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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:fcoex.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings fcoex_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/fcoex.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘fcoex/DESCRIPTION’ ... OK
* this is package ‘fcoex’ 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 ‘fcoex’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’
See ‘/home/biocbuild/bbs-3.17-bioc/meat/fcoex.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 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
discretize,fcoex: no visible global function definition for ‘as’
initialize,fcoex: no visible global function definition for ‘as’
mod_ora,fcoex: no visible global function definition for ‘is’
Undefined global functions or variables:
  as is
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Documented arguments not in \usage in documentation object '.plot_one_interaction':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘fcoex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mod_ora
> ### Title: Over Representation Analysis (ORA)
> ### Aliases: mod_ora mod_ora,fcoex-method
> 
> ### ** Examples
> 
> data("fc")
> gmt_fname <- system.file("extdata", "pathways.gmt", package = "CEMiTool")
> gmt_in <- pathwayPCA::read_gmt(gmt_fname)
Warning in file(con, "rb") :
  file("") only supports open = "w+" and open = "w+b": using the former
Warning in readChar(file, nchars = nChars, useBytes = TRUE) :
  text connection used with readChar(), results may be incorrect
Error in readChar(file, nchars = nChars, useBytes = TRUE) : 
  invalid 'nchars' argument
Calls: <Anonymous> -> readChar
Execution halted
* 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 ...
  ‘fcoex.Rmd’ using ‘UTF-8’... OK
  ‘fcoex_and_seurat.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘fcoex.Rmd’ using rmarkdown
Quitting from lines 130-143 (fcoex.Rmd) 
Error: processing vignette 'fcoex.Rmd' failed with diagnostics:
object 'gmt_in' not found
--- failed re-building ‘fcoex.Rmd’

--- re-building ‘fcoex_and_seurat.Rmd’ using rmarkdown
Quitting from lines 67-75 (fcoex_and_seurat.Rmd) 
Error: processing vignette 'fcoex_and_seurat.Rmd' failed with diagnostics:
invalid 'nchars' argument
--- failed re-building ‘fcoex_and_seurat.Rmd’

SUMMARY: processing the following files failed:
  ‘fcoex.Rmd’ ‘fcoex_and_seurat.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/fcoex.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL fcoex
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘fcoex’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB

Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’
in method for ‘mod_ora’ with signature ‘"fcoex"’: no definition for class “fcoex”
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’
in method for ‘mod_ora’ with signature ‘"fcoex"’: no definition for class “fcoex”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’
** testing if installed package keeps a record of temporary installation path
* DONE (fcoex)

R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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(fcoex)

Warning message:
replacing previous import 'Matrix::head' by 'utils::head' when loading 'fcoex' 
> 
> test_check("fcoex")
[1] "Number of features features =  40"
[1] "Number of prospective features =  14"
[1] "Number of final features =  7"
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 10.905   0.622  11.515