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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiCExperiment.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiCExperiment_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HiCExperiment.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘HiCExperiment/DESCRIPTION’ ... OK
* this is package ‘HiCExperiment’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES'
 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 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 loading without being on the library search path ... 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: 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')
Error in value[[3L]](cond) : failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
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:
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─HiContactsData::HiContactsData("yeast_wt", "cool") at ./setup.R:3:1
   15. │                         └─ExperimentHub::ExperimentHub()
   16. │                           └─AnnotationHub::.Hub(...)
   17. │                             └─base::tryCatch(...)
   18. │                               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   19. │                                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   20. │                                   └─value[[3L]](cond)
   21. │                                     └─base::stop(...)
   22. └─base::.handleSimpleError(...)
   23.   └─testthat (local) h(simpleError(msg, call))
   24.     └─cli::cli_abort(...)
   25.       └─rlang::abort(...)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/HiCExperiment.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL HiCExperiment
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘HiCExperiment’ ...
** this is package ‘HiCExperiment’ version ‘1.10.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
Error in `source_dir()`:
! Failed to evaluate './setup.R'.
Caused by error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
     ▆
  1. ├─testthat::test_check("HiCExperiment")
  2. │ └─testthat::test_dir(...)
  3. │   └─testthat:::test_files(...)
  4. │     └─testthat:::test_files_serial(...)
  5. │       └─testthat:::test_files_setup_state(...)
  6. │         └─testthat::source_test_setup(".", env)
  7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
  8. │             └─base::lapply(...)
  9. │               └─testthat (local) FUN(X[[i]], ...)
 10. │                 └─testthat::source_file(...)
 11. │                   ├─base::withCallingHandlers(...)
 12. │                   └─base::eval(exprs, env)
 13. │                     └─base::eval(exprs, env)
 14. │                       └─HiContactsData::HiContactsData("yeast_wt", "cool") at ./setup.R:3:1
 15. │                         └─ExperimentHub::ExperimentHub()
 16. │                           └─AnnotationHub::.Hub(...)
 17. │                             └─base::tryCatch(...)
 18. │                               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 19. │                                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 20. │                                   └─value[[3L]](cond)
 21. │                                     └─base::stop(...)
 22. └─base::.handleSimpleError(...)
 23.   └─testthat (local) h(simpleError(msg, call))
 24.     └─cli::cli_abort(...)
 25.       └─rlang::abort(...)
Execution halted