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: 2016-04-22 22:25:53 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:27:42 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 108.2 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 3.2.4 (2016-03-10)
* 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 ... [6s/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 ... [51s/52s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotBioNetCircos 6.558  0.320   6.946
bioNetLegend     6.462  0.315   7.087
* 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	0	0
CA_OMICS_NAME	0.000	0.000	0.001
CA_OMICS_NA_STRING	0.001	0.000	0.000
CNVDemoData	0.021	0.002	0.023
RNA2miRNA	0.002	0.001	0.003
RNASeq	0.003	0.002	0.005
RNASeqDemoData	0.003	0.001	0.003
bioMatrixLegend	0.237	0.012	0.248
bioNetCircosPlot	1.574	0.132	1.719
bioNetLegend	6.462	0.315	7.087
biomatrixPlotDemoData	0.003	0.001	0.063
bionetPlotDemoData	0.004	0.002	0.005
convertToZScores	0.008	0.001	0.008
drawBioNetNodeBackground	4.064	0.199	4.306
eraseBioNetNode	1.976	0.149	2.160
getBezierCurve	0.002	0.000	0.001
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.004	0.001	0.004
getBioNetNodeLinkLine	0.002	0.000	0.002
getBioNetParameters	0.526	0.077	0.602
getBioNetPlotLocations	0.447	0.084	0.532
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0	0	0
getCaOmicsVPlotTypes	0.000	0.000	0.001
getDefaultNaStrings	0.001	0.000	0.000
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.034	0.006	0.041
getPlotOmicsData	0.011	0.004	0.015
getPlotSampleData	0.003	0.001	0.004
getPlotSummaryData	0.010	0.002	0.012
getRelatedPlotData	0.074	0.003	0.077
initializeBioMatrixPlot	0.002	0.000	0.002
initializeBioNetCircos	0.523	0.072	0.595
labelBioNetNodeNames	1.741	0.126	1.905
linkBioNetNodes	1.308	0.120	1.494
linkBioNetSamples	1.309	0.101	1.439
methylDemoData	0.003	0.001	0.004
miRNA	0.002	0.002	0.004
miRNADemoData	0.002	0.001	0.003
plotBioMatrix	0.618	0.016	0.663
plotBioMatrixBars	0.011	0.002	0.015
plotBioMatrixBinaryData	0.003	0.001	0.004
plotBioMatrixCategoryData	0.004	0.000	0.005
plotBioMatrixHeatmap	0.007	0.001	0.009
plotBioMatrixRowNames	0.020	0.001	0.021
plotBioMatrixSampleData	0.006	0.001	0.006
plotBioMatrixSampleNames	0.003	0.000	0.004
plotBioNetBars	1.637	0.126	1.764
plotBioNetCircos	6.558	0.320	6.946
plotBioNetHeatmap	4.485	0.205	4.763
plotBioNetLines	3.188	0.171	3.391
plotBioNetPoints	2.857	0.163	3.052
plotBioNetPolygons	2.919	0.148	3.104
plotHeatmapColorScale	1.293	0.026	1.353
resetBioNetNodePlotAreaBoundary	0.001	0.000	0.001
sampleDemoData	0.001	0.000	0.002
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.002	0.000	0.003
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0.000	0.000	0.001
setBioNetNodeLayout	0.473	0.073	0.546
setBioNetPlotAreaBackground	0.082	0.010	0.092
setBioNetPlotParameters	0.000	0.000	0.001
setCaOmicsVColors	0.001	0.000	0.001
setDefaultNaStrings	0.001	0.000	0.001
showBioMatrixPlotLayout	0.026	0.001	0.028
showBioNetNodesLayout	0.918	0.099	1.019
showSupportedBioNetCircosPlotType	0.001	0.000	0.001
sortClinicalData	0.003	0.000	0.003
sortOmicsDataByColumn	0.003	0.000	0.004
sortOmicsDataByRow	0.005	0.001	0.007

BioC 3.2: CHECK report for caOmicsV on oaxaca

Summary

Command output