Multiple platform build/check report for BioC 3.9 - CHECK report for GenomeGraphs on tokay2

Package: GenomeGraphs

Version: 1.44.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeGraphs.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GenomeGraphs_1.44.0.tar.gz

StartedAt: 2019-10-16 03:58:00 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:00:41 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 160.5 seconds

RetCode: 0

Status: OK

CheckDir: GenomeGraphs.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeGraphs.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GenomeGraphs_1.44.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomeGraphs.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.44.0'
* 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 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 ... 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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
gdPlot       1.1   0.00    6.22
DisplayPars  0.5   0.13    7.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
DisplayPars 0.59   0.05   10.31
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomeGraphs.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GenomeGraphs_1.44.0.tar.gz && rm -rf GenomeGraphs.buildbin-libdir && mkdir GenomeGraphs.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomeGraphs.buildbin-libdir GenomeGraphs_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GenomeGraphs_1.44.0.zip && rm GenomeGraphs_1.44.0.tar.gz GenomeGraphs_1.44.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  166k  100  166k    0     0  2097k      0 --:--:-- --:--:-- --:--:-- 2275k

install for i386

* installing *source* package 'GenomeGraphs' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomeGraphs'
    finding HTML links ... done
    AnnotationTrack-class                   html  
    BaseTrack-class                         html  
    DisplayPars-class                       html  
    DisplayPars                             html  
    ExonArray-class                         html  
    Gene-class                              html  
    GeneModel-class                         html  
    GeneRegion-class                        html  
    GenericArray-class                      html  
    GenomeAxis-class                        html  
    HighlightRegion-class                   html  
    Ideogram-class                          html  
    ImplementsTrackOverlay-class            html  
    Legend-class                            html  
    MappedRead-class                        html  
    Overlay-class                           html  
    RectangleOverlay-class                  html  
    Segmentation-class                      html  
    Smoothing-class                         html  
    TextOverlay-class                       html  
    Title-class                             html  
    TrackOverlay-class                      html  
    Transcript-class                        html  
    TranscriptRegion-class                  html  
    cn                                      html  
    drawGD                                  html  
    drawTrackOverlay-methods                html  
    exonProbePos                            html  
    gdObject-class                          html  
    gdPlot                                  html  
    geneBiomart                             html  
    geneRegionBiomart                       html  
    getGenomicRange                         html  
    getPar                                  html  
    getSize                                 html  
    ideogramTab                             html  
    intensity                               html  
    makeAnnotationTrack                     html  
    makeBaseTrack                           html  
    makeExonArray                           html  
    makeGene                                html  
    makeGeneModel                           html  
    makeGeneRegion                          html  
    makeGenericArray                        html  
    makeGenomeAxis                          html  
    makeIdeogram                            html  
    makeLegend                              html  
    makeRectangleOverlay                    html  
    makeSegmentation                        html  
    makeSmoothing                           html  
    makeTextOverlay                         html  
    makeTitle                               html  
    makeTranscript                          html  
    probestart                              html  
    segEnd                                  html  
    segStart                                html  
    segments                                html  
    seqDataEx                               html  
    setPar                                  html  
    showDisplayOptions                      html  
    unrData                                 html  
    unrNProbes                              html  
    unrPositions                            html  
    yeastCons1                              html  
** 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

install for x64

* installing *source* package 'GenomeGraphs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomeGraphs' as GenomeGraphs_1.44.0.zip
* DONE (GenomeGraphs)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GenomeGraphs' successfully unpacked and MD5 sums checked

CHECK report for GenomeGraphs on tokay2

Summary

Command output

Installation output

Tests output

Example timings