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: 2013-03-24 05:37:03 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 05:38:21 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 77.9 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 beta (2013-03-21 r62346)
* 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 '1.19.0'
* 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/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 ... [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	0.010	0.003	0.012
BaseTrack-class	0.009	0.002	0.012
DisplayPars-class	0.018	0.005	0.023
DisplayPars	0.556	0.027	2.754
ExonArray-class	0.045	0.002	0.048
Gene-class	0.102	0.002	0.104
GeneModel-class	0.141	0.012	0.154
GeneRegion-class	0.017	0.001	0.018
GenericArray-class	0.016	0.001	0.017
GenomeAxis-class	0.010	0.001	0.012
HighlightRegion-class	0.013	0.001	0.016
Ideogram-class	0.015	0.001	0.016
ImplementsTrackOverlay-class	0.008	0.001	0.010
Legend-class	0.009	0.000	0.010
MappedRead-class	0.009	0.001	0.009
Overlay-class	0.011	0.001	0.013
RectangleOverlay-class	0.015	0.001	0.016
Segmentation-class	0.011	0.001	0.012
Smoothing-class	0.008	0.001	0.010
TextOverlay-class	0.008	0.001	0.009
Title-class	0.010	0.001	0.011
TrackOverlay-class	0.010	0.000	0.012
Transcript-class	0.012	0.001	0.014
TranscriptRegion-class	0.011	0.001	0.012
cn	0.006	0.000	0.007
exonProbePos	0.007	0.001	0.008
gdObject-class	0.013	0.001	0.017
gdPlot	2.192	0.049	4.457
getPar	0.014	0.001	0.015
getSize	0.012	0.001	0.012
ideogramTab	0.020	0.001	0.020
intensity	0.125	0.001	0.127
makeAnnotationTrack	0.050	0.003	0.056
makeBaseTrack	0.021	0.001	0.022
makeExonArray	0.020	0.003	0.023
makeGene	0.015	0.002	0.016
makeGeneModel	0.014	0.002	0.016
makeGeneRegion	0.018	0.003	0.021
makeGenericArray	0.010	0.002	0.012
makeGenomeAxis	0.015	0.002	0.018
makeIdeogram	0.019	0.003	0.022
makeLegend	0.016	0.003	0.019
makeRectangleOverlay	0.109	0.007	0.118
makeSegmentation	0.097	0.007	0.105
makeSmoothing	0.126	0.007	0.135
makeTextOverlay	0.118	0.008	0.129
makeTitle	0.016	0.001	0.017
makeTranscript	0.020	0.001	0.021
probestart	0.007	0.001	0.007
segEnd	0.007	0.001	0.007
segStart	0.007	0.000	0.006
segments	0.009	0.000	0.009
seqDataEx	0.042	0.008	0.051
setPar	0.027	0.001	0.033
showDisplayOptions	0.010	0.001	0.011
unrData	0.009	0.000	0.010
unrNProbes	0.010	0.001	0.012
unrPositions	0.008	0.000	0.008
yeastCons1	0.007	0.000	0.008