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CHECK report for ALDEx2 on tokay1

This page was generated on 2021-01-22 11:54:48 -0500 (Fri, 22 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: 2021-01-21 14:42:12 -0500 (Thu, 21 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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ALDEx2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ALDEx2_1.22.0.tar.gz
StartedAt: 2021-01-22 00:35:29 -0500 (Fri, 22 Jan 2021)
EndedAt: 2021-01-22 00:44:30 -0500 (Fri, 22 Jan 2021)
EllapsedTime: 541.0 seconds
RetCode: 0
Status:  OK  
CheckDir: ALDEx2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ALDEx2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ALDEx2_1.22.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ALDEx2.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
aldex.corr       85.29   1.03   86.33
aldex.glm.effect  8.39   0.01    8.40
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
aldex.corr       99.11   1.17  100.29
aldex.glm.effect  7.81   0.00    7.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ALDEx2_1.22.0.tar.gz && rm -rf ALDEx2.buildbin-libdir && mkdir ALDEx2.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ALDEx2.buildbin-libdir ALDEx2_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ALDEx2_1.22.0.zip && rm ALDEx2_1.22.0.tar.gz ALDEx2_1.22.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1895k  100 1895k    0     0  24.5M      0 --:--:-- --:--:-- --:--:-- 26.0M

install for i386

* installing *source* package 'ALDEx2' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ALDEx2'
    finding HTML links ... done
    ALDEx2m-package                         html  
    aldex                                   html  
    aldex.clr-class                         html  
    aldex.clr.function-methods              html  
    aldex.corr                              html  
    aldex.effect                            html  
    aldex.glm                               html  
    aldex.glm.effect                        html  
    aldex.kw                                html  
    aldex.plotFeature                       html  
    aldex.set.mode                          html  
    aldex.ttest                             html  
    expectedDistance                        html  
    getDenom-method                         html  
    getFeatureNames-method                  html  
    getFeatures-method                      html  
    getMonteCarloInstances-method           html  
    getMonteCarloReplicate-method           html  
    getMonteCarloSample-method              html  
    getReads-method                         html  
    getSampleIDs-method                     html  
    numConditions-method                    html  
    numFeatures-method                      html  
    numMCInstances-method                   html  
    plot.aldex                              html  
    selex                                   html  
    synth2                                  html  
** 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

install for x64

* installing *source* package 'ALDEx2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ALDEx2' as ALDEx2_1.22.0.zip
* DONE (ALDEx2)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ALDEx2' successfully unpacked and MD5 sums checked

Tests output

ALDEx2.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  46.40    2.15   48.56 

ALDEx2.Rcheck/tests_x64/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-w64-mingw32/x64 (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 
  54.67    1.20   55.87 

Example timings

ALDEx2.Rcheck/examples_i386/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package000
aldex1.891.213.09
aldex.clr-class0.110.010.13
aldex.clr.function-methods0.080.000.08
aldex.corr85.29 1.0386.33
aldex.effect4.900.024.90
aldex.glm1.200.001.21
aldex.glm.effect8.390.018.40
aldex.kw2.150.002.14
aldex.plotFeature0.120.020.14
aldex.set.mode0.060.000.06
aldex.ttest0.160.000.16
expectedDistance0.420.080.50
getDenom-method0.090.000.09
getFeatureNames-method0.070.000.06
getFeatures-method0.040.000.05
getMonteCarloInstances-method0.070.010.08
getMonteCarloReplicate-method0.070.000.08
getMonteCarloSample-method0.100.020.11
getReads-method0.060.000.06
getSampleIDs-method0.060.000.06
numConditions-method0.070.000.06
numFeatures-method0.060.000.07
numMCInstances-method0.060.000.06
plot.aldex000

ALDEx2.Rcheck/examples_x64/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package000
aldex1.880.862.73
aldex.clr-class0.060.000.06
aldex.clr.function-methods0.040.000.05
aldex.corr 99.11 1.17100.29
aldex.effect3.820.003.82
aldex.glm1.010.001.01
aldex.glm.effect7.810.007.81
aldex.kw1.780.001.78
aldex.plotFeature0.110.000.11
aldex.set.mode0.060.000.06
aldex.ttest0.140.000.14
expectedDistance0.440.010.46
getDenom-method0.100.000.09
getFeatureNames-method0.040.000.05
getFeatures-method0.030.030.06
getMonteCarloInstances-method0.070.000.06
getMonteCarloReplicate-method0.060.000.06
getMonteCarloSample-method0.050.000.05
getReads-method0.060.020.08
getSampleIDs-method0.040.000.05
numConditions-method0.050.020.06
numFeatures-method0.060.000.06
numMCInstances-method0.050.000.05
plot.aldex000