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CHECK report for BioNetStat on tokay1

This page was generated on 2019-04-13 11:29:14 -0400 (Sat, 13 Apr 2019).

Package 155/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNetStat 1.2.2
Vinicius Jardim
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 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
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNetStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BioNetStat_1.2.2.tar.gz
StartedAt: 2019-04-13 00:49:36 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:54:52 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 316.5 seconds
RetCode: 0
Status:  OK  
CheckDir: BioNetStat.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNetStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BioNetStat_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BioNetStat.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'BioNetStat' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
centralityPathPlot 9.22   2.22   13.12
pathPlot           7.06   1.73    8.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
centralityPathPlot 7.61   2.21   12.37
pathPlot           6.00   2.06    8.06
* 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
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BioNetStat_1.2.2.tar.gz && rm -rf BioNetStat.buildbin-libdir && mkdir BioNetStat.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioNetStat.buildbin-libdir BioNetStat_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BioNetStat_1.2.2.zip && rm BioNetStat_1.2.2.tar.gz BioNetStat_1.2.2.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2695k  100 2695k    0     0  34.7M      0 --:--:-- --:--:-- --:--:-- 36.5M

install for i386

* installing *source* package 'BioNetStat' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BioNetStat'
    finding HTML links ... done
    KLdegree                                html  
    KLspectrum                              html  
    adjacencyMatrix                         html  
    bnsDataTest                             html  
    centralityPathPlot                      html  
    diffNetAnalysis                         html  
    doLabels                                html  
    labels                                  html  
    nDegreeDensities                        html  
    nSpectralDensities                      html  
    networkFeature                          html  
    networkTest                             html  
    nodeScores                              html  
    nodeTest                                html  
    pathPlot                                html  
    readGmtFile                             html  
    readVarFile                             html  
    runBioNetStat                           html  
    varFile                                 html  
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'BioNetStat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioNetStat' as BioNetStat_1.2.2.zip
* DONE (BioNetStat)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BioNetStat' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

BioNetStat.Rcheck/examples_i386/BioNetStat-Ex.timings

nameusersystemelapsed
KLdegree0.000.020.02
KLspectrum0.010.010.03
adjacencyMatrix000
centralityPathPlot 9.22 2.2213.12
diffNetAnalysis2.030.052.08
doLabels0.160.000.53
labels0.000.010.02
nDegreeDensities0.060.000.06
nSpectralDensities0.050.000.05
networkFeature0.140.020.17
networkTest0.30.00.3
nodeScores0.040.000.04
nodeTest0.190.000.19
pathPlot7.061.738.80
readGmtFile0.070.000.19
readVarFile0.110.000.11
runBioNetStat000
varFile0.000.020.01

BioNetStat.Rcheck/examples_x64/BioNetStat-Ex.timings

nameusersystemelapsed
KLdegree0.050.000.06
KLspectrum0.040.000.03
adjacencyMatrix0.010.000.02
centralityPathPlot 7.61 2.2112.37
diffNetAnalysis1.390.011.41
doLabels0.110.000.11
labels000
nDegreeDensities0.030.000.03
nSpectralDensities0.030.000.03
networkFeature0.090.020.11
networkTest0.240.000.24
nodeScores0.030.010.04
nodeTest0.110.020.13
pathPlot6.002.068.06
readGmtFile0.040.000.05
readVarFile0.110.000.11
runBioNetStat000
varFile0.020.000.02