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This page was generated on 2025-10-06 11:41 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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 217/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.10.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2025-10-02 13:40 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/BioNAR
git_branch: RELEASE_3_21
git_last_commit: d3036b1
git_last_commit_date: 2025-04-15 12:58:11 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BioNAR on kunpeng2

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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2025-10-03 07:02:18 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 07:10:30 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 491.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNAR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BioNAR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.10.0’
* 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
calcEntropy              14.588  0.068  14.697
clusteringSummary        13.851  0.016  13.891
plotEntropy              13.793  0.060  13.889
getEntropy               13.426  0.087  13.549
addEdgeAtts              13.123  0.119  13.272
getCentralityMatrix      12.475  0.048  12.560
getGraphCentralityECDF   12.486  0.027  12.545
annotateTopOntoOVG       11.241  0.044  11.315
runPermDisease            8.019  0.015   8.061
annotateSCHanno           7.626  0.032   7.680
annotateGOont             6.117  0.056   6.217
annotateGoBP              6.075  0.048   6.140
normModularity            5.859  0.028   5.900
calcSparsness             5.681  0.004   5.697
annotateGoMF              5.572  0.031   5.619
calcAllClustering         5.134  0.000   5.148
FitDegree                 1.360  0.077   8.143
getRandomGraphCentrality  0.815  0.012  14.879
* 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-3.21-bioc/meat/BioNAR.Rcheck/00check.log’
for details.


Installation output

BioNAR.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘BioNAR’ ...
** this is package ‘BioNAR’ version ‘1.10.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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 
 46.193   1.282  64.117 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.3600.0778.143
addEdgeAtts13.123 0.11913.272
annotateGOont6.1170.0566.217
annotateGeneNames0.3570.0200.400
annotateGoBP6.0750.0486.140
annotateGoCC4.9500.0204.985
annotateGoMF5.5720.0315.619
annotatePresynaptic2.2350.0042.246
annotateSCHanno7.6260.0327.680
annotateTopOntoOVG11.241 0.04411.315
annotateVertex0.0040.0000.004
applpMatrixToGraph0.0020.0000.002
buildNetwork0.0040.0000.004
calcAllClustering5.1340.0005.148
calcBridgeness0.1040.0000.105
calcCentrality0.1180.0080.128
calcCentralityExternalDistances0.7080.0840.793
calcCentralityInternalDistances0.6840.0040.690
calcClustering0.0060.0000.006
calcDiseasePairs0.6740.0000.675
calcEntropy14.588 0.06814.697
calcMembership0.0080.0000.007
calcReclusterMatrix0.0520.0000.053
calcSparsness5.6810.0045.697
clusterORA0.4940.0000.495
clusteringSummary13.851 0.01613.891
degreeBinnedGDAs0.3550.0000.356
escapeAnnotation0.0000.0000.001
evalCentralitySignificance0.6830.0040.689
findLCC0.0050.0000.006
getAnnotationList0.0780.0000.078
getAnnotationVertexList0.0880.0020.091
getBridgeness0.0920.0010.093
getCentralityMatrix12.475 0.04812.560
getClusterSubgraphByID0.0320.0000.032
getClustering0.0330.0000.033
getCommunityGraph0.0310.0040.035
getDType000
getDYNAMO0.0480.0000.049
getDiseases0.0000.0000.001
getEntropy13.426 0.08713.549
getEntropyRate0.0060.0000.005
getGNP0.0280.0000.027
getGraphCentralityECDF12.486 0.02712.545
getPA0.0280.0000.028
getRandomGraphCentrality 0.815 0.01214.879
getRobustness0.6630.0040.670
layoutByCluster0.4270.0000.429
layoutByRecluster0.2840.0000.286
makeConsensusMatrix0.7490.0080.760
makeMembership0.0030.0000.003
metlMatrix0.0100.0000.011
normModularity5.8590.0285.900
permute000
plotBridgeness0.4920.0040.497
plotEntropy13.793 0.06013.889
prepareGDA0.3250.0040.330
recluster0.0460.0040.050
removeVertexTerm0.0060.0000.006
runPermDisease8.0190.0158.061
sampleDegBinnedGDA0.4660.0040.470
sampleGraphClust0.0360.0000.036
unescapeAnnotation0.0010.0000.001
zeroNA0.0000.0000.001