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This page was generated on 2023-01-02 09:00:55 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for variancePartition on palomino5


To the developers/maintainers of the variancePartition package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2108/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.29.0  (landing page)
Gabriel E. Hoffman
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/variancePartition
git_branch: master
git_last_commit: 49e3278
git_last_commit_date: 2022-11-01 11:11:59 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: variancePartition
Version: 1.29.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:variancePartition.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings variancePartition_1.29.0.tar.gz
StartedAt: 2022-12-29 04:26:10 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 04:31:25 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 315.3 seconds
RetCode: 0
Status:   OK  
CheckDir: variancePartition.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:variancePartition.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings variancePartition_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/variancePartition.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.29.0'
* 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
fitVarPartModel-method        24.47   0.28   24.77
fitExtractVarPartModel-method 20.89   0.37   21.26
getTreat-method               19.36   0.20   19.61
plotCompareP-method           14.61   0.17   14.78
varPartConfInf                12.58   0.14   12.72
extractVarPart                11.70   0.10   11.80
plotPercentBars-method         6.58   0.03    6.61
sortCols-method                6.40   0.11    6.52
plotVarPart-method             6.00   0.07    6.07
dream-method                   3.67   0.11    9.25
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/variancePartition.Rcheck/00check.log'
for details.

Installation output

variancePartition.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL variancePartition
###
##############################################################################
##############################################################################


* installing to library 'F:/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) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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:0.8 s
Dividing work into 1 chunks...

Total:0.8 s
Dividing work into 1 chunks...

Total:0.9 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:0.09 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:5 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:0.3 s
Dividing work into 1 chunks...

Total:6 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:0.3 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...

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

Total:0.9 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:0.2 s
Dividing work into 1 chunks...

Total:0.9 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:7 s
Dividing work into 5 chunks...

Total:7 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:2 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:0.9 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:0.3 s

Total:0.03 s
Dividing work into 1 chunks...

Total:0.3 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:0.4 s


RUNIT TEST PROTOCOL -- Thu Dec 29 04:31:13 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 
There were 31 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
  61.92    1.67   78.78

Example timings

variancePartition.Rcheck/variancePartition-Ex.timings

nameusersystemelapsed
ESS-method0.120.020.14
as.data.frame.varPartResults0.230.040.28
as.matrix-varPartResults-method0.210.000.21
calcVarPart-method0.040.000.04
canCorPairs0.070.000.08
colinearityScore0.280.000.28
dream-method3.670.119.25
extractVarPart11.7 0.111.8
fitExtractVarPartModel-method20.89 0.3721.26
fitVarPartModel-method24.47 0.2824.77
getContrast-method0.000.020.02
getTreat-method19.36 0.2019.61
get_prediction-method0.060.020.07
ggColorHue000
makeContrastsDream1.270.001.27
plotCompareP-method14.61 0.1714.78
plotContrasts0.160.000.16
plotCorrMatrix0.050.000.05
plotCorrStructure0.620.050.70
plotPercentBars-method6.580.036.61
plotStratify0.60.00.6
plotStratifyBy0.560.010.57
plotVarPart-method6.000.076.07
rdf.merMod0.040.000.04
residuals-VarParFitList-method4.930.004.92
sortCols-method6.400.116.52
varPartConfInf12.58 0.1412.72
voomWithDreamWeights2.470.172.64