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CHECK report for GenomeGraphs on celaya2

This page was generated on 2019-10-16 12:46:53 -0400 (Wed, 16 Oct 2019).

Package 650/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeGraphs 1.44.0
Steffen Durinck
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GenomeGraphs
Branch: RELEASE_3_9
Last Commit: bb9d740
Last Changed Date: 2019-05-02 11:53:09 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomeGraphs
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomeGraphs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomeGraphs_1.44.0.tar.gz
StartedAt: 2019-10-16 03:07:32 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:09:56 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 143.5 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 --install=check:GenomeGraphs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomeGraphs_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeGraphs/DESCRIPTION’ ... OK
* this is package ‘GenomeGraphs’ version ‘1.44.0’
* 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 : : no visible global function
  definition for ‘grid.lines’
drawGD,AnnotationTrack : : 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 : : no visible global function
  definition for ‘grid.lines’
drawGD,BaseTrack : dVL : : no visible global function
  definition for ‘gpar’
drawGD,BaseTrack : dVL : : 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 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-3.9-bioc/meat/GenomeGraphs.Rcheck/00check.log’
for details.

Installation output

GenomeGraphs.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenomeGraphs
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GenomeGraphs’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeGraphs)

Tests output

Example timings

GenomeGraphs.Rcheck/GenomeGraphs-Ex.timings

nameusersystemelapsed
AnnotationTrack-class0.0020.0010.003
BaseTrack-class0.0010.0010.002
DisplayPars-class0.0040.0010.004
DisplayPars0.5210.1074.984
ExonArray-class0.0080.0000.008
Gene-class0.0010.0000.001
GeneModel-class0.1400.0050.145
GeneRegion-class0.0010.0000.002
GenericArray-class0.0010.0000.002
GenomeAxis-class0.0010.0000.001
HighlightRegion-class0.0020.0010.003
Ideogram-class0.0010.0010.002
ImplementsTrackOverlay-class0.0010.0010.002
Legend-class0.0010.0010.002
MappedRead-class000
Overlay-class0.0010.0000.001
RectangleOverlay-class0.0010.0010.002
Segmentation-class0.0020.0010.002
Smoothing-class0.0010.0010.001
TextOverlay-class0.0010.0010.002
Title-class0.0010.0000.002
TrackOverlay-class0.0010.0000.001
Transcript-class0.0010.0010.001
TranscriptRegion-class0.0010.0010.002
cn0.0000.0000.001
exonProbePos0.0000.0000.001
gdObject-class0.0020.0000.003
gdPlot0.9360.0593.562
getPar0.0010.0000.002
getSize0.0000.0000.001
ideogramTab0.0020.0010.004
intensity0.0000.0000.001
makeAnnotationTrack0.0340.0020.036
makeBaseTrack0.0040.0000.005
makeExonArray0.0040.0010.005
makeGene0.0010.0010.002
makeGeneModel0.0020.0010.001
makeGeneRegion0.0030.0010.004
makeGenericArray0.0010.0000.002
makeGenomeAxis0.0010.0000.002
makeIdeogram0.0020.0010.002
makeLegend0.0010.0010.002
makeRectangleOverlay0.0450.0210.067
makeSegmentation0.0970.0210.118
makeSmoothing0.0510.0210.072
makeTextOverlay0.0470.0230.070
makeTitle0.0010.0000.001
makeTranscript0.0020.0010.003
probestart0.0010.0000.000
segEnd0.0000.0000.001
segStart0.0010.0000.001
segments0.0000.0000.001
seqDataEx0.0330.0220.056
setPar0.0150.0010.017
showDisplayOptions0.0010.0010.003
unrData0.0000.0010.000
unrNProbes0.0010.0000.001
unrPositions000
yeastCons1000