BioC 2.13: CHECK report for GenomeGraphs on zin1

Package: GenomeGraphs

Version: 1.22.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.22.0.tar.gz

StartedAt: 2014-04-05 01:24:57 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:25:44 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 47.5 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [4s/4s] 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 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 ... [4s/15s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
gdPlot      1.332  0.000   6.657
DisplayPars 0.316  0.008   6.608
* 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
  ‘/home/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	0.004	0.000	0.006
BaseTrack-class	0.008	0.000	0.005
DisplayPars-class	0.012	0.000	0.011
DisplayPars	0.316	0.008	6.608
ExonArray-class	0.008	0.000	0.008
Gene-class	0.004	0.000	0.003
GeneModel-class	0.072	0.004	0.076
GeneRegion-class	0.008	0.000	0.006
GenericArray-class	0.000	0.004	0.007
GenomeAxis-class	0.004	0.000	0.004
HighlightRegion-class	0.004	0.000	0.007
Ideogram-class	0.000	0.004	0.006
ImplementsTrackOverlay-class	0.000	0.004	0.004
Legend-class	0.004	0.000	0.004
MappedRead-class	0.004	0.000	0.005
Overlay-class	0.004	0.000	0.004
RectangleOverlay-class	0.004	0.000	0.004
Segmentation-class	0.004	0.000	0.005
Smoothing-class	0.004	0.000	0.004
TextOverlay-class	0.004	0.000	0.004
Title-class	0.000	0.004	0.004
TrackOverlay-class	0.000	0.004	0.004
Transcript-class	0.004	0.000	0.005
TranscriptRegion-class	0.004	0.000	0.004
cn	0.000	0.004	0.003
exonProbePos	0.000	0.004	0.003
gdObject-class	0.004	0.000	0.006
gdPlot	1.332	0.000	6.657
getPar	0.004	0.000	0.005
getSize	0.004	0.000	0.004
ideogramTab	0.008	0.000	0.006
intensity	0.004	0.000	0.003
makeAnnotationTrack	0.028	0.000	0.030
makeBaseTrack	0.068	0.000	0.067
makeExonArray	0.008	0.000	0.008
makeGene	0.008	0.000	0.005
makeGeneModel	0.004	0.000	0.003
makeGeneRegion	0.000	0.004	0.005
makeGenericArray	0.000	0.000	0.002
makeGenomeAxis	0.004	0.000	0.004
makeIdeogram	0.004	0.000	0.005
makeLegend	0.004	0.000	0.004
makeRectangleOverlay	0.06	0.00	0.06
makeSegmentation	0.044	0.008	0.051
makeSmoothing	0.064	0.004	0.070
makeTextOverlay	0.116	0.000	0.115
makeTitle	0.004	0.000	0.005
makeTranscript	0.008	0.000	0.005
probestart	0.004	0.000	0.001
segEnd	0.004	0.000	0.002
segStart	0.004	0.000	0.002
segments	0.004	0.000	0.002
seqDataEx	0.024	0.000	0.022
setPar	0.012	0.000	0.012
showDisplayOptions	0.004	0.000	0.003
unrData	0.000	0.000	0.002
unrNProbes	0.000	0.000	0.002
unrPositions	0.004	0.000	0.001
yeastCons1	0.004	0.000	0.002