BioC 3.2: CHECK report for caOmicsV on linux1.bioconductor.org

Package: caOmicsV

Version: 1.0.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.0.0.tar.gz

StartedAt: 2015-10-27 01:43:23 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:44:59 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 96.0 seconds

RetCode: 0

Status:  OK

CheckDir: caOmicsV.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/caOmicsV.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.0’
* 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/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 ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
bioNetLegend             9.625  0.148   9.775
plotBioNetCircos         6.660  0.080   6.741
drawBioNetNodeBackground 5.267  0.080   5.348
* 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	0	0
CA_OMICS_NA_STRING	0	0	0
CNVDemoData	0.033	0.000	0.033
RNA2miRNA	0.002	0.000	0.002
RNASeq	0.005	0.000	0.005
RNASeqDemoData	0.002	0.000	0.002
bioMatrixLegend	0.302	0.008	0.310
bioNetCircosPlot	1.777	0.039	1.818
bioNetLegend	9.625	0.148	9.775
biomatrixPlotDemoData	0.003	0.000	0.005
bionetPlotDemoData	0.004	0.000	0.003
convertToZScores	0.006	0.000	0.006
drawBioNetNodeBackground	5.267	0.080	5.348
eraseBioNetNode	2.999	0.020	3.025
getBezierCurve	0.002	0.000	0.001
getBioMatrixDataRowTop	0.001	0.000	0.001
getBioMatrixPlotParameters	0.003	0.000	0.003
getBioNetNodeLinkLine	0.002	0.000	0.001
getBioNetParameters	0.516	0.000	0.516
getBioNetPlotLocations	0.403	0.000	0.403
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0.000	0.000	0.001
getCaOmicsVPlotTypes	0.000	0.000	0.001
getDefaultNaStrings	0.000	0.000	0.001
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.027	0.000	0.027
getPlotOmicsData	0.006	0.004	0.010
getPlotSampleData	0.002	0.000	0.002
getPlotSummaryData	0.008	0.000	0.008
getRelatedPlotData	0.057	0.000	0.057
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.519	0.000	0.519
labelBioNetNodeNames	2.441	0.012	2.453
linkBioNetNodes	1.972	0.016	1.988
linkBioNetSamples	1.482	0.016	1.498
methylDemoData	0.001	0.000	0.001
miRNA	0.001	0.000	0.002
miRNADemoData	0.001	0.000	0.001
plotBioMatrix	0.517	0.004	0.521
plotBioMatrixBars	0.006	0.004	0.010
plotBioMatrixBinaryData	0.003	0.000	0.003
plotBioMatrixCategoryData	0.003	0.000	0.002
plotBioMatrixHeatmap	0.005	0.000	0.005
plotBioMatrixRowNames	0.012	0.000	0.012
plotBioMatrixSampleData	0.000	0.000	0.003
plotBioMatrixSampleNames	0.002	0.000	0.002
plotBioNetBars	1.906	0.020	1.927
plotBioNetCircos	6.660	0.080	6.741
plotBioNetHeatmap	4.433	0.096	4.529
plotBioNetLines	2.954	0.032	2.987
plotBioNetPoints	3.113	0.028	3.144
plotBioNetPolygons	2.911	0.056	2.971
plotHeatmapColorScale	1.099	0.016	1.115
resetBioNetNodePlotAreaBoundary	0.000	0.000	0.001
sampleDemoData	0.001	0.000	0.001
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.001	0.000	0.002
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0	0	0
setBioNetNodeLayout	0.382	0.000	0.381
setBioNetPlotAreaBackground	0.07	0.00	0.07
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0	0	0
setDefaultNaStrings	0.001	0.000	0.000
showBioMatrixPlotLayout	0.020	0.000	0.019
showBioNetNodesLayout	1.046	0.004	1.050
showSupportedBioNetCircosPlotType	0.000	0.000	0.001
sortClinicalData	0.001	0.000	0.002
sortOmicsDataByColumn	0.002	0.000	0.001
sortOmicsDataByRow	0.003	0.000	0.003