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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GEOquery_2.74.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GEOquery.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 ‘GEOquery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEOquery’ version ‘2.74.0’
* 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 ‘GEOquery’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.2Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘curl’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘GEOquery/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("Setting options('download.file.method.GEOquery'='auto')")
    packageStartupMessage("Setting options('GEOquery.inmemory.gpl'=FALSE)")

See section ‘Good practice’ in '?.onAttach'.

.parseGPLTxt: no visible global function definition for ‘new’
.parseGPLWithLimits: no visible global function definition for ‘new’
.parseGSMTxt: no visible global function definition for ‘new’
.parseGSMWithLimits: no visible global function definition for ‘new’
GDS2MA: no visible global function definition for ‘new’
GDS2MA: no visible binding for global variable ‘MA’
GDS2eSet: no visible global function definition for ‘new’
browseGEOAccession: no visible global function definition for
  ‘browseURL’
browseWebsiteRNASeqSearch: no visible global function definition for
  ‘browseURL’
fastTabRead: no visible global function definition for ‘read.table’
fastTabRead: no visible global function definition for ‘read.delim’
getRNASeqData: no visible global function definition for ‘as’
parseGDS: no visible global function definition for ‘new’
parseGSE: no visible global function definition for ‘new’
parseGSEMatrix: no visible global function definition for ‘new’
parseGSEMatrix: no visible binding for global variable ‘.’
parseGSEMatrix: no visible binding for global variable
  ‘characteristics’
parseGSEMatrix: no visible binding for global variable ‘kvpair’
parseGSEMatrix: no visible binding for global variable ‘accession’
parseGSEMatrix: no visible binding for global variable ‘k’
parseGSEMatrix: no visible binding for global variable ‘v’
parseGSEMatrix: no visible global function definition for ‘read.table’
parseGSEMatrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  . MA accession as browseURL characteristics k kvpair new read.delim
  read.table v
Consider adding
  importFrom("methods", "as", "new")
  importFrom("utils", "browseURL", "read.delim", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ‘GEOquery-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGEO
> ### Title: Get a GEO object from NCBI or file
> ### Aliases: getGEO
> ### Keywords: IO
> 
> ### ** Examples
> 
> 
> gds <- getGEO('GDS10')
HTTP 403 Forbidden.File stored at:
/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDk0btO/GDS10.soft.gz
Error in downloadFile(myurl, destfile, mode) : 
  Failed to download /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDk0btO/GDS10.soft.gz!
Calls: 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:
  nrow(res) not equivalent to 12.
  target is NULL, current is numeric
  ── Failure ('test_supp_files.R:22:5'): GSE supplemental file no-download works ──
  ncol(res) not equivalent to 2.
  target is NULL, current is numeric
  ── Failure ('test_supp_files.R:27:5'): GSE Supplemental file filtering works ───
  ncol(res) not equivalent to 2.
  target is NULL, current is numeric
  ── Failure ('test_supp_files.R:28:5'): GSE Supplemental file filtering works ───
  nrow(res) not equivalent to 4.
  target is NULL, current is numeric
  
  [ FAIL 12 | WARN 0 | SKIP 0 | PASS 208 ]
  Error: Test failures
  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 ‘GEOquery.Rmd’ using rmarkdown

Quitting from GEOquery.Rmd:134-139 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GEOquery.Rmd' failed with diagnostics:
HTTP 404 Not Found.
--- failed re-building ‘GEOquery.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/GEOquery.Rcheck/00check.log’
for details.