BioC 2.13: CHECK report for GenomeGraphs on perceval

Package: GenomeGraphs

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.22.0.tar.gz

StartedAt: 2014-04-05 01:33:24 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:34:37 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 72.8 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeGraphs/DESCRIPTION’ ... OK
* this is package ‘GenomeGraphs’ version ‘1.22.0’
* 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 ... [6s/6s] 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GenomeGraphs.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [6s/16s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
gdPlot 1.684  0.049   8.154
* 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 were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.006	0.001	0.006
BaseTrack-class	0.005	0.000	0.006
DisplayPars-class	0.013	0.000	0.014
DisplayPars	0.539	0.028	3.339
ExonArray-class	0.026	0.001	0.027
Gene-class	0.011	0.001	0.011
GeneModel-class	0.113	0.006	0.119
GeneRegion-class	0.011	0.001	0.011
GenericArray-class	0.011	0.001	0.012
GenomeAxis-class	0.012	0.001	0.013
HighlightRegion-class	0.017	0.001	0.017
Ideogram-class	0.017	0.001	0.017
ImplementsTrackOverlay-class	0.012	0.000	0.012
Legend-class	0.006	0.000	0.007
MappedRead-class	0.006	0.000	0.006
Overlay-class	0.006	0.001	0.006
RectangleOverlay-class	0.006	0.001	0.007
Segmentation-class	0.012	0.001	0.014
Smoothing-class	0.009	0.000	0.009
TextOverlay-class	0.008	0.000	0.009
Title-class	0.010	0.001	0.012
TrackOverlay-class	0.008	0.001	0.009
Transcript-class	0.009	0.000	0.009
TranscriptRegion-class	0.008	0.001	0.008
cn	0.006	0.001	0.006
exonProbePos	0.006	0.000	0.006
gdObject-class	0.012	0.000	0.012
gdPlot	1.684	0.049	8.154
getPar	0.011	0.000	0.011
getSize	0.007	0.000	0.007
ideogramTab	0.012	0.000	0.012
intensity	0.006	0.000	0.006
makeAnnotationTrack	0.038	0.002	0.040
makeBaseTrack	0.133	0.003	0.137
makeExonArray	0.019	0.001	0.021
makeGene	0.014	0.001	0.016
makeGeneModel	0.008	0.000	0.009
makeGeneRegion	0.019	0.001	0.021
makeGenericArray	0.006	0.001	0.007
makeGenomeAxis	0.012	0.001	0.012
makeIdeogram	0.016	0.000	0.017
makeLegend	0.014	0.001	0.015
makeRectangleOverlay	0.220	0.007	0.229
makeSegmentation	0.072	0.015	0.091
makeSmoothing	0.092	0.013	0.106
makeTextOverlay	0.079	0.013	0.095
makeTitle	0.010	0.001	0.011
makeTranscript	0.016	0.000	0.019
probestart	0.004	0.000	0.004
segEnd	0.006	0.000	0.005
segStart	0.007	0.000	0.007
segments	0.005	0.000	0.005
seqDataEx	0.032	0.015	0.048
setPar	0.024	0.002	0.028
showDisplayOptions	0.005	0.001	0.006
unrData	0.005	0.000	0.006
unrNProbes	0.005	0.000	0.006
unrPositions	0.007	0.000	0.008
yeastCons1	0.003	0.000	0.003