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CHECK report for caOmicsV on merida2

This page was generated on 2019-04-09 13:31:40 -0400 (Tue, 09 Apr 2019).

Package 208/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.13.1
Henry Zhang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: master
Last Commit: bc9f50a
Last Changed Date: 2019-01-04 13:08:48 -0400 (Fri, 04 Jan 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: caOmicsV
Version: 1.13.1
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_1.13.1.tar.gz
StartedAt: 2019-04-08 23:40:40 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:42:42 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 121.6 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_1.13.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/caOmicsV.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.13.1’
* 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             7.204  0.585   7.829
plotBioNetCircos         6.829  0.517   7.392
plotBioNetHeatmap        6.136  0.432   6.660
drawBioNetNodeBackground 5.132  0.410   5.592
* 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’ ...
** 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_ENV0.0000.0010.000
CA_OMICS_NAME000
CA_OMICS_NA_STRING0.0000.0000.001
CNVDemoData0.0230.0070.031
RNA2miRNA0.0020.0010.004
RNASeq0.0050.0020.007
RNASeqDemoData0.0030.0010.004
bioMatrixLegend0.2050.0330.243
bioNetCircosPlot1.7910.3082.114
bioNetLegend7.2040.5857.829
biomatrixPlotDemoData0.0020.0020.005
bionetPlotDemoData0.0030.0020.005
convertToZScores0.0070.0010.008
drawBioNetNodeBackground5.1320.4105.592
eraseBioNetNode2.2610.2672.553
getBezierCurve000
getBioMatrixDataRowTop0.0010.0010.001
getBioMatrixPlotParameters0.0010.0000.002
getBioNetNodeLinkLine0.0010.0010.001
getBioNetParameters0.3890.1000.493
getBioNetPlotLocations0.3290.1070.440
getBioNetSamplePlotPosition000
getCaOmicsVColors000
getCaOmicsVPlotTypes0.0010.0000.000
getDefaultNaStrings000
getHeatmapColorScales0.0000.0000.001
getPlotDataSet0.0320.0070.039
getPlotOmicsData0.0110.0040.015
getPlotSampleData0.0030.0020.005
getPlotSummaryData0.0110.0020.013
getRelatedPlotData0.0740.0020.077
initializeBioMatrixPlot0.0010.0000.001
initializeBioNetCircos0.4020.1060.511
labelBioNetNodeNames2.2890.1672.485
linkBioNetNodes1.5360.1611.717
linkBioNetSamples1.6510.2351.911
methylDemoData0.0020.0020.003
miRNA0.0020.0010.004
miRNADemoData0.0020.0010.003
plotBioMatrix0.7940.1140.916
plotBioMatrixBars0.0130.0010.015
plotBioMatrixBinaryData0.0040.0020.005
plotBioMatrixCategoryData0.0050.0000.005
plotBioMatrixHeatmap0.0080.0020.011
plotBioMatrixRowNames0.0220.0010.023
plotBioMatrixSampleData0.0040.0010.005
plotBioMatrixSampleNames0.0030.0010.003
plotBioNetBars1.8200.2602.088
plotBioNetCircos6.8290.5177.392
plotBioNetHeatmap6.1360.4326.660
plotBioNetLines3.9710.3324.452
plotBioNetPoints3.7270.3354.114
plotBioNetPolygons3.2230.2493.509
plotHeatmapColorScale1.5860.0291.626
resetBioNetNodePlotAreaBoundary000
sampleDemoData0.0020.0010.004
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea0.0020.0000.003
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.3540.0990.455
setBioNetPlotAreaBackground0.0880.0140.104
setBioNetPlotParameters000
setCaOmicsVColors0.0000.0010.001
setDefaultNaStrings000
showBioMatrixPlotLayout0.0140.0010.014
showBioNetNodesLayout0.7740.1490.939
showSupportedBioNetCircosPlotType0.0000.0000.001
sortClinicalData0.0020.0010.003
sortOmicsDataByColumn0.0020.0010.003
sortOmicsDataByRow0.0040.0010.004