BioC 3.4: CHECK report for caOmicsV on malbec1

Package: caOmicsV

Version: 1.4.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.4.0.tar.gz

StartedAt: 2017-04-14 21:23:52 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:25:29 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 97.2 seconds

RetCode: 0

Status:  OK

CheckDir: caOmicsV.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/caOmicsV.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.0’
* 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 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     7.076  0.072   7.151
plotBioNetCircos 6.788  0.052   6.840
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.4-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	0	0
CNVDemoData	0.012	0.004	0.014
RNA2miRNA	0.004	0.000	0.001
RNASeq	0.004	0.000	0.004
RNASeqDemoData	0.000	0.000	0.001
bioMatrixLegend	0.220	0.000	0.222
bioNetCircosPlot	2.132	0.016	2.162
bioNetLegend	7.076	0.072	7.151
biomatrixPlotDemoData	0.000	0.000	0.002
bionetPlotDemoData	0.000	0.000	0.002
convertToZScores	0.004	0.000	0.004
drawBioNetNodeBackground	3.840	0.048	3.891
eraseBioNetNode	2.060	0.016	2.074
getBezierCurve	0.000	0.000	0.001
getBioMatrixDataRowTop	0	0	0
getBioMatrixPlotParameters	0.000	0.000	0.002
getBioNetNodeLinkLine	0.000	0.000	0.001
getBioNetParameters	0.356	0.000	0.357
getBioNetPlotLocations	0.368	0.000	0.365
getBioNetSamplePlotPosition	0.000	0.000	0.001
getCaOmicsVColors	0.000	0.000	0.001
getCaOmicsVPlotTypes	0	0	0
getDefaultNaStrings	0	0	0
getHeatmapColorScales	0.004	0.000	0.001
getPlotDataSet	0.016	0.000	0.018
getPlotOmicsData	0.004	0.004	0.007
getPlotSampleData	0.004	0.000	0.002
getPlotSummaryData	0.008	0.000	0.006
getRelatedPlotData	0.032	0.000	0.034
initializeBioMatrixPlot	0.000	0.000	0.001
initializeBioNetCircos	0.268	0.000	0.269
labelBioNetNodeNames	1.804	0.020	1.827
linkBioNetNodes	1.456	0.004	1.458
linkBioNetSamples	1.448	0.016	1.467
methylDemoData	0.004	0.000	0.001
miRNA	0.000	0.000	0.002
miRNADemoData	0.000	0.004	0.002
plotBioMatrix	0.504	0.012	0.519
plotBioMatrixBars	0.008	0.000	0.011
plotBioMatrixBinaryData	0.000	0.000	0.003
plotBioMatrixCategoryData	0.000	0.000	0.003
plotBioMatrixHeatmap	0.008	0.000	0.005
plotBioMatrixRowNames	0.012	0.000	0.012
plotBioMatrixSampleData	0.004	0.000	0.003
plotBioMatrixSampleNames	0.004	0.000	0.002
plotBioNetBars	1.896	0.028	1.925
plotBioNetCircos	6.788	0.052	6.840
plotBioNetHeatmap	4.548	0.040	4.589
plotBioNetLines	3.076	0.028	3.105
plotBioNetPoints	3.128	0.020	3.153
plotBioNetPolygons	3.108	0.012	3.121
plotHeatmapColorScale	1.152	0.012	1.164
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.000	0.000	0.001
setBioMatrixBaseCoordinates	0.004	0.000	0.000
setBioMatrixPlotArea	0.000	0.000	0.002
setBioMatrixPlotParameters	0.004	0.000	0.000
setBioNetCircosBasePlotPositions	0	0	0
setBioNetNodeLayout	0.260	0.000	0.259
setBioNetPlotAreaBackground	0.076	0.000	0.075
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0	0	0
setDefaultNaStrings	0	0	0
showBioMatrixPlotLayout	0.016	0.000	0.019
showBioNetNodesLayout	0.992	0.024	1.019
showSupportedBioNetCircosPlotType	0.004	0.000	0.001
sortClinicalData	0.000	0.000	0.002
sortOmicsDataByColumn	0.000	0.004	0.002
sortOmicsDataByRow	0.004	0.000	0.003