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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 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: 2025-09-19 13:45 -0400 (Fri, 19 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: 2025-09-19 19:35:13 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 19:45:06 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 593.1 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_1.11.0.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  6.9Mb
  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              13.360  0.762  14.297
addEdgeAtts              10.220  2.567  15.560
clusteringSummary        12.598  0.098  12.808
getEntropy               11.248  0.709  12.061
calcEntropy              10.327  1.455  12.621
getCentralityMatrix      10.674  0.473  11.252
getGraphCentralityECDF   10.243  0.492  10.812
annotateTopOntoOVG        9.556  0.861  10.998
annotateSCHanno           6.322  0.550   7.103
normModularity            6.067  0.498   6.633
runPermDisease            6.250  0.172   6.488
calcSparsness             5.634  0.461   6.162
annotateGOont             4.729  1.157   6.353
annotateGoBP              4.776  0.591   5.860
FitDegree                 1.149  0.053   6.875
getRandomGraphCentrality  0.696  0.029  14.893
* 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

##############################################################################
##############################################################################
###
### 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 
 39.469   2.526  55.828 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.1490.0536.875
addEdgeAtts10.220 2.56715.560
annotateGOont4.7291.1576.353
annotateGeneNames0.3440.0740.486
annotateGoBP4.7760.5915.860
annotateGoCC3.4400.3654.558
annotateGoMF3.9140.3774.641
annotatePresynaptic2.2600.1732.516
annotateSCHanno6.3220.5507.103
annotateTopOntoOVG 9.556 0.86110.998
annotateVertex0.0030.0010.003
applpMatrixToGraph0.0020.0010.003
buildNetwork0.0050.0020.009
calcAllClustering2.8720.1133.092
calcBridgeness0.0930.0120.154
calcCentrality0.0990.0050.115
calcCentralityExternalDistances0.5590.0621.950
calcCentralityInternalDistances0.5640.0452.767
calcClustering0.0040.0000.005
calcDiseasePairs0.5500.0200.594
calcEntropy10.327 1.45512.621
calcMembership0.0070.0030.014
calcReclusterMatrix0.0430.0060.051
calcSparsness5.6340.4616.162
clusterORA0.4660.0360.507
clusteringSummary12.598 0.09812.808
degreeBinnedGDAs0.3410.0080.352
escapeAnnotation0.0010.0000.002
evalCentralitySignificance0.6070.0130.625
findLCC0.0050.0010.007
getAnnotationList0.0740.0040.079
getAnnotationVertexList0.0900.0120.103
getBridgeness0.0750.0040.080
getCentralityMatrix10.674 0.47311.252
getClusterSubgraphByID0.0290.0020.031
getClustering0.0300.0020.031
getCommunityGraph0.0310.0020.033
getDType0.0000.0000.001
getDYNAMO0.0450.0020.047
getDiseases0.0000.0010.000
getEntropy11.248 0.70912.061
getEntropyRate0.0040.0000.004
getGNP0.0200.0010.021
getGraphCentralityECDF10.243 0.49210.812
getPA0.0250.0020.027
getRandomGraphCentrality 0.696 0.02914.893
getRobustness0.6120.0430.662
layoutByCluster0.1430.0030.146
layoutByRecluster0.1280.0050.134
makeConsensusMatrix0.6370.0430.691
makeMembership0.0020.0010.003
metlMatrix0.0110.0030.014
normModularity6.0670.4986.633
permute0.0010.0000.001
plotBridgeness0.5850.0130.606
plotEntropy13.360 0.76214.297
prepareGDA0.3150.0080.325
recluster0.0410.0030.044
removeVertexTerm0.0050.0010.007
runPermDisease6.2500.1726.488
sampleDegBinnedGDA0.4030.0070.414
sampleGraphClust0.0240.0020.026
unescapeAnnotation0.0000.0010.001
zeroNA0.0000.0000.001