BioC 3.3: CHECK report for caOmicsV on zin2

Package: caOmicsV

Version: 1.2.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.2.0.tar.gz

StartedAt: 2016-10-13 00:09:18 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:11:00 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 102.6 seconds

RetCode: 0

Status:  OK

CheckDir: caOmicsV.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/caOmicsV.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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      8.420  0.151   8.789
plotBioNetCircos  8.089  0.103   8.309
plotBioNetHeatmap 5.108  0.191   5.426
* 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
  ‘/home/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	0.000	0.000	0.001
CA_OMICS_NAME	0.001	0.000	0.000
CA_OMICS_NA_STRING	0.000	0.000	0.001
CNVDemoData	0.016	0.000	0.016
RNA2miRNA	0.002	0.000	0.001
RNASeq	0.003	0.000	0.004
RNASeqDemoData	0.002	0.000	0.002
bioMatrixLegend	0.228	0.000	0.227
bioNetCircosPlot	2.310	0.052	2.461
bioNetLegend	8.420	0.151	8.789
biomatrixPlotDemoData	0.004	0.000	0.010
bionetPlotDemoData	0.003	0.000	0.003
convertToZScores	0.001	0.004	0.006
drawBioNetNodeBackground	4.330	0.124	4.591
eraseBioNetNode	2.328	0.027	2.387
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.000	0.000	0.001
getBioMatrixPlotParameters	0.002	0.000	0.002
getBioNetNodeLinkLine	0.002	0.000	0.001
getBioNetParameters	0.474	0.000	0.474
getBioNetPlotLocations	0.405	0.000	0.405
getBioNetSamplePlotPosition	0.000	0.000	0.001
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0.001	0.000	0.000
getDefaultNaStrings	0.000	0.000	0.001
getHeatmapColorScales	0.000	0.000	0.001
getPlotDataSet	0.021	0.000	0.021
getPlotOmicsData	0.008	0.000	0.008
getPlotSampleData	0.002	0.000	0.002
getPlotSummaryData	0.007	0.000	0.007
getRelatedPlotData	0.041	0.000	0.040
initializeBioMatrixPlot	0.000	0.000	0.001
initializeBioNetCircos	0.515	0.001	0.514
labelBioNetNodeNames	2.006	0.028	2.033
linkBioNetNodes	1.799	0.024	1.828
linkBioNetSamples	1.692	0.020	1.718
methylDemoData	0.002	0.000	0.002
miRNA	0.003	0.000	0.002
miRNADemoData	0.001	0.000	0.002
plotBioMatrix	0.627	0.004	0.631
plotBioMatrixBars	0.014	0.000	0.014
plotBioMatrixBinaryData	0.004	0.000	0.004
plotBioMatrixCategoryData	0.003	0.000	0.004
plotBioMatrixHeatmap	0.007	0.000	0.006
plotBioMatrixRowNames	0.017	0.000	0.016
plotBioMatrixSampleData	0.005	0.000	0.004
plotBioMatrixSampleNames	0.002	0.004	0.003
plotBioNetBars	2.360	0.024	2.389
plotBioNetCircos	8.089	0.103	8.309
plotBioNetHeatmap	5.108	0.191	5.426
plotBioNetLines	3.438	0.060	3.522
plotBioNetPoints	3.528	0.055	3.766
plotBioNetPolygons	3.609	0.048	3.724
plotHeatmapColorScale	1.272	0.016	1.290
resetBioNetNodePlotAreaBoundary	0.001	0.000	0.001
sampleDemoData	0.001	0.000	0.002
setBioMatrixBaseCoordinates	0.001	0.000	0.000
setBioMatrixPlotArea	0.003	0.000	0.003
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0.001	0.000	0.001
setBioNetNodeLayout	0.433	0.004	0.438
setBioNetPlotAreaBackground	0.087	0.004	0.092
setBioNetPlotParameters	0.001	0.000	0.001
setCaOmicsVColors	0	0	0
setDefaultNaStrings	0.000	0.000	0.001
showBioMatrixPlotLayout	0.019	0.004	0.023
showBioNetNodesLayout	1.135	0.004	1.139
showSupportedBioNetCircosPlotType	0.001	0.000	0.001
sortClinicalData	0.003	0.000	0.002
sortOmicsDataByColumn	0.002	0.000	0.003
sortOmicsDataByRow	0.004	0.000	0.003