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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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Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Failure when receiving data from the peer [ftp.ncbi.nlm.nih.gov]: OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 0Error in downloadFile(url, destfile = destfile, mode = "wb") : 
  Failed to download /home/biocbuild/tmp/RtmpDJkl2J/GSE2553_series_matrix.txt.gz!
Calls: .main ... eval -> getGEO -> getAndParseGSEMatrices -> downloadFile

Quitting from GEOquery.qmd:75-79 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `downloadFile()`:
! Failed to download /home/biocbuild/tmp/RtmpDJkl2J/GSE2553_series_matrix.txt.gz!
---
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE2553")
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
Error: processing vignette 'GEOquery.qmd' failed with diagnostics:
✖ Error running quarto cli.
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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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-devel_2025-02-19/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