[BioC] RWebServices failing on mkserver (ant) target.

Michael P Shipway mshipwa1 at jhu.edu
Tue May 19 17:47:43 CEST 2009


I've installed latest Axis: 1.4 Final (April 22, 2006)
After checking that Tomcat was running and that Axis was "happy" 
I re-ran ant gen-wsdl and got the following, which doesn't mention "_PortType":
-----------------------------------
Buildfile: build.xml

-precompile:

gen-wsdl:

web-clean:
   [delete] Deleting directory /tmp/helloWorld/server

gen-wsdl-jms:
    [mkdir] Created dir: /tmp/helloWorld/wsdl

gen-service-wsdl-jms:
     [echo] for service: helloWorld
     [java] Parsing XML file:  /tmp/helloWorld/wsdl/helloWorld.wsdl
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJComplex.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJLogicalMatrix.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJIntegerArray.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJFactor.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJDataFrame.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJArray.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJMatrix.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJRawMatrix.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJIntegerMatrix.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJComplexMatrix.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJComplexArray.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJNumericArray.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJCharMatrix.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJLogicalArray.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJCharArray.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJRawArray.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/packages/rservices/RJNumericMatrix.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJms/services/helloWorld/HelloWorld.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJms/services/helloWorld/HelloWorldSoapBindingStub.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJms/services/helloWorld/helloWorldSoapBindingImpl.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJms/services/helloWorld/HelloWorldService.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJms/services/helloWorld/HelloWorldServiceLocator.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJms/services/helloWorld/HelloWorldServiceTestCase.java
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJms/services/helloWorld/deploy.wsdd
     [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJms/services/helloWorld/undeploy.wsdd

BUILD SUCCESSFUL
Total time: 8 seconds
-----------------------------------


ant debug lists the following properties:
-----------------------------------
Buildfile: build.xml

debug:

basic-prop:
     [echo] os.arch = i386
     [echo] r.home = /usr/lib/R
     [echo] RWebServices.home = /usr/lib/R/library/RWebServices
     [echo] sjava.home = /usr/lib/R/library/SJava
     [echo] sjava.library.path = /usr/lib/R/lib:/usr/lib/R/library/SJava/libs:/opt/jdk1.6.0_11/jre/lib/i386:/opt/jdk1.6.0_11/jre/lib/i386/server
     [echo] ld.library.path.name = LD_LIBRARY_PATH
     [echo] env ld.library.path = /usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/opt/java/bin:/opt/ant/bin:/opt/tomcat/bin:/export/tomcat55/bin:/export/tomcat60/bin:/opt/eclipse:/home/icmdev/bin
     [echo] ld.library.path = /opt/jdk1.6.0_11/jre/lib/i386/client:/opt/jdk1.6.0_11/jre/lib/i386:/opt/jdk1.6.0_11/jre/../lib/i386
     [echo] jni.dir = /opt/jdk1.6.0_11/jre/lib/i386
     [echo] RWebServices.classpath = /usr/lib/R/library/SJava/org/omegahat/Jars/Environment.jar:/usr/lib/R/library/SJava/org/omegahat/Jars/RJava.jar:/usr/lib/R/library/SJava/org/omegahat/Jars/antlr.jar:/usr/lib/R/library/SJava/org/omegahat/Jars/jas.jar:/usr/lib/R/library/SJava/org/omegahat/Jars/jhall.jar:/usr/lib/R/library/RWebServices/lib/junit-4.1.jar:/usr/lib/R/library/RWebServices/lib/rservices.jar
     [echo] r.global.function = ${r.global.function}
     [echo] r.script.demo = ${r.script.demo}
     [echo] sjava configuration? ok

