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

Package: CytoGLMM

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoGLMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CytoGLMM_1.0.0.tar.gz

StartedAt: 2021-10-14 21:50:33 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 21:54:00 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 207.3 seconds

RetCode: 0

Status: OK

CheckDir: CytoGLMM.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoGLMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CytoGLMM_1.0.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CytoGLMM.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 'CytoGLMM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CytoGLMM' version '1.0.0'
* 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 'CytoGLMM' 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
plot_model_selection 7.35   0.06    7.41
cytoflexmix          5.52   0.13    5.64
plot.cytoflexmix     5.32   0.06    5.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
plot_model_selection 6.25   0.01    6.27
* 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/CytoGLMM_1.0.0.tar.gz && rm -rf CytoGLMM.buildbin-libdir && mkdir CytoGLMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoGLMM.buildbin-libdir CytoGLMM_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CytoGLMM_1.0.0.zip && rm CytoGLMM_1.0.0.tar.gz CytoGLMM_1.0.0.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 35343  100 35343    0     0   300k      0 --:--:-- --:--:-- --:--:--  302k

install for i386

* installing *source* package 'CytoGLMM' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CytoGLMM'
    finding HTML links ... done
    cyto_check                              html  
    cytoflexmix                             html  
    cytoglm                                 html  
    cytoglmm                                html  
    cytogroup                               html  
    cytostab                                html  
    generate_data                           html  
    glmm_moment                             html  
    is_unpaired                             html  
    plot.cytoflexmix                        html  
    plot.cytoglm                            html  
    plot.cytoglmm                           html  
    plot.cytogroup                          html  
    plot_coeff                              html  
    plot_heatmap                            html  
    plot_lda                                html  
    plot_mds                                html  
    plot_model_selection                    html  
    plot_prcomp                             html  
    print.cytoglm                           html  
    print.cytoglmm                          html  
    remove_samples                          html  
    summary.cytoglm                         html  
    summary.cytoglmm                        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 'CytoGLMM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CytoGLMM' as CytoGLMM_1.0.0.zip
* DONE (CytoGLMM)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CytoGLMM' 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(CytoGLMM)
> 
> test_check("CytoGLMM")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   3.79    0.57    4.35


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(CytoGLMM)
> 
> test_check("CytoGLMM")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   3.93    0.31    4.21

name	user	system	elapsed
cytoflexmix	5.52	0.13	5.64
cytoglm	1.17	0.00	1.17
cytoglmm	0.25	0.00	0.25
cytogroup	0.82	0.03	0.84
cytostab	0.22	0.00	0.22
generate_data	0.10	0.00	0.09
plot.cytoflexmix	5.32	0.06	5.39
plot.cytoglm	1.41	0.02	1.42
plot.cytoglmm	0.31	0.01	0.33
plot.cytogroup	0.86	0.03	0.89
plot_heatmap	0.42	0.01	0.44
plot_lda	1.58	0.07	1.64
plot_mds	0.45	0.03	0.48
plot_model_selection	7.35	0.06	7.41
plot_prcomp	1.92	0.08	2.00
print.cytoglm	1.31	0.00	1.31
print.cytoglmm	0.22	0.00	0.22
summary.cytoglm	1.22	0.00	1.22
summary.cytoglmm	0.22	0.00	0.22

name	user	system	elapsed
cytoflexmix	4.50	0.03	4.54
cytoglm	1.01	0.00	1.01
cytoglmm	0.17	0.02	0.18
cytogroup	0.48	0.04	0.54
cytostab	0.38	0.02	0.39
generate_data	0.09	0.00	0.09
plot.cytoflexmix	4.56	0.05	4.61
plot.cytoglm	1.22	0.01	1.23
plot.cytoglmm	0.3	0.0	0.3
plot.cytogroup	0.95	0.03	0.99
plot_heatmap	0.14	0.00	0.14
plot_lda	1.57	0.05	1.61
plot_mds	0.39	0.02	0.40
plot_model_selection	6.25	0.01	6.27
plot_prcomp	1.72	0.08	1.79
print.cytoglm	1.12	0.00	1.13
print.cytoglmm	0.19	0.03	0.22
summary.cytoglm	0.89	0.00	0.89
summary.cytoglmm	0.47	0.02	0.48

CHECK results for CytoGLMM on tokay2

Summary

Command output

Installation output

Tests output

Example timings