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BioC 2.12: BUILD report for gwascat on george2

This page was generated on 2013-10-09 09:37:51 -0700 (Wed, 09 Oct 2013).

Package 305/671HostnameOS / ArchBUILDCHECKBUILD BIN
gwascat 1.4.0
VJ Carey
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/gwascat
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64 [ ERROR ] skipped 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  ERROR  skipped  skipped 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  ERROR  skipped  skipped 

Summary

Package: gwascat
Version: 1.4.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gwascat
StartedAt: 2013-10-08 23:03:14 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 23:06:27 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 192.5 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

* 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
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

Loading required package: grid
Loading required package: DBI

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘gwascat.tex’ failed.
LaTeX errors:
!pdfTeX error: /usr/bin/pdflatex (file ./annman.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted