Package: GenomeGraphs

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.19.0.tar.gz

StartedAt: 2013-03-25 02:41:05 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:42:19 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 74.2 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GenomeGraphs.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.19.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'GenomeGraphs' can be installed ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
gdPlot: warning in grid.layout(1, 2, width = c(0.1, 0.9)): partial
  argument match of 'width' to 'widths'
gdPlot: warning in grid.layout(length(vplayout), 1, height = vplayout):
  partial argument match of 'height' to 'heights'
transcriptModule: warning in grid.layout(1, length(vplayout), width =
  vplayout): partial argument match of 'width' to 'widths'
* 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' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [8s/12s] 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GenomeGraphs.Rcheck/00check.log'
for details.

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

name	user	system	elapsed
AnnotationTrack-class	0.007	0.005	0.012
BaseTrack-class	0.007	0.006	0.014
DisplayPars-class	0.012	0.009	0.021
DisplayPars	0.512	0.030	2.690
ExonArray-class	0.019	0.014	0.037
Gene-class	0.009	0.007	0.016
GeneModel-class	0.127	0.015	0.144
GeneRegion-class	0.013	0.008	0.022
GenericArray-class	0.010	0.008	0.018
GenomeAxis-class	0.010	0.007	0.016
HighlightRegion-class	0.010	0.008	0.018
Ideogram-class	0.009	0.007	0.016
ImplementsTrackOverlay-class	0.006	0.004	0.010
Legend-class	0.006	0.004	0.009
MappedRead-class	0.009	0.006	0.015
Overlay-class	0.008	0.006	0.014
RectangleOverlay-class	0.008	0.005	0.014
Segmentation-class	0.011	0.008	0.018
Smoothing-class	0.008	0.006	0.015
TextOverlay-class	0.009	0.006	0.013
Title-class	0.006	0.004	0.011
TrackOverlay-class	0.006	0.004	0.011
Transcript-class	0.008	0.006	0.014
TranscriptRegion-class	0.007	0.005	0.012
cn	0.004	0.004	0.008
exonProbePos	0.054	0.004	0.059
gdObject-class	0.007	0.006	0.013
gdPlot	2.289	0.047	4.594
getPar	0.013	0.006	0.019
getSize	0.009	0.005	0.014
ideogramTab	0.013	0.007	0.020
intensity	0.009	0.005	0.015
makeAnnotationTrack	0.056	0.009	0.065
makeBaseTrack	0.026	0.013	0.038
makeExonArray	0.031	0.013	0.044
makeGene	0.023	0.011	0.034
makeGeneModel	0.010	0.008	0.017
makeGeneRegion	0.014	0.010	0.025
makeGenericArray	0.007	0.005	0.013
makeGenomeAxis	0.011	0.009	0.020
makeIdeogram	0.013	0.009	0.023
makeLegend	0.012	0.008	0.021
makeRectangleOverlay	0.142	0.012	0.155
makeSegmentation	0.133	0.014	0.147
makeSmoothing	0.158	0.014	0.172
makeTextOverlay	0.145	0.014	0.160
makeTitle	0.015	0.009	0.024
makeTranscript	0.016	0.010	0.025
probestart	0.005	0.004	0.010
segEnd	0.006	0.004	0.011
segStart	0.007	0.005	0.011
segments	0.005	0.004	0.010
seqDataEx	0.053	0.008	0.061
setPar	0.033	0.008	0.041
showDisplayOptions	0.012	0.006	0.017
unrData	0.006	0.004	0.010
unrNProbes	0.006	0.005	0.010
unrPositions	0.006	0.004	0.010
yeastCons1	0.006	0.004	0.010