BioC 3.0: CHECK report for GenomeGraphs on moscato1

Package: GenomeGraphs

Version: 1.26.0

Command: rm -rf GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && mkdir GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeGraphs.buildbin-libdir GenomeGraphs_1.26.0.tar.gz >GenomeGraphs.Rcheck\00install.out 2>&1 && cp GenomeGraphs.Rcheck\00install.out GenomeGraphs-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GenomeGraphs.buildbin-libdir --install="check:GenomeGraphs-install.out" --force-multiarch --no-vignettes --timings GenomeGraphs_1.26.0.tar.gz

StartedAt: 2015-04-10 01:30:20 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:33:31 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 191.1 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && mkdir GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeGraphs.buildbin-libdir GenomeGraphs_1.26.0.tar.gz >GenomeGraphs.Rcheck\00install.out 2>&1 && cp GenomeGraphs.Rcheck\00install.out GenomeGraphs-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GenomeGraphs.buildbin-libdir --install="check:GenomeGraphs-install.out" --force-multiarch --no-vignettes --timings GenomeGraphs_1.26.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/GenomeGraphs.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'GenomeGraphs' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [12s] OK
** running examples for arch 'x64' ... [18s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
gdPlot 0.89      0    6.86
* 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
  'D:/biocbld/bbs-3.0-bioc/meat/GenomeGraphs.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'GenomeGraphs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomeGraphs' as GenomeGraphs_1.26.0.zip
* DONE (GenomeGraphs)

name	user	system	elapsed
AnnotationTrack-class	0	0	0
BaseTrack-class	0	0	0
DisplayPars-class	0	0	0
DisplayPars	0.42	0.03	2.46
ExonArray-class	0.01	0.00	0.02
Gene-class	0	0	0
GeneModel-class	0.19	0.00	0.18
GeneRegion-class	0	0	0
GenericArray-class	0	0	0
GenomeAxis-class	0	0	0
HighlightRegion-class	0	0	0
Ideogram-class	0	0	0
ImplementsTrackOverlay-class	0	0	0
Legend-class	0.01	0.00	0.02
MappedRead-class	0	0	0
Overlay-class	0	0	0
RectangleOverlay-class	0	0	0
Segmentation-class	0	0	0
Smoothing-class	0	0	0
TextOverlay-class	0	0	0
Title-class	0	0	0
TrackOverlay-class	0.02	0.00	0.01
Transcript-class	0	0	0
TranscriptRegion-class	0	0	0
cn	0	0	0
exonProbePos	0	0	0
gdObject-class	0	0	0
gdPlot	0.75	0.05	3.31
getPar	0	0	0
getSize	0	0	0
ideogramTab	0	0	0
intensity	0	0	0
makeAnnotationTrack	0.03	0.00	0.04
makeBaseTrack	0	0	0
makeExonArray	0	0	0
makeGene	0	0	0
makeGeneModel	0.02	0.00	0.01
makeGeneRegion	0	0	0
makeGenericArray	0	0	0
makeGenomeAxis	0	0	0
makeIdeogram	0	0	0
makeLegend	0	0	0
makeRectangleOverlay	0.16	0.00	0.16
makeSegmentation	0.14	0.00	0.14
makeSmoothing	0.17	0.00	0.17
makeTextOverlay	0.2	0.0	0.2
makeTitle	0	0	0
makeTranscript	0	0	0
probestart	0	0	0
segEnd	0	0	0
segStart	0	0	0
segments	0	0	0
seqDataEx	0.01	0.00	0.01
setPar	0.02	0.00	0.02
showDisplayOptions	0	0	0
unrData	0	0	0
unrNProbes	0	0	0
unrPositions	0	0	0
yeastCons1	0	0	0

name	user	system	elapsed
AnnotationTrack-class	0	0	0
BaseTrack-class	0	0	0
DisplayPars-class	0	0	0
DisplayPars	0.81	0.08	3.06
ExonArray-class	0.02	0.00	0.01
Gene-class	0	0	0
GeneModel-class	0.34	0.00	0.34
GeneRegion-class	0	0	0
GenericArray-class	0	0	0
GenomeAxis-class	0	0	0
HighlightRegion-class	0	0	0
Ideogram-class	0	0	0
ImplementsTrackOverlay-class	0	0	0
Legend-class	0	0	0
MappedRead-class	0	0	0
Overlay-class	0	0	0
RectangleOverlay-class	0	0	0
Segmentation-class	0	0	0
Smoothing-class	0	0	0
TextOverlay-class	0	0	0
Title-class	0	0	0
TrackOverlay-class	0	0	0
Transcript-class	0	0	0
TranscriptRegion-class	0	0	0
cn	0	0	0
exonProbePos	0	0	0
gdObject-class	0	0	0
gdPlot	0.89	0.00	6.86
getPar	0	0	0
getSize	0	0	0
ideogramTab	0.0	0.0	0.1
intensity	0	0	0
makeAnnotationTrack	0.03	0.00	0.03
makeBaseTrack	0	0	0
makeExonArray	0	0	0
makeGene	0	0	0
makeGeneModel	0	0	0
makeGeneRegion	0	0	0
makeGenericArray	0	0	0
makeGenomeAxis	0	0	0
makeIdeogram	0	0	0
makeLegend	0	0	0
makeRectangleOverlay	0.18	0.00	0.17
makeSegmentation	0.17	0.02	0.19
makeSmoothing	0.2	0.0	0.2
makeTextOverlay	0.2	0.0	0.2
makeTitle	0	0	0
makeTranscript	0.02	0.00	0.02
probestart	0	0	0
segEnd	0	0	0
segStart	0	0	0
segments	0	0	0
seqDataEx	0.03	0.00	0.03
setPar	0.01	0.00	0.01
showDisplayOptions	0	0	0
unrData	0	0	0
unrNProbes	0	0	0
unrPositions	0	0	0
yeastCons1	0	0	0