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CHECK report for BioNetStat on merida1

This page was generated on 2019-04-16 12:09:05 -0400 (Tue, 16 Apr 2019).

Package 155/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNetStat 1.2.2
Vinicius Jardim
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/BioNetStat
Branch: RELEASE_3_8
Last Commit: e9b4a61
Last Changed Date: 2018-12-17 04:54:07 -0400 (Mon, 17 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BioNetStat
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioNetStat_1.2.2.tar.gz
StartedAt: 2019-04-15 22:37:57 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:41:41 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 224.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BioNetStat.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioNetStat_1.2.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/BioNetStat.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNetStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNetStat’ version ‘1.2.2’
* package encoding: UTF-8
* 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 ‘BioNetStat’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.9Mb
    shiny     1.6Mb
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
centralityPathPlot 9.865  1.968  14.559
pathPlot           7.640  1.579   9.290
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/BioNetStat.Rcheck/00check.log’
for details.



Installation output

BioNetStat.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BioNetStat
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BioNetStat’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘BNS_tutorial_by_command_line.Rmd’ using ‘UTF-8’ 
   ‘vignette.Rmd’ using ‘UTF-8’ 
** testing if installed package can be loaded
* DONE (BioNetStat)

Tests output


Example timings

BioNetStat.Rcheck/BioNetStat-Ex.timings

nameusersystemelapsed
KLdegree0.0200.0020.023
KLspectrum0.0370.0010.040
adjacencyMatrix0.0020.0000.002
centralityPathPlot 9.865 1.96814.559
diffNetAnalysis2.0630.3432.047
doLabels0.1940.0210.221
labels0.0020.0030.007
nDegreeDensities0.0530.0090.062
nSpectralDensities0.0310.0050.035
networkFeature0.1170.0190.136
networkTest0.5050.1440.659
nodeScores0.0730.0100.084
nodeTest0.2290.0470.279
pathPlot7.6401.5799.290
readGmtFile0.1410.0020.144
readVarFile0.1720.0030.177
runBioNetStat000
varFile0.0070.0010.010