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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiContacts.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiContacts_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/HiContacts.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84269)
* 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 ‘HiContacts/DESCRIPTION’ ... OK
* this is package ‘HiContacts’ version ‘1.2.0’
* 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 ‘HiContacts’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘HiContacts-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distanceLaw
> ### Title: Compute the law of distance-dependent contact frequency, a.k.a.
> ###   P(s)
> ### Aliases: distanceLaw Ps distanceLaw,HiCExperiment,missing-method
> ###   distanceLaw,PairsFile,missing-method
> ###   distanceLaw,PairsFile,GRanges-method localDistanceLaw
> ###   distanceLaw,HiCExperiment,GRanges-method
> 
> ### ** Examples
> 
> contacts_yeast <- contacts_yeast()
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
  Aborting now.
Calls: contacts_yeast ... import -> FileForFormat -> <Anonymous> -> .check_cool_file
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:
    3. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
    4. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
    5. │   ├─BiocIO::import(FileForFormat(con, format), ...)
    6. │   └─BiocIO::FileForFormat(con, format)
    7. │     └─get(constructorName, ns)(path)
    8. │       └─HiCExperiment:::.check_cool_file(path)
    9. │         └─base::stop("Provided file is not a .cool/.mcool file.\n  Aborting now.")
   10. ├─base::.handleSimpleError(...)
   11. │ └─base (local) h(simpleError(msg, call))
   12. └─base::.handleSimpleError(...)
   13.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 11 | WARN 0 | SKIP 0 | PASS 1 ]
  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 ...
  ‘HiContacts.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘HiContacts.Rmd’ using rmarkdown

Quitting from lines 87-93 [unnamed-chunk-5] (HiContacts.Rmd)
Error: processing vignette 'HiContacts.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'plotMatrix': error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
  Aborting now.
--- failed re-building ‘HiContacts.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/HiContacts.Rcheck/00check.log’
for details.