BioC 3.2: CHECK report for caOmicsV on zin1

Package: caOmicsV

Version: 0.99.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_0.99.2.tar.gz

StartedAt: 2015-08-23 22:15:44 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:17:22 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 97.9 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_0.99.2.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 ‘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 ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
* 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 ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
bioNetLegend      8.216  0.104   8.352
plotBioNetCircos  7.983  0.128   8.156
plotBioNetHeatmap 5.037  0.088   5.140
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/caOmicsV.Rcheck/00check.log’
for details.

* 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	0.000	0.000	0.001
CA_OMICS_NA_STRING	0.001	0.000	0.000
CNVDemoData	0.025	0.004	0.030
RNA2miRNA	0.000	0.000	0.001
RNASeq	0.004	0.000	0.005
RNASeqDemoData	0.002	0.000	0.002
bioMatrixLegend	0.273	0.004	0.276
bioNetCircosPlot	2.064	0.012	2.076
bioNetLegend	8.216	0.104	8.352
biomatrixPlotDemoData	0.003	0.000	0.015
bionetPlotDemoData	0.003	0.000	0.003
convertToZScores	0.005	0.000	0.005
drawBioNetNodeBackground	4.527	0.056	4.594
eraseBioNetNode	2.313	0.032	2.343
getBezierCurve	0.001	0.000	0.001
getBioMatrixDataRowTop	0	0	0
getBioMatrixPlotParameters	0.002	0.000	0.002
getBioNetNodeLinkLine	0.002	0.000	0.002
getBioNetParameters	0.413	0.000	0.423
getBioNetPlotLocations	0.338	0.000	0.338
getBioNetSamplePlotPosition	0	0	0
getCaOmicsVColors	0.000	0.000	0.001
getCaOmicsVPlotTypes	0.000	0.000	0.001
getDefaultNaStrings	0	0	0
getHeatmapColorScales	0.001	0.000	0.001
getPlotDataSet	0.024	0.000	0.024
getPlotOmicsData	0.008	0.000	0.008
getPlotSampleData	0.003	0.000	0.003
getPlotSummaryData	0.007	0.000	0.007
getRelatedPlotData	0.046	0.000	0.046
initializeBioMatrixPlot	0.001	0.000	0.001
initializeBioNetCircos	0.418	0.000	0.418
labelBioNetNodeNames	1.854	0.012	1.864
linkBioNetNodes	1.478	0.012	1.490
linkBioNetSamples	1.712	0.028	1.739
methylDemoData	0.002	0.000	0.002
miRNA	0.000	0.000	0.002
miRNADemoData	0.002	0.000	0.002
plotBioMatrix	0.615	0.008	0.633
plotBioMatrixBars	0.015	0.000	0.015
plotBioMatrixBinaryData	0.004	0.000	0.004
plotBioMatrixCategoryData	0.004	0.000	0.004
plotBioMatrixHeatmap	0.008	0.000	0.008
plotBioMatrixRowNames	0.017	0.000	0.017
plotBioMatrixSampleData	0.005	0.000	0.005
plotBioMatrixSampleNames	0.003	0.000	0.003
plotBioNetBars	2.322	0.056	2.380
plotBioNetCircos	7.983	0.128	8.156
plotBioNetHeatmap	5.037	0.088	5.140
plotBioNetLines	3.365	0.048	3.411
plotBioNetPoints	3.365	0.040	3.411
plotBioNetPolygons	3.329	0.064	3.396
plotHeatmapColorScale	1.143	0.012	1.155
resetBioNetNodePlotAreaBoundary	0.001	0.000	0.000
sampleDemoData	0.001	0.000	0.001
setBioMatrixBaseCoordinates	0	0	0
setBioMatrixPlotArea	0.002	0.000	0.002
setBioMatrixPlotParameters	0	0	0
setBioNetCircosBasePlotPositions	0.001	0.000	0.001
setBioNetNodeLayout	0.395	0.000	0.394
setBioNetPlotAreaBackground	0.081	0.000	0.081
setBioNetPlotParameters	0	0	0
setCaOmicsVColors	0.001	0.000	0.000
setDefaultNaStrings	0.001	0.000	0.001
showBioMatrixPlotLayout	0.02	0.00	0.02
showBioNetNodesLayout	1.178	0.012	1.194
showSupportedBioNetCircosPlotType	0	0	0
sortClinicalData	0.002	0.000	0.002
sortOmicsDataByColumn	0.002	0.000	0.002
sortOmicsDataByRow	0.004	0.000	0.004

BioC 3.2: CHECK report for caOmicsV on zin1

Summary

Command output