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This page was generated on 2025-07-31 11:43 -0400 (Thu, 31 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 2282/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.38.0  (landing page)
Gabriel E. Hoffman
Snapshot Date: 2025-07-28 13:40 -0400 (Mon, 28 Jul 2025)
git_url: https://git.bioconductor.org/packages/variancePartition
git_branch: RELEASE_3_21
git_last_commit: 83803a6
git_last_commit_date: 2025-04-15 10:52:27 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for variancePartition on palomino7

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: 1.38.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:variancePartition.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings variancePartition_1.38.0.tar.gz
StartedAt: 2025-07-29 08:07:39 -0400 (Tue, 29 Jul 2025)
EndedAt: 2025-07-29 08:18:32 -0400 (Tue, 29 Jul 2025)
EllapsedTime: 652.5 seconds
RetCode: 0
Status:   OK  
CheckDir: variancePartition.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:variancePartition.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings variancePartition_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/variancePartition.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 '1.38.0'
* 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 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         38.86   0.31   39.22
fitExtractVarPartModel-method  31.10   0.32   31.45
getTreat-method                27.74   0.22   27.95
plotCompareP-method            22.03   0.19   22.27
extractVarPart                 18.37   0.32   18.72
varPartConfInf                 12.69   0.16   12.86
plotPercentBars-method         10.55   0.08   10.63
plotVarPart-method             10.43   0.09   10.53
sortCols-method                 9.48   0.04    9.53
residuals-VarParFitList-method  8.91   0.10    9.05
mvTest-method                   7.59   0.17   18.34
dream-method                    3.88   0.15   13.45
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/variancePartition.Rcheck/00check.log'
for details.


Installation output

variancePartition.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL variancePartition
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'variancePartition' ...
** this is package 'variancePartition' version '1.38.0'
** 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 ucrt) -- "Great Square Root"
Copyright (C) 2025 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: 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 Jul 29 08:18:16 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 
 210.07    5.98  284.09 

Example timings

variancePartition.Rcheck/variancePartition-Ex.timings

nameusersystemelapsed
ESS-method0.140.030.18
as.data.frame.varPartResults0.480.000.48
as.matrix-varPartResults-method0.40.00.4
augmentPriorCount1.140.061.21
calcVarPart-method0.110.000.10
canCorPairs0.10.00.1
colinearityScore0.560.020.58
deviation-method1.050.031.07
diffVar-method1.400.041.46
dream-method 3.88 0.1513.45
extractVarPart18.37 0.3218.72
fitExtractVarPartModel-method31.10 0.3231.45
fitVarPartModel-method38.86 0.3139.22
getContrast-method0.010.000.02
getTreat-method27.74 0.2227.95
get_prediction-method0.070.030.14
ggColorHue000
makeContrastsDream1.740.031.77
mvTest-method 7.59 0.1718.34
plotCompareP-method22.03 0.1922.27
plotContrasts0.280.000.28
plotCorrMatrix0.090.000.10
plotCorrStructure1.030.061.09
plotPercentBars-method10.55 0.0810.63
plotStratify1.000.031.03
plotStratifyBy0.850.050.89
plotVarPart-method10.43 0.0910.53
rdf0.030.020.05
rdf.merMod0.070.010.09
residuals-VarParFitList-method8.910.109.05
sortCols-method9.480.049.53
varPartConfInf12.69 0.1612.86
vcovSqrt-method0.020.000.02
voomWithDreamWeights3.870.124.00