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

[Shaun Jackman <sjackman@gmail.com>]

Hi Charles,

I've just uploaded IGV 2.0.6-1.

What do I do with the pristine-tar and meta branches? These branches
are new to me.

Cheers,
Shaun

On 28 June 2011 10:38, Shaun Jackman <sjackman@gmail.com> wrote:
> 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$
> org/apache/log4j/RollingFileAppender.class
>
> Cheers,
> Shaun
>
> 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,
>