| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:19 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 2248/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| variancePartition 1.34.0 (landing page) Gabriel E. Hoffman
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 1.34.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings variancePartition_1.34.0.tar.gz |
| StartedAt: 2024-05-31 09:18:40 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 09:36:16 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 1056.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings variancePartition_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/variancePartition.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.34.0’
* 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 code 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 ... NOTE
Unexported object imported by a ':::' call: ‘lmerTest:::as_lmerModLT’
See the note in ?`:::` about the use of this operator.
* 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 Rd file 'residuals.MArrayLM2.Rd':
‘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’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fitVarPartModel-method 25.944 0.131 26.077
fitExtractVarPartModel-method 20.267 0.175 20.444
getTreat-method 17.438 0.037 17.476
plotCompareP-method 13.415 0.312 13.727
extractVarPart 12.807 0.192 12.999
varPartConfInf 9.451 0.036 9.486
sortCols-method 7.096 0.036 7.132
plotPercentBars-method 6.435 0.076 6.510
plotVarPart-method 6.338 0.039 6.378
residuals-VarParFitList-method 5.826 0.032 5.857
mvTest-method 5.023 0.045 11.006
dream-method 3.097 0.049 8.258
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/variancePartition.Rcheck/00check.log’
for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
Removing intercept from test coefficients
Removing intercept from test coefficients
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')
Removing intercept from test coefficients
Removing intercept from test coefficients
Loading required package: Rcpp
Loading required package: RcppZiggurat
Loading required package: RcppParallel
Attaching package: 'RcppParallel'
The following object is masked from 'package:Rcpp':
LdFlags
Rfast: 2.1.0
___ __ __ __ __ __ __ __ __ __ _ _ __ __ __ __ __ __ __ __ __ __ __
| __ __ __ __ | | __ __ __ __ _/ / \ | __ __ __ __ / /__ __ _ _ __ __\
| | | | | | / _ \ | | / /
| | | | | | / / \ \ | | / /
| | | | | | / / \ \ | | / /
| |__ __ __ __| | | |__ __ __ __ / / \ \ | |__ __ __ __ _ / /__/\
| __ __ __ __| | __ __ __ __| / /__ _ __\ \ |_ __ __ __ _ | / ___ /
| \ | | / _ _ _ _ _ _ \ | | \/ / /
| |\ \ | | / / \ \ | | / /
| | \ \ | | / / \ \ | | / /
| | \ \ | | / / \ \ | | / /
| | \ \__ __ _ | | / / \ \ _ __ __ __ _| | / /
|_| \__ __ __\ |_| /_/ \_\ /_ __ __ __ ___| \/ team
Warning:
Variables contain NA's: Disease
Samples with missing data will be dropped.
RUNIT TEST PROTOCOL -- Fri May 31 09:25:43 2024
***********************************************
Number of test functions: 30
Number of errors: 0
Number of failures: 0
1 Test Suite :
variancePartition RUnit Tests - 30 test functions, 0 errors, 0 failures
Number of test functions: 30
Number of errors: 0
Number of failures: 0
There were 29 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
142.347 1.798 183.525
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.132 | 0.015 | 0.148 | |
| as.data.frame.varPartResults | 0.286 | 0.001 | 0.286 | |
| as.matrix-varPartResults-method | 0.259 | 0.000 | 0.258 | |
| augmentPriorCount | 0.769 | 0.008 | 0.776 | |
| calcVarPart-method | 0.049 | 0.000 | 0.048 | |
| canCorPairs | 0.069 | 0.000 | 0.068 | |
| colinearityScore | 0.403 | 0.000 | 0.404 | |
| deviation-method | 1.145 | 0.040 | 1.185 | |
| diffVar-method | 1.099 | 0.012 | 1.112 | |
| dream-method | 3.097 | 0.049 | 8.258 | |
| extractVarPart | 12.807 | 0.192 | 12.999 | |
| fitExtractVarPartModel-method | 20.267 | 0.175 | 20.444 | |
| fitVarPartModel-method | 25.944 | 0.131 | 26.077 | |
| getContrast-method | 0.005 | 0.002 | 0.007 | |
| getTreat-method | 17.438 | 0.037 | 17.476 | |
| get_prediction-method | 0.069 | 0.004 | 0.074 | |
| ggColorHue | 0 | 0 | 0 | |
| makeContrastsDream | 1.337 | 0.004 | 1.341 | |
| mvTest-method | 5.023 | 0.045 | 11.006 | |
| plotCompareP-method | 13.415 | 0.312 | 13.727 | |
| plotContrasts | 0.163 | 0.004 | 0.167 | |
| plotCorrMatrix | 0.067 | 0.003 | 0.070 | |
| plotCorrStructure | 0.724 | 0.009 | 0.731 | |
| plotPercentBars-method | 6.435 | 0.076 | 6.510 | |
| plotStratify | 0.606 | 0.004 | 0.610 | |
| plotStratifyBy | 0.586 | 0.000 | 0.586 | |
| plotVarPart-method | 6.338 | 0.039 | 6.378 | |
| rdf | 0.015 | 0.005 | 0.019 | |
| rdf.merMod | 0.044 | 0.000 | 0.043 | |
| residuals-VarParFitList-method | 5.826 | 0.032 | 5.857 | |
| sortCols-method | 7.096 | 0.036 | 7.132 | |
| varPartConfInf | 9.451 | 0.036 | 9.486 | |
| vcovSqrt-method | 0.012 | 0.002 | 0.015 | |
| voomWithDreamWeights | 2.462 | 0.021 | 2.482 | |