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: 2015-10-27 06:05:59 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:08:11 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 131.5 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/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 ... [64s/66s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
bioNetLegend             7.770  0.427   8.660
plotBioNetCircos         7.579  0.421   8.566
plotBioNetHeatmap        5.992  0.331   6.426
drawBioNetNodeBackground 5.313  0.292   5.717
* 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	0.001
CA_OMICS_NAME	0.001	0.000	0.001
CA_OMICS_NA_STRING	0.001	0.000	0.001
CNVDemoData	0.029	0.003	0.032
RNA2miRNA	0.002	0.001	0.002
RNASeq	0.005	0.002	0.007
RNASeqDemoData	0.002	0.001	0.002
bioMatrixLegend	0.349	0.007	0.355
bioNetCircosPlot	1.991	0.202	2.269
bioNetLegend	7.770	0.427	8.660
biomatrixPlotDemoData	0.004	0.001	0.024
bionetPlotDemoData	0.003	0.000	0.004
convertToZScores	0.008	0.001	0.008
drawBioNetNodeBackground	5.313	0.292	5.717
eraseBioNetNode	2.474	0.196	2.761
getBezierCurve	0.002	0.000	0.001
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.003	0.000	0.004
getBioNetNodeLinkLine	0.002	0.000	0.002
getBioNetParameters	0.454	0.101	0.554
getBioNetPlotLocations	0.589	0.103	0.692
getBioNetSamplePlotPosition	0.000	0.000	0.001
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0.001	0.000	0.001
getDefaultNaStrings	0.001	0.000	0.001
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.030	0.002	0.032
getPlotOmicsData	0.010	0.009	0.019
getPlotSampleData	0.002	0.000	0.004
getPlotSummaryData	0.010	0.000	0.011
getRelatedPlotData	0.062	0.004	0.067
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.606	0.106	0.712
labelBioNetNodeNames	2.044	0.182	2.310
linkBioNetNodes	1.746	0.170	1.984
linkBioNetSamples	1.760	0.163	1.999
methylDemoData	0.002	0.001	0.003
miRNA	0.002	0.001	0.003
miRNADemoData	0.002	0.000	0.002
plotBioMatrix	0.782	0.023	0.883
plotBioMatrixBars	0.019	0.002	0.021
plotBioMatrixBinaryData	0.005	0.001	0.007
plotBioMatrixCategoryData	0.006	0.001	0.024
plotBioMatrixHeatmap	0.008	0.001	0.022
plotBioMatrixRowNames	0.026	0.001	0.036
plotBioMatrixSampleData	0.006	0.001	0.007
plotBioMatrixSampleNames	0.004	0.001	0.018
plotBioNetBars	2.117	0.195	2.364
plotBioNetCircos	7.579	0.421	8.566
plotBioNetHeatmap	5.992	0.331	6.426
plotBioNetLines	3.773	0.218	4.185
plotBioNetPoints	3.619	0.226	3.974
plotBioNetPolygons	3.722	0.225	4.057
plotHeatmapColorScale	1.689	0.039	1.793
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.001	0.000	0.002
setBioMatrixBaseCoordinates	0.000	0.000	0.001
setBioMatrixPlotArea	0.003	0.000	0.004
setBioMatrixPlotParameters	0.001	0.000	0.001
setBioNetCircosBasePlotPositions	0.001	0.000	0.001
setBioNetNodeLayout	0.595	0.096	0.692
setBioNetPlotAreaBackground	0.101	0.014	0.115
setBioNetPlotParameters	0.001	0.000	0.001
setCaOmicsVColors	0.001	0.000	0.001
setDefaultNaStrings	0.000	0.000	0.001
showBioMatrixPlotLayout	0.030	0.001	0.035
showBioNetNodesLayout	1.109	0.142	1.251
showSupportedBioNetCircosPlotType	0.001	0.000	0.001
sortClinicalData	0.003	0.000	0.003
sortOmicsDataByColumn	0.003	0.001	0.003
sortOmicsDataByRow	0.005	0.000	0.006