BioC 2.14: CHECK report for GenomeGraphs on petty

Package: GenomeGraphs

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.24.0.tar.gz

StartedAt: 2014-10-07 22:10:31 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:13:56 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 205.0 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeGraphs/DESCRIPTION’ ... OK
* this is package ‘GenomeGraphs’ version ‘1.24.0’
* 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 ... [20s/21s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/19s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
gdPlot 2.832  0.055   6.257
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.004	0.001	0.004
BaseTrack-class	0.002	0.000	0.003
DisplayPars-class	0.007	0.001	0.008
DisplayPars	0.609	0.015	3.265
ExonArray-class	0.017	0.001	0.019
Gene-class	0.002	0.000	0.002
GeneModel-class	0.179	0.007	0.188
GeneRegion-class	0.003	0.000	0.003
GenericArray-class	0.004	0.000	0.004
GenomeAxis-class	0.002	0.001	0.003
HighlightRegion-class	0.006	0.000	0.006
Ideogram-class	0.003	0.000	0.004
ImplementsTrackOverlay-class	0.001	0.000	0.002
Legend-class	0.001	0.000	0.002
MappedRead-class	0.001	0.001	0.001
Overlay-class	0.002	0.000	0.003
RectangleOverlay-class	0.002	0.000	0.003
Segmentation-class	0.003	0.000	0.003
Smoothing-class	0.003	0.000	0.003
TextOverlay-class	0.003	0.001	0.003
Title-class	0.002	0.000	0.002
TrackOverlay-class	0.002	0.000	0.002
Transcript-class	0.002	0.001	0.002
TranscriptRegion-class	0.002	0.000	0.002
cn	0.001	0.000	0.001
exonProbePos	0.001	0.000	0.001
gdObject-class	0.003	0.001	0.003
gdPlot	2.832	0.055	6.257
getPar	0.003	0.001	0.004
getSize	0.001	0.000	0.001
ideogramTab	0.005	0.001	0.005
intensity	0.001	0.000	0.001
makeAnnotationTrack	0.048	0.002	0.050
makeBaseTrack	0.008	0.001	0.008
makeExonArray	0.008	0.000	0.008
makeGene	0.003	0.000	0.003
makeGeneModel	0.002	0.000	0.003
makeGeneRegion	0.005	0.000	0.006
makeGenericArray	0.002	0.000	0.003
makeGenomeAxis	0.003	0.000	0.003
makeIdeogram	0.005	0.000	0.005
makeLegend	0.003	0.000	0.004
makeRectangleOverlay	0.13	0.01	0.14
makeSegmentation	0.105	0.009	0.116
makeSmoothing	0.139	0.010	0.150
makeTextOverlay	0.126	0.010	0.137
makeTitle	0.003	0.001	0.004
makeTranscript	0.004	0.000	0.005
probestart	0.001	0.000	0.001
segEnd	0.001	0.000	0.001
segStart	0.001	0.001	0.001
segments	0.001	0.000	0.001
seqDataEx	0.041	0.008	0.049
setPar	0.026	0.002	0.030
showDisplayOptions	0.003	0.001	0.003
unrData	0.001	0.000	0.001
unrNProbes	0.001	0.000	0.001
unrPositions	0.001	0.000	0.001
yeastCons1	0.001	0.000	0.001