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

[Martin Morgan]

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('http://bioconductor.org/biocLite.R')
  biocLite('RWebServices')

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

  https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SJava

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?
>
> 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
>
> BUILD FAILED
> /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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-- 
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