RWebServices failing on mkserver (ant) target.
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@michael-p-shipway-3459
Last seen 9.6 years ago
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/or g/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/rse rviceJms/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
RWebServices RWebServices • 1.1k views
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@martin-morgan-1513
Last seen 6 weeks ago
United States
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/r serviceJms/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 > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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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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/rserviceJ ms/services/helloWorld/HelloWorld.java [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJ ms/services/helloWorld/HelloWorldSoapBindingStub.java [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJ ms/services/helloWorld/helloWorldSoapBindingImpl.java [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJ ms/services/helloWorld/HelloWorldService.java [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJ ms/services/helloWorld/HelloWorldServiceLocator.java [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJ ms/services/helloWorld/HelloWorldServiceTestCase.java [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJ ms/services/helloWorld/deploy.wsdd [java] Generating /tmp/helloWorld/wsdl/org/bioconductor/rserviceJ ms/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/SJa va/libs:/opt/jdk1.6.0_11/jre/lib/i386:/opt/jdk1.6.0_11/jre/lib/i386/se rver [echo] ld.library.path.name = LD_LIBRARY_PATH [echo] env ld.library.path = /usr/kerberos/bin:/usr/local/bin:/us r/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:/op t/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/omeg ahat/Jars/Environment.jar:/usr/lib/R/library/SJava/org/omegahat/Jars/R Java.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/or g/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@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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Thank you Martin, your suggestion got me pointed in the correct direction. It seems it was an Axis feature that was tripping me up. I found an Axis mailing list archive entry which seem to apply. http://mail-archives.apache.org/mod_mbox/ws-axis- user/200512.mbox/%3c43A3AE62.8080006 at jp.fujitsu.com%3e Simply put, Axis doesn't like the package name to be the same as an included function. Therefore, it appended "_PortType" to one of them, but didn't use the changed name in all places. When I changed the spelling of the R package name, my problem went away. 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@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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