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CHECK report for ALDEx2 on tokay1

This page was generated on 2020-08-07 12:04:58 -0400 (Fri, 07 Aug 2020).

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 40/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALDEx2 1.21.1
Greg Gloor
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/ALDEx2
Branch: master
Last Commit: 93c54f9
Last Changed Date: 2020-07-07 15:59:33 -0400 (Tue, 07 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
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: 1.21.1
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_1.21.1.tar.gz
StartedAt: 2020-08-07 01:45:57 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 01:55:50 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 593.4 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_1.21.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ALDEx2.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.21.1'
* 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       74.17   1.00   75.17
aldex.glm.effect  6.09   0.02    6.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
aldex.corr       144.72   1.44  149.99
aldex.glm.effect   9.88   0.01    9.90
aldex.effect       5.35   0.08    5.42
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ALDEx2_1.21.1.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_1.21.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ALDEx2_1.21.1.zip && rm ALDEx2_1.21.1.tar.gz ALDEx2_1.21.1.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  31.6M      0 --:--:-- --:--:-- --:--:-- 34.2M

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_1.21.1.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 4.0.2 (2020-06-22) -- "Taking Off Again"
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 
  53.79    2.95   56.81 

ALDEx2.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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 
  43.50    1.28   44.76 

Example timings

ALDEx2.Rcheck/examples_i386/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package000
aldex1.540.772.31
aldex.clr-class0.070.000.06
aldex.clr.function-methods0.060.000.07
aldex.corr74.17 1.0075.17
aldex.effect3.140.013.15
aldex.glm0.940.000.94
aldex.glm.effect6.090.026.11
aldex.kw1.710.001.70
aldex.plotFeature0.090.000.10
aldex.set.mode0.060.000.06
aldex.ttest0.140.000.14
expectedDistance0.430.080.50
getDenom-method0.070.000.08
getFeatureNames-method0.070.000.06
getFeatures-method0.060.000.06
getMonteCarloInstances-method0.030.010.05
getMonteCarloReplicate-method0.050.020.06
getMonteCarloSample-method0.070.000.08
getReads-method0.070.000.06
getSampleIDs-method0.060.000.07
numConditions-method0.050.000.04
numFeatures-method0.060.000.07
numMCInstances-method0.060.000.06
plot.aldex000

ALDEx2.Rcheck/examples_x64/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package000
aldex2.970.913.88
aldex.clr-class0.090.000.10
aldex.clr.function-methods0.090.010.10
aldex.corr144.72 1.44149.99
aldex.effect5.350.085.42
aldex.glm1.230.001.24
aldex.glm.effect9.880.019.90
aldex.kw2.670.002.67
aldex.plotFeature0.110.000.11
aldex.set.mode0.090.000.10
aldex.ttest0.250.000.25
expectedDistance0.660.030.68
getDenom-method0.150.000.16
getFeatureNames-method0.100.000.09
getFeatures-method0.090.000.10
getMonteCarloInstances-method0.060.000.06
getMonteCarloReplicate-method0.070.000.06
getMonteCarloSample-method0.040.000.05
getReads-method0.050.020.06
getSampleIDs-method0.060.000.06
numConditions-method0.050.000.05
numFeatures-method0.050.010.06
numMCInstances-method0.060.000.07
plot.aldex000