| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-02 12:46 -0500 (Mon, 02 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4877 |
| 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 2300/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| variancePartition 1.41.3 (landing page) Gabriel E. Hoffman
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| See other builds for variancePartition in R Universe. | ||||||||||||||
|
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: 1.41.3 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings variancePartition_1.41.3.tar.gz |
| StartedAt: 2026-03-02 05:34:25 -0500 (Mon, 02 Mar 2026) |
| EndedAt: 2026-03-02 05:55:24 -0500 (Mon, 02 Mar 2026) |
| EllapsedTime: 1258.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings variancePartition_1.41.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/variancePartition.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.41.3’
* 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 27.854 0.105 27.960
fitExtractVarPartModel-method 22.241 0.081 22.323
getTreat-method 19.560 0.125 19.685
plotCompareP-method 15.238 0.010 15.249
extractVarPart 13.805 0.088 13.901
varPartConfInf 9.558 0.003 9.562
plotPercentBars-method 7.711 0.004 7.716
sortCols-method 7.269 0.045 7.314
plotVarPart-method 7.004 0.030 7.035
residuals-VarParFitList-method 6.451 0.002 6.453
voomWithDreamWeights 5.848 0.103 5.952
mvTest-method 5.124 0.047 10.998
dream-method 3.540 0.097 8.587
* 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-3.23-bioc/meat/variancePartition.Rcheck/00check.log’
for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘variancePartition’ ... ** this is package ‘variancePartition’ version ‘1.41.3’ ** 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 ‘eBayes’ in package ‘variancePartition’ Creating a new generic function for ‘classifyTestsF’ in package ‘variancePartition’ Creating a new generic function for ‘topTable’ in package ‘variancePartition’ ** help *** 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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 objects are masked from 'package:limma':
eBayes, 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
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
Removing intercept from test coefficients
Removing intercept from test coefficients
calcNormFactors has been renamed to normLibSizes
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
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
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: 2.1.5.2
___ __ __ __ __ __ __ __ __ __ _ _ __ __ __ __ __ __ __ __ __ __ __
| __ __ __ __ | | __ __ __ __ _/ / \ | __ __ __ __ / /__ __ _ _ __ __\
| | | | | | / _ \ | | / /
| | | | | | / / \ \ | | / /
| | | | | | / / \ \ | | / /
| |__ __ __ __| | | |__ __ __ __ / / \ \ | |__ __ __ __ _ / /__/\
| __ __ __ __| | __ __ __ __| / /__ _ __\ \ |_ __ __ __ _ | / ___ /
| \ | | / _ _ _ _ _ _ \ | | \/ / /
| |\ \ | | / / \ \ | | / /
| | \ \ | | / / \ \ | | / /
| | \ \ | | / / \ \ | | / /
| | \ \__ __ _ | | / / \ \ _ __ __ __ _| | / /
|_| \__ __ __\ |_| /_/ \_\ /_ __ __ __ ___| \/ team
Attaching package: 'Rfast'
The following object is masked from 'package:edgeR':
gini
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
Warning:
Variables contain NA's: Disease
Samples with missing data will be dropped.
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
RUNIT TEST PROTOCOL -- Mon Mar 2 05:42:26 2026
***********************************************
Number of test functions: 31
Number of errors: 0
Number of failures: 0
1 Test Suite :
variancePartition RUnit Tests - 31 test functions, 0 errors, 0 failures
Number of test functions: 31
Number of errors: 0
Number of failures: 0
There were 32 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
189.246 4.607 222.443
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.145 | 0.007 | 0.152 | |
| as.data.frame.varPartResults | 0.301 | 0.001 | 0.302 | |
| as.matrix-varPartResults-method | 0.264 | 0.001 | 0.265 | |
| augmentPriorCount | 0.697 | 0.031 | 0.729 | |
| calcVarPart-method | 0.05 | 0.00 | 0.05 | |
| canCorPairs | 0.070 | 0.001 | 0.070 | |
| colinearityScore | 0.416 | 0.000 | 0.416 | |
| deviation-method | 1.055 | 0.045 | 1.100 | |
| diffVar-method | 1.466 | 0.021 | 1.489 | |
| dream-method | 3.540 | 0.097 | 8.587 | |
| extractVarPart | 13.805 | 0.088 | 13.901 | |
| fitExtractVarPartModel-method | 22.241 | 0.081 | 22.323 | |
| fitVarPartModel-method | 27.854 | 0.105 | 27.960 | |
| getContrast-method | 0.007 | 0.000 | 0.007 | |
| getTreat-method | 19.560 | 0.125 | 19.685 | |
| get_prediction-method | 0.060 | 0.010 | 0.071 | |
| ggColorHue | 0.001 | 0.000 | 0.001 | |
| makeContrastsDream | 1.473 | 0.004 | 1.477 | |
| mvTest-method | 5.124 | 0.047 | 10.998 | |
| plotCompareP-method | 15.238 | 0.010 | 15.249 | |
| plotContrasts | 0.279 | 0.000 | 0.280 | |
| plotCorrMatrix | 0.060 | 0.002 | 0.062 | |
| plotCorrStructure | 0.777 | 0.004 | 0.781 | |
| plotPercentBars-method | 7.711 | 0.004 | 7.716 | |
| plotStratify | 0.999 | 0.002 | 1.002 | |
| plotStratifyBy | 0.931 | 0.002 | 0.933 | |
| plotVarPart-method | 7.004 | 0.030 | 7.035 | |
| rdf | 0.017 | 0.002 | 0.019 | |
| rdf.merMod | 0.045 | 0.001 | 0.045 | |
| residuals-VarParFitList-method | 6.451 | 0.002 | 6.453 | |
| sortCols-method | 7.269 | 0.045 | 7.314 | |
| varPartConfInf | 9.558 | 0.003 | 9.562 | |
| vcovSqrt-method | 0.013 | 0.002 | 0.015 | |
| voomWithDreamWeights | 5.848 | 0.103 | 5.952 | |