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BioC 2.12: CHECK report for GenomeGraphs on petty

This page was generated on 2013-10-09 09:39:41 -0700 (Wed, 09 Oct 2013).

Package 267/671HostnameOS / ArchBUILDCHECKBUILD BIN
GenomeGraphs 1.20.0
Steffen Durinck
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GenomeGraphs
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: GenomeGraphs
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.20.0.tar.gz
StartedAt: 2013-10-08 22:32:19 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:33:57 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 97.4 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomeGraphs.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GenomeGraphs.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GenomeGraphs/DESCRIPTION' ... OK
* this is package 'GenomeGraphs' version '1.20.0'
* 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 ... [8s/8s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 examples ... [8s/19s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
gdPlot 2.579  0.044   9.476
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GenomeGraphs.Rcheck/00check.log'
for details.

GenomeGraphs.Rcheck/00install.out:

* 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)

GenomeGraphs.Rcheck/GenomeGraphs-Ex.timings:

nameusersystemelapsed
AnnotationTrack-class0.0090.0010.011
BaseTrack-class0.0070.0000.008
DisplayPars-class0.0170.0010.018
DisplayPars0.6670.0213.979
ExonArray-class0.1140.0020.223
Gene-class0.0110.0010.010
GeneModel-class0.1570.0090.166
GeneRegion-class0.0170.0010.018
GenericArray-class0.0190.0010.020
GenomeAxis-class0.0080.0010.009
HighlightRegion-class0.0150.0010.015
Ideogram-class0.0110.0010.011
ImplementsTrackOverlay-class0.0070.0000.007
Legend-class0.0060.0000.006
MappedRead-class0.0060.0000.007
Overlay-class0.0060.0010.006
RectangleOverlay-class0.0050.0010.006
Segmentation-class0.0080.0010.008
Smoothing-class0.0060.0000.006
TextOverlay-class0.010.000.01
Title-class0.0060.0000.007
TrackOverlay-class0.0030.0000.004
Transcript-class0.0100.0010.011
TranscriptRegion-class0.0060.0010.007
cn0.0920.0010.093
exonProbePos0.0070.0000.008
gdObject-class0.010.000.01
gdPlot2.5790.0449.476
getPar0.0140.0010.014
getSize0.0030.0000.004
ideogramTab0.0090.0000.010
intensity0.0060.0000.007
makeAnnotationTrack0.0560.0010.059
makeBaseTrack0.0190.0010.020
makeExonArray0.0160.0010.016
makeGene0.0120.0010.012
makeGeneModel0.0090.0010.010
makeGeneRegion0.0150.0010.016
makeGenericArray0.0070.0010.008
makeGenomeAxis0.0090.0010.009
makeIdeogram0.0110.0010.011
makeLegend0.0140.0000.016
makeRectangleOverlay0.1380.0110.158
makeSegmentation0.1200.0110.147
makeSmoothing0.1450.0110.160
makeTextOverlay0.1390.0110.153
makeTitle0.0130.0010.013
makeTranscript0.0140.0010.015
probestart0.1040.0010.105
segEnd0.0050.0010.005
segStart0.0090.0010.009
segments0.0060.0010.007
seqDataEx0.0480.0090.057
setPar0.0300.0020.037
showDisplayOptions0.0080.0010.009
unrData0.0060.0000.006
unrNProbes0.0060.0000.006
unrPositions0.0080.0010.009
yeastCons10.0060.0010.006