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(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
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