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BioC 3.0: CHECK report for GenomeGraphs on oaxaca

This page was generated on 2015-04-10 10:02:58 -0700 (Fri, 10 Apr 2015).

Package 362/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeGraphs 1.26.0
Steffen Durinck
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GenomeGraphs
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: GenomeGraphs
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.26.0.tar.gz
StartedAt: 2015-04-09 23:51:52 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:57:04 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 312.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomeGraphs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomeGraphs_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeGraphs/DESCRIPTION’ ... OK
* this is package ‘GenomeGraphs’ version ‘1.26.0’
* 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 ... [14s/14s] 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 ... 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’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/184s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
gdPlot 0.703  0.029 173.571
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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-class0.0020.0000.003
BaseTrack-class0.0010.0000.001
DisplayPars-class0.0030.0000.004
DisplayPars0.2650.0103.386
ExonArray-class0.0090.0000.009
Gene-class0.0010.0010.001
GeneModel-class0.2200.0030.223
GeneRegion-class0.0010.0000.002
GenericArray-class0.0020.0000.002
GenomeAxis-class0.0010.0000.001
HighlightRegion-class0.0030.0000.003
Ideogram-class0.0020.0000.002
ImplementsTrackOverlay-class0.0010.0010.001
Legend-class0.0010.0000.001
MappedRead-class0.0010.0000.001
Overlay-class0.0010.0000.001
RectangleOverlay-class0.0010.0000.001
Segmentation-class0.0010.0000.002
Smoothing-class0.0010.0010.001
TextOverlay-class0.0010.0000.001
Title-class0.0010.0000.001
TrackOverlay-class0.0010.0010.002
Transcript-class0.0010.0000.002
TranscriptRegion-class0.0010.0000.002
cn0.0010.0010.001
exonProbePos0.0010.0000.001
gdObject-class0.0020.0000.002
gdPlot 0.703 0.029173.571
getPar0.0010.0000.002
getSize0.0000.0000.001
ideogramTab0.0030.0000.003
intensity0.0010.0000.000
makeAnnotationTrack0.0320.0010.033
makeBaseTrack0.0040.0000.005
makeExonArray0.0050.0010.005
makeGene0.0030.0000.002
makeGeneModel0.0010.0000.002
makeGeneRegion0.0030.0000.003
makeGenericArray0.0010.0000.002
makeGenomeAxis0.0020.0000.002
makeIdeogram0.0030.0000.003
makeLegend0.0020.0010.002
makeRectangleOverlay0.0800.0080.088
makeSegmentation0.0700.0090.080
makeSmoothing0.0850.0100.096
makeTextOverlay0.0870.0090.097
makeTitle0.0020.0000.003
makeTranscript0.0030.0000.003
probestart000
segEnd000
segStart000
segments0.0010.0000.000
seqDataEx0.0260.0080.034
setPar0.0140.0010.015
showDisplayOptions0.0010.0000.002
unrData0.0000.0000.001
unrNProbes0.0000.0010.001
unrPositions0.0010.0000.001
yeastCons10.0010.0000.001