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 12:07:13 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings variancePartition_1.14.1.tar.gz |
| StartedAt: 2019-10-16 05:39:58 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:44:46 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 287.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings variancePartition_1.14.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/variancePartition.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fitVarPartModel-method 84.019 8.357 28.374
plotCompareP-method 42.318 7.491 16.704
extractVarPart 45.504 3.308 24.608
sortCols-method 33.169 4.853 12.269
voomWithDreamWeights 31.224 3.912 4.245
getContrast-method 23.280 1.843 0.225
fitExtractVarPartModel-method 20.875 3.557 16.505
plotPercentBars 19.179 3.128 12.119
plotVarPart-method 18.659 2.636 11.512
residuals-VarParFitList-method 6.807 1.228 13.807
getVarianceComponents 5.833 1.351 13.402
dream-method 5.778 1.114 3.639
varPartConfInf 5.346 0.689 19.364
plotCorrStructure 2.768 1.200 8.119
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/variancePartition.Rcheck/00check.log’
for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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: 1 s
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
Dividing work into 10 chunks...
Total: 1 s
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
Dividing work into 10 chunks...
Total: 1 s
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
> proc.time()
user system elapsed
10.893 1.927 7.958
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 | 0.250 | 0.024 | 0.292 | |
| as.data.frame-varPartResults-method | 0.969 | 0.211 | 1.300 | |
| as.matrix-varPartResults-method | 0.974 | 0.311 | 0.736 | |
| calcVarPart-method | 0.102 | 0.016 | 0.118 | |
| canCorPairs | 0.095 | 0.010 | 0.105 | |
| colinearityScore | 1.601 | 0.452 | 1.009 | |
| dream-method | 5.778 | 1.114 | 3.639 | |
| extractVarPart | 45.504 | 3.308 | 24.608 | |
| fitExtractVarPartModel-method | 20.875 | 3.557 | 16.505 | |
| fitVarPartModel-method | 84.019 | 8.357 | 28.374 | |
| getContrast-method | 23.280 | 1.843 | 0.225 | |
| getVarianceComponents | 5.833 | 1.351 | 13.402 | |
| ggColorHue | 0.001 | 0.000 | 0.000 | |
| plotCompareP-method | 42.318 | 7.491 | 16.704 | |
| plotContrasts | 0.301 | 0.028 | 0.329 | |
| plotCorrMatrix | 0.077 | 0.000 | 0.077 | |
| plotCorrStructure | 2.768 | 1.200 | 8.119 | |
| plotPercentBars | 19.179 | 3.128 | 12.119 | |
| plotStratify | 0.794 | 0.028 | 0.821 | |
| plotStratifyBy | 0.676 | 0.032 | 0.707 | |
| plotVarPart-method | 18.659 | 2.636 | 11.512 | |
| residuals-VarParFitList-method | 6.807 | 1.228 | 13.807 | |
| sortCols-method | 33.169 | 4.853 | 12.269 | |
| varPartConfInf | 5.346 | 0.689 | 19.364 | |
| voomWithDreamWeights | 31.224 | 3.912 | 4.245 | |