BioC 3.4: CHECK report for caOmicsV on zin1

Package: caOmicsV

Version: 1.3.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.3.0.tar.gz

StartedAt: 2016-09-20 04:06:04 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:07:38 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 93.7 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_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/caOmicsV.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.0’
* 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 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     7.804  0.100   7.924
plotBioNetCircos 7.456  0.108   7.571
* 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	0.000	0.000	0.001
CA_OMICS_NAME	0	0	0
CA_OMICS_NA_STRING	0	0	0
CNVDemoData	0.012	0.000	0.014
RNA2miRNA	0.000	0.000	0.001
RNASeq	0.004	0.000	0.004
RNASeqDemoData	0.000	0.004	0.002
bioMatrixLegend	0.208	0.008	0.217
bioNetCircosPlot	2.120	0.008	2.138
bioNetLegend	7.804	0.100	7.924
biomatrixPlotDemoData	0.004	0.000	0.019
bionetPlotDemoData	0.004	0.000	0.003
convertToZScores	0.008	0.000	0.005
drawBioNetNodeBackground	4.060	0.048	4.110
eraseBioNetNode	2.132	0.016	2.150
getBezierCurve	0.004	0.000	0.001
getBioMatrixDataRowTop	0.000	0.000	0.001
getBioMatrixPlotParameters	0.004	0.000	0.002
getBioNetNodeLinkLine	0.000	0.000	0.001
getBioNetParameters	0.448	0.000	0.449
getBioNetPlotLocations	0.388	0.000	0.388
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0.000	0.004	0.001
getDefaultNaStrings	0.000	0.000	0.001
getHeatmapColorScales	0	0	0
getPlotDataSet	0.024	0.000	0.021
getPlotOmicsData	0.008	0.000	0.008
getPlotSampleData	0.004	0.000	0.002
getPlotSummaryData	0.004	0.000	0.007
getRelatedPlotData	0.04	0.00	0.04
initializeBioMatrixPlot	0.000	0.000	0.001
initializeBioNetCircos	0.472	0.000	0.472
labelBioNetNodeNames	1.848	0.016	1.864
linkBioNetNodes	1.580	0.000	1.581
linkBioNetSamples	1.592	0.008	1.600
methylDemoData	0.004	0.000	0.001
miRNA	0.000	0.000	0.002
miRNADemoData	0.000	0.000	0.001
plotBioMatrix	0.536	0.008	0.542
plotBioMatrixBars	0.012	0.000	0.012
plotBioMatrixBinaryData	0.004	0.000	0.004
plotBioMatrixCategoryData	0.004	0.000	0.003
plotBioMatrixHeatmap	0.008	0.000	0.006
plotBioMatrixRowNames	0.016	0.000	0.015
plotBioMatrixSampleData	0.004	0.000	0.004
plotBioMatrixSampleNames	0.004	0.000	0.002
plotBioNetBars	2.168	0.028	2.206
plotBioNetCircos	7.456	0.108	7.571
plotBioNetHeatmap	4.756	0.060	4.815
plotBioNetLines	3.364	0.028	3.404
plotBioNetPoints	3.212	0.032	3.243
plotBioNetPolygons	3.328	0.040	3.368
plotHeatmapColorScale	1.132	0.012	1.145
resetBioNetNodePlotAreaBoundary	0.000	0.000	0.001
sampleDemoData	0.000	0.000	0.002
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.004	0.000	0.002
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0.004	0.000	0.000
setBioNetNodeLayout	0.404	0.000	0.403
setBioNetPlotAreaBackground	0.08	0.00	0.08
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0.000	0.000	0.001
setDefaultNaStrings	0	0	0
showBioMatrixPlotLayout	0.020	0.000	0.021
showBioNetNodesLayout	1.140	0.012	1.151
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