Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:38:43 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 2218/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
variancePartition 1.33.11 (landing page) Gabriel E. Hoffman
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
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: 1.33.11 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:variancePartition.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings variancePartition_1.33.11.tar.gz |
StartedAt: 2024-03-28 07:45:32 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 07:55:11 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 578.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: variancePartition.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:variancePartition.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings variancePartition_1.33.11.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/variancePartition.Rcheck' * using R Under development (unstable) (2024-03-16 r86144 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'variancePartition/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'variancePartition' version '1.33.11' * 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 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 34.92 0.32 35.25 fitExtractVarPartModel-method 26.86 0.33 27.20 getTreat-method 22.51 0.25 22.81 plotCompareP-method 19.48 0.19 19.67 extractVarPart 16.49 0.19 16.67 varPartConfInf 12.23 0.12 12.36 sortCols-method 9.89 0.05 9.94 plotVarPart-method 9.50 0.09 9.60 plotPercentBars-method 9.43 0.08 9.53 residuals-VarParFitList-method 8.20 0.08 8.28 mvTest-method 7.33 0.16 16.88 dream-method 3.90 0.22 14.38 * 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 'F:/biocbuild/bbs-3.19-bioc/meat/variancePartition.Rcheck/00check.log' for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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: RcppZiggurat Loading required package: RcppParallel Attaching package: 'RcppParallel' The following object is masked from 'package:Rcpp': LdFlags Rfast: 2.1.0 ___ __ __ __ __ __ __ __ __ __ _ _ __ __ __ __ __ __ __ __ __ __ __ | __ __ __ __ | | __ __ __ __ _/ / \ | __ __ __ __ / /__ __ _ _ __ __\ | | | | | | / _ \ | | / / | | | | | | / / \ \ | | / / | | | | | | / / \ \ | | / / | |__ __ __ __| | | |__ __ __ __ / / \ \ | |__ __ __ __ _ / /__/\ | __ __ __ __| | __ __ __ __| / /__ _ __\ \ |_ __ __ __ _ | / ___ / | \ | | / _ _ _ _ _ _ \ | | \/ / / | |\ \ | | / / \ \ | | / / | | \ \ | | / / \ \ | | / / | | \ \ | | / / \ \ | | / / | | \ \__ __ _ | | / / \ \ _ __ __ __ _| | / / |_| \__ __ __\ |_| /_/ \_\ /_ __ __ __ ___| \/ team Warning: Variables contain NA's: Disease Samples with missing data will be dropped. RUNIT TEST PROTOCOL -- Thu Mar 28 07:55:00 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 185.53 6.29 243.31
variancePartition.Rcheck/variancePartition-Ex.timings
name | user | system | elapsed | |
ESS-method | 0.20 | 0.03 | 0.24 | |
as.data.frame.varPartResults | 0.38 | 0.00 | 0.37 | |
as.matrix-varPartResults-method | 0.39 | 0.00 | 0.39 | |
augmentPriorCount | 0.98 | 0.03 | 1.02 | |
calcVarPart-method | 0.08 | 0.02 | 0.09 | |
canCorPairs | 0.06 | 0.03 | 0.09 | |
colinearityScore | 0.64 | 0.02 | 0.66 | |
deviation-method | 1.49 | 0.15 | 1.63 | |
diffVar-method | 1.58 | 0.04 | 1.62 | |
dream-method | 3.90 | 0.22 | 14.38 | |
extractVarPart | 16.49 | 0.19 | 16.67 | |
fitExtractVarPartModel-method | 26.86 | 0.33 | 27.20 | |
fitVarPartModel-method | 34.92 | 0.32 | 35.25 | |
getContrast-method | 0.00 | 0.02 | 0.02 | |
getTreat-method | 22.51 | 0.25 | 22.81 | |
get_prediction-method | 0.08 | 0.03 | 0.14 | |
ggColorHue | 0 | 0 | 0 | |
makeContrastsDream | 1.53 | 0.03 | 1.56 | |
mvTest-method | 7.33 | 0.16 | 16.88 | |
plotCompareP-method | 19.48 | 0.19 | 19.67 | |
plotContrasts | 0.25 | 0.01 | 0.26 | |
plotCorrMatrix | 0.11 | 0.00 | 0.11 | |
plotCorrStructure | 1.02 | 0.03 | 1.05 | |
plotPercentBars-method | 9.43 | 0.08 | 9.53 | |
plotStratify | 0.86 | 0.03 | 0.89 | |
plotStratifyBy | 0.72 | 0.02 | 0.74 | |
plotVarPart-method | 9.50 | 0.09 | 9.60 | |
rdf | 0.03 | 0.00 | 0.04 | |
rdf.merMod | 0.07 | 0.00 | 0.06 | |
residuals-VarParFitList-method | 8.20 | 0.08 | 8.28 | |
sortCols-method | 9.89 | 0.05 | 9.94 | |
varPartConfInf | 12.23 | 0.12 | 12.36 | |
vcovSqrt-method | 0.02 | 0.02 | 0.03 | |
voomWithDreamWeights | 3.59 | 0.09 | 3.69 | |