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BioC 3.4: CHECK report for GenomeGraphs on morelia

This page was generated on 2016-09-21 03:50:03 -0700 (Wed, 21 Sep 2016).

Package 489/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeGraphs 1.33.0
Steffen Durinck
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomeGraphs
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: 1.33.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.33.0.tar.gz
StartedAt: 2016-09-20 07:03:34 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:04:48 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 73.1 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 GenomeGraphs_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.33.0’
* 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 ... 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘GenomeGraphs’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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’
.getRangeFromENS: no visible global function definition for
  ‘callNextMethod’
DisplayPars: no visible global function definition for ‘new’
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’
makeAnnotationTrack: no visible global function definition for
  ‘getClass’
makeAnnotationTrack: no visible global function definition for ‘new’
makeBaseTrack: no visible global function definition for ‘getClass’
makeBaseTrack: no visible global function definition for ‘new’
makeExonArray: no visible global function definition for ‘getClass’
makeExonArray: no visible global function definition for ‘new’
makeGene: no visible global function definition for ‘getClass’
makeGene: no visible global function definition for ‘new’
makeGeneModel: no visible global function definition for ‘getClass’
makeGeneModel: no visible global function definition for ‘new’
makeGeneRegion: no visible global function definition for ‘getClass’
makeGeneRegion: no visible global function definition for ‘new’
makeGenericArray: no visible global function definition for ‘getClass’
makeGenericArray: no visible global function definition for ‘new’
makeGenomeAxis: no visible global function definition for ‘getClass’
makeGenomeAxis: no visible global function definition for ‘new’
makeIdeogram: no visible global function definition for ‘getClass’
makeIdeogram: no visible global function definition for ‘new’
makeLegend: no visible global function definition for ‘getClass’
makeLegend: no visible global function definition for ‘new’
makeRectangleOverlay: no visible global function definition for
  ‘getClass’
makeRectangleOverlay: no visible global function definition for ‘new’
makeSegmentation: no visible global function definition for ‘getClass’
makeSegmentation: no visible global function definition for ‘new’
makeSmoothing: no visible global function definition for ‘getClass’
makeSmoothing: no visible global function definition for ‘new’
makeTextOverlay: no visible global function definition for ‘getClass’
makeTextOverlay: no visible global function definition for ‘new’
makeTitle: no visible global function definition for ‘getClass’
makeTitle: no visible global function definition for ‘new’
makeTranscript: no visible global function definition for ‘getClass’
makeTranscript: no visible global function definition for ‘new’
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: no visible global function definition for
  ‘pushViewport’
drawGD,AnnotationTrack: no visible global function definition for
  ‘dataViewport’
drawGD,AnnotationTrack: no visible global function definition for
  ‘grid.rect’
drawGD,AnnotationTrack: no visible global function definition for
  ‘gpar’
drawGD,AnnotationTrack: no visible global function definition for
  ‘grid.text’
drawGD,AnnotationTrack : <anonymous>: no visible global function
  definition for ‘grid.lines’
drawGD,AnnotationTrack : <anonymous>: no visible global function
  definition for ‘gpar’
drawGD,AnnotationTrack: no visible global function definition for
  ‘popViewport’
drawGD,BaseTrack: no visible global function definition for
  ‘pushViewport’
drawGD,BaseTrack: no visible global function definition for
  ‘dataViewport’
drawGD,BaseTrack : dP: no visible global function definition for
  ‘grid.points’
drawGD,BaseTrack : dP: no visible global function definition for ‘gpar’
drawGD,BaseTrack : dP: no visible global function definition for ‘unit’
drawGD,BaseTrack : dVL : <anonymous>: no visible global function
  definition for ‘grid.lines’
drawGD,BaseTrack : dVL : <anonymous>: no visible global function
  definition for ‘gpar’
drawGD,BaseTrack : dVL : <anonymous>: no visible global function
  definition for ‘unit’
drawGD,BaseTrack : dCL: no visible global function definition for
  ‘grid.lines’
drawGD,BaseTrack : dCL: no visible global function definition for
  ‘gpar’
drawGD,BaseTrack : dCL: no visible global function definition for
  ‘unit’
