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BioC 3.5: CHECK report for caOmicsV on malbec2

This page was generated on 2017-08-16 13:16:44 -0400 (Wed, 16 Aug 2017).

Package 172/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.6.0
Henry Zhang
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/caOmicsV
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -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: 2017-08-15 21:42:36 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:44:23 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 107.3 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 3.4.1 (2017-06-30)
* 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  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
* 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      9.428  0.088   9.524
plotBioNetCircos  7.112  0.092   7.208
plotBioNetHeatmap 5.328  0.140   5.480
* 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_ENV000
CA_OMICS_NAME0.0000.0000.001
CA_OMICS_NA_STRING000
CNVDemoData0.0160.0040.021
RNA2miRNA0.0000.0000.001
RNASeq0.0000.0000.003
RNASeqDemoData0.0000.0000.001
bioMatrixLegend0.3360.0040.339
bioNetCircosPlot2.1600.0402.213
bioNetLegend9.4280.0889.524
biomatrixPlotDemoData0.0040.0000.040
bionetPlotDemoData0.0040.0000.005
convertToZScores0.0080.0000.007
drawBioNetNodeBackground4.7760.1844.965
eraseBioNetNode2.0960.0242.123
getBezierCurve0.0000.0000.001
getBioMatrixDataRowTop0.0520.0000.052
getBioMatrixPlotParameters0.0040.0000.002
getBioNetNodeLinkLine0.0000.0000.001
getBioNetParameters0.5000.0000.501
getBioNetPlotLocations0.4000.0000.404
getBioNetSamplePlotPosition0.0000.0000.001
getCaOmicsVColors000
getCaOmicsVPlotTypes000
getDefaultNaStrings000
getHeatmapColorScales0.0040.0000.000
getPlotDataSet0.0160.0000.019
getPlotOmicsData0.0080.0000.008
getPlotSampleData0.0040.0000.002
getPlotSummaryData0.0600.0000.062
getRelatedPlotData0.0400.0000.038
initializeBioMatrixPlot0.0000.0000.001
initializeBioNetCircos0.2640.0000.261
labelBioNetNodeNames1.8960.0121.907
linkBioNetNodes1.5920.0161.608
linkBioNetSamples1.8880.0081.897
methylDemoData0.0000.0000.001
miRNA0.0000.0000.002
miRNADemoData0.0040.0000.001
plotBioMatrix0.8800.0080.890
plotBioMatrixBars0.0160.0000.017
plotBioMatrixBinaryData0.0040.0000.005
plotBioMatrixCategoryData0.0040.0000.005
plotBioMatrixHeatmap0.0040.0040.009
plotBioMatrixRowNames0.0200.0000.021
plotBioMatrixSampleData0.0000.0040.006
plotBioMatrixSampleNames0.0040.0000.004
plotBioNetBars2.0280.0242.055
plotBioNetCircos7.1120.0927.208
plotBioNetHeatmap5.3280.1405.480
plotBioNetLines3.1760.0323.211
plotBioNetPoints3.0960.0283.125
plotBioNetPolygons3.6160.0323.649
plotHeatmapColorScale1.5280.0121.542
resetBioNetNodePlotAreaBoundary0.0000.0000.001
sampleDemoData0.0040.0000.003
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea0.0000.0000.002
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.4360.0080.448
setBioNetPlotAreaBackground0.0640.0000.065
setBioNetPlotParameters0.0000.0000.001
setCaOmicsVColors0.0000.0000.001
setDefaultNaStrings000
showBioMatrixPlotLayout0.0120.0000.011
showBioNetNodesLayout1.2080.0121.222
showSupportedBioNetCircosPlotType0.0040.0000.001
sortClinicalData0.0040.0000.003
sortOmicsDataByColumn0.0040.0000.004
sortOmicsDataByRow0.0080.0000.006