Gabriel E. Hoffman
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/variancePartition |
| Branch: RELEASE_3_7 |
| Last Commit: 4455edd |
| Last Changed Date: 2018-10-11 19:15:43 -0400 (Thu, 11 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:27:53 -0400 (Wed, 17 Oct 2018).
| Package 1530/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| variancePartition 1.10.4 Gabriel E. Hoffman
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: variancePartition |
| Version: 1.10.4 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings variancePartition_1.10.4.tar.gz |
| StartedAt: 2018-10-16 04:23:26 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 04:27:51 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 264.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings variancePartition_1.10.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/variancePartition.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.4’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fitVarPartModel-method 26.636 1.500 41.677
extractVarPart 11.612 0.748 21.332
getVarianceComponents 6.100 1.028 13.550
varPartConfInf 4.260 0.768 16.400
residuals-VarParFitList-method 3.916 1.032 11.643
plotCompareP-method 0.936 0.592 12.297
fitExtractVarPartModel-method 1.068 0.380 14.736
plotPercentBars 0.840 0.476 7.911
plotVarPart-method 0.628 0.500 8.182
sortCols-method 0.572 0.504 7.294
dream-method 0.484 0.080 5.526
* 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: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘variancePartition’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘eBayes’ from package ‘limma’ in package ‘variancePartition’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (variancePartition)
variancePartition.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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")'.
Projected run time: ˜ 0.5 min
Loading required package: Matrix
Attaching package: 'lmerTest'
The following object is masked from 'package:lme4':
lmer
The following object is masked from 'package:stats':
step
Projected run time: ˜ 0.2 min
Projected run time: ˜ 0.2 min
RUNIT TEST PROTOCOL -- Tue Oct 16 04:27:48 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
variancePartition RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning message:
executing %dopar% sequentially: no parallel backend registered
>
> proc.time()
user system elapsed
32.992 0.108 33.146
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.236 | 0.004 | 0.238 | |
| as.data.frame-varPartResults-method | 0.396 | 0.004 | 0.401 | |
| as.matrix-varPartResults-method | 0.388 | 0.000 | 0.388 | |
| calcVarPart-method | 0.084 | 0.000 | 0.080 | |
| canCorPairs | 0.064 | 0.000 | 0.064 | |
| colinearityScore | 0.44 | 0.00 | 0.44 | |
| dream-method | 0.484 | 0.080 | 5.526 | |
| extractVarPart | 11.612 | 0.748 | 21.332 | |
| fitExtractVarPartModel-method | 1.068 | 0.380 | 14.736 | |
| fitVarPartModel-method | 26.636 | 1.500 | 41.677 | |
| getContrast-method | 0.144 | 0.020 | 0.167 | |
| getVarianceComponents | 6.100 | 1.028 | 13.550 | |
| ggColorHue | 0.004 | 0.000 | 0.001 | |
| plotCompareP-method | 0.936 | 0.592 | 12.297 | |
| plotCorrMatrix | 0.08 | 0.00 | 0.08 | |
| plotCorrStructure | 0.808 | 0.468 | 4.905 | |
| plotPercentBars | 0.840 | 0.476 | 7.911 | |
| plotStratify | 0.884 | 0.056 | 0.956 | |
| plotStratifyBy | 0.792 | 0.064 | 0.854 | |
| plotVarPart-method | 0.628 | 0.500 | 8.182 | |
| residuals-VarParFitList-method | 3.916 | 1.032 | 11.643 | |
| sortCols-method | 0.572 | 0.504 | 7.294 | |
| varPartConfInf | 4.260 | 0.768 | 16.400 | |