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BioC 3.5: CHECK report for caOmicsV on veracruz2

This page was generated on 2017-10-18 14:33:22 -0400 (Wed, 18 Oct 2017).

Package 172/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.6.0
Henry Zhang
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/caOmicsV
Branch: RELEASE_3_5
Last Commit: 534bcd6
Last Changed Date: 2017-04-24 15:45:44 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.6.0.tar.gz
StartedAt: 2017-10-18 01:21:17 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:23:05 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 108.1 seconds
RetCode: 0
Status:  OK 
CheckDir: caOmicsV.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/caOmicsV.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘caOmicsV’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
* 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     6.867  0.345   7.556
plotBioNetCircos 5.579  0.296   6.227
* 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-3.5-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_ENV0.0010.0000.001
CA_OMICS_NAME0.0010.0000.001
CA_OMICS_NA_STRING0.0000.0000.001
CNVDemoData0.0220.0030.026
RNA2miRNA0.0010.0000.002
RNASeq0.0030.0020.004
RNASeqDemoData0.0020.0010.002
bioMatrixLegend0.4200.0120.442
bioNetCircosPlot1.5930.1571.795
bioNetLegend6.8670.3457.556
biomatrixPlotDemoData0.0020.0010.008
bionetPlotDemoData0.0030.0000.004
convertToZScores0.0060.0010.007
drawBioNetNodeBackground3.9710.2174.376
eraseBioNetNode1.7400.1451.952
getBezierCurve0.0010.0000.001
getBioMatrixDataRowTop0.0630.0000.064
getBioMatrixPlotParameters0.0030.0010.003
getBioNetNodeLinkLine0.0010.0000.002
getBioNetParameters0.4020.0710.492
getBioNetPlotLocations0.3060.0760.395
getBioNetSamplePlotPosition0.0010.0000.001
getCaOmicsVColors000
getCaOmicsVPlotTypes0.0000.0000.001
getDefaultNaStrings0.0000.0000.001
getHeatmapColorScales0.0000.0000.001
getPlotDataSet0.0200.0050.030
getPlotOmicsData0.0090.0020.013
getPlotSampleData0.0030.0010.004
getPlotSummaryData0.0740.0010.084
getRelatedPlotData0.0490.0020.053
initializeBioMatrixPlot0.0010.0000.001
initializeBioNetCircos0.2790.0690.353
labelBioNetNodeNames1.6380.1291.843
linkBioNetNodes1.2840.1281.472
linkBioNetSamples1.2910.1161.527
methylDemoData0.0020.0010.002
miRNA0.0010.0010.002
miRNADemoData0.0010.0000.002
plotBioMatrix0.7700.0170.847
plotBioMatrixBars0.0140.0010.016
plotBioMatrixBinaryData0.0040.0010.005
plotBioMatrixCategoryData0.0040.0000.005
plotBioMatrixHeatmap0.0050.0010.006
plotBioMatrixRowNames0.0180.0000.019
plotBioMatrixSampleData0.0050.0010.005
plotBioMatrixSampleNames0.0040.0010.004
plotBioNetBars1.4280.1371.652
plotBioNetCircos5.5790.2966.227
plotBioNetHeatmap4.5370.2044.881
plotBioNetLines2.3810.1502.588
plotBioNetPoints2.4340.1582.664
plotBioNetPolygons2.5520.1562.845
plotHeatmapColorScale1.2550.0261.346
resetBioNetNodePlotAreaBoundary0.0000.0000.001
sampleDemoData0.0010.0010.002
setBioMatrixBaseCoordinates0.0010.0000.001
setBioMatrixPlotArea0.0020.0010.003
setBioMatrixPlotParameters0.0010.0000.001
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.4250.0760.528
setBioNetPlotAreaBackground0.0630.0100.077
setBioNetPlotParameters000
setCaOmicsVColors0.0010.0000.000
setDefaultNaStrings0.0010.0000.001
showBioMatrixPlotLayout0.0130.0000.014
showBioNetNodesLayout0.6440.1090.790
showSupportedBioNetCircosPlotType0.0010.0000.001
sortClinicalData0.0030.0010.003
sortOmicsDataByColumn0.0030.0010.004
sortOmicsDataByRow0.0040.0000.005