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BioC 3.2: CHECK report for caOmicsV on zin1

This page was generated on 2016-04-23 10:14:48 -0700 (Sat, 23 Apr 2016).

Package 139/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.0.0
Henry Zhang
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/caOmicsV
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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: 2016-04-22 22:47:04 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:48:42 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 97.6 seconds
RetCode: 0
Status:  OK 
CheckDir: caOmicsV.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/caOmicsV.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ... [4s/4s] 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 ... [53s/53s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
bioNetLegend     7.762  0.055   7.838
plotBioNetCircos 7.581  0.105   7.703
* 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

caOmicsV.Rcheck/00install.out:

* 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)

caOmicsV.Rcheck/caOmicsV-Ex.timings:

nameusersystemelapsed
CA_OMICS_ENV0.0010.0000.000
CA_OMICS_NAME0.0000.0000.001
CA_OMICS_NA_STRING0.0010.0000.000
CNVDemoData0.0160.0000.017
RNA2miRNA0.0020.0000.001
RNASeq0.0050.0000.004
RNASeqDemoData0.0020.0000.002
bioMatrixLegend0.2530.0000.253
bioNetCircosPlot2.0090.0162.023
bioNetLegend7.7620.0557.838
biomatrixPlotDemoData0.0010.0040.024
bionetPlotDemoData0.0030.0000.003
convertToZScores0.0060.0000.006
drawBioNetNodeBackground4.1720.0364.211
eraseBioNetNode2.1850.0202.204
getBezierCurve0.0010.0000.001
getBioMatrixDataRowTop0.0010.0000.000
getBioMatrixPlotParameters0.0020.0000.002
getBioNetNodeLinkLine0.0020.0000.001
getBioNetParameters0.4090.0000.408
getBioNetPlotLocations0.3190.0000.319
getBioNetSamplePlotPosition000
getCaOmicsVColors0.0010.0000.001
getCaOmicsVPlotTypes0.0000.0000.001
getDefaultNaStrings000
getHeatmapColorScales0.0010.0000.000
getPlotDataSet0.0230.0000.023
getPlotOmicsData0.0080.0000.008
getPlotSampleData0.0020.0000.002
getPlotSummaryData0.0020.0010.006
getRelatedPlotData0.0420.0000.042
initializeBioMatrixPlot0.0010.0000.001
initializeBioNetCircos0.4120.0000.411
labelBioNetNodeNames1.8340.0081.842
linkBioNetNodes1.5250.0201.549
linkBioNetSamples1.5000.0321.536
methylDemoData0.0020.0000.002
miRNA0.0020.0000.002
miRNADemoData0.0020.0000.002
plotBioMatrix0.5480.0030.552
plotBioMatrixBars0.0130.0010.012
plotBioMatrixBinaryData0.0030.0000.003
plotBioMatrixCategoryData0.0030.0000.004
plotBioMatrixHeatmap0.0060.0000.006
plotBioMatrixRowNames0.0150.0000.015
plotBioMatrixSampleData0.0040.0000.004
plotBioMatrixSampleNames0.0030.0000.002
plotBioNetBars2.1540.0112.177
plotBioNetCircos7.5810.1057.703
plotBioNetHeatmap4.7960.0724.868
plotBioNetLines3.2940.0203.326
plotBioNetPoints3.1890.0323.219
plotBioNetPolygons3.5440.0283.583
plotHeatmapColorScale1.1320.0201.151
resetBioNetNodePlotAreaBoundary000
sampleDemoData0.0020.0000.002
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea0.0020.0000.002
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.4190.0000.419
setBioNetPlotAreaBackground0.0820.0000.081
setBioNetPlotParameters000
setCaOmicsVColors0.0010.0000.000
setDefaultNaStrings0.0010.0000.000
showBioMatrixPlotLayout0.0200.0000.021
showBioNetNodesLayout1.1840.0121.194
showSupportedBioNetCircosPlotType000
sortClinicalData0.0030.0000.002
sortOmicsDataByColumn0.0020.0000.003
sortOmicsDataByRow0.0040.0000.004