Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:30 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 213/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BioNAR 1.6.0 (landing page) Anatoly Sorokin
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the BioNAR package: - 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: 1.6.0 |
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_1.6.0.tar.gz |
StartedAt: 2024-05-06 19:59:49 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 20:02:01 -0400 (Mon, 06 May 2024) |
EllapsedTime: 132.5 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_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/BioNAR.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BioNAR/DESCRIPTION’ ... OK * this is package ‘BioNAR’ version ‘1.6.0’ * 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 ... NOTE 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 ... NOTE clusterORA : forafun: no visible binding for global variable ‘pathway’ clusterORA : forafun: no visible binding for global variable ‘size’ clusterORA : forafun: no visible binding for global variable ‘overlap’ clusterORA : forafun: no visible binding for global variable ‘pval’ clusterORA : forafun: no visible binding for global variable ‘padj’ clusterORA : forafun: no visible binding for global variable ‘overlapGenes’ clusterORA : forafun: no visible binding for global variable ‘FL’ clusterORA : forafun: no visible binding for global variable ‘N’ clusterORA : forafun: no visible binding for global variable ‘Fn’ clusterORA : forafun: no visible binding for global variable ‘Cn’ clusterORA : forafun: no visible binding for global variable ‘Mu’ clusterORA : forafun: no visible binding for global variable ‘OR’ clusterORA : forafun: no visible binding for global variable ‘CIw’ clusterORA : forafun: no visible binding for global variable ‘Fe’ clusterORA : forafun: no visible binding for global variable ‘Fc’ clusterORA : forafun: no visible binding for global variable ‘palt’ plotSigmoid: no visible binding for global variable ‘yiR1’ plotSigmoid: no visible binding for global variable ‘yiR2’ plotSigmoid: no visible binding for global variable ‘yiR3’ plotSigmoid: no visible binding for global variable ‘yiR4’ plotSigmoid: no visible binding for global variable ‘yiR5’ Undefined global functions or variables: CIw Cn Fc Fe FL Fn Mu N OR overlap overlapGenes padj palt pathway pval size yiR1 yiR2 yiR3 yiR4 yiR5 * checking Rd files ... NOTE checkRd: (-1) calcEntropy.Rd:52: Lost braces; missing escapes or markup? 52 | Other {Entropy Functions}: | ^ checkRd: (-1) FitDegree.Rd:34: Lost braces 34 | \item{legpos}{position of the legend @seealso{legend}} | ^ checkRd: (-1) getEntropy.Rd:66: Lost braces; missing escapes or markup? 66 | Other {Entropy Functions}: | ^ checkRd: (-1) getEntropyRate.Rd:41: Lost braces; missing escapes or markup? 41 | Other {Entropy Functions}: | ^ checkRd: (-1) getRobustness.Rd:49: Lost braces; missing escapes or markup? 49 | Other {Robustness functions}: | ^ checkRd: (-1) makeConsensusMatrix.Rd:69: Lost braces; missing escapes or markup? 69 | Other {Robustness functions}: | ^ checkRd: (-1) plotEntropy.Rd:57: Lost braces; missing escapes or markup? 