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BioC 3.4: CHECK report for caOmicsV on malbec1

This page was generated on 2017-04-15 16:13:03 -0400 (Sat, 15 Apr 2017).

Package 162/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.4.0
Henry Zhang
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/caOmicsV
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: caOmicsV
Version: 1.4.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.4.0.tar.gz
StartedAt: 2017-04-14 21:23:52 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:25:29 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 97.2 seconds
RetCode: 0
Status:  OK 
CheckDir: caOmicsV.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/caOmicsV.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.0’
* 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 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     7.076  0.072   7.151
plotBioNetCircos 6.788  0.052   6.840
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.4-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_NAME000
CA_OMICS_NA_STRING000
CNVDemoData0.0120.0040.014
RNA2miRNA0.0040.0000.001
RNASeq0.0040.0000.004
RNASeqDemoData0.0000.0000.001
bioMatrixLegend0.2200.0000.222
bioNetCircosPlot2.1320.0162.162
bioNetLegend7.0760.0727.151
biomatrixPlotDemoData0.0000.0000.002
bionetPlotDemoData0.0000.0000.002
convertToZScores0.0040.0000.004
drawBioNetNodeBackground3.8400.0483.891
eraseBioNetNode2.0600.0162.074
getBezierCurve0.0000.0000.001
getBioMatrixDataRowTop000
getBioMatrixPlotParameters0.0000.0000.002
getBioNetNodeLinkLine0.0000.0000.001
getBioNetParameters0.3560.0000.357
getBioNetPlotLocations0.3680.0000.365
getBioNetSamplePlotPosition0.0000.0000.001
getCaOmicsVColors0.0000.0000.001
getCaOmicsVPlotTypes000
getDefaultNaStrings000
getHeatmapColorScales0.0040.0000.001
getPlotDataSet0.0160.0000.018
getPlotOmicsData0.0040.0040.007
getPlotSampleData0.0040.0000.002
getPlotSummaryData0.0080.0000.006
getRelatedPlotData0.0320.0000.034
initializeBioMatrixPlot0.0000.0000.001
initializeBioNetCircos0.2680.0000.269
labelBioNetNodeNames1.8040.0201.827
linkBioNetNodes1.4560.0041.458
linkBioNetSamples1.4480.0161.467
methylDemoData0.0040.0000.001
miRNA0.0000.0000.002
miRNADemoData0.0000.0040.002
plotBioMatrix0.5040.0120.519
plotBioMatrixBars0.0080.0000.011
plotBioMatrixBinaryData0.0000.0000.003
plotBioMatrixCategoryData0.0000.0000.003
plotBioMatrixHeatmap0.0080.0000.005
plotBioMatrixRowNames0.0120.0000.012
plotBioMatrixSampleData0.0040.0000.003
plotBioMatrixSampleNames0.0040.0000.002
plotBioNetBars1.8960.0281.925
plotBioNetCircos6.7880.0526.840
plotBioNetHeatmap4.5480.0404.589
plotBioNetLines3.0760.0283.105
plotBioNetPoints3.1280.0203.153
plotBioNetPolygons3.1080.0123.121
plotHeatmapColorScale1.1520.0121.164
resetBioNetNodePlotAreaBoundary000
sampleDemoData0.0000.0000.001
setBioMatrixBaseCoordinates0.0040.0000.000
setBioMatrixPlotArea0.0000.0000.002
setBioMatrixPlotParameters0.0040.0000.000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.2600.0000.259
setBioNetPlotAreaBackground0.0760.0000.075
setBioNetPlotParameters000
setCaOmicsVColors000
setDefaultNaStrings000
showBioMatrixPlotLayout0.0160.0000.019
showBioNetNodesLayout0.9920.0241.019
showSupportedBioNetCircosPlotType0.0040.0000.001
sortClinicalData0.0000.0000.002
sortOmicsDataByColumn0.0000.0040.002
sortOmicsDataByRow0.0040.0000.003