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BioC 3.1: CHECK report for GenomeGraphs on moscato2

This page was generated on 2015-10-09 09:28:14 -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: rm -rf GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && mkdir GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeGraphs.buildbin-libdir GenomeGraphs_1.28.0.tar.gz >GenomeGraphs.Rcheck\00install.out 2>&1 && cp GenomeGraphs.Rcheck\00install.out GenomeGraphs-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GenomeGraphs.buildbin-libdir --install="check:GenomeGraphs-install.out" --force-multiarch --no-vignettes --timings GenomeGraphs_1.28.0.tar.gz
StartedAt: 2015-10-09 02:07:14 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:09:38 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 143.5 seconds
RetCode: 0
Status:  OK  
CheckDir: GenomeGraphs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && mkdir GenomeGraphs.buildbin-libdir GenomeGraphs.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeGraphs.buildbin-libdir GenomeGraphs_1.28.0.tar.gz >GenomeGraphs.Rcheck\00install.out 2>&1 && cp GenomeGraphs.Rcheck\00install.out GenomeGraphs-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GenomeGraphs.buildbin-libdir --install="check:GenomeGraphs-install.out" --force-multiarch --no-vignettes --timings GenomeGraphs_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/GenomeGraphs.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [11s] OK
** running examples for arch 'x64' ... [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
  'E:/biocbld/bbs-3.1-bioc/meat/GenomeGraphs.Rcheck/00check.log'
for details.


GenomeGraphs.Rcheck/00install.out:


install for i386

* 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'

install for x64

* installing *source* package 'GenomeGraphs' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'GenomeGraphs' as GenomeGraphs_1.28.0.zip
* DONE (GenomeGraphs)

GenomeGraphs.Rcheck/examples_i386/GenomeGraphs-Ex.timings:

nameusersystemelapsed
AnnotationTrack-class000
BaseTrack-class000
DisplayPars-class000
DisplayPars0.630.032.76
ExonArray-class0.010.000.01
Gene-class000
GeneModel-class0.240.020.25
GeneRegion-class000
GenericArray-class000
GenomeAxis-class000
HighlightRegion-class0.010.000.02
Ideogram-class000
ImplementsTrackOverlay-class000
Legend-class000
MappedRead-class000
Overlay-class000
RectangleOverlay-class000
Segmentation-class000
Smoothing-class000
TextOverlay-class0.010.000.02
Title-class000
TrackOverlay-class000
Transcript-class000
TranscriptRegion-class000
cn000
exonProbePos000
gdObject-class000
gdPlot0.940.003.36
getPar000
getSize000
ideogramTab000
intensity000
makeAnnotationTrack0.030.000.04
makeBaseTrack000
makeExonArray000
makeGene000
makeGeneModel000
makeGeneRegion000
makeGenericArray000
makeGenomeAxis000
makeIdeogram0.020.000.01
makeLegend000
makeRectangleOverlay0.230.000.24
makeSegmentation0.220.000.21
makeSmoothing0.250.000.25
makeTextOverlay0.240.000.24
makeTitle000
makeTranscript000
probestart000
segEnd000
segStart000
segments000
seqDataEx0.050.000.05
setPar0.010.000.02
showDisplayOptions000
unrData000
unrNProbes000
unrPositions000
yeastCons10.020.000.01

GenomeGraphs.Rcheck/examples_x64/GenomeGraphs-Ex.timings:

nameusersystemelapsed
AnnotationTrack-class000
BaseTrack-class000
DisplayPars-class0.020.000.01
DisplayPars0.420.062.67
ExonArray-class000
Gene-class000
GeneModel-class0.220.000.22
GeneRegion-class000
GenericArray-class000
GenomeAxis-class000
HighlightRegion-class000
Ideogram-class000
ImplementsTrackOverlay-class000
Legend-class000
MappedRead-class000
Overlay-class000
RectangleOverlay-class000
Segmentation-class000
Smoothing-class000
TextOverlay-class0.010.000.01
Title-class000
TrackOverlay-class000
Transcript-class000
TranscriptRegion-class000
cn000
exonProbePos000
gdObject-class000
gdPlot0.790.003.45
getPar000
getSize000
ideogramTab0.020.000.01
intensity000
makeAnnotationTrack0.020.000.02
makeBaseTrack000
makeExonArray000
makeGene000
makeGeneModel000
makeGeneRegion000
makeGenericArray000
makeGenomeAxis000
makeIdeogram000
makeLegend000
makeRectangleOverlay0.150.000.16
makeSegmentation0.140.000.14
makeSmoothing0.170.000.17
makeTextOverlay0.160.000.15
makeTitle000
makeTranscript000
probestart000
segEnd000
segStart000
segments000
seqDataEx0.010.000.01
setPar0.020.000.02
showDisplayOptions000
unrData000
unrNProbes000
unrPositions000
yeastCons1000