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CHECK report for caOmicsV on merida1

This page was generated on 2020-10-01 11:02:25 -0400 (Thu, 01 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE caOmicsV PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 225/1923HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.19.0
Henry Zhang
Snapshot Date: 2020-09-30 14:42:00 -0400 (Wed, 30 Sep 2020)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: master
Last Commit: 2d96ecc
Last Changed Date: 2020-04-27 14:49:25 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] NA 

Summary

Package: caOmicsV
Version: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2020-10-01 02:29:02 -0400 (Thu, 01 Oct 2020)
EndedAt: 2020-10-01 02:31:33 -0400 (Thu, 01 Oct 2020)
EllapsedTime: 150.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: caOmicsV.Rcheck
Warnings: 1

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_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/caOmicsV.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.19.0’
* 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 ‘text’
Undefined global functions or variables:
  col2rgb dist gray grey legend lines palette par 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.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 ... WARNING
Undocumented code objects:
  ‘getBioMatrixBasePositions’ ‘getBioMatrixColumnPadding’
  ‘getBioMatrixDataAreaWidth’ ‘getBioMatrixGeneLabelWidth’
  ‘getBioMatrixGeneNumber’ ‘getBioMatrixLegendHeight’
  ‘getBioMatrixPhenotypeNumber’ ‘getBioMatrixPlotAreaHeigth’
  ‘getBioMatrixPlotAreaWidth’ ‘getBioMatrixRemarkWidth’
  ‘getBioMatrixRowPadding’ ‘getBioMatrixSampleHeight’
  ‘getBioMatrixSampleIDHeight’ ‘getBioMatrixSampleNumber’
  ‘getBioMatrixSampleWidth’ ‘getBioNetBasePositions’ ‘getBioNetGraph’
  ‘getBioNetNodePaddingScale’ ‘getBioNetNodeParameters’
  ‘getBioNetNodePlotAreaBoundary’ ‘getBioNetNodeRadius’
  ‘getBioNetPlotAreaWidth’ ‘getBioNetPlotSampleWidth’
  ‘getBioNetPlotTotalSample’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 (user + system) or elapsed time > 5s
                          user system elapsed
bioNetLegend             7.900  0.456   8.456
plotBioNetCircos         7.629  0.405   8.112
plotBioNetHeatmap        5.853  0.230   6.098
drawBioNetNodeBackground 5.005  0.233   5.251
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-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/4.0/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_STRING0.0000.0010.000
CNVDemoData0.0240.0080.032
RNA2miRNA0.0020.0020.004
RNASeq0.0050.0020.008
RNASeqDemoData0.0020.0030.005
bioMatrixLegend0.2470.0430.288
bioNetCircosPlot1.9750.2232.201
bioNetLegend7.9000.4568.456
biomatrixPlotDemoData0.0020.0020.005
bionetPlotDemoData0.0030.0020.005
convertToZScores0.0090.0020.010
drawBioNetNodeBackground5.0050.2335.251
eraseBioNetNode2.2170.1672.390
getBezierCurve0.0000.0000.001
getBioMatrixDataRowTop0.0010.0000.001
getBioMatrixPlotParameters0.0020.0010.002
getBioNetNodeLinkLine0.0010.0010.002
getBioNetParameters0.3750.0460.421
getBioNetPlotLocations0.3890.0600.449
getBioNetSamplePlotPosition0.0000.0000.001
getCaOmicsVColors000
getCaOmicsVPlotTypes0.0000.0010.000
getDefaultNaStrings0.0010.0000.001
getHeatmapColorScales0.0000.0000.001
getPlotDataSet0.0210.0090.031
getPlotOmicsData0.0120.0030.015
getPlotSampleData0.0010.0010.003
getPlotSummaryData0.0110.0020.012
getRelatedPlotData0.0910.0050.096
initializeBioMatrixPlot0.0000.0000.001
initializeBioNetCircos0.3940.0340.428
labelBioNetNodeNames1.9470.1282.082
linkBioNetNodes1.4960.1161.621
linkBioNetSamples1.7980.1241.933
methylDemoData0.0030.0020.004
miRNA0.0020.0020.005
miRNADemoData0.0010.0020.004
plotBioMatrix0.7620.0250.795
plotBioMatrixBars0.0170.0020.019
plotBioMatrixBinaryData0.0040.0010.005
plotBioMatrixCategoryData0.0050.0010.005
plotBioMatrixHeatmap0.0140.0120.025
plotBioMatrixRowNames0.0220.0010.024
plotBioMatrixSampleData0.0050.0010.006
plotBioMatrixSampleNames0.0030.0010.004
plotBioNetBars1.9580.1822.143
plotBioNetCircos7.6290.4058.112
plotBioNetHeatmap5.8530.2306.098
plotBioNetLines3.6530.1803.850
plotBioNetPoints3.4620.1773.655
plotBioNetPolygons3.5580.1853.758
plotHeatmapColorScale1.7190.0211.750
resetBioNetNodePlotAreaBoundary0.0000.0000.001
sampleDemoData0.0020.0020.004
setBioMatrixBaseCoordinates0.0000.0000.001
setBioMatrixPlotArea0.0020.0000.004
setBioMatrixPlotParameters0.0010.0000.001
setBioNetCircosBasePlotPositions0.0000.0000.001
setBioNetNodeLayout0.3880.0410.430
setBioNetPlotAreaBackground0.0920.0030.095
setBioNetPlotParameters000
setCaOmicsVColors0.0010.0000.001
setDefaultNaStrings0.0000.0010.001
showBioMatrixPlotLayout0.0510.0020.053
showBioNetNodesLayout0.9280.0961.025
showSupportedBioNetCircosPlotType0.0010.0000.001
sortClinicalData0.0020.0020.005
sortOmicsDataByColumn0.0030.0030.005
sortOmicsDataByRow0.0060.0020.008