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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 2248/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.34.0  (landing page)
Gabriel E. Hoffman
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/variancePartition
git_branch: RELEASE_3_19
git_last_commit: 41b3a88
git_last_commit_date: 2023-11-02 16:11:02 -0400 (Thu, 02 Nov 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for variancePartition on lconway

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: 1.34.0
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_1.34.0.tar.gz
StartedAt: 2024-06-09 23:44:48 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 23:53:17 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 509.3 seconds
RetCode: 0
Status:   OK  
CheckDir: variancePartition.Rcheck
Warnings: 0

Command output

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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_1.34.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/variancePartition.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.34.0’
* 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 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         29.902  0.074  30.011
fitExtractVarPartModel-method  23.149  0.057  23.232
getTreat-method                20.722  0.059  20.805
plotCompareP-method            16.237  0.084  16.372
extractVarPart                 14.700  0.058  14.777
varPartConfInf                 10.361  0.054  10.449
sortCols-method                 7.761  0.023   7.797
plotVarPart-method              7.424  0.022   7.457
plotPercentBars-method          7.209  0.038   7.275
residuals-VarParFitList-method  7.215  0.019   7.246
mvTest-method                   6.353  0.098  13.266
dream-method                    3.655  0.077  20.611
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/variancePartition.Rcheck/00check.log’
for details.


Installation output

variancePartition.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL variancePartition
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output

variancePartition.Rcheck/tests/runTests.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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 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 -- Sun Jun  9 23:53:09 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 
152.347   4.281 211.057 

Example timings

variancePartition.Rcheck/variancePartition-Ex.timings

nameusersystemelapsed
ESS-method0.1400.0170.159
as.data.frame.varPartResults0.2580.0030.261
as.matrix-varPartResults-method0.3480.0040.353
augmentPriorCount0.7450.0960.843
calcVarPart-method0.0670.0040.071
canCorPairs0.0720.0060.078
colinearityScore0.4660.0150.481
deviation-method1.2330.1151.352
diffVar-method1.3520.0731.430
dream-method 3.655 0.07720.611
extractVarPart14.700 0.05814.777
fitExtractVarPartModel-method23.149 0.05723.232
fitVarPartModel-method29.902 0.07430.011
getContrast-method0.0060.0020.007
getTreat-method20.722 0.05920.805
get_prediction-method0.0920.0110.104
ggColorHue0.0000.0000.001
makeContrastsDream1.6600.0081.671
mvTest-method 6.353 0.09813.266
plotCompareP-method16.237 0.08416.372
plotContrasts0.1870.0060.194
plotCorrMatrix0.0640.0060.070
plotCorrStructure0.7170.0260.749
plotPercentBars-method7.2090.0387.275
plotStratify0.7540.0090.765
plotStratifyBy0.7850.0110.799
plotVarPart-method7.4240.0227.457
rdf0.0430.0020.046
rdf.merMod0.0500.0020.053
residuals-VarParFitList-method7.2150.0197.246
sortCols-method7.7610.0237.797
varPartConfInf10.361 0.05410.449
vcovSqrt-method0.0160.0020.018
voomWithDreamWeights2.9380.0753.018