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

Package: proDA

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings proDA_1.2.0.tar.gz

StartedAt: 2020-10-17 07:04:49 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 07:13:05 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 496.1 seconds

RetCode: 0

Status: OK

CheckDir: proDA.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:proDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings proDA_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/proDA.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 'proDA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'proDA' version '1.2.0'
* 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 'proDA' 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
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
abundances 1.88   0.13    7.67
* 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/proDA_1.2.0.tar.gz && rm -rf proDA.buildbin-libdir && mkdir proDA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proDA.buildbin-libdir proDA_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL proDA_1.2.0.zip && rm proDA_1.2.0.tar.gz proDA_1.2.0.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 1355k  100 1355k    0     0  10.0M      0 --:--:-- --:--:-- --:--:-- 10.6M

install for i386

* installing *source* package 'proDA' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'proDA'
    finding HTML links ... done
    abundances                              html  
    accessor_methods                        html  
    as_replicate                            html  
    cash-proDAFit-method                    html  
    coefficient_variance_matrices           html  
    coefficients                            html  
    convergence                             html  
    dist_approx                             html  
    dist_approx_impl                        html  
    distance_sq                             html  
    feature_parameters                      html  
    generate_synthetic_data                 html  
    grapes-zero_dom_mat_mult-grapes         html  
    hyper_parameters                        html  
    invprobit                               html  
    invprobit_fast                          html  
    median_normalization                    html  
    mply_dbl                                html  
    pd_lm                                   html  
    pd_lm.fit                               html  
    pd_row_t_test                           html  
    predict-proDAFit-method                 html  
    proDA                                   html  
    proDAFit-class                          html  
    proDA_package                           html  
    reference_level                         html  
    result_names                            html  
    test_diff                               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 'proDA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'proDA' as proDA_1.2.0.zip
* DONE (proDA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'proDA' 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(proDA)
> 
> test_check("proDA")
== testthat results  ===========================================================
[ OK: 107 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 119.59    1.50  121.07


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(proDA)
> 
> test_check("proDA")
== testthat results  ===========================================================
[ OK: 107 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 143.12    0.37  143.53

name	user	system	elapsed
abundances	1.47	0.32	1.78
as_replicate	0	0	0
cash-proDAFit-method	1.07	0.01	1.09
coefficient_variance_matrices	1.11	0.00	1.11
coefficients	0.91	0.00	0.91
convergence	0.77	0.00	0.76
dist_approx	1.23	0.00	1.24
dist_approx_impl	1.7	0.0	1.7
feature_parameters	1.00	0.03	1.03
generate_synthetic_data	0.03	0.00	0.03
hyper_parameters	0.75	0.02	0.77
invprobit	0.02	0.00	0.01
median_normalization	0	0	0
mply_dbl	0	0	0
pd_lm	0.02	0.00	0.02
pd_row_t_test	1.81	0.00	1.81
proDA	1.90	0.00	1.91
reference_level	0.72	0.00	0.72
result_names	0.83	0.00	0.82
test_diff	3.61	0.08	3.69

name	user	system	elapsed
abundances	1.88	0.13	7.67
as_replicate	0	0	0
cash-proDAFit-method	1.05	0.01	1.07
coefficient_variance_matrices	0.86	0.00	0.86
coefficients	1.30	0.00	1.29
convergence	1.31	0.00	1.32
dist_approx	1.26	0.00	1.26
dist_approx_impl	1.19	0.02	1.20
feature_parameters	0.96	0.00	0.96
generate_synthetic_data	0.03	0.00	0.03
hyper_parameters	0.76	0.00	0.76
invprobit	0.02	0.00	0.02
median_normalization	0	0	0
mply_dbl	0.00	0.02	0.02
pd_lm	0.01	0.00	0.01
pd_row_t_test	1.86	0.00	1.88
proDA	2.05	0.00	2.06
reference_level	0.64	0.00	0.64
result_names	0.71	0.00	0.72
test_diff	3.19	0.00	3.19

CHECK report for proDA on tokay2

Summary

Command output

Installation output

Tests output

Example timings