BioC 2.13: BUILD report for virtualArray on moscato1

* checking for file 'virtualArray/DESCRIPTION' ... OK
* preparing 'virtualArray':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"D:/biocbld/bbs-2.13-bioc/R/bin/i386/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
 ERROR
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated,
    eval, evalq, get, intersect, is.unsorted, lapply, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rep.int, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unlist

Loading required package: plyr
Loading required package: preprocessCore
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Setting options('download.file.method.GEOquery'='auto')
Warning: replacing previous import by 'methods::new' when loading 'virtualArray'
Warning: replacing previous import by 'stats::density' when loading 'virtualArray'
Warning: replacing previous import by 'utils::installed.packages' when loading 'virtualArray'
Warning: replacing previous import by 'utils::read.csv' when loading 'virtualArray'
Warning: replacing previous import by 'utils::read.table' when loading 'virtualArray'
Warning: replacing previous import by 'utils::write.table' when loading 'virtualArray'
To support our work please cite:
Thanks.
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages
    'citation("pkgname")'.

Found 1 file(s)
GSE23402_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE23nnn/GSE23402/matrix/GSE23402_series_matrix.txt.gz'
ftp data connection made, file length 6015535 bytes
opened URL
downloaded 5.7 Mb

File stored at: 
D:\biocbld\bbs-2.13-bioc\tmpdir\Rtmp8yWICl/GPL570.soft
Found 1 file(s)
GSE26428_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26428/matrix/GSE26428_series_matrix.txt.gz'
ftp data connection made, file length 706277 bytes
opened URL
downloaded 689 Kb

File stored at: 
D:\biocbld\bbs-2.13-bioc\tmpdir\Rtmp8yWICl/GPL6480.soft
Loading required package: BiocParallel
Now preprocessing raw data of GSE23402: Loading annotations...
Usinghgu133plus2as Bioconductor annotation package for datasetGSE23402.
Loading required package: hgu133plus2.db
Loading required package: AnnotationDbi
Loading required package: org.Hs.eg.db
Loading required package: DBI


Now preprocessing raw data of GSE23402: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE23402: Annotating expression values with SYMBOL...
Size of expression matrix of GSE23402: 19851 rows and 24 columns.
Now preprocessing raw data of GSE26428: Loading annotations...
Usinghgug4112aas Bioconductor annotation package for datasetGSE26428.
Loading required package: hgug4112a.db

Now preprocessing raw data of GSE26428: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE26428: Annotating expression values with SYMBOL...
Size of expression matrix of GSE26428: 18946 rows and 3 columns.
Now preprocessing raw data of GSE23402: Loading annotations...
Usinghgu133plus2as Bioconductor annotation package for datasetGSE23402.
Now preprocessing raw data of GSE23402: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE23402: Annotating expression values with SYMBOL...
Size of expression matrix of GSE23402: 19851 rows and 24 columns.
Now preprocessing raw data of GSE26428: Loading annotations...
Usinghgug4112aas Bioconductor annotation package for datasetGSE26428.
Now preprocessing raw data of GSE26428: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE26428: Annotating expression values with SYMBOL...
Size of expression matrix of GSE26428: 18946 rows and 3 columns.
Now combining pData of all data sets...
Now setting up pData of GSE23402...
Now setting up pData of GSE26428...
Matching and merging all data sets. This could take some time...
Size of expression matrix of whole dataset: 17674 rows and 27 columns.
Using columns as information for batch effect removal.
The numbers of overlapping genes/identifiers between each pair of datasets and the final result were as follows:

Error: processing vignette 'virtualArray.Rnw' failed with diagnostics:
 chunk 12 
Error in data.frame(full = structure(c("19851", "18946", "17674"), class = "AsIs"),  : 
  duplicate row.names: 
Execution halted
BioC 2.13: BUILD report for virtualArray on moscato1

Summary

Command output
