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This page was generated on 2025-09-13 12:02 -0400 (Sat, 13 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4719
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4538
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4522
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4543
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 218/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.11.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2025-09-12 13:45 -0400 (Fri, 12 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: 2025-09-12 21:23:18 -0400 (Fri, 12 Sep 2025)
EndedAt: 2025-09-12 21:34:10 -0400 (Fri, 12 Sep 2025)
EllapsedTime: 652.0 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 Patched (2025-08-23 r88802)
* 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        15.437  0.044  15.749
getGraphCentralityECDF   12.334  0.458  13.072
getEntropy               12.529  0.203  12.911
plotEntropy              11.474  0.216  12.162
addEdgeAtts              11.377  0.129  11.699
calcEntropy              11.108  0.140  11.608
getCentralityMatrix      10.105  0.175  11.048
annotateTopOntoOVG        9.506  0.123  10.009
calcAllClustering         7.341  0.036   8.099
annotateSCHanno           7.345  0.024   7.955
runPermDisease            6.894  0.053   7.108
annotateGoBP              6.084  0.077   6.383
annotateGOont             5.598  0.095   5.874
normModularity            5.399  0.122   5.681
FitDegree                 1.527  0.077   8.585
getRandomGraphCentrality  0.663  0.046  13.126
* 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 Patched (2025-08-23 r88802) -- "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 
 50.653   2.106  69.945 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.5270.0778.585
addEdgeAtts11.377 0.12911.699
annotateGOont5.5980.0955.874
annotateGeneNames0.3030.0010.303
annotateGoBP6.0840.0776.383
annotateGoCC4.2730.0294.518
annotateGoMF4.5680.0044.997
annotatePresynaptic2.6010.0682.850
annotateSCHanno7.3450.0247.955
annotateTopOntoOVG 9.506 0.12310.009
annotateVertex0.0050.0000.005
applpMatrixToGraph0.0020.0000.002
buildNetwork0.0030.0010.004
calcAllClustering7.3410.0368.099
calcBridgeness0.0800.0130.092
calcCentrality0.1330.0250.166
calcCentralityExternalDistances0.6190.0730.695
calcCentralityInternalDistances0.5260.0000.526
calcClustering0.0040.0000.004
calcDiseasePairs0.5420.0150.619
calcEntropy11.108 0.14011.608
calcMembership0.0060.0000.005
calcReclusterMatrix0.040.000.04
calcSparsness4.4170.0174.459
clusterORA0.3940.0070.400
clusteringSummary15.437 0.04415.749
degreeBinnedGDAs0.3230.0530.403
escapeAnnotation000
evalCentralitySignificance0.5460.0250.571
findLCC0.0050.0010.005
getAnnotationList0.0700.0030.074
getAnnotationVertexList0.0770.0020.080
getBridgeness0.1040.0060.136
getCentralityMatrix10.105 0.17511.048
getClusterSubgraphByID0.0230.0020.024
getClustering0.0240.0010.024
getCommunityGraph0.0270.0000.026
getDType000
getDYNAMO0.0460.0010.047
getDiseases000
getEntropy12.529 0.20312.911
getEntropyRate0.0060.0010.006
getGNP0.0300.0010.031
getGraphCentralityECDF12.334 0.45813.072
getPA0.0220.0010.030
getRandomGraphCentrality 0.663 0.04613.126
getRobustness0.5580.0300.592
layoutByCluster0.1660.0000.166
layoutByRecluster0.1740.0310.206
makeConsensusMatrix0.5770.0380.624
makeMembership0.0030.0000.003
metlMatrix0.0100.0020.011
normModularity5.3990.1225.681
permute000
plotBridgeness0.5290.0320.560
plotEntropy11.474 0.21612.162
prepareGDA0.3810.0270.423
recluster0.0510.0010.052
removeVertexTerm0.0050.0010.006
runPermDisease6.8940.0537.108
sampleDegBinnedGDA0.3680.0040.372
sampleGraphClust0.0290.0000.029
unescapeAnnotation000
zeroNA000