Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:14:35 -0400 (Tue, 09 Apr 2019).
Package 1668/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
variancePartition 1.13.6 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 | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: variancePartition |
Version: 1.13.6 |
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_1.13.6.tar.gz |
StartedAt: 2019-04-09 06:13:27 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 06:20:34 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 427.2 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_1.13.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/variancePartition.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * 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 ‘1.13.6’ * 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 32.733 4.950 50.836 extractVarPart 17.162 2.419 31.805 getVarianceComponents 7.690 1.345 17.304 varPartConfInf 6.473 0.195 27.454 residuals-VarParFitList-method 5.170 1.080 13.997 fitExtractVarPartModel-method 1.761 0.254 26.665 plotCompareP-method 1.590 0.105 16.245 plotCorrStructure 1.369 0.128 8.926 plotPercentBars 1.372 0.096 14.126 sortCols-method 1.142 0.160 14.734 plotVarPart-method 1.078 0.115 13.770 dream-method 1.082 0.070 10.238 * 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’ ** 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" 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, colMeans, colSums, 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, 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: 17 s Projected memory usage: > 4.6 Mb Finished... Total: 15 s Projected memory usage: > 4.6 Mb Finished... Total: 14 s RUNIT TEST PROTOCOL -- Tue Apr 9 06:20:28 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 51.375 0.934 52.258
variancePartition.Rcheck/variancePartition-Ex.timings
name | user | system | elapsed | |
ESS-method | 0.548 | 0.063 | 0.614 | |
as.data.frame-varPartResults-method | 0.583 | 0.015 | 0.598 | |
as.matrix-varPartResults-method | 0.780 | 0.013 | 0.793 | |
calcVarPart-method | 0.156 | 0.005 | 0.161 | |
canCorPairs | 0.083 | 0.009 | 0.093 | |
colinearityScore | 0.828 | 0.013 | 0.842 | |
dream-method | 1.082 | 0.070 | 10.238 | |
extractVarPart | 17.162 | 2.419 | 31.805 | |
fitExtractVarPartModel-method | 1.761 | 0.254 | 26.665 | |
fitVarPartModel-method | 32.733 | 4.950 | 50.836 | |
getContrast-method | 0.300 | 0.058 | 0.359 | |
getVarianceComponents | 7.690 | 1.345 | 17.304 | |
ggColorHue | 0.000 | 0.001 | 0.001 | |
plotCompareP-method | 1.590 | 0.105 | 16.245 | |
plotContrasts | 0.475 | 0.005 | 0.481 | |
plotCorrMatrix | 0.107 | 0.007 | 0.115 | |
plotCorrStructure | 1.369 | 0.128 | 8.926 | |
plotPercentBars | 1.372 | 0.096 | 14.126 | |
plotStratify | 1.282 | 0.008 | 1.292 | |
plotStratifyBy | 1.089 | 0.006 | 1.096 | |
plotVarPart-method | 1.078 | 0.115 | 13.770 | |
residuals-VarParFitList-method | 5.170 | 1.080 | 13.997 | |
sortCols-method | 1.142 | 0.160 | 14.734 | |
varPartConfInf | 6.473 | 0.195 | 27.454 | |