| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:52 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 2179/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| variancePartition 1.30.2 (landing page) Gabriel E. Hoffman
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: variancePartition |
| Version: 1.30.2 |
| 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_1.30.2.tar.gz |
| StartedAt: 2023-10-16 02:00:40 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 02:16:47 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 967.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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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_1.30.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/variancePartition.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.30.2’
* 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 23.866 0.128 23.995
fitExtractVarPartModel-method 20.455 0.172 20.627
getTreat-method 18.740 0.078 18.818
plotCompareP-method 15.060 0.032 15.091
extractVarPart 12.573 0.316 12.889
varPartConfInf 11.256 0.016 11.273
plotPercentBars-method 6.337 0.020 6.358
plotVarPart-method 6.272 0.000 6.273
sortCols-method 6.126 0.004 6.131
residuals-VarParFitList-method 5.080 0.056 5.136
dream-method 3.469 0.090 9.468
* 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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
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: 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:0.4 s
Dividing work into 1 chunks...
Total:0.9 s
Dividing work into 1 chunks...
Total:1 s
Dividing work into 1 chunks...
Total:1 s
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:0.9 s
Dividing work into 1 chunks...
Total:0.9 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: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:0.4 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:0.3 s
Dividing work into 1 chunks...
Total:0.9 s
Dividing work into 1 chunks...
Total:0.9 s
Removing intercept from test coefficients
Removing intercept from test coefficients
Dividing work into 1 chunks...
Total:0.1 s
Dividing work into 1 chunks...
Total:0.7 s
Dividing work into 1 chunks...
Total:0.1 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
Loading required package: Rcpp
Loading required package: RcppZiggurat
Rfast: 2.0.8
___ __ __ __ __ __ __ __ __ __ _ _ __ __ __ __ __ __ __ __ __ __ __
| __ __ __ __ | | __ __ __ __ _/ / \ | __ __ __ __ / /__ __ _ _ __ __\
| | | | | | / _ \ | | / /
| | | | | | / / \ \ | | / /
| | | | | | / / \ \ | | / /
| |__ __ __ __| | | |__ __ __ __ / / \ \ | |__ __ __ __ _ / /__/\
| __ __ __ __| | __ __ __ __| / /__ _ __\ \ |_ __ __ __ _ | / ___ /
| \ | | / _ _ _ _ _ _ \ | | \/ / /
| |\ \ | | / / \ \ | | / /
| | \ \ | | / / \ \ | | / /
| | \ \ | | / / \ \ | | / /
| | \ \__ __ _ | | / / \ \ _ __ __ __ _| | / /
|_| \__ __ __\ |_| /_/ \_\ /_ __ __ __ ___| \/ team
Memory usage to store result: >5 Kb
Dividing work into 1 chunks...
Total:0.07 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:2 s
Dividing work into 5 chunks...
Total:7 s
Dividing work into 5 chunks...
Total:7 s
Dividing work into 5 chunks...
Total:7 s
Memory usage to store result: >248.4 Kb
Dividing work into 5 chunks...
Total:2 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
Dividing work into 1 chunks...
Total:0.9 s
Dividing work into 1 chunks...
Total:0.9 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:0.4 s
RUNIT TEST PROTOCOL -- Mon Oct 16 02:06:09 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
79.749 1.672 97.434
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.145 | 0.000 | 0.145 | |
| as.data.frame.varPartResults | 0.228 | 0.004 | 0.233 | |
| as.matrix-varPartResults-method | 0.218 | 0.000 | 0.218 | |
| calcVarPart-method | 0.051 | 0.000 | 0.050 | |
| canCorPairs | 0.067 | 0.000 | 0.067 | |
| colinearityScore | 0.384 | 0.004 | 0.389 | |
| deviation-method | 1.197 | 0.051 | 1.249 | |
| diffVar-method | 0.892 | 0.021 | 0.912 | |
| dream-method | 3.469 | 0.090 | 9.468 | |
| extractVarPart | 12.573 | 0.316 | 12.889 | |
| fitExtractVarPartModel-method | 20.455 | 0.172 | 20.627 | |
| fitVarPartModel-method | 23.866 | 0.128 | 23.995 | |
| getContrast-method | 0.003 | 0.006 | 0.008 | |
| getTreat-method | 18.740 | 0.078 | 18.818 | |
| get_prediction-method | 0.057 | 0.008 | 0.066 | |
| ggColorHue | 0 | 0 | 0 | |
| makeContrastsDream | 1.299 | 0.000 | 1.299 | |
| mvTest-method | 2.51 | 0.06 | 2.57 | |
| plotCompareP-method | 15.060 | 0.032 | 15.091 | |
| plotContrasts | 0.164 | 0.000 | 0.163 | |
| plotCorrMatrix | 0.067 | 0.004 | 0.071 | |
| plotCorrStructure | 0.708 | 0.012 | 0.719 | |
| plotPercentBars-method | 6.337 | 0.020 | 6.358 | |
| plotStratify | 0.679 | 0.000 | 0.680 | |
| plotStratifyBy | 0.680 | 0.004 | 0.685 | |
| plotVarPart-method | 6.272 | 0.000 | 6.273 | |
| rdf.merMod | 0.046 | 0.000 | 0.046 | |
| residuals-VarParFitList-method | 5.080 | 0.056 | 5.136 | |
| sortCols-method | 6.126 | 0.004 | 6.131 | |
| varPartConfInf | 11.256 | 0.016 | 11.273 | |
| voomWithDreamWeights | 2.966 | 0.008 | 2.974 | |