Thursday, September 29, 2011

Contribute to Practical Code Solutions

Practical Code Solutions has three active authors now and they post blog entries about programming, open source software, networking, scripting and other issues about computers. Since it is not a private site,we are calling new participants which have aimed to write about the issues stated above.

Also the authors which are interested in web programming, desktop programming, databases, operating systems, compilers and interpreters, algorithms, statistics, operations research are welcome!. Requirements are average level of plain English and being a professional or hobbyist on one or more of the subjects described.

Please contact one of the authors of Practical Code Solutions or leave a message under this post to participate. Do not hesitate to share new ideas with us.

DHCP server configuration on Linux.

This page is about configuring a dhcp3-server on a Debian system. You can install the service library with following command;

sudo atp-get install dhcp3-server

When you install dhcp3-server service, you will see dhcp3 directory in folder /etc. That directory contains dhcp3-server configuration file dhcpd.conf. My dhcp3-server service configuration file seems like this;

ddns-update-style none;
option domain-name "sample-dom.sample-com";
option domain-name-servers,;

default-lease-time 600;
max-lease-time 7200;

subnet netmask {
option subnet-mask;
option broadcast-address;
option routers;

host printer {
hardware ethernet 00:26:73:04:08:3f;

host printer1 {
hardware ethernet 00:00:f0:a6:ef:5b;

host AccessPoint_Symbol {
hardware ethernet 00:A0:F8:A7:77:88;

log-facility local7;

First 3 lines are abo ut dn s settings. You can set the domain in domain-name line and you can set dns servers on domai-name-servers line. You can also set multiple dns servers in a single line. If a client gets an ip address and never opens it for 7200 seconds, all information will be deleted for that client. So this date is called expiration date. subnet netmask part defines a scope between "{" and "}" characters. Scope properties are located between parentheses. For example, I want service to distribute ips only from the range of and I don't want the service to distribute ips from the range of and I also want to use this range to special purposes. And then, there are other options needed. subnet-mask, broadcast address and router address. Router address is usually called default gateway.

Host part is used for reservation. printer, printer1 and AccessPoint_Sympol parts are name of the reservations. You have to define a MAC address in a hardware ethernet line and you have to define some reserved ip addresses in fixed-address line. if you use "authoritative" line (you can delete it), all of the clients will record themself to dns server. The last line is just for defining the logging level.

Finally, you will need to start the service. You can use /etc/init.d/dhcp3-server shell script with start, stop, restart, force-reload or status options. If you execute that script without any parameter, it cats the possible options defined below:

Usage: /etc/init.d/dhcp3-server {start|stop|restart|force-reload|status}

Wednesday, September 28, 2011

How to configure site to site VPN profile on Linux,

In this little page I will describe how to configure a vpn connection between two different networks. This connection is usually called site2site vpn.

I used ipsectools and recoon projects to establish a vpn tunnel. In Debian distributions, to install required packages we type:

# sudo apt-get install ipsec-tools racoon

We have to edit some configuration files. I want to explain the related services using the sample configuration. We call Branche Office for the node on the left and central office for the other one. The vpn tunnel is shown in the picture above. The branche office, which is the one we are talking about is a Linux installed machine and the central office is using Nortel Contivity 1740 VPN BOX. The branch office has got / 24 network address. The central office has got / 16 network address. / 16 is for to contain the brache office segment.

But as you know, If you look at from branch office, all other branch offices are behind the central office. So first of all, we have to fix this problem.

The problem is that, if we will define the destination network as, our vpn box device sends packets through the tunnel interface for accessing to / 24 segment. But / 24 segment is already connected to itself! In this sample, our vpn destination network is / 0. Because, this is a branch office and we want to have full control on internet access requests from the branch office. The spd.conf file (/etc/spd.conf) seems like that;

spdadd any -P in none;
spdadd any -P out none;
spdadd any -P out ipsec ah/tunnel/;
spdadd any -P in ipsec ah/tunnel/;

first two lines are required to fix the problem. Last two lines are required to establish vpn tunnel. These are define tunnel source/destination networks and tunnel source/destinatio ends. (aa.aa.aa.aa is ip address of vpn catcher device on the central office and is ip address of branch office box. So it is our linux ip address.)

