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CHECK report for BioNetStat on malbec1

This page was generated on 2020-08-11 11:24:49 -0400 (Tue, 11 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 173/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNetStat 1.9.4
Vinicius Jardim
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 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  NA 
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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BioNetStat_1.9.4.tar.gz
StartedAt: 2020-08-11 04:06:12 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 04:10:06 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 234.5 seconds
RetCode: 0
Status:  OK 
CheckDir: BioNetStat.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BioNetStat_1.9.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BioNetStat.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (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 ‘1.9.4’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
networkTest        14.972  0.016  15.009
centralityPathPlot  9.948  0.568  12.611
pathPlot            7.320  0.088   7.430
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/BioNetStat.Rcheck/00check.log’
for details.



Installation output

BioNetStat.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BioNetStat
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BioNetStat’ ...
** using staged installation
** 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 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 (BioNetStat)

Tests output


Example timings

BioNetStat.Rcheck/BioNetStat-Ex.timings

nameusersystemelapsed
KLdegree0.0120.0000.012
KLspectrum0.0200.0000.021
adjacencyMatrix0.0000.0000.001
centralityPathPlot 9.948 0.56812.611
diffNetAnalysis1.5160.0161.545
doLabels0.0840.0000.088
edgeTest0.0560.0000.059
labels0.0000.0000.001
nDegreeDensities0.0600.0000.061
nSpectralDensities0.1040.0040.105
networkFeature0.0760.0040.080
networkTest14.972 0.01615.009
nodeScores0.1120.0000.112
nodeTest0.1560.0000.155
pathPlot7.3200.0887.430
readSetFile0.1680.0000.237
readVarFile0.1560.0040.163
runBioNetStat000
varFile0.0040.0040.009