##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BeadArrayUseCases
###
##############################################################################
##############################################################################


* checking for file ‘BeadArrayUseCases/DESCRIPTION’ ... OK
* preparing ‘BeadArrayUseCases’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BeadArrayUseCases.rnw’ using Sweave
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, saveRDS, setdiff, table, tapply, union,
    unique, unsplit, which.max, which.min

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")'.

Loading required package: hexbin
Welcome to beadarray version 2.56.0
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: org.Hs.eg.db



Sample Sheet /home/biocbuild/bbs-3.20-data-experiment/tmpdir/RtmpNsqwwa/Rinst39ba3b12aef8b3/BeadArrayUseCases/extdata/Chips/sampleSheet.csv will be used to read the data
Processing section 4613710017_B
Processing section 4613710052_B
Processing section 4613710054_B
Processing section 4616443079_B
Processing section 4616443093_B
Processing section 4616443115_B
Processing section 4616443081_B
Processing section 4616443081_H
Processing section 4616443092_B
Processing section 4616443107_A
Processing section 4616443136_A
Processing section 4616494005_A
HULKing section 4613710017_B
Calculating Neighbourhood
Using locs file to generate neighbours matrix
Loading required package: illuminaHumanv3.db

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: GenomicRanges

Attaching package: ‘limma’

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

    imageplot

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

    plotMA


Error: processing vignette 'BeadArrayUseCases.rnw' failed with diagnostics:
 chunk 48 (label = readFromGEO) 
Error in open.connection(x, "rb") : cannot open the connection

--- failed re-building ‘BeadArrayUseCases.rnw’

SUMMARY: processing the following file failed:
  ‘BeadArrayUseCases.rnw’

Error: Vignette re-building failed.
Execution halted