BioC 3.1: BUILD report for virtualArray on petty

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data virtualArray
###
##############################################################################
##############################################################################


* checking for file ‘virtualArray/DESCRIPTION’ ... OK
* preparing ‘virtualArray’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... 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’:

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

Loading required package: plyr
Loading required package: preprocessCore
Warning: replacing previous import by ‘utils::relist’ when loading ‘virtualArray’
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")'.

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE23nnn/GSE23402/matrix/
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 6015532 bytes
opened URL
==================================================
downloaded 5.7 Mb

File stored at: 
/tmp/RtmpPmIu35/GPL570.soft
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26428/matrix/
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 706280 bytes
opened URL
==================================================
downloaded 689 Kb

File stored at: 
/tmp/RtmpPmIu35/GPL6480.soft
Loading required package: BiocParallel
Loading required package: futile.logger
Now preprocessing raw data of GSE26428: Loading annotations...
Now preprocessing raw data of GSE23402: Loading annotations...
Usinghgu133plus2as Bioconductor annotation package for datasetGSE23402.
Usinghgug4112aas Bioconductor annotation package for datasetGSE26428.
Loading required package: hgu133plus2.db
Packagehgug4112a.dbnot available. Atempting to install it.
Bioconductor version 3.0 (BiocInstaller 1.15.5), ?biocLite
  for help
Installing package into ‘/private/tmp/RtmpKJruyp/Rinst3faa3e660767’
(as ‘lib’ is unspecified)
also installing the dependency ‘org.Hs.eg.db’

trying URL 'http://bioconductor.org/packages/3.0/data/annotation/bin/macosx/contrib/3.2/org.Hs.eg.db_3.0.0.tgz'
Content type 'application/x-gzip' length 61536737 bytes (58.7 Mb)
opened URL
=================================================
downloaded 58.7 Mb

trying URL 'http://bioconductor.org/packages/3.0/data/annotation/bin/macosx/contrib/3.2/hgug4112a.db_3.0.0.tgz'
Content type 'application/x-gzip' length 1631523 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb

Package hgug4112a.db has been successfully installed!
Loading required package: hgug4112a.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: GenomeInfoDb
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:plyr’:

    rename

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:plyr’:

    desc


Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:GenomeInfoDb’:

    species

Loading required package: org.Hs.eg.db
Loading required package: DBI


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...

Error: processing vignette 'virtualArray.Rnw' failed with diagnostics:
 chunk 12 
Error : 2 errors; first error:
  Error in eval(expr, envir, enclos): object 'hgu133plus2SYMBOL' not found

For more information, use bplasterror(). To resume
  calculation, re-call the function and set the
  argument 'BPRESUME' to TRUE or wrap the previous
  call in bpresume().

First traceback:
  49: tools::buildVignettes(dir = ".", tangle = TRUE)
  48: tryCatch({
          engine$weave(file, quiet = quiet)
          setwd(startdir)
          find_vignette_product(name, by = "weave", engine = engine)
      }, error = function(e) {
          stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", 
              file, conditionMessage(e)), domain = NA, call. = FALSE)
      })
  47: tryCatchList(expr, classes, parentenv, handlers)
  46: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  45: doTryCatch(return(expr), name, parentenv, handler)
  44: engine$weave(file, quiet = quiet)
  43: ut
Execution halted
BioC 3.1: BUILD report for virtualArray on petty

Summary

Command output
