##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:phantasusLite.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings phantasusLite_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/phantasusLite.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'phantasusLite/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phantasusLite' version '1.3.0'
* 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 '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 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: inferCondition
> ### Title: Adds condition to the annotation.
> ### Aliases: inferCondition
> 
> ### ** Examples
> 
> ess <- GEOquery::getGEO("GSE143903")
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error in open.connection(x, "rb") : HTTP error 403.
Calls: <Anonymous> ... getAndParseGSEMatrices -> getDirListing -> <Anonymous> -> read_html.default
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 3 | WARN 0 | SKIP 0 | PASS 20 ]
  Error: Test failures
  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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/phantasusLite.Rcheck/00check.log'
for details.