[BioC] Unknown failure in virtualArrayLoadRaw

Robert Soeldner [guest] guest at bioconductor.org
Mon Apr 28 10:38:47 CEST 2014

Hello everyone,

I've tried to use the virtualArray-Package with this http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22153
rawfile and this code:

path<- "/path/to/GSE"
setwd( path )


vArray <- virtualArrayLoadRaw(root_dir = path)
eSet <- virtualArrayCompile(virtualArray=vArray)

The output:

Created directory tree in /path/to/GSE/ . 
Please copy your raw data files into the appropriate directories.

Now starting to compile "sample_info.txt" for later use with the "virtualArrayComBat" function to remove batch effects.

The file "sample_info.txt" has been written to /path/to/GSE/ .
Please edit the "Covariate 1" column to your needs and save before proceeding.

Starting to load raw data files stored in /path/to/GSE/ .
This could take some time, please be patient.

All raw data has been loaded.

Error in eval(as.name(names(sort(sapply(X = ls(envir = virtualArray, pattern = "annot_"),  : 
  error in evaluating the argument 'expr' in selecting a method for function 'eval': Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 
  'x' must be atomic

Is this a bug ?


 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.3 (2014-03-06)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] mogene10stv1cdf_2.13.0 hgu133plus2cdf_2.13.0  affy_1.40.0            GEOquery_2.28.0        virtualArray_1.6.0     preprocessCore_1.24.0 
 [7] plyr_1.8.1             BiocInstaller_1.12.1   AnnotationDbi_1.24.0   Biobase_2.22.0         BiocGenerics_0.8.0    

loaded via a namespace (and not attached):
 [1] affyio_1.30.0     affyPLM_1.38.0    Biostrings_2.30.1 DBI_0.2-7         gcrma_2.34.0      grid_3.0.3        IRanges_1.20.7    lattice_0.20-29  
 [9] outliers_0.14     quadprog_1.5-5    Rcpp_0.11.1       RCurl_1.95-4.1    reshape2_1.4      RSQLite_0.11.4    splines_3.0.3     stats4_3.0.3     
[17] stringr_0.6.2     tools_3.0.3       tseries_0.10-32   XML_3.98-1.1      XVector_0.2.0     zlibbioc_1.8.0    zoo_1.7-11       

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