[BioC] RWebServices createMap(): Error in dots[[1L]][[1L]] : subscript out of bounds

[Martin Morgan]

Michael Shipway wrote:
> Can anyone help me with this, I cannot recreate a web service on a 2nd
> machine?
> 
> I've developed and tested an RWebservices based web service on CentOS
> release 5.3 (Final) running in a VM on my windows XP box.
> 
> However, when I transferred the code to my production machine, CentOS
> release 5.4 (Final),  I cannot map the package (e.g. generate Java code).
> 
> Other differences between the two setups:
> 
> Feature                                   Dev          Production
> 
> RWebServices Version       1.8.0      1.10.0
> 
> R version                                 2.8.1       2.10.0
> 
>  
> 
> I've confirmed that my R package is installed and functioning correctly on
> both machines.
> 
> When I run "ant -Dpkg=natreeV3 map-package" on the production machine, I get
> the error message:
> 
> "Error in dots[[1L]][[1L]] : subscript out of bounds"

I think the issue is in your package documentation, though am not sure.
Does R CMD build <your_pkg> && R CMD check <your_package>_<vers> suggest
anything? Some more below...

> 
>  
> 
> Below is the full verbose output of the map-package
> 
> --------------------------------------------------------------------
> 
> Buildfile: build.xml
> 
>  
> 
> -user-tuning-properties-exist:
> 
>  
> 
> -unpack-tuning-properties:
> 
>  
> 
> map-package:
> 
>      [exec] >
> 
>      [exec] >             library(RWebServices)
> 
>      [exec] Loading required package: SJava
> 
>      [exec] Loading required package: TypeInfo
> 
>      [exec] Loading required package: tools
> 
>      [exec] >             createMap(pkgs="natreeV3",
> 
>      [exec] +             generateTests=TRUE,
> 
>      [exec] +             outputDirectory="/home/mshipwa1/natreeV3",
> 
>      [exec] +             typeMode="javalib",
> 
>      [exec] +             deployMode="jms",
> 
>      [exec] +             wsdlStyle="WRAPPED",
> 
>      [exec] +             wsdlUse="LITERAL",
> 
>      [exec] +             extraClasses="",
> 
>      [exec] +             pkgRoot="org.bioconductor",
> 
>      [exec] +             verbose=TRUE)
> 

the command above ('createMap(...)') can be executed in an R session,
after library(RWebServices). You can then debug the error message using,
e.g., traceback() or debug(). A little more below...

>      [exec] Loading required package: tree
> 
>      [exec] ********************************************
> 
>      [exec]  ***   resolve all data type mapping    *****
> 
>      [exec]  ********************************************
> 
>      [exec] >>>>>> Generate data map for extraClasses:
> 
>      [exec] >>>>>> Generate data map for R function:
> 
>      [exec] character test1(numeric depth)      data map for:  character
> 
>      [exec]     data map for:  numeric
> 
>      [exec] >>>>>> Generate data map for R function:
> 
>      [exec] list test2(numeric depth)   data map for:  list
> 
>      [exec]     data map for:  numeric
> 
>      [exec] >>>>>> Generate data map for R function:
> 
>      [exec] character naTree5(character dataFileName, numeric ndays, numeric
> features, numeric treeDepth)       data map for:  character
> 
>      [exec]     data map for:  character
> 
>      [exec]     data map for:  numeric
> 
>      [exec]     data map for:  numeric
> 
>      [exec]     data map for:  numeric
> 
>      [exec] >>>>>> Generate data map for R function:
> 
>      [exec] list naTree(character dataFileName, numeric ndays, numeric
> features, numeric treeDepth)     data map for:  list
> 
>      [exec]     data map for:  character
> 
>      [exec]     data map for:  numeric
> 
>      [exec]     data map for:  numeric
> 
>      [exec]     data map for:  numeric
> 
>      [exec] ---------------------------------------------------------------
> 
>      [exec] [R Type]  =>  [Java Type]  [Java Package]  [R Package]
> [TypeGroup]  [R->Java]  [Java->R]
> 
>      [exec] ---------------------------------------------------------------
> 
>      [exec] ---------------------------------------------------------------
> 
>      [exec] ********************************************
> 
>      [exec]  ****     resolve function mapping      *****
> 
>      [exec]  ********************************************
> 
>      [exec] >>>>>> Generate function map for R package:  natreeV3
> 
>      [exec] >> (1) java function signature:
> 
>      [exec] [[1]]
> 
>      [exec] String[] test1(double[] depth)
> 
>      [exec] [[2]]
> 
>      [exec] Object[] test2(double[] depth)
> 
>      [exec] [[3]]
> 
>      [exec] String[] naTree5(String[] dataFileName, double[] ndays, double[]
> features, double[] treeDepth)
> 
>      [exec] [[4]]
> 
>      [exec] Object[] naTree(String[] dataFileName, double[] ndays, double[]
> features, double[] treeDepth)
> 
>      [exec] Error in dots[[1L]][[1L]] : subscript out of bounds
> 
>      [exec] Calls: createMap ... .local -> getFunctionDoc -> mapply -> .Call
> -> <Anonymous>

getFunctionDoc is the clue here that is a documentation problem. Likely
it is one of these (ugly) lines

        db_alias_texts <- mapply(tools:::.Rd_get_section, db,
            which = "alias")
        db_description_texts <- mapply(tools:::.Rd_get_section,
            db, which = "description")
        db_value_texts <- mapply(tools:::.Rd_get_section, db,
            which = "value")
        db_arg_texts <- mapply(tools:::.Rd_get_section, db,
            which = "arguments")

Martin

>      [exec] Execution halted
> 
>      [exec] Result: 1
> 
>    [delete] Deleting: /home/mshipwa1/natreeV3/null1969125778
> 
>  
> 
> BUILD SUCCESSFUL
> 
> Total time: 2 seconds
> 
> 
> 	[[alternative HTML version deleted]]
> 
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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