Crashes, freezes and other bugs

Troubleshooting

Freezing bugs

1. Problem: I tried to choose a template set (such as "Rings") in the MarvinSketch applet on my webpage, but the applet does not respond.

   Solution: The most likely cause is that the applet is improperly installed or there is a wrong ARCHIVE or CODEBASE setting in the applet tag, so it cannot find the chemaxon/marvin/templates directory. If Marvin is installed into "somedirectory", then
   

   use this:	ARCHIVE="marvin.jar" CODEBASE="somedirectory"
   NOT this (WRONG!):	ARCHIVE="somedirectory/marvin.jar"

2. P: I tried to do ... but the applet on my page does not respond, and I found a message in the Java Console: "Cannot preload module: ..."

   S: The most likely cause is that the applet is improperly installed or there is a wrong ARCHIVE or CODEBASE setting in the applet tag, so it cannot find the class files in the chemaxon/marvin/modules/ directory. If Marvin is installed into "somedirectory", then
   

   use this:	ARCHIVE="marvin.jar" CODEBASE="somedirectory"
   NOT this (WRONG!):	ARCHIVE="somedirectory/marvin.jar"

3. P: When trying to print a molecule in the applet, it asks "An applet would like to print" (Yes/No) several times, then the applet freezes.

   S: You might use a buggy Java plugin version such as 1.4.0. You should upgrade (or downgrade) Java.
   Detailed explanation: In Java 1.4.0, one Toolkit.getPrintJob() call results in two or more confirm dialogs asking the same question, then one PrintJob.getGraphics() call results in even more questions and freezing when called from an unsigned applet.

4. P: Microsoft Internet Explorer freezes before the applet is finished loading. The following message in shown the status bar:
   "Opening Java class: http://my.site/mydir/chemaxon/marvin/modules/XXX.class"

   S: This is a bug in Microsoft's old Java 1.1 virtual machine, that appears under certain circumstances. As a workaround, you should preload the XXX module. If it still freezes but at class YYY, then you should preload YYY too, etc. See the MarvinView Example XYZ Animations.

5. P: Netscape 6 (Sun JRE 1.3) and Mozilla freeze in Linux when an applet method like MSketch.getMol() is called from JavaScript.

   S: This is a browser/JVM bug that occurs if an applet method is called from JavaScript that requests downloading a class file from the web (with http protocol). The workaround is to preload the extra classes that will be used by the method (see MarvinSketch Example - Import/export of built-in and user defined molecule formats in JavaScript). Another solution is to upgrade Java on the user's machine. The problem does not exist in JRE 1.4.

6. P: MarvinSketch and MarvinView applications sometimes crash under Windows with Java 1.4.1_01.

   S: JRE 1.4.1_01 is a buggy Java version. Many Java applications beside Marvin freeze with this version or other serious problems can occur. See on bugparade.

7. P: MarvinSketch and MarvinView applications can freeze with Java 1.4.1

   S: In wireframe display mode with visible "atom symbols" and "all hydrogens" settings sometimes the JRE cannot draw short lines and this may causes freezing. See on Sun's Bug Parade

Function does not work

• Question: When I select the menu XXX or press button YYY in the applet, I get an error message.
  When I click the "Stack Trace" button, it shows a ClassNotFoundException, ClassFormatError, IncompatibleClassChangeError or something similar.
  Is it my fault (1), a Marvin installation problem (2) or a browser bug (3)?
• Answer: These are all possibilities.
  
  1. If jchem.jar, MarvinBeans.jar or some other JAR file containing Marvin classes is in your CLASSPATH, then it can interfere with the applet.
     Please remove them from the CLASSPATH. Additional libraries such as Marvin should only be specified in a local CLASSPATH inside a script or a Makefile, but not in the global one that is also seen by the web browser.
  2. Marvin might be installed improperly, mixing the new files with an older installation.
     If this is the case, then remove all files and reinstall it again.
  3. There might also be a cache problem with your web browser.
     In Netscape, you can reload all classes with Shift+Reload. If you still have the bug, then try to clear the cache with Edit -> Preferences > Advanced -> Cache and restart the browser.

Browser crashes

• Q: My Netscape 4.x browser crashed when I closed a window containing frames, tables and MarvinView applets. Is it a Marvin bug?

  A: No! It probably has nothing to do with Marvin. Pages containing frames, tables and applets may crash Netscape under certain circumstances. Such crashes are independent of the applet code.

• P: When selecting Print from the browser's File Menu, the applet area is printed in black or it doesn't appear on the paper.

  S: This is a browser/JVM bug, can be found on SUN's Bug Parade site with 4519411 bug Id.
  A fix is integrated into the 1.3.1_03, 1.4.0_01 and above update releases.

• P: Netscape 6 and Netscape 7.0 (Sun JRE 1.3.1) crash in Linux when a signed MarvinView applet tries to evaluate a JavaScript expression.

  S: This is a browser/JVM bug that occurs if netscape.javascript.JSObject.getWindow(applet) is called from Java code. This bug occurs in the following buggy Java versions: 1.3.1_b24, 1.3.1_02-b02. They are found in Netscape 6.x and in Netscape 7.0 as built-in JVM. The only solution is to upgrade Java on the user's machine and set the new Java Environment to the browser. The problem does not exist in JRE 1.3.1_01 and JRE 1.4.x.

• P: Under Linux, reloading an applet a lot of times can cause an out of memory error in the browser.

  S: It is a Java bug in the Linux version of JRE 1.4.2. If there is any reference to the applet in JavaScript, this JRE can not destroy the applet. E.g.:

  if(document.msketch != null) {
          // do someting
  }

  You can find more info about this bug in Sun's Bug Parade. To avoid this memory leak, update your JRE to 1.5.

Other bugs

• Q: How can I report a Marvin bug?

  A: Send an email to describing the circumstances:

  1. What happened, and what did you exactly do before it happened.
  2. The Stack Trace.
     If an error window is popped up, please press "Stack Trace" and send its full contents to us. If you have no error window, then please send the full contents of the Java Console (in Netscape: Communicator/Tools/Java Console).
  3. The http address if you found the bug on an internet web page, otherwise please send us the full page.
  4. Which applet? (MarvinView or MarvinSketch)
  5. Marvin version (see Help/About).