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: 2013-03-25 01:53:58 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:55:18 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 79.1 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ... [8s/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 ... [9s/13s] 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
  ‘/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	0.016	0.004	0.019
BaseTrack-class	0.012	0.008	0.020
DisplayPars-class	0.012	0.020	0.032
DisplayPars	0.616	0.032	2.796
ExonArray-class	0.180	0.004	0.193
Gene-class	0.024	0.000	0.037
GeneModel-class	0.128	0.012	0.174
GeneRegion-class	0.024	0.000	0.023
GenericArray-class	0.032	0.000	0.035
GenomeAxis-class	0.016	0.000	0.017
HighlightRegion-class	0.028	0.000	0.029
Ideogram-class	0.02	0.00	0.02
ImplementsTrackOverlay-class	0.016	0.000	0.018
Legend-class	0.020	0.000	0.017
MappedRead-class	0.016	0.000	0.015
Overlay-class	0.036	0.004	0.036
RectangleOverlay-class	0.016	0.000	0.018
Segmentation-class	0.012	0.000	0.012
Smoothing-class	0.012	0.000	0.013
TextOverlay-class	0.016	0.000	0.014
Title-class	0.012	0.000	0.013
TrackOverlay-class	0.012	0.000	0.010
Transcript-class	0.012	0.004	0.014
TranscriptRegion-class	0.012	0.000	0.010
cn	0.192	0.000	0.190
exonProbePos	0.016	0.000	0.015
gdObject-class	0.024	0.000	0.023
gdPlot	2.448	0.056	4.779
getPar	0.020	0.000	0.021
getSize	0.008	0.004	0.010
ideogramTab	0.020	0.000	0.023
intensity	0.016	0.000	0.015
makeAnnotationTrack	0.06	0.00	0.06
makeBaseTrack	0.032	0.000	0.033
makeExonArray	0.032	0.000	0.035
makeGene	0.024	0.004	0.030
makeGeneModel	0.024	0.000	0.024
makeGeneRegion	0.172	0.012	0.191
makeGenericArray	0.012	0.000	0.011
makeGenomeAxis	0.020	0.000	0.023
makeIdeogram	0.02	0.00	0.02
makeLegend	0.016	0.000	0.016
makeRectangleOverlay	0.1	0.0	0.1
makeSegmentation	0.084	0.000	0.087
makeSmoothing	0.108	0.000	0.110
makeTextOverlay	0.100	0.000	0.099
makeTitle	0.016	0.000	0.014
makeTranscript	0.016	0.000	0.017
probestart	0.008	0.004	0.009
segEnd	0.008	0.000	0.009
segStart	0.016	0.000	0.017
segments	0.008	0.000	0.007
seqDataEx	0.040	0.000	0.039
setPar	0.032	0.000	0.034
showDisplayOptions	0.012	0.000	0.013
unrData	0.012	0.000	0.010
unrNProbes	0.008	0.000	0.010
unrPositions	0.012	0.000	0.013
yeastCons1	0.016	0.000	0.016