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CHECK report for caOmicsV on celaya2

This page was generated on 2019-10-16 12:55:50 -0400 (Wed, 16 Oct 2019).

Package 211/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.14.0
Henry Zhang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: RELEASE_3_9
Last Commit: 5ed9bdf
Last Changed Date: 2019-05-02 11:53:55 -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: caOmicsV
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings caOmicsV_1.14.0.tar.gz
StartedAt: 2019-10-16 01:09:37 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:12:15 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 158.2 seconds
RetCode: 0
Status:  OK 
CheckDir: caOmicsV.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings caOmicsV_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/caOmicsV.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 ‘caOmicsV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘caOmicsV’ version ‘1.14.0’
* 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 ‘caOmicsV’ 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bioMatrixLegend: no visible global function definition for ‘text’
bioMatrixLegend: no visible global function definition for ‘legend’
bioNetLegend: no visible global function definition for ‘text’
bioNetLegend: no visible global function definition for ‘legend’
convertToZScores: no visible global function definition for ‘sd’
drawBioNetNodeBackground: no visible global function definition for
  ‘gray’
drawBioNetNodeBackground: no visible global function definition for
  ‘col2rgb’
drawBioNetNodeBackground: no visible global function definition for
  ‘rgb’
drawBioNetNodeBackground: no visible global function definition for
  ‘polygon’
eraseBioNetNode: no visible global function definition for ‘polygon’
getHeatmapColorScales: no visible global function definition for ‘rgb’
labelBioNetNodeNames: no visible global function definition for ‘text’
linkBioNetNodes: no visible global function definition for ‘col2rgb’
linkBioNetNodes: no visible global function definition for ‘rgb’
linkBioNetNodes: no visible global function definition for ‘polygon’
linkBioNetSamples: no visible global function definition for ‘lines’
plotBioMatrix: no visible global function definition for ‘par’
plotBioMatrix: no visible global function definition for ‘rainbow’
plotBioMatrix: no visible global function definition for ‘legend’
plotBioMatrixBars: no visible global function definition for ‘rect’
plotBioMatrixBinaryData: no visible global function definition for
  ‘points’
plotBioMatrixCategoryData: no visible global function definition for
  ‘palette’
plotBioMatrixCategoryData: no visible global function definition for
  ‘rect’
plotBioMatrixRowNames: no visible global function definition for ‘text’
plotBioMatrixSampleData: no visible global function definition for
  ‘rect’
plotBioMatrixSampleNames: no visible global function definition for
  ‘text’
plotBioNetBars: no visible global function definition for ‘polygon’
plotBioNetCircos: no visible global function definition for ‘par’
plotBioNetCircos: no visible global function definition for ‘rainbow’
plotBioNetHeatmap: no visible global function definition for ‘polygon’
plotBioNetLines: no visible global function definition for ‘lines’
plotBioNetPoints: no visible global function definition for ‘points’
plotBioNetPolygons: no visible global function definition for ‘rainbow’
plotBioNetPolygons: no visible global function definition for ‘polygon’
plotHeatmapColorScale: no visible global function definition for ‘rect’
plotHeatmapColorScale: no visible global function definition for ‘text’
setBioMatrixPlotArea: no visible global function definition for
  ‘plot.new’
setBioMatrixPlotArea: no visible global function definition for
  ‘plot.window’
setBioNetNodeLayout: no visible global function definition for ‘dist’
setBioNetPlotAreaBackground: no visible global function definition for
  ‘grey’
setBioNetPlotAreaBackground: no visible global function definition for
  ‘col2rgb’
setBioNetPlotAreaBackground: no visible global function definition for
  ‘rgb’
setBioNetPlotAreaBackground: no visible global function definition for
  ‘polygon’
showBioNetNodesLayout: no visible global function definition for ‘grey’
showBioNetNodesLayout: no visible global function definition for ‘plot’
showBioNetNodesLayout: no visible global function definition for ‘text’
Undefined global functions or variables:
  col2rgb dist gray grey legend lines palette par plot plot.new
  plot.window points polygon rainbow rect rgb sd text
Consider adding
  importFrom("grDevices", "col2rgb", "gray", "grey", "palette",
             "rainbow", "rgb")
  importFrom("graphics", "legend", "lines", "par", "plot", "plot.new",
             "plot.window", "points", "polygon", "rect", "text")
  importFrom("stats", "dist", "sd")
to your NAMESPACE file.
* 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
Examples with CPU or elapsed time > 5s
                          user system elapsed
bioNetLegend             8.320  0.977   9.312
plotBioNetCircos         8.314  0.980   9.397
plotBioNetHeatmap        5.804  0.504   6.399
drawBioNetNodeBackground 4.679  0.507   5.239
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/caOmicsV.Rcheck/00check.log’
for details.



