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CHECK report for caOmicsV on tokay1

This page was generated on 2021-05-06 12:30:07 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the caOmicsV package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 233/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.20.0  (landing page)
Henry Zhang
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: RELEASE_3_12
Last Commit: bd4a780
Last Changed Date: 2020-10-27 11:05:49 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: caOmicsV
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:caOmicsV.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings caOmicsV_1.20.0.tar.gz
StartedAt: 2021-05-06 01:07:59 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:11:22 -0400 (Thu, 06 May 2021)
EllapsedTime: 202.6 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: caOmicsV.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:caOmicsV.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings caOmicsV_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/caOmicsV.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.20.0'
* 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 ... 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
* 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
* 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 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 'text'
Undefined global functions or variables:
  col2rgb dist gray grey legend lines palette par 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.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 ... WARNING
Undocumented code objects:
  'getBioMatrixBasePositions' 'getBioMatrixColumnPadding'
  'getBioMatrixDataAreaWidth' 'getBioMatrixGeneLabelWidth'
  'getBioMatrixGeneNumber' 'getBioMatrixLegendHeight'
  'getBioMatrixPhenotypeNumber' 'getBioMatrixPlotAreaHeigth'
  'getBioMatrixPlotAreaWidth' 'getBioMatrixRemarkWidth'
  'getBioMatrixRowPadding' 'getBioMatrixSampleHeight'
  'getBioMatrixSampleIDHeight' 'getBioMatrixSampleNumber'
  'getBioMatrixSampleWidth' 'getBioNetBasePositions' 'getBioNetGraph'
  'getBioNetNodePaddingScale' 'getBioNetNodeParameters'
  'getBioNetNodePlotAreaBoundary' 'getBioNetNodeRadius'
  'getBioNetPlotAreaWidth' 'getBioNetPlotSampleWidth'
  'getBioNetPlotTotalSample'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
bioNetLegend             9.13   0.18    9.32
plotBioNetCircos         8.64   0.20    8.84
plotBioNetHeatmap        5.88   0.13    6.00
drawBioNetNodeBackground 4.97   0.22    5.18
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
bioNetLegend             10.23   0.29   10.52
plotBioNetCircos          8.41   0.21    8.61
plotBioNetHeatmap         5.85   0.17    6.03
drawBioNetNodeBackground  5.30   0.20    5.50
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/caOmicsV.Rcheck/00check.log'
for details.



Installation output

caOmicsV.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/caOmicsV_1.20.0.tar.gz && rm -rf caOmicsV.buildbin-libdir && mkdir caOmicsV.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=caOmicsV.buildbin-libdir caOmicsV_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL caOmicsV_1.20.0.zip && rm caOmicsV_1.20.0.tar.gz caOmicsV_1.20.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  171k  100  171k    0     0  17.6M      0 --:--:-- --:--:-- --:--:-- 20.8M

