Greg Gloor
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ALDEx2 |
| Branch: RELEASE_3_7 |
| Last Commit: 9efde42 |
| Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:53:38 -0400 (Wed, 17 Oct 2018).
| Package 35/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ALDEx2 1.12.0 Greg Gloor
| 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: ALDEx2 |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ALDEx2_1.12.0.tar.gz |
| StartedAt: 2018-10-16 19:49:37 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 19:53:10 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 212.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ALDEx2.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ALDEx2_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ALDEx2.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 ‘ALDEx2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ALDEx2’ version ‘1.12.0’ * 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 ‘ALDEx2’ 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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
ALDEx2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ALDEx2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘ALDEx2’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ALDEx2)
ALDEx2.Rcheck/tests/testthat.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.
> library(testthat)
> library(ALDEx2)
>
> test_check("ALDEx2")
[1] "aldex.clr: generating Monte-Carlo instances and clr values"
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "aldex.ttest: doing t-test"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "aldex.effect: calculating effect sizes"
[1] "operating in serial mode"
[1] "aldex.clr: generating Monte-Carlo instances and clr values"
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "aldex.glm: doing Kruskal Wallace and glm test"
[1] "operating in serial mode"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "operating in serial mode"
[1] "computing center with all features"
══ testthat results ═══════════════════════════════════════════════════════════
OK: 18 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
56.165 1.244 57.969
ALDEx2.Rcheck/ALDEx2-Ex.timings
| name | user | system | elapsed | |
| ALDEx2m-package | 0.001 | 0.000 | 0.001 | |
| aldex | 1.424 | 0.232 | 1.697 | |
| aldex.clr-class | 0.059 | 0.002 | 0.061 | |
| aldex.clr.function-methods | 0.066 | 0.004 | 0.071 | |
| aldex.corr | 0.002 | 0.000 | 0.002 | |
| aldex.effect | 3.324 | 0.038 | 3.399 | |
| aldex.glm | 2.812 | 0.077 | 2.935 | |
| aldex.set.mode | 0.052 | 0.002 | 0.056 | |
| aldex.ttest | 0.334 | 0.005 | 0.343 | |
| getDenom-method | 0.204 | 0.004 | 0.209 | |
| getFeatureNames-method | 0.067 | 0.003 | 0.070 | |
| getFeatures-method | 0.063 | 0.002 | 0.066 | |
| getMonteCarloInstances-method | 0.074 | 0.004 | 0.078 | |
| getMonteCarloReplicate-method | 0.074 | 0.003 | 0.077 | |
| getReads-method | 0.076 | 0.004 | 0.080 | |
| getSampleIDs-method | 0.066 | 0.004 | 0.070 | |
| numConditions-method | 0.064 | 0.004 | 0.067 | |
| numFeatures-method | 0.068 | 0.005 | 0.073 | |
| numMCInstances-method | 0.074 | 0.007 | 0.081 | |
| plot.aldex | 0.001 | 0.000 | 0.000 | |