| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:23 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 2132/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| variancePartition 1.28.9 (landing page) Gabriel E. Hoffman
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: variancePartition |
| Version: 1.28.9 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings variancePartition_1.28.9.tar.gz |
| StartedAt: 2023-04-11 00:45:27 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 00:58:17 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 769.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings variancePartition_1.28.9.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/variancePartition.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.28.9’
* 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 26.113 0.104 26.216
fitExtractVarPartModel-method 23.930 0.211 24.141
getTreat-method 21.699 0.044 21.743
plotCompareP-method 16.845 0.064 16.909
extractVarPart 14.168 0.220 14.389
varPartConfInf 14.222 0.036 14.259
sortCols-method 9.297 0.036 9.334
plotVarPart-method 7.391 0.024 7.417
plotPercentBars-method 7.320 0.000 7.319
residuals-VarParFitList-method 5.966 0.000 5.966
dream-method 3.217 0.107 9.327
* 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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.16-bioc/meat/variancePartition.Rcheck/00check.log’
for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
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:0.7 s
Dividing work into 1 chunks...
Total:2 s
Dividing work into 1 chunks...
Total:1 s
Dividing work into 1 chunks...
Total:1 s
Dividing work into 1 chunks...
Total:0.3 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:0.7 s
Dividing work into 1 chunks...
Total:6 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
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:0.3 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:1 s
Dividing work into 1 chunks...
Total:0.9 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:0.8 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:0.08 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:8 s
Dividing work into 5 chunks...
Total:8 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:4 s
Dividing work into 5 chunks...
Total:3 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:0.07 s
Dividing work into 1 chunks...
Total:0.4 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...
Total:0.5 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...
Total:0.5 s
RUNIT TEST PROTOCOL -- Tue Apr 11 00:51:35 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
89.158 1.377 107.313
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.196 | 0.008 | 0.204 | |
| as.data.frame.varPartResults | 0.457 | 0.000 | 0.459 | |
| as.matrix-varPartResults-method | 0.371 | 0.000 | 0.371 | |
| calcVarPart-method | 0.066 | 0.008 | 0.073 | |
| canCorPairs | 0.103 | 0.000 | 0.102 | |
| colinearityScore | 0.439 | 0.000 | 0.439 | |
| deviation-method | 1.422 | 0.400 | 1.822 | |
| diffVar-method | 0.881 | 0.016 | 0.897 | |
| dream-method | 3.217 | 0.107 | 9.327 | |
| extractVarPart | 14.168 | 0.220 | 14.389 | |
| fitExtractVarPartModel-method | 23.930 | 0.211 | 24.141 | |
| fitVarPartModel-method | 26.113 | 0.104 | 26.216 | |
| getContrast-method | 0.007 | 0.000 | 0.007 | |
| getTreat-method | 21.699 | 0.044 | 21.743 | |
| get_prediction-method | 0.078 | 0.000 | 0.078 | |
| ggColorHue | 0.001 | 0.000 | 0.000 | |
| makeContrastsDream | 1.481 | 0.012 | 1.493 | |
| mvTest-method | 3.144 | 0.076 | 3.220 | |
| plotCompareP-method | 16.845 | 0.064 | 16.909 | |
| plotContrasts | 0.173 | 0.000 | 0.174 | |
| plotCorrMatrix | 0.072 | 0.000 | 0.072 | |
| plotCorrStructure | 0.795 | 0.008 | 0.802 | |
| plotPercentBars-method | 7.320 | 0.000 | 7.319 | |
| plotStratify | 0.738 | 0.000 | 0.737 | |
| plotStratifyBy | 0.685 | 0.004 | 0.689 | |
| plotVarPart-method | 7.391 | 0.024 | 7.417 | |
| rdf.merMod | 0.052 | 0.000 | 0.052 | |
| residuals-VarParFitList-method | 5.966 | 0.000 | 5.966 | |
| sortCols-method | 9.297 | 0.036 | 9.334 | |
| varPartConfInf | 14.222 | 0.036 | 14.259 | |
| voomWithDreamWeights | 3.074 | 0.060 | 3.134 | |