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

Michael P Shipway mshipwa1 at jhu.edu
Tue May 19 00:27:33 CEST 2009

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?

Here is the execution and error output:
[icmdev at localhost helloWorld]$ sudo ant mkserver
Buildfile: build.xml


   [delete] Deleting directory /tmp/helloWorld/server
    [mkdir] Created dir: /tmp/helloWorld/server/lib
     [copy] Copying 10 files to /tmp/helloWorld/server/lib

     [echo] for service: helloWorld
    [mkdir] Created dir: /tmp/helloWorld/server/helloWorld/src
    [mkdir] Created dir: /tmp/helloWorld/server/helloWorld/bin
    [mkdir] Created dir: /tmp/helloWorld/server/helloWorld/lib
     [copy] Copying 2 files to /tmp/helloWorld/server/helloWorld
     [copy] Copying 1 file to /tmp/helloWorld/server/helloWorld/src
     [copy] Copying 2 files to /tmp/helloWorld/server/helloWorld/src
     [copy] Copying 1 file to /tmp/helloWorld/server/helloWorld/src/org/bioconductor/rserviceJms/services/helloWorld
     [echo] **** javac srcdir= /tmp/helloWorld/server/helloWorld/src  destdir=/tmp/helloWorld/server/helloWorld/bin ****
    [javac] Compiling 3 source files to /tmp/helloWorld/server/helloWorld/bin
    [javac] /tmp/helloWorld/server/helloWorld/src/org/bioconductor/rserviceJms/services/helloWorld/helloWorldSoapBindingImpl.java:10: cannot find symbol
    [javac] symbol  : class HelloWorld_PortType
    [javac] location: package org.bioconductor.rserviceJms.services.helloWorld
    [javac] public class helloWorldSoapBindingImpl implements org.bioconductor.rserviceJms.services.helloWorld.HelloWorld_PortType {
    [javac]                                                                                                   ^
    [javac] 1 error

/usr/lib/R/library/RWebServices/scripts/build.xml:1213: The following error occurred while executing this line:
/usr/lib/R/library/RWebServices/scripts/build.xml:945: The following error occurred while executing this line:
/usr/lib/R/library/RWebServices/scripts/build.xml:956: The following error occurred while executing this line:
/usr/lib/R/library/RWebServices/scripts/build.xml:629: Compile failed; see the compiler error output for details.

Total time: 7 seconds

Note that the line number for the build.xml (629) is a little high
because I've inserted a couple <echo> lines while trying to find the problem.
It should be more like 622, the line which reads:
     <javac srcdir="${destdir}/src" destdir="${destdir}/bin">

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 

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