| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:57 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2044/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| variancePartition 1.25.5 (landing page) Gabriel E. Hoffman
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: variancePartition |
| Version: 1.25.5 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:variancePartition.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings variancePartition_1.25.5.tar.gz |
| StartedAt: 2022-03-17 20:34:32 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:39:41 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 308.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:variancePartition.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings variancePartition_1.25.5.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/variancePartition.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'variancePartition/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'variancePartition' version '1.25.5'
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getTreat-method 24.01 0.04 24.27
fitExtractVarPartModel-method 23.53 0.04 23.58
fitVarPartModel-method 23.22 0.03 23.25
plotCompareP-method 15.52 0.00 15.52
extractVarPart 12.08 0.02 12.09
varPartConfInf 9.16 0.02 9.17
plotPercentBars-method 7.15 0.02 7.17
sortCols-method 6.16 0.00 6.16
plotVarPart-method 5.87 0.01 5.89
dream-method 3.78 0.06 8.74
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/variancePartition.Rcheck/00check.log'
for details.
variancePartition.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL variancePartition
###
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* installing to library 'D:/biocbuild/bbs-3.15-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'
** help
Loading required namespace: variancePartition
*** installing help indices
converting help for package 'variancePartition'
finding HTML links ... done
ESS-method html
FMT-class html
FMT html
FMT.ZI html
MArrayLM2-class html
VarParCIList-class html
VarParFitList-class html
applyQualityWeights html
as.data.frame.varPartResults html
as.matrix-varPartResults-method html
calcVarPart-method html
canCorPairs html
classifyTestsF-MArrayLM2-method html
classifyTestsF html
colinearityScore html
dot-getAllUniContrasts html
dot-isMixedModelFormula html
dot-standard_transform html
dream-method html
dscchisq html
eBayes-method html
eBayesFMT html
extractVarPart html
fitExtractVarPartModel-method html
fitVarPartModel-method html
getContrast-method html
getTreat-method html
get_prediction-method html
ggColorHue html
isRunableFormula html
makeContrastsDream html
plotCompareP-method html
plotContrasts html
plotCorrMatrix html
plotCorrStructure html
plotPercentBars-method html
plotStratify html
plotStratifyBy html
plotVarPart-method html
plotVarianceEstimates html
rdf.merMod html
rdf_from_matrices html
reOnly html
residuals-MArrayLM-method html
residuals-MArrayLM2-method html
residuals-VarParFitList-method html
residuals.MArrayLM2 html
shrinkageMetric html
sortCols-method html
subset.MArrayLM2-method html
toptable-method html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-variancePartition/00new/variancePartition/help/toptable+2CFMT-method.html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-variancePartition/00new/variancePartition/help/toptable+2CMArrayLM2-method.html
varParFrac-class html
varPartConfInf html
varPartDEdata html
varPartData html
varPartResults-class html
voomWithDreamWeights html
** 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)
Making 'packages.html' ... done
variancePartition.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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")
Loading required package: Matrix
Dividing work into 1 chunks...
Total:0.9 s
Dividing work into 1 chunks...
Total:1 s
Dividing work into 1 chunks...
Total:1 s
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:0.09 s
Removing intercept from test coefficients
Removing intercept from test coefficients
Dividing work into 1 chunks...
Total:1 s
Dividing work into 1 chunks...
Total:0.8 s
Dividing work into 1 chunks...
Total:5 s
Dividing work into 1 chunks...
Total:0.07 s
Dividing work into 1 chunks...
Total:0.3 s
Dividing work into 1 chunks...
Total:0.3 s
Dividing work into 1 chunks...
Total:4 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...
Total:0.3 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...
Total:0.3 s
Memory usage to store result: >487.7 Kb
Dividing work into 1 chunks...
Total:5 s
Dividing work into 1 chunks...
Total:0.8 s
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Dividing work into 1 chunks...
Total:1 s
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Dividing work into 1 chunks...
Total:0.2 s
Dividing work into 1 chunks...