Installation output

caOmicsV.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘caOmicsV’ ...
** using staged installation
** R
** data
** demo
** 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 (caOmicsV)

Tests output


Example timings

caOmicsV.Rcheck/caOmicsV-Ex.timings

nameusersystemelapsed
CA_OMICS_ENV0.0000.0010.001
CA_OMICS_NAME0.0000.0000.001
CA_OMICS_NA_STRING0.0000.0000.001
CNVDemoData0.0300.0130.044
RNA2miRNA0.0020.0030.005
RNASeq0.0060.0050.010
RNASeqDemoData0.0030.0030.006
bioMatrixLegend0.2350.0660.301
bioNetCircosPlot2.0570.4862.546
bioNetLegend8.3200.9779.312
biomatrixPlotDemoData0.0040.0030.007
bionetPlotDemoData0.0030.0030.007
convertToZScores0.0090.0030.012
drawBioNetNodeBackground4.6790.5075.239
eraseBioNetNode2.5070.4112.950
getBezierCurve0.0010.0010.001
getBioMatrixDataRowTop0.0010.0000.001
getBioMatrixPlotParameters0.0030.0010.003
getBioNetNodeLinkLine0.0020.0000.001
getBioNetParameters0.6950.2530.950
getBioNetPlotLocations0.5080.2300.739
getBioNetSamplePlotPosition0.0000.0000.001
getCaOmicsVColors0.0010.0000.001
getCaOmicsVPlotTypes000
getDefaultNaStrings0.0000.0000.001
getHeatmapColorScales0.0000.0000.001
getPlotDataSet0.0420.0160.060
getPlotOmicsData0.0140.0060.019
getPlotSampleData0.0040.0030.007
getPlotSummaryData0.0110.0020.013
getRelatedPlotData0.0790.0070.086
initializeBioMatrixPlot0.0010.0000.001
initializeBioNetCircos0.4620.1930.655
labelBioNetNodeNames2.2150.3392.591
linkBioNetNodes1.6190.3341.986
linkBioNetSamples1.7440.3292.082
methylDemoData0.0030.0030.006
miRNA0.0040.0030.006
miRNADemoData0.0030.0030.005
plotBioMatrix0.7800.0410.837
plotBioMatrixBars0.0150.0020.019
plotBioMatrixBinaryData0.0050.0010.006
plotBioMatrixCategoryData0.0050.0010.007
plotBioMatrixHeatmap0.0090.0040.014
plotBioMatrixRowNames0.0200.0010.021
plotBioMatrixSampleData0.0060.0010.008
plotBioMatrixSampleNames0.0030.0010.004
plotBioNetBars2.3030.4162.730
plotBioNetCircos8.3140.9809.397
plotBioNetHeatmap5.8040.5046.399
plotBioNetLines3.6070.4354.061
plotBioNetPoints3.3780.4743.868
plotBioNetPolygons3.4480.3653.846
plotHeatmapColorScale1.5080.0411.563
resetBioNetNodePlotAreaBoundary000
sampleDemoData0.0020.0020.004
setBioMatrixBaseCoordinates0.0010.0000.001
setBioMatrixPlotArea0.0030.0010.007
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.5820.1830.764
setBioNetPlotAreaBackground0.1020.0380.140
setBioNetPlotParameters0.0010.0000.001
setCaOmicsVColors0.0010.0010.000
setDefaultNaStrings0.0000.0000.001
showBioMatrixPlotLayout0.0490.0030.054
showBioNetNodesLayout0.9030.2791.187
showSupportedBioNetCircosPlotType0.0000.0000.001
sortClinicalData0.0040.0020.006
sortOmicsDataByColumn0.0040.0020.006
sortOmicsDataByRow0.0070.0030.010