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This page was generated on 2025-09-22 12:04 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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

Package 218/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.11.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 Sep 2025)
git_url: https://git.bioconductor.org/packages/BioNAR
git_branch: devel
git_last_commit: ac4d792
git_last_commit_date: 2025-04-15 12:58:11 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BioNAR on lconway

To the developers/maintainers of the BioNAR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioNAR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BioNAR
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNAR_1.11.0.tar.gz
StartedAt: 2025-09-21 19:39:07 -0400 (Sun, 21 Sep 2025)
EndedAt: 2025-09-21 19:49:10 -0400 (Sun, 21 Sep 2025)
EllapsedTime: 603.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNAR.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNAR_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BioNAR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.11.0’
* 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 ‘BioNAR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   6.1Mb
* 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 code 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
Package in Depends field not imported from: ‘Rdpack’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘addNoise’ ‘gofs’ ‘highlightRate’ ‘plotSigmoid’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘clusterCons’ in Rd xrefs
* 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 LazyData ... 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
plotEntropy              13.468  0.755  14.392
addEdgeAtts              11.153  2.815  16.705
clusteringSummary        12.642  0.102  12.864
getEntropy               11.777  0.675  12.562
calcEntropy               9.241  1.515  11.100
getCentralityMatrix      10.180  0.552  10.850
getGraphCentralityECDF    9.563  0.543  10.177
annotateTopOntoOVG        9.295  0.775  10.907
annotateSCHanno           6.381  0.678   7.363
calcSparsness             6.131  0.926   7.745
runPermDisease            6.595  0.177   6.839
normModularity            6.142  0.557   6.777
annotateGOont             4.602  1.054   7.121
annotateGoBP              4.745  0.536   5.475
FitDegree                 1.135  0.051   7.428
getRandomGraphCentrality  0.703  0.029  14.133
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/BioNAR.Rcheck/00check.log’
for details.


Installation output

BioNAR.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioNAR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘BioNAR’ ...
** this is package ‘BioNAR’ version ‘1.11.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (BioNAR)

Tests output

BioNAR.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(BioNAR)
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: poweRlaw
Loading required package: latex2exp
Loading required package: RSpectra
Loading required package: Rdpack



Attaching package: 'BioNAR'

The following object is masked from 'package:igraph':

    permute

> 
> test_check("BioNAR")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 125 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test_bridgeness.R:38:5', 'test_bridgeness.R:81:5'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 125 ]
> 
> proc.time()
   user  system elapsed 
 40.096   2.563  56.796 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.1350.0517.428
addEdgeAtts11.153 2.81516.705
annotateGOont4.6021.0547.121
annotateGeneNames0.3060.0230.334
annotateGoBP4.7450.5365.475
annotateGoCC3.8560.3684.310
annotateGoMF3.7080.3984.426
annotatePresynaptic1.9910.1672.520
annotateSCHanno6.3810.6787.363
annotateTopOntoOVG 9.295 0.77510.907
annotateVertex0.0040.0010.005
applpMatrixToGraph0.0020.0020.005
buildNetwork0.0040.0010.005
calcAllClustering2.8940.1063.107
calcBridgeness0.0870.0100.101
calcCentrality0.1030.0140.128
calcCentralityExternalDistances0.6660.0690.771
calcCentralityInternalDistances0.6240.0512.053
calcClustering0.0050.0010.005
calcDiseasePairs0.4800.0370.920
calcEntropy 9.241 1.51511.100
calcMembership0.0060.0010.007
calcReclusterMatrix0.0450.0030.051
calcSparsness6.1310.9267.745
clusterORA0.3560.0760.609
clusteringSummary12.642 0.10212.864
degreeBinnedGDAs0.3330.0100.345
escapeAnnotation0.0000.0010.001
evalCentralitySignificance0.6340.0200.662
findLCC0.0050.0020.007
getAnnotationList0.0750.0050.080
getAnnotationVertexList0.0930.0260.122
getBridgeness0.0850.0050.091
getCentralityMatrix10.180 0.55210.850
getClusterSubgraphByID0.0280.0010.030
getClustering0.0300.0010.032
getCommunityGraph0.0320.0010.034
getDType0.0000.0000.001
getDYNAMO0.0440.0020.045
getDiseases0.0010.0000.000
getEntropy11.777 0.67512.562
getEntropyRate0.0050.0010.006
getGNP0.0220.0020.024
getGraphCentralityECDF 9.563 0.54310.177
getPA0.0250.0020.026
getRandomGraphCentrality 0.703 0.02914.133
getRobustness0.6420.0430.691
layoutByCluster0.1390.0030.144
layoutByRecluster0.1180.0050.122
makeConsensusMatrix0.6550.0410.703
makeMembership0.0030.0010.004
metlMatrix0.0100.0020.013
normModularity6.1420.5576.777
permute0.0000.0000.001
plotBridgeness0.5790.0160.603
plotEntropy13.468 0.75514.392
prepareGDA0.3420.0120.359
recluster0.0790.0080.089
removeVertexTerm0.0060.0020.008
runPermDisease6.5950.1776.839
sampleDegBinnedGDA0.4780.0150.499
sampleGraphClust0.0350.0020.038
unescapeAnnotation0.0010.0010.002
zeroNA0.0000.0000.001