This site to site vpn tunnel is using pre-shared key mechanism. So we need a pre-shared key configuration file. The file seems like that;

aa.aa.aa.aa [pre-shared key]

This file must be located in /etc/racoon directory in our defined system. The other configuration file that located in /etc/rac oon directory is racoon.conf:

listen {
adminsock "/var/run/racoon.sock" "root" "wheel" 0660;
path pre_shared_key "/etc/racoon/psk.txt";

path certificate "/etc";

remote aa.aa.aa.aa {
exchange_mode aggressive;
my_identifier fqdn "BranchOfficeName";

peers_identifier address aa.aa.aa.aa;
initial_contact on;
ike_frag on;
support_proxy on;
proposal_check obey;

proposal {
encryption_algorithm 3des;
hash_algorithm md5;
authentication_method pre_shared_key;
dh_group 2;

sainfo address any address any {
encryption_algorithm des,3des;
authentication_algorithm hmac_sha1,hmac_md5;
compression_algorithm deflate;
lifetime time 5 min;
pfs_group 2;

the racoon.conf file contains this tunnel configuration, source and destionation network addresses and some ipsec option selections. So you can select different encryption options in this file. But the important point is, each ends should have the same selections. might be a problem for you if it's changeable. If this ip address is changeable, you have to recognize the current value and you have to update it in /etc/spd.conf file. And then, you have to update it on the running service. You can use setkey command to manage tunnel properties.

setkey -D
setkey -DP
setkey -F
/etc/init.d/setkey {start|stop|restart|force-reload}

-D Dump the SAD entries, -F Flush the SAD entries and /etc/init.d/setkey is initialize shell script.

If you create new spd.conf file in different path, you have to kill existing setkey process (or you can use '/usr/sbin/setkey -F -FP' command) and load new conf file with following command:

kill existing setkey process;

/usr/sbin/setkey -F -FP

start setkey with new spd.conf file

/usr/sbin/setkey -f /etc/spd.conf

Finally, if your Linux box's public ip address is changable you can sense current ip address on external interface and update spd.conf file with following php script. It reads some informations from racoon.conf file. If you don't need these parts, you can mark the line with "#" to make it commented.

The filename is createSpd.php (full path: /root/fwscripts/createSpd.php):

$k = 0;
$i = 1;
while($k < 5){
$lan = exec("/sbin/ifconfig eth0 | /bin/grep 'inet addr' | /usr/bin/gawk -F ' ' '{print $2}' | /usr/bin/gawk -F ':' '{print $2}'");
$wan = exec("/sbin/ifconfig ppp0 | /bin/grep 'inet addr' | /usr/bin/gawk -F ' ' '{print $2}' | /usr/bin/gawk -F ':' '{print $2}'");
//$peer = 'aa.aa.aa.aa'; // you can use this line or following line.
$peer = exec("/bin/grep remote /etc/racoon/racoon.conf | /usr/bin/gawk -F ' ' '{ print $2 }'");

$localNet = exec("/bin/grep sainfo /etc/racoon/racoon.conf | /usr/bin/gawk -F ' ' '{ print $3 }'");
$remoteNet = exec("/bin/grep sainfo /etc/racoon/racoon.conf | /usr/bin/gawk -F ' ' '{ print $6 }'");

$blan = strlen($lan);
$bwan = strlen($wan);

echo "strlen($lan):$blan,strlen($wan):$bwan \n";

if($blan < "6" || $bwan < "6" ) {
echo "LAN or WAN hasn't got usable ip address.\n";
echo "The script wait and will be try again!!! ($i) # # # # # # # # # # # \n";
} else {
echo "writing to /etc/spd.conf file as collected information:\n";
exec("/bin/rm -rf /etc/spd.conf.old;/bin/mv /etc/spd.conf /etc/spd.conf.old");
exec("echo 'spdadd any -P out none;' > /etc/spd.conf");
exec("echo 'spdadd any -P in none;' >> /etc/spd.conf");
exec("echo 'spdadd $localNet $localNet any -P in none;' >> /etc/spd.conf");
exec("echo 'spdadd $localNet $localNet any -P out none;' >> /etc/spd.conf");
exec("echo 'spdadd $localNet $remoteNet any -P out ipsec ah/tunnel/$wan-$peer/require;' >> /etc/spd.conf");
exec("echo 'spdadd $remoteNet $localNet any -P in ipsec ah/tunnel/$peer-$wan/require;' >> /etc/spd.conf");
$k = 5;
if($i > 5){
$k = 7;
echo "FNSH\n";

If you want to manage the setkey process with a shell script, you can practically use the following script.


