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This page was generated on 2025-09-04 12:07 -0400 (Thu, 04 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4822
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4617
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4564
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 217/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.11.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2025-09-03 13:45 -0400 (Wed, 03 Sep 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: 2025-09-02 04:49:20 -0000 (Tue, 02 Sep 2025)
EndedAt: 2025-09-02 04:58:38 -0000 (Tue, 02 Sep 2025)
EllapsedTime: 557.8 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        13.849  0.004  13.872
plotEntropy              13.121  0.167  13.328
calcEntropy              12.617  0.020  12.678
getEntropy               12.034  0.032  12.102
getGraphCentralityECDF   11.904  0.000  11.942
getCentralityMatrix      11.534  0.036  11.605
addEdgeAtts              11.480  0.039  11.553
annotateTopOntoOVG        9.682  0.075   9.784
runPermDisease            8.536  0.112   8.669
annotateSCHanno           6.638  0.000   6.661
annotateGOont             5.578  0.136   5.916
normModularity            5.486  0.108   5.610
annotateGoBP              5.545  0.020   5.586
calcAllClustering         5.150  0.000   5.158
annotateGoMF              5.012  0.005   5.034
FitDegree                 1.353  0.031   7.667
getRandomGraphCentrality  0.863  0.131  14.322
* 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 
 45.042   1.218  61.026 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.3530.0317.667
addEdgeAtts11.480 0.03911.553
annotateGOont5.5780.1365.916
annotateGeneNames0.3050.0080.316
annotateGoBP5.5450.0205.586
annotateGoCC4.5660.0034.587
annotateGoMF5.0120.0055.034
annotatePresynaptic1.9860.0001.992
annotateSCHanno6.6380.0006.661
annotateTopOntoOVG9.6820.0759.784
annotateVertex0.0040.0000.004
applpMatrixToGraph0.0020.0000.002
buildNetwork0.0040.0000.004
calcAllClustering5.1500.0005.158
calcBridgeness0.0980.0000.099
calcCentrality0.1450.0040.152
calcCentralityExternalDistances0.6600.0080.670
calcCentralityInternalDistances0.7310.0120.745
calcClustering0.0050.0000.005
calcDiseasePairs0.6120.0200.633
calcEntropy12.617 0.02012.678
calcMembership0.0080.0000.007
calcReclusterMatrix0.0490.0000.049
calcSparsness4.9450.0004.959
clusterORA0.4860.0040.492
clusteringSummary13.849 0.00413.872
degreeBinnedGDAs0.3030.0000.304
escapeAnnotation0.0010.0000.000
evalCentralitySignificance0.7010.0040.707
findLCC0.0050.0000.006
getAnnotationList0.0730.0000.074
getAnnotationVertexList0.0860.0000.086
getBridgeness0.0890.0000.089
getCentralityMatrix11.534 0.03611.605
getClusterSubgraphByID0.0260.0040.030
getClustering0.0310.0000.032
getCommunityGraph0.0330.0000.033
getDType000
getDYNAMO0.0480.0000.049
getDiseases0.0000.0000.001
getEntropy12.034 0.03212.102
getEntropyRate0.0020.0040.005
getGNP0.0180.0080.027
getGraphCentralityECDF11.904 0.00011.942
getPA0.0260.0000.026
getRandomGraphCentrality 0.863 0.13114.322
getRobustness0.7780.0960.877
layoutByCluster0.4330.0320.466
layoutByRecluster0.3110.0120.324
makeConsensusMatrix0.7220.0990.825
makeMembership0.0010.0040.004
metlMatrix0.0150.0000.015
normModularity5.4860.1085.610
permute000
plotBridgeness0.5880.0280.617
plotEntropy13.121 0.16713.328
prepareGDA0.3170.0080.325
recluster0.0490.0000.049
removeVertexTerm0.0060.0000.005
runPermDisease8.5360.1128.669
sampleDegBinnedGDA0.3710.0080.380
sampleGraphClust0.0270.0080.035
unescapeAnnotation000
zeroNA000