Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 216/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BioNAR 1.11.0 (landing page) Anatoly Sorokin
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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. |
Package: BioNAR |
Version: 1.11.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNAR_1.11.0.tar.gz |
StartedAt: 2025-08-08 18:21:31 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 18:23:48 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 136.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BioNAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNAR_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BioNAR.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * 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 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 * 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 ‘/Users/biocbuild/bbs-3.22-bioc/meat/BioNAR.Rcheck/00check.log’ for details.
BioNAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioNAR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 12.317 0.913 17.209
BioNAR.Rcheck/BioNAR-Ex.timings
name | user | system | elapsed | |
FitDegree | 0.307 | 0.027 | 1.839 | |
addEdgeAtts | 3.684 | 1.031 | 4.774 | |
annotateGOont | 1.689 | 0.281 | 2.001 | |
annotateGeneNames | 0.088 | 0.005 | 0.094 | |
annotateGoBP | 1.300 | 0.309 | 1.644 | |
annotateGoCC | 0.958 | 0.275 | 1.240 | |
annotateGoMF | 1.175 | 0.343 | 1.540 | |
annotatePresynaptic | 0.424 | 0.144 | 0.571 | |
annotateSCHanno | 1.906 | 0.453 | 2.370 | |
annotateTopOntoOVG | 2.889 | 0.474 | 3.370 | |
annotateVertex | 0.001 | 0.000 | 0.002 | |
applpMatrixToGraph | 0.000 | 0.001 | 0.000 | |
buildNetwork | 0.000 | 0.000 | 0.001 | |
calcAllClustering | 1.703 | 0.004 | 1.712 | |
calcBridgeness | 0.020 | 0.001 | 0.021 | |
calcCentrality | 0.026 | 0.001 | 0.027 | |
calcCentralityExternalDistances | 0.129 | 0.010 | 0.227 | |
calcCentralityInternalDistances | 0.130 | 0.004 | 0.133 | |
calcClustering | 0.001 | 0.000 | 0.001 | |
calcDiseasePairs | 0.199 | 0.010 | 0.210 | |
calcEntropy | 3.522 | 0.533 | 4.084 | |
calcMembership | 0.002 | 0.000 | 0.002 | |
calcReclusterMatrix | 0.010 | 0.000 | 0.011 | |
calcSparsness | 1.508 | 0.368 | 1.884 | |
clusterORA | 0.105 | 0.010 | 0.114 | |
clusteringSummary | 3.959 | 0.012 | 3.971 | |
degreeBinnedGDAs | 0.084 | 0.005 | 0.090 | |
escapeAnnotation | 0 | 0 | 0 | |
evalCentralitySignificance | 0.125 | 0.008 | 0.132 | |
findLCC | 0.001 | 0.000 | 0.002 | |
getAnnotationList | 0.019 | 0.002 | 0.021 | |
getAnnotationVertexList | 0.023 | 0.003 | 0.026 | |
getBridgeness | 0.018 | 0.002 | 0.020 | |
getCentralityMatrix | 2.653 | 0.518 | 3.185 | |
getClusterSubgraphByID | 0.007 | 0.000 | 0.007 | |
getClustering | 0.007 | 0.000 | 0.007 | |
getCommunityGraph | 0.007 | 0.000 | 0.007 | |
getDType | 0 | 0 | 0 | |
getDYNAMO | 0.010 | 0.000 | 0.011 | |
getDiseases | 0 | 0 | 0 | |
getEntropy | 3.296 | 0.968 | 4.281 | |
getEntropyRate | 0.001 | 0.000 | 0.001 | |
getGNP | 0.005 | 0.000 | 0.006 | |
getGraphCentralityECDF | 2.660 | 0.575 | 3.261 | |
getPA | 0.006 | 0.000 | 0.006 | |
getRandomGraphCentrality | 0.144 | 0.010 | 3.786 | |
getRobustness | 0.140 | 0.008 | 0.148 | |
layoutByCluster | 0.035 | 0.002 | 0.037 | |
layoutByRecluster | 0.030 | 0.001 | 0.031 | |
makeConsensusMatrix | 0.137 | 0.007 | 0.144 | |
makeMembership | 0.001 | 0.000 | 0.001 | |
metlMatrix | 0.002 | 0.000 | 0.003 | |
normModularity | 1.700 | 0.454 | 2.159 | |
permute | 0 | 0 | 0 | |
plotBridgeness | 0.114 | 0.007 | 0.122 | |
plotEntropy | 3.367 | 0.443 | 3.821 | |
prepareGDA | 0.085 | 0.007 | 0.092 | |
recluster | 0.01 | 0.00 | 0.01 | |
removeVertexTerm | 0.001 | 0.001 | 0.001 | |
runPermDisease | 2.931 | 0.097 | 3.042 | |
sampleDegBinnedGDA | 0.107 | 0.011 | 0.118 | |
sampleGraphClust | 0.008 | 0.000 | 0.009 | |
unescapeAnnotation | 0.000 | 0.001 | 0.000 | |
zeroNA | 0 | 0 | 0 | |