case "$1" in
echo "Running ipsec VPN rules file: /etc/spd.conf";
/usr/sbin/setkey -f /etc/spd.conf
echo "Remove ipsec VPN rules file: /etc/spd.conf"
/usr/sbin/setkey -F -FP
echo "Remove ipsec VPN rules file: /etc/spd.conf"
/usr/sbin/setkey -F -FP
echo "Running ipsec VPN rules file: /etc/spd.conf";
/usr/sbin/setkey -f /etc/spd.conf
echo "Usage: /etc/init.d/setkeyHandle {start|stop|restart}"

exit 0

And then, if you want to add this script to boot progress, you can use update-rc.d command in Debian based Linuxs like following,

# update-rc.d setkeyHandle defaults
Adding system startup for /etc/init.d/setkeyHandle ...
/etc/rc0.d/K20setkeyHandle -> ../init.d/setkeyHandle
/etc/rc1.d/K20setkeyHandle -> ../init.d/setkeyHandle
/etc/rc6.d/K20setkeyHandle -> ../init.d/setkeyHandle
/etc/rc2.d/S20setkeyHandle -> ../init.d/setkeyHandle
/etc/rc3.d/S20setkeyHandle -> ../init.d/setkeyHandle
/etc/rc4.d/S20setkeyHandle -> ../init.d/setkeyHandle
/etc/rc5.d/S20setkeyHandle -> ../init.d/setkeyHandle

If you don't want to use default values, you can define your values in the update-rc.d command like following;

# update-rc.d setkeyHandle start 20 2 3 4 5 . stop 80 0 1 6 .

Passing plain Java objects to R using RCaller

Well, you are using RCaller for your statistical calculations. Probably, you are passing your double arrays to R and type some R commands in order to get the desired outputs. After a calculation process, you handle the returned arrays through the parser. This is the general use of RCaller.

Suppose that you have got a Java class which has got some variables with data types int, short, long, float, double and String. This class also includes some arrays of types int[], double[], ..., String[]. Of course it may include some functions, constructors or anything else. But we don't care about this for now.  How about passing this class with its publicly defined variables to R? Yeah! It is possible in its last submitted revision.

Have a look at the Java class below:

class TestClass {

  public int i = 9;
  public float f = 10.0f;
  public double d = 3.14;
  public boolean b = true;
  public String s = "test";

This class simply includes five publicly defined variables with basic data types. Our other class inherits the TestClass and defines some additional arrays:

class TestClassWithArrays extends TestClass {

  public int[] ia = new int[]{1, 2, 3, 4, 5};
  public double[] da = new double[]{1.0, 2.0, 3.0, 4.0, 9.9, 10.1};
  public String[] sa = new String[]{"One", "Two", "Three"};
  public boolean[] ba = new boolean[]{true, true, false};

Ok, they are very simple but there is no reason those classes not to have any methods. Whatever those classes have methods, we consider them as data structures.

Lets pass this data structure to R:

TestClassWithArrays tcwa = new TestClassWithArrays();
    JavaObject jo = new JavaObject("tcwa", tcwa);

    RCaller rcaller = new RCaller();


Well, if there is no expection we have the results in a R list named "tcwa". This R list includes all of the elements that included in TestClassWithArrays and TestClass with their values.

This is an example of proof, the related @Test method is ready for browsing in the Google Code:

  public void TestClassWithArrays() throws IllegalAccessException, IOException {
    TestClassWithArrays tcwa = new TestClassWithArrays();
    JavaObject jo = new JavaObject("tcwa", tcwa);

    RCaller rcaller = new RCaller();


    int[] expectedIntArray = rcaller.getParser().getAsIntArray("ia");
    for (int i = 0; i < tcwa.ia.length; i++) {
      assertEquals(expectedIntArray[i], tcwa.ia[i]);

    double[] expectedDoubleArray = rcaller.getParser().getAsDoubleArray("da");
    for (int i = 0; i < tcwa.da.length; i++) {
      assertEquals(expectedDoubleArray[i], tcwa.da[i], delta);

    String[] expectedStringArray = rcaller.getParser().getAsStringArray("sa");
    for (int i = 0; i <; i++) {


It is shown that in examples, in R side, we can access to elements with their original names that defined in the Java class. That sounds good.

Finally, we can pass our Java objects with defined contents. This use of RCaller narrows the code of addDoubleArray, addIntArray and reduce all of them to simple command of

 JavaObject jo = new JavaObject("tcwa", tcwa);
rcaller.addRCode ( jo.produceRCode() );

It is simplicity...

