Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:53:24 -0400 (Wed, 17 Oct 2018).
Package 1162/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
quantro 1.14.0 Stephanie Hicks
| 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: quantro |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:quantro.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings quantro_1.14.0.tar.gz |
StartedAt: 2018-10-16 23:27:08 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 23:32:06 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 297.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: quantro.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:quantro.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings quantro_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/quantro.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘quantro/DESCRIPTION’ ... OK * this is package ‘quantro’ version ‘1.14.0’ * 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 ‘quantro’ 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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
quantro.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL quantro ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘quantro’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘quantro-vignette.Rnw’ ** testing if installed package can be loaded * DONE (quantro)
quantro.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-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. > require("quantro") || stop("unable to load quantro") Loading required package: quantro Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) [1] TRUE > BiocGenerics:::testPackage("quantro") Loading required package: BiocGenerics Loading required package: parallel 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 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 Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Loading required package: bumphunter Loading required package: foreach Loading required package: iterators Loading required package: locfit locfit 1.5-9.1 2013-03-22 [quantro] Average medians of the distributions are not equal across groups. [quantro] Calculating the quantro test statistic. [quantro] No permutation testing performed. Use B > 0 for permutation testing. [quantro] Average medians of the distributions are not equal across groups. [quantro] Calculating the quantro test statistic. [quantro] No permutation testing performed. Use B > 0 for permutation testing. Loading required package: doParallel [quantro] Average medians of the distributions are not equal across groups. [quantro] Calculating the quantro test statistic. [quantro] Starting permutation testing. [quantro] Parallelizing using 4 workers/cores (backend: doParallelMC, version: 1.0.14). RUNIT TEST PROTOCOL -- Tue Oct 16 23:31:56 2018 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : quantro RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 18.821 2.201 17.992
quantro.Rcheck/quantro-Ex.timings
name | user | system | elapsed | |
MSbetween | 2.022 | 0.082 | 2.105 | |
MSwithin | 0.785 | 0.064 | 0.851 | |
anova | 1.360 | 0.051 | 1.414 | |
matboxplot | 0.623 | 0.040 | 0.664 | |
matdensity | 0.729 | 0.062 | 0.793 | |
quantro | 0.711 | 0.058 | 0.771 | |
quantroPlot | 0.001 | 0.000 | 0.001 | |
quantroPvalPerm | 1.278 | 0.044 | 1.324 | |
quantroStat | 0.694 | 0.038 | 0.733 | |
quantroStatPerm | 1.381 | 0.044 | 1.429 | |
summary | 0.759 | 0.044 | 0.804 | |