Package: gwascat

Version: 1.0.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gwascat

StartedAt: 2012-03-31 23:04:45 -0700 (Sat, 31 Mar 2012)

EndedAt: 2012-03-31 23:05:53 -0700 (Sat, 31 Mar 2012)

EllapsedTime: 67.7 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

* 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

Attaching package: 'BiocGenerics'

The following object(s) are masked from 'package:stats':

    xtabs

The following object(s) are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
    colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: GenomicRanges
Loading required package: snpStats
Loading required package: survival
Loading required package: splines
Loading required package: Matrix
Loading required package: lattice
Loading required package: graph
'gwcat' data frame now available, provides NHGRI GWAS cat records of 2012.03.20.
building 'gwrngs', GRanges for studies with located variants...done.
'gwcat' data frame now available, provides NHGRI GWAS cat records of 2012.03.20.
building 'gwrngs', GRanges for studies with located variants...done.
Warning in .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr23, chr3, chr4, chr5, chr6, chr7, chr8, chr9
  - in 'y': chr0
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).
Warning in .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr23, chr3, chr4, chr5, chr6, chr7, chr8, chr9
  - in 'y': chr0
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).
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")'.

Loading required package: DBI
Loading required package: SNPlocs.Hsapiens.dbSNP.20110815
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gwascat.tex' failed.
LaTeX errors:
! Package auto-pst-pdf Error: 
    "shell escape" (or "write18") is not enabled:
    auto-pst-pdf will not work!
.
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted