[BioC] lumi-package problem: nuID [e.g. nuID2EntrezID()] from vignette example throws an error on my system

[Franz-Josef Müller [guest]]

Dear All,

I am having trouble running this example code from the lumi-vignette:

library(lumi)
## load example data
data(example.lumi)
if (require(lumiHumanIDMapping)) {
  nuIDs <- featureNames(example.lumi)
  mappingInfo <- nuID2EntrezID(nuIDs, lib.mapping=lumiHumanIDMapping)
  head(mappingInfo)
}

Then I am seeing this:

Error in paste("package", package, sep = ":") : 
  cannot coerce type 'closure' to vector of type 'character'

I have come across this problem first when I tried to annotate my own data, but it seems also to happen on my system with every of the nuID mapping commands.

Thanks for your help and advise in advance!

Best

Franzef 



 -- output of sessionInfo(): 

R version 3.0.3 (2014-03-06)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lumiHumanIDMapping_1.10.0 RSQLite_0.11.4            DBI_0.2-7                
[4] AnnotationDbi_1.22.6      lumi_2.12.0               Biobase_2.20.0           
[7] BiocGenerics_0.6.0       

loaded via a namespace (and not attached):
 [1] affy_1.38.1           affyio_1.28.0         annotate_1.38.0       beanplot_1.1         
 [5] BiocInstaller_1.10.2  Biostrings_2.28.0     colorspace_1.2-2      GenomicRanges_1.12.4 
 [9] grid_3.0.3            illuminaio_0.2.0      IRanges_1.18.1        KernSmooth_2.23-10   
[13] lattice_0.20-27       limma_3.16.5          MASS_7.3-29           Matrix_1.1-2         
[17] matrixStats_0.8.1     mclust_4.1            methylumi_2.6.1       mgcv_1.7-28          
[21] minfi_1.6.0           multtest_2.16.0       nleqslv_2.0           nlme_3.1-113         
[25] nor1mix_1.1-4         preprocessCore_1.22.0 R.methodsS3_1.4.2     RColorBrewer_1.0-5   
[29] reshape_0.8.4         siggenes_1.34.0       splines_3.0.3         stats4_3.0.3         
[33] survival_2.37-7       tools_3.0.3           XML_3.95-0.2          xtable_1.7-1         
[37] zlibbioc_1.6.0  

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