| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:57 -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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:variancePartition.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings variancePartition_1.28.9.tar.gz |
| StartedAt: 2023-04-11 07:04:51 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 07:11:39 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 407.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:variancePartition.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings variancePartition_1.28.9.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/variancePartition.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.28.9'
* 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 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 29.59 0.20 29.92
fitExtractVarPartModel-method 25.67 0.43 26.15
getTreat-method 23.45 0.20 23.66
plotCompareP-method 18.55 0.23 18.78
varPartConfInf 15.16 0.10 15.25
extractVarPart 14.80 0.15 14.97
plotPercentBars-method 8.11 0.06 8.17
sortCols-method 8.11 0.03 8.14
plotVarPart-method 7.78 0.06 7.85
residuals-VarParFitList-method 5.50 0.09 5.59
dream-method 3.53 0.08 9.99
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/variancePartition.Rcheck/00check.log'
for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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:1 s
Dividing work into 1 chunks...
Total:1 s
Dividing work into 1 chunks...
Total:1 s
Dividing work into 1 chunks...
Total:0.1 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: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:0.4 s
Dividing work into 1 chunks...
Total:0.5 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:0.3 s
Dividing work into 1 chunks...
Total:0.5 s
Memory usage to store result: >455.2 Kb
Dividing work into 1 chunks...
Total:0.5 s
Memory usage to store result: >455.2 Kb
Dividing work into 1 chunks...
Total:0.5 s
Dividing work into 1 chunks...
Total:2 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:0.2 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:1 s
Loading required package: Rcpp
Loading required package: RcppZiggurat
Memory usage to store result: >5 Kb
Dividing work into 1 chunks...
Total:0.06 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:9 s
Dividing work into 5 chunks...
Total:8 s
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
Dividing work into 1 chunks...
Total:0.9 s
Dividing work into 1 chunks...
Total:1 s
Dividing work into 1 chunks...
Total:0.3 s
Total:0.03 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 07:11:23 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
88.60 2.07 109.17
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.22 | 0.02 | 0.23 | |
| as.data.frame.varPartResults | 0.44 | 0.02 | 0.46 | |
| as.matrix-varPartResults-method | 0.44 | 0.01 | 0.45 | |
| calcVarPart-method | 0.11 | 0.00 | 0.11 | |
| canCorPairs | 0.08 | 0.02 | 0.10 | |
| colinearityScore | 0.50 | 0.01 | 0.51 | |
| deviation-method | 1.64 | 0.03 | 1.67 | |
| diffVar-method | 1.05 | 0.16 | 1.20 | |
| dream-method | 3.53 | 0.08 | 9.99 | |
| extractVarPart | 14.80 | 0.15 | 14.97 | |
| fitExtractVarPartModel-method | 25.67 | 0.43 | 26.15 | |
| fitVarPartModel-method | 29.59 | 0.20 | 29.92 | |
| getContrast-method | 0 | 0 | 0 | |
| getTreat-method | 23.45 | 0.20 | 23.66 | |
| get_prediction-method | 0.08 | 0.00 | 0.09 | |
| ggColorHue | 0 | 0 | 0 | |
| makeContrastsDream | 1.50 | 0.05 | 1.55 | |
| mvTest-method | 3.11 | 0.14 | 3.25 | |
| plotCompareP-method | 18.55 | 0.23 | 18.78 | |
| plotContrasts | 0.2 | 0.0 | 0.2 | |
| plotCorrMatrix | 0.08 | 0.00 | 0.08 | |
| plotCorrStructure | 0.76 | 0.02 | 0.78 | |
| plotPercentBars-method | 8.11 | 0.06 | 8.17 | |
| plotStratify | 0.97 | 0.02 | 0.99 | |
| plotStratifyBy | 1.02 | 0.00 | 1.01 | |
| plotVarPart-method | 7.78 | 0.06 | 7.85 | |
| rdf.merMod | 0.04 | 0.00 | 0.04 | |
| residuals-VarParFitList-method | 5.50 | 0.09 | 5.59 | |
| sortCols-method | 8.11 | 0.03 | 8.14 | |
| varPartConfInf | 15.16 | 0.10 | 15.25 | |
| voomWithDreamWeights | 3.43 | 0.26 | 3.70 | |