install for i386

* installing *source* package 'caOmicsV' ...
** using staged installation
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'caOmicsV'
    finding HTML links ... done
    CA_OMICS_ENV                            html  
    CA_OMICS_NAME                           html  
    CA_OMICS_NA_STRING                      html  
    CNVDemoData                             html  
    RNA2miRNA                               html  
    RNASeq                                  html  
    RNASeqDemoData                          html  
    bioMatrixLegend                         html  
    bioNetCircosPlot                        html  
    bioNetLegend                            html  
    biomatrixPlotDemoData                   html  
    bionetPlotDemoData                      html  
    caOmicsV-package                        html  
    convertToZScores                        html  
    drawBioNetNodeBackground                html  
    eraseBioNetNode                         html  
    getBezierCurve                          html  
    getBioMatrixDataRowTop                  html  
    getBioMatrixPlotParameters              html  
    getBioNetNodeLinkLine                   html  
    getBioNetParameters                     html  
    getBioNetPlotLocations                  html  
    getBioNetSamplePlotPosition             html  
    getCaOmicsVColors                       html  
    getCaOmicsVPlotTypes                    html  
    getDefaultNaStrings                     html  
    getHeatmapColorScales                   html  
    getPlotDataSet                          html  
    getPlotOmicsData                        html  
    getPlotSampleData                       html  
    getPlotSummaryData                      html  
    getRelatedPlotData                      html  
    initializeBioMatrixPlot                 html  
    initializeBioNetCircos                  html  
    labelBioNetNodeNames                    html  
    linkBioNetNodes                         html  
    linkBioNetSamples                       html  
    methylDemoData                          html  
    miRNA                                   html  
    miRNADemoData                           html  
    plotBioMatrix                           html  
    plotBioMatrixBars                       html  
    plotBioMatrixBinaryData                 html  
    plotBioMatrixCategoryData               html  
    plotBioMatrixHeatmap                    html  
    plotBioMatrixRowNames                   html  
    plotBioMatrixSampleData                 html  
    plotBioMatrixSampleNames                html  
    plotBioNetBars                          html  
    plotBioNetCircos                        html  
    plotBioNetHeatmap                       html  
    plotBioNetLines                         html  
    plotBioNetPoints                        html  
    plotBioNetPolygons                      html  
    plotHeatmapColorScale                   html  
    resetBioNetNodePlotAreaBoundary         html  
    sampleDemoData                          html  
    setBioMatrixBaseCoordinates             html  
    setBioMatrixPlotArea                    html  
    setBioMatrixPlotParameters              html  
    setBioNetCircosBasePlotPositions        html  
    setBioNetNodeLayout                     html  
    setBioNetPlotAreaBackground             html  
    setBioNetPlotParameters                 html  
    setCaOmicsVColors                       html  
    setDefaultNaStrings                     html  
    showBioMatrixPlotLayout                 html  
    showBioNetNodesLayout                   html  
    showSupportedBioNetCircosPlotType       html  
    sortClinicalData                        html  
    sortOmicsDataByColumn                   html  
    sortOmicsDataByRow                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'caOmicsV' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'caOmicsV' as caOmicsV_1.20.0.zip
* DONE (caOmicsV)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'caOmicsV' successfully unpacked and MD5 sums checked

Tests output


Example timings

caOmicsV.Rcheck/examples_i386/caOmicsV-Ex.timings

nameusersystemelapsed
CA_OMICS_ENV000
CA_OMICS_NAME000
CA_OMICS_NA_STRING000
CNVDemoData0.030.000.03
RNA2miRNA000
RNASeq0.020.000.01
RNASeqDemoData000
bioMatrixLegend0.170.030.21
bioNetCircosPlot2.390.132.93
bioNetLegend9.130.189.32
biomatrixPlotDemoData0.010.000.01
bionetPlotDemoData000
convertToZScores0.020.000.02
drawBioNetNodeBackground4.970.225.18
eraseBioNetNode2.570.032.61
getBezierCurve000
getBioMatrixDataRowTop000
getBioMatrixPlotParameters000
getBioNetNodeLinkLine000
getBioNetParameters0.330.020.35
getBioNetPlotLocations0.350.000.34
getBioNetSamplePlotPosition000
getCaOmicsVColors000
getCaOmicsVPlotTypes000
getDefaultNaStrings000
getHeatmapColorScales000
getPlotDataSet0.030.000.03
getPlotOmicsData0.000.010.02
getPlotSampleData0.000.020.01
getPlotSummaryData000
getRelatedPlotData0.040.000.05
initializeBioMatrixPlot000
initializeBioNetCircos0.290.030.31
labelBioNetNodeNames2.110.052.16
linkBioNetNodes1.700.061.77
linkBioNetSamples1.670.111.78
methylDemoData000
miRNA0.000.020.01
miRNADemoData000
plotBioMatrix0.690.000.69
plotBioMatrixBars0.010.000.02
plotBioMatrixBinaryData0.020.000.01
plotBioMatrixCategoryData000
plotBioMatrixHeatmap0.000.010.02
plotBioMatrixRowNames0.030.000.03
plotBioMatrixSampleData000
plotBioMatrixSampleNames0.020.000.01
plotBioNetBars2.370.052.43
plotBioNetCircos8.640.208.84
plotBioNetHeatmap5.880.136.00
plotBioNetLines3.760.093.86
plotBioNetPoints3.710.093.80
plotBioNetPolygons3.700.193.89
plotHeatmapColorScale1.450.031.49
resetBioNetNodePlotAreaBoundary000
sampleDemoData000
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea000
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.310.030.35
setBioNetPlotAreaBackground0.090.000.09
setBioNetPlotParameters000
setCaOmicsVColors000
setDefaultNaStrings000
showBioMatrixPlotLayout0.050.000.05
showBioNetNodesLayout1.160.061.21
showSupportedBioNetCircosPlotType000
sortClinicalData000
sortOmicsDataByColumn0.010.000.02
sortOmicsDataByRow000

