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BioC 3.1: CHECK report for GenomeGraphs on zin2

This page was generated on 2015-10-09 09:23:35 -0700 (Fri, 09 Oct 2015).

Package 392/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeGraphs 1.28.0
Steffen Durinck
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GenomeGraphs
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomeGraphs
Version: 1.28.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.28.0.tar.gz
StartedAt: 2015-10-09 01:39:24 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:41:16 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 111.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomeGraphs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeGraphs/DESCRIPTION’ ... OK
* this is package ‘GenomeGraphs’ version ‘1.28.0’
* 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 ... [7s/10s] 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’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘pushViewport’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘dataViewport’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘grid.rect’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘gpar’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘grid.text’
drawGD,AnnotationTrack : .local : <anonymous>: no visible global
  function definition for ‘grid.lines’
drawGD,AnnotationTrack : .local : <anonymous>: no visible global
  function definition for ‘gpar’
drawGD,AnnotationTrack : .local: no visible global function definition
  for ‘popViewport’
drawGD,BaseTrack : .local: no visible global function definition for
  ‘pushViewport’
drawGD,BaseTrack : .local: no visible global function definition for
  ‘dataViewport’
drawGD,BaseTrack : .local : dP: no visible global function definition
  for ‘grid.points’
drawGD,BaseTrack : .local : dP: no visible global function definition
  for ‘gpar’
drawGD,BaseTrack : .local : dP: no visible global function definition
  for ‘unit’
drawGD,BaseTrack : .local : dVL : <anonymous>: no visible global
  function definition for ‘grid.lines’
drawGD,BaseTrack : .local : dVL : <anonymous>: no visible global
  function definition for ‘gpar’
drawGD,BaseTrack : .local : dVL : <anonymous>: no visible global
  function definition for ‘unit’
drawGD,BaseTrack : .local : dCL: no visible global function definition
  for ‘grid.lines’
drawGD,BaseTrack : .local : dCL: no visible global function definition
  for ‘gpar’
drawGD,BaseTrack : .local : dCL: no visible global function definition
  for ‘unit’
drawGD,BaseTrack : .local: no visible global function definition for
  ‘grid.yaxis’
drawGD,BaseTrack : .local: no visible global function definition for
  ‘popViewport’
drawGD,ExonArray : .local: no visible global function definition for
  ‘pushViewport’
drawGD,ExonArray : .local: no visible global function definition for
  ‘viewport’
drawGD,ExonArray : .local: no visible global function definition for
  ‘grid.layout’
drawGD,ExonArray : .local: no visible global function definition for
  ‘dataViewport’
drawGD,ExonArray : .local: no visible global function definition for
  ‘grid.lines’
drawGD,ExonArray : .local: no visible global function definition for
  ‘gpar’
drawGD,ExonArray : .local: no visible global function definition for
  ‘grid.text’
drawGD,ExonArray : .local: no visible global function definition for
  ‘grid.yaxis’
drawGD,ExonArray : .local: no visible global function definition for
  ‘popViewport’
drawGD,Gene : .local: no visible global function definition for
  ‘pushViewport’
drawGD,Gene : .local: no visible global function definition for
  ‘dataViewport’
drawGD,Gene : .local: no visible global function definition for
  ‘grid.rect’
drawGD,Gene : .local: no visible global function definition for ‘gpar’
drawGD,Gene : .local: no visible global function definition for
  ‘grid.text’
drawGD,Gene : .local: no visible global function definition for
  ‘grid.lines’
drawGD,Gene : .local: no visible global function definition for
  ‘popViewport’
drawGD,GeneModel : .local: no visible global function definition for
  ‘pushViewport’
drawGD,GeneModel : .local: no visible global function definition for
  ‘dataViewport’
drawGD,GeneModel : .local: no visible global function definition for
  ‘grid.rect’
drawGD,GeneModel : .local: no visible global function definition for
  ‘gpar’
drawGD,GeneModel : .local: no visible global function definition for
  ‘grid.lines’
drawGD,GeneModel : .local: no visible global function definition for
  ‘popViewport’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘pushViewport’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘dataViewport’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘grid.rect’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘gpar’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘grid.text’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘grid.lines’
drawGD,GeneRegion : .local: no visible global function definition for
  ‘popViewport’
drawGD,GenericArray : .local: no visible global function definition for
  ‘pushViewport’
drawGD,GenericArray : .local: no visible global function definition for
  ‘dataViewport’
drawGD,GenericArray : .local: no visible global function definition for
  ‘grid.lines’
drawGD,GenericArray : .local: no visible global function definition for
  ‘gpar’
drawGD,GenericArray : .local: no visible global function definition for
  ‘grid.points’
drawGD,GenericArray : .local: no visible global function definition for
  ‘unit’
drawGD,GenericArray : .local: no visible global function definition for
  ‘grid.yaxis’
drawGD,GenericArray : .local: no visible global function definition for
  ‘popViewport’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘pushViewport’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘dataViewport’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘grid.lines’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘grid.text’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘gpar’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘grid.segments’
drawGD,GenomeAxis : .local: no visible global function definition for
  ‘popViewport’
drawGD,Ideogram : .local: no visible binding for global variable
  ‘ideogramTab’
drawGD,Ideogram : .local: no visible global function definition for
  ‘pushViewport’
drawGD,Ideogram : .local: no visible global function definition for
  ‘dataViewport’
drawGD,Ideogram : .local: no visible global function definition for
  ‘grid.rect’
drawGD,Ideogram : .local: no visible global function definition for
  ‘gpar’
drawGD,Ideogram : .local: no visible global function definition for
  ‘grid.lines’
drawGD,Ideogram : .local: no visible global function definition for
  ‘popViewport’
drawGD,Legend : .local: no visible global function definition for
  ‘pushViewport’
drawGD,Legend : .local: no visible global function definition for
  ‘dataViewport’
drawGD,Legend : .local: no visible global function definition for
  ‘grid.text’
drawGD,Legend : .local: no visible global function definition for
  ‘gpar’
drawGD,Legend : .local: no visible global function definition for
  ‘grid.rect’
drawGD,Legend : .local: no visible global function definition for
  ‘popViewport’
drawGD,MappedRead : .local: no visible global function definition for
  ‘pushViewport’
drawGD,MappedRead : .local: no visible global function definition for
  ‘dataViewport’
drawGD,MappedRead : .local: no visible global function definition for
  ‘gpar’
drawGD,MappedRead : .local: no visible global function definition for
  ‘grid.lines’
drawGD,MappedRead : .local: no visible global function definition for
  ‘popViewport’
drawGD,Title : .local: no visible global function definition for
  ‘pushViewport’
drawGD,Title : .local: no visible global function definition for
  ‘viewport’
drawGD,Title : .local: no visible global function definition for
  ‘grid.text’
drawGD,Title : .local: no visible global function definition for ‘gpar’
drawGD,Title : .local: no visible global function definition for
  ‘popViewport’
drawGD,Transcript : .local: no visible global function definition for
  ‘pushViewport’
drawGD,Transcript : .local: no visible global function definition for
  ‘viewport’
drawGD,Transcript : .local: no visible global function definition for
  ‘grid.layout’
drawGD,Transcript : .local: no visible global function definition for
  ‘dataViewport’
drawGD,Transcript : .local: no visible global function definition for
  ‘grid.text’
drawGD,Transcript : .local: no visible global function definition for
  ‘gpar’
drawGD,Transcript : .local: no visible global function definition for
  ‘grid.rect’
drawGD,Transcript : .local: no visible global function definition for
  ‘grid.lines’
drawGD,Transcript : .local: no visible global function definition for
  ‘popViewport’
drawOverlay,RectangleOverlay : .local: no visible global function
  definition for ‘grid.rect’
drawOverlay,RectangleOverlay : .local: no visible global function
  definition for ‘gpar’
drawOverlay,TextOverlay : .local: no visible global function definition
  for ‘grid.text’
drawOverlay,TextOverlay : .local: no visible global function definition
  for ‘gpar’
drawTrackOverlay,Segmentation : .local: no visible global function
  definition for ‘grid.lines’
drawTrackOverlay,Segmentation : .local: no visible global function
  definition for ‘gpar’
drawTrackOverlay,Smoothing : .local: no visible global function
  definition for ‘grid.lines’
drawTrackOverlay,Smoothing : .local: no visible global function
  definition for ‘gpar’
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 ... [4s/11s] OK
* 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

