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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:phantasusLite.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings phantasusLite_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/phantasusLite.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘phantasusLite/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phantasusLite’ version ‘1.4.0’
* 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 ‘phantasusLite’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘rhdf5client:::submitRequest’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getCountsMetaPart: no visible binding for global variable ‘file_name’
loadCountsFromH5FileHSDS: no visible binding for global variable
  ‘file_name’
loadCountsFromHSDS: no visible global function definition for ‘.’
loadCountsFromHSDS: no visible binding for global variable ‘directory’
loadCountsFromHSDS: no visible binding for global variable ‘accession’
loadCountsFromHSDS: no visible binding for global variable
  ‘collection_type’
updateARCHS4meta: no visible global function definition for ‘H5Fopen’
updateARCHS4meta: no visible global function definition for ‘H5Lexists’
updateIndexH5: no visible binding for global variable ‘list_dirs’
validateCountsCollection: no visible binding for global variable
  ‘file_name’
validateCountsCollection: no visible global function definition for
  ‘H5Lexists’
Undefined global functions or variables:
  . H5Fopen H5Lexists accession collection_type directory file_name
  list_dirs
* 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 ... ERROR
Running examples in ‘phantasusLite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loadCountsFromH5FileHSDS
> ### Title: Load count matrix from remote HDF5-file
> ### Aliases: loadCountsFromH5FileHSDS
> 
> ### ** Examples
> 
> ess <- GEOquery::getGEO("GSE53053")
Found 0 file(s)
NA
HTTP 404 Not Found.File stored at:
/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2MvpY2/NA
Error in downloadFile(url, destfile = destfile, mode = "wb") : 
  Failed to download /home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2MvpY2/NA!
Calls: <Anonymous> -> getAndParseGSEMatrices -> downloadFile
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:
    2.   └─GEOquery:::getAndParseGSEMatrices(...)
    3.     └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO))
    4.       ├─xml2::read_html(url)
    5.       └─xml2:::read_html.default(url)
    6.         ├─base::suppressWarnings(...)
    7.         │ └─base::withCallingHandlers(...)
    8.         ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
    9.         └─xml2:::read_xml.character(...)
   10.           └─xml2:::read_xml.connection(...)
   11.             ├─base::open(x, "rb")
   12.             └─base::open.connection(x, "rb")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 25 ]
  Error: Test failures
  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-3.20-bioc/meat/phantasusLite.Rcheck/00check.log’
for details.