Friday, September 23, 2011

How to follow up temperature of system room,

able to visit following link For more example and with different devices like hp, cisco, netscreen..;
also should be check article. This article contain a mobile phone client application to follow up to system room temperature..

I needed to find a solution for the question above for the company which I'm working for. I wanna talk about my quick solution in this article.

There are several IMB Blade chassis, cisco routers, Juniper devices, HP / IBM rock mountable servers, Cisco/Hp/Nortel swithces etc. in my system room.. Actually, there are many alternatives but I selected the IBM Blade chassis to read data of temperature. Because, It contains a lot of blade servers and they are really business critical. Somehow that blade chassis should always be powered on..

I have a Linux server for monitoring the network and something like that. It has got Apache Http Server, MySQL server, a Perl interpreter, a Php interpreter installed. I created a DB and a table to record temperature values. I wrote a script to connect to IBM blade chassis and get temperature value. This script gets the values and record them to a text file;

Read data from IBM Blade Chassis (;

use Net::Telnet ();
$t = new Net::Telnet (Timeout => 10);
$t->login("USERID", "password");
$t->cmd("env -T system:mt[1]");
@lines = $t->cmd("temps");
#print @lines;

open (HEDEF, ">/root/ibmTemperature/lastTemp.txt") || die ("Could not open file
print HEDEF "@lines";
close (HEDEF);

recorded data to the lastTemp.txt file is like this;

Value Warning Reset
----- ------- -------
25.00 38.00 33.00

I need the first value; the value of 25.00 at line 1. Use following command to eleminate unwanted parts.

echo `/usr/bin/head -4 /root/ibmTemperature/lastTemp.txt | /usr/bin/tail -1 | /usr/bin/gawk -F ' ' ' {print $1} '`> /root/ibmTemperature/tempfile.txt

Write data to MySQL table (write.php);

I decide to use different languages for each step. The following php script reads the data from blade chassis, writes the data to mysql database server


I did set to execution permission to the script given above. I also wrote the interpreter path to head of the script source. So therefore, I can execute it directly. I also have to say, I almost always use the full path names in all scripts. Because, if I use relative paths in the scripts, I need login on the treminal / console to execute it to get $PATH variable value from environmental values structure. But, If I use full path in my scripts, I can execute it from everywhere (for example, execute from crontab)

shell script for execute all (,

echo `/usr/bin/head -4 /root/ibmTemperature/lastTemp.txt | /usr/bin/tail -1 | /usr/bin/gawk -F ' ' ' {print $1} '`> /root/ibmTemperature/tempfile.txt

Now, I can add script in the crontab for executing it once a minute and script to be able to trigger the, write.php and some linux commands. And now, I have to explain that linux commands;

a) The head is captured from first 4 lines of lastTemp.txt text file. The pipe captures an output from that head and inputs to tail command. So tail command captures the last line from the output of head command and next pipe creates an input for gawk..

This structure is being executed once a minute for adding the current temperature information to MySQL table with mktime date/time format. The following php script creates a clear output for users on a web-page. (my webpage hosted on /systemRoom/ directory in web root directory.)


System room temperature graphic (Last 24 Hours):";
echo "";
echo "";
echo "\n";
$k = 0;
while($line = mysql_fetch_array($result)) {
$current = (3*$line["temp"]);
$current_temp = $line["temp"];

if($current < "72") { $color = "lightblue.PNG"; } elseif($current < "85") { $color = "blue.PNG"; } else { $color = "red.PNG"; } if($k == 0) { $now = $line["date"]; } else { if(strlen($line["date"]) > 5) {
$end = $line["date"];

echo "\n";
echo "";
//echo "";
echo "

echo "";
echo "";
//echo "Now (0 point on graphic): ".date("Y/m/d - H:i:s", $now)."
Oldest (End point on graphic): ".date("Y/m/d - H:i:s", $end)."

echo "";
echo "

: Recommended Values Range

: Acceptable Values Range

: Dangerous Values Range

Thursday, September 22, 2011

How to Connect Juniper Netscreen Device using Perl Scripts

The site contains a usable and easy library to connect netscreen devices. Name of the library is Net::Telnet::Netscreen. Its use is straightforward:

use Net::Telnet ();
$t = new Net::Telnet (Timeout => 10,
Prompt => '/ns5gt-adsl->/');

$t->login(netscreenUsername, Password);
@lines = $t->cmd("get policy id X");
print @lines;

IP_ADDR_of_NetscreenDevice, netscreenUsername and Password expressions can be replaced with an address, an username and a password, respectively.