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/GenomeGraphs.Rcheck/00check.log’
for details.


GenomeGraphs.Rcheck/00install.out:

* installing *source* package ‘GenomeGraphs’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (GenomeGraphs)

GenomeGraphs.Rcheck/GenomeGraphs-Ex.timings:

nameusersystemelapsed
AnnotationTrack-class0.0020.0000.002
BaseTrack-class0.0010.0000.001
DisplayPars-class0.0020.0000.002
DisplayPars0.1350.0122.575
ExonArray-class0.0040.0000.007
Gene-class0.0010.0000.001
GeneModel-class0.0750.0040.105
GeneRegion-class0.0010.0000.001
GenericArray-class0.0010.0000.000
GenomeAxis-class0.0010.0000.001
HighlightRegion-class0.0020.0000.001
Ideogram-class0.0010.0000.001
ImplementsTrackOverlay-class0.0010.0000.001
Legend-class0.0010.0000.000
MappedRead-class0.0000.0000.004
Overlay-class0.0010.0000.001
RectangleOverlay-class0.0010.0000.001
Segmentation-class0.0010.0000.001
Smoothing-class0.0010.0000.000
TextOverlay-class0.0010.0000.001
Title-class0.0010.0000.001
TrackOverlay-class0.0010.0000.001
Transcript-class0.0000.0040.001
TranscriptRegion-class0.0000.0000.001
cn0.0000.0000.001
exonProbePos0.0010.0000.000
gdObject-class0.0020.0000.001
gdPlot0.5560.0273.550
getPar0.0010.0000.001
getSize0.0000.0000.001
ideogramTab0.0020.0000.006
intensity0.0010.0000.000
makeAnnotationTrack0.0180.0000.038
makeBaseTrack0.0020.0000.002
makeExonArray0.0020.0000.002
makeGene0.0010.0000.005
makeGeneModel0.0010.0000.001
makeGeneRegion0.0010.0000.006
makeGenericArray0.0010.0000.000
makeGenomeAxis0.0010.0000.001
makeIdeogram0.0010.0000.002
makeLegend0.0010.0000.002
makeRectangleOverlay0.0470.0040.122
makeSegmentation0.0380.0040.078
makeSmoothing0.0600.0000.064
makeTextOverlay0.0460.0040.100
makeTitle0.0010.0000.001
makeTranscript0.0010.0000.001
probestart0.0010.0000.001
segEnd0.0010.0000.000
segStart0.0000.0000.001
segments0.0000.0000.001
seqDataEx0.0200.0000.045
setPar0.0090.0000.018
showDisplayOptions0.0010.0000.001
unrData0.0000.0000.001
unrNProbes0.0000.0000.001
unrPositions0.0010.0000.000
yeastCons1000