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### Running command:
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###   /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
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BioNAR.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.10.0’
* 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
calcEntropy              19.972  4.076  28.565
plotEntropy              20.924  1.061  22.275
clusteringSummary        21.526  0.215  24.969
getEntropy               18.645  0.993  19.931
addEdgeAtts              15.503  3.320  21.810
getCentralityMatrix      17.423  0.668  18.455
getGraphCentralityECDF   17.241  0.829  18.159
annotateTopOntoOVG       16.656  0.875  17.965
runPermDisease           11.397  0.177  11.727
annotateSCHanno          10.769  0.761  12.278
calcSparsness             9.363  1.674  13.274
annotateGOont             8.326  1.526  11.507
normModularity            8.652  0.771   9.463
annotateGoBP              8.615  0.492   9.928
annotateGoMF              6.934  0.427   8.362
annotateGoCC              6.796  0.424   7.795
calcAllClustering         6.508  0.025   6.559
FitDegree                 2.289  0.086  13.501
getRandomGraphCentrality  1.380  0.035  23.929
* 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.