Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-01 11:36:13 -0400 (Wed, 01 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
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 2248/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
variancePartition 1.34.0 (landing page) Gabriel E. Hoffman
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.34.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings variancePartition_1.34.0.tar.gz |
StartedAt: 2024-05-01 10:33:05 -0400 (Wed, 01 May 2024) |
EndedAt: 2024-05-01 10:53:10 -0400 (Wed, 01 May 2024) |
EllapsedTime: 1204.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: variancePartition.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings variancePartition_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/variancePartition.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘variancePartition/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘variancePartition’ version ‘1.34.0’ * 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 33.728 0.152 33.881 fitExtractVarPartModel-method 28.356 0.143 28.501 getTreat-method 23.149 0.060 23.209 extractVarPart 18.900 0.168 19.068 plotCompareP-method 17.245 0.405 17.651 varPartConfInf 10.973 0.004 10.979 residuals-VarParFitList-method 9.213 0.024 9.237 plotVarPart-method 8.887 0.036 8.924 sortCols-method 7.730 0.004 7.736 plotPercentBars-method 7.276 0.048 7.325 mvTest-method 5.314 0.097 16.785 dream-method 3.955 0.066 12.602 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/variancePartition.Rcheck/00check.log’ for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘variancePartition’ ... ** 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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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: Matrix boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') Attaching package: 'lmerTest' The following object is masked from 'package:lme4': lmer The following object is masked from 'package:stats': step 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 Warning: Variables contain NA's: Disease Samples with missing data will be dropped. Loading required package: Rcpp Loading required package: RcppZiggurat Loading required package: RcppParallel Attaching package: 'RcppParallel' The following object is masked from 'package:Rcpp': LdFlags Rfast: 2.1.0 ___ __ __ __ __ __ __ __ __ __ _ _ __ __ __ __ __ __ __ __ __ __ __ | __ __ __ __ | | __ __ __ __ _/ / \ | __ __ __ __ / /__ __ _ _ __ __\ | | | | | | / _ \ | | / / | | | | | | / / \ \ | | / / | | | | | | / / \ \ | | / / | |__ __ __ __| | | |__ __ __ __ / / \ \ | |__ __ __ __ _ / /__/\ | __ __ __ __| | __ __ __ __| / /__ _ __\ \ |_ __ __ __ _ | / ___ / | \ | | / _ _ _ _ _ _ \ | | \/ / / | |\ \ | | / / \ \ | | / / | | \ \ | | / / \ \ | | / / | | \ \ | | / / \ \ | | / / | | \ \__ __ _ | | / / \ \ _ __ __ __ _| | / / |_| \__ __ __\ |_| /_/ \_\ /_ __ __ __ ___| \/ team RUNIT TEST PROTOCOL -- Wed May 1 10:42:14 2024 *********************************************** 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 170.588 1.660 229.203
variancePartition.Rcheck/variancePartition-Ex.timings
name | user | system | elapsed | |
ESS-method | 0.352 | 0.016 | 0.368 | |
as.data.frame.varPartResults | 0.288 | 0.052 | 0.339 | |
as.matrix-varPartResults-method | 0.262 | 0.032 | 0.294 | |
augmentPriorCount | 0.706 | 0.024 | 0.730 | |
calcVarPart-method | 0.078 | 0.000 | 0.078 | |
canCorPairs | 0.085 | 0.000 | 0.085 | |
colinearityScore | 0.426 | 0.012 | 0.438 | |
deviation-method | 1.014 | 0.020 | 1.034 | |
diffVar-method | 1.480 | 0.044 | 1.526 | |
dream-method | 3.955 | 0.066 | 12.602 | |
extractVarPart | 18.900 | 0.168 | 19.068 | |
fitExtractVarPartModel-method | 28.356 | 0.143 | 28.501 | |
fitVarPartModel-method | 33.728 | 0.152 | 33.881 | |
getContrast-method | 0.008 | 0.000 | 0.008 | |
getTreat-method | 23.149 | 0.060 | 23.209 | |
get_prediction-method | 0.099 | 0.032 | 0.133 | |
ggColorHue | 0.001 | 0.000 | 0.000 | |
makeContrastsDream | 1.514 | 0.019 | 1.533 | |
mvTest-method | 5.314 | 0.097 | 16.785 | |
plotCompareP-method | 17.245 | 0.405 | 17.651 | |
plotContrasts | 0.297 | 0.004 | 0.301 | |
plotCorrMatrix | 0.091 | 0.000 | 0.092 | |
plotCorrStructure | 1.020 | 0.051 | 1.073 | |
plotPercentBars-method | 7.276 | 0.048 | 7.325 | |
plotStratify | 0.663 | 0.004 | 0.667 | |
plotStratifyBy | 0.666 | 0.004 | 0.669 | |
plotVarPart-method | 8.887 | 0.036 | 8.924 | |
rdf | 0.047 | 0.000 | 0.047 | |
rdf.merMod | 0.101 | 0.000 | 0.101 | |
residuals-VarParFitList-method | 9.213 | 0.024 | 9.237 | |
sortCols-method | 7.730 | 0.004 | 7.736 | |
varPartConfInf | 10.973 | 0.004 | 10.979 | |
vcovSqrt-method | 0.017 | 0.000 | 0.017 | |
voomWithDreamWeights | 2.797 | 0.020 | 2.817 | |