BioC 3.2: CHECK report for caOmicsV on oaxaca

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 22:16:06 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:18:13 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 126.8 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 (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 ‘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 ... [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 ... [59s/60s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
bioNetLegend      7.742  0.378   8.227
plotBioNetCircos  7.376  0.347   7.803
plotBioNetHeatmap 5.243  0.247   5.542
* 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	0.001	0.001
CA_OMICS_NAME	0.001	0.000	0.001
CA_OMICS_NA_STRING	0.001	0.000	0.001
CNVDemoData	0.022	0.003	0.025
RNA2miRNA	0.002	0.001	0.003
RNASeq	0.004	0.002	0.008
RNASeqDemoData	0.002	0.000	0.002
bioMatrixLegend	0.305	0.016	0.325
bioNetCircosPlot	1.888	0.174	2.105
bioNetLegend	7.742	0.378	8.227
biomatrixPlotDemoData	0.004	0.001	0.018
bionetPlotDemoData	0.003	0.000	0.004
convertToZScores	0.007	0.001	0.008
drawBioNetNodeBackground	4.581	0.225	4.866
eraseBioNetNode	2.260	0.162	2.462
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.003	0.000	0.004
getBioNetNodeLinkLine	0.001	0.000	0.002
getBioNetParameters	0.534	0.079	0.627
getBioNetPlotLocations	0.448	0.084	0.546
getBioNetSamplePlotPosition	0.001	0.000	0.000
getCaOmicsVColors	0.001	0.000	0.001
getCaOmicsVPlotTypes	0.000	0.000	0.001
getDefaultNaStrings	0	0	0
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.037	0.003	0.043
getPlotOmicsData	0.012	0.004	0.015
getPlotSampleData	0.003	0.000	0.004
getPlotSummaryData	0.011	0.001	0.012
getRelatedPlotData	0.076	0.001	0.078
initializeBioMatrixPlot	0.001	0.000	0.002
initializeBioNetCircos	0.520	0.078	0.599
labelBioNetNodeNames	1.945	0.147	2.127
linkBioNetNodes	1.530	0.125	1.689
linkBioNetSamples	1.609	0.129	1.821
methylDemoData	0.002	0.000	0.003
miRNA	0.002	0.000	0.003
miRNADemoData	0.002	0.000	0.002
plotBioMatrix	0.682	0.015	0.758
plotBioMatrixBars	0.016	0.001	0.027
plotBioMatrixBinaryData	0.005	0.001	0.006
plotBioMatrixCategoryData	0.005	0.000	0.020
plotBioMatrixHeatmap	0.008	0.001	0.009
plotBioMatrixRowNames	0.023	0.001	0.025
plotBioMatrixSampleData	0.006	0.000	0.007
plotBioMatrixSampleNames	0.003	0.001	0.004
plotBioNetBars	2.061	0.160	2.249
plotBioNetCircos	7.376	0.347	7.803
plotBioNetHeatmap	5.243	0.247	5.542
plotBioNetLines	3.537	0.195	3.786
plotBioNetPoints	3.348	0.187	3.666
plotBioNetPolygons	3.449	0.192	3.726
plotHeatmapColorScale	1.422	0.029	1.504
resetBioNetNodePlotAreaBoundary	0	0	0
sampleDemoData	0.002	0.001	0.002
setBioMatrixBaseCoordinates	0.000	0.000	0.001
setBioMatrixPlotArea	0.002	0.001	0.004
setBioMatrixPlotParameters	0.000	0.000	0.001
setBioNetCircosBasePlotPositions	0.001	0.000	0.001
setBioNetNodeLayout	0.533	0.081	0.618
setBioNetPlotAreaBackground	0.094	0.011	0.116
setBioNetPlotParameters	0.001	0.000	0.001
setCaOmicsVColors	0.001	0.000	0.001
setDefaultNaStrings	0.000	0.000	0.001
showBioMatrixPlotLayout	0.026	0.001	0.032
showBioNetNodesLayout	1.048	0.119	1.176
showSupportedBioNetCircosPlotType	0.001	0.000	0.000
sortClinicalData	0.003	0.000	0.003
sortOmicsDataByColumn	0.003	0.000	0.003
sortOmicsDataByRow	0.005	0.001	0.005

BioC 3.2: CHECK report for caOmicsV on oaxaca

Summary

Command output