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CHECK report for ALDEx2 on merida1

This page was generated on 2021-04-15 12:23:52 -0400 (Thu, 15 Apr 2021).

To the developers/maintainers of the ALDEx2 package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 42/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALDEx2 1.22.0  (landing page)
Greg Gloor
Snapshot Date: 2021-04-14 14:50:05 -0400 (Wed, 14 Apr 2021)
URL: https://git.bioconductor.org/packages/ALDEx2
Branch: RELEASE_3_12
Last Commit: ac7f0ab
Last Changed Date: 2020-10-27 10:59:20 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ALDEx2
Version: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2021-04-14 22:38:40 -0400 (Wed, 14 Apr 2021)
EndedAt: 2021-04-14 22:44:39 -0400 (Wed, 14 Apr 2021)
EllapsedTime: 358.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ALDEx2.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ALDEx2.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.22.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
aldex.corr       117.517  4.277 123.016
aldex.glm.effect   7.337  0.040   7.388
* 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:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ALDEx2
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ALDEx2’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ALDEx2)

Tests output

ALDEx2.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
Loading required package: zCompositions
Loading required package: MASS
Loading required package: NADA
Loading required package: survival

Attaching package: 'NADA'

The following object is masked from 'package:stats':

    cor

Loading required package: truncnorm
> 
> test_check("ALDEx2")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
 51.304   1.253  52.635 

Example timings

ALDEx2.Rcheck/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package000
aldex2.1970.4632.684
aldex.clr-class0.0790.0070.086
aldex.clr.function-methods0.0770.0050.082
aldex.corr117.517 4.277123.016
aldex.effect3.6210.0173.641
aldex.glm1.4690.0081.478
aldex.glm.effect7.3370.0407.388
aldex.kw2.6750.0142.691
aldex.plotFeature0.1150.0030.118
aldex.set.mode0.0700.0030.073
aldex.ttest0.2020.0040.207
expectedDistance0.4480.0270.476
getDenom-method0.1210.0030.123
getFeatureNames-method0.0780.0020.080
getFeatures-method0.0710.0020.073
getMonteCarloInstances-method0.0680.0030.071
getMonteCarloReplicate-method0.0650.0030.067
getMonteCarloSample-method0.0740.0020.075
getReads-method0.0710.0020.074
getSampleIDs-method0.0750.0030.077
numConditions-method0.0550.0020.056
numFeatures-method0.0550.0020.057
numMCInstances-method0.0540.0020.057
plot.aldex000