How to Connect Cisco Router with Perl Scripts

( Click for PHP version: )

First of all, I have to explain how to configure the Cisco router for telnet connectivity. Because, the Cisco router supports the telnet password and privilege password, It also supports username and password combination for logging in. So there are two different type to logging in.

The following explanation of Cisco router configurations are from stratch. So we have to connect to router via console cable (rollover cable) and serial port on computer and terminal application. If you use MS Windows operating system, you can use Hyper terminal or different third party terminal applications. If you use Linux operating system, you have several choices. I usually use the minicom in my personel use laptop . But the problem is that It hasn't got any serial ports. The solution is to use the usb to serial converter adapter with requisite drivers installed in my Linux.

Router-A Configuration:
Router> Enable
Router# configure Terminal
Enter configuration commands, one per line. End with CNTL/Z.
Router(config)# enable secret 0 cisco
Router(config)# line vty 0 4
% Login disabled on line 6, until 'password' is set
% Login disabled on line 7, until 'password' is set
% Login disabled on line 8, until 'password' is set
% Login disabled on line 9, until 'password' is set
% Login disabled on line 10, until 'password' is set
Router(config-line)#password cisco
00:00:54: %SYS-5-CONFIG_I: Configured from console by console
Router(config-line)# ^Z
Router#write memory

The following perl script to connect to Router-A without AAA;


use Net::Telnet::Cisco;
my $session = Net::Telnet::Cisco->new(Host => 'x.x.x.x');
$session->login('', 'password');

# Execute a command
my @output = $session->cmd('show version');
print @output;

# Enable mode
if ($session->enable("enable_password") ) {
@output = $session->cmd('show privilege');
print "My privileges: @output\n";
} else {
warn "Can't enable: " . $session->errmsg;


After than write this perl script above, of course you have to add execution permission to script file. For example, if the file name of this script is then simply type

chmod +x

Router-B Configuration (Updating to AAA model):

Router(config)#aaa new-model
Router(config)#username TelnetUser privilege 15 password 0 TelnetPassword

The following perl script to connect to Router-B;

The difference between the first sample and the second sample is that,
first router configuration is done with telnet password and password.

Anyway you can use the Net::Telnet::Cisco Library which is written in Perl. If you are using a Linux Distro, probably your package manager already contains it.


use Net::Telnet::Cisco;

my $session = Net::Telnet::Cisco->new(Host => 'x.x.x.x');
$session->login('TelnetUser', 'TelnetPassword');

# Execute a command
my @output = $session->cmd('show version');
print @output;

# Enable mode
@output = $session-> cmd('show privilege');
print "My privileges: @output\n";

If you want to add "Net::Telnet:Cisco" or something like that manually, you can search the related perl library on site
For Example link is used in the sample we have just given.
And you can also download compressed file.

After extracting it, enter extracted directory. Execute perl Makefile.PL.
The "make" and "make install" commands produces the output below:

user@hostn:~/DIR> tar xvfz Net-Telnet-Cisco-1.10.tar.gz 
user@hostn:~/DIR> cd Net-Telnet-Cisco-1.10/
user@hostn:~/DIR/Net-Telnet-Cisco-1.10> perl Makefile.PL

Checking if your kit is complete...
Looks good
Writing Makefile for Net::Telnet::Cisco
user@hostn:~/DIR/Net-Telnet-Cisco-1.10> make
cp blib/lib/Net/Telnet/
AutoSplitting blib/lib/Net/Telnet/ (blib/lib/auto/Net/Telnet/Cisco)
Manifying blib/man3/Net::Telnet::Cisco.3pm
user@hostn:~/DIR/Net-Telnet-Cisco-1.10> make install
ERROR: Can't create '/usr/lib/perl5/site_perl/5.12.3/Net/Telnet'
Do not have write permissions on '/usr/lib/perl5/site_perl/5.12.3/Net/Telnet'
at -e line 1
make: *** [pure_site_install] Error 13
user@hostn:~/DIR/Net-Telnet-Cisco-1.10> sudo make install
root's password:
Appending installation info to /usr/lib/perl5/5.12.3/i586-linux-thread-multi/perllocal.pod

The last step is installing which is required root permissions. So When used without root permission, It returned an error than used "sudo" to get root permission, It finally successful.

