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CHECK report for variancePartition on malbec1

This page was generated on 2019-04-16 11:51:30 -0400 (Tue, 16 Apr 2019).

Package 1616/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.12.3
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)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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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


Installation output

variancePartition.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL variancePartition
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* 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)

Tests output

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 

Example timings

variancePartition.Rcheck/variancePartition-Ex.timings

nameusersystemelapsed
ESS-method0.6160.0080.622
as.data.frame-varPartResults-method0.4200.0200.442
as.matrix-varPartResults-method0.4160.0000.416
calcVarPart-method0.0720.0040.078
canCorPairs0.0680.0000.065
colinearityScore0.5760.0000.580
dream-method0.9600.1407.005
extractVarPart15.340 0.74827.291
fitExtractVarPartModel-method 1.568 0.38420.329
fitVarPartModel-method32.648 1.95251.766
getContrast-method0.1440.0200.173
getVarianceComponents 7.656 1.51616.876
ggColorHue000
plotCompareP-method 1.364 0.76815.483
plotContrasts0.5240.0160.539
plotCorrMatrix0.1240.0040.134
plotCorrStructure1.2560.7887.579
plotPercentBars 0.936 0.74011.280
plotStratify1.0760.0681.145
plotStratifyBy0.8280.0640.891
plotVarPart-method 0.848 0.64410.178
residuals-VarParFitList-method 5.276 1.21214.202
sortCols-method 0.824 0.68811.142
varPartConfInf 6.200 1.12022.608