Package: GenomeGraphs

Version: 1.19.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.19.0.tar.gz

StartedAt: 2013-01-16 02:52:13 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:53:08 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 55.2 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GenomeGraphs.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.19.0’
* 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 ... 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 ... 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
  ‘/loc/home/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	0.008	0.004	0.012
BaseTrack-class	0.012	0.000	0.010
DisplayPars-class	0.024	0.000	0.025
DisplayPars	0.464	0.016	2.789
ExonArray-class	0.016	0.000	0.017
Gene-class	0.004	0.000	0.007
GeneModel-class	0.100	0.000	0.101
GeneRegion-class	0.008	0.000	0.008
GenericArray-class	0.012	0.000	0.012
GenomeAxis-class	0.012	0.000	0.012
HighlightRegion-class	0.020	0.000	0.022
Ideogram-class	0.008	0.000	0.010
ImplementsTrackOverlay-class	0.012	0.000	0.010
Legend-class	0.008	0.000	0.009
MappedRead-class	0.008	0.000	0.008
Overlay-class	0.008	0.000	0.008
RectangleOverlay-class	0.100	0.008	0.108
Segmentation-class	0.012	0.000	0.009
Smoothing-class	0.008	0.000	0.007
TextOverlay-class	0.008	0.000	0.008
Title-class	0.008	0.000	0.007
TrackOverlay-class	0.008	0.000	0.007
Transcript-class	0.008	0.000	0.009
TranscriptRegion-class	0.004	0.000	0.007
cn	0.004	0.000	0.005
exonProbePos	0.008	0.000	0.006
gdObject-class	0.016	0.000	0.014
gdPlot	1.500	0.008	3.835
getPar	0.016	0.000	0.017
getSize	0.004	0.000	0.006
ideogramTab	0.004	0.008	0.012
intensity	0.004	0.004	0.008
makeAnnotationTrack	0.032	0.000	0.033
makeBaseTrack	0.028	0.000	0.025
makeExonArray	0.016	0.004	0.020
makeGene	0.012	0.004	0.015
makeGeneModel	0.012	0.000	0.012
makeGeneRegion	0.012	0.004	0.016
makeGenericArray	0.008	0.000	0.009
makeGenomeAxis	0.008	0.004	0.010
makeIdeogram	0.008	0.000	0.007
makeLegend	0.008	0.000	0.008
makeRectangleOverlay	0.064	0.000	0.064
makeSegmentation	0.056	0.000	0.056
makeSmoothing	0.076	0.000	0.079
makeTextOverlay	0.080	0.000	0.078
makeTitle	0.004	0.012	0.014
makeTranscript	0.004	0.012	0.015
probestart	0.008	0.000	0.007
segEnd	0.008	0.000	0.007
segStart	0.004	0.000	0.005
segments	0.008	0.000	0.007
seqDataEx	0.028	0.000	0.028
setPar	0.024	0.004	0.028
showDisplayOptions	0.008	0.004	0.011
unrData	0.008	0.000	0.006
unrNProbes	0.004	0.000	0.006
unrPositions	0.004	0.000	0.004
yeastCons1	0.004	0.000	0.004