BioC 3.2: CHECK report for GenomeGraphs on oaxaca

Package: GenomeGraphs

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.30.0.tar.gz

StartedAt: 2015-10-27 03:59:00 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:00:54 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 114.1 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 GenomeGraphs_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeGraphs/DESCRIPTION’ ... OK
* this is package ‘GenomeGraphs’ version ‘1.30.0’
* 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 ... [10s/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’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘pushViewport’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘dataViewport’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘grid.rect’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘gpar’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘grid.text’
drawGD,AnnotationTrack : .local : <anonymous>: no visible global
  function definition for ‘grid.lines’
drawGD,AnnotationTrack : .local : <anonymous>: no visible global
  function definition for ‘gpar’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘popViewport’
drawGD,BaseTrack : .local: no visible global function definition for
  ‘pushViewport’
drawGD,BaseTrack : .local: no visible global function definition for
  ‘dataViewport’
drawGD,BaseTrack : .local : dP: no visible global function definition
  for ‘grid.points’
drawGD,BaseTrack : .local : dP: no visible global function definition
  for ‘gpar’
drawGD,BaseTrack : .local : dP: no visible global function definition
  for ‘unit’
drawGD,BaseTrack : .local : dVL : <anonymous>: no visible global
  function definition for ‘grid.lines’
drawGD,BaseTrack : .local : dVL : <anonymous>: no visible global
  function definition for ‘gpar’
drawGD,BaseTrack : .local : dVL : <anonymous>: no visible global
  function definition for ‘unit’
drawGD,BaseTrack : .local : dCL: no visible global function definition
  for ‘grid.lines’
drawGD,BaseTrack : .local : dCL: no visible global function definition
  for ‘gpar’
drawGD,BaseTrack : .local : dCL: no visible global function definition
  for ‘unit’
drawGD,BaseTrack : .local: no visible global function definition for
  ‘grid.yaxis’
drawGD,BaseTrack : .local: no visible global function definition for
  ‘popViewport’
drawGD,ExonArray : .local: no visible global function definition for
  ‘pushViewport’
drawGD,ExonArray : .local: no visible global function definition for
  ‘viewport’
drawGD,ExonArray : .local: no visible global function definition for
  ‘grid.layout’
drawGD,ExonArray : .local: no visible global function definition for
  ‘dataViewport’
drawGD,ExonArray : .local: no visible global function definition for
  ‘grid.lines’
drawGD,ExonArray : .local: no visible global function definition for
  ‘gpar’
drawGD,ExonArray : .local: no visible global function definition for
  ‘grid.text’
drawGD,ExonArray : .local: no visible global function definition for
  ‘grid.yaxis’
drawGD,ExonArray : .local: no visible global function definition for
  ‘popViewport’
drawGD,Gene : .local: no visible global function definition for
  ‘pushViewport’
drawGD,Gene : .local: no visible global function definition for
  ‘dataViewport’
drawGD,Gene : .local: no visible global function definition for
  ‘grid.rect’
drawGD,Gene : .local: no visible global function definition for ‘gpar’
drawGD,Gene : .local: no visible global function definition for
  ‘grid.text’
drawGD,Gene : .local: no visible global function definition for
  ‘grid.lines’
drawGD,Gene : .local: no visible global function definition for
  ‘popViewport’
drawGD,GeneModel : .local: no visible global function definition for
  ‘pushViewport’
drawGD,GeneModel : .local: no visible global function definition for
  ‘dataViewport’
drawGD,GeneModel : .local: no visible global function definition for
  ‘grid.rect’
drawGD,GeneModel : .local: no visible global function definition for
  ‘gpar’
drawGD,GeneModel : .local: no visible global function definition for
  ‘grid.lines’
drawGD,GeneModel : .local: no visible global function definition for
  ‘popViewport’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘pushViewport’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘dataViewport’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘grid.rect’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘gpar’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘grid.text’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘grid.lines’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘popViewport’
drawGD,GenericArray : .local: no visible global function definition for
  ‘pushViewport’
drawGD,GenericArray : .local: no visible global function definition for
  ‘dataViewport’
drawGD,GenericArray : .local: no visible global function definition for
  ‘grid.lines’
drawGD,GenericArray : .local: no visible global function definition for
  ‘gpar’
drawGD,GenericArray : .local: no visible global function definition for
  ‘grid.points’
drawGD,GenericArray : .local: no visible global function definition for
  ‘unit’
drawGD,GenericArray : .local: no visible global function definition for
  ‘grid.yaxis’
drawGD,GenericArray : .local: no visible global function definition for
  ‘popViewport’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘pushViewport’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘dataViewport’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘grid.lines’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘grid.text’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘gpar’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘grid.segments’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘popViewport’
drawGD,Ideogram : .local: no visible binding for global variable
  ‘ideogramTab’
drawGD,Ideogram : .local: no visible global function definition for
  ‘pushViewport’
drawGD,Ideogram : .local: no visible global function definition for
  ‘dataViewport’
drawGD,Ideogram : .local: no visible global function definition for
  ‘grid.rect’
drawGD,Ideogram : .local: no visible global function definition for
  ‘gpar’
drawGD,Ideogram : .local: no visible global function definition for
  ‘grid.lines’
drawGD,Ideogram : .local: no visible global function definition for
  ‘popViewport’
drawGD,Legend : .local: no visible global function definition for
  ‘pushViewport’
drawGD,Legend : .local: no visible global function definition for
  ‘dataViewport’
drawGD,Legend : .local: no visible global function definition for
  ‘grid.text’
drawGD,Legend : .local: no visible global function definition for
  ‘gpar’
drawGD,Legend : .local: no visible global function definition for
  ‘grid.rect’
drawGD,Legend : .local: no visible global function definition for
  ‘popViewport’
drawGD,MappedRead : .local: no visible global function definition for
  ‘pushViewport’
drawGD,MappedRead : .local: no visible global function definition for
  ‘dataViewport’
drawGD,MappedRead : .local: no visible global function definition for
  ‘gpar’
drawGD,MappedRead : .local: no visible global function definition for
  ‘grid.lines’
drawGD,MappedRead : .local: no visible global function definition for
  ‘popViewport’
drawGD,Title : .local: no visible global function definition for
  ‘pushViewport’
drawGD,Title : .local: no visible global function definition for
  ‘viewport’
drawGD,Title : .local: no visible global function definition for
  ‘grid.text’
drawGD,Title : .local: no visible global function definition for ‘gpar’
drawGD,Title : .local: no visible global function definition for
  ‘popViewport’
drawGD,Transcript : .local: no visible global function definition for
  ‘pushViewport’
drawGD,Transcript : .local: no visible global function definition for
  ‘viewport’
drawGD,Transcript : .local: no visible global function definition for
  ‘grid.layout’
drawGD,Transcript : .local: no visible global function definition for
  ‘dataViewport’
drawGD,Transcript : .local: no visible global function definition for
  ‘grid.text’
drawGD,Transcript : .local: no visible global function definition for
  ‘gpar’
drawGD,Transcript : .local: no visible global function definition for
  ‘grid.rect’
drawGD,Transcript : .local: no visible global function definition for
  ‘grid.lines’
drawGD,Transcript : .local: no visible global function definition for
  ‘popViewport’
drawOverlay,RectangleOverlay : .local: no visible global function
  definition for ‘grid.rect’
drawOverlay,RectangleOverlay : .local: no visible global function
  definition for ‘gpar’
drawOverlay,TextOverlay : .local: no visible global function definition
  for ‘grid.text’
drawOverlay,TextOverlay : .local: no visible global function definition
  for ‘gpar’
drawTrackOverlay,Segmentation : .local: no visible global function
  definition for ‘grid.lines’
drawTrackOverlay,Segmentation : .local: no visible global function
  definition for ‘gpar’
drawTrackOverlay,Smoothing : .local: no visible global function
  definition for ‘grid.lines’
drawTrackOverlay,Smoothing : .local: no visible global function
  definition for ‘gpar’
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 ... [6s/10s] 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

