BioC 3.2: CHECK report for caOmicsV on perceval

Package: caOmicsV

Version: 0.99.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_0.99.2.tar.gz

StartedAt: 2015-08-23 22:52:02 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:54:25 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 142.8 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_0.99.2.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 (2015-08-14 r69078)
* 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 ‘0.99.2’
* 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 ... [7s/7s] 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 ... [68s/69s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
bioNetLegend             8.006  0.587   8.691
plotBioNetCircos         7.559  0.537   8.212
plotBioNetHeatmap        6.198  0.476   6.724
drawBioNetNodeBackground 5.356  0.418   5.799
* 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	0.000	0.000	0.001
CA_OMICS_NAME	0.001	0.000	0.001
CA_OMICS_NA_STRING	0.000	0.000	0.001
CNVDemoData	0.030	0.004	0.035
RNA2miRNA	0.002	0.000	0.002
RNASeq	0.005	0.010	0.015
RNASeqDemoData	0.002	0.001	0.002
bioMatrixLegend	0.42	0.01	0.43
bioNetCircosPlot	2.056	0.310	2.379
bioNetLegend	8.006	0.587	8.691
biomatrixPlotDemoData	0.005	0.002	0.028
bionetPlotDemoData	0.003	0.001	0.005
convertToZScores	0.008	0.001	0.009
drawBioNetNodeBackground	5.356	0.418	5.799
eraseBioNetNode	2.507	0.297	2.824
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.001	0.001	0.001
getBioMatrixPlotParameters	0.003	0.000	0.003
getBioNetNodeLinkLine	0.001	0.000	0.002
getBioNetParameters	0.500	0.165	0.666
getBioNetPlotLocations	0.770	0.192	0.963
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	0.031	0.003	0.032
getPlotOmicsData	0.011	0.006	0.017
getPlotSampleData	0.003	0.001	0.004
getPlotSummaryData	0.012	0.001	0.013
getRelatedPlotData	0.074	0.008	0.081
initializeBioMatrixPlot	0.002	0.000	0.002
initializeBioNetCircos	0.812	0.217	1.029
labelBioNetNodeNames	2.184	0.309	2.519
linkBioNetNodes	1.853	0.281	2.166
linkBioNetSamples	1.891	0.255	2.177
methylDemoData	0.003	0.001	0.004
miRNA	0.003	0.001	0.005
miRNADemoData	0.002	0.000	0.002
plotBioMatrix	0.783	0.035	0.837
plotBioMatrixBars	0.017	0.002	0.020
plotBioMatrixBinaryData	0.004	0.000	0.005
plotBioMatrixCategoryData	0.005	0.000	0.006
plotBioMatrixHeatmap	0.009	0.001	0.010
plotBioMatrixRowNames	0.020	0.002	0.022
plotBioMatrixSampleData	0.006	0.001	0.011
plotBioMatrixSampleNames	0.004	0.000	0.005
plotBioNetBars	2.141	0.260	2.422
plotBioNetCircos	7.559	0.537	8.212
plotBioNetHeatmap	6.198	0.476	6.724
plotBioNetLines	3.856	0.343	4.242
plotBioNetPoints	3.743	0.334	4.110
plotBioNetPolygons	3.815	0.339	4.186
plotHeatmapColorScale	1.742	0.064	1.825
resetBioNetNodePlotAreaBoundary	0.001	0.000	0.000
sampleDemoData	0.002	0.000	0.003
setBioMatrixBaseCoordinates	0.001	0.000	0.001
setBioMatrixPlotArea	0.003	0.001	0.004
setBioMatrixPlotParameters	0.000	0.000	0.001
setBioNetCircosBasePlotPositions	0.000	0.001	0.000
setBioNetNodeLayout	0.731	0.157	0.888
setBioNetPlotAreaBackground	0.093	0.019	0.113
setBioNetPlotParameters	0.001	0.001	0.001
setCaOmicsVColors	0.001	0.000	0.000
setDefaultNaStrings	0.001	0.000	0.001
showBioMatrixPlotLayout	0.031	0.002	0.035
showBioNetNodesLayout	1.183	0.219	1.402
showSupportedBioNetCircosPlotType	0.001	0.000	0.001
sortClinicalData	0.003	0.001	0.003
sortOmicsDataByColumn	0.003	0.001	0.004
sortOmicsDataByRow	0.005	0.001	0.005

BioC 3.2: CHECK report for caOmicsV on perceval

Summary

Command output