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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data altcdfenvs
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* checking for file ‘altcdfenvs/DESCRIPTION’ ... OK
* preparing ‘altcdfenvs’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘altcdfenvs.Rnw’ using Sweave
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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: 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: affy
Loading required package: makecdfenv
Loading required package: affyio
Loading required package: Biostrings
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: hypergraph
Loading required package: graph

Attaching package: ‘graph’

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

    complement

Loading required package: AnnotationDbi
Loading required package: grid

Attaching package: ‘grid’

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

    pattern


Attaching package: ‘Rgraphviz’

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

    from, to

The following objects are masked from ‘package:S4Vectors’:

    from, to


Error: processing vignette 'altcdfenvs.Rnw' failed with diagnostics:
 chunk 10 (label = plotGraph) 
Error in buildEdgeList(graph, recipEdges, edgeAttrs, subGList, attrs$edge) : 
  attempt to set index 66/66 in SET_STRING_ELT

--- failed re-building ‘altcdfenvs.Rnw’

--- re-building ‘modify.Rnw’ using Sweave
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘plasmodiumanophelescdf’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘plasmodiumanophelescdf’

--- finished re-building ‘modify.Rnw’

--- re-building ‘ngenomeschips.Rnw’ using Sweave
Read 5407 items
--- finished re-building ‘ngenomeschips.Rnw’

SUMMARY: processing the following file failed:
  ‘altcdfenvs.Rnw’

Error: Vignette re-building failed.
Execution halted