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CHECK report for ALDEx2 on malbec1

This page was generated on 2021-01-25 11:48:00 -0500 (Mon, 25 Jan 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
Greg Gloor
Snapshot Date: 2021-01-24 14:40:16 -0500 (Sun, 24 Jan 2021)
URL: https://git.bioconductor.org/packages/ALDEx2
Branch: RELEASE_3_12
Last Commit: ac7f0ab
Last Changed Date: 2020-10-27 10:59:20 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ALDEx2_1.22.0.tar.gz
StartedAt: 2021-01-24 23:21:54 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 23:27:40 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 345.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ALDEx2.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ALDEx2_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ALDEx2.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.22.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
aldex.corr       114.352  1.200 115.921
aldex.glm.effect   7.628  0.004   7.652
* 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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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ALDEx2
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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)
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")
══ Warnings ════════════════════════════════════════════════════════════════════
── Warning (test-clr-conds.R:11:1): (code run outside of `test_that()`) ────────
values are unreliable when estimated with so few MC smps
Backtrace:
 1. ALDEx2::aldex.clr(selex.sub, conds, mc.samples = 2) test-clr-conds.R:11:0
 2. ALDEx2::aldex.clr(selex.sub, conds, mc.samples = 2)
 3. ALDEx2::aldex.clr.function(...)
── Warning (test-clr-conds.R:12:1): (code run outside of `test_that()`) ────────
values are unreliable when estimated with so few MC smps
Backtrace:
 1. ALDEx2::aldex.clr(selex.sub, conds3, mc.samples = 2) test-clr-conds.R:12:0
 2. ALDEx2::aldex.clr(selex.sub, conds3, mc.samples = 2)
 3. ALDEx2::aldex.clr.function(...)
── Warning (test-clr-conds.R:13:1): (code run outside of `test_that()`) ────────
values are unreliable when estimated with so few MC smps
Backtrace:
 1. ALDEx2::aldex.clr(selex.sub, mm, mc.samples = 2) test-clr-conds.R:13:0
 2. ALDEx2::aldex.clr(selex.sub, mm, mc.samples = 2)
 3. ALDEx2::aldex.clr.function(...)
── Warning (test-clr-conds.R:14:1): (code run outside of `test_that()`) ────────
values are unreliable when estimated with so few MC smps
Backtrace:
 1. ALDEx2::aldex.clr(selex.sub, cont, mc.samples = 2) test-clr-conds.R:14:0
 2. ALDEx2::aldex.clr(selex.sub, cont, mc.samples = 2)
 3. ALDEx2::aldex.clr.function(...)

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
 49.576   0.528  50.294 

Example timings

ALDEx2.Rcheck/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package000
aldex2.0240.0842.142
aldex.clr-class0.0560.0040.061
aldex.clr.function-methods0.0560.0040.059
aldex.corr114.352 1.200115.921
aldex.effect4.0400.0004.047
aldex.glm1.6560.0041.660
aldex.glm.effect7.6280.0047.652
aldex.kw3.1040.0003.119
aldex.plotFeature0.1560.0000.157
aldex.set.mode0.0880.0000.089
aldex.ttest0.2240.0000.225
expectedDistance0.4760.0080.481
getDenom-method0.1400.0040.152
getFeatureNames-method0.0920.0000.090
getFeatures-method0.0920.0000.094
getMonteCarloInstances-method0.0920.0000.090
getMonteCarloReplicate-method0.0880.0040.091
getMonteCarloSample-method0.1000.0000.101
getReads-method0.0880.0000.091
getSampleIDs-method0.0840.0000.087
numConditions-method0.0840.0000.088
numFeatures-method0.0880.0000.088
numMCInstances-method0.0920.0000.090
plot.aldex0.0000.0000.001