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This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
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 217/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.11.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 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: 2025-08-29 19:26:47 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 19:36:35 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 587.6 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 (2025-06-13)
* 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
addEdgeAtts              12.560  2.076  14.978
calcEntropy              12.082  0.753  13.046
plotEntropy              11.869  0.881  12.838
getEntropy               10.200  1.618  12.666
clusteringSummary        10.414  0.697  11.453
getGraphCentralityECDF    9.805  0.946  11.560
annotateTopOntoOVG        9.939  0.621  10.706
getCentralityMatrix       7.625  1.179   8.931
annotateSCHanno           6.893  0.706   8.002
runPermDisease            6.571  0.214   6.834
annotateGOont             5.882  0.828   6.816
normModularity            5.501  0.630   6.183
calcSparsness             4.902  0.765   5.822
annotateGoBP              4.867  0.500   5.569
FitDegree                 1.044  0.056   6.404
getRandomGraphCentrality  0.658  0.026  13.880
* 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 (2025-06-13) -- "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 
 39.446   2.475  56.114 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.0440.0566.404
addEdgeAtts12.560 2.07614.978
annotateGOont5.8820.8286.816
annotateGeneNames0.3180.0120.333
annotateGoBP4.8670.5005.569
annotateGoCC3.9750.3654.513
annotateGoMF4.1790.3624.717
annotatePresynaptic1.4720.2111.961
annotateSCHanno6.8930.7068.002
annotateTopOntoOVG 9.939 0.62110.706
annotateVertex0.0020.0000.004
applpMatrixToGraph0.0020.0000.003
buildNetwork0.0030.0000.004
calcAllClustering3.8310.0343.895
calcBridgeness0.0940.0060.100
calcCentrality0.1090.0040.116
calcCentralityExternalDistances0.5810.0180.604
calcCentralityInternalDistances0.5420.0060.551
calcClustering0.0050.0010.005
calcDiseasePairs0.5100.0160.530
calcEntropy12.082 0.75313.046
calcMembership0.0070.0010.009
calcReclusterMatrix0.0390.0020.042
calcSparsness4.9020.7655.822
clusterORA0.3690.0660.461
clusteringSummary10.414 0.69711.453
degreeBinnedGDAs0.2530.0470.314
escapeAnnotation0.0010.0000.001
evalCentralitySignificance0.4270.0590.495
findLCC0.0040.0010.004
getAnnotationList0.0500.0030.053
getAnnotationVertexList0.0600.0090.069
getBridgeness0.0480.0030.051
getCentralityMatrix7.6251.1798.931
getClusterSubgraphByID0.0210.0070.031
getClustering0.0170.0010.018
getCommunityGraph0.0180.0010.019
getDType000
getDYNAMO0.0260.0010.028
getDiseases0.0000.0010.000
getEntropy10.200 1.61812.666
getEntropyRate0.0060.0010.007
getGNP0.0230.0020.025
getGraphCentralityECDF 9.805 0.94611.560
getPA0.0230.0010.024
getRandomGraphCentrality 0.658 0.02613.880
getRobustness0.5580.0360.662
layoutByCluster0.1170.0030.192
layoutByRecluster0.1030.0040.134
makeConsensusMatrix0.5480.0380.611
makeMembership0.0020.0010.003
metlMatrix0.0090.0010.011
normModularity5.5010.6306.183
permute0.0000.0010.001
plotBridgeness0.4480.0770.556
plotEntropy11.869 0.88112.838
prepareGDA0.3230.0090.333
recluster0.0420.0030.045
removeVertexTerm0.0050.0020.007
runPermDisease6.5710.2146.834
sampleDegBinnedGDA0.4090.0110.422
sampleGraphClust0.0260.0020.027
unescapeAnnotation0.0010.0010.002
zeroNA0.0000.0010.001