BioC 2.14: CHECK report for GenomeGraphs on moscato2

Package: GenomeGraphs

Version: 1.24.0

Command: rm -rf GenomeGraphs.buildbin-libdir && mkdir GenomeGraphs.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeGraphs.buildbin-libdir GenomeGraphs_1.24.0.tar.gz >GenomeGraphs-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=GenomeGraphs.buildbin-libdir --install="check:GenomeGraphs-install.out" --force-multiarch --no-vignettes --timings GenomeGraphs_1.24.0.tar.gz

StartedAt: 2014-10-08 01:27:42 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:30:24 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 161.7 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 && mkdir GenomeGraphs.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeGraphs.buildbin-libdir GenomeGraphs_1.24.0.tar.gz >GenomeGraphs-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=GenomeGraphs.buildbin-libdir --install="check:GenomeGraphs-install.out" --force-multiarch --no-vignettes --timings GenomeGraphs_1.24.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/GenomeGraphs.Rcheck'
* using R version 3.1.1 (2014-07-10)
* 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 '1.24.0'
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gdPlot: warning in grid.layout(1, 2, width = c(0.1, 0.9)): partial
  argument match of 'width' to 'widths'
gdPlot: warning in grid.layout(length(vplayout), 1, height = vplayout):
  partial argument match of 'height' to 'heights'
transcriptModule: warning in grid.layout(1, length(vplayout), width =
  vplayout): partial argument match of 'width' to 'widths'
* 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' ... [23s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
DisplayPars  0.4   0.03   14.54
** running examples for arch 'x64' ... [21s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
DisplayPars 0.52   0.04   11.74
* 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

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.14-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_1.24.0.zip
* DONE (GenomeGraphs)

name	user	system	elapsed
AnnotationTrack-class	0	0	0
BaseTrack-class	0	0	0
DisplayPars-class	0	0	0
DisplayPars	0.40	0.03	14.54
ExonArray-class	0	0	0
Gene-class	0	0	0
GeneModel-class	0.18	0.00	0.17
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	0.02	0.00	0.02
Transcript-class	0	0	0
TranscriptRegion-class	0	0	0
cn	0	0	0
exonProbePos	0	0	0
gdObject-class	0	0	0
gdPlot	1.26	0.00	3.91
getPar	0	0	0
getSize	0	0	0
ideogramTab	0.00	0.02	0.02
intensity	0	0	0
makeAnnotationTrack	0.03	0.00	0.03
makeBaseTrack	0	0	0
makeExonArray	0	0	0
makeGene	0.02	0.00	0.02
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	0.14	0.00	0.14
makeSegmentation	0.14	0.00	0.14
makeSmoothing	0.15	0.00	0.15
makeTextOverlay	0.14	0.02	0.16
makeTitle	0.02	0.00	0.02
makeTranscript	0	0	0
probestart	0	0	0
segEnd	0	0	0
segStart	0	0	0
segments	0	0	0
seqDataEx	0.03	0.00	0.03
setPar	0.02	0.00	0.01
showDisplayOptions	0	0	0
unrData	0	0	0
unrNProbes	0	0	0
unrPositions	0	0	0
yeastCons1	0	0	0

name	user	system	elapsed
AnnotationTrack-class	0	0	0
BaseTrack-class	0	0	0
DisplayPars-class	0	0	0
DisplayPars	0.52	0.04	11.74
ExonArray-class	0	0	0
Gene-class	0	0	0
GeneModel-class	0.21	0.00	0.21
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	0.01	0.00	0.02
exonProbePos	0	0	0
gdObject-class	0	0	0
gdPlot	1.44	0.00	4.03
getPar	0	0	0
getSize	0	0	0
ideogramTab	0	0	0
intensity	0	0	0
makeAnnotationTrack	0.03	0.00	0.15
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	0.17	0.00	0.17
makeSegmentation	0.16	0.00	0.16
makeSmoothing	0.17	0.02	0.19
makeTextOverlay	0.17	0.00	0.17
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	0.02	0.00	0.02
setPar	0.02	0.00	0.02
showDisplayOptions	0	0	0
unrData	0	0	0
unrNProbes	0	0	0
unrPositions	0.01	0.00	0.01
yeastCons1	0	0	0