Package: caOmicsV

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings caOmicsV_1.10.0.tar.gz

StartedAt: 2018-10-16 20:15:39 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:17:38 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 119.8 seconds

RetCode: 0

Status:  OK

CheckDir: caOmicsV.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings caOmicsV_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/caOmicsV.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotBioNetCircos         7.913  0.464   8.449
bioNetLegend             7.237  0.480   7.798
plotBioNetHeatmap        6.034  0.284   6.373
drawBioNetNodeBackground 4.913  0.266   5.221
* 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-3.7-bioc/meat/caOmicsV.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL caOmicsV
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘caOmicsV’ ...
** R
** data
** demo
** inst
** byte-compile and prepare 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	0.002
CA_OMICS_NAME	0.001	0.001	0.001
CA_OMICS_NA_STRING	0.001	0.000	0.001
CNVDemoData	0.022	0.006	0.028
RNA2miRNA	0.003	0.002	0.004
RNASeq	0.005	0.002	0.007
RNASeqDemoData	0.004	0.001	0.004
bioMatrixLegend	0.220	0.032	0.254
bioNetCircosPlot	1.605	0.215	1.837
bioNetLegend	7.237	0.480	7.798
biomatrixPlotDemoData	0.004	0.002	0.006
bionetPlotDemoData	0.004	0.001	0.005
convertToZScores	0.008	0.001	0.009
drawBioNetNodeBackground	4.913	0.266	5.221
eraseBioNetNode	2.107	0.180	2.311
getBezierCurve	0.001	0.001	0.002
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.004	0.000	0.004
getBioNetNodeLinkLine	0.002	0.000	0.002
getBioNetParameters	0.335	0.100	0.444
getBioNetPlotLocations	0.394	0.098	0.494
getBioNetSamplePlotPosition	0.001	0.000	0.001
getCaOmicsVColors	0.001	0.000	0.001
getCaOmicsVPlotTypes	0.001	0.000	0.001
getDefaultNaStrings	0.001	0.000	0.001
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.039	0.009	0.047
getPlotOmicsData	0.011	0.003	0.014
getPlotSampleData	0.003	0.002	0.005
getPlotSummaryData	0.009	0.001	0.010
getRelatedPlotData	0.067	0.004	0.071
initializeBioMatrixPlot	0.003	0.000	0.003
initializeBioNetCircos	0.420	0.113	0.540
labelBioNetNodeNames	1.975	0.168	2.167
linkBioNetNodes	1.462	0.164	1.646
linkBioNetSamples	1.420	0.150	1.584
methylDemoData	0.003	0.001	0.004
miRNA	0.003	0.001	0.004
miRNADemoData	0.002	0.001	0.003
plotBioMatrix	0.748	0.022	0.781
plotBioMatrixBars	0.014	0.002	0.016
plotBioMatrixBinaryData	0.004	0.001	0.004
plotBioMatrixCategoryData	0.006	0.000	0.007
plotBioMatrixHeatmap	0.009	0.002	0.012
plotBioMatrixRowNames	0.022	0.001	0.022
plotBioMatrixSampleData	0.005	0.001	0.006
plotBioMatrixSampleNames	0.005	0.001	0.005
plotBioNetBars	2.072	0.212	2.321
plotBioNetCircos	7.913	0.464	8.449
plotBioNetHeatmap	6.034	0.284	6.373
plotBioNetLines	3.267	0.208	3.502
plotBioNetPoints	3.356	0.236	3.624
plotBioNetPolygons	3.230	0.214	3.474
plotHeatmapColorScale	1.672	0.031	1.718
resetBioNetNodePlotAreaBoundary	0.002	0.000	0.001
sampleDemoData	0.003	0.001	0.005
setBioMatrixBaseCoordinates	0.001	0.001	0.002
setBioMatrixPlotArea	0.003	0.000	0.004
setBioMatrixPlotParameters	0.002	0.000	0.002
setBioNetCircosBasePlotPositions	0.002	0.000	0.001
setBioNetNodeLayout	0.327	0.097	0.425
setBioNetPlotAreaBackground	0.076	0.012	0.088
setBioNetPlotParameters	0.001	0.000	0.001
setCaOmicsVColors	0.001	0.000	0.001
setDefaultNaStrings	0.001	0.000	0.001
showBioMatrixPlotLayout	0.017	0.001	0.018
showBioNetNodesLayout	0.884	0.150	1.044
showSupportedBioNetCircosPlotType	0.001	0.000	0.002
sortClinicalData	0.004	0.001	0.005
sortOmicsDataByColumn	0.003	0.001	0.004
sortOmicsDataByRow	0.005	0.001	0.006