ip:3838/sample-apps/dbhello.

Should anything go wrong, check the logs (/var/log/shiny-server) for clues. Have fun!

 

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