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CHECK report for ALDEx2 on malbec1

This page was generated on 2018-04-12 13:12:45 -0400 (Thu, 12 Apr 2018).

Package 34/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALDEx2 1.10.0
Greg Gloor
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/ALDEx2
Branch: RELEASE_3_6
Last Commit: e43f99e
Last Changed Date: 2017-10-30 12:40:39 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ALDEx2
Version: 1.10.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ALDEx2_1.10.0.tar.gz
StartedAt: 2018-04-11 21:22:37 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 21:25:05 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 148.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ALDEx2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ALDEx2_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ALDEx2.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 ‘ALDEx2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ALDEx2’ version ‘1.10.0’
* 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 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
* 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

* installing *source* package ‘ALDEx2’ ...
** 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 (ALDEx2)

Tests output

ALDEx2.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(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 
 35.124   0.184  35.346 

Example timings

ALDEx2.Rcheck/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package0.0040.0000.000
aldex1.1600.0601.224
aldex.clr-class0.1440.0000.143
aldex.clr.function-methods0.0440.0000.046
aldex.corr000
aldex.effect2.2240.0122.237
aldex.glm1.7760.0041.778
aldex.set.mode0.0440.0000.045
aldex.ttest0.1640.0080.173
getDenom-method0.0800.0000.082
getFeatureNames-method0.0640.0000.062
getFeatures-method0.0400.0000.042
getMonteCarloInstances-method0.0440.0000.043
getMonteCarloReplicate-method0.0400.0000.042
getReads-method0.0480.0000.046
getSampleIDs-method0.0440.0000.043
numConditions-method0.0440.0000.044
numFeatures-method0.0400.0040.042
numMCInstances-method0.0440.0000.043
plot.aldex000