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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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: 2025-10-13 13:40 -0400 (Mon, 13 Oct 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    ERROR  
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


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: 2025-10-14 14:24:11 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 14:31:29 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 437.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BioNAR.Rcheck
Warnings: NA

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              11.330  3.047  14.540
calcEntropy              11.988  1.916  14.084
plotEntropy              12.213  1.279  13.607
getEntropy               11.158  1.710  12.983
clusteringSummary        11.807  0.037  11.921
getGraphCentralityECDF    9.882  0.925  10.917
annotateTopOntoOVG        9.858  0.881  10.869
getCentralityMatrix       8.978  1.393  10.516
runPermDisease            8.859  0.214   9.176
annotateSCHanno           6.356  0.791   7.225
calcSparsness             5.956  1.122   7.173
normModularity            5.398  0.932   6.378
annotateGOont             5.129  0.749   5.992
annotateGoBP              4.590  0.977   5.769
calcAllClustering         5.348  0.021   5.421
annotateGoMF              4.051  0.878   5.314
FitDegree                 1.058  0.067   6.021
getRandomGraphCentrality  0.527  0.065  12.370
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 124 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test_bridgeness.R:38:5', 'test_bridgeness.R:81:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_bridgeness.R:101:5'): Norm Modularity ────────────────────────
  `nm` (`actual`) not equal to 0.009390085 (`expected`).
  
    `actual`: 0.0070
  `expected`: 0.0094
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 124 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 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.fail


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 1 | WARN 0 | SKIP 2 | PASS 124 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_bridgeness.R:101:5'): Norm Modularity ────────────────────────
`nm` (`actual`) not equal to 0.009390085 (`expected`).

  `actual`: 0.0070
`expected`: 0.0094

[ FAIL 1 | WARN 0 | SKIP 2 | PASS 124 ]
Error: Test failures
Execution halted

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.0580.0676.021
addEdgeAtts11.330 3.04714.540
annotateGOont5.1290.7495.992
annotateGeneNames0.2590.0090.269
annotateGoBP4.5900.9775.769
annotateGoCC3.1560.8454.246
annotateGoMF4.0510.8785.314
annotatePresynaptic1.4320.2361.737
annotateSCHanno6.3560.7917.225
annotateTopOntoOVG 9.858 0.88110.869
annotateVertex0.0040.0010.004
applpMatrixToGraph0.0020.0000.003
buildNetwork0.0040.0010.005
calcAllClustering5.3480.0215.421
calcBridgeness0.0720.0040.079
calcCentrality0.0960.0030.104
calcCentralityExternalDistances0.4980.0430.545
calcCentralityInternalDistances0.5060.0170.530
calcClustering0.0050.0010.007
calcDiseasePairs0.6530.0310.689
calcEntropy11.988 1.91614.084
calcMembership0.0070.0010.009
calcReclusterMatrix0.0610.0070.071
calcSparsness5.9561.1227.173
clusterORA0.3850.0260.416
clusteringSummary11.807 0.03711.921
degreeBinnedGDAs0.2780.0090.294
escapeAnnotation0.0010.0000.001
evalCentralitySignificance0.5010.0230.527
findLCC0.0060.0010.007
getAnnotationList0.0590.0040.063
getAnnotationVertexList0.0720.0110.084
getBridgeness0.0960.0080.104
getCentralityMatrix 8.978 1.39310.516
getClusterSubgraphByID0.0220.0010.024
getClustering0.0240.0010.025
getCommunityGraph0.0260.0010.028
getDType0.0010.0000.000
getDYNAMO0.0380.0020.040
getDiseases000
getEntropy11.158 1.71012.983
getEntropyRate0.0050.0000.006
getGNP0.0210.0020.023
getGraphCentralityECDF 9.882 0.92510.917
getPA0.0210.0020.024
getRandomGraphCentrality 0.527 0.06512.370
getRobustness0.4950.0420.540
layoutByCluster0.1130.0050.120
layoutByRecluster0.0990.0070.106
makeConsensusMatrix0.4970.0290.531
makeMembership0.0020.0010.003
metlMatrix0.0110.0020.012
normModularity5.3980.9326.378
permute0.0000.0010.000
plotBridgeness0.4890.0110.504
plotEntropy12.213 1.27913.607
prepareGDA0.2610.0140.280
recluster0.0370.0030.040
removeVertexTerm0.0060.0010.008
runPermDisease8.8590.2149.176
sampleDegBinnedGDA0.3770.0370.419
sampleGraphClust0.0280.0010.030
unescapeAnnotation0.0010.0010.002
zeroNA0.0000.0010.000