| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:33 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R 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 | ||||
|
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. |
| Package 2156/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| variancePartition 1.29.0 (landing page) Gabriel E. Hoffman
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
| 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 00:20:17 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 00:29:20 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 542.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: variancePartition.Rcheck |
| Warnings: NA |
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### Running command:
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### /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 version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-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 ‘1.29.0’
* 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 27.055 0.112 27.169
fitExtractVarPartModel-method 23.108 0.196 23.304
getTreat-method 21.278 0.092 21.371
plotCompareP-method 17.035 0.044 17.079
extractVarPart 14.397 0.192 14.589
varPartConfInf 13.434 0.036 13.471
sortCols-method 7.634 0.016 7.651
plotPercentBars-method 7.269 0.028 7.297
plotVarPart-method 7.100 0.000 7.099
residuals-VarParFitList-method 5.606 0.044 5.651
dream-method 3.733 0.077 9.608
* 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.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
variancePartition.Rcheck/tests/runTests.Rout
R version 4.3.0 alpha (2023-04-03 r84154)
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:2 s
Dividing work into 1 chunks...
Total:2 s
Dividing work into 1 chunks...
Total:6 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: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: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:1 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:0.4 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:2 s
Dividing work into 5 chunks...
Total:9 s
Dividing work into 5 chunks...
Total:9 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:0.4 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...
Total:0.5 s
RUNIT TEST PROTOCOL -- Wed Apr 12 00:25:58 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
77.486 1.687 94.826
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.159 | 0.008 | 0.168 | |
| as.data.frame.varPartResults | 0.283 | 0.000 | 0.283 | |
| as.matrix-varPartResults-method | 0.238 | 0.000 | 0.238 | |
| calcVarPart-method | 0.056 | 0.000 | 0.056 | |
| canCorPairs | 0.068 | 0.000 | 0.067 | |
| colinearityScore | 0.433 | 0.000 | 0.432 | |
| dream-method | 3.733 | 0.077 | 9.608 | |
| extractVarPart | 14.397 | 0.192 | 14.589 | |
| fitExtractVarPartModel-method | 23.108 | 0.196 | 23.304 | |
| fitVarPartModel-method | 27.055 | 0.112 | 27.169 | |
| getContrast-method | 0.009 | 0.000 | 0.009 | |
| getTreat-method | 21.278 | 0.092 | 21.371 | |
| get_prediction-method | 0.061 | 0.012 | 0.075 | |
| ggColorHue | 0 | 0 | 0 | |
| makeContrastsDream | 1.428 | 0.008 | 1.437 | |
| plotCompareP-method | 17.035 | 0.044 | 17.079 | |
| plotContrasts | 0.18 | 0.00 | 0.18 | |
| plotCorrMatrix | 0.071 | 0.000 | 0.071 | |
| plotCorrStructure | 0.745 | 0.008 | 0.753 | |
| plotPercentBars-method | 7.269 | 0.028 | 7.297 | |
| plotStratify | 0.654 | 0.004 | 0.657 | |
| plotStratifyBy | 0.710 | 0.004 | 0.714 | |
| plotVarPart-method | 7.100 | 0.000 | 7.099 | |
| rdf.merMod | 0.068 | 0.000 | 0.068 | |
| residuals-VarParFitList-method | 5.606 | 0.044 | 5.651 | |
| sortCols-method | 7.634 | 0.016 | 7.651 | |
| varPartConfInf | 13.434 | 0.036 | 13.471 | |
| voomWithDreamWeights | 2.864 | 0.028 | 2.892 | |