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CHECK report for caOmicsV on merida2

This page was generated on 2018-01-19 07:35:04 -0500 (Fri, 19 Jan 2018).

Package 181/1482HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.9.0
Henry Zhang
Snapshot Date: 2018-01-18 17:01:21 -0500 (Thu, 18 Jan 2018)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: master
Last Commit: ce3bf3a
Last Changed Date: 2017-10-30 12:54:10 -0500 (Mon, 30 Oct 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
merida2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: caOmicsV
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.9.0.tar.gz
StartedAt: 2018-01-18 22:20:46 -0500 (Thu, 18 Jan 2018)
EndedAt: 2018-01-18 22:23:17 -0500 (Thu, 18 Jan 2018)
EllapsedTime: 150.8 seconds
RetCode: 0
Status:  OK 
CheckDir: caOmicsV.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/caOmicsV.Rcheck’
* using R Under development (unstable) (2017-12-04 r73829)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.9.0’
* 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   5.0Mb
* 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 sizes of PDF files under ‘inst/doc’ ... 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             10.556  0.550  12.847
plotBioNetCircos          8.314  0.463   9.106
plotBioNetHeatmap         6.470  0.333   7.307
drawBioNetNodeBackground  5.753  0.293   6.927
* 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
  ‘/Users/biocbuild/bbs-3.7-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_ENV0.0020.0000.001
CA_OMICS_NAME0.0010.0010.001
CA_OMICS_NA_STRING0.0010.0000.003
CNVDemoData0.0230.0080.034
RNA2miRNA0.0030.0020.004
RNASeq0.0050.0030.009
RNASeqDemoData0.0030.0020.006
bioMatrixLegend0.4150.0350.486
bioNetCircosPlot2.3580.2772.813
bioNetLegend10.556 0.55012.847
biomatrixPlotDemoData0.0040.0010.006
bionetPlotDemoData0.0040.0010.010
convertToZScores0.0110.0020.014
drawBioNetNodeBackground5.7530.2936.927
eraseBioNetNode2.5250.2042.913
getBezierCurve0.0020.0010.002
getBioMatrixDataRowTop0.1090.0010.117
getBioMatrixPlotParameters0.0040.0000.005
getBioNetNodeLinkLine0.0030.0000.003
getBioNetParameters0.4220.1010.550
getBioNetPlotLocations0.4200.1000.549
getBioNetSamplePlotPosition0.0010.0000.001
getCaOmicsVColors0.0010.0000.001
getCaOmicsVPlotTypes0.0010.0000.001
getDefaultNaStrings0.0010.0000.002
getHeatmapColorScales0.0010.0000.001
getPlotDataSet0.0380.0080.050
getPlotOmicsData0.0120.0030.016
getPlotSampleData0.0040.0020.005
getPlotSummaryData0.1260.0030.138
getRelatedPlotData0.0830.0040.088
initializeBioMatrixPlot0.0010.0000.002
initializeBioNetCircos0.4110.1030.535
labelBioNetNodeNames2.2550.1872.581
linkBioNetNodes1.7840.1762.043
linkBioNetSamples1.7630.1742.024
methylDemoData0.0030.0010.004
miRNA0.0030.0020.005
miRNADemoData0.0030.0010.004
plotBioMatrix1.1100.0271.191
plotBioMatrixBars0.0190.0010.022
plotBioMatrixBinaryData0.0060.0000.007
plotBioMatrixCategoryData0.0060.0000.006
plotBioMatrixHeatmap0.0090.0010.012
plotBioMatrixRowNames0.0270.0010.029
plotBioMatrixSampleData0.0060.0010.008
plotBioMatrixSampleNames0.0050.0010.006
plotBioNetBars2.3430.2092.645
plotBioNetCircos8.3140.4639.106
plotBioNetHeatmap6.4700.3337.307
plotBioNetLines3.9980.2954.756
plotBioNetPoints3.6430.2584.021
plotBioNetPolygons3.7820.2374.125
plotHeatmapColorScale1.7870.0421.957
resetBioNetNodePlotAreaBoundary0.0010.0000.001
sampleDemoData0.0020.0010.004
setBioMatrixBaseCoordinates0.0010.0000.001
setBioMatrixPlotArea0.0040.0000.004
setBioMatrixPlotParameters0.0010.0000.000
setBioNetCircosBasePlotPositions0.0010.0000.001
setBioNetNodeLayout0.3800.0970.492
setBioNetPlotAreaBackground0.0960.0140.115
setBioNetPlotParameters0.0010.0000.001
setCaOmicsVColors0.0010.0000.001
setDefaultNaStrings0.0010.0000.001
showBioMatrixPlotLayout0.0180.0010.020
showBioNetNodesLayout0.9820.1601.175
showSupportedBioNetCircosPlotType0.0010.0000.002
sortClinicalData0.0040.0010.005
sortOmicsDataByColumn0.0040.0010.006
sortOmicsDataByRow0.0070.0010.009