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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MSstatsSampleSize.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MSstatsSampleSize_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsSampleSize.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsSampleSize/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsSampleSize’ version ‘1.16.0’
* 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 ‘MSstatsSampleSize’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'MSstatsSampleSize' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsSampleSize.Rcheck/00install.out’ for details.
* 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 ... 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 ... WARNING
Functions or methods with usage in documentation object '.classification' but not in code:
  ‘.classification’

* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                             old_size new_size compress
  classification_results.rda    1.8Mb    1.3Mb       xz
  simulated_datasets.rda        656Kb    511Kb       xz
  variance_estimation.rda       690Kb    321Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MSstatsSampleSize-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: designSampleSizeClassification
> ### Title: Estimate the mean predictive accuracy and mean protein
> ###   importance over all the simulated datasets
> ### Aliases: designSampleSizeClassification
> 
> ### ** Examples
> 
> data(OV_SRM_train)
> data(OV_SRM_train_annotation)
> 
> # num_simulations = 10: simulate 10 times
> # expected_FC = "data": fold change estimated from OV_SRM_train
> # select_simulated_proteins = "proportion":
> # select the simulated proteins based on the proportion of total proteins
> # simulate_valid = FALSE: use input OV_SRM_train as validation set
> # valid_samples_per_group = 50: 50 samples per condition
> simulated_datasets <- simulateDataset(data = OV_SRM_train,
+                                       annotation = OV_SRM_train_annotation,
+                                       num_simulations = 10,
+                                       expected_FC = "data",
+                                       list_diff_proteins =  NULL,
+                                       select_simulated_proteins = "proportion",
+                                       protein_proportion = 1.0,
+                                       protein_number = 1000,
+                                       samples_per_group = 50,
+                                       simulate_valid = FALSE,
+                                       valid_samples_per_group = 50)
 Preparing variance analysis...
 Variance analysis completed.
 Preparing simulation...
 Size of training data to simulate: 100
 Number of proteins to simulate: 67
 Start to run the simulation...
  Simulation: 1
  Simulation: 2
  Simulation: 3
  Simulation: 4
  Simulation: 5
  Simulation: 6
  Simulation: 7
  Simulation: 8
  Simulation: 9
  Simulation: 10
 Simulation completed.
> 
> # run classification on simulated datasets without parallel computation
> classification_results <- designSampleSizeClassification(simulations = simulated_datasets,
+                                                          parallel = FALSE)
 classifier: rf
 Start to train classifier...
Error: Required packages are missing: randomForest
Execution halted
* 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:
  ── Error ('test-designSampleSizeClassification.R:6:5'): designSampleSizeClassification works ──
  Error: Required packages are missing: randomForest
  Backtrace:
      ▆
   1. └─MSstatsSampleSize::designSampleSizeClassification(simulations = MSstatsSampleSize::simulated_datasets) at test-designSampleSizeClassification.R:6:5
   2.   └─base::lapply(...)
   3.     └─MSstatsSampleSize (local) FUN(X[[i]], ...)
   4.       └─MSstatsSampleSize:::.classificationModel(x = x, y = y, classifier = classifier)
   5.         ├─caret::train(...)
   6.         └─caret:::train.default(...)
   7.           └─caret::checkInstall(models$library)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
  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 ...
  ‘MSstatsSampleSize.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘MSstatsSampleSize.Rmd’
  ...
 Simulation completed.

> classification_results <- designSampleSizeClassification(simulations = simulated_datasets, 
+     parallel = FALSE)
 classifier: rf
 Start to train classifier...

  When sourcing ‘MSstatsSampleSize.R’:
Error: Required packages are missing: randomForest
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
  ...
--- re-building ‘MSstatsSampleSize.Rmd’ using rmarkdown

Quitting from lines  at lines 213-217 [unnamed-chunk-7] (MSstatsSampleSize.Rmd)
Error: processing vignette 'MSstatsSampleSize.Rmd' failed with diagnostics:
Required packages are missing: randomForest
--- failed re-building ‘MSstatsSampleSize.Rmd’

SUMMARY: processing the following file failed:
  ‘MSstatsSampleSize.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsSampleSize.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MSstatsSampleSize
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘MSstatsSampleSize’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
Warning: Package 'MSstatsSampleSize' is deprecated and will be removed from
  Bioconductor version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'MSstatsSampleSize' is deprecated and will be removed from
  Bioconductor version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsSampleSize)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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(MSstatsSampleSize)
Warning message:
Package 'MSstatsSampleSize' is deprecated and will be removed from
  Bioconductor version 3.19 
> 
> test_check("MSstatsSampleSize")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-designSampleSizeClassification.R:6:5'): designSampleSizeClassification works ──
Error: Required packages are missing: randomForest
Backtrace:
    ▆
 1. └─MSstatsSampleSize::designSampleSizeClassification(simulations = MSstatsSampleSize::simulated_datasets) at test-designSampleSizeClassification.R:6:5
 2.   └─base::lapply(...)
 3.     └─MSstatsSampleSize (local) FUN(X[[i]], ...)
 4.       └─MSstatsSampleSize:::.classificationModel(x = x, y = y, classifier = classifier)
 5.         ├─caret::train(...)
 6.         └─caret:::train.default(...)
 7.           └─caret::checkInstall(models$library)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
Error: Test failures
Execution halted