drawGD,BaseTrack: no visible global function definition for
  ‘grid.yaxis’
drawGD,BaseTrack: no visible global function definition for
  ‘popViewport’
drawGD,ExonArray: no visible global function definition for
  ‘pushViewport’
drawGD,ExonArray: no visible global function definition for ‘viewport’
drawGD,ExonArray: no visible global function definition for
  ‘grid.layout’
drawGD,ExonArray: no visible global function definition for
  ‘dataViewport’
drawGD,ExonArray: no visible global function definition for
  ‘grid.lines’
drawGD,ExonArray: no visible global function definition for ‘gpar’
drawGD,ExonArray: no visible global function definition for ‘grid.text’
drawGD,ExonArray: no visible global function definition for
  ‘grid.yaxis’
drawGD,ExonArray: no visible global function definition for
  ‘popViewport’
drawGD,Gene: no visible global function definition for ‘pushViewport’
drawGD,Gene: no visible global function definition for ‘dataViewport’
drawGD,Gene: no visible global function definition for ‘grid.rect’
drawGD,Gene: no visible global function definition for ‘gpar’
drawGD,Gene: no visible global function definition for ‘grid.text’
drawGD,Gene: no visible global function definition for ‘grid.lines’
drawGD,Gene: no visible global function definition for ‘popViewport’
drawGD,GeneModel: no visible global function definition for
  ‘pushViewport’
drawGD,GeneModel: no visible global function definition for
  ‘dataViewport’
drawGD,GeneModel: no visible global function definition for ‘grid.rect’
drawGD,GeneModel: no visible global function definition for ‘gpar’
drawGD,GeneModel: no visible global function definition for
  ‘grid.lines’
drawGD,GeneModel: no visible global function definition for
  ‘popViewport’
drawGD,GeneRegion: no visible global function definition for
  ‘pushViewport’
drawGD,GeneRegion: no visible global function definition for
  ‘dataViewport’
drawGD,GeneRegion: no visible global function definition for
  ‘grid.rect’
drawGD,GeneRegion: no visible global function definition for ‘gpar’
drawGD,GeneRegion: no visible global function definition for
  ‘grid.text’
drawGD,GeneRegion: no visible global function definition for
  ‘grid.lines’
drawGD,GeneRegion: no visible global function definition for
  ‘popViewport’
drawGD,GenericArray: no visible global function definition for
  ‘pushViewport’
drawGD,GenericArray: no visible global function definition for
  ‘dataViewport’
drawGD,GenericArray: no visible global function definition for
  ‘grid.lines’
drawGD,GenericArray: no visible global function definition for ‘gpar’
drawGD,GenericArray: no visible global function definition for
  ‘grid.points’
drawGD,GenericArray: no visible global function definition for ‘unit’
drawGD,GenericArray: no visible global function definition for
  ‘grid.yaxis’
drawGD,GenericArray: no visible global function definition for
  ‘popViewport’
drawGD,GenomeAxis: no visible global function definition for
  ‘pushViewport’
drawGD,GenomeAxis: no visible global function definition for
  ‘dataViewport’
drawGD,GenomeAxis: no visible global function definition for
  ‘grid.lines’
drawGD,GenomeAxis: no visible global function definition for
  ‘grid.text’
drawGD,GenomeAxis: no visible global function definition for ‘gpar’
drawGD,GenomeAxis: no visible global function definition for
  ‘grid.segments’
drawGD,GenomeAxis: no visible global function definition for
  ‘popViewport’
drawGD,Ideogram: no visible global function definition for ‘data’
drawGD,Ideogram: no visible binding for global variable ‘ideogramTab’
drawGD,Ideogram: no visible global function definition for
  ‘pushViewport’
drawGD,Ideogram: no visible global function definition for
  ‘dataViewport’
drawGD,Ideogram: no visible global function definition for ‘grid.rect’
drawGD,Ideogram: no visible global function definition for ‘gpar’
drawGD,Ideogram: no visible global function definition for
  ‘colorRampPalette’
drawGD,Ideogram: no visible global function definition for ‘grid.lines’
drawGD,Ideogram: no visible global function definition for
  ‘popViewport’
drawGD,Legend: no visible global function definition for ‘pushViewport’
drawGD,Legend: no visible global function definition for ‘dataViewport’
drawGD,Legend: no visible global function definition for ‘grid.text’
drawGD,Legend: no visible global function definition for ‘gpar’
drawGD,Legend: no visible global function definition for ‘grid.rect’
drawGD,Legend: no visible global function definition for ‘popViewport’
drawGD,MappedRead: no visible global function definition for
  ‘pushViewport’
drawGD,MappedRead: no visible global function definition for
  ‘dataViewport’
drawGD,MappedRead: no visible global function definition for ‘gpar’
drawGD,MappedRead: no visible global function definition for
  ‘grid.lines’
drawGD,MappedRead: no visible global function definition for
  ‘popViewport’
drawGD,Title: no visible global function definition for ‘pushViewport’
