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This page was generated on 2023-05-10 10:04:43 -0000 (Wed, 10 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6211
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CHECK results for variancePartition on kunpeng1


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 2143/2194HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.31.0  (landing page)
Gabriel E. Hoffman
Snapshot Date: 2023-05-08 19:11:19 -0000 (Mon, 08 May 2023)
git_url: https://git.bioconductor.org/packages/variancePartition
git_branch: devel
git_last_commit: efbb1bd
git_last_commit_date: 2023-04-25 14:40:45 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    ERROR  

Summary

Package: variancePartition
Version: 1.31.0
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_1.31.0.tar.gz
StartedAt: 2023-05-10 07:53:37 -0000 (Wed, 10 May 2023)
EndedAt: 2023-05-10 08:17:13 -0000 (Wed, 10 May 2023)
EllapsedTime: 1415.8 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_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/variancePartition.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.31.0’
* package encoding: UTF-8
* 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         33.801  0.096  33.897
fitExtractVarPartModel-method  29.589  0.140  29.728
getTreat-method                28.445  0.100  28.546
plotCompareP-method            22.614  0.036  22.650
varPartConfInf                 18.030  0.044  18.074
extractVarPart                 17.836  0.124  17.960
plotPercentBars-method          9.726  0.048   9.775
plotVarPart-method              9.521  0.008   9.530
sortCols-method                 9.439  0.004   9.442
residuals-VarParFitList-method  7.265  0.028   7.294
dream-method                    4.578  0.085  11.790
* 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
  ‘multivariate_tests.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
--- finished re-building ‘dream.Rmd’

--- re-building ‘multivariate_tests.Rmd’ using rmarkdown
Quitting from lines 115-124 (multivariate_tests.Rmd) 
Error: processing vignette 'multivariate_tests.Rmd' failed with diagnostics:
there is no package called 'zenith'
--- failed re-building ‘multivariate_tests.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:
  ‘multivariate_tests.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-devel_2023-03-12_r83975-bin/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) (2023-03-12 r83975) -- "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: lme4
Loading required package: Matrix

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:0.5 s
Dividing work into 1 chunks...

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

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

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

Total:0.2 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:0.5 s
Dividing work into 1 chunks...

Total:0.6 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:2 s
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
Dividing work into 1 chunks...

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

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

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

Total:0.4 s
Memory usage to store result: >455.2 Kb
Dividing work into 1 chunks...

Total:0.4 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
Loading required package: clusterGeneration
Loading required package: grid
Loading required package: reshape2
Dividing work into 1 chunks...

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

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

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

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

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

Total:2 s
Loading required package: Rcpp
Loading required package: RcppZiggurat
Memory usage to store result: >5 Kb
Dividing work into 1 chunks...

Total:0.1 s
Warning: 
Variables contain NA's: Disease 
Samples with missing data will be dropped.

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:10 s
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
Dividing work into 1 chunks...

Total:1 s
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:0.5 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 -- Wed May 10 08:01:09 2023 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
variancePartition RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
There were 29 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
109.337   1.100 129.680

Example timings

variancePartition.Rcheck/variancePartition-Ex.timings

nameusersystemelapsed
ESS-method0.1770.0050.181
as.data.frame.varPartResults0.3980.0000.398
as.matrix-varPartResults-method0.3720.0000.371
calcVarPart-method0.0650.0040.069
canCorPairs0.0820.0000.082
colinearityScore0.4810.0110.494
deviation-method1.5970.0291.625
diffVar-method1.2500.0351.285
dream-method 4.578 0.08511.790
extractVarPart17.836 0.12417.960
fitExtractVarPartModel-method29.589 0.14029.728
fitVarPartModel-method33.801 0.09633.897
getContrast-method0.0090.0000.009
getTreat-method28.445 0.10028.546
get_prediction-method0.0790.0000.082
ggColorHue000
makeContrastsDream1.8420.0021.845
mvTest-method3.5250.0163.542
plotCompareP-method22.614 0.03622.650
plotContrasts0.2380.0000.238
plotCorrMatrix0.0830.0000.082
plotCorrStructure0.9410.0000.941
plotPercentBars-method9.7260.0489.775
plotStratify0.9390.0040.943
plotStratifyBy0.9450.0040.949
plotVarPart-method9.5210.0089.530
rdf.merMod0.0690.0000.069
residuals-VarParFitList-method7.2650.0287.294
sortCols-method9.4390.0049.442
varPartConfInf18.030 0.04418.074
voomWithDreamWeights3.4940.0323.526