Hi everybody, I'm using NetBeans and RCaller to build a little GUI in Java. Within the code I'm reading .fcs files using read.FCS from the flowCore package. When I add the code to the R console everything works fine. If I run the code in Netbeans the following error occurs: Error: Error in isVersioned(object) : Error: error in evaluating the argument 'object' Error: for function 'isVersioned': error in `[<-`(`*tmp*`, names(versions), value = list()) : Error: could not find function "loadMethod" Error:Calls: as ... asMethod -> new -> initialize -> initialize -> .local -> [<- Error:Calls: read.FCS ... validObject -> anyStrings -> validityMethod -> isVersioned Error: Execution stopped I set: caller.setRscriptExecutable("../R-3.1.0/bin/x64/Rscript.exe"); and caller.setRExecutable(".../R-3.1.0/bin/x64/R.exe"); I would be very thankful for any help. Joachim -- output of sessionInfo(): R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Runiversal_1.0.2 EBImage_4.7.0 flowViz_1.29.0 lattice_0.20-29 [5] flowCore_1.31.1 loaded via a namespace (and not attached): [1] abind_1.4-0 Biobase_2.25.0 BiocGenerics_0.11.0 [4] corpcor_1.6.6 DEoptimR_1.0-1 graph_1.43.0 [7] grid_3.1.0 hexbin_1.26.3 IDPmisc_1.1.17 [10] jpeg_0.1-8 KernSmooth_2.23-12 ks_1.9.1 [13] latticeExtra_0.6-26 locfit_1.5-9.1 MASS_7.3-31 [16] misc3d_0.8-4 mvtnorm_0.9-9998 parallel_3.1.0 [19] pcaPP_1.9-49 png_0.1-7 RColorBrewer_1.0-5 [22] rgl_0.93.996 robustbase_0.90-2 rrcov_1.3-4 [25] stats4_3.1.0 tiff_0.1-5 tools_3.1.0 -- Sent via the guest posting facility at bioconductor.org.

On 04/16/2014 04:46 AM, Joachim Schumann [guest] wrote: > > Hi everybody, > > I'm using NetBeans and RCaller to build a little GUI in Java. Within the code I'm reading .fcs files using read.FCS from the flowCore package. When I add the code to the R console everything works fine. If I run the code in Netbeans the following error occurs: > Error: Error in isVersioned(object) : > Error: error in evaluating the argument 'object' > Error: for function 'isVersioned': error in `[<-`(`*tmp*`, names(versions), value = list()) : > Error: could not find function "loadMethod" > Error:Calls: as ... asMethod -> new -> initialize -> initialize -> .local -> [<- > Error:Calls: read.FCS ... validObject -> anyStrings -> validityMethod -> isVersioned > Error: Execution stopped > > I set: > caller.setRscriptExecutable("../R-3.1.0/bin/x64/Rscript.exe"); > and > caller.setRExecutable(".../R-3.1.0/bin/x64/R.exe"); > > I would be very thankful for any help. I think the embedded R is running without the 'methods' package attached, and what you're actually seeing is a missing import(methods) in one of the package NAMESPACE files. It would help to have a minimal example of the R code that causes the problem; I think it could be emulated for some script trouble.R with Rscript -f trouble.R, since Rscript doesn't load the methods package either. The work-around in your code is I think to explicitly load the methods package at the start of your session. It would be good to have a reproducible example, if possible... Good luck wiht the gui! Martin > > Joachim > > -- output of sessionInfo(): > > R version 3.1.0 (2014-04-10) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Runiversal_1.0.2 EBImage_4.7.0 flowViz_1.29.0 lattice_0.20-29 > [5] flowCore_1.31.1 > > loaded via a namespace (and not attached): > [1] abind_1.4-0 Biobase_2.25.0 BiocGenerics_0.11.0 > [4] corpcor_1.6.6 DEoptimR_1.0-1 graph_1.43.0 > [7] grid_3.1.0 hexbin_1.26.3 IDPmisc_1.1.17 > [10] jpeg_0.1-8 KernSmooth_2.23-12 ks_1.9.1 > [13] latticeExtra_0.6-26 locfit_1.5-9.1 MASS_7.3-31 > [16] misc3d_0.8-4 mvtnorm_0.9-9998 parallel_3.1.0 > [19] pcaPP_1.9-49 png_0.1-7 RColorBrewer_1.0-5 > [22] rgl_0.93.996 robustbase_0.90-2 rrcov_1.3-4 > [25] stats4_3.1.0 tiff_0.1-5 tools_3.1.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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