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CHECK report for caOmicsV on malbec1

This page was generated on 2018-04-12 13:13:45 -0400 (Thu, 12 Apr 2018).

Package 180/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.8.0
Henry Zhang
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: RELEASE_3_6
Last Commit: 7c17e17
Last Changed Date: 2017-10-30 12:40:52 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: caOmicsV
Version: 1.8.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.8.0.tar.gz
StartedAt: 2018-04-11 22:00:49 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:02:32 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 102.5 seconds
RetCode: 0
Status:  OK 
CheckDir: caOmicsV.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/caOmicsV.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.0’
* 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 ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
bioNetLegend      8.756  0.088   8.855
plotBioNetCircos  7.636  0.092   7.733
plotBioNetHeatmap 5.272  0.080   5.361
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/caOmicsV.Rcheck/00check.log’
for details.



Installation output

caOmicsV.Rcheck/00install.out

* installing *source* package ‘caOmicsV’ ...
** R
** data
** demo
** inst
** preparing 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_ENV0.0000.0040.000
CA_OMICS_NAME000
CA_OMICS_NA_STRING0.0000.0000.001
CNVDemoData0.020.000.02
RNA2miRNA0.0000.0040.001
RNASeq0.0040.0000.004
RNASeqDemoData0.0040.0000.002
bioMatrixLegend0.2040.0080.212
bioNetCircosPlot2.7040.0362.778
bioNetLegend8.7560.0888.855
biomatrixPlotDemoData0.0040.0000.045
bionetPlotDemoData0.0040.0000.002
convertToZScores0.0040.0000.004
drawBioNetNodeBackground4.5320.0764.612
eraseBioNetNode2.4000.0442.450
getBezierCurve0.0000.0000.001
getBioMatrixDataRowTop0.0520.0000.053
getBioMatrixPlotParameters0.0000.0000.001
getBioNetNodeLinkLine0.0000.0000.001
getBioNetParameters0.3840.0000.383
getBioNetPlotLocations0.3680.0000.367
getBioNetSamplePlotPosition0.0000.0000.001
getCaOmicsVColors0.0000.0000.001
getCaOmicsVPlotTypes0.0040.0000.001
getDefaultNaStrings0.0000.0000.001
getHeatmapColorScales000
getPlotDataSet0.0200.0000.021
getPlotOmicsData0.0080.0000.009
getPlotSampleData0.0000.0040.002
getPlotSummaryData0.0600.0000.059
getRelatedPlotData0.0400.0000.039
initializeBioMatrixPlot0.0000.0000.001
initializeBioNetCircos0.2840.0000.284
labelBioNetNodeNames1.9920.0202.014
linkBioNetNodes1.5480.0121.561
linkBioNetSamples1.5600.0161.576
methylDemoData0.0040.0000.001
miRNA0.0000.0000.002
miRNADemoData0.0000.0000.001
plotBioMatrix0.7240.0080.729
plotBioMatrixBars0.0120.0000.012
plotBioMatrixBinaryData0.0040.0000.004
plotBioMatrixCategoryData0.0040.0000.002
plotBioMatrixHeatmap0.0040.0000.006
plotBioMatrixRowNames0.0160.0000.012
plotBioMatrixSampleData0.0040.0000.003
plotBioMatrixSampleNames0.0000.0000.002
plotBioNetBars2.1520.0202.173
plotBioNetCircos7.6360.0927.733
plotBioNetHeatmap5.2720.0805.361
plotBioNetLines4.0440.0404.090
plotBioNetPoints3.4480.0323.484
plotBioNetPolygons3.1600.0363.200
plotHeatmapColorScale1.3520.0161.367
resetBioNetNodePlotAreaBoundary0.0040.0000.000
sampleDemoData0.0000.0000.003
setBioMatrixBaseCoordinates0.0000.0000.001
setBioMatrixPlotArea0.0040.0000.003
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.4280.0000.428
setBioNetPlotAreaBackground0.0840.0000.083
setBioNetPlotParameters000
setCaOmicsVColors0.0000.0000.001
setDefaultNaStrings0.0000.0000.001
showBioMatrixPlotLayout0.0120.0000.012
showBioNetNodesLayout1.0360.0041.042
showSupportedBioNetCircosPlotType000
sortClinicalData0.0000.0000.003
sortOmicsDataByColumn0.0000.0000.002
sortOmicsDataByRow0.0040.0000.003