[BioC] Error in isVersioned(object)

[Martin Morgan]

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.
>
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