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This page was generated on 2023-05-31 05:44:46 -0000 (Wed, 31 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4219
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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 2146/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.31.0  (landing page)
Gabriel E. Hoffman
Snapshot Date: 2023-05-29 10:19:22 -0000 (Mon, 29 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/R/R-4.3.0/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings variancePartition_1.31.0.tar.gz
StartedAt: 2023-05-30 22:15:08 -0000 (Tue, 30 May 2023)
EndedAt: 2023-05-30 22:39:28 -0000 (Tue, 30 May 2023)
EllapsedTime: 1459.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: variancePartition.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings variancePartition_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/variancePartition.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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         35.869  0.096  35.962
fitExtractVarPartModel-method  31.903  0.156  32.057
getTreat-method                29.533  0.100  29.631
plotCompareP-method            22.930  0.052  22.981
extractVarPart                 19.105  0.163  19.269
varPartConfInf                 18.936  0.044  18.978
plotPercentBars-method         10.073  0.000  10.072
sortCols-method                 9.926  0.044   9.969
plotVarPart-method              9.727  0.040   9.767
residuals-VarParFitList-method  7.449  0.000   7.448
dream-method                    4.892  0.086  12.552
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  
   
  1 Test Suite : 
  variancePartition RUnit Tests - 21 test functions, 1 error, 0 failures
  ERROR in test_vcov2: Error in library(Rfast) : there is no package called 'Rfast'
  
  Test files with failing tests
  
     test_vcov.R 
       test_vcov2 
  
  
  Error in BiocGenerics:::testPackage("variancePartition") : 
    unit tests failed for package variancePartition
  Execution halted
* 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 [zenith] (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: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/variancePartition.Rcheck/00check.log’
for details.

Installation output

variancePartition.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL variancePartition
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/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.fail


R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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:8 s
Dividing work into 1 chunks...

Total:0.2 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:0.5 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:0.3 s
Dividing work into 1 chunks...

Total:1 s
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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
Timing stopped at: 0.001 0 0.001
Error in library(Rfast) : there is no package called 'Rfast'
In addition: There were 29 warnings (use warnings() to see them)
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:11 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
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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:0.5 s

Total:0.07 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 May 30 22:22:56 2023 
*********************************************** 
Number of test functions: 21 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
variancePartition RUnit Tests - 21 test functions, 1 error, 0 failures
ERROR in test_vcov2: Error in library(Rfast) : there is no package called 'Rfast'

Test files with failing tests

   test_vcov.R 
     test_vcov2 


Error in BiocGenerics:::testPackage("variancePartition") : 
  unit tests failed for package variancePartition
Execution halted

Example timings

variancePartition.Rcheck/variancePartition-Ex.timings

nameusersystemelapsed
ESS-method0.2130.0040.218
as.data.frame.varPartResults0.4140.0000.414
as.matrix-varPartResults-method0.330.000.33
calcVarPart-method0.0730.0000.073
canCorPairs0.0970.0000.097
colinearityScore0.5920.0240.616
deviation-method1.5570.0521.609
diffVar-method1.2900.0241.314
dream-method 4.892 0.08612.552
extractVarPart19.105 0.16319.269
fitExtractVarPartModel-method31.903 0.15632.057
fitVarPartModel-method35.869 0.09635.962
getContrast-method0.010.000.01
getTreat-method29.533 0.10029.631
get_prediction-method0.1100.0040.116
ggColorHue0.0010.0000.000
makeContrastsDream2.0250.0082.032
mvTest-method4.0750.0324.106
plotCompareP-method22.930 0.05222.981
plotContrasts0.2560.0160.272
plotCorrMatrix0.0810.0040.086
plotCorrStructure0.9710.0200.991
plotPercentBars-method10.073 0.00010.072
plotStratify1.0010.0001.002
plotStratifyBy0.9690.0120.981
plotVarPart-method9.7270.0409.767
rdf.merMod0.0750.0040.079
residuals-VarParFitList-method7.4490.0007.448
sortCols-method9.9260.0449.969
varPartConfInf18.936 0.04418.978
voomWithDreamWeights3.6330.0123.644