Saturday, September 17, 2011

RCaller: Support for sequential commands with a single process

I think, this revision will be the foundation of the version  2.1. RCaller is supposed to be slow but the easiest way of calling R from Java.

Finally I have implemented the method runAndReturnResultOnline() for running sequential commands in a single process. What does this stand for? Let me give an example to explain this:

Suppose that you want to perform a simulation study to measure the success of your new procedure. For this, you decide to draw random numbers from a distribution and calculate something and handle the results in Java. RCaller creates  Rscript processes for each single iteration. This cause to too many operating system calls.

Latest release of RCaller includes the method for this. Lets have a look at the Test file:

  public void onlineCalculationTest() {
    RCaller rcaller = new RCaller();
    assertEquals(rcaller.getParser().getAsIntArray("a")[0], 1);

    assertEquals(rcaller.getParser().getAsDoubleArray("m")[0], 5.5, 0.000001);

    assertEquals(rcaller.getParser().getAsDoubleArray("k")[0], 50.0, 0.000001);

In first stage,we are creating an integer vector and getting the first element. In the second one, we are creating the same integer vector with a different name and calculating the arithmetic mean. In the last one, we are recreating the vector a and getting the median, which is equal to 50.

This example uses the same RCaller object. In first stage, the R executable file (it is /usr/bin/R in my Ubuntu Linux) is created once. In second stage the same R file is used and no longer processes are created again. In this stage, the vector a is accessible and still remains alive. At the last stage, b is alive again and a is recreated. So this example does not cause the R to open and close three times but only once.

This modification speeds up the RCaller, but it can be still considered as slow.
However, it is still easy to implement and much more faster than the previous implementation.

Have Fun!

Thursday, September 15, 2011

Handling R lists with RCaller 2.0

Since RCaller creates an Rscript process for each single run, it is said to be in-efficient for most cases. But there are useful non-hack methods to improve the method. Suppose that your aim is to calculate medians of two double vector like this:

  public void singleResultTest() {
    double delta = 0.0000001;
    RCaller rcaller = new RCaller();
    rcaller.addRCode("x <- c(6 ,8, 3.4, 1, 2)");
    rcaller.addRCode("med <- median(x)");


    double[] result = rcaller.getParser().getAsDoubleArray("med");

    assertEquals(result[0], 3.4, delta);

However, this example considers only computing the median of x, effort for computing medians of three variables needs three process which is very slow. Lists are "vector of vector" objects but they are different from matrices. A list object in R can handle several types of vector with their names. For example

alist <- list (
s = c("string1", "string2", "string3") , 
i = c(5,4,7,6),
d = c(5.5, 6.7, 8.9)

the list object alist is formed by three different kind of vectors: string vector s, integer vector i and double vector d. Also their names are s, i and d, respectively. Accessing elements of this list is straightforward. There are two ways to access to elements. First one is conventional way using indices. When the example above runs, strvec is set to String vector s.

alist <- list (
strvec <- alist[1]
While a list object can handle R objects with their names, we can handle more than more result in a single RCaller run. Back to our example, we wanted to calculate medians of three double vectors in a single run.
  public void TestLists2()throws Exception {
    double delta = 0.0000001;
    RCaller rcaller = new RCaller();
    rcaller.addRCode("x <- c(6 ,8, 3.4, 1, 2)");
    rcaller.addRCode("med1 <- median(x)");

    rcaller.addRCode("y <- c(16 ,18, 13.4, 11,12)");
    rcaller.addRCode("med2 <- median(y)");

    rcaller.addRCode("z <- c(116 ,118, 113.4,111,112)");
    rcaller.addRCode("med3 <- median(z)");

    rcaller.addRCode("results <- list(m1 = med1, m2 = med2, m3 = med3)");


    double[] result = rcaller.getParser().getAsDoubleArray("m1");
    assertEquals(result[0], 3.4, delta);

    result = rcaller.getParser().getAsDoubleArray("m2");
    assertEquals(result[0], 13.4, delta);

    result = rcaller.getParser().getAsDoubleArray("m3");
    assertEquals(result[0], 113.4, delta);
This code passes the tests. By the result at hand, we have three medians of three different vectors with one pass calculation. With this way, an huge number of vectors can be accepted as a result from R and this method may be considered efficient... these test files were integrated to source structure of project in

hope works!

