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This page was generated on 2022-06-24 12:05:32 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 nebbiolo1


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 2093/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.26.0  (landing page)
Gabriel E. Hoffman
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/variancePartition
git_branch: RELEASE_3_15
git_last_commit: b173129
git_last_commit_date: 2022-04-26 11:26:31 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: variancePartition
Version: 1.26.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings variancePartition_1.26.0.tar.gz
StartedAt: 2022-06-23 22:30:38 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 22:36:45 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 366.7 seconds
RetCode: 0
Status:   OK  
CheckDir: variancePartition.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings variancePartition_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/variancePartition.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.26.0’
* 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         30.771  0.188  30.959
fitExtractVarPartModel-method  27.660  0.160  27.819
getTreat-method                23.621  0.080  23.701
plotCompareP-method            19.431  0.059  19.493
extractVarPart                 15.205  0.132  15.337
varPartConfInf                 14.638  0.000  14.639
sortCols-method                 8.658  0.020   8.678
plotPercentBars-method          8.228  0.040   8.268
plotVarPart-method              7.872  0.000   7.872
residuals-VarParFitList-method  6.372  0.000   6.372
dream-method                    3.594  0.279   9.829
* 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-3.15-bioc/meat/variancePartition.Rcheck/00check.log’
for details.



Installation output

variancePartition.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL variancePartition
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
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:1 s
Dividing work into 1 chunks...

Total:7 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:6 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:0.4 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...

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

Total:2 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:0.4 s
Dividing work into 1 chunks...

Total:0.4 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:9 s
Dividing work into 5 chunks...

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

Total:9 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:0.3 s

Total:0.04 s
Dividing work into 1 chunks...

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

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

Total:0.5 s


RUNIT TEST PROTOCOL -- Thu Jun 23 22:36:42 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 
 73.940   1.090  92.249 

Example timings

variancePartition.Rcheck/variancePartition-Ex.timings

nameusersystemelapsed
ESS-method0.2450.0040.249
as.data.frame.varPartResults0.3860.0000.385
as.matrix-varPartResults-method0.3310.0040.335
calcVarPart-method0.0700.0040.074
canCorPairs0.0740.0040.078
colinearityScore0.4480.0000.448
dream-method3.5940.2799.829
eBayesFMT1.4400.0161.457
extractVarPart15.205 0.13215.337
fitExtractVarPartModel-method27.660 0.16027.819
fitVarPartModel-method30.771 0.18830.959
getContrast-method0.0090.0000.008
getTreat-method23.621 0.08023.701
get_prediction-method0.0810.0080.090
ggColorHue0.0000.0010.000
makeContrastsDream1.6600.0301.689
plotCompareP-method19.431 0.05919.493
plotContrasts0.1650.0000.165
plotCorrMatrix0.0750.0000.075
plotCorrStructure0.7800.0080.789
plotPercentBars-method8.2280.0408.268
plotStratify0.6130.0040.617
plotStratifyBy0.5990.0040.604
plotVarPart-method7.8720.0007.872
rdf.merMod0.0470.0040.052
residuals-VarParFitList-method6.3720.0006.372
sortCols-method8.6580.0208.678
varPartConfInf14.638 0.00014.639
voomWithDreamWeights3.0040.0683.072