## Installation of the Server Version

Rpad has been setup with Linux using the Apache server, with either Apache 1.3 or Apache 2.0. It may well work on others, but this was the easiest option. Under windows, it has also been tested with Apache (although it doesn't seem as responsive as apache under linux). I have also had good experiences using Rpad with coLinux (www.colinux.org) under win2k with R, Apache, and mod_perl. Rpad can be installed using CGI for the perl portion or with mod_perl. These directions describe installation with mod_perl:

The main steps to installing Rpad on a server are:

- Install R.
- Install the R2HTML package from CRAN.
- Install the Rpad package from CRAN.
- Install Apache.
- Install mod_perl. This is optional. Rpad can also be run with CGI.
- Copy the directory basehtml in Rpad's package directory to /www/var (or wherever your server root is). Rename as appropriate. For example:

    cp -r /usr/lib/R/library/Rpad/basehtml /var/www/Rpad

- Enable write access to the Rpad directory as well as the Rpad/server directory.
- Enable execution of all of the Rpad/server/*.pl files (chmod a+x).
- Install the Statistics-R_perl_interface that comes with Rpad in the serverversion directory. This version has slight modifications to Graciliano's R-Statistics version 0.02).
- Change the server configuration as appropriate to enable CGI and/or mod_perl. Tell the browser not to cache some files which might change during a session, using the mod_expires module. Here is the portion of the httpd.conf for Apache 1.3 to do this for Rpad files in /var/www/Rpad:

    <Directory /var/www/Rpad/server*>
      <IfModule mod_perl.c>
        <Files *.pl> # requires mod_perl
          SetHandler perl-script
          PerlHandler Apache::Registry
          Options +ExecCGI
          PerlSendHeader ON
        </Files>
      </IfModule>
      Options +ExecCGI
      AddHandler cgi-script .pl
      <IfModule mod_expires.c>
        ExpiresActive on
        ExpiresDefault "now plus 0 seconds"
      </IfModule>
    </Directory>
    AddType text/x-component .htc
    AddType text/html .Rpad

- Here's a portion of the httpd.conf to configure Rpad for Apache2 for files in /var/www/Rpad:

    <Directory /var/www/Rpad/server*>
      <IfModule mod_perl.c>
        <Files *.pl> # requires mod_perl
          SetHandler perl-script
          PerlResponseHandler ModPerl::PerlRun
          PerlOptions +ParseHeaders
          Options -Indexes +ExecCGI
        </Files>
      </IfModule>
      Options +ExecCGI
      AddHandler cgi-script .pl
      <IfModule mod_expires.c>
        ExpiresActive on
        ExpiresDefault "now plus 0 seconds"
      </IfModule>
    </Directory>
    AddType text/x-component .htc
    AddType text/html .Rpad

- Add a mime type to tell the server to serve .Rpad files as text/html (done in the httpd.conf files above).
- To get the help menu item to work, create a symlink R to /usr/lib/R in the /www/var/Rpad directory (ln -s /usr/lib/R /var/www/Rpad/R).
- To update the javascript database for the R keyword search page (SearchRKeywords.html), source makeHelpTemplate.R from within R in the main Rpad directory.

## Notes on Debian

This is the main platform that Debian's been tested on, and www.Rpad.org is a Debian server. Debian packages for Rpad are available at www.Rpad.org. Installing the Rpad package does all of the installation steps described above. Under Debian, Rpad will work with apache or apache2, and it will work with or without mod_perl on either version of apache.

