Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-04-22 13:17 -0400 (Tue, 22 Apr 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
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 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | 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 | ![]() | ||||||||
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: 2025-04-22 00:17:07 -0400 (Tue, 22 Apr 2025) |
EndedAt: 2025-04-22 00:26:18 -0400 (Tue, 22 Apr 2025) |
EllapsedTime: 550.5 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 4.5.0 RC (2025-04-04 r88126) * 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 33.139 0.147 33.401 fitExtractVarPartModel-method 27.453 0.125 27.718 getTreat-method 22.735 0.090 22.898 plotCompareP-method 17.462 0.101 17.652 extractVarPart 16.984 0.090 17.166 varPartConfInf 11.099 0.085 11.280 plotVarPart-method 8.541 0.056 8.651 plotPercentBars-method 8.428 0.051 8.526 sortCols-method 8.363 0.064 8.499 residuals-VarParFitList-method 7.963 0.046 8.066 mvTest-method 5.951 0.091 13.290 dream-method 3.653 0.076 20.650 * 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 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 Apr 22 00:26:08 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 171.413 3.916 230.660
variancePartition.Rcheck/variancePartition-Ex.timings
name | user | system | elapsed | |
ESS-method | 0.169 | 0.015 | 0.185 | |
as.data.frame.varPartResults | 0.376 | 0.005 | 0.384 | |
as.matrix-varPartResults-method | 0.344 | 0.004 | 0.350 | |
augmentPriorCount | 0.747 | 0.088 | 0.843 | |
calcVarPart-method | 0.068 | 0.005 | 0.074 | |
canCorPairs | 0.068 | 0.005 | 0.073 | |
colinearityScore | 0.542 | 0.015 | 0.561 | |
deviation-method | 1.167 | 0.074 | 1.250 | |
diffVar-method | 1.204 | 0.074 | 1.293 | |
dream-method | 3.653 | 0.076 | 20.650 | |
extractVarPart | 16.984 | 0.090 | 17.166 | |
fitExtractVarPartModel-method | 27.453 | 0.125 | 27.718 | |
fitVarPartModel-method | 33.139 | 0.147 | 33.401 | |
getContrast-method | 0.006 | 0.002 | 0.009 | |
getTreat-method | 22.735 | 0.090 | 22.898 | |
get_prediction-method | 0.092 | 0.009 | 0.104 | |
ggColorHue | 0 | 0 | 0 | |
makeContrastsDream | 1.694 | 0.014 | 1.716 | |
mvTest-method | 5.951 | 0.091 | 13.290 | |
plotCompareP-method | 17.462 | 0.101 | 17.652 | |
plotContrasts | 0.166 | 0.002 | 0.169 | |
plotCorrMatrix | 0.058 | 0.006 | 0.065 | |
plotCorrStructure | 0.877 | 0.027 | 0.912 | |
plotPercentBars-method | 8.428 | 0.051 | 8.526 | |
plotStratify | 0.755 | 0.009 | 0.771 | |
plotStratifyBy | 0.730 | 0.008 | 0.742 | |
plotVarPart-method | 8.541 | 0.056 | 8.651 | |
rdf | 0.032 | 0.003 | 0.036 | |
rdf.merMod | 0.072 | 0.003 | 0.075 | |
residuals-VarParFitList-method | 7.963 | 0.046 | 8.066 | |
sortCols-method | 8.363 | 0.064 | 8.499 | |
varPartConfInf | 11.099 | 0.085 | 11.280 | |
vcovSqrt-method | 0.023 | 0.002 | 0.025 | |
voomWithDreamWeights | 3.079 | 0.068 | 3.171 | |