BioC 3.2: CHECK report for caOmicsV on oaxaca

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 01:59:20 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:01:24 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 124.3 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 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... [5s/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 ... [55s/61s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
bioNetLegend      7.089  0.358   7.741
plotBioNetCircos  6.792  0.338   7.902
plotBioNetHeatmap 5.019  0.239   5.353
plotBioNetPoints  3.217  0.174   5.669
* 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	0.001	0.001
CNVDemoData	0.019	0.002	0.027
RNA2miRNA	0.001	0.000	0.001
RNASeq	0.004	0.002	0.006
RNASeqDemoData	0.002	0.000	0.002
bioMatrixLegend	0.289	0.018	0.318
bioNetCircosPlot	1.726	0.157	1.983
bioNetLegend	7.089	0.358	7.741
biomatrixPlotDemoData	0.003	0.001	0.032
bionetPlotDemoData	0.003	0.000	0.003
convertToZScores	0.005	0.000	0.006
drawBioNetNodeBackground	4.307	0.211	4.549
eraseBioNetNode	2.136	0.148	2.550
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.002	0.000	0.002
getBioNetNodeLinkLine	0.001	0.000	0.001
getBioNetParameters	0.571	0.087	0.660
getBioNetPlotLocations	0.402	0.080	0.483
getBioNetSamplePlotPosition	0.000	0.001	0.001
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0	0	0
getDefaultNaStrings	0.001	0.000	0.001
getHeatmapColorScales	0.001	0.000	0.000
getPlotDataSet	0.033	0.001	0.083
getPlotOmicsData	0.011	0.003	0.014
getPlotSampleData	0.003	0.000	0.003
getPlotSummaryData	0.010	0.000	0.011
getRelatedPlotData	0.066	0.001	0.067
initializeBioMatrixPlot	0.002	0.000	0.002
initializeBioNetCircos	0.523	0.082	0.606
labelBioNetNodeNames	1.874	0.143	2.115
linkBioNetNodes	1.505	0.133	2.004
linkBioNetSamples	1.537	0.128	1.882
methylDemoData	0.002	0.000	0.002
miRNA	0.002	0.000	0.002
miRNADemoData	0.001	0.000	0.001
plotBioMatrix	0.654	0.017	0.705
plotBioMatrixBars	0.014	0.001	0.016
plotBioMatrixBinaryData	0.005	0.000	0.006
plotBioMatrixCategoryData	0.004	0.000	0.004
plotBioMatrixHeatmap	0.005	0.001	0.007
plotBioMatrixRowNames	0.021	0.001	0.022
plotBioMatrixSampleData	0.005	0.001	0.006
plotBioMatrixSampleNames	0.003	0.001	0.100
plotBioNetBars	1.955	0.158	2.114
plotBioNetCircos	6.792	0.338	7.902
plotBioNetHeatmap	5.019	0.239	5.353
plotBioNetLines	3.253	0.182	3.564
plotBioNetPoints	3.217	0.174	5.669
plotBioNetPolygons	3.243	0.188	3.526
plotHeatmapColorScale	1.392	0.029	1.473
resetBioNetNodePlotAreaBoundary	0.001	0.000	0.001
sampleDemoData	0.002	0.000	0.002
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.002	0.000	0.006
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0.000	0.000	0.001
setBioNetNodeLayout	0.523	0.078	0.603
setBioNetPlotAreaBackground	0.085	0.011	0.097
setBioNetPlotParameters	0.001	0.000	0.000
setCaOmicsVColors	0.001	0.000	0.001
setDefaultNaStrings	0	0	0
showBioMatrixPlotLayout	0.024	0.002	0.026
showBioNetNodesLayout	0.966	0.111	1.078
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	0.004