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###
### Running command:
###
###   /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.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL HiCExperiment
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘HiCExperiment’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HiCExperiment)

R version 4.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(HiCExperiment)
Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
> 
> test_check("HiCExperiment")
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
resolutions(1): 1000

see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
resolutions(5): 1000 2000 4000 8000 16000

resolutions(5): 1000 2000 4000 8000 16000

HicFile object
.hic file: /home/biocbuild/.cache/R/ExperimentHub/a1ea07ab6977e_7836 
resolution: 1000 
pairs file: 
metadata(0):
HicproFile object
HiC-Pro files:
  $ matrix:   /home/biocbuild/.cache/R/ExperimentHub/a1ea03bf6b736_7837 
  $ regions:  /home/biocbuild/.cache/R/ExperimentHub/a1ea028d68c4c_7838 
resolution: 1000 
pairs file: 
metadata(0):
Going through preflight checklist...
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 80 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-CoolFile.R:10:5'): CoolFile works ──────────────────────────────
Error in `.check_cool_file(path)`: Provided file is not a .cool/.mcool file.
  Aborting now.
Backtrace:
    ▆
 1. └─HiCExperiment::CoolFile(mcoolPath) at test-CoolFile.R:10:4
 2.   └─HiCExperiment:::.check_cool_file(path)
── Error ('test-HiCExperiment-methods.R:1:1'): (code run outside of `test_that()`) ──
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.
Backtrace:
     ▆
  1. ├─HiCExperiment::contacts_yeast() at test-HiCExperiment-methods.R:1:0
  2. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
  3. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
  4. │   ├─BiocIO::import(FileForFormat(con, format), ...)
  5. │   └─BiocIO::FileForFormat(con, format)
  6. │     └─get(constructorName, ns)(path)
  7. │       └─HiCExperiment:::.check_cool_file(path)
  8. │         └─base::stop("Provided file is not a .cool/.mcool file.\n  Aborting now.")
  9. └─base::.handleSimpleError(...)
 10.   └─base (local) h(simpleError(msg, call))
── Error ('test-aggrHicExperiment.R:3:5'): AggrHiCExperiment methods work ──────
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