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This page was generated on 2021-11-26 15:05:43 -0500 (Fri, 26 Nov 2021).

CHECK results for BioNetStat on machv2

To the developers/maintainers of the BioNetStat package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioNetStat.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 189/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNetStat 1.14.0  (landing page)
Vinicius Jardim
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/BioNetStat
git_branch: RELEASE_3_14
git_last_commit: 8ff3b2a
git_last_commit_date: 2021-10-26 12:44:15 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BioNetStat
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNetStat_1.14.0.tar.gz
StartedAt: 2021-11-25 14:21:47 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 14:26:13 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 266.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNetStat.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNetStat_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BioNetStat.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.0’
* 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  5.4Mb
  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’ ‘markdown’
  ‘pheatmap’ ‘plyr’ ‘rmarkdown’ ‘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’
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:
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
networkTest        14.046  0.202  14.257
centralityPathPlot 10.297  0.616  14.394
pathPlot            7.226  0.456   7.687
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/BioNetStat.Rcheck/00check.log’
for details.



Installation output

BioNetStat.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioNetStat
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
** 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
KLdegree0.0150.0020.018
KLspectrum0.0320.0030.036
adjacencyMatrix0.0020.0000.002
centralityPathPlot10.297 0.61614.394
diffNetAnalysis1.7270.0281.757
doLabels0.0950.0020.098
edgeTest0.1150.0120.126
labels0.0020.0030.004
nDegreeDensities0.0730.0070.081
nSpectralDensities0.1020.0090.111
networkFeature0.1260.0070.133
networkTest14.046 0.20214.257
nodeScores0.0840.0120.097
nodeTest0.1880.0160.204
pathPlot7.2260.4567.687
readSetFile0.1610.0020.162
readVarFile0.1540.0030.158
runBioNetStat000
varFile0.0090.0020.012