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  1. Jalview
  2. JAL-2285

CLI operation fails in Jalview 2.10.0 when given incorrect ext.dirs path

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Trivial
    • Resolution: Not A Bug
    • Affects Version/s: 2.10.0
    • Fix Version/s: None
    • Component/s: Command Line Interface
    • Labels:
      None
    • Environment:
      OSX 10.9.5, OSX 10.11.6

      Description

      This issue was discovered this afternoon during a meeting I had with Fabio.

      Attempting to run Jalview 2.10.0 from command line fails with an exception. See stack trace below:

      Java version: 1.8.0_25
      x86_64 Mac OS X 10.11.6
      Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/log4j/Layout
      at jalview.bin.Jalview.doMain(Jalview.java:209)
      at jalview.bin.Jalview.main(Jalview.java:179)
      Caused by: java.lang.ClassNotFoundException: org.apache.log4j.Layout
      at java.net.URLClassLoader$1.run(URLClassLoader.java:372)
      at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.net.URLClassLoader.findClass(URLClassLoader.java:360)
      at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
      at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
      at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
      ... 2 more

      Seems like something is screwed up with the packaging. Initially we thought it was a class path issue but couldn't get it resolved by specifying the class path with the command. We also tried downloading the latest log4j lib to the class path and that didn't work either.





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            Assignee:
            jprocter Jim Procter
            Reporter:
            tcnofoegbu Tochukwu Charles N Ofoegbu
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              Dates

              Created:
              Updated:
              Resolved: