##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GEOquery_2.79.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GEOquery.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-27 04:59:00 UTC
* checking for file ‘GEOquery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEOquery’ version ‘2.79.0’
* 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 ... INFO
  installed size is 13.3Mb
  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 ... NOTE
Argument items with no description in Rd file 'getGEOSuppFileURL.Rd':
  ‘GEO’
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
getRNASeqData 5.053  0.351   9.745
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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.qmd’ using html


processing file: GEOquery.qmd
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
  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
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

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

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/GEOquery.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GEOquery
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘GEOquery’ ...
** this is package ‘GEOquery’ version ‘2.79.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GEOquery)

R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(GEOquery)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("GEOquery")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 242 ]
> 
> proc.time()
   user  system elapsed 
 68.979   9.823 113.634