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.000	0.002
BaseTrack-class	0.001	0.000	0.001
DisplayPars-class	0.003	0.000	0.004
DisplayPars	0.223	0.008	2.293
ExonArray-class	0.009	0.001	0.009
Gene-class	0.001	0.000	0.000
GeneModel-class	0.092	0.003	0.095
GeneRegion-class	0.001	0.001	0.002
GenericArray-class	0.001	0.000	0.002
GenomeAxis-class	0.001	0.000	0.001
HighlightRegion-class	0.003	0.001	0.003
Ideogram-class	0.001	0.000	0.002
ImplementsTrackOverlay-class	0.001	0.000	0.001
Legend-class	0.001	0.000	0.001
MappedRead-class	0	0	0
Overlay-class	0.001	0.000	0.001
RectangleOverlay-class	0.001	0.000	0.002
Segmentation-class	0.002	0.000	0.002
Smoothing-class	0.001	0.000	0.002
TextOverlay-class	0.001	0.000	0.002
Title-class	0.001	0.000	0.002
TrackOverlay-class	0.001	0.001	0.002
Transcript-class	0.001	0.000	0.002
TranscriptRegion-class	0.001	0.000	0.001
cn	0.001	0.001	0.001
exonProbePos	0.001	0.000	0.001
gdObject-class	0.002	0.000	0.003
gdPlot	0.791	0.024	3.207
getPar	0.002	0.000	0.001
getSize	0.000	0.000	0.001
ideogramTab	0.003	0.001	0.004
intensity	0.001	0.000	0.001
makeAnnotationTrack	0.022	0.001	0.024
makeBaseTrack	0.004	0.000	0.004
makeExonArray	0.005	0.000	0.005
makeGene	0.003	0.000	0.003
makeGeneModel	0.001	0.000	0.002
makeGeneRegion	0.002	0.000	0.003
makeGenericArray	0.001	0.001	0.002
makeGenomeAxis	0.002	0.000	0.002
makeIdeogram	0.003	0.001	0.002
makeLegend	0.001	0.000	0.001
makeRectangleOverlay	0.069	0.003	0.072
makeSegmentation	0.056	0.003	0.059
makeSmoothing	0.071	0.004	0.076
makeTextOverlay	0.065	0.003	0.069
makeTitle	0.002	0.000	0.002
makeTranscript	0.002	0.001	0.002
probestart	0.001	0.000	0.000
segEnd	0	0	0
segStart	0.000	0.001	0.001
segments	0.000	0.000	0.001
seqDataEx	0.023	0.002	0.025
setPar	0.012	0.001	0.013
showDisplayOptions	0.000	0.001	0.001
unrData	0	0	0
unrNProbes	0.001	0.000	0.001
unrPositions	0.001	0.000	0.000
yeastCons1	0.001	0.000	0.000