Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-07-25 12:13 -0400 (Fri, 25 Jul 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" | 4793 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4531 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4574 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4515 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4512 |
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 2253/2311 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
variancePartition 1.39.0 (landing page) Gabriel E. Hoffman
| 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 | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: variancePartition |
Version: 1.39.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings variancePartition_1.39.0.tar.gz |
StartedAt: 2025-07-25 14:07:54 -0000 (Fri, 25 Jul 2025) |
EndedAt: 2025-07-25 14:18:35 -0000 (Fri, 25 Jul 2025) |
EllapsedTime: 640.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: variancePartition.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings variancePartition_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/variancePartition.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 ‘variancePartition/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘variancePartition’ version ‘1.39.0’ * 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 loading without being on the library search path ... 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 42.180 0.132 42.414 fitExtractVarPartModel-method 33.030 0.207 33.314 getTreat-method 28.910 0.068 29.061 plotCompareP-method 22.218 0.004 22.285 extractVarPart 20.838 0.443 21.332 varPartConfInf 13.880 0.004 13.921 plotPercentBars-method 10.588 0.004 10.618 sortCols-method 10.477 0.032 10.538 plotVarPart-method 10.372 0.064 10.464 residuals-VarParFitList-method 9.344 0.000 9.366 mvTest-method 7.669 0.075 15.707 dream-method 4.724 0.102 11.283 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/variancePartition.Rcheck/00check.log’ for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘variancePartition’ ... ** this is package ‘variancePartition’ version ‘1.39.0’ ** 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 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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 -- Fri Jul 25 14:18:29 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 227.152 2.736 278.979
variancePartition.Rcheck/variancePartition-Ex.timings
name | user | system | elapsed | |
ESS-method | 0.202 | 0.008 | 0.211 | |
as.data.frame.varPartResults | 0.478 | 0.000 | 0.480 | |
as.matrix-varPartResults-method | 0.402 | 0.108 | 0.511 | |
augmentPriorCount | 1.042 | 0.398 | 1.442 | |
calcVarPart-method | 0.068 | 0.007 | 0.076 | |
canCorPairs | 0.104 | 0.004 | 0.108 | |
colinearityScore | 0.592 | 0.008 | 0.602 | |
deviation-method | 1.253 | 0.008 | 1.263 | |
diffVar-method | 1.669 | 0.044 | 1.716 | |
dream-method | 4.724 | 0.102 | 11.283 | |
extractVarPart | 20.838 | 0.443 | 21.332 | |
fitExtractVarPartModel-method | 33.030 | 0.207 | 33.314 | |
fitVarPartModel-method | 42.180 | 0.132 | 42.414 | |
getContrast-method | 0.009 | 0.000 | 0.009 | |
getTreat-method | 28.910 | 0.068 | 29.061 | |
get_prediction-method | 0.092 | 0.004 | 0.098 | |
ggColorHue | 0 | 0 | 0 | |
makeContrastsDream | 2.006 | 0.000 | 2.011 | |
mvTest-method | 7.669 | 0.075 | 15.707 | |
plotCompareP-method | 22.218 | 0.004 | 22.285 | |
plotContrasts | 0.268 | 0.000 | 0.268 | |
plotCorrMatrix | 0.081 | 0.000 | 0.082 | |
plotCorrStructure | 1.076 | 0.004 | 1.083 | |
plotPercentBars-method | 10.588 | 0.004 | 10.618 | |
plotStratify | 0.993 | 0.000 | 0.996 | |
plotStratifyBy | 0.948 | 0.000 | 0.950 | |
plotVarPart-method | 10.372 | 0.064 | 10.464 | |
rdf | 0.032 | 0.000 | 0.032 | |
rdf.merMod | 0.066 | 0.004 | 0.070 | |
residuals-VarParFitList-method | 9.344 | 0.000 | 9.366 | |
sortCols-method | 10.477 | 0.032 | 10.538 | |
varPartConfInf | 13.880 | 0.004 | 13.921 | |
vcovSqrt-method | 0.019 | 0.000 | 0.020 | |
voomWithDreamWeights | 4.166 | 0.024 | 4.200 | |