Greg Gloor
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ALDEx2 |
| Branch: RELEASE_3_8 |
| Last Commit: a8b970c |
| Last Changed Date: 2019-01-04 13:03:23 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:50:50 -0400 (Tue, 16 Apr 2019).
| Package 38/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ALDEx2 1.14.1 Greg Gloor
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ALDEx2 |
| Version: 1.14.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ALDEx2_1.14.1.tar.gz |
| StartedAt: 2019-04-15 22:08:47 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:11:53 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 186.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ALDEx2.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ALDEx2_1.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ALDEx2.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 ‘ALDEx2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ALDEx2’ version ‘1.14.1’ * 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 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: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ALDEx2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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 3.5.3 (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.
> 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
51.188 0.512 51.812
ALDEx2.Rcheck/ALDEx2-Ex.timings
| name | user | system | elapsed | |
| ALDEx2m-package | 0 | 0 | 0 | |
| aldex | 2.108 | 0.116 | 2.227 | |
| aldex.clr-class | 0.048 | 0.000 | 0.046 | |
| aldex.clr.function-methods | 0.044 | 0.004 | 0.051 | |
| aldex.corr | 0 | 0 | 0 | |
| aldex.effect | 3.804 | 0.008 | 3.840 | |
| aldex.glm | 2.292 | 0.048 | 2.343 | |
| aldex.set.mode | 0.06 | 0.00 | 0.06 | |
| aldex.ttest | 0.324 | 0.004 | 0.329 | |
| getDenom-method | 0.224 | 0.004 | 0.229 | |
| getFeatureNames-method | 0.072 | 0.004 | 0.079 | |
| getFeatures-method | 0.084 | 0.000 | 0.086 | |
| getMonteCarloInstances-method | 0.048 | 0.000 | 0.048 | |
| getMonteCarloReplicate-method | 0.044 | 0.000 | 0.043 | |
| getReads-method | 0.044 | 0.000 | 0.043 | |
| getSampleIDs-method | 0.044 | 0.000 | 0.043 | |
| numConditions-method | 0.048 | 0.000 | 0.046 | |
| numFeatures-method | 0.044 | 0.000 | 0.046 | |
| numMCInstances-method | 0.056 | 0.000 | 0.053 | |
| plot.aldex | 0 | 0 | 0 | |