Hi Chris,
The KEGG search works fine for me, so the problem should be elsewhere..
Can you try to compile & run it without IntelliJ?
Running 'mvn package' in the command line will do it.
Tomas
On Mar 9, 2012, at 6:01 PM, Pudney Chris (ext) GBJH wrote:
G'day,
Also getting the following error for KEGG searches:
[16:57:37|SEVERE|WorkerThread]: Unhandled exception
java.lang.NoClassDefFoundError: Could not initialize class
org.apache.axis.client.AxisClient while processing task Peak
identification of 476.308 using KEGG Compound
Database(java.lang.NoClassDefFoundError: Could not initialize class
org.apache.axis.client.axiscli...@org.apache.axis.client.Service.getAxisClient<mailto:org.apache.axis.client.axiscli...@org.apache.axis.client.Service.getAxisClient>(Service.java:104))
java.lang.NoClassDefFoundError: Could not initialize class
org.apache.axis.client.AxisClient
at org.apache.axis.client.Service.getAxisClient(Service.java:104)
This is a bit odd since lib/ contains axis-1.4.jar which has holds
org.apache.axis.client.Service.getAxisClient
Regards,
Chris.
On 09/03/12 16:10, Pudney Chris (ext) GBJH wrote:
G'day,
I got this working with IntelliJ.
I've done some limited testing and got a ClassNotFoundException for
ChemSpider searches indicating that Apache Commons Discovery is missing.
[15:53:02|SEVERE|WorkerThread]: Unhandled exception
java.lang.NoClassDefFoundError:
org/apache/commons/discovery/tools/DiscoverSingleton while processing
task Peak identification of 274.911 using ChemSpider
Database(java.lang.NoClassDefFoundError:
org/apache/commons/discovery/tools/discoversingle...@org.apache.axis.components.logger.LogFactory$1.run(LogFactory.java:45))
java.lang.NoClassDefFoundError:
org/apache/commons/discovery/tools/DiscoverSingleton
A quick comparison of the old lib/ directory with the new
target/MZmine-*/lib/ directory shows the following are missing:
commons-discovery
jcommon-xml
ostermillerutils
resolver
saaj
serializer
wsdl4j
xercesSamples
Regards,
Chris.
Hi Chris, Sandra, everyone else,
As I mentioned previously, I have switched the MZmine build system
from ant to maven. I am committing the changes at the moment.
It seems to work fine, but there might still be hidden problems, so
please be careful when using the trunk over next few days.
One of the required changes was to move the src/ folder to
src/main/java/ (standard folder structure required by maven). I am
not sure what this change might cause when you update your branch
sources... so please make sure to keep a backup of your files, just
in case :)
I created a fake maven repository in lib/ to include some of the
dependencies that do not (yet) have their own maven repository.
To build MZmine from scratch, please run 'mvn package'.
The build should appear in the target/MZmine-version/ folder.
So far I tried using Eclipse and it seems to have a reasonably good
integration of maven.
Let me know if you have any other questions.
Cheers,
Tomas
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
TEL: +81-98-966-8684
This message may contain confidential information. If you are not the
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Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
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===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
TEL: +81-98-966-8684
------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
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