There's also a script that will install the Rpad html files. It is located in the serverversion directory within the Rpad package directory. It's called installRpadWWW.sh. This creates another Rpad directory. In addition to copying the base html files, it sets permissions and configures apache properly for that directory. Here's an example:

    /usr/local/lib/R/site-library/Rpad/installRpadWWW.sh /var/www/RpadTesting

I normally add a cron job to restart the Apache server once a day. This clears out any R processes that didn't get killed for whatever reason. I create the following as the file /etc/cron.daily/Rpad-cleanup:

       apachectl restart
       rm -rf /var/www/Rpad/server/dd*

## Notes on Apache 1.3 under Windows

    # Installing apache_1.3.33-win32-x86-no_src.msi downloaded from
    # www.apache.org using CGI
    # Windows 2000
    # Perl 5.8.4 installed at C:/apps/perl
    # Installed Apache at C:/Program Files/Apache Group/Apache
    # WWW root is at C:/Program Files/Apache Group/Apache/htdocs

    # Copied the directory basehtml directory to htdocs\Rpad
    xcopy/I/S "C:\Program Files\R\rw2001\library\Rpad\basehtml" "C:\Program Files\Apache Group\Apache\htdocs\Rpad"

    # Added a mime type for .Rpad files in conf\mime.types as follows:
    text/html			Rpad

    #Installed Statistics-R_perl_interface:
    cd C:\Program Files\R\rw2001\library\Rpad\serverversion\Statistics-R_perl_interface
    perl Makefile.pl
    nmake
    nmake install
    # you can also just copy the directory
    # C:\Program Files\R\rw2001\library\Rpad\serverversion\Statistics-R_perl_interface\lib\Statistics
    # to C:\apps\perl\site\lib (or wherever your perl lib's are)

    # Add the following to the conf\httpd.conf file to read .pl files as CGI:
    AddHandler cgi-script .pl

    # Changed the following in the conf\httpd.conf file to enable CGI:
        Options Indexes FollowSymLinks MultiViews
    # to
        Options Indexes FollowSymLinks MultiViews ExecCGI

    # Added the following line as the first line to the 3 perl files in
    # htdocs\Rpad\server to point to perl
    #!c:/apps/perl/bin/perl.exe

    # I also futzed with the permissions on these files, but I don't know
    # that it was necessary.

    # Used R's png driver rather than ghostscript: in .RpadStartup.R,
    # uncommented the following line:
    #
    graphoptions(type="Rpng")

    That was it. I had ghostscript installed, so the default
    graphoptions(type="pngalpha")
    also worked.

    On my system, a number of stranded Rterm.exe files built
    up. Restarting apache didn't get rid of them. The task manager
    wouldn't get rid of them either. So, I used the "process"
    command downloaded from
    http://www.beyondlogic.org/solutions/processutil/processutil.htm
    to kill them as:
    process -k Rterm.exe

    You also probably need to lock down the file system. Apache
    starting as a service has access to the whole file system.
    You need to change the user for the apache service and
    set permissions for that user to prevent access to unwanted
    parts of your hard drive. Google for "apache localsystem ntfs permissions".

## Notes on Apache 2.0 under Windows

Installing Rpad on an apache2 installation (cgi mode) on Windows 2000 worked exactly the same as the Apache 1.3 installation.

I briefly tried Rpad with apache2/modperl under windows. In very limited testing, it worked okay. Modperl under windows can make Apache very slow, at least to start and stop. A server restart can take over 10 seconds on my win2k laptop.

## Notes on the Windows IIS server

WARNING: Users (including me) have reported problems installing Rpad on IIS. I've got a Windows 2000 machine with IIS running fine. In another installation on XP (also using IIS v5.1), it refuses to start R (the perl part works, it just won't spawn another process).

Installing Rpad on the IIS server that came with Windows 2000 worked mainly the same as the Apache 1.3 installation. Here are some further notes:

    # Copied the directory basehtml directory to wwwroot\Rpad
    xcopy/I/S "C:\Program Files\R\rw2001\library\Rpad\basehtml" "C:\Inetpub\wwwroot\Rpad"

    #Installed the Statistics-R_perl_interface as outlined above.

