Package: caOmicsV

Version: 1.16.0

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_1.16.0.tar.gz

StartedAt: 2020-04-15 00:56:32 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:58:39 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 127.3 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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/caOmicsV.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.16.0’
* 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             7.544  0.559   8.171
plotBioNetCircos         6.604  0.525   7.470
plotBioNetHeatmap        5.914  0.432   6.547
drawBioNetNodeBackground 4.846  0.409   5.284
* 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-3.10-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	0.000	0.001
CA_OMICS_NAME	0	0	0
CA_OMICS_NA_STRING	0	0	0
CNVDemoData	0.017	0.006	0.023
RNA2miRNA	0.002	0.001	0.003
RNASeq	0.004	0.002	0.006
RNASeqDemoData	0.002	0.002	0.004
bioMatrixLegend	0.238	0.038	0.277
bioNetCircosPlot	1.751	0.289	2.055
bioNetLegend	7.544	0.559	8.171
biomatrixPlotDemoData	0.002	0.002	0.004
bionetPlotDemoData	0.002	0.001	0.003
convertToZScores	0.007	0.001	0.009
drawBioNetNodeBackground	4.846	0.409	5.284
eraseBioNetNode	2.186	0.297	2.519
getBezierCurve	0.001	0.000	0.000
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.002	0.000	0.001
getBioNetNodeLinkLine	0.001	0.001	0.001
getBioNetParameters	0.373	0.098	0.480
getBioNetPlotLocations	0.373	0.104	0.487
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0.000	0.000	0.001
getCaOmicsVPlotTypes	0.001	0.000	0.000
getDefaultNaStrings	0	0	0
getHeatmapColorScales	0.001	0.000	0.000
getPlotDataSet	0.034	0.008	0.043
getPlotOmicsData	0.010	0.004	0.013
getPlotSampleData	0.002	0.001	0.003
getPlotSummaryData	0.011	0.001	0.013
getRelatedPlotData	0.062	0.008	0.071
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.385	0.101	0.494
labelBioNetNodeNames	1.773	0.170	2.172
linkBioNetNodes	1.443	0.163	1.616
linkBioNetSamples	1.450	0.248	1.717
methylDemoData	0.002	0.002	0.004
miRNA	0.003	0.002	0.004
miRNADemoData	0.002	0.001	0.003
plotBioMatrix	0.717	0.055	0.782
plotBioMatrixBars	0.016	0.002	0.018
plotBioMatrixBinaryData	0.005	0.001	0.006
plotBioMatrixCategoryData	0.003	0.000	0.003
plotBioMatrixHeatmap	0.007	0.001	0.008
plotBioMatrixRowNames	0.019	0.001	0.020
plotBioMatrixSampleData	0.003	0.001	0.004
plotBioMatrixSampleNames	0.003	0.000	0.004
plotBioNetBars	1.537	0.232	1.774
plotBioNetCircos	6.604	0.525	7.470
plotBioNetHeatmap	5.914	0.432	6.547
plotBioNetLines	3.492	0.315	4.037
plotBioNetPoints	3.046	0.324	3.531
plotBioNetPolygons	3.057	0.275	3.613
plotHeatmapColorScale	1.575	0.044	1.646
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.001	0.001	0.002
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.002	0.000	0.004
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0.000	0.000	0.001
setBioNetNodeLayout	0.365	0.106	0.475
setBioNetPlotAreaBackground	0.087	0.016	0.102
setBioNetPlotParameters	0.000	0.000	0.001
setCaOmicsVColors	0.000	0.000	0.001
setDefaultNaStrings	0.000	0.001	0.001
showBioMatrixPlotLayout	0.049	0.001	0.052
showBioNetNodesLayout	0.975	0.156	1.302
showSupportedBioNetCircosPlotType	0.000	0.000	0.001
sortClinicalData	0.002	0.001	0.003
sortOmicsDataByColumn	0.002	0.001	0.003
sortOmicsDataByRow	0.006	0.001	0.007