| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:15 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| 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 2178/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| variancePartition 1.35.0 (landing page) Gabriel E. Hoffman
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | NA | ||||||||
|
To the developers/maintainers of the variancePartition package: - 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: 1.35.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings variancePartition_1.35.0.tar.gz |
| StartedAt: 2024-05-13 06:21:48 -0400 (Mon, 13 May 2024) |
| EndedAt: 2024-05-13 06:30:29 -0400 (Mon, 13 May 2024) |
| EllapsedTime: 520.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings variancePartition_1.35.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/variancePartition.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.35.0’
* 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 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 29.465 0.113 30.048
fitExtractVarPartModel-method 23.208 0.088 23.390
getTreat-method 20.459 0.071 20.606
plotCompareP-method 15.052 0.068 15.331
extractVarPart 14.622 0.065 14.763
varPartConfInf 10.379 0.037 10.445
sortCols-method 7.879 0.031 7.947
plotPercentBars-method 7.580 0.032 7.634
plotVarPart-method 7.533 0.028 7.586
residuals-VarParFitList-method 7.056 0.025 7.121
mvTest-method 6.027 0.089 12.807
dream-method 3.580 0.081 20.737
* 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
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/variancePartition.Rcheck/00check.log’
for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 -- Mon May 13 06:30:17 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
162.287 4.507 222.954
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.164 | 0.017 | 0.182 | |
| as.data.frame.varPartResults | 0.325 | 0.004 | 0.330 | |
| as.matrix-varPartResults-method | 0.321 | 0.004 | 0.326 | |
| augmentPriorCount | 1.043 | 0.080 | 1.132 | |
| calcVarPart-method | 0.067 | 0.005 | 0.072 | |
| canCorPairs | 0.072 | 0.005 | 0.077 | |
| colinearityScore | 0.466 | 0.011 | 0.481 | |
| deviation-method | 1.563 | 0.088 | 1.664 | |
| diffVar-method | 1.467 | 0.075 | 1.547 | |
| dream-method | 3.580 | 0.081 | 20.737 | |
| extractVarPart | 14.622 | 0.065 | 14.763 | |
| fitExtractVarPartModel-method | 23.208 | 0.088 | 23.390 | |
| fitVarPartModel-method | 29.465 | 0.113 | 30.048 | |
| getContrast-method | 0.010 | 0.003 | 0.013 | |
| getTreat-method | 20.459 | 0.071 | 20.606 | |
| get_prediction-method | 0.072 | 0.010 | 0.083 | |
| ggColorHue | 0 | 0 | 0 | |
| makeContrastsDream | 1.498 | 0.012 | 1.517 | |
| mvTest-method | 6.027 | 0.089 | 12.807 | |
| plotCompareP-method | 15.052 | 0.068 | 15.331 | |
| plotContrasts | 0.184 | 0.005 | 0.191 | |
| plotCorrMatrix | 0.070 | 0.009 | 0.078 | |
| plotCorrStructure | 0.856 | 0.029 | 0.890 | |
| plotPercentBars-method | 7.580 | 0.032 | 7.634 | |
| plotStratify | 0.649 | 0.008 | 0.658 | |
| plotStratifyBy | 0.677 | 0.009 | 0.689 | |
| plotVarPart-method | 7.533 | 0.028 | 7.586 | |
| rdf | 0.027 | 0.002 | 0.029 | |
| rdf.merMod | 0.062 | 0.002 | 0.064 | |
| residuals-VarParFitList-method | 7.056 | 0.025 | 7.121 | |
| sortCols-method | 7.879 | 0.031 | 7.947 | |
| varPartConfInf | 10.379 | 0.037 | 10.445 | |
| vcovSqrt-method | 0.020 | 0.003 | 0.022 | |
| voomWithDreamWeights | 3.025 | 0.074 | 3.111 | |