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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘GEOquery.qmd’ using html


processing file: GEOquery.qmd
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12/47 [tbl-search-fields] 
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14/47 [tbl-example-search]
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38/47 [unnamed-chunk-16]  
Error in `open.connection()`:
! cannot open the connection
Backtrace:
    ▆
 1. └─GEOquery::getGSEDataTables("GSE3494")
 2.   ├─xml2::read_xml(url)
 3.   └─xml2:::read_xml.character(url)
 4.     └─xml2:::read_xml.connection(...)
 5.       ├─base::open(x, "rb")
 6.       └─base::open.connection(x, "rb")

Quitting from GEOquery.qmd:252-257 [unnamed-chunk-16]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─GEOquery::getGSEDataTables("GSE3494")
 2.   ├─xml2::read_xml(url)
 3.   └─xml2:::read_xml.character(url)
 4.     └─xml2:::read_xml.connection(...)
 5.       ├─base::open(x, "rb")
 6.       └─base::open.connection(x, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
WARN: Error encountered when rendering files
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]
  17/47
  18/47 [unnamed-chunk-6]
  19/47
  20/47 [unnamed-chunk-7]
  21/47
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  35/47
  36/47 [unnamed-chunk-15]
  37/47
  38/47 [unnamed-chunk-16]
  Error in `open.connection()`:
  ! cannot open the connection
  Backtrace:
  ▆
  1. └─GEOquery::getGSEDataTables("GSE3494")
  2.  ├─xml2::read_xml(url)
  3.  └─xml2:::read_xml.character(url)
  4.  └─xml2:::read_xml.connection(...)
  5.  ├─base::open(x, "rb")
  6.  └─base::open.connection(x, "rb")
  
  Quitting from GEOquery.qmd:252-257 [unnamed-chunk-16]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `open.connection()`:
  ! cannot open the connection
  ---
  Backtrace:
  ▆
  1. └─GEOquery::getGSEDataTables("GSE3494")
  2.  ├─xml2::read_xml(url)
  3.  └─xml2:::read_xml.character(url)
  4.  └─xml2:::read_xml.connection(...)
  5.  ├─base::open(x, "rb")
  6.  └─base::open.connection(x, "rb")
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Execution halted
  WARN: Error encountered when rendering files
  
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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21/22 [unnamed-chunk-11]
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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/bbs-3.23-bioc/R/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