Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-07-31 11:45 -0400 (Thu, 31 Jul 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 2282/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
variancePartition 1.38.0 (landing page) Gabriel E. Hoffman
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
To the developers/maintainers of the variancePartition package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/variancePartition.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: variancePartition |
Version: 1.38.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings variancePartition_1.38.0.tar.gz |
StartedAt: 2025-07-29 12:11:06 -0400 (Tue, 29 Jul 2025) |
EndedAt: 2025-07-29 12:30:42 -0400 (Tue, 29 Jul 2025) |
EllapsedTime: 1175.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: variancePartition.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings variancePartition_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/variancePartition.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘variancePartition/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘variancePartition’ version ‘1.38.0’ * 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 ‘variancePartition’ can be installed ... OK * checking installed package size ... OK * 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 Unexported object imported by a ':::' call: ‘lmerTest:::as_lmerModLT’ See the note in ?`:::` about the use of this operator. * 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 ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE S3 methods shown with full name in Rd file 'residuals.MArrayLM2.Rd': ‘residuals.MArrayLM2’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fitVarPartModel-method 71.993 0.246 78.910 fitExtractVarPartModel-method 56.281 0.264 61.419 getTreat-method 48.044 0.177 50.989 plotCompareP-method 36.665 0.148 37.604 extractVarPart 35.298 0.170 38.311 varPartConfInf 22.852 0.066 23.124 plotPercentBars-method 17.920 0.099 18.349 sortCols-method 17.498 0.052 17.728 plotVarPart-method 17.195 0.053 17.310 residuals-VarParFitList-method 16.098 0.035 16.189 mvTest-method 11.863 0.131 26.806 dream-method 7.477 0.135 43.480 voomWithDreamWeights 6.223 0.087 6.369 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/variancePartition.Rcheck/00check.log’ for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘variancePartition’ ... ** this is package ‘variancePartition’ version ‘1.38.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘calcVarPart’ with signature ‘"negbin"’: no definition for class “negbin” in method for ‘checkModelStatus’ with signature ‘"negbin"’: no definition for class “negbin” Creating a new generic function for ‘classifyTestsF’ in package ‘variancePartition’ Creating a new generic function for ‘topTable’ in package ‘variancePartition’ ** help Loading required namespace: variancePartition *** installing help indices *** copying figures ** 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 (variancePartition)
variancePartition.Rcheck/tests/runTests.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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. > BiocGenerics:::testPackage("variancePartition") Attaching package: 'variancePartition' The following object is masked from 'package:limma': topTable Loading required package: lme4 Loading required package: Matrix Attaching package: 'lmerTest' The following object is masked from 'package:lme4': lmer The following object is masked from 'package:stats': step boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') Removing intercept from test coefficients Removing intercept from test coefficients boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') Removing intercept from test coefficients Removing intercept from test coefficients Loading required package: Rcpp Loading required package: zigg Loading required package: RcppParallel Attaching package: 'RcppParallel' The following object is masked from 'package:Rcpp': LdFlags Rfast: 2.1.5.1 ___ __ __ __ __ __ __ __ __ __ _ _ __ __ __ __ __ __ __ __ __ __ __ | __ __ __ __ | | __ __ __ __ _/ / \ | __ __ __ __ / /__ __ _ _ __ __\ | | | | | | / _ \ | | / / | | | | | | / / \ \ | | / / | | | | | | / / \ \ | | / / | |__ __ __ __| | | |__ __ __ __ / / \ \ | |__ __ __ __ _ / /__/\ | __ __ __ __| | __ __ __ __| / /__ _ __\ \ |_ __ __ __ _ | / ___ / | \ | | / _ _ _ _ _ _ \ | | \/ / / | |\ \ | | / / \ \ | | / / | | \ \ | | / / \ \ | | / / | | \ \ | | / / \ \ | | / / | | \ \__ __ _ | | / / \ \ _ __ __ __ _| | / / |_| \__ __ __\ |_| /_/ \_\ /_ __ __ __ ___| \/ team Attaching package: 'Rfast' The following object is masked from 'package:edgeR': gini Warning: Variables contain NA's: Disease Samples with missing data will be dropped. RUNIT TEST PROTOCOL -- Tue Jul 29 12:30:25 2025 *********************************************** Number of test functions: 30 Number of errors: 0 Number of failures: 0 1 Test Suite : variancePartition RUnit Tests - 30 test functions, 0 errors, 0 failures Number of test functions: 30 Number of errors: 0 Number of failures: 0 There were 29 warnings (use warnings() to see them) > > proc.time() user system elapsed 380.909 5.755 513.574
variancePartition.Rcheck/variancePartition-Ex.timings
name | user | system | elapsed | |
ESS-method | 0.332 | 0.025 | 0.361 | |
as.data.frame.varPartResults | 0.809 | 0.011 | 0.826 | |
as.matrix-varPartResults-method | 0.679 | 0.008 | 0.691 | |
augmentPriorCount | 1.478 | 0.128 | 1.657 | |
calcVarPart-method | 0.113 | 0.007 | 0.121 | |
canCorPairs | 0.132 | 0.010 | 0.146 | |
colinearityScore | 1.097 | 0.010 | 1.115 | |
deviation-method | 1.928 | 0.107 | 2.056 | |
diffVar-method | 2.632 | 0.096 | 2.747 | |
dream-method | 7.477 | 0.135 | 43.480 | |
extractVarPart | 35.298 | 0.170 | 38.311 | |
fitExtractVarPartModel-method | 56.281 | 0.264 | 61.419 | |
fitVarPartModel-method | 71.993 | 0.246 | 78.910 | |
getContrast-method | 0.015 | 0.003 | 0.022 | |
getTreat-method | 48.044 | 0.177 | 50.989 | |
get_prediction-method | 0.163 | 0.029 | 0.198 | |
ggColorHue | 0.000 | 0.001 | 0.001 | |
makeContrastsDream | 3.412 | 0.027 | 3.508 | |
mvTest-method | 11.863 | 0.131 | 26.806 | |
plotCompareP-method | 36.665 | 0.148 | 37.604 | |
plotContrasts | 0.418 | 0.009 | 0.451 | |
plotCorrMatrix | 0.134 | 0.011 | 0.146 | |
plotCorrStructure | 1.823 | 0.054 | 1.896 | |
plotPercentBars-method | 17.920 | 0.099 | 18.349 | |
plotStratify | 1.493 | 0.011 | 1.508 | |
plotStratifyBy | 1.560 | 0.010 | 1.631 | |
plotVarPart-method | 17.195 | 0.053 | 17.310 | |
rdf | 0.048 | 0.004 | 0.061 | |
rdf.merMod | 0.124 | 0.004 | 0.137 | |
residuals-VarParFitList-method | 16.098 | 0.035 | 16.189 | |
sortCols-method | 17.498 | 0.052 | 17.728 | |
varPartConfInf | 22.852 | 0.066 | 23.124 | |
vcovSqrt-method | 0.029 | 0.003 | 0.033 | |
voomWithDreamWeights | 6.223 | 0.087 | 6.369 | |