Package: caOmicsV

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.8.0.tar.gz

StartedAt: 2018-04-12 01:18:34 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:20:14 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 99.8 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/caOmicsV.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.8.0’
* 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 ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
* 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             6.758  0.281   7.119
plotBioNetCircos         5.508  0.272   5.817
drawBioNetNodeBackground 4.247  0.202   5.024
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-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	0.000	0.000	0.001
CA_OMICS_NA_STRING	0.001	0.000	0.001
CNVDemoData	0.016	0.004	0.024
RNA2miRNA	0.001	0.001	0.003
RNASeq	0.004	0.003	0.006
RNASeqDemoData	0.002	0.001	0.003
bioMatrixLegend	0.304	0.015	0.320
bioNetCircosPlot	1.712	0.164	1.893
bioNetLegend	6.758	0.281	7.119
biomatrixPlotDemoData	0.004	0.001	0.005
bionetPlotDemoData	0.002	0.001	0.003
convertToZScores	0.005	0.002	0.007
drawBioNetNodeBackground	4.247	0.202	5.024
eraseBioNetNode	1.987	0.141	2.708
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.074	0.001	0.090
getBioMatrixPlotParameters	0.003	0.000	0.004
getBioNetNodeLinkLine	0.002	0.000	0.002
getBioNetParameters	0.336	0.076	0.523
getBioNetPlotLocations	0.437	0.080	0.650
getBioNetSamplePlotPosition	0.001	0.000	0.001
getCaOmicsVColors	0.001	0.000	0.000
getCaOmicsVPlotTypes	0.001	0.000	0.001
getDefaultNaStrings	0.001	0.000	0.001
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.028	0.006	0.040
getPlotOmicsData	0.010	0.003	0.020
getPlotSampleData	0.003	0.001	0.004
getPlotSummaryData	0.075	0.002	0.095
getRelatedPlotData	0.055	0.002	0.075
initializeBioMatrixPlot	0.002	0.000	0.002
initializeBioNetCircos	0.433	0.077	0.651
labelBioNetNodeNames	1.704	0.134	1.967
linkBioNetNodes	1.144	0.108	1.263
linkBioNetSamples	1.240	0.114	1.372
methylDemoData	0.002	0.001	0.003
miRNA	0.002	0.001	0.003
miRNADemoData	0.002	0.002	0.003
plotBioMatrix	0.750	0.015	0.780
plotBioMatrixBars	0.012	0.001	0.012
plotBioMatrixBinaryData	0.004	0.000	0.005
plotBioMatrixCategoryData	0.004	0.000	0.005
plotBioMatrixHeatmap	0.008	0.002	0.009
plotBioMatrixRowNames	0.016	0.001	0.017
plotBioMatrixSampleData	0.005	0.000	0.005
plotBioMatrixSampleNames	0.004	0.000	0.004
plotBioNetBars	1.495	0.129	1.646
plotBioNetCircos	5.508	0.272	5.817
plotBioNetHeatmap	4.471	0.214	4.715
plotBioNetLines	2.777	0.148	2.971
plotBioNetPoints	2.576	0.154	2.771
plotBioNetPolygons	2.690	0.157	2.868
plotHeatmapColorScale	1.229	0.024	1.262
resetBioNetNodePlotAreaBoundary	0.000	0.000	0.001
sampleDemoData	0.002	0.000	0.002
setBioMatrixBaseCoordinates	0.000	0.001	0.000
setBioMatrixPlotArea	0.002	0.000	0.003
setBioMatrixPlotParameters	0.000	0.000	0.001
setBioNetCircosBasePlotPositions	0.000	0.000	0.001
setBioNetNodeLayout	0.297	0.073	0.371
setBioNetPlotAreaBackground	0.056	0.008	0.064
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0.001	0.000	0.001
setDefaultNaStrings	0.000	0.000	0.001
showBioMatrixPlotLayout	0.010	0.001	0.012
showBioNetNodesLayout	0.663	0.091	0.764
showSupportedBioNetCircosPlotType	0.001	0.000	0.001
sortClinicalData	0.003	0.001	0.003
sortOmicsDataByColumn	0.003	0.001	0.004
sortOmicsDataByRow	0.003	0.000	0.004