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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FCBF.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings FCBF_2.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FCBF.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* 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 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘FCBF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FCBF’ version ‘2.12.0’
* 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 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 loading without being on the library search path ... 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 ... 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                                21.312  0.336  21.648
scDengue                            14.557  0.140  14.698
su_plot                              8.789  0.160   8.950
get_su_for_feature_table_and_vector  8.235  0.188   8.423
get_ig_for_feature_table_and_vector  7.604  0.068   7.671
discretize_exprs                     4.837  0.232   5.069
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘FCBF-Vignette.Rmd’ using rmarkdown

Quitting from 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
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/FCBF.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL FCBF
###
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* installing to library ‘/home/biocbuild/bbs-3.19-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
Warning in fun(libname, pkgname) :
  Package 'FCBF' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'FCBF' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (FCBF)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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)
Warning message:
In fun(libname, pkgname) :
  Package 'FCBF' is deprecated and will be removed from Bioconductor
  version 3.20
> 
> 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 
  7.715   0.429   8.132