BioC 3.5: CHECK report for caOmicsV on oaxaca

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: 2017-03-04 00:06:48 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 00:08:26 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 97.8 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 r72177)
* 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
plotBioNetCircos 5.822  0.328   6.299
bioNetLegend     5.846  0.278   6.174
* 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	0	0
CA_OMICS_NAME	0.001	0.000	0.001
CA_OMICS_NA_STRING	0.001	0.000	0.000
CNVDemoData	0.022	0.003	0.026
RNA2miRNA	0.001	0.001	0.002
RNASeq	0.005	0.003	0.007
RNASeqDemoData	0.002	0.001	0.003
bioMatrixLegend	0.312	0.007	0.329
bioNetCircosPlot	1.375	0.126	1.626
bioNetLegend	5.846	0.278	6.174
biomatrixPlotDemoData	0.002	0.002	0.068
bionetPlotDemoData	0.002	0.001	0.003
convertToZScores	0.005	0.000	0.005
drawBioNetNodeBackground	3.489	0.155	3.670
eraseBioNetNode	1.660	0.106	1.795
getBezierCurve	0.001	0.001	0.001
getBioMatrixDataRowTop	0.092	0.000	0.093
getBioMatrixPlotParameters	0.003	0.000	0.004
getBioNetNodeLinkLine	0.001	0.000	0.002
getBioNetParameters	0.355	0.058	0.414
getBioNetPlotLocations	0.233	0.057	0.291
getBioNetSamplePlotPosition	0.001	0.000	0.000
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0.000	0.000	0.001
getDefaultNaStrings	0.000	0.000	0.001
getHeatmapColorScales	0	0	0
getPlotDataSet	0.018	0.003	0.021
getPlotOmicsData	0.007	0.003	0.010
getPlotSampleData	0.001	0.001	0.002
getPlotSummaryData	0.057	0.001	0.057
getRelatedPlotData	0.044	0.003	0.048
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.363	0.061	0.424
labelBioNetNodeNames	1.543	0.113	1.687
linkBioNetNodes	1.170	0.111	1.314
linkBioNetSamples	1.342	0.110	1.494
methylDemoData	0.001	0.000	0.002
miRNA	0.002	0.000	0.002
miRNADemoData	0.002	0.001	0.002
plotBioMatrix	0.767	0.016	0.851
plotBioMatrixBars	0.011	0.001	0.034
plotBioMatrixBinaryData	0.003	0.000	0.004
plotBioMatrixCategoryData	0.004	0.000	0.005
plotBioMatrixHeatmap	0.005	0.001	0.006
plotBioMatrixRowNames	0.014	0.000	0.015
plotBioMatrixSampleData	0.004	0.000	0.004
plotBioMatrixSampleNames	0.002	0.001	0.003
plotBioNetBars	1.371	0.135	1.531
plotBioNetCircos	5.822	0.328	6.299
plotBioNetHeatmap	4.309	0.212	4.572
plotBioNetLines	2.931	0.166	3.247
plotBioNetPoints	2.446	0.145	2.656
plotBioNetPolygons	2.727	0.154	3.010
plotHeatmapColorScale	1.326	0.025	1.381
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.001	0.000	0.002
setBioMatrixBaseCoordinates	0.000	0.000	0.001
setBioMatrixPlotArea	0.002	0.001	0.003
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0	0	0
setBioNetNodeLayout	0.238	0.054	0.292
setBioNetPlotAreaBackground	0.055	0.009	0.064
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0	0	0
setDefaultNaStrings	0.001	0.000	0.001
showBioMatrixPlotLayout	0.020	0.001	0.021
showBioNetNodesLayout	0.652	0.080	0.732
showSupportedBioNetCircosPlotType	0.001	0.000	0.000
sortClinicalData	0.002	0.000	0.002
sortOmicsDataByColumn	0.002	0.000	0.003
sortOmicsDataByRow	0.004	0.001	0.004