| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 2179/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| variancePartition 1.30.2 (landing page) Gabriel E. Hoffman
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
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: 1.30.2 |
| 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_1.30.2.tar.gz |
| StartedAt: 2023-10-19 09:19:17 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 09:32:20 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 782.8 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_1.30.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/variancePartition.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.30.2’
* 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 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 31.626 0.292 57.090
fitExtractVarPartModel-method 28.607 0.262 51.537
getTreat-method 25.890 0.236 46.535
plotCompareP-method 20.469 0.186 36.820
extractVarPart 16.818 0.200 29.037
varPartConfInf 16.738 0.151 30.284
sortCols-method 8.993 0.089 16.240
plotPercentBars-method 8.934 0.088 16.112
plotVarPart-method 8.758 0.084 15.817
residuals-VarParFitList-method 6.723 0.067 12.112
dream-method 4.168 0.083 19.044
mvTest-method 3.630 0.059 6.563
voomWithDreamWeights 3.196 0.059 5.827
* 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
‘/Users/biocbuild/bbs-3.17-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/4.3-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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:0.8 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
Dividing work into 1 chunks...
Total:0.2 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:2 s
Dividing work into 1 chunks...
Total:14 s
Dividing work into 1 chunks...
Total:0.2 s
Dividing work into 1 chunks...
Total:0.8 s
Dividing work into 1 chunks...
Total:0.9 s
Dividing work into 1 chunks...
Total:12 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...
Total:0.7 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...
Total:0.7 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...
Total:11 s
Dividing work into 1 chunks...
Total:3 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:2 s
Dividing work into 1 chunks...
Total:2 s
Dividing work into 1 chunks...
Total:0.8 s
Dividing work into 1 chunks...
Total:0.7 s
Memory usage to store result: >455.2 Kb
Dividing work into 1 chunks...
Total:0.7 s
Memory usage to store result: >455.2 Kb
Dividing work into 1 chunks...
Total:0.7 s
Dividing work into 1 chunks...
Total:2 s
Dividing work into 1 chunks...
Total:2 s
Removing intercept from test coefficients
Removing intercept from test coefficients
Dividing work into 1 chunks...
Total:0.3 s
Dividing work into 1 chunks...
Total:2 s
Dividing work into 1 chunks...
Total:0.4 s
Dividing work into 1 chunks...
Total:3 s
Dividing work into 1 chunks...
Total:4 s
Dividing work into 1 chunks...
Total:3 s
Loading required package: Rcpp
Loading required package: RcppZiggurat
Memory usage to store result: >5 Kb
Dividing work into 1 chunks...
Total:0.2 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:4 s
Dividing work into 5 chunks...
Total:17 s
Dividing work into 5 chunks...
Total:17 s
Dividing work into 5 chunks...
Total:17 s
Memory usage to store result: >248.4 Kb
Dividing work into 5 chunks...
Total:5 s
Dividing work into 5 chunks...
Total:6 s
Dividing work into 5 chunks...
Total:7 s
Dividing work into 5 chunks...
Total:7 s
Dividing work into 1 chunks...
Total:2 s
Dividing work into 1 chunks...
Total:2 s
Dividing work into 1 chunks...
Total:0.8 s
Total:0.1 s
Dividing work into 1 chunks...
Total:0.9 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...
Total:1 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...
Total:1 s
RUNIT TEST PROTOCOL -- Thu Oct 19 09:31:53 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
101.178 1.624 216.026
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.218 | 0.011 | 0.356 | |
| as.data.frame.varPartResults | 0.359 | 0.006 | 0.556 | |
| as.matrix-varPartResults-method | 0.300 | 0.005 | 0.477 | |
| calcVarPart-method | 0.085 | 0.006 | 0.158 | |
| canCorPairs | 0.084 | 0.006 | 0.163 | |
| colinearityScore | 0.503 | 0.008 | 0.818 | |
| deviation-method | 1.309 | 0.053 | 2.087 | |
| diffVar-method | 1.044 | 0.038 | 1.652 | |
| dream-method | 4.168 | 0.083 | 19.044 | |
| extractVarPart | 16.818 | 0.200 | 29.037 | |
| fitExtractVarPartModel-method | 28.607 | 0.262 | 51.537 | |
| fitVarPartModel-method | 31.626 | 0.292 | 57.090 | |
| getContrast-method | 0.008 | 0.002 | 0.016 | |
| getTreat-method | 25.890 | 0.236 | 46.535 | |
| get_prediction-method | 0.091 | 0.012 | 0.185 | |
| ggColorHue | 0 | 0 | 0 | |
| makeContrastsDream | 1.792 | 0.020 | 3.227 | |
| mvTest-method | 3.630 | 0.059 | 6.563 | |
| plotCompareP-method | 20.469 | 0.186 | 36.820 | |
| plotContrasts | 0.208 | 0.005 | 0.378 | |
| plotCorrMatrix | 0.069 | 0.008 | 0.138 | |
| plotCorrStructure | 0.879 | 0.036 | 1.635 | |
| plotPercentBars-method | 8.934 | 0.088 | 16.112 | |
| plotStratify | 0.859 | 0.014 | 1.539 | |
| plotStratifyBy | 0.859 | 0.013 | 1.542 | |
| plotVarPart-method | 8.758 | 0.084 | 15.817 | |
| rdf.merMod | 0.076 | 0.003 | 0.140 | |
| residuals-VarParFitList-method | 6.723 | 0.067 | 12.112 | |
| sortCols-method | 8.993 | 0.089 | 16.240 | |
| varPartConfInf | 16.738 | 0.151 | 30.284 | |
| voomWithDreamWeights | 3.196 | 0.059 | 5.827 | |