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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:FCBF.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings FCBF_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FCBF.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 ‘FCBF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FCBF’ version ‘2.10.0’
* 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 ‘FCBF’ 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 ... 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 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
fcbf                                22.792  0.217  23.010
get_ig_for_feature_table_and_vector 15.393  0.060  15.592
scDengue                            15.094  0.084  15.178
get_su_for_feature_table_and_vector 10.740  0.172  11.332
su_plot                              8.793  0.032   8.824
discretize_exprs                     7.850  0.360   8.289
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘FCBF-Vignette.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘FCBF-Vignette.Rmd’
  ...

> control <- trainControl(method = "cv", number = 5, 
+     classProbs = TRUE, summaryFunction = twoClassSummary)

> svm_fcbf <- train(target_variable ~ ., metric = "ROC", 
+     data = dataset_fcbf, method = "svmRadial", trControl = control)

  When sourcing ‘FCBF-Vignette.R’:
Error: Required packages are missing: kernlab
Execution halted

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

Quitting from lines  at lines 178-205 [unnamed-chunk-10] (FCBF-Vignette.Rmd)
Error: processing vignette 'FCBF-Vignette.Rmd' failed with diagnostics:
Required packages are missing: kernlab
--- failed re-building ‘FCBF-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘FCBF-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/FCBF.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL FCBF
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘FCBF’ ...
** using staged installation
** R
** data
** 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 (FCBF)

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(FCBF)
> 
> test_check("FCBF")
[1] "Number of features features =  8"
[1] "Number of prospective features =  7"
[1] "Number of final features =  2"
[1] "Number of features features =  8"
[1] "Number of prospective features =  1"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  8.161   0.411   8.562