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CHECK report for caOmicsV on merida1

This page was generated on 2020-04-15 12:42:02 -0400 (Wed, 15 Apr 2020).

Package 225/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.16.0
Henry Zhang
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: RELEASE_3_10
Last Commit: f404be7
Last Changed Date: 2019-10-29 13:09:20 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: caOmicsV
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2020-04-15 00:56:32 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:58:39 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 127.3 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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/caOmicsV.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.16.0’
* 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             7.544  0.559   8.171
plotBioNetCircos         6.604  0.525   7.470
plotBioNetHeatmap        5.914  0.432   6.547
drawBioNetNodeBackground 4.846  0.409   5.284
* 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-3.10-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_ENV0.0000.0000.001
CA_OMICS_NAME000
CA_OMICS_NA_STRING000
CNVDemoData0.0170.0060.023
RNA2miRNA0.0020.0010.003
RNASeq0.0040.0020.006
RNASeqDemoData0.0020.0020.004
bioMatrixLegend0.2380.0380.277
bioNetCircosPlot1.7510.2892.055
bioNetLegend7.5440.5598.171
biomatrixPlotDemoData0.0020.0020.004
bionetPlotDemoData0.0020.0010.003
convertToZScores0.0070.0010.009
drawBioNetNodeBackground4.8460.4095.284
eraseBioNetNode2.1860.2972.519
getBezierCurve0.0010.0000.000
getBioMatrixDataRowTop0.0010.0000.001
getBioMatrixPlotParameters0.0020.0000.001
getBioNetNodeLinkLine0.0010.0010.001
getBioNetParameters0.3730.0980.480
getBioNetPlotLocations0.3730.1040.487
getBioNetSamplePlotPosition000
getCaOmicsVColors0.0000.0000.001
getCaOmicsVPlotTypes0.0010.0000.000
getDefaultNaStrings000
getHeatmapColorScales0.0010.0000.000
getPlotDataSet0.0340.0080.043
getPlotOmicsData0.0100.0040.013
getPlotSampleData0.0020.0010.003
getPlotSummaryData0.0110.0010.013
getRelatedPlotData0.0620.0080.071
initializeBioMatrixPlot0.0010.0000.001
initializeBioNetCircos0.3850.1010.494
labelBioNetNodeNames1.7730.1702.172
linkBioNetNodes1.4430.1631.616
linkBioNetSamples1.4500.2481.717
methylDemoData0.0020.0020.004
miRNA0.0030.0020.004
miRNADemoData0.0020.0010.003
plotBioMatrix0.7170.0550.782
plotBioMatrixBars0.0160.0020.018
plotBioMatrixBinaryData0.0050.0010.006
plotBioMatrixCategoryData0.0030.0000.003
plotBioMatrixHeatmap0.0070.0010.008
plotBioMatrixRowNames0.0190.0010.020
plotBioMatrixSampleData0.0030.0010.004
plotBioMatrixSampleNames0.0030.0000.004
plotBioNetBars1.5370.2321.774
plotBioNetCircos6.6040.5257.470
plotBioNetHeatmap5.9140.4326.547
plotBioNetLines3.4920.3154.037
plotBioNetPoints3.0460.3243.531
plotBioNetPolygons3.0570.2753.613
plotHeatmapColorScale1.5750.0441.646
resetBioNetNodePlotAreaBoundary000
sampleDemoData0.0010.0010.002
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea0.0020.0000.004
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions0.0000.0000.001
setBioNetNodeLayout0.3650.1060.475
setBioNetPlotAreaBackground0.0870.0160.102
setBioNetPlotParameters0.0000.0000.001
setCaOmicsVColors0.0000.0000.001
setDefaultNaStrings0.0000.0010.001
showBioMatrixPlotLayout0.0490.0010.052
showBioNetNodesLayout0.9750.1561.302
showSupportedBioNetCircosPlotType0.0000.0000.001
sortClinicalData0.0020.0010.003
sortOmicsDataByColumn0.0020.0010.003
sortOmicsDataByRow0.0060.0010.007