WARNING: java.io.EOFException

what system? Sikuli version?

how did you run the script?

name of the script and path?

32 bit window xp 2002.
Sikuli X r930 (Portable version for 32bit Windows. For 64bit Windows, please run the Sikuli-IDE-w.bat instead of Sikuli-IDE.exe. )

SIKULI_H

_include("../sahisource/business/Report.sah");
_include("../sahisource/business/GandivaCommon.sah");
_include("../sahisource/business/IformInstance.sah");

compatePDFUsingSikuli({"cardId":"CUCD1", "pageNo":2});
function compatePDFUsingSikuli($inputObject)
{
 try
 {
  _log("compatePDFUsingSikuli Started");
  var $dirPathSikuli;
  $dirPathSikuli = _getGlobal("importDIR");
  var $fitToPageIcon = $dirPathSikuli+"sikuli/image/fitToPage.png";
  var $nextArrowIcon = $dirPathSikuli+"sikuli/image/nextArrow.png";
  var $downloadedPdf = $dirPathSikuli+"sikuli/pdf/"+$inputObject.cardId+".pdf";
  var $closePDF = $dirPathSikuli+"sikuli/image/closePDF.png";
  var $pages = $inputObject.pageNo;

  $obj = java.lang.Runtime.getRuntime();
  $obj.gc();
  $cmdline = "C:/Program Files/Adobe/Reader 9.0/Reader/AcroRd32.exe " + $downloadedPdf;
  var $appObj = org.sikuli.script.App.open($cmdline); //Failing At this line
  $appObj = org.sikuli.script.App.focus($cmdline);
  var $screenObj= new org.sikuli.script.Screen();
  $screenObj.wait($fitToPageIcon, 5000);
  $clickIcon = $screenObj.find($fitToPageIcon);
  $clickIcon.click($fitToPageIcon);
  for(var $i=1;$i<=$pages;$i++)
  {
    var $baseImage = $dirPathSikuli+"sikuli/image/"+$inputObject.cardId+"_base"+$i+".png";
    var $matchObj = $screenObj.find($baseImage);
    var $screenScore = parseFloat($matchObj.getScore());
       _assertEqual(true, ($screenScore > 0.987), "Image Match with SIKULI");
    var $nextIcon = $screenObj.find($nextArrowIcon);
     $nextIcon.click($nextArrowIcon);
  }
  $closeIcon = $screenObj.find($closePDF);
  $closeIcon.click($closePDF);
  $obj.gc();
  _log("compatePDFUsingSikuli End");
 }
 catch(e)
 {
  handleFailure(e);
 }
}
.............................................................................................
Set Under User Variable:

SAHI_HOME => D:\sahiPro

SIKULI_HOME => D:\Sikuli-IDE\

PATH => D:\Sikuli-IDE\libs;

Set JAVA_HOME

Set PATH= C:\Program Files \Java\jre6\bin

Seems to be some Java based scripting language/system you are using.

Since the error comes up the first time you are trying to access the Sikuli java stuff and in the stack trace only non-Sikuli items are listed, I guess there is some class path information missing for the Sikuli stuff (sikuli-script.jar).