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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiCExperiment.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiCExperiment_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/HiCExperiment.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 ‘HiCExperiment/DESCRIPTION’ ... OK
* this is package ‘HiCExperiment’ version ‘1.0.0’
* 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 ‘HiCExperiment’ 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 ... NOTE
Foreign function call to a different package:
  .Call("_H5Fis_hdf5", ..., PACKAGE = "rhdf5")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
File ‘HiCExperiment/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("Consider using the `HiContacts` package to perform advanced genomic operations \non `HiCExperiment` objects.\n\nRead \"Orchestrating Hi-C analysis with Bioconductor\" online book to learn more:\nhttps://js2264.github.io/OHCA/")

See section ‘Good practice’ in '?.onAttach'.
* 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 ... ERROR
Running examples in ‘HiCExperiment-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AggrHiCExperiment
> ### Title: 'AggrHiCExperiment' S4 class
> ### Aliases: AggrHiCExperiment AggrHiCExperiment-class
> ###   slices,AggrHiCExperiment,missing-method
> ###   slices,AggrHiCExperiment,character-method
> ###   slices,AggrHiCExperiment,numeric-method show,AggrHiCExperiment-method
> 
> ### ** Examples
> 
> fpath <- HiContactsData::HiContactsData('yeast_wt', 'mcool')
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
> data(centros_yeast)
> x <- AggrHiCExperiment(
+   file = fpath, 
+   resolution = 8000,
+   targets = centros_yeast[c(4, 7)]
+ )
Going through preflight checklist...
Error in .multi2DQuery(file, resolution, pairs = pairs, bed = bed, BPPARAM = BPPARAM,  : 
  object 'allBins' not found
Calls: AggrHiCExperiment -> .multi2DQuery
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 in `.multi2DQuery(file, resolution, pairs = pairs, bed = bed, BPPARAM = BPPARAM, 
      maxDistance = maxDistance)`: object 'allBins' not found
  Backtrace:
      ▆
   1. └─HiCExperiment::AggrHiCExperiment(...) at test-aggrHicExperiment.R:3:4
   2.   └─HiCExperiment:::.multi2DQuery(...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 80 ]
  Error: Test failures
  In addition: Warning messages:
  1: In for (i in seq_along(extends)) { :
    closing unused connection 5 (/home/biocbuild/.cache/R/ExperimentHub/3e92c6715d6198_7752)
  2: In for (i in seq_along(extends)) { :
    closing unused connection 4 (/home/biocbuild/.cache/R/ExperimentHub/3e92c6715d6198_7752)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘HiCExperiment.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘HiCExperiment.Rmd’ using rmarkdown

Quitting from lines 99-103 [load_lib] (HiCExperiment.Rmd)
Error: processing vignette 'HiCExperiment.Rmd' failed with diagnostics:
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 ‘HiCExperiment.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/HiCExperiment.Rcheck/00check.log’
for details.