Back to Multiple platform build/check report for BioC 3.7
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for caOmicsV on malbec2

This page was generated on 2018-10-17 08:27:43 -0400 (Wed, 17 Oct 2018).

Package 188/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.10.0
Henry Zhang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: RELEASE_3_7
Last Commit: c6c83f6
Last Changed Date: 2018-04-30 10:35:37 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: caOmicsV
Version: 1.10.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings caOmicsV_1.10.0.tar.gz
StartedAt: 2018-10-15 22:58:58 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:00:29 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 91.1 seconds
RetCode: 0
Status:  OK 
CheckDir: caOmicsV.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings caOmicsV_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/caOmicsV.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
bioNetLegend      7.460  0.100   7.564
plotBioNetCircos  6.768  0.072   6.846
plotBioNetHeatmap 4.940  0.068   5.010
* 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-3.7-bioc/meat/caOmicsV.Rcheck/00check.log’
for details.



Installation output

caOmicsV.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL caOmicsV
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘caOmicsV’ ...
** 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
* DONE (caOmicsV)

Tests output


Example timings

caOmicsV.Rcheck/caOmicsV-Ex.timings

nameusersystemelapsed
CA_OMICS_ENV0.0000.0000.001
CA_OMICS_NAME0.0000.0000.001
CA_OMICS_NA_STRING000
CNVDemoData0.0080.0040.015
RNA2miRNA0.0000.0000.001
RNASeq0.0040.0000.004
RNASeqDemoData0.0040.0000.002
bioMatrixLegend0.1120.0120.123
bioNetCircosPlot1.8520.0321.903
bioNetLegend7.4600.1007.564
biomatrixPlotDemoData0.0040.0000.016
bionetPlotDemoData0.0000.0000.002
convertToZScores0.0040.0000.006
drawBioNetNodeBackground4.6840.0804.767
eraseBioNetNode2.1160.0402.160
getBezierCurve0.0000.0000.001
getBioMatrixDataRowTop0.0000.0000.001
getBioMatrixPlotParameters0.0000.0000.002
getBioNetNodeLinkLine0.0040.0000.001
getBioNetParameters0.2160.0000.216
getBioNetPlotLocations0.2680.0000.267
getBioNetSamplePlotPosition0.0000.0000.001
getCaOmicsVColors0.0040.0000.000
getCaOmicsVPlotTypes0.0000.0000.001
getDefaultNaStrings0.0000.0000.001
getHeatmapColorScales000
getPlotDataSet0.0240.0040.030
getPlotOmicsData0.0080.0000.011
getPlotSampleData0.0000.0000.003
getPlotSummaryData0.0080.0000.010
getRelatedPlotData0.0560.0000.057
initializeBioMatrixPlot0.0000.0000.001
initializeBioNetCircos0.3280.0000.325
labelBioNetNodeNames1.8520.0161.870
linkBioNetNodes1.5360.0201.555
linkBioNetSamples1.7120.0321.745
methylDemoData0.0000.0040.003
miRNA0.0000.0000.002
miRNADemoData0.0000.0000.002
plotBioMatrix0.6800.0080.689
plotBioMatrixBars0.0160.0000.017
plotBioMatrixBinaryData0.0040.0000.005
plotBioMatrixCategoryData0.0040.0000.005
plotBioMatrixHeatmap0.0080.0000.009
plotBioMatrixRowNames0.0200.0040.020
plotBioMatrixSampleData0.0040.0040.006
plotBioMatrixSampleNames0.0040.0000.003
plotBioNetBars1.9240.0361.962
plotBioNetCircos6.7680.0726.846
plotBioNetHeatmap4.9400.0685.010
plotBioNetLines3.1080.0283.136
plotBioNetPoints3.2120.0163.232
plotBioNetPolygons3.0760.0523.133
plotHeatmapColorScale1.3520.0161.372
resetBioNetNodePlotAreaBoundary000
sampleDemoData0.0000.0000.001
setBioMatrixBaseCoordinates0.0000.0000.001
setBioMatrixPlotArea0.0040.0000.003
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.2400.0000.239
setBioNetPlotAreaBackground0.0680.0000.067
setBioNetPlotParameters0.0040.0000.001
setCaOmicsVColors0.0000.0000.001
setDefaultNaStrings000
showBioMatrixPlotLayout0.0160.0000.013
showBioNetNodesLayout0.8680.0400.909
showSupportedBioNetCircosPlotType0.0040.0000.000
sortClinicalData0.0000.0000.002
sortOmicsDataByColumn0.0000.0000.003
sortOmicsDataByRow0.0000.0000.003