BioC 3.4: CHECK report for caOmicsV on morelia

Package: caOmicsV

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.3.0.tar.gz

StartedAt: 2016-09-20 04:03:01 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:04:25 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 84.3 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/caOmicsV.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.0’
* 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     5.232  0.215   5.486
plotBioNetCircos 5.131  0.236   5.400
* 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	0.000	0.000
CA_OMICS_NAME	0.001	0.000	0.000
CA_OMICS_NA_STRING	0	0	0
CNVDemoData	0.018	0.003	0.021
RNA2miRNA	0.002	0.001	0.002
RNASeq	0.004	0.004	0.008
RNASeqDemoData	0.002	0.001	0.003
bioMatrixLegend	0.251	0.015	0.266
bioNetCircosPlot	1.343	0.102	1.472
bioNetLegend	5.232	0.215	5.486
biomatrixPlotDemoData	0.003	0.001	0.035
bionetPlotDemoData	0.002	0.001	0.003
convertToZScores	0.004	0.000	0.005
drawBioNetNodeBackground	3.545	0.156	3.733
eraseBioNetNode	1.718	0.119	1.866
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.001	0.000	0.002
getBioMatrixPlotParameters	0.004	0.001	0.003
getBioNetNodeLinkLine	0.001	0.000	0.002
getBioNetParameters	0.424	0.060	0.484
getBioNetPlotLocations	0.358	0.047	0.404
getBioNetSamplePlotPosition	0.000	0.000	0.001
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0	0	0
getDefaultNaStrings	0.001	0.000	0.001
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.018	0.003	0.021
getPlotOmicsData	0.007	0.003	0.010
getPlotSampleData	0.002	0.001	0.002
getPlotSummaryData	0.006	0.001	0.007
getRelatedPlotData	0.043	0.005	0.049
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.470	0.064	0.534
labelBioNetNodeNames	1.407	0.098	1.535
linkBioNetNodes	1.091	0.091	1.216
linkBioNetSamples	1.065	0.090	1.491
methylDemoData	0.001	0.001	0.002
miRNA	0.002	0.001	0.002
miRNADemoData	0.002	0.000	0.002
plotBioMatrix	0.567	0.013	0.609
plotBioMatrixBars	0.014	0.001	0.016
plotBioMatrixBinaryData	0.004	0.001	0.005
plotBioMatrixCategoryData	0.004	0.000	0.004
plotBioMatrixHeatmap	0.006	0.001	0.007
plotBioMatrixRowNames	0.023	0.000	0.024
plotBioMatrixSampleData	0.005	0.000	0.005
plotBioMatrixSampleNames	0.003	0.001	0.004
plotBioNetBars	1.442	0.119	1.561
plotBioNetCircos	5.131	0.236	5.400
plotBioNetHeatmap	4.108	0.170	4.309
plotBioNetLines	2.560	0.125	2.722
plotBioNetPoints	2.670	0.144	2.848
plotBioNetPolygons	2.548	0.137	2.736
plotHeatmapColorScale	1.136	0.021	1.414
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.001	0.001	0.002
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.001	0.000	0.002
setBioMatrixPlotParameters	0.001	0.001	0.000
setBioNetCircosBasePlotPositions	0.001	0.000	0.001
setBioNetNodeLayout	0.260	0.054	0.314
setBioNetPlotAreaBackground	0.066	0.008	0.074
setBioNetPlotParameters	0.001	0.000	0.000
setCaOmicsVColors	0.001	0.000	0.001
setDefaultNaStrings	0.001	0.000	0.001
showBioMatrixPlotLayout	0.024	0.001	0.026
showBioNetNodesLayout	0.745	0.084	0.829
showSupportedBioNetCircosPlotType	0	0	0
sortClinicalData	0.002	0.001	0.003
sortOmicsDataByColumn	0.002	0.000	0.002
sortOmicsDataByRow	0.003	0.000	0.003