Multiple platform build/check report for BioC 3.11 - CHECK report for ALDEx2 on tokay2

Package: ALDEx2

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ALDEx2.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ALDEx2_1.20.0.tar.gz

StartedAt: 2020-10-17 01:30:00 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 01:35:54 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 353.5 seconds

RetCode: 0

Status: OK

CheckDir: ALDEx2.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ALDEx2.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ALDEx2_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-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 '1.20.0'
* 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       9.53   0.22    9.77
aldex.glm.effect 7.02   0.00    7.02
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
aldex.corr       8.76   0.09    8.86
aldex.glm.effect 8.64   0.00    8.64
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ALDEx2_1.20.0.tar.gz && rm -rf ALDEx2.buildbin-libdir && mkdir ALDEx2.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ALDEx2.buildbin-libdir ALDEx2_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ALDEx2_1.20.0.zip && rm ALDEx2_1.20.0.tar.gz ALDEx2_1.20.0.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 1890k  100 1890k    0     0  23.4M      0 --:--:-- --:--:-- --:--:-- 25.2M

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_1.20.0.zip
* DONE (ALDEx2)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ALDEx2' successfully unpacked and MD5 sums checked


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")
== testthat results  ===========================================================
[ OK: 22 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  41.70    2.18   43.89


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")
== testthat results  ===========================================================
[ OK: 22 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  44.06    1.37   45.42

name	user	system	elapsed
ALDEx2m-package	0	0	0
aldex	1.69	1.27	2.96
aldex.clr-class	0.06	0.00	0.06
aldex.clr.function-methods	0.06	0.00	0.06
aldex.corr	9.53	0.22	9.77
aldex.effect	3.63	0.00	3.63
aldex.glm	1	0	1
aldex.glm.effect	7.02	0.00	7.02
aldex.kw	1.97	0.00	1.97
aldex.plotFeature	0.09	0.03	0.12
aldex.set.mode	0.05	0.01	0.06
aldex.ttest	0.12	0.02	0.14
expectedDistance	0.58	0.03	0.61
getDenom-method	0.14	0.02	0.16
getFeatureNames-method	0.06	0.01	0.08
getFeatures-method	0.07	0.00	0.06
getMonteCarloInstances-method	0.06	0.00	0.06
getMonteCarloReplicate-method	0.05	0.02	0.06
getMonteCarloSample-method	0.06	0.00	0.07
getReads-method	0.06	0.00	0.06
getSampleIDs-method	0.05	0.00	0.05
numConditions-method	0.06	0.00	0.06
numFeatures-method	0.06	0.00	0.06
numMCInstances-method	0.07	0.00	0.06
plot.aldex	0	0	0

name	user	system	elapsed
ALDEx2m-package	0	0	0
aldex	1.83	0.84	2.68
aldex.clr-class	0.06	0.00	0.06
aldex.clr.function-methods	0.05	0.00	0.05
aldex.corr	8.76	0.09	8.86
aldex.effect	4.64	0.02	4.65
aldex.glm	1.64	0.00	1.64
aldex.glm.effect	8.64	0.00	8.64
aldex.kw	2.36	0.00	2.36
aldex.plotFeature	0.08	0.03	0.11
aldex.set.mode	0.11	0.00	0.11
aldex.ttest	0.19	0.00	0.19
expectedDistance	0.48	0.03	0.51
getDenom-method	0.08	0.00	0.08
getFeatureNames-method	0.04	0.00	0.05
getFeatures-method	0.07	0.00	0.06
getMonteCarloInstances-method	0.06	0.00	0.06
getMonteCarloReplicate-method	0.03	0.02	0.05
getMonteCarloSample-method	0.05	0.01	0.06
getReads-method	0.06	0.00	0.06
getSampleIDs-method	0.05	0.00	0.05
numConditions-method	0.04	0.00	0.05
numFeatures-method	0.06	0.00	0.06
numMCInstances-method	0.06	0.00	0.07
plot.aldex	0	0	0

CHECK report for ALDEx2 on tokay2

Summary

Command output

Installation output

Tests output

Example timings