Package: GenomeGraphs

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.14.0.tar.gz

StartedAt: 2012-03-24 01:20:37 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:21:52 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 74.8 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 2.14.2 (2012-02-29)
* 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 '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using 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	0.003	0.001	0.003
BaseTrack-class	0.000	0.000	0.001
DisplayPars-class	0.002	0.000	0.002
DisplayPars	0.528	0.028	2.836
ExonArray-class	0.003	0.001	0.003
Gene-class	0	0	0
GeneModel-class	0.131	0.008	0.139
GeneRegion-class	0.000	0.001	0.001
GenericArray-class	0.001	0.000	0.001
GenomeAxis-class	0	0	0
HighlightRegion-class	0.001	0.000	0.001
Ideogram-class	0.000	0.000	0.001
ImplementsTrackOverlay-class	0.001	0.000	0.001
Legend-class	0.001	0.000	0.001
MappedRead-class	0.001	0.000	0.001
Overlay-class	0.001	0.000	0.001
RectangleOverlay-class	0.001	0.001	0.001
Segmentation-class	0.001	0.000	0.001
Smoothing-class	0.001	0.001	0.001
TextOverlay-class	0.001	0.000	0.001
Title-class	0.001	0.000	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	0.001	0.000
exonProbePos	0.001	0.000	0.000
gdObject-class	0.001	0.001	0.002
gdPlot	2.225	0.034	4.482
getPar	0.002	0.001	0.003
getSize	0	0	0
ideogramTab	0.004	0.001	0.004
intensity	0	0	0
makeAnnotationTrack	0.039	0.002	0.042
makeBaseTrack	0.001	0.001	0.002
makeExonArray	0.002	0.000	0.002
makeGene	0.000	0.000	0.001
makeGeneModel	0.001	0.000	0.001
makeGeneRegion	0.001	0.000	0.001
makeGenericArray	0.001	0.001	0.001
makeGenomeAxis	0.001	0.000	0.000
makeIdeogram	0.000	0.001	0.001
makeLegend	0.001	0.000	0.001
makeRectangleOverlay	0.136	0.005	0.141
makeSegmentation	0.117	0.004	0.122
makeSmoothing	0.167	0.004	0.175
makeTextOverlay	0.196	0.005	0.203
makeTitle	0.001	0.000	0.001
makeTranscript	0.001	0.001	0.001
probestart	0.000	0.000	0.001
segEnd	0	0	0
segStart	0	0	0
segments	0	0	0
seqDataEx	0.044	0.002	0.046
setPar	0.017	0.001	0.019
showDisplayOptions	0.001	0.001	0.002
unrData	0	0	0
unrNProbes	0.000	0.000	0.001
unrPositions	0	0	0
yeastCons1	0	0	0