Gabriel E. Hoffman
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/variancePartition |
| Branch: RELEASE_3_10 |
| Last Commit: b3f2867 |
| Last Changed Date: 2020-01-06 21:23:55 -0400 (Mon, 06 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:25:17 -0400 (Wed, 15 Apr 2020).
| Package 1783/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| variancePartition 1.16.1 Gabriel E. Hoffman
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: variancePartition |
| Version: 1.16.1 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings variancePartition_1.16.1.tar.gz |
| StartedAt: 2020-04-15 07:19:35 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:36:49 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 1034.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings variancePartition_1.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/variancePartition.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.16.1'
* 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 ... 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 ... 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 or elapsed time > 5s
user system elapsed
fitVarPartModel-method 23.44 3.83 69.53
extractVarPart 14.67 3.43 54.25
fitExtractVarPartModel-method 5.17 1.24 40.88
getVarianceComponents 5.05 1.25 26.29
residuals-VarParFitList-method 5.43 0.82 24.58
plotCompareP-method 3.36 0.60 24.53
varPartConfInf 3.92 0.01 23.69
plotPercentBars 2.72 0.52 24.48
sortCols-method 2.52 0.71 25.94
plotVarPart-method 2.63 0.47 21.95
voomWithDreamWeights 2.50 0.22 21.82
dream-method 2.50 0.14 30.17
plotCorrStructure 1.71 0.15 15.14
colinearityScore 0.75 0.07 10.28
as.data.frame-varPartResults-method 0.60 0.01 11.92
as.matrix-varPartResults-method 0.55 0.02 9.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fitVarPartModel-method 22.42 2.70 66.53
extractVarPart 13.00 1.87 46.71
getVarianceComponents 5.55 0.94 26.20
fitExtractVarPartModel-method 4.92 1.24 39.11
residuals-VarParFitList-method 4.83 0.76 18.80
plotCompareP-method 3.74 0.39 24.33
varPartConfInf 4.05 0.00 19.53
dream-method 2.88 0.23 35.50
plotPercentBars 2.17 0.29 18.78
sortCols-method 2.06 0.39 21.42
plotVarPart-method 1.73 0.56 19.39
voomWithDreamWeights 1.69 0.14 17.95
plotCorrStructure 1.42 0.07 13.92
colinearityScore 0.94 0.08 10.82
as.data.frame-varPartResults-method 0.78 0.06 12.58
as.matrix-varPartResults-method 0.62 0.00 11.46
* 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: OK
variancePartition.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/variancePartition_1.16.1.tar.gz && rm -rf variancePartition.buildbin-libdir && mkdir variancePartition.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=variancePartition.buildbin-libdir variancePartition_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL variancePartition_1.16.1.zip && rm variancePartition_1.16.1.tar.gz variancePartition_1.16.1.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 1381k 100 1381k 0 0 7722k 0 --:--:-- --:--:-- --:--:-- 7936k
install for i386
* installing *source* package 'variancePartition' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'eBayes' from package 'limma' in package 'variancePartition'
Creating a new generic function for 'classifyTestsF' in package 'variancePartition'
Creating a generic function for 'topTable' from package 'limma' in package 'variancePartition'
** help
*** installing help indices
converting help for package 'variancePartition'
finding HTML links ... done
ESS-method 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
extractVarPart html
fitExtractVarPartModel-method html
fitVarPartModel-method html
getContrast-method html
getVarianceComponents html
ggColorHue html
plotCompareP-method html
plotContrasts html
plotCorrMatrix html
plotCorrStructure html
plotPercentBars html
plotStratify html
plotStratifyBy html
plotVarPart-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_1.16.1.zip
* DONE (variancePartition)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'variancePartition' successfully unpacked and MD5 sums checked
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variancePartition.Rcheck/tests_i386/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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 10 chunks...
Total:8 s
Dividing work into 10 chunks...
Total:9 s
Dividing work into 10 chunks...
Total:11 s
> proc.time()
user system elapsed
5.10 0.43 32.48
Warning messages:
1: In dream(geneExpr[1:10, ], form, info, L1) :
Contrasts with only a single non-zero term are already evaluated by default.
2: In eBayes(fit1) :
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
3: In dream(geneExpr[1:10, ], form, info, L2) :
Contrasts with only a single non-zero term are already evaluated by default.
4: In eBayes(fit2) :
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
5: In dream(geneExpr[1:10, ], form, info, L) :
Contrasts with only a single non-zero term are already evaluated by default.
6: In eBayes(fit) :
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
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variancePartition.Rcheck/tests_x64/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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 10 chunks...
Total:9 s
Dividing work into 10 chunks...
Total:12 s
Dividing work into 10 chunks...
Total:8 s
> proc.time()
user system elapsed
5.09 0.40 32.82
Warning messages:
1: In dream(geneExpr[1:10, ], form, info, L1) :
Contrasts with only a single non-zero term are already evaluated by default.
2: In eBayes(fit1) :
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
3: In dream(geneExpr[1:10, ], form, info, L2) :
Contrasts with only a single non-zero term are already evaluated by default.
4: In eBayes(fit2) :
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
5: In dream(geneExpr[1:10, ], form, info, L) :
Contrasts with only a single non-zero term are already evaluated by default.
6: In eBayes(fit) :
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
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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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