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CHECK report for caOmicsV on merida2

This page was generated on 2018-04-21 09:41:30 -0400 (Sat, 21 Apr 2018).

Package 185/1551HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.9.0
Henry Zhang
Snapshot Date: 2018-04-20 16:45:23 -0400 (Fri, 20 Apr 2018)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: master
Last Commit: ce3bf3a
Last Changed Date: 2017-10-30 12:54:10 -0400 (Mon, 30 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: caOmicsV
Version: 1.9.0
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_1.9.0.tar.gz
StartedAt: 2018-04-20 22:22:19 -0400 (Fri, 20 Apr 2018)
EndedAt: 2018-04-20 22:24:16 -0400 (Fri, 20 Apr 2018)
EllapsedTime: 117.0 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_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/caOmicsV.Rcheck’
* using R version 3.5.0 RC (2018-04-16 r74612)
* 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 ‘1.9.0’
* 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             8.121  0.501   8.695
plotBioNetCircos         6.911  0.418   7.388
plotBioNetHeatmap        5.705  0.260   6.012
drawBioNetNodeBackground 5.044  0.281   5.366
* 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-3.7-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
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘caOmicsV’ ...
** 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
* DONE (caOmicsV)

Tests output


Example timings

caOmicsV.Rcheck/caOmicsV-Ex.timings

nameusersystemelapsed
CA_OMICS_ENV0.0010.0000.001
CA_OMICS_NAME0.0010.0010.002
CA_OMICS_NA_STRING000
CNVDemoData0.0160.0050.021
RNA2miRNA0.0020.0010.003
RNASeq0.0040.0020.005
RNASeqDemoData0.0020.0010.003
bioMatrixLegend0.2140.0340.250
bioNetCircosPlot1.7250.2351.978
bioNetLegend8.1210.5018.695
biomatrixPlotDemoData0.0030.0020.006
bionetPlotDemoData0.0040.0020.006
convertToZScores0.0130.0020.015
drawBioNetNodeBackground5.0440.2815.366
eraseBioNetNode2.1720.1902.374
getBezierCurve0.0020.0000.001
getBioMatrixDataRowTop0.0010.0000.002
getBioMatrixPlotParameters0.0030.0000.003
getBioNetNodeLinkLine0.0030.0000.003
getBioNetParameters0.3920.1070.501
getBioNetPlotLocations0.3430.1050.448
getBioNetSamplePlotPosition0.0010.0000.001
getCaOmicsVColors000
getCaOmicsVPlotTypes0.0010.0000.000
getDefaultNaStrings0.0000.0000.001
getHeatmapColorScales0.0010.0000.001
getPlotDataSet0.0240.0060.030
getPlotOmicsData0.0100.0020.013
getPlotSampleData0.0050.0010.006
getPlotSummaryData0.0130.0020.015
getRelatedPlotData0.0500.0040.055
initializeBioMatrixPlot0.0010.0000.001
initializeBioNetCircos0.3820.1000.482
labelBioNetNodeNames1.8720.1592.045
linkBioNetNodes1.4200.1671.602
linkBioNetSamples1.4830.1501.655
methylDemoData0.0040.0020.005
miRNA0.0030.0020.005
miRNADemoData0.0020.0010.003
plotBioMatrix0.7850.0260.822
plotBioMatrixBars0.0150.0010.016
plotBioMatrixBinaryData0.0060.0010.007
plotBioMatrixCategoryData0.0060.0020.007
plotBioMatrixHeatmap0.0100.0020.012
plotBioMatrixRowNames0.0210.0000.022
plotBioMatrixSampleData0.0040.0000.005
plotBioMatrixSampleNames0.0050.0010.006
plotBioNetBars1.7970.1922.014
plotBioNetCircos6.9110.4187.388
plotBioNetHeatmap5.7050.2606.012
plotBioNetLines3.3730.2193.610
plotBioNetPoints3.3270.2333.585
plotBioNetPolygons3.3460.2443.630
plotHeatmapColorScale1.6990.0321.752
resetBioNetNodePlotAreaBoundary0.0010.0010.001
sampleDemoData0.0020.0010.004
setBioMatrixBaseCoordinates0.0010.0000.001
setBioMatrixPlotArea0.0030.0000.004
setBioMatrixPlotParameters0.0010.0000.001
setBioNetCircosBasePlotPositions0.0010.0000.001
setBioNetNodeLayout0.3630.0980.464
setBioNetPlotAreaBackground0.0720.0110.084
setBioNetPlotParameters0.0010.0000.002
setCaOmicsVColors0.0010.0000.001
setDefaultNaStrings0.0010.0000.002
showBioMatrixPlotLayout0.0160.0000.016
showBioNetNodesLayout0.8710.1431.037
showSupportedBioNetCircosPlotType0.0010.0000.001
sortClinicalData0.0030.0010.005
sortOmicsDataByColumn0.0030.0010.005
sortOmicsDataByRow0.0060.0010.007