BioC 3.1: BUILD report for charm on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data charm
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* checking for file ‘charm/DESCRIPTION’ ... OK
* preparing ‘charm’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view
    with 'browseVignettes()'. To cite Bioconductor,
    see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

Loading required package: SQN
Loading required package: mclust
Package 'mclust' version 5.0.2
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: nor1mix
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.2-1 (2015-09-30) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: ‘spam’

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

    backsolve, forwardsolve

Loading required package: maps

 # ATTENTION: maps v3.0 has an updated 'world' map.        #
 # Many country borders and names have changed since 1990. #
 # Type '?world' or 'news(package="maps")'. See README_v3. #



Attaching package: ‘maps’

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

    map


Attaching package: ‘fields’

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

    ozone

Loading required package: RColorBrewer
Loading required package: genefilter
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’

Attaching package: ‘genefilter’

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

    anyNA

Welcome to charm version 2.14.0
Loading required package: pd.charm.hg18.example
Loading required package: RSQLite
Loading required package: DBI
Loading required package: oligoClasses
Welcome to oligoClasses version 1.30.0
Loading required package: oligo
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘stats4’

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

    mle

Loading required package: IRanges
Loading required package: XVector
============================================================
Welcome to oligo version 1.32.0
============================================================
Filenames:
  fileNameColumn not specified. Trying to guess.

  OK - Found in column1
Sample names:
  sampleNameColumn column not specified. Trying to guess.
  OK - Found in column2
Group labels:
  groupColumn column not specified. Trying to guess.
  OK - Found in column3
The following columns in sampleKey contain discrepant values between channels and are being removed: 1
Platform design info loaded.
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: rtracklayer
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Warning: 'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")

Error: processing vignette 'charm.Rnw' failed with diagnostics:
 chunk 10 (label = getControlIndex) 
Error : error reading from connection
Execution halted
BioC 3.1: BUILD report for charm on petty

Summary

Command output
