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CHECK report for microbiomeDASim on tokay1

This page was generated on 2021-01-19 11:55:48 -0500 (Tue, 19 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE microbiomeDASim PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1094/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeDASim 1.4.0
Justin Williams
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/microbiomeDASim
Branch: RELEASE_3_12
Last Commit: 55fb35a
Last Changed Date: 2020-10-27 11:49:06 -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: microbiomeDASim
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiomeDASim.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings microbiomeDASim_1.4.0.tar.gz
StartedAt: 2021-01-19 04:52:29 -0500 (Tue, 19 Jan 2021)
EndedAt: 2021-01-19 04:58:14 -0500 (Tue, 19 Jan 2021)
EllapsedTime: 345.1 seconds
RetCode: 0
Status:  OK  
CheckDir: microbiomeDASim.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:microbiomeDASim.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings microbiomeDASim_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/microbiomeDASim.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 'microbiomeDASim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'microbiomeDASim' version '1.4.0'
* package encoding: UTF-8
* 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 'microbiomeDASim' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
gen_norm_microbiome_obs 25.17   0.11   25.30
simulate2MRexperiment   11.85   0.00   11.84
simulate2phyloseq       11.73   0.02   11.75
gen_norm_microbiome      7.02   0.06    7.07
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
gen_norm_microbiome_obs 25.80   0.14   26.07
simulate2MRexperiment    9.62   0.02    9.64
simulate2phyloseq        9.60   0.00    9.63
gen_norm_microbiome      7.53   0.00    7.54
* 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

microbiomeDASim.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/microbiomeDASim_1.4.0.tar.gz && rm -rf microbiomeDASim.buildbin-libdir && mkdir microbiomeDASim.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=microbiomeDASim.buildbin-libdir microbiomeDASim_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL microbiomeDASim_1.4.0.zip && rm microbiomeDASim_1.4.0.tar.gz microbiomeDASim_1.4.0.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 1288k  100 1288k    0     0  23.9M      0 --:--:-- --:--:-- --:--:-- 25.6M

install for i386

* installing *source* package 'microbiomeDASim' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'microbiomeDASim'
    finding HTML links ... done
    IP_form_check                           html  
    final_output_gen                        html  
    form_beta_check                         html  
    gen_microbiome_norm_feature_check       html  
    gen_norm_microbiome                     html  
    gen_norm_microbiome_obs                 html  
    ggplot_spaghetti                        html  
    mean_trend                              html  
    mean_trend_beta_vec                     html  
    mean_trend_design_mat                   html  
    mvrnorm_corr_gen                        html  
    mvrnorm_sim                             html  
    mvrnorm_sim_obs                         html  
    sigma_corr_function                     html  
    simulate2MRexperiment                   html  
    finding level-2 HTML links ... done

    simulate2phyloseq                       html  
    timepoint_process                       html  
    trunc_bugs                              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 'microbiomeDASim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'microbiomeDASim' as microbiomeDASim_1.4.0.zip
* DONE (microbiomeDASim)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'microbiomeDASim' successfully unpacked and MD5 sums checked

Tests output

microbiomeDASim.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(microbiomeDASim)
> 
> test_check("microbiomeDASim")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  10.21    0.73   10.93 

microbiomeDASim.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(microbiomeDASim)
> 
> test_check("microbiomeDASim")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  12.43    0.48   12.90 

Example timings

microbiomeDASim.Rcheck/examples_i386/microbiomeDASim-Ex.timings

nameusersystemelapsed
gen_norm_microbiome7.020.067.07
gen_norm_microbiome_obs25.17 0.1125.30
ggplot_spaghetti4.150.114.26
mean_trend0.640.020.66
mvrnorm_corr_gen0.440.000.44
mvrnorm_sim3.840.013.88
mvrnorm_sim_obs4.700.084.78
simulate2MRexperiment11.85 0.0011.84
simulate2phyloseq11.73 0.0211.75

microbiomeDASim.Rcheck/examples_x64/microbiomeDASim-Ex.timings

nameusersystemelapsed
gen_norm_microbiome7.530.007.54
gen_norm_microbiome_obs25.80 0.1426.07
ggplot_spaghetti3.890.043.94
mean_trend0.630.000.64
mvrnorm_corr_gen0.420.020.45
mvrnorm_sim3.910.013.93
mvrnorm_sim_obs4.560.024.57
simulate2MRexperiment9.620.029.64
simulate2phyloseq9.600.009.63