BioC 3.3: CHECK report for caOmicsV on oaxaca

Package: caOmicsV

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.2.0.tar.gz

StartedAt: 2016-10-12 23:53:14 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 23:55:05 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 111.4 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-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 ‘1.2.0’
* 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      7.760  0.384   8.308
plotBioNetCircos  6.857  0.333   7.350
plotBioNetHeatmap 4.918  0.239   5.190
* 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	0	0
CA_OMICS_NAME	0.000	0.000	0.001
CA_OMICS_NA_STRING	0	0	0
CNVDemoData	0.015	0.003	0.018
RNA2miRNA	0.002	0.001	0.003
RNASeq	0.004	0.011	0.015
RNASeqDemoData	0.002	0.001	0.003
bioMatrixLegend	0.269	0.012	0.282
bioNetCircosPlot	1.908	0.154	2.066
bioNetLegend	7.760	0.384	8.308
biomatrixPlotDemoData	0.003	0.002	0.005
bionetPlotDemoData	0.003	0.001	0.004
convertToZScores	0.008	0.001	0.010
drawBioNetNodeBackground	4.443	0.217	4.690
eraseBioNetNode	2.123	0.146	2.305
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.003	0.001	0.003
getBioNetNodeLinkLine	0.002	0.000	0.002
getBioNetParameters	0.584	0.084	0.668
getBioNetPlotLocations	0.516	0.068	0.585
getBioNetSamplePlotPosition	0.001	0.000	0.001
getCaOmicsVColors	0.001	0.000	0.001
getCaOmicsVPlotTypes	0.001	0.000	0.000
getDefaultNaStrings	0.001	0.000	0.000
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.025	0.005	0.030
getPlotOmicsData	0.011	0.008	0.019
getPlotSampleData	0.003	0.001	0.003
getPlotSummaryData	0.008	0.001	0.009
getRelatedPlotData	0.075	0.004	0.078
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.621	0.087	0.709
labelBioNetNodeNames	1.861	0.140	2.040
linkBioNetNodes	1.426	0.129	1.587
linkBioNetSamples	1.481	0.136	1.651
methylDemoData	0.002	0.001	0.003
miRNA	0.002	0.000	0.002
miRNADemoData	0.001	0.000	0.003
plotBioMatrix	0.663	0.018	0.716
plotBioMatrixBars	0.015	0.001	0.018
plotBioMatrixBinaryData	0.005	0.001	0.005
plotBioMatrixCategoryData	0.005	0.000	0.005
plotBioMatrixHeatmap	0.008	0.001	0.009
plotBioMatrixRowNames	0.021	0.001	0.021
plotBioMatrixSampleData	0.005	0.001	0.005
plotBioMatrixSampleNames	0.003	0.001	0.004
plotBioNetBars	1.912	0.154	2.069
plotBioNetCircos	6.857	0.333	7.350
plotBioNetHeatmap	4.918	0.239	5.190
plotBioNetLines	3.208	0.171	3.413
plotBioNetPoints	3.225	0.182	3.442
plotBioNetPolygons	3.242	0.191	3.468
plotHeatmapColorScale	1.383	0.029	1.493
resetBioNetNodePlotAreaBoundary	0.000	0.000	0.001
sampleDemoData	0.002	0.001	0.003
setBioMatrixBaseCoordinates	0.001	0.001	0.001
setBioMatrixPlotArea	0.003	0.000	0.004
setBioMatrixPlotParameters	0.001	0.001	0.001
setBioNetCircosBasePlotPositions	0.000	0.000	0.001
setBioNetNodeLayout	0.414	0.079	0.495
setBioNetPlotAreaBackground	0.083	0.010	0.094
setBioNetPlotParameters	0.001	0.000	0.000
setCaOmicsVColors	0.000	0.000	0.001
setDefaultNaStrings	0.001	0.000	0.000
showBioMatrixPlotLayout	0.025	0.001	0.027
showBioNetNodesLayout	0.964	0.117	1.082
showSupportedBioNetCircosPlotType	0.001	0.000	0.000
sortClinicalData	0.003	0.001	0.004
sortOmicsDataByColumn	0.003	0.001	0.004
sortOmicsDataByRow	0.004	0.001	0.005