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: 2017-10-17 21:45:35 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 21:47:17 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 102.0 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 3.4.2 (2017-09-28)
* 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  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
* 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      8.208  0.056   8.269
plotBioNetCircos  7.024  0.056   7.088
plotBioNetHeatmap 4.996  0.076   5.077
* 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	0.000	0.000	0.001
CA_OMICS_NAME	0	0	0
CA_OMICS_NA_STRING	0	0	0
CNVDemoData	0.008	0.008	0.014
RNA2miRNA	0.000	0.000	0.002
RNASeq	0.004	0.000	0.004
RNASeqDemoData	0.000	0.000	0.001
bioMatrixLegend	0.328	0.000	0.328
bioNetCircosPlot	2.272	0.016	2.306
bioNetLegend	8.208	0.056	8.269
biomatrixPlotDemoData	0.004	0.000	0.031
bionetPlotDemoData	0.004	0.000	0.004
convertToZScores	0.008	0.000	0.007
drawBioNetNodeBackground	4.660	0.172	4.835
eraseBioNetNode	2.060	0.048	2.109
getBezierCurve	0.000	0.000	0.001
getBioMatrixDataRowTop	0.048	0.000	0.048
getBioMatrixPlotParameters	0.000	0.000	0.002
getBioNetNodeLinkLine	0.004	0.000	0.001
getBioNetParameters	0.356	0.000	0.357
getBioNetPlotLocations	0.240	0.000	0.239
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0.004	0.000	0.000
getCaOmicsVPlotTypes	0	0	0
getDefaultNaStrings	0	0	0
getHeatmapColorScales	0	0	0
getPlotDataSet	0.012	0.004	0.018
getPlotOmicsData	0.008	0.000	0.007
getPlotSampleData	0.004	0.000	0.002
getPlotSummaryData	0.052	0.000	0.054
getRelatedPlotData	0.032	0.004	0.034
initializeBioMatrixPlot	0	0	0
initializeBioNetCircos	0.368	0.000	0.371
labelBioNetNodeNames	1.744	0.024	1.767
linkBioNetNodes	1.436	0.024	1.461
linkBioNetSamples	1.544	0.016	1.564
methylDemoData	0.000	0.000	0.001
miRNA	0.004	0.000	0.001
miRNADemoData	0.000	0.000	0.001
plotBioMatrix	0.708	0.004	0.710
plotBioMatrixBars	0.012	0.000	0.011
plotBioMatrixBinaryData	0.000	0.004	0.003
plotBioMatrixCategoryData	0.004	0.000	0.003
plotBioMatrixHeatmap	0.004	0.000	0.005
plotBioMatrixRowNames	0.012	0.000	0.012
plotBioMatrixSampleData	0.000	0.000	0.003
plotBioMatrixSampleNames	0.000	0.000	0.002
plotBioNetBars	1.800	0.024	1.825
plotBioNetCircos	7.024	0.056	7.088
plotBioNetHeatmap	4.996	0.076	5.077
plotBioNetLines	3.028	0.020	3.048
plotBioNetPoints	3.180	0.048	3.228
plotBioNetPolygons	3.532	0.036	3.572
plotHeatmapColorScale	1.452	0.012	1.468
resetBioNetNodePlotAreaBoundary	0.000	0.000	0.001
sampleDemoData	0.004	0.000	0.003
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.000	0.000	0.003
setBioMatrixPlotParameters	0.000	0.000	0.001
setBioNetCircosBasePlotPositions	0.000	0.000	0.001
setBioNetNodeLayout	0.516	0.000	0.518
setBioNetPlotAreaBackground	0.092	0.000	0.094
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0.000	0.000	0.001
setDefaultNaStrings	0.000	0.000	0.002
showBioMatrixPlotLayout	0.012	0.004	0.015
showBioNetNodesLayout	1.404	0.024	1.430
showSupportedBioNetCircosPlotType	0	0	0
sortClinicalData	0.004	0.000	0.002
sortOmicsDataByColumn	0.004	0.000	0.002
sortOmicsDataByRow	0.004	0.000	0.003