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: 2017-10-18 01:21:17 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:23:05 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 108.1 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 3.4.2 (2017-09-28)
* 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  5.3Mb
  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     6.867  0.345   7.556
plotBioNetCircos 5.579  0.296   6.227
* 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	0.001
CA_OMICS_NAME	0.001	0.000	0.001
CA_OMICS_NA_STRING	0.000	0.000	0.001
CNVDemoData	0.022	0.003	0.026
RNA2miRNA	0.001	0.000	0.002
RNASeq	0.003	0.002	0.004
RNASeqDemoData	0.002	0.001	0.002
bioMatrixLegend	0.420	0.012	0.442
bioNetCircosPlot	1.593	0.157	1.795
bioNetLegend	6.867	0.345	7.556
biomatrixPlotDemoData	0.002	0.001	0.008
bionetPlotDemoData	0.003	0.000	0.004
convertToZScores	0.006	0.001	0.007
drawBioNetNodeBackground	3.971	0.217	4.376
eraseBioNetNode	1.740	0.145	1.952
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.063	0.000	0.064
getBioMatrixPlotParameters	0.003	0.001	0.003
getBioNetNodeLinkLine	0.001	0.000	0.002
getBioNetParameters	0.402	0.071	0.492
getBioNetPlotLocations	0.306	0.076	0.395
getBioNetSamplePlotPosition	0.001	0.000	0.001
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0.000	0.000	0.001
getDefaultNaStrings	0.000	0.000	0.001
getHeatmapColorScales	0.000	0.000	0.001
getPlotDataSet	0.020	0.005	0.030
getPlotOmicsData	0.009	0.002	0.013
getPlotSampleData	0.003	0.001	0.004
getPlotSummaryData	0.074	0.001	0.084
getRelatedPlotData	0.049	0.002	0.053
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.279	0.069	0.353
labelBioNetNodeNames	1.638	0.129	1.843
linkBioNetNodes	1.284	0.128	1.472
linkBioNetSamples	1.291	0.116	1.527
methylDemoData	0.002	0.001	0.002
miRNA	0.001	0.001	0.002
miRNADemoData	0.001	0.000	0.002
plotBioMatrix	0.770	0.017	0.847
plotBioMatrixBars	0.014	0.001	0.016
plotBioMatrixBinaryData	0.004	0.001	0.005
plotBioMatrixCategoryData	0.004	0.000	0.005
plotBioMatrixHeatmap	0.005	0.001	0.006
plotBioMatrixRowNames	0.018	0.000	0.019
plotBioMatrixSampleData	0.005	0.001	0.005
plotBioMatrixSampleNames	0.004	0.001	0.004
plotBioNetBars	1.428	0.137	1.652
plotBioNetCircos	5.579	0.296	6.227
plotBioNetHeatmap	4.537	0.204	4.881
plotBioNetLines	2.381	0.150	2.588
plotBioNetPoints	2.434	0.158	2.664
plotBioNetPolygons	2.552	0.156	2.845
plotHeatmapColorScale	1.255	0.026	1.346
resetBioNetNodePlotAreaBoundary	0.000	0.000	0.001
sampleDemoData	0.001	0.001	0.002
setBioMatrixBaseCoordinates	0.001	0.000	0.001
setBioMatrixPlotArea	0.002	0.001	0.003
setBioMatrixPlotParameters	0.001	0.000	0.001
setBioNetCircosBasePlotPositions	0	0	0
setBioNetNodeLayout	0.425	0.076	0.528
setBioNetPlotAreaBackground	0.063	0.010	0.077
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0.001	0.000	0.000
setDefaultNaStrings	0.001	0.000	0.001
showBioMatrixPlotLayout	0.013	0.000	0.014
showBioNetNodesLayout	0.644	0.109	0.790
showSupportedBioNetCircosPlotType	0.001	0.000	0.001
sortClinicalData	0.003	0.001	0.003
sortOmicsDataByColumn	0.003	0.001	0.004
sortOmicsDataByRow	0.004	0.000	0.005