Package: caOmicsV

Version: 1.13.1

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_1.13.1.tar.gz

StartedAt: 2019-04-08 23:40:40 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:42:42 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 121.6 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_1.13.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/caOmicsV.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.13.1’
* 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             7.204  0.585   7.829
plotBioNetCircos         6.829  0.517   7.392
plotBioNetHeatmap        6.136  0.432   6.660
drawBioNetNodeBackground 5.132  0.410   5.592
* 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’ ...
** 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	0.001	0.000
CA_OMICS_NAME	0	0	0
CA_OMICS_NA_STRING	0.000	0.000	0.001
CNVDemoData	0.023	0.007	0.031
RNA2miRNA	0.002	0.001	0.004
RNASeq	0.005	0.002	0.007
RNASeqDemoData	0.003	0.001	0.004
bioMatrixLegend	0.205	0.033	0.243
bioNetCircosPlot	1.791	0.308	2.114
bioNetLegend	7.204	0.585	7.829
biomatrixPlotDemoData	0.002	0.002	0.005
bionetPlotDemoData	0.003	0.002	0.005
convertToZScores	0.007	0.001	0.008
drawBioNetNodeBackground	5.132	0.410	5.592
eraseBioNetNode	2.261	0.267	2.553
getBezierCurve	0	0	0
getBioMatrixDataRowTop	0.001	0.001	0.001
getBioMatrixPlotParameters	0.001	0.000	0.002
getBioNetNodeLinkLine	0.001	0.001	0.001
getBioNetParameters	0.389	0.100	0.493
getBioNetPlotLocations	0.329	0.107	0.440
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0.001	0.000	0.000
getDefaultNaStrings	0	0	0
getHeatmapColorScales	0.000	0.000	0.001
getPlotDataSet	0.032	0.007	0.039
getPlotOmicsData	0.011	0.004	0.015
getPlotSampleData	0.003	0.002	0.005
getPlotSummaryData	0.011	0.002	0.013
getRelatedPlotData	0.074	0.002	0.077
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.402	0.106	0.511
labelBioNetNodeNames	2.289	0.167	2.485
linkBioNetNodes	1.536	0.161	1.717
linkBioNetSamples	1.651	0.235	1.911
methylDemoData	0.002	0.002	0.003
miRNA	0.002	0.001	0.004
miRNADemoData	0.002	0.001	0.003
plotBioMatrix	0.794	0.114	0.916
plotBioMatrixBars	0.013	0.001	0.015
plotBioMatrixBinaryData	0.004	0.002	0.005
plotBioMatrixCategoryData	0.005	0.000	0.005
plotBioMatrixHeatmap	0.008	0.002	0.011
plotBioMatrixRowNames	0.022	0.001	0.023
plotBioMatrixSampleData	0.004	0.001	0.005
plotBioMatrixSampleNames	0.003	0.001	0.003
plotBioNetBars	1.820	0.260	2.088
plotBioNetCircos	6.829	0.517	7.392
plotBioNetHeatmap	6.136	0.432	6.660
plotBioNetLines	3.971	0.332	4.452
plotBioNetPoints	3.727	0.335	4.114
plotBioNetPolygons	3.223	0.249	3.509
plotHeatmapColorScale	1.586	0.029	1.626
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.002	0.001	0.004
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.002	0.000	0.003
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0	0	0
setBioNetNodeLayout	0.354	0.099	0.455
setBioNetPlotAreaBackground	0.088	0.014	0.104
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0.000	0.001	0.001
setDefaultNaStrings	0	0	0
showBioMatrixPlotLayout	0.014	0.001	0.014
showBioNetNodesLayout	0.774	0.149	0.939
showSupportedBioNetCircosPlotType	0.000	0.000	0.001
sortClinicalData	0.002	0.001	0.003
sortOmicsDataByColumn	0.002	0.001	0.003
sortOmicsDataByRow	0.004	0.001	0.004