Package: BioNetStat

Version: 1.4.3

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_1.4.3.tar.gz

StartedAt: 2019-10-16 00:58:34 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:04:08 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 334.5 seconds

RetCode: 0

Status:  OK

CheckDir: BioNetStat.Rcheck

Warnings: 0

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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_1.4.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BioNetStat.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.3’
* 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 ... 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:
  ‘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 : : no visible global function definition
  for ‘cor’
adjacencyMatrix : : 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 : : no visible global function
  definition for ‘dist’
clusteringCoefficientTest :  : : 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 : : 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 : : 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 or elapsed time > 5s
                     user system elapsed
centralityPathPlot 13.699  2.149  18.515
networkTest        14.653  0.865  15.529
pathPlot           10.005  2.779  12.744
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/BioNetStat.Rcheck/00check.log’
for details.

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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/3.6/Resources/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)

name	user	system	elapsed
KLdegree	0.020	0.005	0.063
KLspectrum	0.034	0.003	0.037
adjacencyMatrix	0.002	0.001	0.002
centralityPathPlot	13.699	2.149	18.515
diffNetAnalysis	1.904	0.115	2.020
doLabels	0.193	0.005	0.201
edgeTest	0.127	0.010	0.136
labels	0.003	0.003	0.005
nDegreeDensities	0.053	0.005	0.057
nSpectralDensities	0.031	0.009	0.040
networkFeature	0.142	0.018	0.161
networkTest	14.653	0.865	15.529
nodeScores	0.116	0.018	0.134
nodeTest	0.218	0.023	0.241
pathPlot	10.005	2.779	12.744
readGmtFile	0.176	0.003	0.181
readVarFile	0.207	0.006	0.213
runBioNetStat	0	0	0
varFile	0.007	0.003	0.011