Package: GenomeGraphs

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.20.0.tar.gz

StartedAt: 2013-05-01 05:56:33 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:57:49 -0700 (Wed, 01 May 2013)

EllapsedTime: 76.3 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GenomeGraphs.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GenomeGraphs/DESCRIPTION' ... OK
* this is package 'GenomeGraphs' version '1.20.0'
* 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/8s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [7s/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
** testing if installed package can be loaded
* DONE (GenomeGraphs)

name	user	system	elapsed
AnnotationTrack-class	0.010	0.002	0.013
BaseTrack-class	0.010	0.002	0.013
DisplayPars-class	0.017	0.004	0.025
DisplayPars	0.512	0.028	3.155
ExonArray-class	0.113	0.004	0.121
Gene-class	0.011	0.002	0.013
GeneModel-class	0.123	0.012	0.139
GeneRegion-class	0.010	0.001	0.010
GenericArray-class	0.013	0.001	0.014
GenomeAxis-class	0.012	0.001	0.013
HighlightRegion-class	0.017	0.001	0.019
Ideogram-class	0.012	0.001	0.013
ImplementsTrackOverlay-class	0.007	0.001	0.008
Legend-class	0.007	0.001	0.008
MappedRead-class	0.006	0.000	0.006
Overlay-class	0.007	0.001	0.008
RectangleOverlay-class	0.007	0.001	0.006
Segmentation-class	0.009	0.001	0.010
Smoothing-class	0.009	0.001	0.011
TextOverlay-class	0.006	0.000	0.007
Title-class	0.007	0.001	0.007
TrackOverlay-class	0.007	0.001	0.009
Transcript-class	0.010	0.001	0.011
TranscriptRegion-class	0.008	0.001	0.009
cn	0.006	0.000	0.007
exonProbePos	0.096	0.001	0.101
gdObject-class	0.011	0.001	0.012
gdPlot	1.945	0.049	4.452
getPar	0.016	0.000	0.016
getSize	0.008	0.001	0.010
ideogramTab	0.013	0.002	0.016
intensity	0.009	0.001	0.010
makeAnnotationTrack	0.044	0.003	0.050
makeBaseTrack	0.017	0.002	0.019
makeExonArray	0.016	0.002	0.018
makeGene	0.015	0.002	0.018
makeGeneModel	0.012	0.002	0.015
makeGeneRegion	0.015	0.002	0.017
makeGenericArray	0.008	0.002	0.010
makeGenomeAxis	0.012	0.002	0.013
makeIdeogram	0.013	0.002	0.018
makeLegend	0.013	0.002	0.016
makeRectangleOverlay	0.099	0.010	0.112
makeSegmentation	0.091	0.008	0.103
makeSmoothing	0.124	0.010	0.138
makeTextOverlay	0.111	0.010	0.124
makeTitle	0.132	0.003	0.141
makeTranscript	0.019	0.001	0.020
probestart	0.008	0.001	0.009
segEnd	0.005	0.000	0.005
segStart	0.006	0.001	0.006
segments	0.008	0.001	0.008
seqDataEx	0.044	0.015	0.059
setPar	0.028	0.002	0.031
showDisplayOptions	0.013	0.001	0.015
unrData	0.008	0.000	0.009
unrNProbes	0.008	0.001	0.009
unrPositions	0.015	0.000	0.015
yeastCons1	0.007	0.001	0.008