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This page was generated on 2025-10-03 12:07 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
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: 2025-10-02 13:45 -0400 (Thu, 02 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: 2025-10-03 05:04:51 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 05:20:36 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 945.0 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        13.842  0.012  13.870
plotEntropy              13.374  0.287  13.702
calcEntropy              13.115  0.032  13.192
getEntropy               12.080  0.095  12.214
getCentralityMatrix      12.056  0.068  12.162
getGraphCentralityECDF   12.052  0.020  12.110
addEdgeAtts              11.033  0.187  11.252
annotateTopOntoOVG       10.567  0.084  10.684
runPermDisease            8.180  0.116   8.319
annotateSCHanno           6.807  0.012   6.839
normModularity            6.025  0.438   6.482
annotateGoBP              6.012  0.104   6.134
annotateGOont             5.338  0.124   5.500
calcAllClustering         5.191  0.015   5.215
annotateGoMF              5.132  0.040   5.189
FitDegree                 1.440  0.059   8.002
getRandomGraphCentrality  0.961  0.287  15.292
* 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 
 46.278   1.278  61.921 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.4400.0598.002
addEdgeAtts11.033 0.18711.252
annotateGOont5.3380.1245.500
annotateGeneNames0.3110.0000.315
annotateGoBP6.0120.1046.134
annotateGoCC4.9560.0084.982
annotateGoMF5.1320.0405.189
annotatePresynaptic2.6670.0832.760
annotateSCHanno6.8070.0126.839
annotateTopOntoOVG10.567 0.08410.684
annotateVertex0.0050.0000.005
applpMatrixToGraph0.0020.0000.002
buildNetwork0.0040.0000.004
calcAllClustering5.1910.0155.215
calcBridgeness0.1010.0030.105
calcCentrality0.1360.0000.139
calcCentralityExternalDistances0.7740.0240.801
calcCentralityInternalDistances0.7660.0040.772
calcClustering0.0060.0000.006
calcDiseasePairs0.6410.0200.663
calcEntropy13.115 0.03213.192
calcMembership0.0080.0000.008
calcReclusterMatrix0.0520.0040.056
calcSparsness4.9770.0004.991
clusterORA0.4970.0040.504
clusteringSummary13.842 0.01213.870
degreeBinnedGDAs0.3020.0160.318
escapeAnnotation0.0010.0000.000
evalCentralitySignificance0.7160.0120.730
findLCC0.0060.0000.005
getAnnotationList0.0690.0000.069
getAnnotationVertexList0.0810.0000.082
getBridgeness0.0890.0000.089
getCentralityMatrix12.056 0.06812.162
getClusterSubgraphByID0.0280.0040.032
getClustering0.0330.0000.034
getCommunityGraph0.0360.0000.037
getDType0.0000.0000.001
getDYNAMO0.0520.0000.053
getDiseases000
getEntropy12.080 0.09512.214
getEntropyRate0.0050.0000.005
getGNP0.0260.0000.026
getGraphCentralityECDF12.052 0.02012.110
getPA0.0250.0030.028
getRandomGraphCentrality 0.961 0.28715.292
getRobustness0.8190.1811.003
layoutByCluster0.4330.0050.438
layoutByRecluster0.2830.0040.288
makeConsensusMatrix0.7470.0320.781
makeMembership0.0030.0000.003
metlMatrix0.0130.0000.012
normModularity6.0250.4386.482
permute000
plotBridgeness0.6670.0040.672
plotEntropy13.374 0.28713.702
prepareGDA0.3040.0080.313
recluster0.0840.0000.084
removeVertexTerm0.0060.0000.006
runPermDisease8.1800.1168.319
sampleDegBinnedGDA0.3930.0200.415
sampleGraphClust0.0350.0040.038
unescapeAnnotation0.0010.0000.001
zeroNA000