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Re: Update of the Integrative Genomics Viewer to version 2.0 ?

Hi Charles,

I'm going to be pretty busy for about two weeks. I probably won't have
time to look into this until then. If 1.5.65 compiles cleanly and
works, there's no harm in uploading that in the mean time. I can take
a look into the 2.0 log4j issue two weeks from now. The
RollingFileAppender class is at least present in the jar:

$ strings /usr/share/java/log4j-1.2-1.2.15.jar |grep /RollingFileAppender.class$


On 27 June 2011 23:17, Charles Plessy <plessy@debian.org> wrote:
> Dear Shaun and everybody,
> There is a major update of the IGV, which may be interesting to follow.
> Unfortunately, I have tried to build it from source but could not produce a JAR
> file that can be executed.  I have been reluctant to modify the master branch
> of the Git repository where we manage the igv package, as there is a version
> 1.5.65 on the upstream download area, but not in their changelog, which
> suggests that there may be some maintainance.
> What shall I do: share work on version 2.0 in our master branch, make a
> separate branch for the moment, or provide a temporary fork separately ?
> For the record, the error I get is:
> log4j:ERROR Could not find value for key log4j.appender.R
> log4j:ERROR Could not instantiate appender named "R".
> ERROR [2011-06-28 15:16:26,637]  [DefaultExceptionHandler.java:42] [main]  Unhandled exception
> java.lang.NoClassDefFoundError: org/apache/log4j/RollingFileAppender
>        at org.broad.igv.ui.Main.initializeLog(Main.java:225)
>        at org.broad.igv.ui.Main.initApplication(Main.java:94)
>        at org.broad.igv.ui.Main.main(Main.java:70)
> Caused by: java.lang.ClassNotFoundException: org.apache.log4j.RollingFileAppender
>        at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
>        at java.security.AccessController.doPrivileged(Native Method)
>        at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
>        at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
>        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
>        at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
>        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:334)
>        ... 3 more
> Have a nice day,

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