Gabriel E. Hoffman
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/variancePartition |
| Branch: RELEASE_3_8 |
| Last Commit: ffd2458 |
| Last Changed Date: 2019-03-21 16:41:42 -0400 (Thu, 21 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:51:30 -0400 (Tue, 16 Apr 2019).
| Package 1616/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| variancePartition 1.12.3 Gabriel E. Hoffman
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: variancePartition |
| Version: 1.12.3 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings variancePartition_1.12.3.tar.gz |
| StartedAt: 2019-04-16 03:37:22 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:42:58 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 335.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings variancePartition_1.12.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/variancePartition.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.3’
* 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 32.648 1.952 51.766
extractVarPart 15.340 0.748 27.291
getVarianceComponents 7.656 1.516 16.876
varPartConfInf 6.200 1.120 22.608
residuals-VarParFitList-method 5.276 1.212 14.202
plotCompareP-method 1.364 0.768 15.483
plotCorrStructure 1.256 0.788 7.579
fitExtractVarPartModel-method 1.568 0.384 20.329
plotPercentBars 0.936 0.740 11.280
sortCols-method 0.824 0.688 11.142
plotVarPart-method 0.848 0.644 10.178
dream-method 0.960 0.140 7.005
* 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-3.8-bioc/R/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
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, 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 memory usage: > 4.6 Mb
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
Finished...
Total: 14 s
Projected memory usage: > 4.6 Mb
Finished...
Total: 12 s
Projected memory usage: > 4.6 Mb
Finished...
Total: 13 s
RUNIT TEST PROTOCOL -- Tue Apr 16 03:42:54 2019
***********************************************
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
44.228 0.140 44.453
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.616 | 0.008 | 0.622 | |
| as.data.frame-varPartResults-method | 0.420 | 0.020 | 0.442 | |
| as.matrix-varPartResults-method | 0.416 | 0.000 | 0.416 | |
| calcVarPart-method | 0.072 | 0.004 | 0.078 | |
| canCorPairs | 0.068 | 0.000 | 0.065 | |
| colinearityScore | 0.576 | 0.000 | 0.580 | |
| dream-method | 0.960 | 0.140 | 7.005 | |
| extractVarPart | 15.340 | 0.748 | 27.291 | |
| fitExtractVarPartModel-method | 1.568 | 0.384 | 20.329 | |
| fitVarPartModel-method | 32.648 | 1.952 | 51.766 | |
| getContrast-method | 0.144 | 0.020 | 0.173 | |
| getVarianceComponents | 7.656 | 1.516 | 16.876 | |
| ggColorHue | 0 | 0 | 0 | |
| plotCompareP-method | 1.364 | 0.768 | 15.483 | |
| plotContrasts | 0.524 | 0.016 | 0.539 | |
| plotCorrMatrix | 0.124 | 0.004 | 0.134 | |
| plotCorrStructure | 1.256 | 0.788 | 7.579 | |
| plotPercentBars | 0.936 | 0.740 | 11.280 | |
| plotStratify | 1.076 | 0.068 | 1.145 | |
| plotStratifyBy | 0.828 | 0.064 | 0.891 | |
| plotVarPart-method | 0.848 | 0.644 | 10.178 | |
| residuals-VarParFitList-method | 5.276 | 1.212 | 14.202 | |
| sortCols-method | 0.824 | 0.688 | 11.142 | |
| varPartConfInf | 6.200 | 1.120 | 22.608 | |