| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-08 11:41:32 -0400 (Wed, 08 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" | 4707 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: variancePartition |
| Version: 1.34.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings variancePartition_1.34.0.tar.gz |
| StartedAt: 2024-05-08 13:00:52 -0000 (Wed, 08 May 2024) |
| EndedAt: 2024-05-08 13:11:25 -0000 (Wed, 08 May 2024) |
| EllapsedTime: 633.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.34.0’
* 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 39.852 0.128 40.069
fitExtractVarPartModel-method 31.246 0.152 31.469
getTreat-method 27.099 0.039 27.201
plotCompareP-method 21.193 0.320 21.560
extractVarPart 19.639 0.335 20.020
varPartConfInf 12.796 0.052 12.879
sortCols-method 10.215 0.024 10.260
plotPercentBars-method 10.023 0.071 10.117
plotVarPart-method 9.912 0.060 9.995
residuals-VarParFitList-method 9.184 0.020 9.226
mvTest-method 7.826 0.042 16.253
dream-method 4.614 0.031 11.297
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* 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/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 -- Wed May 8 13:11:20 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
229.674 1.846 280.594
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.179 | 0.020 | 0.199 | |
| as.data.frame.varPartResults | 0.443 | 0.000 | 0.444 | |
| as.matrix-varPartResults-method | 0.391 | 0.000 | 0.392 | |
| augmentPriorCount | 1.051 | 0.028 | 1.080 | |
| calcVarPart-method | 0.08 | 0.00 | 0.08 | |
| canCorPairs | 0.094 | 0.000 | 0.094 | |
| colinearityScore | 0.604 | 0.000 | 0.605 | |
| deviation-method | 1.752 | 0.040 | 1.795 | |
| diffVar-method | 1.785 | 0.016 | 1.805 | |
| dream-method | 4.614 | 0.031 | 11.297 | |
| extractVarPart | 19.639 | 0.335 | 20.020 | |
| fitExtractVarPartModel-method | 31.246 | 0.152 | 31.469 | |
| fitVarPartModel-method | 39.852 | 0.128 | 40.069 | |
| getContrast-method | 0.008 | 0.000 | 0.009 | |
| getTreat-method | 27.099 | 0.039 | 27.201 | |
| get_prediction-method | 0.085 | 0.004 | 0.092 | |
| ggColorHue | 0.001 | 0.000 | 0.000 | |
| makeContrastsDream | 2.007 | 0.004 | 2.015 | |
| mvTest-method | 7.826 | 0.042 | 16.253 | |
| plotCompareP-method | 21.193 | 0.320 | 21.560 | |
| plotContrasts | 0.263 | 0.000 | 0.264 | |
| plotCorrMatrix | 0.086 | 0.000 | 0.087 | |
| plotCorrStructure | 1.038 | 0.008 | 1.049 | |
| plotPercentBars-method | 10.023 | 0.071 | 10.117 | |
| plotStratify | 0.924 | 0.000 | 0.926 | |
| plotStratifyBy | 0.932 | 0.000 | 0.934 | |
| plotVarPart-method | 9.912 | 0.060 | 9.995 | |
| rdf | 0.033 | 0.002 | 0.034 | |
| rdf.merMod | 0.073 | 0.000 | 0.074 | |
| residuals-VarParFitList-method | 9.184 | 0.020 | 9.226 | |
| sortCols-method | 10.215 | 0.024 | 10.260 | |
| varPartConfInf | 12.796 | 0.052 | 12.879 | |
| vcovSqrt-method | 0.019 | 0.000 | 0.020 | |
| voomWithDreamWeights | 3.725 | 0.036 | 3.769 | |