Package: GenomeGraphs

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.13.0.tar.gz

StartedAt: 2011-05-09 14:47:55 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:50:00 -0700 (Mon, 09 May 2011)

EllapsedTime: 124.3 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/GenomeGraphs.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeGraphs/DESCRIPTION’ ... OK
* this is package ‘GenomeGraphs’ version ‘1.13.0’
* checking package name space 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 3126Kb to 452Kb
  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 ...
*** tangling vignette sources ...
   ‘GenomeGraphs.Rnw’ 
** testing if installed package can be loaded

* DONE (GenomeGraphs)

name	user	system	elapsed
AnnotationTrack-class	0.002	0.000	0.002
BaseTrack-class	0.002	0.000	0.002
DisplayPars-class	0.006	0.001	0.006
DisplayPars	0.475	0.020	3.282
ExonArray-class	0.018	0.001	0.018
Gene-class	0.001	0.000	0.001
GeneModel-class	0.202	0.005	0.207
GeneRegion-class	0.002	0.001	0.002
GenericArray-class	0.002	0.000	0.002
GenomeAxis-class	0.001	0.001	0.002
HighlightRegion-class	0.005	0.000	0.005
Ideogram-class	0.002	0.000	0.003
ImplementsTrackOverlay-class	0.001	0.000	0.002
Legend-class	0.001	0.001	0.001
MappedRead-class	0.001	0.000	0.000
Overlay-class	0.001	0.000	0.001
RectangleOverlay-class	0.002	0.000	0.002
Segmentation-class	0.001	0.000	0.002
Smoothing-class	0.002	0.000	0.002
TextOverlay-class	0.001	0.000	0.002
Title-class	0.001	0.000	0.001
TrackOverlay-class	0.001	0.000	0.001
Transcript-class	0.001	0.001	0.002
TranscriptRegion-class	0.002	0.000	0.002
cn	0.000	0.000	0.001
exonProbePos	0.001	0.000	0.000
gdObject-class	0.002	0.000	0.002
gdPlot	2.452	0.029	59.100
getPar	0.003	0.000	0.002
getSize	0.000	0.000	0.001
ideogramTab	0.004	0.001	0.005
intensity	0.001	0.000	0.001
makeAnnotationTrack	0.097	0.000	0.099
makeBaseTrack	0.007	0.000	0.007
makeExonArray	0.008	0.001	0.008
makeGene	0.003	0.000	0.003
makeGeneModel	0.002	0.000	0.002
makeGeneRegion	0.004	0.000	0.005
makeGenericArray	0.001	0.000	0.002
makeGenomeAxis	0.002	0.000	0.002
makeIdeogram	0.003	0.000	0.003
makeLegend	0.002	0.001	0.003
makeRectangleOverlay	0.139	0.003	0.142
makeSegmentation	0.109	0.003	0.111
makeSmoothing	0.159	0.004	0.162
makeTextOverlay	0.125	0.003	0.129
makeTitle	0.003	0.000	0.003
makeTranscript	0.003	0.001	0.004
probestart	0	0	0
segEnd	0	0	0
segStart	0.000	0.000	0.001
segments	0	0	0
seqDataEx	0.046	0.003	0.049
setPar	0.023	0.000	0.023
showDisplayOptions	0.005	0.000	0.006
unrData	0	0	0
unrNProbes	0	0	0
unrPositions	0.001	0.001	0.000
yeastCons1	0.000	0.000	0.001