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CodonCode AlignerPhredPhrapConsedPolyPhredTraceViewer |
Known Problems and WorkaroundsThis page describes known problems with the current release of CodonCode Aligner, and how to work around the problems. Problem: Problems running Aligner License Server or CodonCode Aligner on OS X 10.4.10 or 10.4.11 after December 13, 2007 Description: 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: 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: 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: 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: 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:
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: 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:
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: 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:
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