BioC 2.12: BUILD report for gwascat on lamb2

* checking for file ‘gwascat/DESCRIPTION’ ... OK
* preparing ‘gwascat’:
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: IRanges
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, as.data.frame,
    cbind, colnames, duplicated, eval, get, intersect, 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

Loading required package: GenomicRanges
Loading required package: snpStats
Loading required package: survival
Loading required package: splines
Loading required package: Matrix
Loading required package: lattice

Attaching package: ‘Matrix’

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

    expand

Loading required package: graph
NOTE: input data had non-ASCII characters replaced by ‘*’.
‘gwcat’ data frame now available, provides NHGRI GWAS cat records of 2012.09.22.
building ‘gwrngs’, GRanges for studies with located variants...
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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")’.

NOTE: input data had non-ASCII characters replaced by ‘*’.
‘gwcat’ data frame now available, provides NHGRI GWAS cat records of 2012.09.22.
building ‘gwrngs’, GRanges for studies with located variants...
Loading required package: ggplot2
No methods found in "GenomicRanges" for requests: summary
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: ‘ggbio’

The following objects are masked from ‘package:ggplot2’:

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

Warning in `[<-.factor`(`*tmp*`, oth, value = "Other") :
  invalid factor level, NA generated
Warning in .local(con, format, text, ...) :
  Starting with BioC 2.12, the default value for the ‘asRangedData’ argument
  of import() has changed from TRUE to FALSE. Explicitly provide a
  value for this argument to avoid this warning e.g. with
    import(..., asRangedData=FALSE)
  to get a GRanges object, or with
    import(..., asRangedData=TRUE)
  to get a RangedData object. This warning will be removed in BioC 2.13
Loading required package: grid
No methods found in "IRanges" for requests: nlevels
Loading required package: DBI


Error: processing vignette ‘gwascat.Rnw’ failed with diagnostics:
 chunk 18 (label = getstr) 
Error in `[[<-.data.frame`(`*tmp*`, a, value = character(0)) : 
  replacement has 0 rows, data has 41
Execution halted
Summary

Command output
