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CHECK report for caOmicsV on merida2

This page was generated on 2018-07-19 11:14:32 -0400 (Thu, 19 Jul 2018).

Package 188/1560HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.10.0
Henry Zhang
Snapshot Date: 2018-07-18 16:45:10 -0400 (Wed, 18 Jul 2018)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: RELEASE_3_7
Last Commit: c6c83f6
Last Changed Date: 2018-04-30 10:35:37 -0400 (Mon, 30 Apr 2018)
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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2018-07-18 22:24:33 -0400 (Wed, 18 Jul 2018)
EndedAt: 2018-07-18 22:26:30 -0400 (Wed, 18 Jul 2018)
EllapsedTime: 117.3 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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/caOmicsV.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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             7.182  0.455   7.703
plotBioNetCircos         6.866  0.416   7.348
plotBioNetHeatmap        6.339  0.318   6.715
drawBioNetNodeBackground 5.055  0.291   5.420
* 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
###
##############################################################################
##############################################################################


* 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_ENV0.0010.0010.001
CA_OMICS_NAME0.0010.0000.001
CA_OMICS_NA_STRING0.0010.0000.001
CNVDemoData0.0230.0060.029
RNA2miRNA0.0030.0010.003
RNASeq0.0050.0030.007
RNASeqDemoData0.0030.0020.005
bioMatrixLegend0.1880.0310.220
bioNetCircosPlot1.7550.2372.006
bioNetLegend7.1820.4557.703
biomatrixPlotDemoData0.0030.0010.004
bionetPlotDemoData0.0050.0020.007
convertToZScores0.0110.0010.013
drawBioNetNodeBackground5.0550.2915.420
eraseBioNetNode2.0890.1602.266
getBezierCurve0.0010.0000.001
getBioMatrixDataRowTop0.0020.0000.002
getBioMatrixPlotParameters0.0060.0000.007
getBioNetNodeLinkLine0.0030.0010.003
getBioNetParameters0.3720.1120.487
getBioNetPlotLocations0.3430.0950.441
getBioNetSamplePlotPosition0.0010.0000.001
getCaOmicsVColors0.0010.0000.001
getCaOmicsVPlotTypes0.0010.0000.001
getDefaultNaStrings0.0010.0000.002
getHeatmapColorScales0.0010.0000.001
getPlotDataSet0.0350.0070.042
getPlotOmicsData0.0120.0040.015
getPlotSampleData0.0040.0010.005
getPlotSummaryData0.0120.0020.013
getRelatedPlotData0.0620.0040.067
initializeBioMatrixPlot0.0010.0000.002
initializeBioNetCircos0.3680.0980.468
labelBioNetNodeNames1.9420.1612.120
linkBioNetNodes1.5420.1821.741
linkBioNetSamples1.3820.1441.540
methylDemoData0.0030.0020.005
miRNA0.0030.0020.005
miRNADemoData0.0030.0010.005
plotBioMatrix0.8040.0230.844
plotBioMatrixBars0.0150.0010.016
plotBioMatrixBinaryData0.0060.0000.006
plotBioMatrixCategoryData0.0060.0000.007
plotBioMatrixHeatmap0.0100.0020.012
plotBioMatrixRowNames0.0210.0010.022
plotBioMatrixSampleData0.0040.0000.005
plotBioMatrixSampleNames0.0050.0000.006
plotBioNetBars1.7380.1881.942
plotBioNetCircos6.8660.4167.348
plotBioNetHeatmap6.3390.3186.715
plotBioNetLines3.6630.2413.936
plotBioNetPoints3.3890.2363.659
plotBioNetPolygons3.4270.2253.677
plotHeatmapColorScale1.6860.0261.733
resetBioNetNodePlotAreaBoundary0.0010.0000.002
sampleDemoData0.0030.0010.005
setBioMatrixBaseCoordinates0.0010.0000.001
setBioMatrixPlotArea0.0030.0000.004
setBioMatrixPlotParameters0.0010.0010.001
setBioNetCircosBasePlotPositions0.0010.0000.002
setBioNetNodeLayout0.3840.0980.485
setBioNetPlotAreaBackground0.0880.0150.104
setBioNetPlotParameters0.0010.0000.001
setCaOmicsVColors0.0010.0000.001
setDefaultNaStrings0.0010.0000.001
showBioMatrixPlotLayout0.0140.0000.016
showBioNetNodesLayout0.8140.1420.967
showSupportedBioNetCircosPlotType0.0010.0000.001
sortClinicalData0.0040.0020.005
sortOmicsDataByColumn0.0050.0020.006
sortOmicsDataByRow0.0070.0010.008