BioC 3.2: CHECK report for GenomeGraphs on moscato1

Package: GenomeGraphs

Version: 1.30.0

Command: rm -rf GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && mkdir GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeGraphs.buildbin-libdir GenomeGraphs_1.30.0.tar.gz >GenomeGraphs.Rcheck\00install.out 2>&1 && cp GenomeGraphs.Rcheck\00install.out GenomeGraphs-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GenomeGraphs.buildbin-libdir --install="check:GenomeGraphs-install.out" --force-multiarch --no-vignettes --timings GenomeGraphs_1.30.0.tar.gz

StartedAt: 2016-04-23 02:42:43 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:47:39 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 296.2 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && mkdir GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeGraphs.buildbin-libdir GenomeGraphs_1.30.0.tar.gz >GenomeGraphs.Rcheck\00install.out 2>&1 && cp GenomeGraphs.Rcheck\00install.out GenomeGraphs-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GenomeGraphs.buildbin-libdir --install="check:GenomeGraphs-install.out" --force-multiarch --no-vignettes --timings GenomeGraphs_1.30.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/GenomeGraphs.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [53s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
gdPlot      1.10   0.02   23.39
DisplayPars 0.34   0.04   22.85
** running examples for arch 'x64' ... [52s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
gdPlot      1.17   0.00   24.10
DisplayPars 0.41   0.04   22.85
* 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
  'D:/biocbld/bbs-3.2-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_1.30.0.zip
* DONE (GenomeGraphs)

name	user	system	elapsed
AnnotationTrack-class	0	0	0
BaseTrack-class	0	0	0
DisplayPars-class	0	0	0
DisplayPars	0.34	0.04	22.85
ExonArray-class	0	0	0
Gene-class	0	0	0
GeneModel-class	0.08	0.00	0.08
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	0.02	0.00	0.02
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	1.10	0.02	23.39
getPar	0	0	0
getSize	0	0	0
ideogramTab	0.00	0.01	0.01
intensity	0	0	0
makeAnnotationTrack	0.04	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	0.01	0.00	0.01
makeLegend	0	0	0
makeRectangleOverlay	0.16	0.00	0.16
makeSegmentation	0.14	0.00	0.14
makeSmoothing	0.15	0.00	0.15
makeTextOverlay	0.24	0.00	0.32
makeTitle	0	0	0
makeTranscript	0.01	0.00	0.01
probestart	0	0	0
segEnd	0	0	0
segStart	0	0	0
segments	0	0	0
seqDataEx	0.04	0.02	0.05
setPar	0.01	0.00	0.02
showDisplayOptions	0.02	0.00	0.01
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	0.41	0.04	22.85
ExonArray-class	0	0	0
Gene-class	0	0	0
GeneModel-class	0.13	0.00	0.12
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	0.02	0.00	0.01
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	1.17	0.00	24.10
getPar	0	0	0
getSize	0	0	0
ideogramTab	0	0	0
intensity	0	0	0
makeAnnotationTrack	0.03	0.00	0.03
makeBaseTrack	0	0	0
makeExonArray	0.02	0.00	0.01
makeGene	0	0	0
makeGeneModel	0	0	0
makeGeneRegion	0	0	0
makeGenericArray	0.01	0.00	0.02
makeGenomeAxis	0	0	0
makeIdeogram	0	0	0
makeLegend	0	0	0
makeRectangleOverlay	0.27	0.00	0.26
makeSegmentation	0.23	0.00	0.24
makeSmoothing	0.30	0.00	0.29
makeTextOverlay	0.28	0.00	0.28
makeTitle	0	0	0
makeTranscript	0	0	0
probestart	0	0	0
segEnd	0.01	0.00	0.02
segStart	0	0	0
segments	0	0	0
seqDataEx	0.05	0.00	0.05
setPar	0.02	0.00	0.01
showDisplayOptions	0	0	0
unrData	0	0	0
unrNProbes	0	0	0
unrPositions	0	0	0
yeastCons1	0	0	0