Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:59 -0400 (Fri, 15 Oct 2021).

CHECK results for BioNetStat on tokay2

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 187/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNetStat 1.12.0  (landing page)
Vinicius Jardim
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/BioNetStat
git_branch: RELEASE_3_13
git_last_commit: 1bd4d5e
git_last_commit_date: 2021-05-19 12:35:18 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNetStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BioNetStat_1.12.0.tar.gz
StartedAt: 2021-10-14 20:16:27 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 20:21:04 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 277.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNetStat.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNetStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BioNetStat_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BioNetStat.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BioNetStat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNetStat' version '1.12.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
networkTest        13.63   0.11   13.73
centralityPathPlot  6.74   1.66    9.82
pathPlot            6.20   1.41    7.61
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
networkTest        11.67   0.03   11.70
centralityPathPlot  7.20   0.99    9.67
pathPlot            6.45   1.27    9.28
* 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/BioNetStat.Rcheck/00check.log'
for details.



Installation output

BioNetStat.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BioNetStat_1.12.0.tar.gz && rm -rf BioNetStat.buildbin-libdir && mkdir BioNetStat.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioNetStat.buildbin-libdir BioNetStat_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BioNetStat_1.12.0.zip && rm BioNetStat_1.12.0.tar.gz BioNetStat_1.12.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 33 2937k   33  980k    0     0  1551k      0  0:00:01 --:--:--  0:00:01 1552k
100 2937k  100 2937k    0     0  2133k      0  0:00:01  0:00:01 --:--:-- 2134k

install for i386

* installing *source* package 'BioNetStat' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BioNetStat'
    finding HTML links ... done
    KLdegree                                html  
    KLspectrum                              html  
    adjacencyMatrix                         html  
    centralityPathPlot                      html  
    diffNetAnalysis                         html  
    doLabels                                html  
    edgeTest                                html  
    labels                                  html  
    nDegreeDensities                        html  
    nSpectralDensities                      html  
    networkFeature                          html  
    networkTest                             html  
    nodeScores                              html  
    nodeTest                                html  
    pathPlot                                html  
    readSetFile                             html  
    readVarFile                             html  
    runBioNetStat                           html  
    varFile                                 html  
** 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

install for x64

* installing *source* package 'BioNetStat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioNetStat' as BioNetStat_1.12.0.zip
* DONE (BioNetStat)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BioNetStat' successfully unpacked and MD5 sums checked

Tests output


Example timings

BioNetStat.Rcheck/examples_i386/BioNetStat-Ex.timings

nameusersystemelapsed
KLdegree0.040.000.03
KLspectrum0.010.010.04
adjacencyMatrix000
centralityPathPlot6.741.669.82
diffNetAnalysis2.060.032.15
doLabels0.090.000.09
edgeTest0.070.000.06
labels000
nDegreeDensities0.070.000.08
nSpectralDensities0.140.000.14
networkFeature0.080.000.08
networkTest13.63 0.1113.73
nodeScores0.120.000.13
nodeTest0.210.000.20
pathPlot6.201.417.61
readSetFile0.120.000.56
readVarFile0.190.000.39
runBioNetStat000
varFile0.030.010.05

BioNetStat.Rcheck/examples_x64/BioNetStat-Ex.timings

nameusersystemelapsed
KLdegree0.020.000.01
KLspectrum0.010.000.01
adjacencyMatrix000
centralityPathPlot7.200.999.67
diffNetAnalysis1.340.011.36
doLabels0.100.000.09
edgeTest0.060.000.07
labels000
nDegreeDensities0.060.000.06
nSpectralDensities0.130.000.13
networkFeature0.080.000.08
networkTest11.67 0.0311.70
nodeScores0.040.000.05
nodeTest0.100.000.09
pathPlot6.451.279.28
readSetFile0.070.000.08
readVarFile0.160.000.16
runBioNetStat000
varFile0.020.000.01