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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings variancePartition_1.39.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/variancePartition.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.39.1’
* 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 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         33.115  0.146  33.371
fitExtractVarPartModel-method  25.999  0.128  26.243
getTreat-method                22.676  0.108  22.869
plotCompareP-method            17.855  0.080  18.012
extractVarPart                 16.127  0.087  16.285
varPartConfInf                 11.296  0.064  11.436
plotPercentBars-method          8.628  0.056   8.740
sortCols-method                 8.497  0.064   8.633
plotVarPart-method              7.944  0.048   8.046
residuals-VarParFitList-method  7.659  0.051   7.762
mvTest-method                   5.802  0.114  13.123
dream-method                    3.633  0.064  20.921
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
    Length mismatch: comparison on first 4 components
  Component "weights": Mean relative difference: 0.06105003
  
  
  Test files with failing tests
  
     test_voomWithDreamWeights.R 
       test_reweigthing_voom 
       test_voomLmFit 
       test_voomWithDreamWeights 
  
  
  Error in BiocGenerics:::testPackage("variancePartition") : 
    unit tests failed for package variancePartition
  Execution halted
* 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: 1 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/variancePartition.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL variancePartition
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘variancePartition’ ...
** this is package ‘variancePartition’ version ‘1.39.1’
** 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
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)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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
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.

Timing stopped at: 3.049 0.17 3.238
Error in checkEqualsNumeric(vobj1$weights, vobj2$weights) : 
  Mean relative difference: 0.0838729

In addition: There were 32 warnings (use warnings() to see them)
Timing stopped at: 16.26 0.465 16.8
Error in checkEquals(fit1, fit2) : 
  Component "coefficients": Mean relative difference: 0.0007980718
Component "stdev.unscaled": Mean relative difference: 0.003669761
Component "sigma": Mean relative difference: 0.01160843
Component "EList": Component "weights": Mean relative difference: 0.1072408

Timing stopped at: 0.561 0.048 0.612
Error in checkEquals(vobj1, vobj2) : 
  Length mismatch: comparison on first 4 components
Component "weights": Mean relative difference: 0.06105003



RUNIT TEST PROTOCOL -- Tue Sep  2 00:40:26 2025 
*********************************************** 
Number of test functions: 31 
Number of errors: 0 
Number of failures: 3 

 
1 Test Suite : 
variancePartition RUnit Tests - 31 test functions, 0 errors, 3 failures
FAILURE in test_reweigthing_voom: Error in checkEqualsNumeric(vobj1$weights, vobj2$weights) : 
  Mean relative difference: 0.0838729

FAILURE in test_voomLmFit: Error in checkEquals(fit1, fit2) : 
  Component "coefficients": Mean relative difference: 0.0007980718
Component "stdev.unscaled": Mean relative difference: 0.003669761
Component "sigma": Mean relative difference: 0.01160843
Component "EList": Component "weights": Mean relative difference: 0.1072408

FAILURE in test_voomWithDreamWeights: Error in checkEquals(vobj1, vobj2) : 
  Length mismatch: comparison on first 4 components
Component "weights": Mean relative difference: 0.06105003


Test files with failing tests

   test_voomWithDreamWeights.R 
     test_reweigthing_voom 
     test_voomLmFit 
     test_voomWithDreamWeights 


Error in BiocGenerics:::testPackage("variancePartition") : 
  unit tests failed for package variancePartition
Execution halted