Package: caOmicsV

Version: 1.17.0

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_1.17.0.tar.gz

StartedAt: 2020-01-16 02:30:23 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:33:23 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 180.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: caOmicsV.Rcheck

Warnings: 1

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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_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/caOmicsV.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.17.0’
* 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 ... WARNING
Undocumented code objects:
  ‘getBioMatrixBasePositions’ ‘getBioMatrixColumnPadding’
  ‘getBioMatrixDataAreaWidth’ ‘getBioMatrixGeneLabelWidth’
  ‘getBioMatrixGeneNumber’ ‘getBioMatrixLegendHeight’
  ‘getBioMatrixPhenotypeNumber’ ‘getBioMatrixPlotAreaHeigth’
  ‘getBioMatrixPlotAreaWidth’ ‘getBioMatrixRemarkWidth’
  ‘getBioMatrixRowPadding’ ‘getBioMatrixSampleHeight’
  ‘getBioMatrixSampleIDHeight’ ‘getBioMatrixSampleNumber’
  ‘getBioMatrixSampleWidth’ ‘getBioNetBasePositions’ ‘getBioNetGraph’
  ‘getBioNetNodePaddingScale’ ‘getBioNetNodeParameters’
  ‘getBioNetNodePlotAreaBoundary’ ‘getBioNetNodeRadius’
  ‘getBioNetPlotAreaWidth’ ‘getBioNetPlotSampleWidth’
  ‘getBioNetPlotTotalSample’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 (user + system) or elapsed time > 5s
                          user system elapsed
bioNetLegend             9.744  1.536  20.466
plotBioNetCircos         7.827  0.784   8.717
plotBioNetHeatmap        5.882  0.552   6.694
drawBioNetNodeBackground 5.333  0.570   6.020
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/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	0.001	0.001	0.001
CA_OMICS_NAME	0.001	0.000	0.000
CA_OMICS_NA_STRING	0.000	0.000	0.001
CNVDemoData	0.031	0.013	0.044
RNA2miRNA	0.003	0.004	0.006
RNASeq	0.005	0.004	0.010
RNASeqDemoData	0.003	0.004	0.007
bioMatrixLegend	0.351	0.077	0.429
bioNetCircosPlot	2.137	0.478	2.796
bioNetLegend	9.744	1.536	20.466
biomatrixPlotDemoData	0.005	0.006	0.114
bionetPlotDemoData	0.004	0.004	0.007
convertToZScores	0.010	0.002	0.013
drawBioNetNodeBackground	5.333	0.570	6.020
eraseBioNetNode	2.273	0.355	2.722
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.001	0.001	0.001
getBioMatrixPlotParameters	0.002	0.001	0.003
getBioNetNodeLinkLine	0.001	0.001	0.002
getBioNetParameters	0.496	0.201	0.697
getBioNetPlotLocations	0.534	0.217	0.750
getBioNetSamplePlotPosition	0.001	0.000	0.000
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0.000	0.000	0.001
getDefaultNaStrings	0	0	0
getHeatmapColorScales	0.000	0.000	0.001
getPlotDataSet	0.044	0.014	0.057
getPlotOmicsData	0.014	0.006	0.020
getPlotSampleData	0.004	0.003	0.006
getPlotSummaryData	0.012	0.003	0.015
getRelatedPlotData	0.068	0.006	0.075
initializeBioMatrixPlot	0.000	0.001	0.001
initializeBioNetCircos	0.468	0.222	0.691
labelBioNetNodeNames	1.974	0.307	2.310
linkBioNetNodes	1.643	0.311	1.981
linkBioNetSamples	1.579	0.298	1.914
methylDemoData	0.003	0.004	0.006
miRNA	0.003	0.002	0.004
miRNADemoData	0.002	0.001	0.003
plotBioMatrix	0.756	0.048	0.819
plotBioMatrixBars	0.019	0.001	0.021
plotBioMatrixBinaryData	0.005	0.001	0.006
plotBioMatrixCategoryData	0.005	0.001	0.006
plotBioMatrixHeatmap	0.010	0.003	0.013
plotBioMatrixRowNames	0.024	0.002	0.025
plotBioMatrixSampleData	0.006	0.001	0.007
plotBioMatrixSampleNames	0.003	0.001	0.004
plotBioNetBars	2.165	0.362	2.546
plotBioNetCircos	7.827	0.784	8.717
plotBioNetHeatmap	5.882	0.552	6.694
plotBioNetLines	3.787	0.511	4.530
plotBioNetPoints	3.560	0.467	4.145
plotBioNetPolygons	3.663	0.437	4.206
plotHeatmapColorScale	1.612	0.050	1.705
resetBioNetNodePlotAreaBoundary	0.001	0.000	0.001
sampleDemoData	0.002	0.003	0.005
setBioMatrixBaseCoordinates	0.000	0.000	0.001
setBioMatrixPlotArea	0.002	0.001	0.003
setBioMatrixPlotParameters	0.000	0.000	0.001
setBioNetCircosBasePlotPositions	0.000	0.000	0.001
setBioNetNodeLayout	0.489	0.197	0.687
setBioNetPlotAreaBackground	0.121	0.033	0.156
setBioNetPlotParameters	0.001	0.001	0.000
setCaOmicsVColors	0.001	0.000	0.001
setDefaultNaStrings	0.001	0.000	0.001
showBioMatrixPlotLayout	0.050	0.003	0.070
showBioNetNodesLayout	1.002	0.297	1.315
showSupportedBioNetCircosPlotType	0.001	0.000	0.001
sortClinicalData	0.004	0.002	0.006
sortOmicsDataByColumn	0.003	0.002	0.005
sortOmicsDataByRow	0.006	0.003	0.016