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CHECK report for ALDEx2 on merida1

This page was generated on 2019-04-16 11:57:59 -0400 (Tue, 16 Apr 2019).

Package 38/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALDEx2 1.14.1
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)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ALDEx2
Version: 1.14.1
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_1.14.1.tar.gz
StartedAt: 2019-04-15 22:19:03 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:22:34 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 211.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ALDEx2.Rcheck
Warnings: 0

Command output

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### 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_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ALDEx2.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.1’
* 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 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


Installation output

ALDEx2.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ALDEx2
###
##############################################################################
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* 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)

Tests output

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-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 
 58.475   1.296  60.411 

Example timings

ALDEx2.Rcheck/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package0.0000.0000.001
aldex2.0570.2412.318
aldex.clr-class0.0650.0030.068
aldex.clr.function-methods0.0560.0040.061
aldex.corr0.0000.0000.001
aldex.effect3.2790.0413.343
aldex.glm2.7520.0862.857
aldex.set.mode0.0760.0030.080
aldex.ttest0.2890.0050.296
getDenom-method0.2080.0040.214
getFeatureNames-method0.0720.0040.078
getFeatures-method0.0910.0060.097
getMonteCarloInstances-method0.0660.0020.068
getMonteCarloReplicate-method0.0720.0030.077
getReads-method0.0720.0030.076
getSampleIDs-method0.0760.0030.081
numConditions-method0.0780.0050.083
numFeatures-method0.0610.0030.065
numMCInstances-method0.0830.0050.089
plot.aldex000