57 | Other {Entropy Functions}: | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/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/4.4-arm64/Resources/library’ * installing *source* package ‘BioNAR’ ... ** 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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 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 129 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test_bridgeness.R:38:5', 'test_bridgeness.R:81:5' [ FAIL 0 | WARN 0 | SKIP 2 | PASS 129 ] > > proc.time() user system elapsed 11.984 0.629 16.600
BioNAR.Rcheck/BioNAR-Ex.timings
name | user | system | elapsed | |
FitDegree | 0.271 | 0.011 | 1.668 | |
addEdgeAtts | 3.492 | 0.829 | 4.326 | |
annotateGOont | 1.558 | 0.191 | 1.752 | |
annotateGeneNames | 0.083 | 0.004 | 0.088 | |
annotateGoBP | 1.144 | 0.293 | 1.441 | |
annotateGoCC | 0.806 | 0.240 | 1.047 | |
annotateGoMF | 0.951 | 0.267 | 1.219 | |
annotatePresynaptic | 0.327 | 0.097 | 0.425 | |
annotateSCHanno | 1.831 | 0.393 | 2.227 | |
annotateTopOntoOVG | 2.637 | 0.430 | 3.073 | |
annotateVertex | 0.001 | 0.000 | 0.002 | |
applpMatrixToGraph | 0.001 | 0.000 | 0.001 | |
buildNetwork | 0.001 | 0.000 | 0.001 | |
calcAllClustering | 1.745 | 0.005 | 1.751 | |
calcBridgeness | 0.020 | 0.001 | 0.021 | |
calcCentrality | 0.012 | 0.001 | 0.013 | |
calcCentralityExternalDistances | 0.096 | 0.005 | 0.100 | |
calcCentralityInternalDistances | 0.103 | 0.003 | 0.106 | |
calcClustering | 0.001 | 0.000 | 0.001 | |
calcDiseasePairs | 0.199 | 0.007 | 0.206 | |
calcEntropy | 3.554 | 0.625 | 4.192 | |
calcMembership | 0.002 | 0.001 | 0.002 | |
calcReclusterMatrix | 0.005 | 0.000 | 0.006 | |
calcSparsness | 1.516 | 0.348 | 1.867 | |
clusterORA | 0.101 | 0.008 | 0.110 | |
clusteringSummary | 3.868 | 0.003 | 3.871 | |
degreeBinnedGDAs | 0.098 | 0.005 | 0.104 | |
escapeAnnotation | 0.001 | 0.000 | 0.000 | |
evalCentralitySignificance | 0.094 | 0.002 | 0.096 | |
findLCC | 0.001 | 0.000 | 0.002 | |
getAnnotationList | 0.019 | 0.002 | 0.020 | |
getAnnotationVertexList | 0.023 | 0.003 | 0.025 | |
getBridgeness | 0.018 | 0.001 | 0.019 | |
getCentralityMatrix | 2.531 | 0.430 | 2.965 | |
getClusterSubgraphByID | 0.002 | 0.000 | 0.002 | |
getClustering | 0.002 | 0.001 | 0.002 | |
getCommunityGraph | 0.002 | 0.000 | 0.002 | |
getDType | 0 | 0 | 0 | |
getDYNAMO | 0.011 | 0.001 | 0.012 | |
getDiseases | 0.001 | 0.000 | 0.000 | |
getEntropy | 3.231 | 0.816 | 4.069 | |
getEntropyRate | 0.001 | 0.000 | 0.002 | |
getGNP | 0.000 | 0.001 | 0.001 | |
getGraphCentralityECDF | 2.356 | 0.464 | 2.823 | |
getPA | 0.001 | 0.000 | 0.001 | |
getRandomGraphCentrality | 0.120 | 0.009 | 3.790 | |
getRobustness | 0.138 | 0.013 | 0.150 | |
layoutByCluster | 0.026 | 0.001 | 0.026 | |
layoutByRecluster | 0.021 | 0.001 | 0.023 | |
makeConsensusMatrix | 0.129 | 0.013 | 0.141 | |
metlMatrix | 0.002 | 0.000 | 0.003 | |
normModularity | 1.643 | 0.402 | 2.046 | |
permute | 0.000 | 0.000 | 0.001 | |
plotBridgeness | 0.103 | 0.002 | 0.106 | |
plotEntropy | 3.403 | 0.814 | 4.221 | |
prepareGDA | 0.094 | 0.007 | 0.100 | |
recluster | 0.004 | 0.000 | 0.005 | |
removeVertexTerm | 0.001 | 0.001 | 0.002 | |
runPermDisease | 2.852 | 0.089 | 2.945 | |
sampleDegBinnedGDA | 0.112 | 0.009 | 0.121 | |
sampleGraphClust | 0.003 | 0.001 | 0.003 | |
unescapeAnnotation | 0.000 | 0.000 | 0.001 | |
zeroNA | 0 | 0 | 0 | |