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

Martin Morgan mtmorgan at fhcrc.org
Tue May 19 04:43:21 CEST 2009

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.,


from within the development version of R, or (not encouraged) using
svn from



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?
> Here is the execution and error output:
> ————————————————-
> [icmdev at localhost helloWorld]$ sudo ant mkserver
> Password: 
> Buildfile: build.xml
> mkserver:
> mkserver-jms:
>    [delete] Deleting directory /tmp/helloWorld/server
>     [mkdir] Created dir: /tmp/helloWorld/server/lib
>      [copy] Copying 10 files to /tmp/helloWorld/server/lib
> make-service-server-jms:
>      [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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> https://stat.ethz.ch/mailman/listinfo/bioconductor
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

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