Total:0.3 s
Memory usage to store result: >454.7 Kb
Dividing work into 1 chunks...
Total:0.2 s
Memory usage to store result: >454.7 Kb
Dividing work into 1 chunks...
Total:0.2 s
Dividing work into 1 chunks...
Total:0.8 s
Dividing work into 1 chunks...
Total:0.8 s
Removing intercept from test coefficients
Removing intercept from test coefficients
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Memory usage to store result: >248.4 Kb
Dividing work into 5 chunks...
Total:2 s
Dividing work into 5 chunks...
Total:6 s
Dividing work into 5 chunks...
Total:6 s
Dividing work into 5 chunks...
Total:6 s
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Memory usage to store result: >248.4 Kb
Dividing work into 5 chunks...
Total:2 s
Dividing work into 5 chunks...
Total:2 s
Dividing work into 5 chunks...
Total:2 s
Dividing work into 5 chunks...
Total:2 s
Fixed effect model, using limma directly...
Dividing work into 1 chunks...
Total:0.8 s
Fixed effect model, using limma directly...
User can apply eBayes() afterwards...
Dividing work into 1 chunks...
Total:0.7 s
Dividing work into 1 chunks...
Total:0.2 s
Total:0.03 s
Dividing work into 1 chunks...
Total:0.3 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...
Total:0.3 s
Memory usage to store result: >49.7 Kb
Dividing work into 1 chunks...
Total:0.3 s
RUNIT TEST PROTOCOL -- Thu Mar 17 20:39:33 2022
***********************************************
Number of test functions: 15
Number of errors: 0
Number of failures: 0
1 Test Suite :
variancePartition RUnit Tests - 15 test functions, 0 errors, 0 failures
Number of test functions: 15
Number of errors: 0
Number of failures: 0
There were 31 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
52.48 0.89 66.20
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.11 | 0.00 | 0.11 | |
| as.data.frame.varPartResults | 0.31 | 0.00 | 0.32 | |
| as.matrix-varPartResults-method | 0.31 | 0.00 | 0.31 | |
| calcVarPart-method | 0.04 | 0.00 | 0.05 | |
| canCorPairs | 0.07 | 0.00 | 0.06 | |
| colinearityScore | 0.36 | 0.02 | 0.39 | |
| dream-method | 3.78 | 0.06 | 8.74 | |
| eBayesFMT | 0.92 | 0.00 | 0.92 | |
| extractVarPart | 12.08 | 0.02 | 12.09 | |
| fitExtractVarPartModel-method | 23.53 | 0.04 | 23.58 | |
| fitVarPartModel-method | 23.22 | 0.03 | 23.25 | |
| getContrast-method | 0 | 0 | 0 | |
| getTreat-method | 24.01 | 0.04 | 24.27 | |
| get_prediction-method | 0.07 | 0.00 | 0.08 | |
| ggColorHue | 0 | 0 | 0 | |
| makeContrastsDream | 1.37 | 0.01 | 1.40 | |
| plotCompareP-method | 15.52 | 0.00 | 15.52 | |
| plotContrasts | 0.19 | 0.00 | 0.19 | |
| plotCorrMatrix | 0.11 | 0.00 | 0.11 | |
| plotCorrStructure | 0.72 | 0.00 | 0.72 | |
| plotPercentBars-method | 7.15 | 0.02 | 7.17 | |
| plotStratify | 0.55 | 0.00 | 0.55 | |
| plotStratifyBy | 0.47 | 0.00 | 0.46 | |
| plotVarPart-method | 5.87 | 0.01 | 5.89 | |
| rdf.merMod | 0.05 | 0.00 | 0.05 | |
| residuals-VarParFitList-method | 4.56 | 0.00 | 4.56 | |
| sortCols-method | 6.16 | 0.00 | 6.16 | |
| varPartConfInf | 9.16 | 0.02 | 9.17 | |
| voomWithDreamWeights | 2.25 | 0.06 | 2.31 | |