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This page was generated on 2025-10-02 12:06 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4844
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4576
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 219/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.11.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2025-10-01 13:45 -0400 (Wed, 01 Oct 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: BioNAR
Version: 1.11.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BioNAR_1.11.0.tar.gz
StartedAt: 2025-09-30 06:24:02 -0000 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 06:34:01 -0000 (Tue, 30 Sep 2025)
EllapsedTime: 599.0 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BioNAR_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BioNAR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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  6.8Mb
  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        13.863  0.012  13.901
plotEntropy              13.288  0.063  13.399
calcEntropy              12.811  0.056  12.910
getEntropy               12.461  0.068  12.566
getGraphCentralityECDF   12.038  0.048  12.123
getCentralityMatrix      11.845  0.051  11.931
addEdgeAtts              11.087  0.127  11.246
annotateTopOntoOVG       10.610  0.068  10.713
runPermDisease            8.616  0.008   8.653
annotateSCHanno           6.962  0.020   7.006
annotateGoBP              6.285  0.076   6.383
normModularity            5.978  0.032   6.031
annotateGOont             5.342  0.123   5.514
calcAllClustering         5.175  0.020   5.205
calcSparsness             5.017  0.012   5.044
FitDegree                 1.435  0.028   8.163
getRandomGraphCentrality  0.838  0.016  14.336
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/BioNAR.Rcheck/00check.log’
for details.


Installation output

BioNAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BioNAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 46.132   1.035  61.809 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.4350.0288.163
addEdgeAtts11.087 0.12711.246
annotateGOont5.3420.1235.514
annotateGeneNames0.3090.0160.348
annotateGoBP6.2850.0766.383
annotateGoCC4.9380.0154.971
annotateGoMF4.8590.0124.888
annotatePresynaptic2.6620.0152.687
annotateSCHanno6.9620.0207.006
annotateTopOntoOVG10.610 0.06810.713
annotateVertex0.0040.0000.005
applpMatrixToGraph0.0020.0000.002
buildNetwork0.0040.0000.004
calcAllClustering5.1750.0205.205
calcBridgeness0.1180.0040.123
calcCentrality0.1360.0080.145
calcCentralityExternalDistances0.7680.0480.818
calcCentralityInternalDistances0.7540.0000.757
calcClustering0.0060.0000.006
calcDiseasePairs0.6400.0080.649
calcEntropy12.811 0.05612.910
calcMembership0.0080.0000.007
calcReclusterMatrix0.0490.0040.052
calcSparsness5.0170.0125.044
clusterORA0.5200.0000.522
clusteringSummary13.863 0.01213.901
degreeBinnedGDAs0.3060.0040.311
escapeAnnotation0.0000.0000.001
evalCentralitySignificance0.7250.0140.741
findLCC0.0000.0050.005
getAnnotationList0.0690.0030.071
getAnnotationVertexList0.0800.0040.084
getBridgeness0.0910.0040.095
getCentralityMatrix11.845 0.05111.931
getClusterSubgraphByID0.0290.0000.030
getClustering0.0310.0000.031
getCommunityGraph0.0330.0000.033
getDType0.0010.0000.000
getDYNAMO0.0470.0000.048
getDiseases000
getEntropy12.461 0.06812.566
getEntropyRate0.0050.0000.005
getGNP0.0280.0000.028
getGraphCentralityECDF12.038 0.04812.123
getPA0.0270.0000.027
getRandomGraphCentrality 0.838 0.01614.336
getRobustness0.7090.0360.749
layoutByCluster0.4210.0080.429
layoutByRecluster0.2830.0040.287
makeConsensusMatrix0.7310.0160.749
makeMembership0.0020.0000.003
metlMatrix0.0100.0000.011
normModularity5.9780.0326.031
permute0.0000.0000.001
plotBridgeness0.6400.0040.647
plotEntropy13.288 0.06313.399
prepareGDA0.2830.0080.292
recluster0.0730.0070.081
removeVertexTerm0.0060.0000.006
runPermDisease8.6160.0088.653
sampleDegBinnedGDA0.3890.0040.394
sampleGraphClust0.0330.0040.036
unescapeAnnotation0.0010.0000.001
zeroNA0.0010.0000.000