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

Franz-Josef Müller [guest] guest at bioconductor.org
Mon Mar 31 21:04:29 CEST 2014

Dear All,

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

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

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!



 -- output of sessionInfo(): 

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

[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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