BioC 3.6: CHECK report for caOmicsV on veracruz1

Package: caOmicsV

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.7.0.tar.gz

StartedAt: 2017-08-16 00:46:27 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:48:08 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 101.5 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 --no-vignettes --timings caOmicsV_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/caOmicsV.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.7.0’
* 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 ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
bioNetLegend     7.169  0.290   8.941
plotBioNetCircos 5.228  0.261   5.595
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/caOmicsV.Rcheck/00check.log’
for details.

* installing *source* package ‘caOmicsV’ ...
** R
** data
** demo
** inst
** preparing 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	0	0
CA_OMICS_NAME	0	0	0
CA_OMICS_NA_STRING	0.001	0.000	0.001
CNVDemoData	0.020	0.004	0.025
RNA2miRNA	0.002	0.001	0.002
RNASeq	0.003	0.001	0.004
RNASeqDemoData	0.002	0.001	0.002
bioMatrixLegend	0.359	0.013	0.385
bioNetCircosPlot	1.497	0.138	1.648
bioNetLegend	7.169	0.290	8.941
biomatrixPlotDemoData	0.003	0.002	0.006
bionetPlotDemoData	0.003	0.001	0.004
convertToZScores	0.007	0.001	0.010
drawBioNetNodeBackground	4.009	0.183	4.512
eraseBioNetNode	1.599	0.110	1.738
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.068	0.000	0.069
getBioMatrixPlotParameters	0.002	0.000	0.002
getBioNetNodeLinkLine	0.002	0.000	0.001
getBioNetParameters	0.350	0.061	0.413
getBioNetPlotLocations	0.236	0.067	0.304
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0.001	0.000	0.000
getCaOmicsVPlotTypes	0.000	0.000	0.001
getDefaultNaStrings	0.001	0.000	0.000
getHeatmapColorScales	0	0	0
getPlotDataSet	0.022	0.006	0.027
getPlotOmicsData	0.007	0.002	0.009
getPlotSampleData	0.003	0.001	0.004
getPlotSummaryData	0.049	0.001	0.050
getRelatedPlotData	0.048	0.002	0.049
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.275	0.066	0.343
labelBioNetNodeNames	1.507	0.109	1.631
linkBioNetNodes	1.135	0.110	1.277
linkBioNetSamples	1.221	0.105	1.353
methylDemoData	0.001	0.000	0.002
miRNA	0.002	0.001	0.002
miRNADemoData	0.002	0.001	0.003
plotBioMatrix	0.735	0.015	0.765
plotBioMatrixBars	0.013	0.001	0.015
plotBioMatrixBinaryData	0.004	0.000	0.005
plotBioMatrixCategoryData	0.003	0.000	0.003
plotBioMatrixHeatmap	0.006	0.001	0.007
plotBioMatrixRowNames	0.017	0.001	0.020
plotBioMatrixSampleData	0.005	0.001	0.005
plotBioMatrixSampleNames	0.003	0.000	0.003
plotBioNetBars	1.254	0.114	1.381
plotBioNetCircos	5.228	0.261	5.595
plotBioNetHeatmap	4.331	0.193	4.585
plotBioNetLines	2.497	0.145	2.682
plotBioNetPoints	2.529	0.145	2.702
plotBioNetPolygons	2.552	0.141	2.752
plotHeatmapColorScale	1.252	0.023	1.298
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.002	0.001	0.003
setBioMatrixBaseCoordinates	0.000	0.000	0.001
setBioMatrixPlotArea	0.002	0.000	0.002
setBioMatrixPlotParameters	0.001	0.000	0.001
setBioNetCircosBasePlotPositions	0.001	0.001	0.000
setBioNetNodeLayout	0.247	0.059	0.309
setBioNetPlotAreaBackground	0.058	0.008	0.067
setBioNetPlotParameters	0.001	0.000	0.001
setCaOmicsVColors	0.000	0.000	0.001
setDefaultNaStrings	0.001	0.000	0.000
showBioMatrixPlotLayout	0.013	0.001	0.014
showBioNetNodesLayout	0.503	0.081	0.586
showSupportedBioNetCircosPlotType	0.000	0.001	0.001
sortClinicalData	0.002	0.000	0.002
sortOmicsDataByColumn	0.001	0.001	0.002
sortOmicsDataByRow	0.003	0.001	0.004