Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:15:21 -0400 (Thu, 12 Apr 2018).
Package 36/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
alpine 1.4.0 Michael Love
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: alpine |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings alpine_1.4.0.tar.gz |
StartedAt: 2018-04-11 21:22:53 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 21:27:17 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 263.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: alpine.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings alpine_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/alpine.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘alpine/DESCRIPTION’ ... OK * this is package ‘alpine’ version ‘1.4.0’ * 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 ‘alpine’ 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed fitBiasModels 12.636 0.568 14.269 estimateAbundance 11.024 0.424 12.365 predictCoverage 5.396 0.124 5.595 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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
alpine.Rcheck/00install.out
* installing *source* package ‘alpine’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (alpine)
alpine.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On" 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. > library(testthat) > library(alpine) > test_check("alpine") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 1 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 46.388 1.700 49.060
alpine.Rcheck/alpine-Ex.timings
name | user | system | elapsed | |
buildFragtypes | 3.516 | 0.076 | 4.309 | |
estimateAbundance | 11.024 | 0.424 | 12.365 | |
extractAlpine | 0.024 | 0.000 | 0.024 | |
fitBiasModels | 12.636 | 0.568 | 14.269 | |
getFragmentWidths | 2.012 | 0.020 | 2.284 | |
getReadLength | 1.104 | 0.008 | 1.213 | |
mergeGenes | 0.216 | 0.000 | 0.217 | |
normalizeDESeq | 0.004 | 0.000 | 0.002 | |
plotFragLen | 0.012 | 0.000 | 0.012 | |
plotGC | 0.024 | 0.004 | 0.027 | |
plotGRL | 0.228 | 0.000 | 0.229 | |
plotOrder0 | 0.036 | 0.000 | 0.035 | |
plotRelPos | 0.012 | 0.000 | 0.012 | |
predictCoverage | 5.396 | 0.124 | 5.595 | |
splitGenesAcrossChroms | 0.296 | 0.004 | 0.301 | |
splitLongGenes | 0.428 | 0.004 | 0.433 | |