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CHECK report for caOmicsV on malbec2

This page was generated on 2020-10-17 11:54:31 -0400 (Sat, 17 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 230/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.18.0
Henry Zhang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: RELEASE_3_11
Last Commit: dcd3e5d
Last Changed Date: 2020-04-27 14:49:25 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: caOmicsV
Version: 1.18.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings caOmicsV_1.18.0.tar.gz
StartedAt: 2020-10-16 23:33:49 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:35:43 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 114.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: caOmicsV.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings caOmicsV_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/caOmicsV.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotBioNetCircos 8.843  0.124   8.976
bioNetLegend     7.898  0.104   8.003
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/caOmicsV.Rcheck/00check.log’
for details.



Installation output

caOmicsV.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL caOmicsV
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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_ENV0.0010.0010.000
CA_OMICS_NAME000
CA_OMICS_NA_STRING000
CNVDemoData0.0160.0030.020
RNA2miRNA0.0010.0000.002
RNASeq0.0030.0000.003
RNASeqDemoData0.0020.0000.002
bioMatrixLegend0.2090.0080.217
bioNetCircosPlot2.2090.0322.256
bioNetLegend7.8980.1048.003
biomatrixPlotDemoData0.0040.0000.028
bionetPlotDemoData0.0030.0000.003
convertToZScores0.0080.0000.007
drawBioNetNodeBackground4.0880.0724.160
eraseBioNetNode1.9790.0242.002
getBezierCurve0.0010.0000.000
getBioMatrixDataRowTop0.0010.0000.000
getBioMatrixPlotParameters0.0010.0000.000
getBioNetNodeLinkLine0.0010.0000.000
getBioNetParameters0.2410.0000.241
getBioNetPlotLocations0.2360.0000.237
getBioNetSamplePlotPosition0.0000.0000.001
getCaOmicsVColors000
getCaOmicsVPlotTypes000
getDefaultNaStrings000
getHeatmapColorScales0.0010.0000.000
getPlotDataSet0.0150.0000.014
getPlotOmicsData0.0030.0040.007
getPlotSampleData0.0020.0000.001
getPlotSummaryData0.0050.0000.006
getRelatedPlotData0.0370.0000.037
initializeBioMatrixPlot0.0010.0000.000
initializeBioNetCircos0.2380.0040.242
labelBioNetNodeNames1.8320.0201.852
linkBioNetNodes1.5000.0241.524
linkBioNetSamples1.6700.0281.698
methylDemoData0.0020.0000.002
miRNA0.0020.0000.003
miRNADemoData0.0000.0020.002
plotBioMatrix0.6690.0160.702
plotBioMatrixBars0.0110.0000.011
plotBioMatrixBinaryData0.0030.0000.003
plotBioMatrixCategoryData0.0030.0000.003
plotBioMatrixHeatmap0.0050.0000.005
plotBioMatrixRowNames0.0120.0000.011
plotBioMatrixSampleData0.0030.0000.003
plotBioMatrixSampleNames0.0020.0000.001
plotBioNetBars2.2260.0312.262
plotBioNetCircos8.8430.1248.976
plotBioNetHeatmap4.6300.0764.706
plotBioNetLines3.4520.0403.492
plotBioNetPoints4.1020.0324.133
plotBioNetPolygons3.9000.0283.928
plotHeatmapColorScale1.6140.0121.626
resetBioNetNodePlotAreaBoundary000
sampleDemoData0.0020.0000.002
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea0.0020.0000.003
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions0.0010.0000.000
setBioNetNodeLayout0.3890.0000.390
setBioNetPlotAreaBackground0.1370.0000.136
setBioNetPlotParameters0.0000.0010.000
setCaOmicsVColors0.0000.0010.000
setDefaultNaStrings0.0000.0010.000
showBioMatrixPlotLayout0.0450.0040.049
showBioNetNodesLayout1.4420.0041.447
showSupportedBioNetCircosPlotType000
sortClinicalData0.0030.0000.002
sortOmicsDataByColumn0.0000.0030.002
sortOmicsDataByRow0.0000.0040.005