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CHECK report for BioNetStat on tokay1

This page was generated on 2020-08-10 12:24:30 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BioNetStat PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 173/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNetStat 1.9.4
Vinicius Jardim
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/BioNetStat
Branch: master
Last Commit: a7e646c
Last Changed Date: 2020-05-31 18:41:56 -0400 (Sun, 31 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BioNetStat
Version: 1.9.4
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNetStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BioNetStat_1.9.4.tar.gz
StartedAt: 2020-08-10 04:40:15 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 04:46:15 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 359.8 seconds
RetCode: 0
Status:  OK  
CheckDir: BioNetStat.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNetStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BioNetStat_1.9.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BioNetStat.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.9.4'
* 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 whether package 'BioNetStat' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.9Mb
    shiny     1.9Mb
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION
Most likely 'inst/CITATION' should be used instead.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  'BiocParallel' 'RColorBrewer' 'RJSONIO' 'ggplot2' 'knitr' 'pheatmap'
  'plyr' 'stats' 'utils' 'whisker' 'yaml'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'DT' 'shiny' 'shinyBS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
adjacencyMatrix : <anonymous>: no visible global function definition
  for 'cor'
adjacencyMatrix : <anonymous>: no visible global function definition
  for 'p.adjust'
betweennessCentralityTest: no visible global function definition for
  'bplapply'
betweennessCentralityVertexTest: no visible global function definition
  for 'bplapply'
betweennessEdgesCentrality: no visible global function definition for
  'adjacencyMatrix1'
closenessCentralityTest: no visible global function definition for
  'bplapply'
closenessCentralityVertexTest: no visible global function definition
  for 'bplapply'
clusteringCoefficientTest : <anonymous>: no visible global function
  definition for 'dist'
clusteringCoefficientTest : <anonymous> : <anonymous>: no visible
  global function definition for 'dist'
clusteringCoefficientTest: no visible global function definition for
  'bplapply'
clusteringCoefficientVertexTest: no visible global function definition
  for 'bplapply'
degreeCentralityTest: no visible global function definition for
  'bplapply'
degreeCentralityVertexTest: no visible global function definition for
  'bplapply'
degreeDistributionTest: no visible global function definition for
  'bplapply'
diffNetAnalysis: no visible binding for global variable 'expr'
diffNetAnalysis: no visible global function definition for 'p.adjust'
doLabels: no visible global function definition for 'read.csv'
edgeBetweennessEdgeTest: no visible global function definition for
  'bplapply'
edgeBetweennessTest: no visible global function definition for
  'bplapply'
edgesResInt : <anonymous>: no visible global function definition for
  'dist'
eigenvectorCentralityTest: no visible global function definition for
  'bplapply'
eigenvectorCentralityVertexTest: no visible global function definition
  for 'bplapply'
gaussianDensity: no visible global function definition for 'bw.nrd0'
gaussianDensity: no visible global function definition for 'density'
pathPlot: no visible binding for global variable 'median'
readVarFile: no visible global function definition for 'read.table'
resInt : <anonymous>: no visible global function definition for 'dist'
retEdgesTable: no visible global function definition for 'p.adjust'
retTable: no visible global function definition for 'p.adjust'
spectralDistributionTest: no visible global function definition for
  'bplapply'
spectralEntropyTest: no visible global function definition for
  'bplapply'
var.list: no visible global function definition for 'aggregate'
Undefined global functions or variables:
  adjacencyMatrix1 aggregate bplapply bw.nrd0 cor density dist expr
  median p.adjust read.csv read.table
Consider adding
  importFrom("stats", "aggregate", "bw.nrd0", "cor", "density", "dist",
             "median", "p.adjust")
  importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.
* 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 (user + system) or elapsed time > 5s
                    user system elapsed
networkTest        13.68   0.17   13.85
centralityPathPlot  7.93   2.43   11.66
pathPlot            6.53   1.12    7.65
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
networkTest        11.14   0.05   11.18
centralityPathPlot  7.35   0.88    9.45
pathPlot            6.59   0.66    7.25
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-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/3.12/bioc/src/contrib/BioNetStat_1.9.4.tar.gz && rm -rf BioNetStat.buildbin-libdir && mkdir BioNetStat.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioNetStat.buildbin-libdir BioNetStat_1.9.4.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BioNetStat_1.9.4.zip && rm BioNetStat_1.9.4.tar.gz BioNetStat_1.9.4.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 2932k  100 2932k    0     0  13.6M      0 --:--:-- --:--:-- --:--:-- 13.9M

install for i386

* installing *source* package 'BioNetStat' ...
** using staged installation
** 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  
    edgeTest                                html  
    labels                                  html  
    nDegreeDensities                        html  
    nSpectralDensities                      html  
    networkFeature                          html  
    networkTest                             html  
    nodeScores                              html  
    nodeTest                                html  
    pathPlot                                html  
    readSetFile                             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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BioNetStat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioNetStat' as BioNetStat_1.9.4.zip
* DONE (BioNetStat)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BioNetStat' successfully unpacked and MD5 sums checked

Tests output


Example timings

BioNetStat.Rcheck/examples_i386/BioNetStat-Ex.timings

nameusersystemelapsed
KLdegree000
KLspectrum0.010.000.02
adjacencyMatrix000
centralityPathPlot 7.93 2.4311.66
diffNetAnalysis1.630.031.76
doLabels0.110.000.11
edgeTest0.060.000.06
labels000
nDegreeDensities0.080.000.08
nSpectralDensities0.120.000.12
networkFeature0.090.000.09
networkTest13.68 0.1713.85
nodeScores0.070.000.08
nodeTest0.100.020.11
pathPlot6.531.127.65
readSetFile0.050.000.22
readVarFile0.120.000.13
runBioNetStat000
varFile0.020.000.01

BioNetStat.Rcheck/examples_x64/BioNetStat-Ex.timings

nameusersystemelapsed
KLdegree0.010.000.01
KLspectrum0.020.020.03
adjacencyMatrix0.010.000.02
centralityPathPlot7.350.889.45
diffNetAnalysis1.400.001.41
doLabels0.090.000.09
edgeTest0.080.000.08
labels0.020.000.01
nDegreeDensities0.070.000.10
nSpectralDensities0.130.000.12
networkFeature0.110.010.13
networkTest11.14 0.0511.18
nodeScores0.060.010.08
nodeTest0.130.000.13
pathPlot6.590.667.25
readSetFile0.050.000.04
readVarFile0.090.020.11
runBioNetStat000
varFile000