BioC 3.3: CHECK report for caOmicsV on morelia

Package: caOmicsV

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings caOmicsV_1.1.0.tar.gz

StartedAt: 2015-10-22 04:09:43 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 04:11:11 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 87.6 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/caOmicsV.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.1.0’
* 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 ... [4s/4s] 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 ... [41s/42s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
bioNetLegend     5.045  0.257   6.232
plotBioNetCircos 4.855  0.230   5.118
* 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	0.000	0.000
CA_OMICS_NAME	0.001	0.000	0.001
CA_OMICS_NA_STRING	0.000	0.000	0.001
CNVDemoData	0.013	0.002	0.015
RNA2miRNA	0.001	0.001	0.001
RNASeq	0.003	0.002	0.006
RNASeqDemoData	0.002	0.001	0.003
bioMatrixLegend	0.212	0.006	0.218
bioNetCircosPlot	1.266	0.113	1.391
bioNetLegend	5.045	0.257	6.232
biomatrixPlotDemoData	0.002	0.001	0.041
bionetPlotDemoData	0.002	0.001	0.003
convertToZScores	0.006	0.000	0.006
drawBioNetNodeBackground	3.430	0.162	3.616
eraseBioNetNode	1.593	0.098	1.726
getBezierCurve	0.001	0.000	0.000
getBioMatrixDataRowTop	0.000	0.000	0.001
getBioMatrixPlotParameters	0.002	0.000	0.002
getBioNetNodeLinkLine	0.001	0.000	0.001
getBioNetParameters	0.384	0.064	0.449
getBioNetPlotLocations	0.267	0.058	0.325
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0.000	0.000	0.001
getCaOmicsVPlotTypes	0	0	0
getDefaultNaStrings	0.001	0.001	0.000
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.018	0.001	0.019
getPlotOmicsData	0.006	0.003	0.009
getPlotSampleData	0.002	0.000	0.002
getPlotSummaryData	0.006	0.001	0.007
getRelatedPlotData	0.039	0.001	0.041
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.350	0.057	0.407
labelBioNetNodeNames	1.380	0.094	1.505
linkBioNetNodes	1.020	0.090	1.142
linkBioNetSamples	1.174	0.108	1.316
methylDemoData	0.001	0.000	0.001
miRNA	0.001	0.000	0.002
miRNADemoData	0.001	0.000	0.001
plotBioMatrix	0.545	0.013	0.590
plotBioMatrixBars	0.015	0.001	0.018
plotBioMatrixBinaryData	0.003	0.000	0.004
plotBioMatrixCategoryData	0.003	0.001	0.005
plotBioMatrixHeatmap	0.006	0.001	0.007
plotBioMatrixRowNames	0.014	0.000	0.014
plotBioMatrixSampleData	0.003	0.001	0.005
plotBioMatrixSampleNames	0.003	0.000	0.002
plotBioNetBars	1.309	0.106	1.416
plotBioNetCircos	4.855	0.230	5.118
plotBioNetHeatmap	3.865	0.177	4.068
plotBioNetLines	2.396	0.123	2.555
plotBioNetPoints	2.590	0.143	2.768
plotBioNetPolygons	2.508	0.138	2.681
plotHeatmapColorScale	1.176	0.022	1.229
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.002	0.001	0.002
setBioMatrixBaseCoordinates	0.001	0.000	0.001
setBioMatrixPlotArea	0.002	0.001	0.003
setBioMatrixPlotParameters	0.001	0.000	0.001
setBioNetCircosBasePlotPositions	0.001	0.000	0.001
setBioNetNodeLayout	0.387	0.060	0.447
setBioNetPlotAreaBackground	0.105	0.009	0.114
setBioNetPlotParameters	0.001	0.000	0.001
setCaOmicsVColors	0.001	0.000	0.001
setDefaultNaStrings	0.001	0.000	0.000
showBioMatrixPlotLayout	0.026	0.001	0.027
showBioNetNodesLayout	0.711	0.090	0.801
showSupportedBioNetCircosPlotType	0	0	0
sortClinicalData	0.002	0.001	0.003
sortOmicsDataByColumn	0.001	0.000	0.001
sortOmicsDataByRow	0.004	0.001	0.003