R, rApache and TwoRavens

Eventually, this document may be split into several parts, dedicated to individual components - such as R, rApache and the TwoRavens applications. Particularly, if the TwoRavens team creates an “official” distribution with their own installation manual.


a. httpd (Apache):

yum install httpd

Disable SELinux on httpd:

setenforce permissive


https strongly recommended (required?); signed cert recommended.

b. R:

yum install R R-devel

(EPEL distribution recommended; version 3.* required; 3.1.* recommended as of writing this)

c. rApache:

rpm distribution from the HMDC systems group is recommended; download and install the latest available rpm (1.2.6, as of writing this):


d. Install libcurl-devel:

(provides /usr/bin/curl-config, needed by some 3rd-party R packages; package installation will fail silently if it’s not found!):

yum install libcurl-devel

Make sure you have the standard GNU compilers installed (needed for 3rd-party R packages to build themselves).

1. Set Up R

R is used both by the Dataverse application, directly, and the TwoRavens companion app.

Two distinct interfaces are used to access R: Dataverse uses Rserve; and TwoRavens sends jobs to R running under rApache using Rook interface.

We provide a shell script (conf/R/r-setup.sh in the Dataverse source tree; you will need the other 3 files in that directory as well - https://github.com/IQSS/dataverse/conf/R/r-setup.sh) that will attempt to install the required 3rd party packages; it will also configure Rserve and rserve user. rApache configuration will be addressed in its own section.

The script will attempt to download the packages from CRAN (or a mirror) and GitHub, so the system must have access to the internet. On a server fully firewalled from the world, packages can be installed from downloaded sources. This is left as an exercise for the reader. Consult the script for insight.

2. Install the TwoRavens Application

b. unzip

and rename the resulting directory dataexplore. Place it in the web root directory of your apache server; so that it is visible from the outside at

https://<rapache server>:<rapache port>/dataexplore

We’ll assume /var/www/html/dataexplore in the examples below.

c. run the installer

a scripted, interactive installer is provided at the top level of the TwoRavens distribution (https://github.com/IQSS/TwoRavens/blob/master/install.pl). Run it as


The installer will ask you to provide the following:

Setting default Comment
TwoRavens directory /var/www/html/dataexplore File directory where TwoRavens is installed.
Apache config dir. /etc/httpd rApache config file for TwoRavens will be placed under conf.d/ there.
Apache web dir. /var/www/html  
Apache host address local hostname  
Apache host port 443  
Apache web protocol https http or https (https recommended)
Dataverse URL   URL of the Dataverse from which TwoRavens will be receiving metadata and data files. For example, https://thedata.harvard.edu.

This should be it!


Explained below are the steps needed to manually configure TwoRavens to run under rApache (these are performed by the install.pl script above). Provided for reference.

I. Configure the TwoRavens web (Javascript) application.

Edit the file /var/www/html/dataexplore/app_ddi.js.

find and edit the following 3 lines:

  1. var production=false;

    and change it to true;

  2. hostname="localhost:8080";

    so that it points to the dataverse app, from which TwoRavens will be obtaining the metadata and data files. (don’t forget to change 8080 to the correct port number!)


  3. var rappURL = "";

    set this to the URL of your rApache server, i.e.


II. Configure the R applications to run under rApache

rApache is a loadable httpd module that provides a link between Apache and R. When you installed the rApache rpm, under 0., it placed the module in the Apache library directory and added a configuration entry to the config file (/etc/httpd/conf/httpd.conf).

Now we need to configure rApache to serve several R “mini-apps”, from the R sources provided with TwoRavens.

a. Edit the following files:

in dataexplore/rook:

rookdata.R, rookzelig.R, rooksubset.R, rooktransform.R, rookselector.R, rooksource.R

and replace every instance of production<-FALSE line with production<-TRUE.

(yeah, that’s why we provide that installer script...)

b. Edit dataexplore/rook/rooksource.R

and change the following line:




(or your dataexplore directory, if different from the above)

c. Edit the following lines in dataexplore/rook/rookutils.R:

url <- paste("https://dataverse-internal.iq.harvard.edu/custom/preprocess_dir/preprocessSubset_",sessionid,".txt",sep="")


imageVector[[qicount]]<<-paste("https://dataverse-internal.iq.harvard.edu/custom/pic_dir/", mysessionid,"_",mymodelcount,qicount,".png", sep = "")

and change the URL to reflect the correct location of your rApache instance - make sure that the protocol and the port number are correct too, not just the host name!

d. Add the following lines to /etc/httpd/conf/httpd.conf:

(This configuration is now supplied in its own config file tworavens-rapache.conf, it can be dropped into the Apache’s /etc/httpd/conf.d. Again, the scripted installer will do this for you automatically.)

RSourceOnStartup "/var/www/html/dataexplore/rook/rooksource.R"
<Location /custom/zeligapp>
   SetHandler r-handler
   RFileEval /var/www/html/dataexplore/rook/rookzelig.R:Rook::Server$call(zelig.app)
<Location /custom/subsetapp>
   SetHandler r-handler
   RFileEval /var/www/html/dataexplore/rook/rooksubset.R:Rook::Server$call(subset.app)
<Location /custom/transformapp>
   SetHandler r-handler
   RFileEval /var/www/html/dataexplore/rook/rooktransform.R:Rook::Server$call(transform.app)
<Location /custom/dataapp>
   SetHandler r-handler
   RFileEval /var/www/html/dataexplore/rook/rookdata.R:Rook::Server$call(data.app)

e. Create the following directories and chown them user apache:

mkdir --parents /var/www/html/custom/pic_dir

mkdir --parents /var/www/html/custom/preprocess_dir

chown -R apache.apache /var/www/html/custom

f. chown the dataexplore directory

to user apache:

chown -R apache /var/www/html/dataexplore

g. restart httpd

service httpd restart