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This page was generated on 2023-04-12 10:55:43 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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:
- 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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 2156/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.29.0  (landing page)
Gabriel E. Hoffman
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/variancePartition
git_branch: devel
git_last_commit: 49e3278
git_last_commit_date: 2022-11-01 11:11:59 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    ERROR  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  

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/site-library --timings variancePartition_1.29.0.tar.gz
StartedAt: 2023-04-12 10:07:00 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 10:16:48 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 588.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: variancePartition.Rcheck
Warnings: NA

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/site-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) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 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 loading without being on the library search path ... 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         32.658  0.148  32.807
fitExtractVarPartModel-method  26.998  0.160  27.159
getTreat-method                22.928  0.072  23.000
plotCompareP-method            19.585  0.044  19.634
varPartConfInf                 15.175  0.004  15.180
extractVarPart                 14.414  0.148  14.563
sortCols-method                 7.802  0.040   7.845
plotVarPart-method              7.828  0.008   7.837
plotPercentBars-method          7.639  0.032   7.671
residuals-VarParFitList-method  6.284  0.000   6.284
dream-method                    4.151  0.135  10.761
* 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 ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘FAQ.Rmd’ using rmarkdown
--- finished re-building ‘FAQ.Rmd’

--- re-building ‘additional_visualization.Rmd’ using rmarkdown
--- finished re-building ‘additional_visualization.Rmd’

--- re-building ‘dream.Rmd’ using rmarkdown
Quitting from lines 110-129 (dream.Rmd) 
Error: processing vignette 'dream.Rmd' failed with diagnostics:
statmod package required but is not installed (or can't be loaded)
--- failed re-building ‘dream.Rmd’

--- re-building ‘theory_practice_random_effects.Rmd’ using rmarkdown
--- finished re-building ‘theory_practice_random_effects.Rmd’

--- re-building ‘variancePartition.Rnw’ using knitr
--- finished re-building ‘variancePartition.Rnw’

SUMMARY: processing the following file failed:
  ‘dream.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 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/site-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) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 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")

Attaching package: 'variancePartition'

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

    topTable

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:0.4 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:10 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:0.5 s
Dividing work into 1 chunks...

Total:0.6 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:8 s
Dividing work into 5 chunks...

Total:9 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: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:0.4 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:0.5 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...

Total:0.5 s


RUNIT TEST PROTOCOL -- Wed Apr 12 10:13:11 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 
 78.716   1.572 100.666

Example timings

variancePartition.Rcheck/variancePartition-Ex.timings

nameusersystemelapsed
ESS-method0.1530.0040.157
as.data.frame.varPartResults0.3380.0000.338
as.matrix-varPartResults-method0.3060.0000.306
calcVarPart-method0.0570.0030.061
canCorPairs0.0660.0040.070
colinearityScore0.3750.0000.376
dream-method 4.151 0.13510.761
extractVarPart14.414 0.14814.563
fitExtractVarPartModel-method26.998 0.16027.159
fitVarPartModel-method32.658 0.14832.807
getContrast-method0.0160.0000.016
getTreat-method22.928 0.07223.000
get_prediction-method0.0870.0040.091
ggColorHue000
makeContrastsDream1.6310.0041.635
plotCompareP-method19.585 0.04419.634
plotContrasts0.210.000.21
plotCorrMatrix0.0700.0040.074
plotCorrStructure0.7840.0200.804
plotPercentBars-method7.6390.0327.671
plotStratify0.7270.0000.727
plotStratifyBy0.6980.0040.702
plotVarPart-method7.8280.0087.837
rdf.merMod0.0840.0000.084
residuals-VarParFitList-method6.2840.0006.284
sortCols-method7.8020.0407.845
varPartConfInf15.175 0.00415.180
voomWithDreamWeights2.9070.0522.959