Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-18 12:03:37 -0400 (Mon, 18 Oct 2021).

CHECK results for BioNetStat on nebbiolo2

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 185/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNetStat 1.13.0  (landing page)
Vinicius Jardim
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/BioNetStat
git_branch: master
git_last_commit: 85644a4
git_last_commit_date: 2021-05-19 12:35:18 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BioNetStat
Version: 1.13.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BioNetStat_1.13.0.tar.gz
StartedAt: 2021-10-17 19:15:34 -0400 (Sun, 17 Oct 2021)
EndedAt: 2021-10-17 19:18:35 -0400 (Sun, 17 Oct 2021)
EllapsedTime: 180.9 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNetStat.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BioNetStat_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/BioNetStat.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.13.0’
* 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        10.448  0.100  10.548
centralityPathPlot  9.330  0.827  13.561
pathPlot            6.361  0.520   6.881
* 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-3.14-bioc/meat/BioNetStat.Rcheck/00check.log’
for details.



Installation output

BioNetStat.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL BioNetStat
###
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* installing to library ‘/home/biocbuild/bbs-3.14-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
** 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
KLdegree0.0110.0000.011
KLspectrum0.0180.0000.018
adjacencyMatrix0.0000.0000.001
centralityPathPlot 9.330 0.82713.561
diffNetAnalysis1.2910.0281.319
doLabels0.0810.0000.080
edgeTest0.0560.0000.056
labels0.0010.0000.001
nDegreeDensities0.0580.0000.059
nSpectralDensities0.1000.0040.103
networkFeature0.0660.0040.070
networkTest10.448 0.10010.548
nodeScores0.0540.0030.058
nodeTest0.0920.0170.108
pathPlot6.3610.5206.881
readSetFile0.0880.0030.092
readVarFile0.1390.0010.139
runBioNetStat000
varFile0.0070.0000.007