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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCExperiment.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings HiCExperiment_1.7.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/HiCExperiment.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'HiCExperiment/DESCRIPTION' ... OK
* this is package 'HiCExperiment' version '1.7.0'
* 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 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 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 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 ... 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'.

.pairs2gi: no visible global function definition for 'read.delim'
.pairs2gi: no visible global function definition for 'tail'
Undefined global functions or variables:
  read.delim tail
Consider adding
  importFrom("utils", "read.delim", "tail")
to your NAMESPACE file.
* 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: CoolFile-class
> ### Title: 'CoolFile' S4 class
> ### Aliases: CoolFile-class McoolFile-class CoolFile CoolFile-methods
> ###   show,CoolFile-method
> 
> ### ** Examples
> 
> mcoolPath <- HiContactsData::HiContactsData('yeast_wt', 'mcool')
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
> pairsPath <- HiContactsData::HiContactsData('yeast_wt', 'pairs.gz')
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
> cf <- CoolFile(
+   mcoolPath, 
+   resolution = 2000, 
+   pairsFile = pairsPath, 
+   metadata = list(info = 'Yeast WT Hi-C exp.')
+ )
Error in .check_cool_file(path) : 
  Provided file is not a .cool/.mcool file.
  Aborting now.
Calls: CoolFile -> .check_cool_file
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
AggrHiCExperiment 13.03   2.34   40.94
* 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:3:5
   2.   └─HiCExperiment:::.multi2DQuery(...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 80 ]
  Error: Test failures
  In addition: Warning messages:
  1: In for (i in 1L:d2) { :
    closing unused connection 5 (E:/biocbuild/ExperimentHub_cache/1d7a433a86cb7_7752)
  2: In for (i in 1L:d2) { :
    closing unused connection 4 (E:/biocbuild/ExperimentHub_cache/1d7a433a86cb7_7752)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/HiCExperiment.Rcheck/00check.log'
for details.