BioC 3.6: CHECK report for caOmicsV on malbec1

Package: caOmicsV

Version: 1.7.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.7.0.tar.gz

StartedAt: 2017-08-15 21:45:20 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:47:05 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 105.2 seconds

RetCode: 0

Status:  OK

CheckDir: caOmicsV.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘1.7.0’
* 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  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
* 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      8.308  0.124   8.440
plotBioNetCircos  7.356  0.052   7.412
plotBioNetHeatmap 5.036  0.052   5.093
* 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-3.6-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	0.012	0.008	0.021
RNA2miRNA	0.004	0.000	0.001
RNASeq	0.004	0.000	0.003
RNASeqDemoData	0.000	0.000	0.002
bioMatrixLegend	0.336	0.004	0.343
bioNetCircosPlot	2.124	0.036	2.172
bioNetLegend	8.308	0.124	8.440
biomatrixPlotDemoData	0.004	0.000	0.028
bionetPlotDemoData	0.004	0.000	0.004
convertToZScores	0.008	0.000	0.007
drawBioNetNodeBackground	4.436	0.056	4.494
eraseBioNetNode	2.040	0.020	2.059
getBezierCurve	0.000	0.000	0.001
getBioMatrixDataRowTop	0.052	0.000	0.052
getBioMatrixPlotParameters	0.000	0.000	0.002
getBioNetNodeLinkLine	0.004	0.000	0.001
getBioNetParameters	0.376	0.000	0.375
getBioNetPlotLocations	0.236	0.000	0.236
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0.004	0.000	0.000
getDefaultNaStrings	0	0	0
getHeatmapColorScales	0.000	0.000	0.001
getPlotDataSet	0.020	0.000	0.017
getPlotOmicsData	0.008	0.000	0.007
getPlotSampleData	0.000	0.000	0.003
getPlotSummaryData	0.056	0.000	0.058
getRelatedPlotData	0.032	0.004	0.035
initializeBioMatrixPlot	0.000	0.000	0.001
initializeBioNetCircos	0.244	0.000	0.244
labelBioNetNodeNames	1.896	0.020	1.919
linkBioNetNodes	1.460	0.008	1.467
linkBioNetSamples	1.592	0.012	1.606
methylDemoData	0.000	0.000	0.001
miRNA	0.004	0.000	0.002
miRNADemoData	0.000	0.000	0.001
plotBioMatrix	0.712	0.008	0.720
plotBioMatrixBars	0.008	0.000	0.011
plotBioMatrixBinaryData	0.000	0.000	0.002
plotBioMatrixCategoryData	0.000	0.000	0.003
plotBioMatrixHeatmap	0.004	0.000	0.006
plotBioMatrixRowNames	0.012	0.000	0.011
plotBioMatrixSampleData	0.004	0.000	0.004
plotBioMatrixSampleNames	0.004	0.000	0.003
plotBioNetBars	1.912	0.020	1.932
plotBioNetCircos	7.356	0.052	7.412
plotBioNetHeatmap	5.036	0.052	5.093
plotBioNetLines	3.600	0.032	3.646
plotBioNetPoints	4.180	0.036	4.218
plotBioNetPolygons	3.128	0.036	3.167
plotHeatmapColorScale	1.396	0.012	1.406
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.000	0.000	0.001
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.000	0.000	0.002
setBioMatrixPlotParameters	0.004	0.000	0.001
setBioNetCircosBasePlotPositions	0.000	0.000	0.001
setBioNetNodeLayout	0.356	0.004	0.361
setBioNetPlotAreaBackground	0.068	0.000	0.065
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0	0	0
setDefaultNaStrings	0	0	0
showBioMatrixPlotLayout	0.008	0.000	0.012
showBioNetNodesLayout	0.876	0.004	0.883
showSupportedBioNetCircosPlotType	0.004	0.000	0.000
sortClinicalData	0.000	0.000	0.002
sortOmicsDataByColumn	0.004	0.000	0.002
sortOmicsDataByRow	0.004	0.000	0.003