drawGD,Title: no visible global function definition for ‘viewport’
drawGD,Title: no visible global function definition for ‘grid.text’
drawGD,Title: no visible global function definition for ‘gpar’
drawGD,Title: no visible global function definition for ‘popViewport’
drawGD,Transcript: no visible global function definition for
  ‘pushViewport’
drawGD,Transcript: no visible global function definition for ‘viewport’
drawGD,Transcript: no visible global function definition for
  ‘grid.layout’
drawGD,Transcript: no visible global function definition for
  ‘dataViewport’
drawGD,Transcript: no visible global function definition for
  ‘grid.text’
drawGD,Transcript: no visible global function definition for ‘gpar’
drawGD,Transcript: no visible global function definition for
  ‘grid.rect’
drawGD,Transcript: no visible global function definition for
  ‘grid.lines’
drawGD,Transcript: no visible global function definition for
  ‘popViewport’
drawOverlay,RectangleOverlay: no visible global function definition for
  ‘rgb’
drawOverlay,RectangleOverlay: no visible global function definition for
  ‘col2rgb’
drawOverlay,RectangleOverlay: no visible global function definition for
  ‘grid.rect’
drawOverlay,RectangleOverlay: no visible global function definition for
  ‘gpar’
drawOverlay,TextOverlay: no visible global function definition for
  ‘grid.text’
drawOverlay,TextOverlay: no visible global function definition for
  ‘gpar’
drawTrackOverlay,Segmentation: no visible global function definition
  for ‘grid.lines’
drawTrackOverlay,Segmentation: no visible global function definition
  for ‘gpar’
drawTrackOverlay,Smoothing: no visible global function definition for
  ‘grid.lines’
drawTrackOverlay,Smoothing: no visible global function definition for
  ‘gpar’
initialize,AnnotationTrack: no visible global function definition for
  ‘callNextMethod’
initialize,Gene: no visible global function definition for
  ‘callNextMethod’
initialize,Gene: no visible global function definition for ‘getBM’
initialize,GeneRegion: no visible global function definition for
  ‘callNextMethod’
initialize,GeneRegion: no visible global function definition for
  ‘getBM’
initialize,Transcript: no visible global function definition for
  ‘callNextMethod’
initialize,Transcript: no visible global function definition for
  ‘getBM’
initialize,gdObject: no visible global function definition for
  ‘callNextMethod’
show,BaseTrack: no visible global function definition for ‘show’
show,ExonArray: no visible global function definition for ‘show’
show,GenericArray: no visible global function definition for ‘show’
showDisplayOptions,character: no visible global function definition for
  ‘getClass’
Undefined global functions or variables:
  callNextMethod col2rgb colorRampPalette data dataViewport getBM
  getClass gpar grid.layout grid.lines grid.newpage grid.points
  grid.rect grid.segments grid.text grid.yaxis ideogramTab new
  popViewport pushViewport rgb show unit viewport
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "rgb")
  importFrom("methods", "callNextMethod", "getClass", "new", "show")
  importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-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-class0.0010.0000.001
BaseTrack-class0.0010.0000.001
DisplayPars-class0.0040.0000.004
DisplayPars0.4970.0091.387
ExonArray-class0.0090.0000.009
Gene-class0.0020.0010.001
GeneModel-class0.1050.0030.109
GeneRegion-class0.0010.0000.001
GenericArray-class0.0020.0000.001
GenomeAxis-class0.0010.0000.001
HighlightRegion-class0.0030.0000.003
Ideogram-class0.0020.0000.002
ImplementsTrackOverlay-class0.0010.0010.001
Legend-class0.0010.0000.002
MappedRead-class0.0000.0000.001
Overlay-class0.0010.0000.001
RectangleOverlay-class0.0010.0000.001
Segmentation-class0.0010.0000.001
Smoothing-class0.0010.0000.001
TextOverlay-class0.0000.0000.001
Title-class0.0010.0000.001
TrackOverlay-class0.0010.0000.000
Transcript-class0.0010.0000.001
TranscriptRegion-class0.0010.0000.001
cn000
exonProbePos0.0000.0010.000
gdObject-class0.0010.0000.001
gdPlot0.5630.0291.944
getPar0.0010.0000.001
getSize0.0000.0000.001
ideogramTab0.0030.0010.004
intensity000
makeAnnotationTrack0.0180.0010.019
makeBaseTrack0.0020.0000.003
makeExonArray0.0020.0010.003
makeGene0.0020.0000.002
makeGeneModel0.0010.0000.002
makeGeneRegion0.0030.0010.004
makeGenericArray0.0010.0000.002
makeGenomeAxis0.0010.0010.002
makeIdeogram0.0030.0000.002
makeLegend0.0020.0000.001
makeRectangleOverlay0.0530.0050.058
makeSegmentation0.0580.0060.064
makeSmoothing0.0600.0080.079
makeTextOverlay0.0510.0050.065
makeTitle0.0010.0000.001
makeTranscript0.0020.0010.002
probestart0.0010.0000.001
segEnd0.0010.0000.000
segStart0.0010.0000.000
segments0.0010.0000.000
seqDataEx0.0160.0050.021
setPar0.0080.0010.009
showDisplayOptions0.0010.0000.001
unrData000
unrNProbes0.0000.0000.001
unrPositions0.0000.0000.001
yeastCons1000