Back to Multiple platform build/check report for BioC 3.22:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-15 12:04 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 216/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.11.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 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
palomino8Windows Server 2022 Datacenter / x64  OK    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: 2025-08-14 20:31:05 -0400 (Thu, 14 Aug 2025)
EndedAt: 2025-08-14 20:38:56 -0400 (Thu, 14 Aug 2025)
EllapsedTime: 471.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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        11.345  0.001  11.347
plotEntropy               9.149  0.019   9.169
calcEntropy               9.019  0.028   9.049
addEdgeAtts               8.432  0.052   8.504
getEntropy                8.210  0.030   8.240
annotateTopOntoOVG        7.269  0.066   7.335
getCentralityMatrix       7.273  0.028   7.302
getGraphCentralityECDF    7.144  0.036   7.181
runPermDisease            6.388  0.014   6.402
annotateGOont             4.748  0.116   5.105
FitDegree                 0.869  0.023   5.508
getRandomGraphCentrality  0.531  0.006  10.085
* 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

##############################################################################
##############################################################################
###
### 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 
 33.127   0.888  44.798 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree0.8690.0235.508
addEdgeAtts8.4320.0528.504
annotateGOont4.7480.1165.105
annotateGeneNames0.2710.0040.276
annotateGoBP4.6910.0284.737
annotateGoCC3.4780.0023.492
annotateGoMF3.8380.0023.843
annotatePresynaptic1.4850.0301.515
annotateSCHanno4.6730.0034.677
annotateTopOntoOVG7.2690.0667.335
annotateVertex0.0190.0010.019
applpMatrixToGraph0.0020.0000.002
buildNetwork0.0030.0000.003
calcAllClustering4.5980.0014.600
calcBridgeness0.0650.0000.065
calcCentrality0.0820.0010.083
calcCentralityExternalDistances0.4530.0300.483
calcCentralityInternalDistances0.4630.0010.463
calcClustering0.0020.0000.004
calcDiseasePairs0.4770.0200.499
calcEntropy9.0190.0289.049
calcMembership0.0060.0000.005
calcReclusterMatrix0.0350.0010.034
calcSparsness3.2870.0003.288
clusterORA0.3670.0020.370
clusteringSummary11.345 0.00111.347
degreeBinnedGDAs0.2420.0010.244
escapeAnnotation0.0000.0000.001
evalCentralitySignificance0.4720.0000.472
findLCC0.0040.0000.004
getAnnotationList0.0700.0000.071
getAnnotationVertexList0.0780.0010.079
getBridgeness0.0590.0000.059
getCentralityMatrix7.2730.0287.302
getClusterSubgraphByID0.020.000.02
getClustering0.0210.0000.021
getCommunityGraph0.0220.0000.022
getDType000
getDYNAMO0.0320.0010.033
getDiseases000
getEntropy8.210.038.24
getEntropyRate0.0040.0000.004
getGNP0.0170.0010.018
getGraphCentralityECDF7.1440.0367.181
getPA0.0190.0000.019
getRandomGraphCentrality 0.531 0.00610.085
getRobustness0.4780.0000.478
layoutByCluster0.1080.0010.109
layoutByRecluster0.0960.0000.096
makeConsensusMatrix0.4440.0000.444
makeMembership0.0010.0010.002
metlMatrix0.0080.0000.008
normModularity3.8780.0213.899
permute000
plotBridgeness0.3910.0010.392
plotEntropy9.1490.0199.169
prepareGDA0.2730.0020.276
recluster0.0330.0000.033
removeVertexTerm0.0040.0000.004
runPermDisease6.3880.0146.402
sampleDegBinnedGDA0.3010.0010.302
sampleGraphClust0.0250.0000.025
unescapeAnnotation0.0010.0000.001
zeroNA000