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BioC 3.5: CHECK report for caOmicsV on malbec2

This page was generated on 2017-10-18 14:16:55 -0400 (Wed, 18 Oct 2017).

Package 172/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.6.0
Henry Zhang
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: RELEASE_3_5
Last Commit: 534bcd6
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: caOmicsV
Version: 1.6.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.6.0.tar.gz
StartedAt: 2017-10-17 21:45:35 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 21:47:17 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 102.0 seconds
RetCode: 0
Status:  OK 
CheckDir: caOmicsV.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/caOmicsV.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.6.0’
* 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  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
* 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      8.208  0.056   8.269
plotBioNetCircos  7.024  0.056   7.088
plotBioNetHeatmap 4.996  0.076   5.077
* 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-3.5-bioc/meat/caOmicsV.Rcheck/00check.log’
for details.


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)

caOmicsV.Rcheck/caOmicsV-Ex.timings:

nameusersystemelapsed
CA_OMICS_ENV0.0000.0000.001
CA_OMICS_NAME000
CA_OMICS_NA_STRING000
CNVDemoData0.0080.0080.014
RNA2miRNA0.0000.0000.002
RNASeq0.0040.0000.004
RNASeqDemoData0.0000.0000.001
bioMatrixLegend0.3280.0000.328
bioNetCircosPlot2.2720.0162.306
bioNetLegend8.2080.0568.269
biomatrixPlotDemoData0.0040.0000.031
bionetPlotDemoData0.0040.0000.004
convertToZScores0.0080.0000.007
drawBioNetNodeBackground4.6600.1724.835
eraseBioNetNode2.0600.0482.109
getBezierCurve0.0000.0000.001
getBioMatrixDataRowTop0.0480.0000.048
getBioMatrixPlotParameters0.0000.0000.002
getBioNetNodeLinkLine0.0040.0000.001
getBioNetParameters0.3560.0000.357
getBioNetPlotLocations0.2400.0000.239
getBioNetSamplePlotPosition000
getCaOmicsVColors0.0040.0000.000
getCaOmicsVPlotTypes000
getDefaultNaStrings000
getHeatmapColorScales000
getPlotDataSet0.0120.0040.018
getPlotOmicsData0.0080.0000.007
getPlotSampleData0.0040.0000.002
getPlotSummaryData0.0520.0000.054
getRelatedPlotData0.0320.0040.034
initializeBioMatrixPlot000
initializeBioNetCircos0.3680.0000.371
labelBioNetNodeNames1.7440.0241.767
linkBioNetNodes1.4360.0241.461
linkBioNetSamples1.5440.0161.564
methylDemoData0.0000.0000.001
miRNA0.0040.0000.001
miRNADemoData0.0000.0000.001
plotBioMatrix0.7080.0040.710
plotBioMatrixBars0.0120.0000.011
plotBioMatrixBinaryData0.0000.0040.003
plotBioMatrixCategoryData0.0040.0000.003
plotBioMatrixHeatmap0.0040.0000.005
plotBioMatrixRowNames0.0120.0000.012
plotBioMatrixSampleData0.0000.0000.003
plotBioMatrixSampleNames0.0000.0000.002
plotBioNetBars1.8000.0241.825
plotBioNetCircos7.0240.0567.088
plotBioNetHeatmap4.9960.0765.077
plotBioNetLines3.0280.0203.048
plotBioNetPoints3.1800.0483.228
plotBioNetPolygons3.5320.0363.572
plotHeatmapColorScale1.4520.0121.468
resetBioNetNodePlotAreaBoundary0.0000.0000.001
sampleDemoData0.0040.0000.003
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea0.0000.0000.003
setBioMatrixPlotParameters0.0000.0000.001
setBioNetCircosBasePlotPositions0.0000.0000.001
setBioNetNodeLayout0.5160.0000.518
setBioNetPlotAreaBackground0.0920.0000.094
setBioNetPlotParameters000
setCaOmicsVColors0.0000.0000.001
setDefaultNaStrings0.0000.0000.002
showBioMatrixPlotLayout0.0120.0040.015
showBioNetNodesLayout1.4040.0241.430
showSupportedBioNetCircosPlotType000
sortClinicalData0.0040.0000.002
sortOmicsDataByColumn0.0040.0000.002
sortOmicsDataByRow0.0040.0000.003