Gabriel E. Hoffman
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/variancePartition |
| Branch: master |
| Last Commit: 09d4853 |
| Last Changed Date: 2020-01-02 16:53:11 -0500 (Thu, 02 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:42:58 -0500 (Thu, 16 Jan 2020).
| Package 1778/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| variancePartition 1.17.1 Gabriel E. Hoffman
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: variancePartition |
| Version: 1.17.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings variancePartition_1.17.1.tar.gz |
| StartedAt: 2020-01-16 09:45:14 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 09:56:44 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 689.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings variancePartition_1.17.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/variancePartition.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.17.1’
* 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 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 ... 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 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 199.290 68.800 113.465
plotCompareP-method 102.343 49.374 36.218
extractVarPart 102.434 31.209 64.976
sortCols-method 77.395 31.172 26.898
voomWithDreamWeights 66.428 27.516 11.658
fitExtractVarPartModel-method 54.457 26.158 40.791
plotVarPart-method 47.252 22.965 24.551
getContrast-method 51.987 17.912 0.832
plotPercentBars 46.188 20.496 25.876
residuals-VarParFitList-method 24.106 11.090 43.879
getVarianceComponents 19.211 11.267 41.571
dream-method 13.487 6.750 31.171
varPartConfInf 10.026 1.424 42.533
plotCorrStructure 6.524 4.109 14.683
colinearityScore 4.971 3.207 3.804
* 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: OK
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * 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 ** 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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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:3 s
Dividing work into 10 chunks...
Total:3 s
Dividing work into 10 chunks...
Total:3 s
> proc.time()
user system elapsed
24.404 10.383 17.090
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
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.579 | 0.103 | 0.682 | |
| as.data.frame-varPartResults-method | 2.857 | 1.478 | 2.349 | |
| as.matrix-varPartResults-method | 2.603 | 1.618 | 2.118 | |
| calcVarPart-method | 0.229 | 0.052 | 0.281 | |
| canCorPairs | 0.128 | 0.032 | 0.160 | |
| colinearityScore | 4.971 | 3.207 | 3.804 | |
| dream-method | 13.487 | 6.750 | 31.171 | |
| extractVarPart | 102.434 | 31.209 | 64.976 | |
| fitExtractVarPartModel-method | 54.457 | 26.158 | 40.791 | |
| fitVarPartModel-method | 199.290 | 68.800 | 113.465 | |
| getContrast-method | 51.987 | 17.912 | 0.832 | |
| getVarianceComponents | 19.211 | 11.267 | 41.571 | |
| ggColorHue | 0.000 | 0.001 | 0.001 | |
| plotCompareP-method | 102.343 | 49.374 | 36.218 | |
| plotContrasts | 0.660 | 0.107 | 0.767 | |
| plotCorrMatrix | 0.107 | 0.018 | 0.126 | |
| plotCorrStructure | 6.524 | 4.109 | 14.683 | |
| plotPercentBars | 46.188 | 20.496 | 25.876 | |
| plotStratify | 1.346 | 0.106 | 1.452 | |
| plotStratifyBy | 1.742 | 0.264 | 2.006 | |
| plotVarPart-method | 47.252 | 22.965 | 24.551 | |
| residuals-VarParFitList-method | 24.106 | 11.090 | 43.879 | |
| sortCols-method | 77.395 | 31.172 | 26.898 | |
| varPartConfInf | 10.026 | 1.424 | 42.533 | |
| voomWithDreamWeights | 66.428 | 27.516 | 11.658 | |