BioC 3.5: CHECK report for caOmicsV on veracruz2

Package: caOmicsV

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.6.0.tar.gz

StartedAt: 2017-08-16 00:36:32 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:38:19 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 106.1 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘1.6.0’
* 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  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
* 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     6.653  0.293   7.323
plotBioNetCircos 5.215  0.270   5.580
* 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-3.5-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	0.001	0.000	0.003
CA_OMICS_NAME	0.001	0.000	0.001
CA_OMICS_NA_STRING	0.000	0.001	0.000
CNVDemoData	0.023	0.004	0.032
RNA2miRNA	0.002	0.001	0.002
RNASeq	0.004	0.001	0.005
RNASeqDemoData	0.002	0.001	0.003
bioMatrixLegend	0.404	0.013	0.531
bioNetCircosPlot	1.753	0.155	2.383
bioNetLegend	6.653	0.293	7.323
biomatrixPlotDemoData	0.002	0.001	0.003
bionetPlotDemoData	0.003	0.002	0.004
convertToZScores	0.004	0.001	0.006
drawBioNetNodeBackground	3.822	0.205	4.075
eraseBioNetNode	1.641	0.121	1.787
getBezierCurve	0.001	0.001	0.001
getBioMatrixDataRowTop	0.05	0.00	0.05
getBioMatrixPlotParameters	0.002	0.000	0.002
getBioNetNodeLinkLine	0.001	0.000	0.001
getBioNetParameters	0.372	0.065	0.443
getBioNetPlotLocations	0.232	0.058	0.297
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0.000	0.000	0.001
getCaOmicsVPlotTypes	0	0	0
getDefaultNaStrings	0.000	0.001	0.000
getHeatmapColorScales	0	0	0
getPlotDataSet	0.015	0.003	0.019
getPlotOmicsData	0.006	0.002	0.007
getPlotSampleData	0.002	0.000	0.003
getPlotSummaryData	0.063	0.001	0.065
getRelatedPlotData	0.044	0.002	0.047
initializeBioMatrixPlot	0.000	0.000	0.001
initializeBioNetCircos	0.263	0.067	0.346
labelBioNetNodeNames	1.572	0.121	1.716
linkBioNetNodes	1.177	0.115	1.305
linkBioNetSamples	1.255	0.103	1.395
methylDemoData	0.002	0.001	0.002
miRNA	0.003	0.001	0.003
miRNADemoData	0.001	0.000	0.002
plotBioMatrix	0.732	0.016	0.761
plotBioMatrixBars	0.014	0.001	0.015
plotBioMatrixBinaryData	0.004	0.001	0.005
plotBioMatrixCategoryData	0.004	0.000	0.005
plotBioMatrixHeatmap	0.004	0.001	0.006
plotBioMatrixRowNames	0.019	0.001	0.020
plotBioMatrixSampleData	0.004	0.000	0.004
plotBioMatrixSampleNames	0.003	0.000	0.002
plotBioNetBars	1.341	0.127	1.485
plotBioNetCircos	5.215	0.270	5.580
plotBioNetHeatmap	4.401	0.206	4.664
plotBioNetLines	2.516	0.152	2.709
plotBioNetPoints	2.535	0.152	2.717
plotBioNetPolygons	2.574	0.146	2.758
plotHeatmapColorScale	1.268	0.022	1.325
resetBioNetNodePlotAreaBoundary	0.001	0.000	0.000
sampleDemoData	0.002	0.001	0.002
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.002	0.001	0.002
setBioMatrixPlotParameters	0.001	0.000	0.001
setBioNetCircosBasePlotPositions	0.001	0.000	0.000
setBioNetNodeLayout	0.269	0.069	0.338
setBioNetPlotAreaBackground	0.060	0.008	0.069
setBioNetPlotParameters	0.001	0.000	0.000
setCaOmicsVColors	0.001	0.000	0.001
setDefaultNaStrings	0.000	0.000	0.001
showBioMatrixPlotLayout	0.013	0.001	0.014
showBioNetNodesLayout	0.637	0.094	0.734
showSupportedBioNetCircosPlotType	0.000	0.000	0.001
sortClinicalData	0.002	0.000	0.003
sortOmicsDataByColumn	0.003	0.001	0.004
sortOmicsDataByRow	0.003	0.001	0.003