| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:59 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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: - 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. |
| Package 2037/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| variancePartition 1.24.1 (landing page) Gabriel E. Hoffman
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: variancePartition |
| Version: 1.24.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings variancePartition_1.24.1.tar.gz |
| StartedAt: 2022-04-12 19:48:04 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 19:58:27 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 623.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings variancePartition_1.24.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/variancePartition.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.24.1’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fitVarPartModel-method 51.843 0.488 52.419
fitExtractVarPartModel-method 44.657 0.395 45.086
getTreat-method 44.411 0.420 44.903
plotCompareP-method 34.638 0.311 34.980
extractVarPart 27.676 0.247 27.953
varPartConfInf 24.650 0.176 24.844
plotVarPart-method 14.351 0.219 14.638
plotPercentBars-method 14.358 0.131 14.501
sortCols-method 14.293 0.133 14.439
residuals-VarParFitList-method 10.897 0.111 11.023
dream-method 6.472 0.107 17.081
* 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
‘/Users/biocbuild/bbs-3.14-bioc/meat/variancePartition.Rcheck/00check.log’
for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)
variancePartition.Rcheck/tests/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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:2 s
Dividing work into 1 chunks...
Total:2 s
Dividing work into 1 chunks...
Total:2 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:11 s
Dividing work into 1 chunks...
Total:0.2 s
Dividing work into 1 chunks...
Total:0.8 s
Dividing work into 1 chunks...
Total:0.8 s
Dividing work into 1 chunks...
Total:9 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...
Total:0.8 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...
Total:0.7 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...
Total:9 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:2 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:0.6 s
Memory usage to store result: >455.2 Kb
Dividing work into 1 chunks...
Total:0.6 s
Dividing work into 1 chunks...
Total:2 s
Dividing work into 1 chunks...
Total:2 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:4 s
Dividing work into 5 chunks...
Total:16 s
Dividing work into 5 chunks...
Total:15 s
Dividing work into 5 chunks...
Total:15 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:5 s
Dividing work into 5 chunks...
Total:6 s
Dividing work into 5 chunks...
Total:6 s
Dividing work into 5 chunks...
Total:6 s
Fixed effect model, using limma directly...
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:2 s
Dividing work into 1 chunks...
Total:0.6 s
Total:0.06 s
Dividing work into 1 chunks...
Total:0.8 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...
Total:0.7 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...
Total:0.9 s
RUNIT TEST PROTOCOL -- Tue Apr 12 19:58:18 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
>
> proc.time()
user system elapsed
125.273 1.928 153.890
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.283 | 0.011 | 0.294 | |
| as.data.frame.varPartResults | 0.649 | 0.012 | 0.662 | |
| as.matrix-varPartResults-method | 0.591 | 0.007 | 0.599 | |
| calcVarPart-method | 0.118 | 0.005 | 0.123 | |
| canCorPairs | 0.131 | 0.008 | 0.138 | |
| colinearityScore | 0.801 | 0.011 | 0.812 | |
| dream-method | 6.472 | 0.107 | 17.081 | |
| eBayesFMT | 2.287 | 0.030 | 2.319 | |
| extractVarPart | 27.676 | 0.247 | 27.953 | |
| fitExtractVarPartModel-method | 44.657 | 0.395 | 45.086 | |
| fitVarPartModel-method | 51.843 | 0.488 | 52.419 | |
| getContrast-method | 0.013 | 0.003 | 0.015 | |
| getTreat-method | 44.411 | 0.420 | 44.903 | |
| get_prediction-method | 0.119 | 0.013 | 0.134 | |
| ggColorHue | 0.001 | 0.000 | 0.000 | |
| makeContrastsDream | 2.776 | 0.027 | 2.805 | |
| plotCompareP-method | 34.638 | 0.311 | 34.980 | |
| plotContrasts | 0.273 | 0.004 | 0.277 | |
| plotCorrMatrix | 0.116 | 0.008 | 0.125 | |
| plotCorrStructure | 1.358 | 0.039 | 1.401 | |
| plotPercentBars-method | 14.358 | 0.131 | 14.501 | |
| plotStratify | 0.951 | 0.006 | 0.959 | |
| plotStratifyBy | 0.903 | 0.005 | 0.909 | |
| plotVarPart-method | 14.351 | 0.219 | 14.638 | |
| rdf.merMod | 0.121 | 0.003 | 0.123 | |
| residuals-VarParFitList-method | 10.897 | 0.111 | 11.023 | |
| sortCols-method | 14.293 | 0.133 | 14.439 | |
| varPartConfInf | 24.650 | 0.176 | 24.844 | |
| voomWithDreamWeights | 4.757 | 0.124 | 4.883 | |