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This page was generated on 2025-06-24 12:06 -0400 (Tue, 24 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4565
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4506
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4544
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4492
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4497
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 2252/2310HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.39.0  (landing page)
Gabriel E. Hoffman
Snapshot Date: 2025-06-23 13:25 -0400 (Mon, 23 Jun 2025)
git_url: https://git.bioconductor.org/packages/variancePartition
git_branch: devel
git_last_commit: 393d8da
git_last_commit_date: 2025-04-15 10:52:27 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for variancePartition on nebbiolo2

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.

raw results


Summary

Package: variancePartition
Version: 1.39.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings variancePartition_1.39.0.tar.gz
StartedAt: 2025-06-24 04:02:21 -0400 (Tue, 24 Jun 2025)
EndedAt: 2025-06-24 04:21:36 -0400 (Tue, 24 Jun 2025)
EllapsedTime: 1155.0 seconds
RetCode: 0
Status:   OK  
CheckDir: variancePartition.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings variancePartition_1.39.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/variancePartition.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* 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         27.915  0.001  27.919
fitExtractVarPartModel-method  22.052  0.033  22.086
getTreat-method                19.377  0.068  19.446
plotCompareP-method            14.750  0.231  14.982
extractVarPart                 13.619  0.059  13.678
varPartConfInf                  9.461  0.051   9.515
plotPercentBars-method          7.297  0.120   7.419
sortCols-method                 7.050  0.066   7.118
plotVarPart-method              6.926  0.065   6.991
residuals-VarParFitList-method  6.438  0.017   6.456
mvTest-method                   5.097  0.045  10.834
dream-method                    3.589  0.061   8.697
* 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-3.22-bioc/meat/variancePartition.Rcheck/00check.log’
for details.


Installation output

variancePartition.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL variancePartition
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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)

Tests output

variancePartition.Rcheck/tests/runTests.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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: 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 Jun 24 04:09:41 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 
151.177   1.240 189.020 

Example timings

variancePartition.Rcheck/variancePartition-Ex.timings

nameusersystemelapsed
ESS-method0.1440.0070.150
as.data.frame.varPartResults0.3280.0010.329
as.matrix-varPartResults-method0.2730.0000.273
augmentPriorCount0.9500.0240.975
calcVarPart-method0.0490.0010.049
canCorPairs0.0750.0020.078
colinearityScore0.4210.0000.421
deviation-method0.9210.0090.929
diffVar-method1.1680.0111.180
dream-method3.5890.0618.697
extractVarPart13.619 0.05913.678
fitExtractVarPartModel-method22.052 0.03322.086
fitVarPartModel-method27.915 0.00127.919
getContrast-method0.0070.0000.007
getTreat-method19.377 0.06819.446
get_prediction-method0.0610.0000.062
ggColorHue000
makeContrastsDream1.3780.0041.381
mvTest-method 5.097 0.04510.834
plotCompareP-method14.750 0.23114.982
plotContrasts0.1780.0000.179
plotCorrMatrix0.0630.0010.063
plotCorrStructure0.7630.0070.770
plotPercentBars-method7.2970.1207.419
plotStratify0.6370.0110.648
plotStratifyBy0.6170.0030.620
plotVarPart-method6.9260.0656.991
rdf0.020.000.02
rdf.merMod0.0440.0020.046
residuals-VarParFitList-method6.4380.0176.456
sortCols-method7.0500.0667.118
varPartConfInf9.4610.0519.515
vcovSqrt-method0.0140.0000.014
voomWithDreamWeights2.9980.0413.040