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CHECK report for caOmicsV on malbec1

This page was generated on 2020-08-10 11:40:51 -0400 (Mon, 10 Aug 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 223/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.19.0
Henry Zhang
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 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
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: caOmicsV
Version: 1.19.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings caOmicsV_1.19.0.tar.gz
StartedAt: 2020-08-10 01:30:13 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 01:32:08 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 115.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: caOmicsV.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings caOmicsV_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/caOmicsV.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.19.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
bioNetLegend      8.684  0.072   8.765
plotBioNetCircos  8.612  0.128   8.749
plotBioNetHeatmap 5.160  0.076   5.238
* 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-3.12-bioc/meat/caOmicsV.Rcheck/00check.log’
for details.



Installation output

caOmicsV.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL caOmicsV
###
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* installing to library ‘/home/biocbuild/bbs-3.12-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_ENV000
CA_OMICS_NAME0.0000.0000.001
CA_OMICS_NA_STRING000
CNVDemoData0.0120.0040.016
RNA2miRNA0.0000.0000.001
RNASeq0.0040.0000.003
RNASeqDemoData0.0040.0000.001
bioMatrixLegend0.1120.0200.134
bioNetCircosPlot2.0600.0322.100
bioNetLegend8.6840.0728.765
biomatrixPlotDemoData0.0040.0000.002
bionetPlotDemoData0.0000.0000.002
convertToZScores0.0040.0000.005
drawBioNetNodeBackground4.1400.0804.222
eraseBioNetNode2.5080.0602.572
getBezierCurve000
getBioMatrixDataRowTop0.0040.0000.001
getBioMatrixPlotParameters0.0000.0000.001
getBioNetNodeLinkLine0.0040.0000.001
getBioNetParameters0.3120.0160.329
getBioNetPlotLocations0.2920.0000.289
getBioNetSamplePlotPosition0.0000.0000.001
getCaOmicsVColors000
getCaOmicsVPlotTypes000
getDefaultNaStrings000
getHeatmapColorScales0.0000.0000.001
getPlotDataSet0.0120.0000.014
getPlotOmicsData0.0080.0000.006
getPlotSampleData0.0040.0000.003
getPlotSummaryData0.0080.0000.009
getRelatedPlotData0.0680.0040.073
initializeBioMatrixPlot0.0000.0000.001
initializeBioNetCircos0.3360.0000.336
labelBioNetNodeNames2.0400.0282.069
linkBioNetNodes2.0160.0402.059
linkBioNetSamples1.8680.0121.885
methylDemoData0.0040.0000.001
miRNA0.0000.0000.001
miRNADemoData0.0040.0000.001
plotBioMatrix0.6880.0080.697
plotBioMatrixBars0.0200.0000.018
plotBioMatrixBinaryData0.0040.0000.005
plotBioMatrixCategoryData0.0040.0000.005
plotBioMatrixHeatmap0.0040.0000.007
plotBioMatrixRowNames0.0200.0000.021
plotBioMatrixSampleData0.0040.0000.005
plotBioMatrixSampleNames0.0000.0000.003
plotBioNetBars2.9240.0282.955
plotBioNetCircos8.6120.1288.749
plotBioNetHeatmap5.1600.0765.238
plotBioNetLines3.2800.0323.324
plotBioNetPoints3.8400.0443.893
plotBioNetPolygons3.7920.0483.853
plotHeatmapColorScale1.4240.0081.434
resetBioNetNodePlotAreaBoundary000
sampleDemoData0.0000.0000.001
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea0.0000.0000.002
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.2280.0000.231
setBioNetPlotAreaBackground0.0840.0000.086
setBioNetPlotParameters000
setCaOmicsVColors000
setDefaultNaStrings000
showBioMatrixPlotLayout0.0440.0000.046
showBioNetNodesLayout1.3320.0001.332
showSupportedBioNetCircosPlotType000
sortClinicalData0.0000.0000.002
sortOmicsDataByColumn0.0040.0000.001
sortOmicsDataByRow0.0040.0000.002