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: 2011-07-07 03:18:54 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 03:21:04 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 130.0 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) (2011-06-22 r56208)
* 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 '1.13.0'
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                  old_size new_size compress
  exampleData.rda     74Kb     35Kb       xz
  ideogram.rda        57Kb     33Kb       xz
  seqDataEx.rda      113Kb     34Kb       xz
* checking sizes of PDF files under 'inst/doc' ... OK
* 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	0.001	0.002
BaseTrack-class	0	0	0
DisplayPars-class	0.002	0.001	0.003
DisplayPars	0.490	0.022	3.230
ExonArray-class	0.006	0.000	0.006
Gene-class	0.001	0.000	0.000
GeneModel-class	0.161	0.004	0.166
GeneRegion-class	0.000	0.000	0.001
GenericArray-class	0.001	0.000	0.001
GenomeAxis-class	0.001	0.000	0.001
HighlightRegion-class	0.001	0.000	0.001
Ideogram-class	0	0	0
ImplementsTrackOverlay-class	0.001	0.000	0.001
Legend-class	0.001	0.001	0.001
MappedRead-class	0.000	0.000	0.001
Overlay-class	0.001	0.001	0.001
RectangleOverlay-class	0.001	0.000	0.002
Segmentation-class	0.001	0.001	0.001
Smoothing-class	0.001	0.000	0.002
TextOverlay-class	0.001	0.001	0.001
Title-class	0.001	0.000	0.001
TrackOverlay-class	0.001	0.001	0.002
Transcript-class	0	0	0
TranscriptRegion-class	0.001	0.001	0.001
cn	0	0	0
exonProbePos	0	0	0
gdObject-class	0.005	0.001	0.005
gdPlot	2.583	0.027	56.309
getPar	0.003	0.000	0.003
getSize	0	0	0
ideogramTab	0.004	0.001	0.005
intensity	0	0	0
makeAnnotationTrack	0.040	0.000	0.041
makeBaseTrack	0.002	0.001	0.002
makeExonArray	0.001	0.000	0.001
makeGene	0.001	0.000	0.001
makeGeneModel	0.001	0.000	0.001
makeGeneRegion	0.001	0.000	0.001
makeGenericArray	0.001	0.000	0.002
makeGenomeAxis	0.001	0.000	0.001
makeIdeogram	0.000	0.000	0.001
makeLegend	0.001	0.000	0.001
makeRectangleOverlay	0.151	0.003	0.155
makeSegmentation	0.125	0.002	0.128
makeSmoothing	0.169	0.004	0.175
makeTextOverlay	0.139	0.004	0.154
makeTitle	0.001	0.001	0.001
makeTranscript	0.001	0.000	0.001
probestart	0.000	0.001	0.000
segEnd	0	0	0
segStart	0	0	0
segments	0	0	0
seqDataEx	0.045	0.002	0.055
setPar	0.019	0.000	0.019
showDisplayOptions	0.002	0.000	0.002
unrData	0	0	0
unrNProbes	0	0	0
unrPositions	0.000	0.000	0.001
yeastCons1	0	0	0