| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 219/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioNAR 1.15.0 (landing page) Anatoly Sorokin
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
| See other builds for BioNAR in R Universe. | ||||||||||||||
|
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: 1.15.0 |
| 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_1.15.0.tar.gz |
| StartedAt: 2026-05-05 07:35:22 -0000 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 08:15:23 -0000 (Tue, 05 May 2026) |
| EllapsedTime: 2400.9 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: BioNAR.Rcheck |
| Warnings: NA |
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### Running command:
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### /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_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.24-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 ‘1.15.0’
* 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 ...
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 ‘1.15.0’ ** 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/BioNAR-Ex.timings
| name | user | system | elapsed | |
| FitDegree | 1.938 | 0.064 | 8.413 | |
| addEdgeAtts | 10.954 | 0.056 | 11.036 | |
| annotateGOont | 5.785 | 0.132 | 5.960 | |
| annotateGeneNames | 0.330 | 0.004 | 0.353 | |
| annotateGoBP | 6.294 | 0.076 | 6.388 | |
| annotateGoCC | 4.956 | 0.011 | 4.982 | |
| annotateGoMF | 5.036 | 0.012 | 5.061 | |
| annotatePresynaptic | 2.815 | 0.043 | 2.866 | |
| annotateSCHanno | 6.892 | 0.032 | 6.944 | |
| annotateTopOntoOVG | 10.952 | 0.032 | 11.014 | |
| annotateVertex | 0.005 | 0.000 | 0.005 | |
| applpMatrixToGraph | 0.003 | 0.000 | 0.002 | |
| buildNetwork | 0.005 | 0.000 | 0.004 | |
| calcAllClustering | 5.205 | 0.004 | 5.223 | |
| calcBridgeness | 0.099 | 0.008 | 0.107 | |
| calcCentrality | 0.143 | 0.000 | 0.146 | |
| calcCentralityExternalDistances | 0.855 | 0.096 | 0.954 | |
| calcCentralityInternalDistances | 0.884 | 0.008 | 0.894 | |
| calcClustering | 0.007 | 0.000 | 0.006 | |
| calcDiseasePairs | 0.681 | 0.008 | 0.691 | |
| calcEntropy | 14.008 | 0.036 | 14.084 | |
| calcMembership | 0.507 | 0.000 | 0.509 | |
| calcReclusterMatrix | 0.051 | 0.000 | 0.051 | |
| calcSparsness | 4.843 | 0.000 | 4.855 | |
| clusterORA | 0.517 | 0.004 | 0.523 | |
| clusteringSummary | 13.931 | 0.016 | 13.974 | |
| degreeBinnedGDAs | 0.309 | 0.016 | 0.325 | |
| escapeAnnotation | 0.001 | 0.000 | 0.000 | |
| evalCentralitySignificance | 0.886 | 0.039 | 0.928 | |
| findLCC | 0.006 | 0.000 | 0.006 | |
| getAnnotationList | 0.073 | 0.000 | 0.073 | |
| getAnnotationVertexList | 0.081 | 0.003 | 0.084 | |
| getBridgeness | 0.099 | 0.000 | 0.100 | |