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This page was generated on 2023-03-01 07:38:53 -0000 (Wed, 01 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4266
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CHECK results for variancePartition on kunpeng1


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 2121/2171HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.29.0  (landing page)
Gabriel E. Hoffman
Snapshot Date: 2023-02-27 07:53:22 -0000 (Mon, 27 Feb 2023)
git_url: https://git.bioconductor.org/packages/variancePartition
git_branch: master
git_last_commit: 49e3278
git_last_commit_date: 2022-11-01 15:11:59 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: variancePartition
Version: 1.29.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings variancePartition_1.29.0.tar.gz
StartedAt: 2023-02-28 18:23:27 -0000 (Tue, 28 Feb 2023)
EndedAt: 2023-02-28 18:40:30 -0000 (Tue, 28 Feb 2023)
EllapsedTime: 1023.3 seconds
RetCode: 0
Status:   OK  
CheckDir: variancePartition.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings variancePartition_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/variancePartition.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.29.0’
* 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         36.741  0.148  36.890
fitExtractVarPartModel-method  31.818  0.179  31.999
getTreat-method                29.962  0.076  30.039
plotCompareP-method            23.949  0.032  23.983
extractVarPart                 19.485  0.279  19.766
varPartConfInf                 18.958  0.044  19.002
plotPercentBars-method         10.194  0.044  10.238
sortCols-method                10.082  0.020  10.102
plotVarPart-method              9.954  0.028   9.982
residuals-VarParFitList-method  7.534  0.004   7.538
dream-method                    4.692  0.091  12.138
* 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 ...
  ‘FAQ.Rmd’ using ‘UTF-8’... OK
  ‘additional_visualization.Rmd’ using ‘UTF-8’... OK
  ‘dream.Rmd’ using ‘UTF-8’... OK
  ‘theory_practice_random_effects.Rmd’ using ‘UTF-8’... OK
  ‘variancePartition.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/variancePartition.Rcheck/00check.log’
for details.

Installation output

variancePartition.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL variancePartition
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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’
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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")

Attaching package: 'variancePartition'

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

    topTable

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

Total:2 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:1 s
Dividing work into 1 chunks...

Total:8 s
Dividing work into 1 chunks...

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

Total:0.5 s
Dividing work into 1 chunks...

Total:0.5 s
Dividing work into 1 chunks...

Total:7 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...

Total:0.5 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...

Total:0.5 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...

Total:7 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:0.5 s
Dividing work into 1 chunks...

Total:0.5 s
Memory usage to store result: >455.2 Kb
Dividing work into 1 chunks...

Total:0.5 s
Memory usage to store result: >455.2 Kb
Dividing work into 1 chunks...

Total:0.4 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:3 s
Dividing work into 5 chunks...

Total:10 s
Dividing work into 5 chunks...

Total:10 s
Dividing work into 5 chunks...

Total:11 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:4 s
Dividing work into 5 chunks...

Total:4 s
Dividing work into 5 chunks...

Total:4 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:0.5 s

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

Total:0.5 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...

Total:0.6 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...

Total:0.6 s


RUNIT TEST PROTOCOL -- Tue Feb 28 18:30:48 2023 
*********************************************** 
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 
There were 31 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 93.765   0.958 115.010

Example timings

variancePartition.Rcheck/variancePartition-Ex.timings

nameusersystemelapsed
ESS-method0.1820.0040.187
as.data.frame.varPartResults0.4190.0000.419
as.matrix-varPartResults-method0.3880.0000.388
calcVarPart-method0.0720.0000.071
canCorPairs0.0840.0000.085
colinearityScore0.4870.0240.510
dream-method 4.692 0.09112.138
extractVarPart19.485 0.27919.766
fitExtractVarPartModel-method31.818 0.17931.999
fitVarPartModel-method36.741 0.14836.890
getContrast-method0.010.000.01
getTreat-method29.962 0.07630.039
get_prediction-method0.0840.0040.091
ggColorHue0.0000.0000.001
makeContrastsDream1.9850.0041.989
plotCompareP-method23.949 0.03223.983
plotContrasts0.2570.0000.257
plotCorrMatrix0.0870.0000.087
plotCorrStructure0.9740.0281.003
plotPercentBars-method10.194 0.04410.238
plotStratify1.0110.0081.018
plotStratifyBy0.990.000.99
plotVarPart-method9.9540.0289.982
rdf.merMod0.070.000.07
residuals-VarParFitList-method7.5340.0047.538
sortCols-method10.082 0.02010.102
varPartConfInf18.958 0.04419.002
voomWithDreamWeights3.8530.0163.868