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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data GEOquery
###
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* checking for file ‘GEOquery/DESCRIPTION’ ... OK
* preparing ‘GEOquery’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GEOquery.qmd’ using html


processing file: GEOquery.qmd
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2/47 [setup]             
3/47                     
4/47 [unnamed-chunk-1]   
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11/47                     
12/47 [tbl-search-fields] 
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14/47 [tbl-example-search]
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16/47 [unnamed-chunk-5]   
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 15000 milliseconds
Backtrace:
     ▆
  1. └─GEOquery::hasRNASeqQuantifications("GSE164073")
  2.   └─GEOquery:::getGSEDownloadPageURLs(accession)
  3.     ├─stringr::str_replace(...)
  4.     │ └─stringr:::check_lengths(string, pattern, replacement)
  5.     │   └─vctrs::vec_size_common(...)
  6.     ├─stringr::str_replace(...)
  7.     │ └─stringr:::check_lengths(string, pattern, replacement)
  8.     │   └─vctrs::vec_size_common(...)
  9.     ├─rvest::html_attr(...)
 10.     │ └─xml2::xml_attr(x, name, default = default)
 11.     ├─rvest::html_nodes(...)
 12.     │ └─rvest::html_elements(...)
 13.     ├─rvest::read_html(...)
 14.     ├─httr2::resp_body_string(...)
 15.     │ └─httr2:::check_response(resp)
 16.     │   └─httr2:::is_response(resp)
 17.     └─httr2::req_perform(...)
 18.       └─httr2:::handle_resp(req, resp, error_call = error_call)
 19.         └─rlang::cnd_signal(resp)

Quitting from GEOquery.qmd:142-146 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
Error: processing vignette 'GEOquery.qmd' failed with diagnostics:
! Error running quarto CLI from R.
Caused by error in `quarto_render()`:
✖ Error returned by quarto CLI.
  -----------------------------
  
  
  processing file: GEOquery.qmd
  1/47
  2/47 [setup]
  3/47
  4/47 [unnamed-chunk-1]
  5/47
  6/47 [unnamed-chunk-2]
  7/47
  8/47 [unnamed-chunk-3]
  9/47
  10/47 [unnamed-chunk-4]
  11/47
  12/47 [tbl-search-fields]
  13/47
  14/47 [tbl-example-search]
  15/47
  16/47 [unnamed-chunk-5]
  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 15000 milliseconds
  Backtrace:
  ▆
  1. └─GEOquery::hasRNASeqQuantifications("GSE164073")
  2.  └─GEOquery:::getGSEDownloadPageURLs(accession)
  3.  ├─stringr::str_replace(...)
  4.  │ └─stringr:::check_lengths(string, pattern, replacement)
  5.  │ └─vctrs::vec_size_common(...)
  6.  ├─stringr::str_replace(...)
  7.  │ └─stringr:::check_lengths(string, pattern, replacement)
  8.  │ └─vctrs::vec_size_common(...)
  9.  ├─rvest::html_attr(...)
  10.  │ └─xml2::xml_attr(x, name, default = default)
  11.  ├─rvest::html_nodes(...)
  12.  │ └─rvest::html_elements(...)
  13.  ├─rvest::read_html(...)
  14.  ├─httr2::resp_body_string(...)
  15.  │ └─httr2:::check_response(resp)
  16.  │ └─httr2:::is_response(resp)
  17.  └─httr2::req_perform(...)
  18.  └─httr2:::handle_resp(req, resp, error_call = error_call)
  19.  └─rlang::cnd_signal(resp)
  
  Quitting from GEOquery.qmd:142-146 [unnamed-chunk-5]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Execution halted
  
Caused by error:
! System command 'quarto' failed
--- failed re-building ‘GEOquery.qmd’

--- re-building ‘single-cell.qmd’ using html


processing file: single-cell.qmd
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18/22                   
19/22 [unnamed-chunk-10]
20/22                   
21/22 [unnamed-chunk-11]
22/22                   
output file: single-cell.knit.md

pandoc 
  to: html
  output-file: single-cell.html
  standalone: true
  embed-resources: true
  wrap: none
  default-image-extension: png
  css:
    - >-
      /home/biocbuild/R/R-4.5.0/site-library/quarto/rmarkdown/template/quarto_vignette/resources/vignette.css
  toc: true
  variables: {}
  
metadata
  document-css: false
  lang: en
  minimal: true
  theme: none
  title: Handling single-cell RNA-seq data in GEOquery
  author: Sean Davis
  date: '2025-08-29'
  last-modified:
    '[object Object]': null
  vignette: |
    %\VignetteIndexEntry{Handling single-cell RNA-seq data in GEOquery} %\VignetteEngine{quarto::html} %\VignetteEncoding{UTF-8}
  
Output created: single-cell.html

--- finished re-building ‘single-cell.qmd’

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

Error: Vignette re-building failed.
Execution halted