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BioC 3.5: CHECK report for caOmicsV on tokay2

This page was generated on 2017-08-16 13:24:39 -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: rm -rf caOmicsV.buildbin-libdir caOmicsV.Rcheck && mkdir caOmicsV.buildbin-libdir caOmicsV.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=caOmicsV.buildbin-libdir caOmicsV_1.6.0.tar.gz >caOmicsV.Rcheck\00install.out 2>&1 && cp caOmicsV.Rcheck\00install.out caOmicsV-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=caOmicsV.buildbin-libdir --install="check:caOmicsV-install.out" --force-multiarch --no-vignettes --timings caOmicsV_1.6.0.tar.gz
StartedAt: 2017-08-15 22:29:02 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:33:04 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 241.8 seconds
RetCode: 0
Status:  OK  
CheckDir: caOmicsV.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf caOmicsV.buildbin-libdir caOmicsV.Rcheck && mkdir caOmicsV.buildbin-libdir caOmicsV.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=caOmicsV.buildbin-libdir caOmicsV_1.6.0.tar.gz >caOmicsV.Rcheck\00install.out 2>&1 && cp caOmicsV.Rcheck\00install.out caOmicsV-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=caOmicsV.buildbin-libdir --install="check:caOmicsV-install.out" --force-multiarch --no-vignettes --timings caOmicsV_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/caOmicsV.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'caOmicsV' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
bioNetLegend             11.57   0.16   11.80
plotBioNetCircos         10.03   0.15   10.17
plotBioNetHeatmap         5.65   0.15    5.81
drawBioNetNodeBackground  5.46   0.14    5.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
bioNetLegend             10.86   0.23   11.09
plotBioNetCircos          8.57   0.16    8.79
plotBioNetHeatmap         5.87   0.11    5.99
drawBioNetNodeBackground  5.07   0.19    5.25
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/caOmicsV.Rcheck/00check.log'
for details.


caOmicsV.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'caOmicsV' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'caOmicsV' as caOmicsV_1.6.0.zip
* DONE (caOmicsV)

caOmicsV.Rcheck/examples_i386/caOmicsV-Ex.timings:

nameusersystemelapsed
CA_OMICS_ENV000
CA_OMICS_NAME000
CA_OMICS_NA_STRING000
CNVDemoData0.030.000.03
RNA2miRNA000
RNASeq0.000.020.02
RNASeqDemoData000
bioMatrixLegend0.360.000.36
bioNetCircosPlot2.880.063.03
bioNetLegend11.57 0.1611.80
biomatrixPlotDemoData000
bionetPlotDemoData0.020.000.02
convertToZScores000
drawBioNetNodeBackground5.460.145.61
eraseBioNetNode2.660.062.72
getBezierCurve000
getBioMatrixDataRowTop0.050.000.04
getBioMatrixPlotParameters0.010.000.02
getBioNetNodeLinkLine000
getBioNetParameters0.410.000.41
getBioNetPlotLocations0.390.000.39
getBioNetSamplePlotPosition000
getCaOmicsVColors000
getCaOmicsVPlotTypes000
getDefaultNaStrings000
getHeatmapColorScales0.010.000.02
getPlotDataSet0.020.020.03
getPlotOmicsData0.010.000.01
getPlotSampleData0.020.000.02
getPlotSummaryData0.060.000.06
getRelatedPlotData0.030.000.03
initializeBioMatrixPlot000
initializeBioNetCircos0.270.010.29
labelBioNetNodeNames2.610.062.67
linkBioNetNodes2.030.042.06
linkBioNetSamples2.030.042.08
methylDemoData000
miRNA000
miRNADemoData0.020.000.01
plotBioMatrix0.810.020.83
plotBioMatrixBars0.010.000.02
plotBioMatrixBinaryData000
plotBioMatrixCategoryData0.020.000.01
plotBioMatrixHeatmap000
plotBioMatrixRowNames0.030.000.03
plotBioMatrixSampleData000
plotBioMatrixSampleNames000
plotBioNetBars3.000.043.05
plotBioNetCircos10.03 0.1510.17
plotBioNetHeatmap5.650.155.81
plotBioNetLines3.740.143.88
plotBioNetPoints3.560.143.70
plotBioNetPolygons3.800.083.87
plotHeatmapColorScale1.370.031.41
resetBioNetNodePlotAreaBoundary000
sampleDemoData000
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea000
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.340.000.34
setBioNetPlotAreaBackground0.050.020.06
setBioNetPlotParameters000
setCaOmicsVColors000
setDefaultNaStrings000
showBioMatrixPlotLayout0.020.000.01
showBioNetNodesLayout1.500.031.53
showSupportedBioNetCircosPlotType000
sortClinicalData0.020.000.02
sortOmicsDataByColumn000
sortOmicsDataByRow0.000.010.02

caOmicsV.Rcheck/examples_x64/caOmicsV-Ex.timings:

nameusersystemelapsed
CA_OMICS_ENV000
CA_OMICS_NAME000
CA_OMICS_NA_STRING000
CNVDemoData0.030.000.03
RNA2miRNA000
RNASeq0.020.000.02
RNASeqDemoData000
bioMatrixLegend0.460.000.47
bioNetCircosPlot2.490.112.59
bioNetLegend10.86 0.2311.09
biomatrixPlotDemoData000
bionetPlotDemoData0.000.020.02
convertToZScores000
drawBioNetNodeBackground5.070.195.25
eraseBioNetNode2.530.032.57
getBezierCurve000
getBioMatrixDataRowTop0.060.000.06
getBioMatrixPlotParameters000
getBioNetNodeLinkLine000
getBioNetParameters0.530.000.53
getBioNetPlotLocations0.30.00.3
getBioNetSamplePlotPosition000
getCaOmicsVColors000
getCaOmicsVPlotTypes0.010.000.01
getDefaultNaStrings000
getHeatmapColorScales000
getPlotDataSet0.020.020.03
getPlotOmicsData0.010.000.02
getPlotSampleData000
getPlotSummaryData0.070.000.07
getRelatedPlotData0.040.000.04
initializeBioMatrixPlot000
initializeBioNetCircos0.330.020.35
labelBioNetNodeNames2.330.012.34
linkBioNetNodes1.640.081.72
linkBioNetSamples2.000.022.02
methylDemoData000
miRNA0.000.010.01
miRNADemoData000
plotBioMatrix0.880.020.89
plotBioMatrixBars0.010.000.02
plotBioMatrixBinaryData000
plotBioMatrixCategoryData0.020.000.01
plotBioMatrixHeatmap000
plotBioMatrixRowNames0.030.000.03
plotBioMatrixSampleData0.010.000.02
plotBioMatrixSampleNames000
plotBioNetBars2.250.002.25
plotBioNetCircos8.570.168.79
plotBioNetHeatmap5.870.115.99
plotBioNetLines4.310.124.59
plotBioNetPoints3.850.133.97
plotBioNetPolygons4.690.144.83
plotHeatmapColorScale1.920.051.97
resetBioNetNodePlotAreaBoundary000
sampleDemoData0.000.010.01
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea000
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.750.030.78
setBioNetPlotAreaBackground0.090.020.11
setBioNetPlotParameters000
setCaOmicsVColors000
setDefaultNaStrings000
showBioMatrixPlotLayout0.020.000.01
showBioNetNodesLayout1.610.071.68
showSupportedBioNetCircosPlotType000
sortClinicalData000
sortOmicsDataByColumn000
sortOmicsDataByRow0.000.010.02