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This page was generated on 2025-09-29 11:39 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4580
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 217/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.10.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2025-09-25 13:40 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/BioNAR
git_branch: RELEASE_3_21
git_last_commit: d3036b1
git_last_commit_date: 2025-04-15 12:58:11 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BioNAR on kjohnson1

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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2025-09-26 14:07:07 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 14:14:18 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 431.1 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BioNAR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.10.0’
* 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
addEdgeAtts              11.188  2.373  13.703
calcEntropy              11.807  1.258  13.213
getEntropy               10.598  2.035  12.790
clusteringSummary        12.466  0.041  12.608
plotEntropy              11.280  1.220  12.736
annotateTopOntoOVG        9.642  1.211  11.323
getGraphCentralityECDF    8.803  1.329  10.252
getCentralityMatrix       8.596  1.209   9.905
runPermDisease            8.081  0.152   8.426
annotateSCHanno           5.926  1.086   7.365
normModularity            6.116  0.779   6.971
annotateGOont             5.099  0.696   5.857
calcSparsness             4.915  0.640   5.589
calcAllClustering         5.355  0.022   5.429
annotateGoBP              4.719  0.485   5.264
FitDegree                 1.661  0.073   6.363
getRandomGraphCentrality  0.528  0.034  12.339
* 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-3.21-bioc/meat/BioNAR.Rcheck/00check.log’
for details.


Installation output

BioNAR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘BioNAR’ ...
** this is package ‘BioNAR’ version ‘1.10.0’
** 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 (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 
 40.476   3.174  57.352 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.6610.0736.363
addEdgeAtts11.188 2.37313.703
annotateGOont5.0990.6965.857
annotateGeneNames0.2930.0150.333
annotateGoBP4.7190.4855.264
annotateGoCC3.2090.7353.991
annotateGoMF3.3540.8094.221
annotatePresynaptic2.1320.3912.553
annotateSCHanno5.9261.0867.365
annotateTopOntoOVG 9.642 1.21111.323
annotateVertex0.0040.0010.005
applpMatrixToGraph0.0010.0010.002
buildNetwork0.0030.0010.004
calcAllClustering5.3550.0225.429
calcBridgeness0.0690.0040.074
calcCentrality0.0870.0030.092
calcCentralityExternalDistances0.4610.0200.487
calcCentralityInternalDistances0.4510.0160.478
calcClustering0.0040.0010.005
calcDiseasePairs0.6160.0230.645
calcEntropy11.807 1.25813.213
calcMembership0.0060.0010.007
calcReclusterMatrix0.0380.0030.040
calcSparsness4.9150.6405.589
clusterORA0.3610.0210.386
clusteringSummary12.466 0.04112.608
degreeBinnedGDAs0.3120.0250.340
escapeAnnotation0.0000.0000.002
evalCentralitySignificance0.4230.0080.434
findLCC0.0050.0000.005
getAnnotationList0.0590.0030.063
getAnnotationVertexList0.0720.0140.086
getBridgeness0.0640.0030.067
getCentralityMatrix8.5961.2099.905
getClusterSubgraphByID0.0190.0010.021
getClustering0.0160.0010.017
getCommunityGraph0.0150.0020.016
getDType0.0000.0000.001
getDYNAMO0.0350.0020.037
getDiseases000
getEntropy10.598 2.03512.790
getEntropyRate0.0040.0010.005
getGNP0.0180.0010.020
getGraphCentralityECDF 8.803 1.32910.252
getPA0.0210.0020.024
getRandomGraphCentrality 0.528 0.03412.339
getRobustness0.4520.0250.479
layoutByCluster0.1130.0020.115
layoutByRecluster0.1590.0050.165
makeConsensusMatrix0.4240.0200.453
makeMembership0.0020.0010.003
metlMatrix0.0080.0020.010
normModularity6.1160.7796.971
permute0.0000.0010.000
plotBridgeness0.4890.0090.506
plotEntropy11.280 1.22012.736
prepareGDA0.2910.0230.322
recluster0.0380.0030.040
removeVertexTerm0.0060.0010.008
runPermDisease8.0810.1528.426
sampleDegBinnedGDA0.3460.0300.384
sampleGraphClust0.0280.0020.030
unescapeAnnotation0.0010.0000.002
zeroNA0.0010.0000.001