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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --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: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: getRNASeqData
> ### Title: Get GEO RNA-seq quantifications as a SummarizedExperiment object
> ### Aliases: getRNASeqData
> 
> ### ** Examples
> 
> se <- getRNASeqData("GSE164073")
Error in `httr2::req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [ncbi.nlm.nih.gov]: Connection timed out after 15002 milliseconds
Backtrace:
     ▆
  1. └─GEOquery::getRNASeqData("GSE164073")
  2.   └─GEOquery:::getRNASeqQuantResults(accession)
  3.     └─GEOquery:::getGSEDownloadPageURLs(gse)
  4.       ├─stringr::str_replace(...)
  5.       │ └─stringr:::check_lengths(string, pattern, replacement)
  6.       │   └─vctrs::vec_size_common(...)
  7.       ├─stringr::str_replace(...)
  8.       │ └─stringr:::check_lengths(string, pattern, replacement)
  9.       │   └─vctrs::vec_size_common(...)
 10.       ├─rvest::html_attr(...)
 11.       │ └─xml2::xml_attr(x, name, default = default)
 12.       ├─rvest::html_nodes(...)
 13.       │ └─rvest::html_elements(...)
 14.       ├─rvest::read_html(...)
 15.       ├─httr2::resp_body_string(...)
 16.       │ └─httr2:::check_response(resp)
 17.       │   └─httr2:::is_response(resp)
 18.       └─httr2::req_perform(...)
 19.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 20.           └─rlang::cnd_signal(resp)
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 14 | WARN 0 | SKIP 0 | PASS 198 ]
  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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/GEOquery.Rcheck/00check.log’
for details.