Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:11 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for BioNetStat on palomino3


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? 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 194/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNetStat 1.16.1  (landing page)
Vinicius Jardim
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/BioNetStat
git_branch: RELEASE_3_15
git_last_commit: 0b6aaac
git_last_commit_date: 2022-06-26 12:48:26 -0400 (Sun, 26 Jun 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / 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: 1.16.1
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNetStat.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BioNetStat_1.16.1.tar.gz
StartedAt: 2022-10-18 22:26:41 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:30:39 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 238.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNetStat.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNetStat.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BioNetStat_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/BioNetStat.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.16.1'
* 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  5.3Mb
  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        12.45   0.37   12.83
centralityPathPlot  8.11   0.81   12.81
pathPlot            7.29   1.16    8.47
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/BioNetStat.Rcheck/00check.log'
for details.



Installation output

BioNetStat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BioNetStat
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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
KLdegree0.020.000.01
KLspectrum0.030.000.04
adjacencyMatrix000
centralityPathPlot 8.11 0.8112.81
diffNetAnalysis1.750.021.77
doLabels0.110.000.11
edgeTest0.060.020.08
labels000
nDegreeDensities0.050.000.04
nSpectralDensities0.110.000.11
networkFeature0.080.000.08
networkTest12.45 0.3712.83
nodeScores0.080.000.08
nodeTest0.110.000.11
pathPlot7.291.168.47
readSetFile0.100.000.34
readVarFile0.150.000.16
runBioNetStat000
varFile000