caOmicsV.Rcheck/examples_x64/caOmicsV-Ex.timings

nameusersystemelapsed
CA_OMICS_ENV000
CA_OMICS_NAME000
CA_OMICS_NA_STRING0.020.000.01
CNVDemoData0.000.010.02
RNA2miRNA000
RNASeq0.000.020.02
RNASeqDemoData000
bioMatrixLegend0.150.010.17
bioNetCircosPlot2.130.112.23
bioNetLegend10.23 0.2910.52
biomatrixPlotDemoData0.020.000.01
bionetPlotDemoData000
convertToZScores0.000.010.02
drawBioNetNodeBackground5.30.25.5
eraseBioNetNode2.960.083.05
getBezierCurve000
getBioMatrixDataRowTop0.020.000.01
getBioMatrixPlotParameters000
getBioNetNodeLinkLine000
getBioNetParameters0.280.000.28
getBioNetPlotLocations0.30.00.3
getBioNetSamplePlotPosition000
getCaOmicsVColors000
getCaOmicsVPlotTypes000
getDefaultNaStrings000
getHeatmapColorScales000
getPlotDataSet0.030.000.03
getPlotOmicsData0.020.000.02
getPlotSampleData000
getPlotSummaryData0.000.020.01
getRelatedPlotData0.040.000.05
initializeBioMatrixPlot000
initializeBioNetCircos0.410.030.44
labelBioNetNodeNames2.050.062.11
linkBioNetNodes1.600.081.68
linkBioNetSamples1.650.031.68
methylDemoData000
miRNA0.000.020.01
miRNADemoData000
plotBioMatrix0.70.00.7
plotBioMatrixBars0.020.000.02
plotBioMatrixBinaryData000
plotBioMatrixCategoryData000
plotBioMatrixHeatmap0.020.000.01
plotBioMatrixRowNames0.030.000.03
plotBioMatrixSampleData000
plotBioMatrixSampleNames000
plotBioNetBars2.300.012.31
plotBioNetCircos8.410.218.61
plotBioNetHeatmap5.850.176.03
plotBioNetLines4.220.094.31
plotBioNetPoints4.530.084.61
plotBioNetPolygons3.750.143.89
plotHeatmapColorScale1.580.031.61
resetBioNetNodePlotAreaBoundary000
sampleDemoData000
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea0.020.000.02
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.420.020.44
setBioNetPlotAreaBackground0.080.000.07
setBioNetPlotParameters000
setCaOmicsVColors000
setDefaultNaStrings000
showBioMatrixPlotLayout0.050.000.05
showBioNetNodesLayout1.120.031.16
showSupportedBioNetCircosPlotType000
sortClinicalData000
sortOmicsDataByColumn0.020.000.01
sortOmicsDataByRow000