Known Problems and Workarounds

This page describes known problems with the current release of CodonCode Aligner, and how to work around the problems.

Problem: Advanced assembly options are missing after upgrading to CodonCode Aligner version 3

Description:
Several users have complained that advanced assembly or alignment options are not available anymore after upgrading to CodonCode Aligner version 3.

Causes:

In older CodonCode Aligner version, several "advanced" assembly options were accessible through a single menu item and toolbar button (including "Compare contigs" and "Assemble in groups (by name)".

All of these functions are still available in CodonCode Aligner version 3. The "Contig" menu has been re-organized so that each of the advanced assembly options now has a separate menu item. Similarly, "Compare contigs" and "Assemble in groups" now have separate toolbar icons; you may need to change the "Toolbars" preferences to see the new icons.

Solution:

Use the specific menu item in the "Advanced Assembly" submenu in the "Contig" menu. Note that the previous option "Merge existing contigs" has been replaced by the "Assembly with Preprocessing" option (if you do not need pre-processing, the simple "Assemble" option will also merge existing contigs).

To add a new icon (e.g. for "Compare Contigs)" to the toolbar in the project window:

Open the preferences (from the "Edit" menu in Windows, or the "CodonCode Aligner" menu on Mac OS X).
Select "Toolbars" on the left.
In the drop down menu at the right side (under "Buttons to show"), select "Project View"
Scroll down the list of toolbar buttons until you see "Compare Contigs"
Click on the check box before "Compare Contigs" to select it
Click "OK" to close the preferences.

Problem: Problems running Aligner License Server or CodonCode Aligner on OS X 10.4.10 or 10.4.11 after December 13, 2007

Description:
Aligner License Server version 1.1.0 and older failed to start on OS X 10.4.10 and 10.4.11 after December 13, 2007. Users of CodonCode Aligner version 2.0.1 and older on OS X 10.4.10 or 10.4.11 experienced problems when saving, exporting, or importing.

Causes:

An Apple software update released between December 13, 2007 and December 17, 2007 broke a library used by Aligner License Server 1.1.0 and older, and by CodonCode Aligner 2.0.1 and older.

Workaround:

Aligner License Server users should update to Aligner License Server version 1.2.0 or newer. Update instructions are available at http://codoncode.net/bb/viewtopic.php?t=62. Please follow the update instructions carefully!

CodonCode Aligner users with a current update and support agreement should update to CodonCode Aligner version 2.0.3 or newer.

Users of CodonCode Aligner version 1.6.3 and older without a current update and support agreement can fix the problem by following the instructions at http://codoncode.net/viewtopic.php?t=14.

Problem: CodonCode Aligner does not start after updating to OS X 10.4.6

Description:
After updating to OS X 10.4.6, CodonCode Aligner does not start up anymore.

Causes:

A bug in the OS X updater that affects some (but not all) computers.

Workaround:

Open a terminal window (/Applications/Utilities/Terminal), and type or paste the following line:

/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Commands/update_sharing 1.4

Press return. When the command prompt returns, Aligner should run without problems. If not, please contact us.

Problem: CodonCode Aligner hangs on OS X 10.2

Description:
On OS X 10.2, CodonCode Aligner 1.5.1 hangs, in particular when trying to open the preferences.

Causes:

A bug that affects only OS X 10.2 (but not OS X 10.3 and newer or Windows).

Workaround:

Please update your version of CodonCode Aligner to version 1.5.2. This problem was fixed in CodonCode Aligner 1.5.1c.

Please note that we have stopped supporting OS X 10.2. Apple has stopped any Java development on OS X 10.2 when they released OS X 10.3, and the Java version on OS X 10.2 has many significant limitations. If you are still using OS X 10.2, we suggest that you update to OS X 10.3 or 10.4, if possible.

Problem: CodonCode Aligner does not start or crashes on OS X 10.3.9

Description:
When trying to run CodonCode Aligner, the Aligner Updater, or the Aligner Installer on OS X 10.3.9, the program icon bounces a few times in the dock, but the application does not start (or crashes).

Causes:

This Quicktime 7.0.4 update (released Jan 10, 2006) contains a bug that causes many Java applications to fail. After installing this update, CodonCode Aligner fails to run.

Workaround:

Please update your version of CodonCode Aligner to the most current version (1.5.1 or newer). This problem was fixed in CodonCode Aligner 1.5.

Note that similar problem occured with the original update to OS X 10.3.9. This update broke Java, causing problems with all Java applications and with Safari. Apple released a Java updates that fixes this problem. For more information, please visit http://www.apple.com/support/downloads/javaupdateformacosx1039.html and http://docs.info.apple.com/article.html?artnum=301380.

Problem: The Aligner application / Aligner Updater / Aligner Installer crashes on OS X 10.3

Description:
When trying to run CodonCode Aligner, the Aligner Updater, or the Aligner Installer on OS X 10.3, the program crashes.

Causes:

A bug in the interaction of Java with the font management on OS X 10.3 can cause Java programs like CodonCode Aligner to crash when fonts are disabled.

Workaround:

Open the "FontBook" application (in /Applications)
Enable all disabled fonts (especially commonly used fonts like Times, Monaco, Geneva, etc.)
Quit the "FontBook" application

Many thanks to Dent Earl for reporting and helping to solve this problem. This problem has been reported to Apple.

Problem: Very slow startup

Description:
When starting CodonCode Aligner, the startup takes a very long time, or Aligner may not start at all.

Causes:

This is caused by automatic scanning of archives by anti-virus software. We have seen this problem with Sophos Anti-Virus, but since scanning archives and compressed files is a known cause of problems for anti-virus software, you may see similar problems if you are using other anti-virus software.

Workaround:

Turn off automatic scanning of archives and compressed files in your anti-virus software

Thanks to Gert Woerheide for reporting and helping to solve this problem. You can read the messages about this problem in our support forum.

Problem: Aligner 1.2.4 crashes on OS X 10.3 (Panther)

Description:
CodonCode Aligner crashes randomly on OS X 10.3 with "KERN_PROTECTION_FAILURE" and similar error messages (actually, Java crashes, but that kills Aligner, which uses Java).

Causes:

This is due to a bug in Java 1.3.1 on OS X 10.3. It has been reported to Apple (bug report ID 3709796). Similar problems have been reported for other Java-based applications, for example ImageJ.

Workaround:

Please download a newer version of the CodonCode Aligner installer. Newer versions of CodonCode Aligner use Java 1.4.2 on OS X 10.3, which crashes much less frequently.
We also suggest that you install any available operating system and Java updates, if you have not already done so.