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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phantasusLite.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phantasusLite_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/phantasusLite.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phantasusLite/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phantasusLite’ version ‘1.0.0’
* 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 ‘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 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 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
createIndexH5: no visible global function definition for ‘h5closeAll’
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
  h5closeAll 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)
Found 1 file(s)
GSE143903_series_matrix.txt.gz
HTTP error 404.File stored at:
/tmp/RtmpwAKeAd/GPL21493.soft.gz
Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE) : 
  Failed to download /tmp/RtmpwAKeAd/GPL21493.soft.gz!
Calls: <Anonymous> ... parseGSEMatrix -> getGEO -> getGEOfile -> 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:
       ▆
    1. └─GEOquery::getGEO("GSE85653", AnnotGPL = TRUE) at test-loadCountsFromH5file.R:36:3
    2.   └─GEOquery:::getAndParseGSEMatrices(...)
    3.     └─GEOquery:::parseGSEMatrix(...)
    4.       └─GEOquery::getGEO(GPL, AnnotGPL = AnnotGPL, destdir = destdir)
    5.         └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
    6.           └─GEOquery:::downloadFile(myurl, destfile, mode = mode, quiet = TRUE)
    7.             └─base::tryCatch(...)
    8.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.                   └─value[[3L]](cond)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 19 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/phantasusLite.Rcheck/00check.log’
for details.