Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:44 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for caOmicsV on machv2


To the developers/maintainers of the caOmicsV package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/caOmicsV.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 245/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.24.0  (landing page)
Henry Zhang
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/caOmicsV
git_branch: RELEASE_3_14
git_last_commit: 8813875
git_last_commit_date: 2021-10-26 12:20:58 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: caOmicsV
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings caOmicsV_1.24.0.tar.gz
StartedAt: 2022-04-12 11:10:51 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 11:13:10 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 138.8 seconds
RetCode: 0
Status:   OK  
CheckDir: caOmicsV.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings caOmicsV_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/caOmicsV.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.24.0’
* 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 ... 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
bioNetLegend             7.729  0.478   8.229
plotBioNetCircos         7.642  0.419   8.080
plotBioNetHeatmap        5.630  0.254   5.894
drawBioNetNodeBackground 4.755  0.233   5.037
* 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


Installation output

caOmicsV.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL caOmicsV
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘caOmicsV’ ...
** using staged installation
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (caOmicsV)

Tests output


Example timings

caOmicsV.Rcheck/caOmicsV-Ex.timings

nameusersystemelapsed
CA_OMICS_ENV0.0000.0000.001
CA_OMICS_NAME0.0010.0010.001
CA_OMICS_NA_STRING0.0000.0000.001
CNVDemoData0.0230.0080.031
RNA2miRNA0.0010.0030.005
RNASeq0.0040.0020.006
RNASeqDemoData0.0020.0020.004
bioMatrixLegend0.1960.0310.226
bioNetCircosPlot1.7700.2071.980
bioNetLegend7.7290.4788.229
biomatrixPlotDemoData0.0020.0030.006
bionetPlotDemoData0.0030.0030.006
convertToZScores0.0060.0020.008
drawBioNetNodeBackground4.7550.2335.037
eraseBioNetNode2.0940.1582.262
getBezierCurve0.0000.0010.001
getBioMatrixDataRowTop0.0010.0000.001
getBioMatrixPlotParameters0.0010.0010.003
getBioNetNodeLinkLine0.0010.0010.001
getBioNetParameters0.4060.0590.466
getBioNetPlotLocations0.3700.0260.396
getBioNetSamplePlotPosition0.0010.0010.000
getCaOmicsVColors0.0010.0000.001
getCaOmicsVPlotTypes000
getDefaultNaStrings0.0000.0000.001
getHeatmapColorScales0.0010.0000.001
getPlotDataSet0.0200.0110.030
getPlotOmicsData0.0130.0030.016
getPlotSampleData0.0020.0010.005
getPlotSummaryData0.0090.0020.011
getRelatedPlotData0.0890.0040.094
initializeBioMatrixPlot0.0000.0010.001
initializeBioNetCircos0.3610.0410.403
labelBioNetNodeNames1.9240.1192.060
linkBioNetNodes1.4510.1081.570
linkBioNetSamples1.6890.1441.862
methylDemoData0.0030.0020.005
miRNA0.0030.0020.005
miRNADemoData0.0020.0020.004
plotBioMatrix0.8320.0200.857
plotBioMatrixBars0.0160.0010.019
plotBioMatrixBinaryData0.0050.0010.006
plotBioMatrixCategoryData0.0050.0010.006
plotBioMatrixHeatmap0.0080.0030.011
plotBioMatrixRowNames0.0220.0010.024
plotBioMatrixSampleData0.0040.0010.006
plotBioMatrixSampleNames0.0030.0010.005
plotBioNetBars2.4120.2042.619
plotBioNetCircos7.6420.4198.080
plotBioNetHeatmap5.6300.2545.894
plotBioNetLines3.5650.1873.807
plotBioNetPoints3.5100.1673.685
plotBioNetPolygons3.5900.1793.782
plotHeatmapColorScale1.5910.0221.621
resetBioNetNodePlotAreaBoundary0.0010.0000.001
sampleDemoData0.0020.0020.003
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea0.0020.0010.003
setBioMatrixPlotParameters0.0000.0000.001
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.3340.0460.379
setBioNetPlotAreaBackground0.5040.0780.582
setBioNetPlotParameters000
setCaOmicsVColors000
setDefaultNaStrings0.0010.0010.000
showBioMatrixPlotLayout0.8640.0140.884
showBioNetNodesLayout0.9670.0951.064
showSupportedBioNetCircosPlotType0.0010.0000.000
sortClinicalData0.0020.0030.005
sortOmicsDataByColumn0.0030.0030.006
sortOmicsDataByRow0.0060.0020.008