Hints for programmers

Map generation

• The following may indicate incomplete documentation (e.g., no man page for a class or function)

ant -Dpkg=<pkg> map-package

> map-package:
>      [exec] >
>      [exec] > library(RWebServices)
>      [exec] Loading required package: SJava
>      [exec] Loading required package: TypeInfo
>      [exec] Loading required package: tools
>      [exec] > createMap(pkgs="<pgk>",
...
>      [exec] Error in get(x, envir, mode, inherits) : invalid first argument
>      [exec] Execution halted
>      [exec] Result: 1

> options(error=recover)
> createMap(pkgs='<pkg>', [etc])
 Error in get(x, envir, mode, inherits) : invalid first argument

Enter a frame number, or 0 to exit

 1: createMap([etc]
 2: createMap([etc]
 3: .local(funcs, pkgs, generateTests, outputDirectory, typeMode, deployMode, v
 4: generateFunctionMap(unlist(sigs, recursive = FALSE), genTest = generateTest
 5: rjSigsToRJMap(rTypeInfo, lookup = lookup, deployMode = deployMode, typeMode
 6: generateDataMap(arg, javaToR = TRUE, deployMode = deployMode, typeMode = ty
 7: updateLookup_jType(rType)
 8: generateJavaBean(rType, jPkgName, slotListJ, typeMode)
 9: createJavaBean(javaType, jPkgName, slotListJ, classDoc, typeMode)
10: paste("\n\t/**\n", "\t* Sets the ", slotName, " value for this ", javaType,
11: get(rSlotName, classDoc)

Equality of data objects in R and Java

ant rservices-test

performs tests to see that numeric values are identical after a round trip to R. These tests should not usually fail.

The default code in test/src/org/bioconductor/rservicesJms/worker/RWorkerDataTest.java checking on data transfer from Java to R use 'identical' on the R side to check that the objects are the same. Thus it is possible to create a custom method for assessing identity on the R side with code like

setMethod("identical",
          signature(x="MyClass", y="MyClass"),
          function(x, y) {
              ## return TRUE if identical,
              ## FALSE or stop("<msg>") otherwise
              TRUE
          })

If you add this to your package (it could also be added to R/<MyClass>.R, starting in the same directory as RWorkerDataTest.java), then be sure to add

exportMethods(identical)

to your NAMESPACE file

Tracking down errors

• Test the function in R alone. Generate the relevant data objects in R and invoke the function.
• Write test cases for data transfer first; there should be templates in test/.../worker/RWorkerDataTest.java. For R to Java, there are facilities to generate a 'mock' data set by calling an R script (in the R/ directory of this class).
• If the data and parameters are transfered correctly, then try evaluating the service

Web service generation

gen-service-wsdl-jms:
     [echo] for service: <pkg>
     [java] Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/discovery/tools/DiscoverSingleton

might indicate that axis.home is not set correctly in RWebServicesEnv.properties. The missing jar file is commons-discovery-*.jar