Gabriel E. Hoffman
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/variancePartition |
| Branch: RELEASE_3_9 |
| Last Commit: 12a60fd |
| Last Changed Date: 2019-10-01 11:56:37 -0400 (Tue, 01 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:56:08 -0400 (Wed, 16 Oct 2019).
| Package 1705/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| variancePartition 1.14.1 Gabriel E. Hoffman
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: variancePartition |
| Version: 1.14.1 |
| 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_1.14.1.tar.gz |
| StartedAt: 2019-10-16 07:39:28 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:47:49 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 501.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running 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_1.14.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/variancePartition.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.14.1’
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
[.MArrayLM2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 or elapsed time > 5s
user system elapsed
fitVarPartModel-method 136.994 34.861 60.505
plotCompareP-method 77.417 28.290 29.002
extractVarPart 68.201 15.185 49.376
sortCols-method 56.706 20.950 20.881
voomWithDreamWeights 53.050 12.635 7.329
fitExtractVarPartModel-method 39.519 18.269 32.392
getContrast-method 40.401 10.201 0.414
plotPercentBars 34.011 11.600 20.842
plotVarPart-method 33.185 9.885 19.907
dream-method 10.155 4.762 6.690
residuals-VarParFitList-method 9.161 4.172 22.254
getVarianceComponents 7.900 4.686 21.507
varPartConfInf 8.567 1.042 35.176
plotCorrStructure 4.436 2.552 12.113
* 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-3.9-bioc/meat/variancePartition.Rcheck/00check.log’
for details.
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/3.6/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
Dividing work into 10 chunks...
Total: 2 s
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
Dividing work into 10 chunks...
Total: 2 s
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
> proc.time()
user system elapsed
21.683 8.292 16.271
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 dream(geneExpr[1:10, ], form, info, L2) :
Contrasts with only a single non-zero term are already evaluated by default.
3: In dream(geneExpr[1:10, ], form, info, L) :
Contrasts with only a single non-zero term are already evaluated by default.
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.479 | 0.031 | 0.511 | |
| as.data.frame-varPartResults-method | 2.322 | 1.078 | 1.946 | |
| as.matrix-varPartResults-method | 1.998 | 1.163 | 1.707 | |
| calcVarPart-method | 0.191 | 0.040 | 0.231 | |
| canCorPairs | 0.126 | 0.029 | 0.155 | |
| colinearityScore | 2.790 | 1.763 | 1.871 | |
| dream-method | 10.155 | 4.762 | 6.690 | |
| extractVarPart | 68.201 | 15.185 | 49.376 | |
| fitExtractVarPartModel-method | 39.519 | 18.269 | 32.392 | |
| fitVarPartModel-method | 136.994 | 34.861 | 60.505 | |
| getContrast-method | 40.401 | 10.201 | 0.414 | |
| getVarianceComponents | 7.900 | 4.686 | 21.507 | |
| ggColorHue | 0.000 | 0.023 | 0.023 | |
| plotCompareP-method | 77.417 | 28.290 | 29.002 | |
| plotContrasts | 0.797 | 0.118 | 0.915 | |
| plotCorrMatrix | 0.147 | 0.040 | 0.188 | |
| plotCorrStructure | 4.436 | 2.552 | 12.113 | |
| plotPercentBars | 34.011 | 11.600 | 20.842 | |
| plotStratify | 1.649 | 0.200 | 1.849 | |
| plotStratifyBy | 1.587 | 0.165 | 1.753 | |
| plotVarPart-method | 33.185 | 9.885 | 19.907 | |
| residuals-VarParFitList-method | 9.161 | 4.172 | 22.254 | |
| sortCols-method | 56.706 | 20.950 | 20.881 | |
| varPartConfInf | 8.567 | 1.042 | 35.176 | |
| voomWithDreamWeights | 53.050 | 12.635 | 7.329 | |