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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:mistyR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings mistyR_1.7.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/mistyR.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘mistyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mistyR’ version ‘1.7.2’
* 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 R 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 loading without being on the library search path ... OK
* checking 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
collect_results 131.327  6.573 137.789
reexports        44.887  1.936  46.790
run_misty        44.431  2.048  46.440
remove_views     27.539  0.115  27.695
add_paraview     22.600  0.144  22.745
add_juxtaview     5.944  0.080   6.024
create_view       5.766  0.012   5.778
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Generating paraview
  
  Generating paraview
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 172 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-misty.R:266:3'): k for cv , n.bags for bagging can be changed and approx works ──
  first.run < second.run is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 172 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘mistyR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/mistyR.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL mistyR
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Training models

Training models

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Generating paraview

Training models

Generating paraview

Training models

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Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Generating paraview

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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

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Training models

Collecting improvements

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Collecting importances

Aggregating
Aggregating subset

Generating paraview

Training models

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Training models

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Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Computing triangulation

Generating juxtaview

Generating paraview

Generating paraview using 20 nearest neighbors per unit

Approximating RBF matrix using the Nystrom method

Computing triangulation

Generating juxtaview

Generating paraview

Computing triangulation

Generating juxtaview

Generating paraview

Computing triangulation

Generating paraview

Generating paraview

Generating paraview using 2 nearest neighbors per unit

Generating paraview

Generating paraview
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 172 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-misty.R:266:3'): k for cv , n.bags for bagging can be changed and approx works ──
first.run < second.run is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 4 | SKIP 0 | PASS 172 ]
Error: Test failures
Execution halted