jms-prop:
     [echo] r.script.jms = ${r.script.jms}
     [echo] jms.home = /usr/lib/incubator-activemq-4.0.2/
     [echo] jms.host = localhost
     [echo] jms.port = 61616
     [echo] jms.classpath = /usr/lib/incubator-activemq-4.0.2/lib/activeio-core-3.0-beta4.jar:/usr/lib/incubator-activemq-4.0.2/lib/activemq-console-4.0.2.jar:/usr/lib/incubator-activemq-4.0.2/lib/activemq-core-4.0.2.jar:/usr/lib/incubator-activemq-4.0.2/lib/backport-util-concurrent-2.1.jar:/usr/lib/incubator-activemq-4.0.2/lib/commons-logging-1.1.jar:/usr/lib/incubator-activemq-4.0.2/lib/geronimo-j2ee-management_1.0_spec-1.0.jar:/usr/lib/incubator-activemq-4.0.2/lib/geronimo-jms_1.1_spec-1.0.jar:/usr/lib/incubator-activemq-4.0.2/lib/mx4j-2.1.1.jar

ws-prop:
     [echo] tomcat.host = localhost
     [echo] tomcat.port = 8080
     [echo] axis.home = /opt/tomcat/webapps/axis
     [echo] axis.classpath = /opt/tomcat/webapps/axis/WEB-INF/lib/axis.jar:/opt/tomcat/webapps/axis/WEB-INF/lib/commons-discovery-0.2.jar:/opt/tomcat/webapps/axis/WEB-INF/lib/commons-logging-1.0.4.jar:/opt/tomcat/webapps/axis/WEB-INF/lib/commons-logging-1.1.jar:/opt/tomcat/webapps/axis/WEB-INF/lib/jaxrpc.jar:/opt/tomcat/webapps/axis/WEB-INF/lib/mail.jar:/opt/tomcat/webapps/axis/WEB-INF/lib/saaj.jar:/opt/tomcat/webapps/axis/WEB-INF/lib/wsdl4j-1.5.1.jar
-----------------------------------

I'm getting the same error message from ant "mkserver".


Michael Shipway
mshipway at jhu.edu
Center for Cardiovascular Bioinformatics and Modeling 
Institute for Computational Medicine 
Johns Hopkins University 
214 Computational Science & Engineering Building
3400 N. Charles St. 
Baltimore, MD 21218 
(410) 516-8616 


----- Original Message -----
From: Martin Morgan <mtmorgan at fhcrc.org>
Date: Monday, May 18, 2009 10:43 pm
Subject: Re: [BioC] RWebServices failing on mkserver (ant) target.
To: mshipway at jhu.edu
Cc: bioconductor at stat.math.ethz.ch


> Hi Michael --
>  
>  Glad to hear you're giving RWebServices a try! I think the problem is
>  occuring in the ant gen-wsdl stage, and suspect that the problem is
>  use of axis other than 1.4. This is just from googling '_PortType'; I
>  don't see these issues with my set-up. Does that help? If not it might
>  help to get the version information on all the tools that are involved
>  -- library(RWebServices); sessionInfo() in R, ant -version, and axis,
>  at least.
>  
>  Also, I'd encourage use of the 'devel' version of R, RWebServices, and
>  SJava, e.g.,
>  
>    source('
>    biocLite('RWebServices')
>  
>  from within the development version of R, or (not encouraged) using
>  svn from
>  
>    
>  
>  Martin
>  
>  Michael P Shipway <mshipwa1 at jhu.edu> writes:
>  
>  > I am trying to install and use RWebServices on a system running 
> CentOS 5 (Linux).
>  > I've installed all the prerequisites, including the optional ones.
>  > I've created a simple R package to test the setup
>  > which takes a single numeric parameter and returns a canned text string.
>  >
>  > I am hung up on step 4.2 of the “Enabling R packages for web or 
> grid services”
>  >  vignette document, which builds a web service server.
>  > One of the java code files which was autogenerated by an earlier 
> step implements 
>  > a java class which does not exist
>  > 
> (org.bioconductor.rserviceJms.services.helloWorld.HelloWorld_PortType 
> ). 
>  >
>  > It appears that this class should also have been autogenerated, 
>  > but I am unable to determine where this should have happened. 
>  >
>  > Can anyone suggest what I may be doing wrong?
>  >

- snip -



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