BioC 2.14: BUILD report for virtualArray on zin2

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data virtualArray
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* 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’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, do.call,
    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
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'='curl')
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
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  2 5874k    2  117k    0     0  86026      0  0:01:09  0:00:01  0:01:08 90570
 92 5874k   92 5433k    0     0  2287k      0  0:00:02  0:00:02 --:--:-- 2358k
100 5874k  100 5874k    0     0  2377k      0  0:00:02  0:00:02 --:--:-- 2447k
File stored at: 
/tmp/RtmpHIRNaB/GPL570.soft
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26428/matrix/
Found 1 file(s)
GSE26428_series_matrix.txt.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  2  689k    2 17376    0     0  14605      0  0:00:48  0:00:01  0:00:47 15528
100  689k  100  689k    0     0   364k      0  0:00:01  0:00:01 --:--:--  378k
File stored at: 
/tmp/RtmpHIRNaB/GPL6480.soft
Loading required package: BiocParallel
Now preprocessing raw data of GSE23402: Loading annotations...
Usinghgu133plus2as Bioconductor annotation package for datasetGSE23402.
Now preprocessing raw data of GSE26428: Loading annotations...
Usinghgug4112aas Bioconductor annotation package for datasetGSE26428.
Loading required package: hgu133plus2.db
Loading required package: hgug4112a.db
Loading required package: AnnotationDbi
Loading required package: AnnotationDbi
Loading required package: GenomeInfoDb
Loading required package: GenomeInfoDb
Loading required package: org.Hs.eg.db
Loading required package: org.Hs.eg.db
Loading required package: DBI
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 GSE23402: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE26428: Annotating expression values with SYMBOL...
Now preprocessing raw data of GSE23402: Annotating expression values with SYMBOL...

Error: processing vignette 'virtualArray.Rnw' failed with diagnostics:
 chunk 12 
Error : 2 errors; first error:
  Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL'

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:
  50: tools::buildVignettes(dir = ".", tangle = TRUE)
  49: 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)
      })
  48: tryCatchList(expr, classes, parentenv, handlers)
  47: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  46: doTryCatch(return(expr), name, parentenv, handler)
Execution halted
BioC 2.14: BUILD report for virtualArray on zin2

Summary

Command output
