BioC 3.2: CHECK report for caOmicsV on perceval

Package: caOmicsV

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.0.0.tar.gz

StartedAt: 2015-11-10 02:53:24 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:55:35 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 130.9 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/caOmicsV.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.0.0’
* 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 ... [6s/6s] 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 ... OK
* 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 ... [63s/67s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
bioNetLegend             7.755  0.419   8.749
plotBioNetCircos         7.552  0.414   8.537
plotBioNetHeatmap        5.976  0.308   6.507
drawBioNetNodeBackground 5.253  0.280   5.730
* 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: OK

* 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	0.001	0.001
CA_OMICS_NAME	0.000	0.000	0.001
CA_OMICS_NA_STRING	0.000	0.000	0.001
CNVDemoData	0.029	0.003	0.032
RNA2miRNA	0.002	0.000	0.002
RNASeq	0.005	0.006	0.009
RNASeqDemoData	0.003	0.000	0.003
bioMatrixLegend	0.341	0.008	0.350
bioNetCircosPlot	1.981	0.195	2.264
bioNetLegend	7.755	0.419	8.749
biomatrixPlotDemoData	0.004	0.002	0.082
bionetPlotDemoData	0.004	0.001	0.004
convertToZScores	0.008	0.001	0.008
drawBioNetNodeBackground	5.253	0.280	5.730
eraseBioNetNode	2.446	0.198	2.787
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.003	0.001	0.003
getBioNetNodeLinkLine	0.001	0.000	0.002
getBioNetParameters	0.439	0.096	0.536
getBioNetPlotLocations	0.578	0.103	0.682
getBioNetSamplePlotPosition	0.000	0.000	0.001
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0.001	0.000	0.001
getDefaultNaStrings	0.001	0.000	0.000
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.030	0.002	0.031
getPlotOmicsData	0.011	0.004	0.014
getPlotSampleData	0.003	0.000	0.003
getPlotSummaryData	0.011	0.000	0.010
getRelatedPlotData	0.060	0.003	0.064
initializeBioMatrixPlot	0.002	0.000	0.001
initializeBioNetCircos	0.591	0.104	0.695
labelBioNetNodeNames	2.024	0.171	2.240
linkBioNetNodes	1.743	0.169	2.018
linkBioNetSamples	1.751	0.160	2.016
methylDemoData	0.002	0.001	0.002
miRNA	0.002	0.000	0.003
miRNADemoData	0.002	0.000	0.002
plotBioMatrix	0.764	0.020	0.843
plotBioMatrixBars	0.018	0.001	0.020
plotBioMatrixBinaryData	0.005	0.000	0.011
plotBioMatrixCategoryData	0.005	0.001	0.020
plotBioMatrixHeatmap	0.008	0.001	0.010
plotBioMatrixRowNames	0.022	0.001	0.029
plotBioMatrixSampleData	0.005	0.000	0.007
plotBioMatrixSampleNames	0.003	0.000	0.015
plotBioNetBars	2.062	0.185	2.326
plotBioNetCircos	7.552	0.414	8.537
plotBioNetHeatmap	5.976	0.308	6.507
plotBioNetLines	3.750	0.214	4.138
plotBioNetPoints	3.579	0.229	3.986
plotBioNetPolygons	3.680	0.227	4.436
plotHeatmapColorScale	1.685	0.044	1.820
resetBioNetNodePlotAreaBoundary	0.001	0.000	0.001
sampleDemoData	0.002	0.001	0.003
setBioMatrixBaseCoordinates	0.001	0.000	0.001
setBioMatrixPlotArea	0.003	0.001	0.003
setBioMatrixPlotParameters	0.001	0.000	0.001
setBioNetCircosBasePlotPositions	0	0	0
setBioNetNodeLayout	0.578	0.094	0.672
setBioNetPlotAreaBackground	0.090	0.013	0.102
setBioNetPlotParameters	0.001	0.000	0.001
setCaOmicsVColors	0.001	0.000	0.001
setDefaultNaStrings	0.000	0.000	0.001
showBioMatrixPlotLayout	0.029	0.001	0.033
showBioNetNodesLayout	1.110	0.139	1.250
showSupportedBioNetCircosPlotType	0.001	0.000	0.001
sortClinicalData	0.003	0.000	0.003
sortOmicsDataByColumn	0.003	0.000	0.004
sortOmicsDataByRow	0.005	0.001	0.005