BioC 3.3: CHECK report for caOmicsV on linux2.bioconductor.org

Package: caOmicsV

Version: 1.1.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.1.0.tar.gz

StartedAt: 2015-10-27 02:18:32 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:20:18 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 106.0 seconds

RetCode: 0

Status:  OK

CheckDir: caOmicsV.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/caOmicsV.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ... [5s/5s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [60s/60s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
bioNetLegend      8.537  0.156   8.700
plotBioNetCircos  7.729  0.168   7.907
plotBioNetHeatmap 6.063  0.072   6.139
* 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	0.000
CA_OMICS_NA_STRING	0.001	0.000	0.000
CNVDemoData	0.013	0.000	0.012
RNA2miRNA	0.002	0.000	0.001
RNASeq	0.004	0.000	0.003
RNASeqDemoData	0.002	0.000	0.001
bioMatrixLegend	0.235	0.000	0.235
bioNetCircosPlot	1.865	0.035	1.903
bioNetLegend	8.537	0.156	8.700
biomatrixPlotDemoData	0.003	0.000	0.004
bionetPlotDemoData	0.003	0.000	0.002
convertToZScores	0.004	0.000	0.004
drawBioNetNodeBackground	4.218	0.064	4.287
eraseBioNetNode	2.684	0.040	2.731
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.002	0.000	0.002
getBioNetNodeLinkLine	0.002	0.000	0.002
getBioNetParameters	0.391	0.000	0.391
getBioNetPlotLocations	0.269	0.004	0.273
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0.001	0.000	0.001
getCaOmicsVPlotTypes	0.001	0.000	0.001
getDefaultNaStrings	0.001	0.000	0.001
getHeatmapColorScales	0	0	0
getPlotDataSet	0.018	0.000	0.018
getPlotOmicsData	0.006	0.000	0.006
getPlotSampleData	0.001	0.000	0.001
getPlotSummaryData	0.005	0.000	0.005
getRelatedPlotData	0.032	0.008	0.040
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.371	0.004	0.375
labelBioNetNodeNames	1.728	0.016	1.744
linkBioNetNodes	1.978	0.040	2.018
linkBioNetSamples	2.080	0.028	2.108
methylDemoData	0.000	0.004	0.002
miRNA	0.000	0.000	0.002
miRNADemoData	0.002	0.000	0.001
plotBioMatrix	0.514	0.004	0.518
plotBioMatrixBars	0.007	0.000	0.011
plotBioMatrixBinaryData	0.003	0.000	0.003
plotBioMatrixCategoryData	0.002	0.000	0.003
plotBioMatrixHeatmap	0.001	0.004	0.005
plotBioMatrixRowNames	0.012	0.000	0.012
plotBioMatrixSampleData	0.003	0.000	0.003
plotBioMatrixSampleNames	0.002	0.000	0.002
plotBioNetBars	1.927	0.008	1.936
plotBioNetCircos	7.729	0.168	7.907
plotBioNetHeatmap	6.063	0.072	6.139
plotBioNetLines	4.093	0.048	4.142
plotBioNetPoints	4.380	0.052	4.434
plotBioNetPolygons	4.528	0.052	4.582
plotHeatmapColorScale	1.464	0.016	1.481
resetBioNetNodePlotAreaBoundary	0.000	0.000	0.001
sampleDemoData	0.002	0.000	0.002
setBioMatrixBaseCoordinates	0.001	0.000	0.001
setBioMatrixPlotArea	0.002	0.000	0.003
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0	0	0
setBioNetNodeLayout	0.536	0.004	0.540
setBioNetPlotAreaBackground	0.112	0.000	0.113
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0	0	0
setDefaultNaStrings	0.001	0.000	0.000
showBioMatrixPlotLayout	0.027	0.000	0.027
showBioNetNodesLayout	1.561	0.020	1.581
showSupportedBioNetCircosPlotType	0	0	0
sortClinicalData	0.003	0.000	0.002
sortOmicsDataByColumn	0.003	0.000	0.003
sortOmicsDataByRow	0.004	0.000	0.005