BioC 3.5: CHECK report for caOmicsV on toluca2

Package: caOmicsV

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.5.0.tar.gz

StartedAt: 2017-04-23 01:22:33 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 01:24:33 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 119.5 seconds

RetCode: 0

Status:  OK

CheckDir: caOmicsV.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/caOmicsV.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.5.0’
* 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     7.869  0.356   8.238
plotBioNetCircos 6.249  0.322   6.581
* 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
  ‘/Users/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	0.001	0.000	0.001
CA_OMICS_NAME	0.001	0.000	0.001
CA_OMICS_NA_STRING	0.001	0.000	0.000
CNVDemoData	0.019	0.004	0.022
RNA2miRNA	0.002	0.000	0.002
RNASeq	0.004	0.002	0.007
RNASeqDemoData	0.002	0.001	0.002
bioMatrixLegend	0.428	0.010	0.440
bioNetCircosPlot	1.900	0.203	2.109
bioNetLegend	7.869	0.356	8.238
biomatrixPlotDemoData	0.004	0.001	0.005
bionetPlotDemoData	0.003	0.001	0.004
convertToZScores	0.007	0.001	0.008
drawBioNetNodeBackground	3.941	0.215	4.812
eraseBioNetNode	1.810	0.142	2.652
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.085	0.001	0.111
getBioMatrixPlotParameters	0.002	0.000	0.003
getBioNetNodeLinkLine	0.001	0.000	0.002
getBioNetParameters	0.449	0.070	0.698
getBioNetPlotLocations	0.334	0.076	0.551
getBioNetSamplePlotPosition	0.000	0.000	0.001
getCaOmicsVColors	0.001	0.000	0.001
getCaOmicsVPlotTypes	0.001	0.000	0.001
getDefaultNaStrings	0.001	0.000	0.001
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.028	0.004	0.043
getPlotOmicsData	0.010	0.006	0.021
getPlotSampleData	0.002	0.001	0.003
getPlotSummaryData	0.095	0.001	0.128
getRelatedPlotData	0.066	0.002	0.092
initializeBioMatrixPlot	0.001	0.000	0.002
initializeBioNetCircos	0.338	0.076	0.556
labelBioNetNodeNames	1.727	0.132	2.282
linkBioNetNodes	1.245	0.115	1.367
linkBioNetSamples	1.363	0.120	1.490
methylDemoData	0.002	0.001	0.003
miRNA	0.003	0.001	0.003
miRNADemoData	0.002	0.001	0.003
plotBioMatrix	0.768	0.019	0.794
plotBioMatrixBars	0.016	0.002	0.016
plotBioMatrixBinaryData	0.004	0.000	0.004
plotBioMatrixCategoryData	0.005	0.001	0.006
plotBioMatrixHeatmap	0.007	0.002	0.008
plotBioMatrixRowNames	0.021	0.002	0.023
plotBioMatrixSampleData	0.003	0.000	0.004
plotBioMatrixSampleNames	0.003	0.001	0.003
plotBioNetBars	1.631	0.146	1.780
plotBioNetCircos	6.249	0.322	6.581
plotBioNetHeatmap	4.548	0.246	4.801
plotBioNetLines	2.844	0.229	3.082
plotBioNetPoints	2.795	0.172	2.974
plotBioNetPolygons	2.795	0.163	2.966
plotHeatmapColorScale	1.287	0.026	1.320
resetBioNetNodePlotAreaBoundary	0.001	0.000	0.001
sampleDemoData	0.002	0.001	0.003
setBioMatrixBaseCoordinates	0.001	0.000	0.001
setBioMatrixPlotArea	0.002	0.000	0.003
setBioMatrixPlotParameters	0.001	0.000	0.001
setBioNetCircosBasePlotPositions	0.000	0.000	0.001
setBioNetNodeLayout	0.430	0.077	0.508
setBioNetPlotAreaBackground	0.080	0.011	0.092
setBioNetPlotParameters	0.001	0.001	0.001
setCaOmicsVColors	0.001	0.000	0.000
setDefaultNaStrings	0	0	0
showBioMatrixPlotLayout	0.024	0.001	0.025
showBioNetNodesLayout	0.754	0.109	0.869
showSupportedBioNetCircosPlotType	0.000	0.000	0.001
sortClinicalData	0.003	0.001	0.004
sortOmicsDataByColumn	0.002	0.001	0.003
sortOmicsDataByRow	0.006	0.001	0.006