Anatoly Sorokin
| Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-26 12:07 -0400 (Fri, 26 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4831 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4619 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4563 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 218/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioNAR 1.11.0 (landing page) Anatoly Sorokin
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
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. |
| 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: 2025-09-26 05:09:21 -0000 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 05:53:06 -0000 (Fri, 26 Sep 2025) |
| EllapsedTime: 2624.2 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: BioNAR.Rcheck |
| Warnings: NA |
##############################################################################
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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_1.11.0.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 ...
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)
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
45.899 1.267 62.251
BioNAR.Rcheck/BioNAR-Ex.timings
| name | user | system | elapsed | |
| FitDegree | 1.482 | 0.035 | 8.369 | |
| addEdgeAtts | 10.900 | 0.092 | 11.027 | |
| annotateGOont | 5.209 | 0.164 | 5.425 | |
| annotateGeneNames | 0.283 | 0.004 | 0.290 | |
| annotateGoBP | 6.100 | 0.064 | 6.189 | |
| annotateGoCC | 4.935 | 0.007 | 4.961 | |
| annotateGoMF | 5.171 | 0.019 | 5.211 | |
| annotatePresynaptic | 2.709 | 0.060 | 2.779 | |
| annotateSCHanno | 6.868 | 0.024 | 6.916 | |
| annotateTopOntoOVG | 10.702 | 0.060 | 10.795 | |
| annotateVertex | 0.005 | 0.000 | 0.005 | |
| applpMatrixToGraph | 0.003 | 0.000 | 0.002 | |
| buildNetwork | 0.004 | 0.000 | 0.005 | |
| calcAllClustering | 5.140 | 0.028 | 5.185 | |
| calcBridgeness | 0.092 | 0.016 | 0.108 | |
| calcCentrality | 0.132 | 0.004 | 0.140 | |
| calcCentralityExternalDistances | 0.763 | 0.012 | 0.777 | |
| calcCentralityInternalDistances | 0.717 | 0.004 | 0.723 | |
| calcClustering | 0.006 | 0.000 | 0.005 | |
| calcDiseasePairs | 0.629 | 0.024 | 0.655 | |
| calcEntropy | 13.123 | 0.028 | 13.198 | |
| calcMembership | 0.009 | 0.000 | 0.008 | |
| calcReclusterMatrix | 0.056 | 0.000 | 0.055 | |
| calcSparsness | 6.004 | 0.000 | 6.021 | |
| clusterORA | 0.512 | 0.004 | 0.518 | |
| clusteringSummary | 13.842 | 0.012 | 13.893 | |
| degreeBinnedGDAs | 0.311 | 0.000 | 0.313 | |
| escapeAnnotation | 0.001 | 0.000 | 0.000 | |
| evalCentralitySignificance | 0.735 | 0.008 | 0.745 | |
| findLCC | 0.006 | 0.000 | 0.006 | |
| getAnnotationList | 0.071 | 0.000 | 0.072 | |
| getAnnotationVertexList | 0.086 | 0.000 | 0.087 | |
| getBridgeness | 0.094 | 0.000 | 0.094 | |
| getCentralityMatrix | 12.179 | 0.602 | 12.821 | |
| getClusterSubgraphByID | 0.032 | 0.004 | 0.037 | |
| getClustering | 0.036 | 0.000 | 0.036 | |
| getCommunityGraph | 0.033 | 0.004 | 0.038 | |
| getDType | 0.000 | 0.000 | 0.001 | |
| getDYNAMO | 0.050 | 0.004 | 0.055 | |
| getDiseases | 0 | 0 | 0 | |
| getEntropy | 12.291 | 0.167 | 12.496 | |
| getEntropyRate | 0.006 | 0.000 | 0.006 | |
| getGNP | 0.024 | 0.004 | 0.027 | |
| getGraphCentralityECDF | 11.791 | 0.080 | 11.906 | |
| getPA | 0.03 | 0.00 | 0.03 | |
| getRandomGraphCentrality | 1.039 | 0.016 | 14.287 | |
| getRobustness | 0.722 | 0.008 | 0.732 | |
| layoutByCluster | 0.424 | 0.004 | 0.429 | |
| layoutByRecluster | 0.283 | 0.008 | 0.291 | |
| makeConsensusMatrix | 0.788 | 0.020 | 0.811 | |
| makeMembership | 0.003 | 0.000 | 0.003 | |
| metlMatrix | 0.011 | 0.000 | 0.011 | |
| normModularity | 5.443 | 0.040 | 5.498 | |
| permute | 0.001 | 0.000 | 0.000 | |
| plotBridgeness | 0.675 | 0.008 | 0.684 | |
| plotEntropy | 13.467 | 0.095 | 13.605 | |
| prepareGDA | 0.293 | 0.004 | 0.297 | |
| recluster | 0.074 | 0.004 | 0.079 | |
| removeVertexTerm | 0.002 | 0.004 | 0.007 | |
| runPermDisease | 8.270 | 0.028 | 8.322 | |
| sampleDegBinnedGDA | 0.423 | 0.004 | 0.428 | |
| sampleGraphClust | 0.035 | 0.000 | 0.036 | |
| unescapeAnnotation | 0 | 0 | 0 | |
| zeroNA | 0 | 0 | 0 | |