BioC experimental data: BUILD report for BeadArrayUseCases on moscato2

Package: BeadArrayUseCases

Version: 1.6.0

Command: chmod a+r BeadArrayUseCases -R && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data BeadArrayUseCases

StartedAt: 2015-10-07 08:38:46 -0700 (Wed, 07 Oct 2015)

EndedAt: 2015-10-07 08:51:50 -0700 (Wed, 07 Oct 2015)

EllapsedTime: 783.2 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   chmod a+r BeadArrayUseCases -R && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data BeadArrayUseCases
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* checking for file 'BeadArrayUseCases/DESCRIPTION' ... OK
* preparing 'BeadArrayUseCases':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"E:/biocbld/bbs-3.1-bioc/R/bin/x64/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,
    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, unsplit

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: ggplot2
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Welcome to beadarray version 2.18.0
beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
Setting options('download.file.method.GEOquery'='auto')
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: IRanges
Loading required package: org.Hs.eg.db
Loading required package: DBI



Sample Sheet E:\biocbld\bbs-3.1-data-experiment\tmpdir\RtmpsRUDvL\Rinstfbc3e507098\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: GenomicRanges

Attaching package: 'limma'

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

    imageplot

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

    plotMA

trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE5350/GSE5350-GPL2507_series_matrix.txt.gz'
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downloaded 5.0 MB

Warning in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
  downloaded length 2038193 != reported length 200
File stored at: 
E:\biocbld\bbs-3.1-data-experiment\tmpdir\RtmpKYlkUQ/GPL2507.soft
Warning: running command '"C:\progra˜2\MiKTeX˜1.9\miktex\bin\texi2dvi.exe" --quiet --pdf "BeadArrayUseCases.tex" --max-iterations=20 -I "E:/biocbld/bbs-3.1-bioc/R/share/texmf/tex/latex" -I "E:/biocbld/bbs-3.1-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'BeadArrayUseCases.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file umvs): Font umvs at 864 not found
 ==> Fatal error occurred, no output PDF file produced!
Execution halted