Build/check report for BioC 3.23 - CHECK results for GEOquery on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4852
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for GEOquery on nebbiolo1

To the developers/maintainers of the GEOquery package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GEOquery.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: GEOquery

Version: 2.79.0

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

StartedAt: 2026-02-01 23:57:45 -0500 (Sun, 01 Feb 2026)

EndedAt: 2026-02-02 00:01:52 -0500 (Mon, 02 Feb 2026)

EllapsedTime: 247.4 seconds

RetCode: 1

Status: ERROR

CheckDir: GEOquery.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GEOquery.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 24.04.3 LTS
* using session charset: UTF-8
* 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 5.235  0.482   8.855
getGEO        4.337  0.224   5.684
* 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:
    6.         │ ├─rlang::eval_bare(...)
    7.         │ ├─base::tryCatch(...)
    8.         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11.         │ └─base::force(expr)
   12.         └─rlang::abort(...)
  ── Failure ('test_supp_files.R:16:5'): GSM Supplemental files downloading to baseDir works ──
  Expected `nrow(res)` to be equivalent to 1.
  target is NULL, current is numeric
  
  [ FAIL 17 | WARN 0 | SKIP 0 | PASS 64 ]
  Error:
  ! Test failures.
  Execution halted
* 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
[31m

processing file: GEOquery.qmd
[39m[31mHTTP 403 Forbidden.[39m[31mError in `downloadFile()`:
! Failed to download /tmp/RtmpDYnd5I/GSE2553_series_matrix.txt.gz!
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE2553")
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
[39m[31m
Quitting from GEOquery.qmd:75-79 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `downloadFile()`:
! Failed to download /tmp/RtmpDYnd5I/GSE2553_series_matrix.txt.gz!
---
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE2553")
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[39m[31mExecution halted
[39m[33mWARN: Error encountered when rendering files[39m
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
  [31mHTTP 403 Forbidden.Error in `downloadFile()`:[39m
  ! Failed to download /tmp/RtmpDYnd5I/GSE2553_series_matrix.txt.gz!
  Backtrace:
  ▆
  1. └─GEOquery::getGEO("GSE2553")
  2.  └─GEOquery:::getAndParseGSEMatrices(...)
  3.  └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  
  Quitting from GEOquery.qmd:75-79 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `downloadFile()`:
  ! Failed to download /tmp/RtmpDYnd5I/GSE2553_series_matrix.txt.gz!
  ---
  Backtrace:
  ▆
  1. └─GEOquery::getGEO("GSE2553")
  2.  └─GEOquery:::getAndParseGSEMatrices(...)
  3.  └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  [31mExecution halted[39m
  [33mWARN: Error encountered when rendering files[39m
  
Caused by error:
! System command 'quarto' failed
--- failed re-building ‘GEOquery.qmd’

--- re-building ‘single-cell.qmd’ using html
[31m

processing file: single-cell.qmd
[39m[31moutput file: single-cell.knit.md

[39m[1mpandoc [22m
  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: {}
  
[1mmetadata[22m
  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: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/GEOquery.Rcheck/00check.log’
for details.

Installation output

GEOquery.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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)

