[BioC] virtualArray: Error at second execution of virtualArrayExpressionSets

Adrian [guest] guest at bioconductor.org
Wed Nov 20 18:36:43 CET 2013

Dear virtualArray maintainer,

I'm facing the following problem.

When I run "virtualArrayExpressionSets" on a few expression sets in a clean R session it works fine,
but if I'm running the function again the exact same way in the same session it gives me the following error:

Error in LastError$store(results = results, is.error = is.error, throw.error = TRUE) : 
  Errors occurred during execution. First error message:
Error in as.character.default(x): no method for coercing this S4 class to a vector

##Code for calling the function
data.combined  <- virtualArrayExpressionSets(
identifier = "SYMBOL", 
collapse_fun = median, 
removeBatcheffect = "EB", 
sampleinfo = FALSE)

I'm probably overlooking something obvious, so any comments are much appreciated.

Thanks a lot!


 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] virtualArray_1.6.0                   hugene10stv1cdf_2.13.0               hgu133plus2cdf_2.13.0               
 [4] affy_1.40.0                          limma_3.18.3                         MergeMaid_2.34.0                    
 [7] MASS_7.3-29                          genefilter_1.44.0                    pvca_1.2.0                          
[10] MetaPCA_0.1.4                        MetaDE_1.0.5                         combinat_0.0-8                      
[13] impute_1.36.0                        survival_2.37-4                      MetaQC_0.1.13                       
[16] iterators_1.0.6                      foreach_1.4.1                        proto_0.3-10                        
[19] hugene10sttranscriptcluster.db_8.0.1 hgu133plus2.db_2.10.1                org.Hs.eg.db_2.10.1                 
[22] RSQLite_0.11.4                       DBI_0.2-7                            AnnotationDbi_1.24.0                
[25] BiocParallel_0.4.1                   preprocessCore_1.24.0                plyr_1.8                            
[28] Biobase_2.22.0                       BiocGenerics_0.8.0                  

loaded via a namespace (and not attached):
 [1] affyio_1.30.0        affyPLM_1.38.0       annotate_1.40.0      BatchJobs_1.1-1135   BBmisc_1.4           BiocInstaller_1.12.0
 [7] Biostrings_2.30.1    brew_1.0-6           codetools_0.2-8      digest_0.6.3         fail_1.2             gcrma_2.34.0        
[13] GEOquery_2.28.0      grid_3.0.1           IRanges_1.20.5       lattice_0.20-24      lme4_1.0-5           Matrix_1.1-0        
[19] minqa_1.2.1          nlme_3.1-111         outliers_0.14        quadprog_1.5-5       RCurl_1.95-4.1       reshape2_1.2.2      
[25] sendmailR_1.1-2      stats4_3.0.1         stringr_0.6.2        tseries_0.10-32      vsn_3.30.0           XML_3.95-0.2        
[31] xtable_1.7-1         XVector_0.2.0        zlibbioc_1.8.0       zoo_1.7-10         

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