BioC 3.0: CHECK report for GenomeGraphs on perceval

Package: GenomeGraphs

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.26.0.tar.gz

StartedAt: 2015-04-10 01:58:00 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:00:50 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 170.6 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_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.26.0’
* 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 ... [16s/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 ... NOTE
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.drawGene: no visible global function definition for ‘pushViewport’
.drawGene: no visible global function definition for ‘dataViewport’
.drawGene: no visible global function definition for ‘grid.rect’
.drawGene: no visible global function definition for ‘gpar’
.drawGene: no visible global function definition for ‘grid.text’
.drawGene: no visible global function definition for ‘grid.lines’
.drawGene: no visible global function definition for ‘popViewport’
exonModule: no visible global function definition for ‘pushViewport’
exonModule: no visible global function definition for ‘dataViewport’
exonModule: no visible global function definition for ‘grid.rect’
exonModule: no visible global function definition for ‘gpar’
exonModule: no visible global function definition for ‘grid.lines’
gdPlot: no visible global function definition for ‘grid.newpage’
gdPlot: no visible global function definition for ‘pushViewport’
gdPlot: no visible global function definition for ‘viewport’
gdPlot: no visible global function definition for ‘grid.layout’
gdPlot: no visible global function definition for ‘grid.text’
gdPlot: no visible global function definition for ‘gpar’
gdPlot: no visible global function definition for ‘popViewport’
geneBiomart: no visible global function definition for ‘getBM’
geneRegionBiomart: no visible global function definition for ‘getBM’
transcriptModule: no visible global function definition for
  ‘pushViewport’
transcriptModule: no visible global function definition for ‘viewport’
transcriptModule: no visible global function definition for
  ‘grid.layout’
initialize,Gene: no visible global function definition for ‘getBM’
initialize,GeneRegion: no visible global function definition for
  ‘getBM’
initialize,Transcript: no visible global function definition for
  ‘getBM’
* 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 ... [10s/15s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.002	0.001	0.002
BaseTrack-class	0.002	0.000	0.001
DisplayPars-class	0.005	0.000	0.006
DisplayPars	0.244	0.024	2.356
ExonArray-class	0.011	0.000	0.010
Gene-class	0.001	0.000	0.002
GeneModel-class	0.359	0.008	0.644
GeneRegion-class	0.002	0.000	0.001
GenericArray-class	0.002	0.000	0.002
GenomeAxis-class	0.002	0.000	0.002
HighlightRegion-class	0.003	0.001	0.004
Ideogram-class	0.001	0.000	0.002
ImplementsTrackOverlay-class	0.001	0.001	0.002
Legend-class	0.001	0.000	0.001
MappedRead-class	0.000	0.001	0.001
Overlay-class	0.001	0.000	0.002
RectangleOverlay-class	0.001	0.001	0.002
Segmentation-class	0.002	0.000	0.002
Smoothing-class	0.001	0.000	0.001
TextOverlay-class	0.001	0.000	0.001
Title-class	0.001	0.000	0.001
TrackOverlay-class	0.002	0.000	0.002
Transcript-class	0.002	0.000	0.001
TranscriptRegion-class	0.002	0.000	0.002
cn	0.001	0.000	0.001
exonProbePos	0.001	0.000	0.001
gdObject-class	0.002	0.001	0.002
gdPlot	0.707	0.035	3.364
getPar	0.001	0.001	0.002
getSize	0.000	0.000	0.001
ideogramTab	0.003	0.001	0.004
intensity	0.001	0.000	0.001
makeAnnotationTrack	0.033	0.001	0.039
makeBaseTrack	0.005	0.001	0.005
makeExonArray	0.006	0.000	0.006
makeGene	0.002	0.000	0.002
makeGeneModel	0.002	0.001	0.002
makeGeneRegion	0.003	0.000	0.004
makeGenericArray	0.002	0.000	0.002
makeGenomeAxis	0.001	0.000	0.002
makeIdeogram	0.002	0.000	0.003
makeLegend	0.002	0.001	0.002
makeRectangleOverlay	0.073	0.007	0.088
makeSegmentation	0.064	0.006	0.076
makeSmoothing	0.079	0.006	0.090
makeTextOverlay	0.070	0.006	0.086
makeTitle	0.002	0.000	0.003
makeTranscript	0.002	0.000	0.003
probestart	0.001	0.000	0.001
segEnd	0.000	0.000	0.001
segStart	0.001	0.001	0.001
segments	0.001	0.000	0.000
seqDataEx	0.024	0.006	0.029
setPar	0.018	0.002	0.033
showDisplayOptions	0.002	0.000	0.003
unrData	0.000	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