BioC 3.3: CHECK report for caOmicsV on morelia

Package: caOmicsV

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.1.0.tar.gz

StartedAt: 2016-04-20 23:57:31 -0700 (Wed, 20 Apr 2016)

EndedAt: 2016-04-20 23:59:27 -0700 (Wed, 20 Apr 2016)

EllapsedTime: 116.2 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/caOmicsV.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.1.0’
* 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 ... [5s/5s] 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 ... [55s/56s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
bioNetLegend      7.298  0.381   7.748
plotBioNetCircos  6.956  0.344   7.345
plotBioNetHeatmap 5.038  0.245   5.316
* 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-3.3-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	0.000	0.000	0.001
CA_OMICS_NA_STRING	0.001	0.000	0.001
CNVDemoData	0.018	0.002	0.021
RNA2miRNA	0.002	0.000	0.002
RNASeq	0.004	0.004	0.008
RNASeqDemoData	0.003	0.001	0.003
bioMatrixLegend	0.327	0.010	0.337
bioNetCircosPlot	1.868	0.169	2.076
bioNetLegend	7.298	0.381	7.748
biomatrixPlotDemoData	0.004	0.001	0.005
bionetPlotDemoData	0.003	0.001	0.005
convertToZScores	0.008	0.001	0.009
drawBioNetNodeBackground	4.342	0.230	4.605
eraseBioNetNode	2.075	0.149	2.257
getBezierCurve	0.002	0.000	0.002
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.003	0.000	0.003
getBioNetNodeLinkLine	0.001	0.000	0.001
getBioNetParameters	0.499	0.079	0.578
getBioNetPlotLocations	0.421	0.087	0.508
getBioNetSamplePlotPosition	0.001	0.000	0.001
getCaOmicsVColors	0.001	0.001	0.000
getCaOmicsVPlotTypes	0.001	0.000	0.000
getDefaultNaStrings	0.001	0.000	0.001
getHeatmapColorScales	0	0	0
getPlotDataSet	0.027	0.005	0.031
getPlotOmicsData	0.011	0.007	0.018
getPlotSampleData	0.004	0.001	0.005
getPlotSummaryData	0.010	0.002	0.012
getRelatedPlotData	0.072	0.006	0.078
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.501	0.090	0.593
labelBioNetNodeNames	1.866	0.147	2.045
linkBioNetNodes	1.505	0.137	1.679
linkBioNetSamples	1.444	0.142	1.624
methylDemoData	0.002	0.001	0.002
miRNA	0.002	0.000	0.002
miRNADemoData	0.002	0.000	0.003
plotBioMatrix	0.638	0.018	0.688
plotBioMatrixBars	0.014	0.001	0.017
plotBioMatrixBinaryData	0.005	0.000	0.005
plotBioMatrixCategoryData	0.004	0.001	0.004
plotBioMatrixHeatmap	0.008	0.002	0.010
plotBioMatrixRowNames	0.021	0.001	0.022
plotBioMatrixSampleData	0.006	0.001	0.007
plotBioMatrixSampleNames	0.004	0.001	0.004
plotBioNetBars	1.812	0.147	2.313
plotBioNetCircos	6.956	0.344	7.345
plotBioNetHeatmap	5.038	0.245	5.316
plotBioNetLines	3.368	0.181	3.591
plotBioNetPoints	3.143	0.183	3.358
plotBioNetPolygons	3.178	0.177	3.396
plotHeatmapColorScale	1.366	0.029	1.461
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.001	0.001	0.002
setBioMatrixBaseCoordinates	0.001	0.000	0.000
setBioMatrixPlotArea	0.002	0.001	0.004
setBioMatrixPlotParameters	0.000	0.000	0.001
setBioNetCircosBasePlotPositions	0	0	0
setBioNetNodeLayout	0.461	0.073	0.533
setBioNetPlotAreaBackground	0.087	0.012	0.099
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0	0	0
setDefaultNaStrings	0.001	0.000	0.001
showBioMatrixPlotLayout	0.026	0.001	0.029
showBioNetNodesLayout	1.072	0.128	1.205
showSupportedBioNetCircosPlotType	0	0	0
sortClinicalData	0.003	0.001	0.004
sortOmicsDataByColumn	0.004	0.001	0.004
sortOmicsDataByRow	0.006	0.001	0.007