Package: GenomeGraphs

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.12.0.tar.gz

StartedAt: 2011-10-20 15:06:33 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:08:38 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 124.7 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/GenomeGraphs.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GenomeGraphs/DESCRIPTION' ... OK
* this is package 'GenomeGraphs' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GenomeGraphs' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'GenomeGraphs.pdf' from 3184Kb to 532Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'GenomeGraphs' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GenomeGraphs)

name	user	system	elapsed
AnnotationTrack-class	0.001	0.000	0.002
BaseTrack-class	0.000	0.000	0.001
DisplayPars-class	0.002	0.000	0.002
DisplayPars	0.531	0.026	4.403
ExonArray-class	0.003	0.000	0.003
Gene-class	0.001	0.000	0.000
GeneModel-class	0.154	0.006	0.163
GeneRegion-class	0.001	0.000	0.001
GenericArray-class	0.000	0.000	0.001
GenomeAxis-class	0.001	0.000	0.000
HighlightRegion-class	0.002	0.000	0.002
Ideogram-class	0.001	0.001	0.001
ImplementsTrackOverlay-class	0.001	0.000	0.001
Legend-class	0.000	0.001	0.001
MappedRead-class	0	0	0
Overlay-class	0.001	0.000	0.001
RectangleOverlay-class	0.001	0.001	0.002
Segmentation-class	0.001	0.000	0.001
Smoothing-class	0.000	0.001	0.001
TextOverlay-class	0.001	0.000	0.001
Title-class	0.001	0.001	0.001
TrackOverlay-class	0.001	0.000	0.001
Transcript-class	0.000	0.001	0.000
TranscriptRegion-class	0.001	0.000	0.001
cn	0.001	0.000	0.000
exonProbePos	0.000	0.000	0.001
gdObject-class	0.002	0.000	0.002
gdPlot	2.520	0.032	58.847
getPar	0.003	0.000	0.003
getSize	0	0	0
ideogramTab	0.003	0.001	0.004
intensity	0	0	0
makeAnnotationTrack	0.04	0.00	0.04
makeBaseTrack	0.002	0.001	0.001
makeExonArray	0.001	0.000	0.001
makeGene	0.001	0.001	0.001
makeGeneModel	0	0	0
makeGeneRegion	0.001	0.001	0.002
makeGenericArray	0.001	0.000	0.001
makeGenomeAxis	0.000	0.001	0.001
makeIdeogram	0.001	0.000	0.001
makeLegend	0.000	0.001	0.001
makeRectangleOverlay	0.132	0.003	0.135
makeSegmentation	0.107	0.003	0.111
makeSmoothing	0.154	0.003	0.158
makeTextOverlay	0.119	0.002	0.122
makeTitle	0.001	0.000	0.001
makeTranscript	0.000	0.000	0.001
probestart	0.000	0.000	0.001
segEnd	0	0	0
segStart	0.000	0.000	0.001
segments	0	0	0
seqDataEx	0.044	0.002	0.046
setPar	0.017	0.000	0.018
showDisplayOptions	0.002	0.000	0.002
unrData	0	0	0
unrNProbes	0.000	0.000	0.001
unrPositions	0	0	0
yeastCons1	0	0	0