    ## NOTE: This step shouldn't be needed anymore! It should figure it out right,
    ## but I left it in so you can try it if things don't work right.
    # In C:\Inetpub\wwwroot\Rpad\server\R_process.pl, change the following
    # lines from:
    my $R = Statistics::Rpad->new(
    #                           log_dir => '/var/www/Rpad/server/' . $Rpad_ID
                               log_dir => $dir . $Rpad_ID
                               ) ;
    # to:
    my $R = Statistics::Rpad->new(
                               log_dir => 'c:/Inetpub/wwwroot/Rpad/server/' . $Rpad_ID
    #                           log_dir => $dir . $Rpad_ID
                               ) ;

    # In the IIS "properties" tab, change the following:
    # Under Http Headers|File Types...|New Type..., entered a Content type
    # of text/html for an Associated Extension of Rpad
    # Under Home Directory|Configuration...|App Mappings,
    # added a Extension for pl with an Executable of
    # C:\apps\Perl\bin\perl5.8.4.exe %s %s

    # Used R's png driver rather than ghostscript:
    # in c:/Inetpub/wwwroot/Rpad/.RpadStartup.R,
    # uncommented the following line:
    #
    graphoptions(type="Rpng")

    # In c:/Inetpub/wwwroot/Rpad/.RpadStartup.R, uncommented
    # the following lines to properly specify the location for graphs.
    #
    ## NOTE: This step shouldn't be needed anymore! It should figure it out right,
    ## but I left it in so you can try it if things don't work right.
    assign("RpadDir", envir = Rpad:::.RpadEnv,
           gsub("c:/Inetpub/wwwroot","", getwd(), ignore.case = TRUE) )

    I didn't know how to disable caching on the pages served from Rpad/server*.

    As with apache, you need to lock down the file permissions. Google
    for IIS and IUSR. Also look for "IIS Lockdown Tool".

## Troubleshouting server installations

Look for directories named /var/www/Rpad/server/dd??????????/ (adjust as needed for your root directory). In those directories, do you see eps and png graphics files? Having the eps files but not the png files might indicate that ghostscript isn't working right. If the directories are not being created it indicates that the perl interface is not working right.

If Rpad code sections return something like the following in your browser, then perl or mod_perl is not set up right:

    <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
    <HTML><HEAD>
    <TITLE>405 Method Not Allowed</TITLE>
    </HEAD><BODY>
    <H1>Method Not Allowed</H1>
    The requested method POST is not allowed for the URL /Rpad/server/R_process.pl.<P>
    <HR>
    <ADDRESS>Apache/1.3.33 Server at tomshort Port 80</ADDRESS>
    </BODY></HTML>

In 'General Example', do you see the HTML table just below the "HTML(head(dataset))" line? If so, that suggests that R2HTML is installed correctly.

In an Rpad page, select an R input section. On the first line of one of these, insert "RpadURL()" and hit the calculate button or F9. It should come back with something like "/Rpad/server/ddNgkIdEnXNA". Does it? If it's pointing to the wrong place, the browser won't be able to find the graphics files. If this happened, the browser would be blank where the graphic was supposed to be.

Make sure the *.pl files in /var/www/Rpad/server/ are set to enable execution.

Check the apache (or other server) error logs for additional information (/var/log/apache/error.log on Debian).

To test out the perl portion of Rpad and the browser access, enter the following in your browser:

http://localhost/Rpad/server/Rpad_process.pl?command=login

This should return a directory name, something like ddqbwuyLueIL. This should make a directory of the same name in Rpad/server. Then take this directory name and make another url as follows (replace the ID=ddqbwuyLueIL with your actual directory name):

http://localhost/Rpad/server/R_process.pl?&ID=ddqbwuyLueIL&command=R_commands&R_commands=print('hello' <http://localhost/Rpad/server/R_process.pl?&ID=ddqbwuyLueIL&command=R_commands&R_commands=print%28%27hello%27>)

This should return [1] "hello" to the browser. If that works, then your connection to R should be right.

If graphics appear locally but not on remote machines, it indicates a problem with finding the URL for the graphics files. You may have to modify the Rpad/.RpadStartup.R to explicitly tell R where to find the graphics files, like:

assign("RpadDir", envir = Rpad:::.RpadEnv, gsub("c:/Inetpub/wwwroot","", getwd(), ignore.case = TRUE) )
by Tom Short, tshort@epri.com, Copyright 2005. EPRI, license: GNU GPL v2 or greater