Tests output

GEOquery.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2026-01-15 r89304) -- "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")
Saving _problems/test_GSE-6.R
Saving _problems/test_GSE-15.R
Saving _problems/test_GSE-21.R
Saving _problems/test_GSE-28.R
Saving _problems/test_GSE-34.R
Saving _problems/test_GSE-47.R
Saving _problems/test_GSE-55.R
Saving _problems/test_GSE-69.R
Saving _problems/test_GSE-102.R
Saving _problems/test_GSE-109.R
Saving _problems/test_GSE-115.R
Saving _problems/test_fetch_GPL_false-5.R
Saving _problems/test_fetch_GPL_false-14.R
Saving _problems/test_geo_rnaseq-62.R
Saving _problems/test_supp_files-5.R
Saving _problems/test_supp_files-10.R
Saving _problems/test_supp_files-16.R
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 64 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_GSE.R:6:5'): empty GSE is handled correctly ────────────────────
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE11413") at test_GSE.R:6:5
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_GSE.R:15:5'): case-mismatched IDs in GSEs handled correctly ────
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE35683") at test_GSE.R:15:5
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_GSE.R:21:5'): single-sample GSE handled correctly ──────────────
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE11595") at test_GSE.R:21:5
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_GSE.R:28:5'): short GSE handled correctly ──────────────────────
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE34145") at test_GSE.R:28:5
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_GSE.R:34:5'): generic SOFT format GSE handled correctly ────────
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE1563", GSEMatrix = FALSE) at test_GSE.R:34:5
  2.   └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
  3.     └─GEOquery:::downloadFile(myurl, destfile, mode)
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_GSE.R:47:3'): GSE with more than one value per characteristic handled ──
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE71989") at test_GSE.R:47:3
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_GSE.R:55:3'): GSE has populated experimentData ─────────────────
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE53986") at test_GSE.R:55:3
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_GSE.R:69:3'): GSE populates experimentData as much as possible ──
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE99709") at test_GSE.R:69:3
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_GSE.R:102:3'): GSE/GPL with integer64 columns handled correctly ──
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE7864") at test_GSE.R:102:3
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_GSE.R:109:3'): Test regression against issue 144 ───────────────
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE225759") at test_GSE.R:109:3
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_GSE.R:115:3'): GSE425 parsing with malformed sample lines ──────
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE425") at test_GSE.R:115:3
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_fetch_GPL_false.R:5:5'): GSE without GPL works ─────────────────
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE2553", getGPL = FALSE) at test_fetch_GPL_false.R:5:5
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_fetch_GPL_false.R:14:5'): GDS without GPL works ────────────────
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GDS10") at test_fetch_GPL_false.R:14:5
  2.   └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
  3.     └─GEOquery:::downloadFile(myurl, destfile, mode)
  4.       ├─base::tryCatch(...)
  5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8.       └─httr2::req_perform(req)
  9.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.             ├─rlang::catch_cnd(...)
 12.             │ ├─rlang::eval_bare(...)
 13.             │ ├─base::tryCatch(...)
 14.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.             │ └─base::force(expr)
 18.             └─rlang::abort(...)
── Error ('test_geo_rnaseq.R:62:3'): getRNASeqData returns SummarizedExperiment ──
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getRNASeqData(gse) at test_geo_rnaseq.R:62:3
  2.   ├─methods::as(getGEO(accession)[[1]], "SummarizedExperiment")
  3.   │ └─methods:::.class1(object)
  4.   └─GEOquery::getGEO(accession)
  5.     └─GEOquery:::getAndParseGSEMatrices(...)
  6.       └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  7.         ├─base::tryCatch(...)
  8.         │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.         │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.         │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11.         └─httr2::req_perform(req)
 12.           └─httr2:::handle_resp(req, resp, error_call = error_call)
 13.             └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 14.               ├─rlang::catch_cnd(...)
 15.               │ ├─rlang::eval_bare(...)
 16.               │ ├─base::tryCatch(...)
 17.               │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 18.               │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 19.               │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 20.               │ └─base::force(expr)
 21.               └─rlang::abort(...)
── Error ('test_supp_files.R:5:5'): GSE Supplemental files downloading works ───
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(httr2::req_url_query(httr2::req_url_path_append(httr2::request(base_url = url), i), tool = "geoquery"), path = destfile)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEOSuppFiles("GSE1000") at test_supp_files.R:5:5
  2.   └─httr2::req_perform(...)
  3.     └─httr2:::handle_resp(req, resp, error_call = error_call)
  4.       └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
  5.         ├─rlang::catch_cnd(...)
  6.         │ ├─rlang::eval_bare(...)
  7.         │ ├─base::tryCatch(...)
  8.         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11.         │ └─base::force(expr)
 12.         └─rlang::abort(...)
── Error ('test_supp_files.R:10:5'): GSM Supplemental files downloading works ──
<httr2_http_403/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(httr2::req_url_query(httr2::req_url_path_append(httr2::request(base_url = url), i), tool = "geoquery"), path = destfile)`: HTTP 403 Forbidden.
Backtrace:
     ▆
  1. └─GEOquery::getGEOSuppFiles("GSM15789") at test_supp_files.R:10:5
  2.   └─httr2::req_perform(...)
  3.     └─httr2:::handle_resp(req, resp, error_call = error_call)
  4.       └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
  5.         ├─rlang::catch_cnd(...)
  6.         │ ├─rlang::eval_bare(...)
  7.         │ ├─base::tryCatch(...)
  8.         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11.         │ └─base::force(expr)
 12.         └─rlang::abort(...)
── Failure ('test_supp_files.R:16:5'): GSM Supplemental files downloading to baseDir works ──
Expected `nrow(res)` to be equivalent to 1.
target is NULL, current is numeric

[ FAIL 17 | WARN 0 | SKIP 0 | PASS 64 ]
Error:
! Test failures.
Execution halted

Example timings

GEOquery.Rcheck/GEOquery-Ex.timings

name	user	system	elapsed
browseGEOAccession	0.001	0.000	0.000
browseWebsiteRNASeqSearch	0	0	0
coercion	0	0	0
getGEO	4.337	0.224	5.684
getGEOSeriesFileListing	0.447	0.074	0.558
getGEOSuppFileURL	0.001	0.000	0.000
getGEOSuppFiles	0.090	0.002	0.137
getGEOfile	0.000	0.000	0.001
getGSEDataTables	0.246	0.040	0.410
getRNASeqData	5.235	0.482	8.855
getRNASeqQuantGenomeInfo	0.011	0.001	0.067
hasRNASeqQuantifications	0.011	0.000	0.069
searchFieldsGEO	0.071	0.005	0.513
searchGEO	0.001	0.000	0.000
urlForAccession	0	0	0