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CHECK report for GenomeGraphs on merida1

This page was generated on 2020-04-15 12:35:27 -0400 (Wed, 15 Apr 2020).

Package 675/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeGraphs 1.46.0
Steffen Durinck
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/GenomeGraphs
Branch: RELEASE_3_10
Last Commit: 8104468
Last Changed Date: 2019-10-29 13:07:55 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomeGraphs
Version: 1.46.0
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_1.46.0.tar.gz
StartedAt: 2020-04-15 02:35:26 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:37:21 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 114.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomeGraphs.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### 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_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.46.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'GenomeGraphs' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/GenomeGraphs.Rcheck/00install.out’ for details.
* 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 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-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
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package can be loaded from final location
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeGraphs)

Tests output

Example timings

GenomeGraphs.Rcheck/GenomeGraphs-Ex.timings

nameusersystemelapsed
AnnotationTrack-class0.0020.0000.002
BaseTrack-class0.0010.0000.001
DisplayPars-class0.0020.0000.002
DisplayPars1.0260.0393.504
ExonArray-class0.0060.0000.006
Gene-class0.0010.0000.001
GeneModel-class0.0720.0010.073
GeneRegion-class0.0010.0000.000
GenericArray-class0.0010.0000.002
GenomeAxis-class0.0010.0000.001
HighlightRegion-class0.0020.0000.002
Ideogram-class0.0010.0000.001
ImplementsTrackOverlay-class0.0010.0000.001
Legend-class000
MappedRead-class0.0000.0000.001
Overlay-class0.0010.0000.001
RectangleOverlay-class0.0010.0000.001
Segmentation-class0.0010.0000.001
Smoothing-class0.0010.0010.000
TextOverlay-class0.0010.0000.002
Title-class0.0010.0010.001
TrackOverlay-class0.0010.0000.002
Transcript-class0.0010.0010.001
TranscriptRegion-class0.0000.0000.001
cn000
exonProbePos000
gdObject-class0.0010.0000.001
gdPlot1.2460.0274.649
getPar0.0000.0000.003
getSize000
ideogramTab0.0010.0010.002
intensity000
makeAnnotationTrack0.0200.0010.021
makeBaseTrack0.0030.0010.004
makeExonArray0.0040.0000.004
makeGene0.0010.0000.002
makeGeneModel0.0010.0000.001
makeGeneRegion0.0020.0000.003
makeGenericArray0.0010.0010.002
makeGenomeAxis0.0010.0000.002
makeIdeogram0.0020.0010.002
makeLegend0.0010.0000.001
makeRectangleOverlay0.0370.0040.041
makeSegmentation0.0840.0020.086
makeSmoothing0.0420.0030.045
makeTextOverlay0.0390.0040.049
makeTitle0.0020.0000.002
makeTranscript0.0010.0010.001
probestart000
segEnd0.0010.0000.000
segStart000
segments000
seqDataEx0.0200.0020.023
setPar0.0090.0010.009
showDisplayOptions0.0010.0000.001
unrData000
unrNProbes000
unrPositions000
yeastCons1000