BioC 3.2: BUILD report for GenomicRanges on moscato1

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### Running command:
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###   chmod a+r GenomicRanges -R && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GenomicRanges
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* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* preparing 'GenomicRanges':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"D:/biocbld/bbs-3.2-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 objects are masked from 'package:stats':

    IQR, mad, 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, grep, grepl, intersect,
    is.unsorted, lapply, lengths, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unlist, unsplit

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Warning in .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Loading required package: SummarizedExperiment
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: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Warning in .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode,  :
  63 pairs (0 proper, 63 not proper) were dropped because the seqname
  or strand of the alignments in the pair were not concordant.
  Note that a GAlignmentPairs object can only hold concordant pairs at the
  moment, that is, pairs where the 2 alignments are on the opposite strands
  of the same reference sequence.
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK

Attaching package: 'AnnotationHub'

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

    cache

updating AnnotationHub metadata: retrieving 1 resource
snapshotDate(): 2016-04-22
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/6789'
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22

Attaching package: 'locfit'

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

    left, right

Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

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

    plotMA

Loading required package: BSgenome
Loading required package: rtracklayer
Loading required package: DBI

KEGG.db contains mappings based on older data because the
  original resource was removed from the the public domain
  before the most recent update was produced. This package
  should now be considered deprecated and future versions of
  Bioconductor may not have it available.  Users who want more
  current data are encouraged to look at the KEGGREST or
  reactome.db packages


Attaching package: 'KEGGgraph'

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

    plot

trying URL 'http://www.genome.jp/kegg-bin/download?entry=hsa05200&format=kgml'
Content type 'text/xml' length 200 bytes
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========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================
downloaded 31 KB

Warning in download.file(kgml, destfile = destfile, method = method, ...) :
  downloaded length 31873 != reported length 200

Error: processing vignette 'GenomicRangesHOWTOs.Rnw' failed with diagnostics:
 chunk 54 (label = cancer_3) 
Error : 1: AttValue: ' expected
2: attributes construct error
3: Couldn't find end of Start Tag graphics line 515
4: Premature end of data in tag entry line 513
5: Premature end of data in tag pathway line 4

Execution halted
BioC 3.2: BUILD report for GenomicRanges on moscato1

Summary

Command output
