Multiple platform build/check report for BioC 3.13 - CHECK results for proDA on tokay2

Package: proDA

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings proDA_1.6.0.tar.gz

StartedAt: 2021-10-15 03:42:36 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 03:50:55 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 499.3 seconds

RetCode: 0

Status: OK

CheckDir: proDA.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings proDA_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/proDA.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.6.0'
* 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
* 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 http://155.52.207.165/BBS/3.13/bioc/src/contrib/proDA_1.6.0.tar.gz && rm -rf proDA.buildbin-libdir && mkdir proDA.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proDA.buildbin-libdir proDA_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL proDA_1.6.0.zip && rm proDA_1.6.0.tar.gz proDA_1.6.0.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
 79 1355k   79 1083k    0     0  1619k      0 --:--:-- --:--:-- --:--:-- 1619k
100 1355k  100 1355k    0     0  1736k      0 --:--:-- --:--:-- --:--:-- 1735k

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_1.6.0.zip
* DONE (proDA)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'proDA' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
== Skipped tests ===============================================================
* Very slow (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 126 ]
> 
> proc.time()
   user  system elapsed 
 142.76    1.25  144.00


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
== Skipped tests ===============================================================
* Very slow (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 126 ]
> 
> proc.time()
   user  system elapsed 
 144.28    0.35  144.62

name	user	system	elapsed
abundances	0.95	0.24	1.19
as_replicate	0	0	0
cash-proDAFit-method	0.7	0.0	0.7
coefficient_variance_matrices	0.72	0.00	0.72
coefficients	0.73	0.00	0.73
convergence	0.71	0.00	0.71
dist_approx	1.61	0.00	1.61
dist_approx_impl	1.53	0.00	1.53
feature_parameters	0.69	0.00	0.69
generate_synthetic_data	0.04	0.00	0.04
hyper_parameters	0.67	0.00	0.67
invprobit	0	0	0
median_normalization	0	0	0
mply_dbl	0.02	0.00	0.02
pd_lm	0	0	0
pd_row_t_test	2.8	0.0	2.8
proDA	1.86	0.00	1.86
reference_level	0.59	0.00	0.59
result_names	0.67	0.00	0.67
test_diff	3.81	0.04	3.86

name	user	system	elapsed
abundances	1.33	0.09	1.46
as_replicate	0	0	0
cash-proDAFit-method	1.36	0.01	1.38
coefficient_variance_matrices	0.83	0.00	0.83
coefficients	0.80	0.00	0.79
convergence	0.76	0.00	0.77
dist_approx	1.75	0.00	1.75
dist_approx_impl	1.63	0.00	1.62
feature_parameters	0.78	0.00	0.78
generate_synthetic_data	0.05	0.00	0.05
hyper_parameters	0.81	0.00	0.81
invprobit	0	0	0
median_normalization	0	0	0
mply_dbl	0.01	0.00	0.02
pd_lm	0	0	0
pd_row_t_test	3.93	0.00	3.92
proDA	2.04	0.00	2.05
reference_level	0.64	0.00	0.64
result_names	0.77	0.00	0.76
test_diff	3.64	0.02	3.66

CHECK results for proDA on tokay2

Summary

Command output

Installation output

Tests output

Example timings