BioC 3.4: CHECK report for caOmicsV on morelia

Package: caOmicsV

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.4.0.tar.gz

StartedAt: 2017-04-14 23:31:55 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:33:34 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 99.4 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/caOmicsV.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.0’
* 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 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     6.367  0.308   6.995
plotBioNetCircos 5.636  0.265   5.960
* 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-3.4-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	0.001	0.001	0.001
CA_OMICS_NAME	0.001	0.000	0.003
CA_OMICS_NA_STRING	0.001	0.000	0.001
CNVDemoData	0.036	0.003	0.040
RNA2miRNA	0.002	0.001	0.003
RNASeq	0.004	0.007	0.011
RNASeqDemoData	0.002	0.001	0.005
bioMatrixLegend	0.329	0.010	0.363
bioNetCircosPlot	1.896	0.171	2.235
bioNetLegend	6.367	0.308	6.995
biomatrixPlotDemoData	0.004	0.002	0.039
bionetPlotDemoData	0.003	0.001	0.005
convertToZScores	0.008	0.002	0.009
drawBioNetNodeBackground	3.697	0.176	3.924
eraseBioNetNode	1.714	0.120	1.875
getBezierCurve	0.000	0.000	0.001
getBioMatrixDataRowTop	0.001	0.000	0.000
getBioMatrixPlotParameters	0.001	0.001	0.002
getBioNetNodeLinkLine	0.001	0.000	0.001
getBioNetParameters	0.459	0.071	0.531
getBioNetPlotLocations	0.430	0.075	0.505
getBioNetSamplePlotPosition	0.001	0.000	0.000
getCaOmicsVColors	0.001	0.000	0.001
getCaOmicsVPlotTypes	0.001	0.000	0.000
getDefaultNaStrings	0	0	0
getHeatmapColorScales	0.000	0.000	0.001
getPlotDataSet	0.020	0.004	0.023
getPlotOmicsData	0.008	0.005	0.013
getPlotSampleData	0.003	0.001	0.004
getPlotSummaryData	0.010	0.001	0.011
getRelatedPlotData	0.064	0.009	0.072
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.321	0.074	0.395
labelBioNetNodeNames	1.535	0.110	1.679
linkBioNetNodes	1.279	0.115	1.431
linkBioNetSamples	1.284	0.101	1.445
methylDemoData	0.002	0.001	0.002
miRNA	0.001	0.001	0.003
miRNADemoData	0.002	0.000	0.002
plotBioMatrix	0.531	0.016	0.580
plotBioMatrixBars	0.013	0.001	0.015
plotBioMatrixBinaryData	0.004	0.000	0.005
plotBioMatrixCategoryData	0.004	0.001	0.005
plotBioMatrixHeatmap	0.008	0.002	0.010
plotBioMatrixRowNames	0.015	0.000	0.016
plotBioMatrixSampleData	0.004	0.000	0.004
plotBioMatrixSampleNames	0.002	0.001	0.002
plotBioNetBars	1.459	0.111	1.581
plotBioNetCircos	5.636	0.265	5.960
plotBioNetHeatmap	4.408	0.205	4.648
plotBioNetLines	2.749	0.149	3.017
plotBioNetPoints	2.659	0.145	2.865
plotBioNetPolygons	2.784	0.152	2.995
plotHeatmapColorScale	1.267	0.023	1.341
resetBioNetNodePlotAreaBoundary	0.001	0.000	0.000
sampleDemoData	0.001	0.001	0.002
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.002	0.001	0.006
setBioMatrixPlotParameters	0.001	0.000	0.000
setBioNetCircosBasePlotPositions	0	0	0
setBioNetNodeLayout	0.336	0.076	0.412
setBioNetPlotAreaBackground	0.073	0.008	0.082
setBioNetPlotParameters	0.001	0.000	0.000
setCaOmicsVColors	0.001	0.000	0.000
setDefaultNaStrings	0.000	0.000	0.001
showBioMatrixPlotLayout	0.026	0.001	0.027
showBioNetNodesLayout	0.825	0.092	0.918
showSupportedBioNetCircosPlotType	0	0	0
sortClinicalData	0.002	0.001	0.003
sortOmicsDataByColumn	0.002	0.001	0.002
sortOmicsDataByRow	0.005	0.000	0.005