Michael Shipway wrote: > I believe I have identified the bug, it is in > RWebServices version 1.10.0, > Function: getFunctionDoc() > File: mkMapUtil.R > Lines: 218-283 > > I do not have a copy of the version 1.8.0 code so I cannot confirm that this > has changed in 1.10.0, only that it exists. > > This function now crashes if the <package>/man directory of the package does > NOT contain "R documentation" file in (Rd) format. > NOTE: it does not need to be the correct Rd file for the package, a random > documentation file from another package seems to work as well. > It does check for the existence of several key elements of the Rd format, so > it must be a valid Rd file at least. This must have been a difficult issue to track down. RWebServices is expecting that the package have appropriate documentation, which is why I suggested R CMD check. R's Rd parser changed a lot leading up to 2.10, so RWebServices also changed; there are no easy alternatives to using the non-exported functions you mention below. Martin > > It appears that getFunctionDoc() uses the Rd_db() function to "build a > database of all Rd sources in the package". > This wrapped in a try() function to trap any errors. > However, it appears that finding zero files in not an error, just a null > result, so the function tries to evaluate the database... and fails. > > As long as at least one valid Rd files is in the /man directory, the ant > "map-package" target will succeed. > > It should also be noted that the R-manual says this about Rd_db(): > Warning > These functions are still experimental. Names, interfaces and values might > change in future versions. > > Michael Shipway > > P.S. The document "Parsing Rd Files" Jan 1, 2010 details the Rd file format. > http://developer.r-project.org/parseRd.pdf > "Prior to this document, the R documentation (Rd) file format did not have a > formal description." > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Martin Morgan > Sent: Thursday, January 07, 2010 1:34 PM > To: Michael Shipway > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] RWebServices createMap(): Error in dots[[1L]][[1L]] : > subscript out of bounds > > 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]] >> >> _______________________________________________ >> 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. 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