BioC 3.0: CHECK report for GenomeGraphs on zin1

Package: GenomeGraphs

Version: 1.26.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.26.0.tar.gz

StartedAt: 2015-04-10 00:19:38 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:21:59 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 141.0 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.26.0’
* 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 ... [11s/11s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/36s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
gdPlot      0.560  0.012  15.289
DisplayPars 0.316  0.004  14.447
* 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
  ‘/home/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	0.004	0.000	0.002
BaseTrack-class	0.000	0.000	0.002
DisplayPars-class	0.000	0.000	0.003
DisplayPars	0.316	0.004	14.447
ExonArray-class	0.004	0.000	0.005
Gene-class	0.000	0.000	0.001
GeneModel-class	0.216	0.000	0.216
GeneRegion-class	0.004	0.000	0.002
GenericArray-class	0.000	0.000	0.001
GenomeAxis-class	0.000	0.000	0.001
HighlightRegion-class	0.000	0.004	0.003
Ideogram-class	0.004	0.000	0.001
ImplementsTrackOverlay-class	0.000	0.000	0.001
Legend-class	0.000	0.000	0.001
MappedRead-class	0	0	0
Overlay-class	0.004	0.000	0.001
RectangleOverlay-class	0.000	0.000	0.001
Segmentation-class	0.000	0.000	0.001
Smoothing-class	0.000	0.000	0.001
TextOverlay-class	0.000	0.000	0.002
Title-class	0.000	0.000	0.001
TrackOverlay-class	0.000	0.000	0.001
Transcript-class	0.004	0.000	0.001
TranscriptRegion-class	0.000	0.000	0.001
cn	0.004	0.000	0.001
exonProbePos	0	0	0
gdObject-class	0.004	0.000	0.002
gdPlot	0.560	0.012	15.289
getPar	0.000	0.000	0.001
getSize	0.000	0.000	0.001
ideogramTab	0.004	0.000	0.002
intensity	0.000	0.000	0.001
makeAnnotationTrack	0.024	0.000	0.023
makeBaseTrack	0.004	0.000	0.003
makeExonArray	0.004	0.000	0.003
makeGene	0.004	0.000	0.002
makeGeneModel	0.000	0.000	0.001
makeGeneRegion	0.000	0.000	0.002
makeGenericArray	0.004	0.000	0.001
makeGenomeAxis	0.000	0.000	0.001
makeIdeogram	0.004	0.000	0.002
makeLegend	0.000	0.000	0.001
makeRectangleOverlay	0.056	0.000	0.059
makeSegmentation	0.048	0.000	0.052
makeSmoothing	0.068	0.004	0.074
makeTextOverlay	0.068	0.000	0.067
makeTitle	0.004	0.000	0.002
makeTranscript	0.004	0.000	0.002
probestart	0	0	0
segEnd	0.000	0.004	0.000
segStart	0.000	0.000	0.001
segments	0	0	0
seqDataEx	0.020	0.000	0.022
setPar	0.012	0.000	0.013
showDisplayOptions	0.000	0.000	0.001
unrData	0	0	0
unrNProbes	0.000	0.000	0.001
unrPositions	0	0	0
yeastCons1	0	0	0