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This page was generated on 2022-04-13 12:06:06 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for variancePartition on nebbiolo2


To the developers/maintainers of the variancePartition package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2037/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.24.1  (landing page)
Gabriel E. Hoffman
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/variancePartition
git_branch: RELEASE_3_14
git_last_commit: c2877be
git_last_commit_date: 2022-04-11 12:53:27 -0400 (Mon, 11 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  YES
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: variancePartition
Version: 1.24.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings variancePartition_1.24.1.tar.gz
StartedAt: 2022-04-12 09:48:49 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 09:54:15 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 326.1 seconds
RetCode: 0
Status:   OK  
CheckDir: variancePartition.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings variancePartition_1.24.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/variancePartition.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.24.1’
* 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 R 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 ... OK
* 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 documentation object 'residuals.MArrayLM2':
  ‘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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
fitVarPartModel-method         26.391  0.184  26.576
getTreat-method                22.890  0.212  23.102
fitExtractVarPartModel-method  22.801  0.276  23.078
plotCompareP-method            17.347  0.124  17.472
extractVarPart                 13.711  0.172  13.883
varPartConfInf                 12.661  0.068  12.729
sortCols-method                 7.504  0.052   7.556
plotPercentBars-method          7.315  0.068   7.383
plotVarPart-method              7.257  0.044   7.301
residuals-VarParFitList-method  5.369  0.084   5.452
dream-method                    3.361  0.110   8.969
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/variancePartition.Rcheck/00check.log’
for details.

Installation output

variancePartition.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL variancePartition
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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’
** 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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")
Loading required package: Matrix
Dividing work into 1 chunks...

Total:1 s
Dividing work into 1 chunks...

Total:1 s
Dividing work into 1 chunks...

Total:1 s

Attaching package: 'lmerTest'

The following object is masked from 'package:lme4':

    lmer

The following object is masked from 'package:stats':

    step

Dividing work into 1 chunks...

Total:0.1 s
Removing intercept from test coefficients
Removing intercept from test coefficients
Dividing work into 1 chunks...

Total:1 s
Dividing work into 1 chunks...

Total:0.9 s
Dividing work into 1 chunks...

Total:6 s
Dividing work into 1 chunks...

Total:0.1 s
Dividing work into 1 chunks...

Total:0.4 s
Dividing work into 1 chunks...

Total:0.4 s
Dividing work into 1 chunks...

Total:5 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...

Total:0.4 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...

Total:0.4 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...

Total:5 s
Dividing work into 1 chunks...

Total:1 s
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Dividing work into 1 chunks...

Total:1 s
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Dividing work into 1 chunks...

Total:0.3 s
Dividing work into 1 chunks...

Total:0.3 s
Memory usage to store result: >455.2 Kb
Dividing work into 1 chunks...

Total:0.3 s
Memory usage to store result: >455.2 Kb
Dividing work into 1 chunks...

Total:0.3 s
Dividing work into 1 chunks...

Total:1 s
Dividing work into 1 chunks...

Total:1 s
Removing intercept from test coefficients
Removing intercept from test coefficients
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Memory usage to store result: >248.4 Kb
Dividing work into 5 chunks...

Total:2 s
Dividing work into 5 chunks...

Total:7 s
Dividing work into 5 chunks...

Total:8 s
Dividing work into 5 chunks...

Total:8 s
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Memory usage to store result: >248.4 Kb
Dividing work into 5 chunks...

Total:3 s
Dividing work into 5 chunks...

Total:3 s
Dividing work into 5 chunks...

Total:3 s
Dividing work into 5 chunks...

Total:3 s
Fixed effect model, using limma directly...
Dividing work into 1 chunks...

Total:1 s
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Dividing work into 1 chunks...

Total:1 s
Dividing work into 1 chunks...

Total:0.4 s

Total:0.05 s
Dividing work into 1 chunks...

Total:0.4 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...

Total:0.4 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...

Total:0.5 s


RUNIT TEST PROTOCOL -- Tue Apr 12 09:54:11 2022 
*********************************************** 
Number of test functions: 15 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
variancePartition RUnit Tests - 15 test functions, 0 errors, 0 failures
Number of test functions: 15 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 66.777   1.021  83.030

Example timings

variancePartition.Rcheck/variancePartition-Ex.timings

nameusersystemelapsed
ESS-method0.1550.0000.155
as.data.frame.varPartResults0.2910.0080.298
as.matrix-varPartResults-method0.2850.0000.285
calcVarPart-method0.0550.0000.054
canCorPairs0.0680.0000.067
colinearityScore0.3970.0000.397
dream-method3.3610.1108.969
eBayesFMT1.1970.0401.237
extractVarPart13.711 0.17213.883
fitExtractVarPartModel-method22.801 0.27623.078
fitVarPartModel-method26.391 0.18426.576
getContrast-method0.0070.0000.008
getTreat-method22.890 0.21223.102
get_prediction-method0.0540.0080.062
ggColorHue000
makeContrastsDream1.4170.0081.426
plotCompareP-method17.347 0.12417.472
plotContrasts0.1260.0000.127
plotCorrMatrix0.0630.0080.071
plotCorrStructure0.7390.0000.739
plotPercentBars-method7.3150.0687.383
plotStratify0.5270.0000.527
plotStratifyBy0.4950.0000.495
plotVarPart-method7.2570.0447.301
rdf.merMod0.0520.0000.053
residuals-VarParFitList-method5.3690.0845.452
sortCols-method7.5040.0527.556
varPartConfInf12.661 0.06812.729
voomWithDreamWeights2.7550.0362.792