BioC 3.5: CHECK report for caOmicsV on malbec2

Package: caOmicsV

Version: 1.6.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.6.0.tar.gz

StartedAt: 2017-08-15 21:42:36 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:44:23 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 107.3 seconds

RetCode: 0

Status:  OK

CheckDir: caOmicsV.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/caOmicsV.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
* 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 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      9.428  0.088   9.524
plotBioNetCircos  7.112  0.092   7.208
plotBioNetHeatmap 5.328  0.140   5.480
* 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
  ‘/home/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	0	0
CA_OMICS_NAME	0.000	0.000	0.001
CA_OMICS_NA_STRING	0	0	0
CNVDemoData	0.016	0.004	0.021
RNA2miRNA	0.000	0.000	0.001
RNASeq	0.000	0.000	0.003
RNASeqDemoData	0.000	0.000	0.001
bioMatrixLegend	0.336	0.004	0.339
bioNetCircosPlot	2.160	0.040	2.213
bioNetLegend	9.428	0.088	9.524
biomatrixPlotDemoData	0.004	0.000	0.040
bionetPlotDemoData	0.004	0.000	0.005
convertToZScores	0.008	0.000	0.007
drawBioNetNodeBackground	4.776	0.184	4.965
eraseBioNetNode	2.096	0.024	2.123
getBezierCurve	0.000	0.000	0.001
getBioMatrixDataRowTop	0.052	0.000	0.052
getBioMatrixPlotParameters	0.004	0.000	0.002
getBioNetNodeLinkLine	0.000	0.000	0.001
getBioNetParameters	0.500	0.000	0.501
getBioNetPlotLocations	0.400	0.000	0.404
getBioNetSamplePlotPosition	0.000	0.000	0.001
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0	0	0
getDefaultNaStrings	0	0	0
getHeatmapColorScales	0.004	0.000	0.000
getPlotDataSet	0.016	0.000	0.019
getPlotOmicsData	0.008	0.000	0.008
getPlotSampleData	0.004	0.000	0.002
getPlotSummaryData	0.060	0.000	0.062
getRelatedPlotData	0.040	0.000	0.038
initializeBioMatrixPlot	0.000	0.000	0.001
initializeBioNetCircos	0.264	0.000	0.261
labelBioNetNodeNames	1.896	0.012	1.907
linkBioNetNodes	1.592	0.016	1.608
linkBioNetSamples	1.888	0.008	1.897
methylDemoData	0.000	0.000	0.001
miRNA	0.000	0.000	0.002
miRNADemoData	0.004	0.000	0.001
plotBioMatrix	0.880	0.008	0.890
plotBioMatrixBars	0.016	0.000	0.017
plotBioMatrixBinaryData	0.004	0.000	0.005
plotBioMatrixCategoryData	0.004	0.000	0.005
plotBioMatrixHeatmap	0.004	0.004	0.009
plotBioMatrixRowNames	0.020	0.000	0.021
plotBioMatrixSampleData	0.000	0.004	0.006
plotBioMatrixSampleNames	0.004	0.000	0.004
plotBioNetBars	2.028	0.024	2.055
plotBioNetCircos	7.112	0.092	7.208
plotBioNetHeatmap	5.328	0.140	5.480
plotBioNetLines	3.176	0.032	3.211
plotBioNetPoints	3.096	0.028	3.125
plotBioNetPolygons	3.616	0.032	3.649
plotHeatmapColorScale	1.528	0.012	1.542
resetBioNetNodePlotAreaBoundary	0.000	0.000	0.001
sampleDemoData	0.004	0.000	0.003
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.000	0.000	0.002
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0	0	0
setBioNetNodeLayout	0.436	0.008	0.448
setBioNetPlotAreaBackground	0.064	0.000	0.065
setBioNetPlotParameters	0.000	0.000	0.001
setCaOmicsVColors	0.000	0.000	0.001
setDefaultNaStrings	0	0	0
showBioMatrixPlotLayout	0.012	0.000	0.011
showBioNetNodesLayout	1.208	0.012	1.222
showSupportedBioNetCircosPlotType	0.004	0.000	0.001
sortClinicalData	0.004	0.000	0.003
sortOmicsDataByColumn	0.004	0.000	0.004
sortOmicsDataByRow	0.008	0.000	0.006