Wednesday, September 14, 2011

about the current Internet Connection in Turkey

30 minutes ago... Something happened. And now: Turkey has a very very slow internet access for the sites out of Turkey. Probably there is something wrong. I wanna share with all quickly.

I checked some news on some web sites and telecommunication companies but I can not find anything about it. Everything is possible. But somebody want to know the reason. :)

Wednesday, September 7, 2011

Embedding R in Java Applications using Renjin

Effort of embedding R in other languages is not a short history for programmers. Rserve, Rjava, RCaller and Renjin are prominent efforts for doing this. Their approaches are completely different. RServe opens server sockets and listens for connections whatever the client is. It uses its own protocol to communicate with clients and it passes commands to R which were sent by clients. This is the neatest idea for me.

RJava uses the JNI (Java Native Library) way to interoperate R and Java. This is the most common and intuitive way for me.

RCaller sends commands to R interpreter by creating a process for each single call. Then it handles the results as XML and parses it. It is the easiest and the most in-efficient way of calling R from Java. But it works.

And finally, Renjin, is a re-implementation of R for the Java Virtual Machine. I think, this will be the most rational way of calling R from Java because it is something like

is not for calling R from Java,
is for calling itself and maybe it can be said that: it is for calling java from java :),
for Java programmers who aimed to use R in their projects

So that is why I participated this project. External function calls are always make pain whatever the way you use.

Renjin is an R implementation in Java.

I think all these paragraphs tell the whole story.

How can we embed Renjin to our Java projects? Lets do something... But we have some requirements:

  1. renjin-core-0.1.2-SNAPSHOT.jar (Download from
  2. commons-vfs-1.0.jar (Part of apache commons)
  3. commons-logging-1.1.1.jar (Part of apache commons)
  4. guava-r07.jar (
  5. commons-math-2.1.jar (Part of apache commons)

Ok. These are the renjin and required Jar files. Lets evaluate the R expression "x<-1:10" which creates a vector of integers from one to ten. Tracking the code is straightforward.
package renjincall;


import r.lang.Context;

import r.lang.SEXP;

import r.parser.ParseOptions;

import r.parser.ParseState;

import r.parser.RLexer;

import r.parser.RParser;

import r.lang.EvalResult;

public class RenjinCall {

  public RenjinCall() {

    Context topLevelContext = Context.newTopLevelContext();

    try {


    } catch (Exception e) {


    StringReader reader = new StringReader("x<-1:10\n");
    ParseOptions options = ParseOptions.defaults();
    ParseState state = new ParseState();
    RLexer lexer = new RLexer(options, state, reader);
    RParser parser = new RParser(options, state, lexer);
    try {
    } catch (Exception e) {
      System.out.println("Cannot parse: " + e.toString());
    SEXP result = parser.getResult();

  public static void main(String[] args) {
    new RenjinCall();

We are initializing the library, creating the lexer and the parser and hadling the result as a SEXP. Finally we are printing the SEXP object (not itself, its String representation)

<-(x, :(1.0, 10.0))
This is the parsed version of our "x<-1:10", it contains the same amount of information but it is a little bit different in form. Since we only parsed the content but it has not been evaluated. Track the code:
EvalResult eva = result.evaluate(topLevelContext, topLevelContext.getEnvironment());

Now, the output is

c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10)

and this is the well known representation of R integer vectors. Of course printing the result in String format is not all the work. We would handle the elements of this array rather than print it. Lets do some work on it:

IntVector vector = (IntVector) eva.getExpression();
    for (int i = 0; i < vector.length(); i++) {
i + ". element of this vector is: " + vector.getElementAsInt(i)

IntVector is defined in renjin core library and is for handling integer vectors. We simple used the .length() and .getElementAsInt() methods like using Java's ArrayList class. Finally the result is

0. element of this vector is: 1
1. element of this vector is: 2
2. element of this vector is: 3
3. element of this vector is: 4
4. element of this vector is: 5
5. element of this vector is: 6
6. element of this vector is: 7
7. element of this vector is: 8
8. element of this vector is: 9
9. element of this vector is: 10

It is nice, hah?

Monday, September 5, 2011

Online R Interpreter - Under development

This is the online R interpreter, Renjin, the Java implementation of the popular statistical programme. Note that it is under development and it includes unimplemented functionality and bugs. But it may be nice to try it online and you can report some bugs or join this project. Link is