Package: GenomeGraphs

Version: 1.14.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.14.0.tar.gz

StartedAt: 2012-03-24 00:34:47 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:36:36 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 108.9 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GenomeGraphs.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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	0.004	0.000	0.001
BaseTrack-class	0	0	0
DisplayPars-class	0.000	0.000	0.002
DisplayPars	0.504	0.024	3.108
ExonArray-class	0.000	0.004	0.004
Gene-class	0.000	0.000	0.001
GeneModel-class	0.104	0.000	0.107
GeneRegion-class	0.000	0.000	0.001
GenericArray-class	0.000	0.000	0.001
GenomeAxis-class	0.000	0.000	0.001
HighlightRegion-class	0.004	0.000	0.001
Ideogram-class	0	0	0
ImplementsTrackOverlay-class	0.004	0.000	0.000
Legend-class	0	0	0
MappedRead-class	0	0	0
Overlay-class	0	0	0
RectangleOverlay-class	0.004	0.000	0.001
Segmentation-class	0.000	0.000	0.001
Smoothing-class	0	0	0
TextOverlay-class	0.004	0.000	0.000
Title-class	0.000	0.000	0.001
TrackOverlay-class	0.000	0.000	0.001
Transcript-class	0.000	0.000	0.001
TranscriptRegion-class	0	0	0
cn	0	0	0
exonProbePos	0	0	0
gdObject-class	0.000	0.004	0.001
gdPlot	1.636	0.016	58.503
getPar	0.000	0.000	0.002
getSize	0	0	0
ideogramTab	0.000	0.000	0.003
intensity	0	0	0
makeAnnotationTrack	0.028	0.000	0.030
makeBaseTrack	0.004	0.000	0.002
makeExonArray	0.004	0.000	0.001
makeGene	0.000	0.000	0.001
makeGeneModel	0	0	0
makeGeneRegion	0.004	0.000	0.001
makeGenericArray	0.000	0.000	0.001
makeGenomeAxis	0	0	0
makeIdeogram	0.004	0.000	0.001
makeLegend	0.000	0.000	0.001
makeRectangleOverlay	0.068	0.000	0.067
makeSegmentation	0.052	0.000	0.052
makeSmoothing	0.068	0.004	0.075
makeTextOverlay	0.060	0.004	0.064
makeTitle	0.000	0.000	0.001
makeTranscript	0.000	0.000	0.001
probestart	0	0	0
segEnd	0	0	0
segStart	0	0	0
segments	0	0	0
seqDataEx	0.02	0.00	0.02
setPar	0.124	0.000	0.124
showDisplayOptions	0.000	0.000	0.001
unrData	0	0	0
unrNProbes	0	0	0
unrPositions	0.000	0.000	0.001
yeastCons1	0	0	0