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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mistyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mistyR_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mistyR.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mistyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mistyR’ version ‘1.13.0’
* 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 for sufficient/correct file permissions ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 whether startup messages can be suppressed ... 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
aggregate_results: no visible binding for global variable ‘measure’
aggregate_results: no visible binding for global variable ‘target’
aggregate_results: no visible binding for global variable ‘value’
aggregate_results: no visible binding for global variable ‘sd’
aggregate_results: no visible binding for global variable ‘view’
aggregate_results: no visible binding for global variable ‘.PT’
aggregate_results: no visible binding for global variable ‘Importance’
aggregate_results_subset: no visible binding for global variable ‘view’
aggregate_results_subset: no visible binding for global variable ‘.PT’
aggregate_results_subset: no visible binding for global variable
  ‘Importance’
bagged_mars_model: no visible binding for global variable ‘index’
bagged_mars_model: no visible binding for global variable ‘prediction’
collect_results : <anonymous>: no visible binding for global variable
  ‘intra.RMSE’
collect_results : <anonymous>: no visible binding for global variable
  ‘multi.RMSE’
collect_results : <anonymous>: no visible binding for global variable
  ‘multi.R2’
collect_results : <anonymous>: no visible binding for global variable
  ‘intra.R2’
collect_results: no visible binding for global variable ‘target’
collect_results : <anonymous>: no visible binding for global variable
  ‘target’
collect_results : <anonymous>: no visible binding for global variable
  ‘view’
collect_results : <anonymous> : <anonymous>: no visible binding for
  global variable ‘value’
collect_results : <anonymous> : <anonymous>: no visible binding for
  global variable ‘Predictor’
collect_results : <anonymous> : <anonymous>: no visible binding for
  global variable ‘Importance’
extract_signature: no visible binding for global variable ‘measure’
extract_signature: no visible binding for global variable ‘target’
extract_signature: no visible binding for global variable ‘ts’
extract_signature: no visible binding for global variable ‘view’
extract_signature: no visible binding for global variable ‘value’
extract_signature : <anonymous>: no visible binding for global variable
  ‘Importance’
extract_signature : <anonymous>: no visible binding for global variable
  ‘Target’
extract_signature : <anonymous>: no visible binding for global variable
  ‘ts’
extract_signature : <anonymous>: no visible binding for global variable
  ‘Predictor’
gradient_boosting_model: no visible binding for global variable ‘index’
linear_model: no visible binding for global variable ‘index’
mars_model: no visible binding for global variable ‘index’
mlp_model: no visible binding for global variable ‘index’
plot_contrast_heatmap: no visible binding for global variable ‘view’
plot_contrast_heatmap: no visible binding for global variable ‘measure’
plot_contrast_heatmap: no visible binding for global variable ‘target’
plot_contrast_heatmap: no visible binding for global variable ‘Target’
plot_contrast_heatmap: no visible binding for global variable
  ‘nsamples’
plot_contrast_heatmap: no visible binding for global variable
  ‘Predictor’
plot_contrast_heatmap: no visible binding for global variable
  ‘Importance’
plot_contrast_results: no visible binding for global variable ‘view’
plot_contrast_results : <anonymous>: no visible binding for global
  variable ‘view’
plot_contrast_results : <anonymous>: no visible binding for global
  variable ‘Predictor’
plot_contrast_results : <anonymous>: no visible binding for global
  variable ‘Target’
plot_contrast_results: no visible binding for global variable ‘measure’
plot_contrast_results: no visible binding for global variable ‘target’
plot_contrast_results : <anonymous>: no visible binding for global
  variable ‘nsamples’
plot_contrast_results : <anonymous>: no visible binding for global
  variable ‘Importance’
plot_improvement_stats: no visible binding for global variable ‘target’
plot_improvement_stats: no visible binding for global variable ‘sd’
plot_interaction_communities: no visible binding for global variable
  ‘nsamples’
plot_interaction_communities: no visible binding for global variable
  ‘Predictor’
plot_interaction_heatmap: no visible binding for global variable
  ‘measure’
plot_interaction_heatmap: no visible binding for global variable
  ‘target’
plot_interaction_heatmap: no visible binding for global variable
  ‘Target’
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_view_contributions: no visible binding for global variable
  ‘measure’
plot_view_contributions: no visible binding for global variable
  ‘target’
plot_view_contributions: no visible binding for global variable
  ‘fraction’
plot_view_contributions: no visible binding for global variable ‘view’
run_misty : <anonymous>: no visible binding for global variable ‘p’
run_misty : <anonymous>: no visible binding for global variable
  ‘intra.RMSE’
run_misty : <anonymous>: no visible binding for global variable
  ‘multi.RMSE’
run_misty : <anonymous>: no visible binding for global variable
  ‘intra.R2’
run_misty : <anonymous>: no visible binding for global variable
  ‘multi.R2’
svm_model: no visible binding for global variable ‘index’
Undefined global functions or variables:
  .PT Importance Predictor Target fraction index intra.R2 intra.RMSE
  measure multi.R2 multi.RMSE nsamples p prediction sd target total ts
  value view
Consider adding
  importFrom("stats", "sd", "ts")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) collect_results.Rd:32: Lost braces; missing escapes or markup?
    32 |             for all performance measures for each {target} over all samples.}
       |                                                   ^
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
collect_results              276.486 17.622 321.078
reexports                     91.614  6.756 107.568
run_misty                     90.962  5.875 102.072
remove_views                  61.092  5.825  73.118
add_paraview                  49.386  2.966  58.729
add_juxtaview                 14.612  0.556  17.297
create_view                   14.973  0.109  17.088
plot_improvement_stats         8.879  0.416   9.917
plot_contrast_results          6.186  0.228   7.184
plot_contrast_heatmap          5.807  0.224   6.770
plot_interaction_heatmap       4.768  0.212   5.470
plot_interaction_communities   4.482  0.216   5.153
plot_view_contributions        4.453  0.209   5.112
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/mistyR.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mistyR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘mistyR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (mistyR)

R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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Aggregating

Training models

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Aggregating

Training models

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Collecting importances

Aggregating

Training models

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Aggregating

Training models

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Aggregating

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Aggregating

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Aggregating

Generating paraview

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Computing triangulation

Generating juxtaview

Generating paraview

Generating paraview using 20 nearest neighbors per unit

Approximating RBF matrix using the Nystrom method

Computing triangulation

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Computing triangulation

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Generating paraview using 2 nearest neighbors per unit

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[ FAIL 0 | WARN 4 | SKIP 0 | PASS 173 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 173 ]
> 
> proc.time()
   user  system elapsed 
791.565   9.990 898.676