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[interhelp #15566] problems with running interproscan #35

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1../interproscan.sh

What is the expected output? What do you see instead?

help menu... instead this:

28/02/2014 16:21:08:143 Welcome to InterProScan-5.3-46.0
Exception in thread "main" 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 'htmlWriter' defined in class path resource 
[spring/jobs/outputWriter/html/htmlWriter-context.xml]: Cannot resolve 
reference to bean 'freeMarkerConfigHtmlWriter' while setting bean property 
'freeMarkerConfig'; nested exception is 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 'freeMarkerConfigHtmlWriter' defined in class path resource 
[spring/jobs/outputWriter/html/htmlWriter-context.xml]: Initialization of bean 
failed; nested exception is org.springframework.beans.FatalBeanException: 
Failed to obtain BeanInfo for class [freemarker.template.Configuration]; nested 
exception is java.beans.IntrospectionException: type mismatch between read and 
write methods
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1360)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1118)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
        at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
        at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:128)
Caused by: org.springframework.beans.factory.BeanCreationException: Error 
creating bean with name 'freeMarkerConfigHtmlWriter' defined in class path 
resource [spring/jobs/outputWriter/html/htmlWriter-context.xml]: Initialization 
of bean failed; nested exception is 
org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for 
class [freemarker.template.Configuration]; nested exception is 
java.beans.IntrospectionException: type mismatch between read and write methods
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
        ... 15 more
Caused by: org.springframework.beans.FatalBeanException: Failed to obtain 
BeanInfo for class [freemarker.template.Configuration]; nested exception is 
java.beans.IntrospectionException: type mismatch between read and write methods
        at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:262)
        at org.springframework.beans.CachedIntrospectionResults.forClass(CachedIntrospectionResults.java:149)
        at org.springframework.beans.BeanWrapperImpl.getCachedIntrospectionResults(BeanWrapperImpl.java:324)
        at org.springframework.beans.BeanWrapperImpl.getPropertyDescriptors(BeanWrapperImpl.java:331)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.filterPropertyDescriptorsForDependencyCheck(AbstractAutowireCapableBeanFactory.java:1242)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1101)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
        ... 21 more
Caused by: java.beans.IntrospectionException: type mismatch between read and 
write methods
        at java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:659)
        at java.beans.PropertyDescriptor.setReadMethod(PropertyDescriptor.java:256)
        at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:282)
        at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:180)
        at org.springframework.beans.ExtendedBeanInfo.<init>(ExtendedBeanInfo.java:100)
        at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:224)
        ... 27 more

What version of the product are you using? On what operating system?

InterProScan-5.3-46.0
Linux pathos 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 
x86_64 x86_64 x86_64 GNU/Linux

java version "1.8.0"
Java(TM) SE Runtime Environment (build 1.8.0-b129)
Java HotSpot(TM) 64-Bit Server VM (build 25.0-b69, mixed mode)
This is perl 5, version 14, subversion 2 (v5.14.2) built for 
x86_64-linux-gnu-thread-multi

Please provide any additional information below.

I followed the installation instructions and I'm not able to run interproscan.

Original issue reported on code.google.com by claudiov...@gmail.com on 28 Feb 2014 at 3:32

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 3 Mar 2014 at 11:51

GoogleCodeExporter commented 9 years ago 
Hi,

The error comes as you are using Java 1.8 and InterProScan 5 will not
work using Java 1.8. You should use Java 1.6 or 1.7. A complete list of
Java requirements for InterProScan 5 can be found on the following page:
https://code.google.com/p/interproscan/wiki/InstallationRequirements

Regards,
Gift

Original comment by nuka....@gmail.com on 6 Mar 2014 at 11:57

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 15 May 2014 at 9:28