Package: caOmicsV

Version: 1.12.1

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_1.12.1.tar.gz

StartedAt: 2019-04-15 22:46:27 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:48:26 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 119.0 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_1.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/caOmicsV.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.1’
* 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             6.995  0.481   7.534
plotBioNetCircos         6.859  0.448   7.375
plotBioNetHeatmap        6.442  0.377   7.009
drawBioNetNodeBackground 4.963  0.252   5.262
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘caOmicsV’ ...
** 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
* DONE (caOmicsV)

name	user	system	elapsed
CA_OMICS_ENV	0.000	0.000	0.001
CA_OMICS_NAME	0	0	0
CA_OMICS_NA_STRING	0.000	0.000	0.001
CNVDemoData	0.018	0.005	0.024
RNA2miRNA	0.002	0.001	0.002
RNASeq	0.003	0.001	0.006
RNASeqDemoData	0.002	0.001	0.004
bioMatrixLegend	0.214	0.035	0.251
bioNetCircosPlot	1.801	0.237	2.057
bioNetLegend	6.995	0.481	7.534
biomatrixPlotDemoData	0.002	0.001	0.003
bionetPlotDemoData	0.003	0.002	0.005
convertToZScores	0.010	0.002	0.011
drawBioNetNodeBackground	4.963	0.252	5.262
eraseBioNetNode	2.204	0.191	2.414
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.001	0.000	0.001
getBioNetNodeLinkLine	0.001	0.000	0.001
getBioNetParameters	0.398	0.105	0.512
getBioNetPlotLocations	0.350	0.097	0.450
getBioNetSamplePlotPosition	0.000	0.001	0.001
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0.001	0.000	0.001
getDefaultNaStrings	0.000	0.001	0.000
getHeatmapColorScales	0	0	0
getPlotDataSet	0.036	0.008	0.045
getPlotOmicsData	0.009	0.004	0.012
getPlotSampleData	0.002	0.001	0.003
getPlotSummaryData	0.008	0.001	0.010
getRelatedPlotData	0.045	0.004	0.049
initializeBioMatrixPlot	0.001	0.000	0.000
initializeBioNetCircos	0.374	0.100	0.477
labelBioNetNodeNames	1.846	0.156	2.025
linkBioNetNodes	1.504	0.173	1.695
linkBioNetSamples	1.493	0.166	1.690
methylDemoData	0.002	0.002	0.004
miRNA	0.002	0.001	0.002
miRNADemoData	0.002	0.001	0.003
plotBioMatrix	0.787	0.040	0.836
plotBioMatrixBars	0.014	0.002	0.014
plotBioMatrixBinaryData	0.003	0.000	0.004
plotBioMatrixCategoryData	0.003	0.001	0.003
plotBioMatrixHeatmap	0.007	0.002	0.008
plotBioMatrixRowNames	0.018	0.001	0.021
plotBioMatrixSampleData	0.005	0.001	0.006
plotBioMatrixSampleNames	0.003	0.001	0.009
plotBioNetBars	1.866	0.181	2.072
plotBioNetCircos	6.859	0.448	7.375
plotBioNetHeatmap	6.442	0.377	7.009
plotBioNetLines	3.794	0.252	4.089
plotBioNetPoints	3.355	0.232	3.639
plotBioNetPolygons	3.472	0.231	3.744
plotHeatmapColorScale	1.698	0.028	1.748
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.002	0.001	0.003
setBioMatrixBaseCoordinates	0.001	0.001	0.000
setBioMatrixPlotArea	0.002	0.000	0.003
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0.001	0.000	0.000
setBioNetNodeLayout	0.411	0.110	0.533
setBioNetPlotAreaBackground	0.080	0.014	0.096
setBioNetPlotParameters	0.000	0.000	0.001
setCaOmicsVColors	0.000	0.000	0.001
setDefaultNaStrings	0.001	0.000	0.001
showBioMatrixPlotLayout	0.015	0.000	0.016
showBioNetNodesLayout	0.890	0.150	1.076
showSupportedBioNetCircosPlotType	0.000	0.001	0.000
sortClinicalData	0.003	0.001	0.005
sortOmicsDataByColumn	0.003	0.001	0.005
sortOmicsDataByRow	0.006	0.001	0.008