[MOBY-l] Problems starting dashboard in trunk

[Björn Usadel]

Hi,

looks very similar to what Marc experienced on his Mac.

I attached his solution below. We don't know if this is the appropriate 
solution, as we are really more into Perl Biomoby than Java Biomoby. But 
this did the trick for Marc. Maybe one of the Java guys can chip in here?

Cheers,
Björn
---------------
Hi Björn,

yes i can comment on this:

When looking at the stack trace of the exception thrown you see that it 
is again  the

java.lang.NoClassDefFoundError: org/apache/commons/collections/map/LinkedMap

error. So you’ll need to get  version 3.2 of the commons-collections 
(commons-collections-3.2.jar)
and put it in the right place. I did this manually on the command line 
since i do know nothing about
“maven dependencies” -  but i guess that if you change 
“commons-collections-2.1.jar” to
“commons-collections-3.2.jar” in the dependency list you’ll be fine 
after rebuilding the dashboard
(and i suggest you do “ant clean” or whatever is the equivalent to this 
in eclipse before rebuilding).

I hope this solves your problem,

bests,
Marc

P.S.: I do not think this is a JVM-related problem as i am using the 
same version of
apple’s JVM.

Andreas Groscurth wrote:
> Hi Ola,
> 
> I hope a apple person can jump in here because I have no idea about
> apples and its JVM.... is it a JRE or a JDK ?
> 
> andreas
> 
> Ola Spjuth wrote:
>> Hi Andreas,
>>
>> Sorry, I should have clarified this:
>>
>> I have apples JVM1.5.0 installed at
>> /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0 with the
>> following structure:
>>
>> Classes
>> Commands
>> Headers
>> Home
>>     bin
>>     lib
>> Libraries
>> Resources
>>
>> The JRE container in Eclipse points to
>> /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home, and
>> setting is to not use deprecated JRE_LIB. I have set the JAVA_HOME in
>> Eclipse and in bash to this as well, so that should not be a problem
>> (don't know why that wasn't picked up by ant). Anyway, I can build
>> jmoby, moses datatypes, run sample clients, but not dashboard. I do
>> see commons-collections-2.1.jar under Maven dependencies in Eclipse.
>>
>> Cheers,
>>
>> /Ola
>>
>> On Mar 27, 2008, at 16:28 , Andreas Groscurth wrote:
>>
>>> Hi Ola,
>>>
>>> the current docs
>>> (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/EclipseAndJMoby.html)
>>> do not suggest to edit any build files... and the 'Home' makes me
>>> wondering - what Java installation is that ? never seen a Java
>>> installation that has a 'Home' directory inside ?!
>>>
>>> which Java version do you work with - is your JAVA_HOME set correctly
>>> and does Eclipse uses the correct JDK (and not some JRE) ?
>>>
>>> Best
>>> andreas
>>>
>>> Ola Spjuth wrote:
>>>> Hi,
>>>>
>>>> After following the docs for jMoby in eclipse (I had to add Home/ to
>>>> line line 108 in build.xml to look like <fileset
>>>> dir="${java.home}/../Home/lib">), and generating datatypes, I tried
>>>> to start dashboard and got the following exception:
>>>>
>>>> dashboard:
>>>> [Dashboard] Exception in thread "main"
>>>> java.lang.NoClassDefFoundError:
>>>> org/apache/commons/collections/map/LinkedMap
>>>> [Dashboard]     at
>>>> org.apache.commons.configuration.BaseConfiguration.<init>(BaseConfiguration.java:54)
>>>>
>>>> [Dashboard]     at
>>>> org.apache.commons.configuration.CompositeConfiguration.clear(CompositeConfiguration.java:159)
>>>>
>>>> [Dashboard]     at
>>>> org.apache.commons.configuration.CompositeConfiguration.<init>(CompositeConfiguration.java:56)
>>>>
>>>> [Dashboard]     at
>>>> org.biomoby.service.dashboard.DashboardConfig.get(DashboardConfig.java:117)
>>>>
>>>> [Dashboard]     at
>>>> org.biomoby.service.dashboard.DashboardConfig.getString(DashboardConfig.java:243)
>>>>
>>>> [Dashboard]     at
>>>> org.biomoby.service.dashboard.Dashboard.getProperty(Dashboard.java:208)
>>>> [Dashboard]     at
>>>> org.biomoby.service.dashboard.Dashboard.getComponent(Dashboard.java:485)
>>>>
>>>> [Dashboard]     at
>>>> org.biomoby.service.dashboard.Dashboard.<init>(Dashboard.java:176)
>>>> [Dashboard]     at
>>>> org.biomoby.service.dashboard.Dashboard.main(Dashboard.java:988)
>>>>
>>>> I am new to maven and don't really now how I should fix this
>>>> dependency.
>>>> Any suggestions for a solution?
>>>>
>>>> Cheers,
>>>>
>>>> /Ola
>>>> _______________________________________________
>>>> moby-l mailing list
>>>> moby-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/moby-l
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