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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:healthyControlsPresenceChecker.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings healthyControlsPresenceChecker_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/healthyControlsPresenceChecker.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘healthyControlsPresenceChecker/DESCRIPTION’ ... OK
* this is package ‘healthyControlsPresenceChecker’ version ‘1.14.0’
* 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 ‘healthyControlsPresenceChecker’ 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 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  
   
  1 Test Suite : 
  healthyControlsPresenceChecker RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in test_healthyControlsCheck: Error in open.connection(x, "rb") : cannot open the connection
  
  Test files with failing tests
  
     test_healthyControlsPresenceChecker.R 
       test_healthyControlsCheck 
  
  
  Error in BiocGenerics:::testPackage("healthyControlsPresenceChecker") : 
    unit tests failed for package healthyControlsPresenceChecker
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘healthyControlsPresenceChecker.Rmd’ using rmarkdown

Quitting from healthyControlsPresenceChecker.Rmd:68-70 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection
---
Backtrace:
     ▆
  1. └─healthyControlsPresenceChecker::healthyControlsCheck(...)
  2.   ├─xml2::read_html("https://ftp.ncbi.nlm.nih.gov/geo/series/")
  3.   └─xml2:::read_html.default("https://ftp.ncbi.nlm.nih.gov/geo/series/")
  4.     ├─base::suppressWarnings(...)
  5.     │ └─base::withCallingHandlers(...)
  6.     ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
  7.     └─xml2:::read_xml.character(...)
  8.       └─xml2:::read_xml.connection(...)
  9.         ├─base::open(x, "rb")
 10.         └─base::open.connection(x, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'healthyControlsPresenceChecker.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘healthyControlsPresenceChecker.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/healthyControlsPresenceChecker.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL healthyControlsPresenceChecker
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘healthyControlsPresenceChecker’ ...
** this is package ‘healthyControlsPresenceChecker’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (healthyControlsPresenceChecker)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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.

> BiocGenerics:::testPackage("healthyControlsPresenceChecker")
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE19nnn/GSE19429
Timing stopped at: 0.216 0.01 0.916
Error in open.connection(x, "rb") : cannot open the connection


RUNIT TEST PROTOCOL -- Tue Nov  4 12:26:02 2025 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
healthyControlsPresenceChecker RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test_healthyControlsCheck: Error in open.connection(x, "rb") : cannot open the connection

Test files with failing tests

   test_healthyControlsPresenceChecker.R 
     test_healthyControlsCheck 


Error in BiocGenerics:::testPackage("healthyControlsPresenceChecker") : 
  unit tests failed for package healthyControlsPresenceChecker
Execution halted