BioC 2.12: CHECK report for GenomeGraphs on george2

Package: GenomeGraphs

Version: 1.20.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.20.0.tar.gz

StartedAt: 2013-10-09 02:04:55 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:06:12 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 76.8 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 3.0.1 (2013-05-16)
* 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 ‘1.20.0’
* 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/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 installed files from ‘inst/doc’ ... OK
* checking examples ... [9s/15s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
gdPlot 2.372  0.028     5.1
* 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
** testing if installed package can be loaded
* DONE (GenomeGraphs)

name	user	system	elapsed
AnnotationTrack-class	0.008	0.008	0.015
BaseTrack-class	0.012	0.004	0.017
DisplayPars-class	0.020	0.012	0.032
DisplayPars	0.860	0.024	3.313
ExonArray-class	0.040	0.004	0.041
Gene-class	0.016	0.000	0.014
GeneModel-class	0.124	0.016	0.140
GeneRegion-class	0.024	0.000	0.021
GenericArray-class	0.032	0.000	0.032
GenomeAxis-class	0.016	0.004	0.021
HighlightRegion-class	0.032	0.000	0.031
Ideogram-class	0.044	0.000	0.045
ImplementsTrackOverlay-class	0.016	0.000	0.017
Legend-class	0.012	0.000	0.013
MappedRead-class	0.016	0.004	0.022
Overlay-class	0.02	0.00	0.02
RectangleOverlay-class	0.024	0.000	0.022
Segmentation-class	0.016	0.004	0.052
Smoothing-class	0.012	0.004	0.033
TextOverlay-class	0.016	0.004	0.022
Title-class	0.192	0.000	0.203
TrackOverlay-class	0.008	0.004	0.014
Transcript-class	0.012	0.000	0.014
TranscriptRegion-class	0.012	0.000	0.013
cn	0.008	0.000	0.008
exonProbePos	0.008	0.000	0.009
gdObject-class	0.016	0.000	0.016
gdPlot	2.372	0.028	5.100
getPar	0.016	0.008	0.024
getSize	0.008	0.008	0.015
ideogramTab	0.040	0.004	0.042
intensity	0.012	0.000	0.013
makeAnnotationTrack	0.048	0.008	0.065
makeBaseTrack	0.036	0.008	0.047
makeExonArray	0.028	0.012	0.038
makeGene	0.028	0.004	0.047
makeGeneModel	0.024	0.008	0.031
makeGeneRegion	0.032	0.008	0.040
makeGenericArray	0.012	0.004	0.017
makeGenomeAxis	0.024	0.008	0.030
makeIdeogram	0.028	0.000	0.026
makeLegend	0.020	0.000	0.022
makeRectangleOverlay	0.092	0.000	0.092
makeSegmentation	0.076	0.004	0.078
makeSmoothing	0.112	0.000	0.164
makeTextOverlay	0.100	0.008	0.106
makeTitle	0.020	0.000	0.023
makeTranscript	0.028	0.000	0.031
probestart	0.012	0.000	0.012
segEnd	0.016	0.000	0.017
segStart	0.008	0.000	0.007
segments	0.012	0.000	0.014
seqDataEx	0.052	0.004	0.056
setPar	0.036	0.000	0.038
showDisplayOptions	0.016	0.000	0.016
unrData	0.012	0.004	0.024
unrNProbes	0.020	0.000	0.049
unrPositions	0.012	0.004	0.015
yeastCons1	0.008	0.000	0.011