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This page was generated on 2025-09-04 12:03 -0400 (Thu, 04 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4822
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4617
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4564
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 217/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.11.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2025-09-03 13:45 -0400 (Wed, 03 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BioNAR_1.11.0.tar.gz
StartedAt: 2025-09-03 21:20:41 -0400 (Wed, 03 Sep 2025)
EndedAt: 2025-09-03 21:31:35 -0400 (Wed, 03 Sep 2025)
EllapsedTime: 654.0 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNAR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BioNAR_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BioNAR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
clusteringSummary        17.560  0.028  18.627
calcEntropy              13.305  0.132  13.655
addEdgeAtts              13.030  0.319  13.821
plotEntropy              12.877  0.356  13.580
getEntropy               12.136  0.140  12.403
getGraphCentralityECDF    9.936  0.016   9.991
annotateTopOntoOVG        9.523  0.116  10.207
getCentralityMatrix       9.461  0.072  10.047
runPermDisease            7.925  0.103   8.363
calcAllClustering         6.853  0.022   7.070
annotateGOont             6.598  0.194   7.003
annotateSCHanno           6.710  0.004   7.078
normModularity            5.995  0.155   6.269
annotateGoBP              5.442  0.099   5.650
calcSparsness             5.429  0.024   5.650
annotateGoMF              4.989  0.144   5.220
FitDegree                 1.071  0.067   7.508
getRandomGraphCentrality  0.731  0.020  14.705
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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


Installation output

BioNAR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BioNAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 45.422   1.177  63.057 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.0710.0677.508
addEdgeAtts13.030 0.31913.821
annotateGOont6.5980.1947.003
annotateGeneNames0.3110.0070.349
annotateGoBP5.4420.0995.650
annotateGoCC4.6870.0244.921
annotateGoMF4.9890.1445.220
annotatePresynaptic2.0670.0222.097
annotateSCHanno6.7100.0047.078
annotateTopOntoOVG 9.523 0.11610.207
annotateVertex0.0050.0000.005
applpMatrixToGraph0.0020.0000.002
buildNetwork0.0050.0000.005
calcAllClustering6.8530.0227.070
calcBridgeness0.0860.0090.131
calcCentrality0.0980.0150.132
calcCentralityExternalDistances0.5890.0691.103
calcCentralityInternalDistances0.5140.0010.858
calcClustering0.0050.0000.005
calcDiseasePairs0.6220.0110.668
calcEntropy13.305 0.13213.655
calcMembership0.0080.0000.008
calcReclusterMatrix0.0520.0010.053
calcSparsness5.4290.0245.650
clusterORA0.4540.0250.527
clusteringSummary17.560 0.02818.627
degreeBinnedGDAs0.3430.0280.381
escapeAnnotation0.0010.0000.001
evalCentralitySignificance0.7580.0110.770
findLCC0.0050.0000.005
getAnnotationList0.0950.0010.096
getAnnotationVertexList0.1140.0020.116
getBridgeness0.0760.0020.078
getCentralityMatrix 9.461 0.07210.047
getClusterSubgraphByID0.0330.0000.033
getClustering0.0350.0000.035
getCommunityGraph0.0360.0010.037
getDType000
getDYNAMO0.0510.0020.053
getDiseases0.0010.0000.000
getEntropy12.136 0.14012.403
getEntropyRate0.0050.0000.006
getGNP0.0520.0020.054
getGraphCentralityECDF9.9360.0169.991
getPA0.0230.0000.023
getRandomGraphCentrality 0.731 0.02014.705
getRobustness0.5490.0440.615
layoutByCluster0.1580.0110.170
layoutByRecluster0.1300.0070.138
makeConsensusMatrix0.6550.0620.717
makeMembership0.0040.0000.003
metlMatrix0.0130.0000.013
normModularity5.9950.1556.269
permute000
plotBridgeness0.4400.0430.508
plotEntropy12.877 0.35613.580
prepareGDA0.2840.0190.349
recluster0.0390.0040.043
removeVertexTerm0.0050.0000.005
runPermDisease7.9250.1038.363
sampleDegBinnedGDA0.3820.0090.395
sampleGraphClust0.0280.0020.029
unescapeAnnotation0.0010.0000.001
zeroNA000