Package: caOmicsV

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings caOmicsV_1.14.0.tar.gz

StartedAt: 2019-10-16 01:09:37 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:12:15 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 158.2 seconds

RetCode: 0

Status:  OK

CheckDir: caOmicsV.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings caOmicsV_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/caOmicsV.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.14.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
bioNetLegend             8.320  0.977   9.312
plotBioNetCircos         8.314  0.980   9.397
plotBioNetHeatmap        5.804  0.504   6.399
drawBioNetNodeBackground 4.679  0.507   5.239
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/caOmicsV.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL caOmicsV
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘caOmicsV’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (caOmicsV)

name	user	system	elapsed
CA_OMICS_ENV	0.000	0.001	0.001
CA_OMICS_NAME	0.000	0.000	0.001
CA_OMICS_NA_STRING	0.000	0.000	0.001
CNVDemoData	0.030	0.013	0.044
RNA2miRNA	0.002	0.003	0.005
RNASeq	0.006	0.005	0.010
RNASeqDemoData	0.003	0.003	0.006
bioMatrixLegend	0.235	0.066	0.301
bioNetCircosPlot	2.057	0.486	2.546
bioNetLegend	8.320	0.977	9.312
biomatrixPlotDemoData	0.004	0.003	0.007
bionetPlotDemoData	0.003	0.003	0.007
convertToZScores	0.009	0.003	0.012
drawBioNetNodeBackground	4.679	0.507	5.239
eraseBioNetNode	2.507	0.411	2.950
getBezierCurve	0.001	0.001	0.001
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.003	0.001	0.003
getBioNetNodeLinkLine	0.002	0.000	0.001
getBioNetParameters	0.695	0.253	0.950
getBioNetPlotLocations	0.508	0.230	0.739
getBioNetSamplePlotPosition	0.000	0.000	0.001
getCaOmicsVColors	0.001	0.000	0.001
getCaOmicsVPlotTypes	0	0	0
getDefaultNaStrings	0.000	0.000	0.001
getHeatmapColorScales	0.000	0.000	0.001
getPlotDataSet	0.042	0.016	0.060
getPlotOmicsData	0.014	0.006	0.019
getPlotSampleData	0.004	0.003	0.007
getPlotSummaryData	0.011	0.002	0.013
getRelatedPlotData	0.079	0.007	0.086
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.462	0.193	0.655
labelBioNetNodeNames	2.215	0.339	2.591
linkBioNetNodes	1.619	0.334	1.986
linkBioNetSamples	1.744	0.329	2.082
methylDemoData	0.003	0.003	0.006
miRNA	0.004	0.003	0.006
miRNADemoData	0.003	0.003	0.005
plotBioMatrix	0.780	0.041	0.837
plotBioMatrixBars	0.015	0.002	0.019
plotBioMatrixBinaryData	0.005	0.001	0.006
plotBioMatrixCategoryData	0.005	0.001	0.007
plotBioMatrixHeatmap	0.009	0.004	0.014
plotBioMatrixRowNames	0.020	0.001	0.021
plotBioMatrixSampleData	0.006	0.001	0.008
plotBioMatrixSampleNames	0.003	0.001	0.004
plotBioNetBars	2.303	0.416	2.730
plotBioNetCircos	8.314	0.980	9.397
plotBioNetHeatmap	5.804	0.504	6.399
plotBioNetLines	3.607	0.435	4.061
plotBioNetPoints	3.378	0.474	3.868
plotBioNetPolygons	3.448	0.365	3.846
plotHeatmapColorScale	1.508	0.041	1.563
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.002	0.002	0.004
setBioMatrixBaseCoordinates	0.001	0.000	0.001
setBioMatrixPlotArea	0.003	0.001	0.007
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0	0	0
setBioNetNodeLayout	0.582	0.183	0.764
setBioNetPlotAreaBackground	0.102	0.038	0.140
setBioNetPlotParameters	0.001	0.000	0.001
setCaOmicsVColors	0.001	0.001	0.000
setDefaultNaStrings	0.000	0.000	0.001
showBioMatrixPlotLayout	0.049	0.003	0.054
showBioNetNodesLayout	0.903	0.279	1.187
showSupportedBioNetCircosPlotType	0.000	0.000	0.001
sortClinicalData	0.004	0.002	0.006
sortOmicsDataByColumn	0.004	0.002	0.006
sortOmicsDataByRow	0.007	0.003	0.010