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CHECK report for BioNetStat on merida2

This page was generated on 2018-10-17 09:00:02 -0400 (Wed, 17 Oct 2018).

Package 145/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNetStat 1.0.4
Vinicius Jardim
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BioNetStat
Branch: RELEASE_3_7
Last Commit: 2a5333a
Last Changed Date: 2018-05-12 15:24:18 -0400 (Sat, 12 May 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BioNetStat
Version: 1.0.4
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_1.0.4.tar.gz
StartedAt: 2018-10-16 20:08:30 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:12:02 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 212.4 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_1.0.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/BioNetStat.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.4’
* 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 9.910  1.957  14.889
pathPlot           7.835  1.749   9.604
* 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-3.7-bioc/meat/BioNetStat.Rcheck/00check.log’
for details.



Installation output

BioNetStat.Rcheck/00install.out

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### Running command:
###
###   /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
KLdegree0.0170.0030.024
KLspectrum0.0400.0010.043
adjacencyMatrix0.0050.0010.004
centralityPathPlot 9.910 1.95714.889
diffNetAnalysis1.7860.3031.792
doLabels0.1770.0210.201
labels0.0030.0030.006
nDegreeDensities0.0400.0090.049
nSpectralDensities0.0350.0100.045
networkFeature0.1350.0210.158
networkTest0.4980.1490.661
nodeScores0.0920.0130.109
nodeTest0.2380.0500.292
pathPlot7.8351.7499.604
readGmtFile0.1310.0020.134
readVarFile0.1450.0030.149
runBioNetStat0.0010.0000.001
varFile0.0070.0020.010