Gabriel E. Hoffman
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/variancePartition |
| Branch: RELEASE_3_12 |
| Last Commit: bd06b39 |
| Last Changed Date: 2020-10-27 11:06:58 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:08 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the variancePartition package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1929/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| variancePartition 1.20.0 (landing page) Gabriel E. Hoffman
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: variancePartition |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings variancePartition_1.20.0.tar.gz |
| StartedAt: 2021-05-06 07:49:54 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 08:07:57 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 1083.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings variancePartition_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/variancePartition.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.20.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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: 'lme4:::reOnly'
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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fitVarPartModel-method 41.59 12.43 108.06
extractVarPart 23.68 7.48 68.14
residuals-VarParFitList-method 15.86 2.00 37.14
fitExtractVarPartModel-method 9.36 3.63 52.15
plotCompareP-method 7.41 1.10 30.25
sortCols-method 5.59 1.13 24.28
plotVarPart-method 4.69 1.36 23.16
plotPercentBars 4.78 1.14 25.31
varPartConfInf 4.93 0.02 33.69
voomWithDreamWeights 2.45 0.11 15.28
dream-method 2.32 0.06 23.96
plotCorrStructure 1.62 0.05 8.27
as.data.frame-varPartResults-method 0.59 0.05 7.30
as.matrix-varPartResults-method 0.53 0.01 6.67
colinearityScore 0.47 0.03 6.43
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fitVarPartModel-method 41.58 5.09 100.81
extractVarPart 25.72 3.66 68.68
fitExtractVarPartModel-method 9.09 2.08 54.09
residuals-VarParFitList-method 9.66 1.49 25.94
plotCompareP-method 6.11 1.41 25.12
plotPercentBars 3.95 1.13 21.14
sortCols-method 4.00 0.86 19.86
plotVarPart-method 3.78 0.76 19.58
varPartConfInf 3.90 0.01 25.33
dream-method 2.72 0.03 23.95
voomWithDreamWeights 1.72 0.05 13.04
plotCorrStructure 1.52 0.01 6.56
as.data.frame-varPartResults-method 1.00 0.03 6.44
colinearityScore 0.62 0.08 7.74
as.matrix-varPartResults-method 0.63 0.03 6.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/variancePartition.Rcheck/00check.log'
for details.
variancePartition.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/variancePartition_1.20.0.tar.gz && rm -rf variancePartition.buildbin-libdir && mkdir variancePartition.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=variancePartition.buildbin-libdir variancePartition_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL variancePartition_1.20.0.zip && rm variancePartition_1.20.0.tar.gz variancePartition_1.20.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1393k 100 1393k 0 0 47.6M 0 --:--:-- --:--:-- --:--:-- 48.6M
install for i386
* installing *source* package 'variancePartition' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'classifyTestsF' in package 'variancePartition'
** help
*** 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
as.data.frame-varPartResults-method 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
eBayes-method html
eBayesFMT html
extractVarPart html
fitExtractVarPartModel-method html
fitVarPartModel-method html
getContrast-method html
get_prediction-method html
ggColorHue html
plotCompareP-method html
plotContrasts html
plotCorrMatrix html
plotCorrStructure html
plotPercentBars html
plotStratify html
plotStratifyBy html
plotVarPart-method html
residuals-MArrayLM-method html
residuals-MArrayLM2-method html
residuals-VarParFitList-method html
sortCols-method html
subset.MArrayLM2-method html
toptable-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
install for x64
* installing *source* package 'variancePartition' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'variancePartition' as variancePartition_1.20.0.zip
* DONE (variancePartition)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'variancePartition' successfully unpacked and MD5 sums checked
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variancePartition.Rcheck/tests_i386/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:limma':
plotMA
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'variancePartition'
The following object is masked from 'package:limma':
classifyTestsF
Dividing work into 1 chunks...
Total:6 s
Dividing work into 1 chunks...
Total:6 s
Dividing work into 1 chunks...
Total:6 s
> proc.time()
user system elapsed
5.32 0.31 22.64
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variancePartition.Rcheck/tests_x64/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:limma':
plotMA
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'variancePartition'
The following object is masked from 'package:limma':
classifyTestsF
Dividing work into 1 chunks...
Total:6 s
Dividing work into 1 chunks...
Total:6 s
Dividing work into 1 chunks...
Total:6 s
> proc.time()
user system elapsed
5.53 0.23 22.71
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variancePartition.Rcheck/examples_i386/variancePartition-Ex.timings
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variancePartition.Rcheck/examples_x64/variancePartition-Ex.timings
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