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

Package: mistyR

Version: 1.0.3

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mistyR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mistyR_1.0.3.tar.gz

StartedAt: 2021-10-15 02:05:59 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 02:21:27 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 927.7 seconds

RetCode: 0

Status: OK

CheckDir: mistyR.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:mistyR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mistyR_1.0.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/mistyR.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 'mistyR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mistyR' version '1.0.3'
* 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 'mistyR' 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 ... NOTE
plot_interaction_heatmap: no visible binding for global variable
  'Importance'
plot_interaction_heatmap: no visible binding for global variable
  'Predictor'
plot_interaction_heatmap: no visible binding for global variable
  'total'
plot_interaction_heatmap: no visible binding for global variable
  'Target'
plot_view_contributions: no visible binding for global variable
  'measure'
plot_view_contributions: no visible binding for global variable
  'target'
Undefined global functions or variables:
  Importance Predictor Target measure target total
* 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
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
collect_results          175.41   2.03  176.92
reexports                 60.13   0.54   60.53
run_misty                 58.17   0.32   58.28
remove_views              28.64   0.10   28.75
add_paraview              21.00   0.13   21.13
plot_improvement_stats     8.81   0.80    8.90
create_view                7.45   0.02    7.47
add_juxtaview              6.08   0.15    6.48
plot_contrast_results      5.13   0.70    5.25
plot_contrast_heatmap      4.76   0.42    4.85
plot_interaction_heatmap   4.56   0.50    4.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
collect_results        163.19   2.05  164.81
reexports               59.34   0.57   59.85
run_misty               53.44   0.37   53.75
remove_views            37.58   0.10   37.67
add_paraview            22.33   0.09   22.42
create_view             11.74   0.00   11.74
plot_improvement_stats   8.66   0.74    8.74
add_juxtaview            6.28   0.13    6.40
plot_contrast_results    5.03   0.26    5.09
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/mistyR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/mistyR_1.0.3.tar.gz && rm -rf mistyR.buildbin-libdir && mkdir mistyR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mistyR.buildbin-libdir mistyR_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL mistyR_1.0.3.zip && rm mistyR_1.0.3.tar.gz mistyR_1.0.3.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
 12 2502k   12  310k    0     0   917k      0  0:00:02 --:--:--  0:00:02  917k
 89 2502k   89 2244k    0     0  1718k      0  0:00:01  0:00:01 --:--:-- 1717k
100 2502k  100 2502k    0     0  1767k      0  0:00:01  0:00:01 --:--:-- 1767k

install for i386

* installing *source* package 'mistyR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mistyR'
    finding HTML links ... done
    add_juxtaview                           html  
    add_paraview                            html  
    add_views                               html  
    clear_cache                             html  
    collect_results                         html  
    create_initial_view                     html  
    create_view                             html  
    plot_contrast_heatmap                   html  
    plot_contrast_results                   html  
    plot_improvement_stats                  html  
    plot_interaction_communities            html  
    plot_interaction_heatmap                html  
    plot_view_contributions                 html  
    reexports                               html  
    remove_views                            html  
    run_misty                               html  
    synthetic                               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 'mistyR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mistyR' as mistyR_1.0.3.zip
* DONE (mistyR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'mistyR' 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(mistyR)
mistyR is able to run computationally intensive functions
  in parallel. Please consider specifying a future::plan(). For example by running
  future::plan(future::multisession) before calling mistyR functions.
> 
> test_check("mistyR")

Generating paraview

Attaching package: 'purrr'

The following object is masked from 'package:testthat':

    is_null

Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models

Generating paraview
Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Generating paraview
Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Generating paraview

Generating paraview
Training models

Generating paraview
Training models

Generating paraview
Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating
Aggregating subset

Computing triangulation

Generating juxtaview

Generating paraview

Generating paraview using 20 nearest neighbors per unit

Approximating RBF matrix using the Nystrom method

Generating paraview

Computing triangulation

Generating juxtaview

Generating paraview

Computing triangulation

Generating juxtaview

Generating paraview

Computing triangulation
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
  37.32    1.57   38.46


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(mistyR)
mistyR is able to run computationally intensive functions
  in parallel. Please consider specifying a future::plan(). For example by running
  future::plan(future::multisession) before calling mistyR functions.
> 
> test_check("mistyR")

Generating paraview

Attaching package: 'purrr'

The following object is masked from 'package:testthat':

    is_null

Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models

Generating paraview
Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Generating paraview
Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Generating paraview

Generating paraview
Training models

Generating paraview
Training models

Generating paraview
Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating
Aggregating subset

Computing triangulation

Generating juxtaview

Generating paraview

Generating paraview using 20 nearest neighbors per unit

Approximating RBF matrix using the Nystrom method

Generating paraview

Computing triangulation

Generating juxtaview

Generating paraview

Computing triangulation

Generating juxtaview

Generating paraview

Computing triangulation
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
  39.46    1.31   40.53

name	user	system	elapsed
add_juxtaview	6.08	0.15	6.48
add_paraview	21.00	0.13	21.13
add_views	0.01	0.00	0.01
clear_cache	0	0	0
collect_results	175.41	2.03	176.92
create_initial_view	0.44	0.03	0.47
create_view	7.45	0.02	7.47
plot_contrast_heatmap	4.76	0.42	4.85
plot_contrast_results	5.13	0.70	5.25
plot_improvement_stats	8.81	0.80	8.90
plot_interaction_communities	4.47	0.48	4.46
plot_interaction_heatmap	4.56	0.50	4.64
plot_view_contributions	3.94	0.56	4.10
reexports	60.13	0.54	60.53
remove_views	28.64	0.10	28.75
run_misty	58.17	0.32	58.28

name	user	system	elapsed
add_juxtaview	6.28	0.13	6.40
add_paraview	22.33	0.09	22.42
add_views	0.01	0.00	0.02
clear_cache	0	0	0
collect_results	163.19	2.05	164.81
create_initial_view	0.43	0.03	0.47
create_view	11.74	0.00	11.74
plot_contrast_heatmap	4.01	0.27	4.04
plot_contrast_results	5.03	0.26	5.09
plot_improvement_stats	8.66	0.74	8.74
plot_interaction_communities	4.12	0.28	4.14
plot_interaction_heatmap	4.55	0.28	4.55
plot_view_contributions	4.41	0.30	4.46
reexports	59.34	0.57	59.85
remove_views	37.58	0.10	37.67
run_misty	53.44	0.37	53.75

CHECK results for mistyR on tokay2

Summary

Command output

Installation output

Tests output

Example timings