Multiple platform build/check report for BioC 3.7 - CHECK report for ALDEx2 on tokay2

Package: ALDEx2

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ALDEx2.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ALDEx2_1.12.0.tar.gz

StartedAt: 2018-10-17 00:27:55 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:32:54 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 299.0 seconds

RetCode: 0

Status: OK

CheckDir: ALDEx2.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ALDEx2.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ALDEx2_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ALDEx2.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.12.0'
* 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
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
aldex.effect 5.13   0.05    5.18
* 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/3.7/bioc/src/contrib/ALDEx2_1.12.0.tar.gz && rm -rf ALDEx2.buildbin-libdir && mkdir ALDEx2.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ALDEx2.buildbin-libdir ALDEx2_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ALDEx2_1.12.0.zip && rm ALDEx2_1.12.0.tar.gz ALDEx2_1.12.0.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 97791  100 97791    0     0  1554k      0 --:--:-- --:--:-- --:--:-- 1768k

install for i386

* installing *source* package 'ALDEx2' ...
** 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.set.mode                          html  
    aldex.ttest                             html  
    getDenom-method                         html  
    getFeatureNames-method                  html  
    getFeatures-method                      html  
    getMonteCarloInstances-method           html  
    getMonteCarloReplicate-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
In R CMD INSTALL

install for x64

* installing *source* package 'ALDEx2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ALDEx2' as ALDEx2_1.12.0.zip
* DONE (ALDEx2)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ALDEx2' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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)
> 
> test_check("ALDEx2")
[1] "aldex.clr: generating Monte-Carlo instances and clr values"
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "aldex.ttest: doing t-test"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "aldex.effect: calculating effect sizes"
[1] "operating in serial mode"
[1] "aldex.clr: generating Monte-Carlo instances and clr values"
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "aldex.glm: doing Kruskal Wallace and glm test"
[1] "operating in serial mode"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "operating in serial mode"
[1] "computing center with all features"
== testthat results  ===========================================================
OK: 18 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  48.85    1.92   50.79


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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)
> 
> test_check("ALDEx2")
[1] "aldex.clr: generating Monte-Carlo instances and clr values"
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "aldex.ttest: doing t-test"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "aldex.effect: calculating effect sizes"
[1] "operating in serial mode"
[1] "aldex.clr: generating Monte-Carlo instances and clr values"
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "aldex.glm: doing Kruskal Wallace and glm test"
[1] "operating in serial mode"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "running tests for each MC instance:"
|------------(25%)----------(50%)----------(75%)----------|
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "operating in serial mode"
[1] "computing center with all features"
== testthat results  ===========================================================
OK: 18 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  54.85    1.32   56.20

name	user	system	elapsed
ALDEx2m-package	0	0	0
aldex	1.61	1.37	3.05
aldex.clr-class	0.08	0.00	0.08
aldex.clr.function-methods	0.08	0.00	0.07
aldex.corr	0	0	0
aldex.effect	3.54	0.02	3.57
aldex.glm	2.19	0.00	2.18
aldex.set.mode	0.11	0.00	0.11
aldex.ttest	0.3	0.0	0.3
getDenom-method	0.22	0.01	0.24
getFeatureNames-method	0.08	0.03	0.11
getFeatures-method	0.13	0.02	0.14
getMonteCarloInstances-method	0.09	0.01	0.11
getMonteCarloReplicate-method	0.09	0.00	0.09
getReads-method	0.07	0.00	0.07
getSampleIDs-method	0.04	0.00	0.04
numConditions-method	0.05	0.00	0.05
numFeatures-method	0.04	0.00	0.04
numMCInstances-method	0.04	0.00	0.05
plot.aldex	0	0	0

name	user	system	elapsed
ALDEx2m-package	0	0	0
aldex	2.10	0.68	2.76
aldex.clr-class	0.07	0.04	0.11
aldex.clr.function-methods	0.12	0.00	0.12
aldex.corr	0	0	0
aldex.effect	5.13	0.05	5.18
aldex.glm	3.29	0.03	3.32
aldex.set.mode	0.1	0.0	0.1
aldex.ttest	0.29	0.00	0.29
getDenom-method	0.18	0.02	0.19
getFeatureNames-method	0.06	0.01	0.08
getFeatures-method	0.08	0.00	0.07
getMonteCarloInstances-method	0.08	0.02	0.10
getMonteCarloReplicate-method	0.08	0.01	0.09
getReads-method	0.08	0.02	0.09
getSampleIDs-method	0.07	0.00	0.08
numConditions-method	0.08	0.00	0.08
numFeatures-method	0.11	0.00	0.11
numMCInstances-method	0.08	0.01	0.09
plot.aldex	0	0	0

CHECK report for ALDEx2 on tokay2

Summary

Command output

Installation output

Tests output

Example timings