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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GEOquery_2.78.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GEOquery.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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
* checking for file ‘GEOquery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEOquery’ version ‘2.78.0’
* 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 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘GEOquery.qmd’ ‘single-cell.qmd’
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/GEOquery.qmd’
   ‘vignettes/single-cell.qmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
getRNASeqData 5.163  0.532    9.26
getGEO        3.909  0.155    5.26
* 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:
   15. │             └─curl::curl_download(url, local_path, quiet = !show_progress)
   16. ├─curl:::raise_libcurl_error(...)
   17. │ └─base::stop(e)
   18. ├─rlang (local) `<fn>`(`<crl_r___>`)
   19. │ └─handlers[[1L]](cnd)
   20. │   └─cli::cli_abort(...)
   21. │     └─rlang::abort(...)
   22. │       └─rlang:::signal_abort(cnd, .file)
   23. │         └─base::signalCondition(cnd)
   24. └─base (local) `<fn>`(`<rlng_rrr>`)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 235 ]
  Error:
  ! Test failures.
  Execution halted
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GEOquery.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GEOquery
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GEOquery’ ...
** this is package ‘GEOquery’ version ‘2.78.0’
** 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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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_geo_rnaseq-43.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 235 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_geo_rnaseq.R:43:3'): readRNAQuantAnnotation returns data.frame ──
Error in `(function (cond)  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = structure("Failed to download <https://www.ncbi.nlm.nih.gov/geo/download/?format=file&type=rnaseq_counts&file=Human.GRCh38.p13.annot.tsv.gz>.", names = ""), trace = structure(list(call = list(readRNAQuantAnnotation(link), as.data.frame(readr::read_tsv(link, show_col_types = FALSE)), readr::read_tsv(link, show_col_types = FALSE), vroom::vroom(file, delim = "\t", col_names = col_names, col_types = col_types, col_select = {     {         col_select     } }, id = id, .name_repair = name_repair, skip = skip, n_max = n_max, na = na, quote = quote, comment = comment, skip_empty_rows = skip_empty_rows, trim_ws = trim_ws, escape_double = TRUE, escape_backslash = FALSE, locale = locale, guess_max = guess_max, show_col_types = show_col_types, progress = progress, altrep = lazy, num_threads = num_threads), standardise_path(file), lapply(path, function(p) {     ext <- tolower(tools::file_ext(p))     local_path <- download_file(p, ext, call = call)     withr::defer(unlink(local_path), envir = call)     switch(ext, gz = gzfile(local_path), bz2 = bzfile(local_path), xz = xzfile(local_path), zip = zipfile(local_path)) }), FUN(X[[i]], ...), download_file(p, ext, call = call), try_fetch(if (requireNamespace("curl", quietly = TRUE)) {     curl::curl_download(url, local_path, quiet = !show_progress) } else {     utils::download.file(url, local_path, mode = "wb", quiet = !show_progress) }, error = function(cnd) {     unlink(local_path)     cli::cli_abort(c("Failed to download {.url {url}}.", x = conditionMessage(cnd)), parent = NA, error = cnd, call = call) }), tryCatch(withCallingHandlers(expr, condition = function(cnd) {     {         .__handler_frame__. <- TRUE         .__setup_frame__. <- frame         if (inherits(cnd, "message")) {             except <- c("warning", "error")         }         else if (inherits(cnd, "warning")) {             except <- "error"         }         else {             except <- ""         }     }     while (!is_null(cnd)) {         if (inherits(cnd, "error")) {             out <- handlers[[1L]](cnd)             if (!inherits(out, "rlang_zap"))                  throw(out)         }         inherit <- .subset2(.subset2(cnd, "rlang"), "inherit")         if (is_false(inherit)) {             return()         }         cnd <- .subset2(cnd, "parent")     } }), stackOverflowError = handlers[[1L]]), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(expr, names, parentenv, handlers[[1L]]), doTryCatch(return(expr), name, parentenv, handler), withCallingHandlers(expr, condition = function(cnd) {     {         .__handler_frame__. <- TRUE         .__setup_frame__. <- frame         if (inherits(cnd, "message")) {             except <- c("warning", "error")         }         else if (inherits(cnd, "warning")) {             except <- "error"         }         else {             except <- ""         }     }     while (!is_null(cnd)) {         if (inherits(cnd, "error")) {             out <- handlers[[1L]](cnd)             if (!inherits(out, "rlang_zap"))                  throw(out)         }         inherit <- .subset2(.subset2(cnd, "rlang"), "inherit")         if (is_false(inherit)) {             return()         }         cnd <- .subset2(cnd, "parent")     } }), curl::curl_download(url, local_path, quiet = !show_progress), raise_libcurl_error(22L, "HTTP response code said error", "The requested URL returned error: 500", "https://www.ncbi.nlm.nih.gov/geo/download/?format=file&type=rnaseq_counts&file=Human.GRCh38.p13.annot.tsv.gz", NULL), stop(e), `<fn>`(`<crl_r___>`), handlers[[1L]](cnd), cli::cli_abort(c("Failed to download {.url {url}}.", x = conditionMessage(cnd)), parent = NA, error = cnd, call = call), rlang::abort(message, ..., call = call, use_cli_format = TRUE,      .frame = .frame)), parent = c(0L, 1L, 1L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 9L, 8L, 0L, 16L, 0L, 18L, 19L, 20L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE), namespace = c("GEOquery", "BiocGenerics", "readr", "vroom", "vroom", "base", "vroom", "vroom", "rlang", "base", "base", "base", "base", "base", "curl", "curl", "base", "rlang", NA, "cli", "rlang"), scope = c(":::", "::", "::", "::",  ":::", "::", "local", ":::", "::", "::", "local", "local", "local", "::", "::", ":::", "::", "local", NA, "::", "::"), error_frame = c(FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE)), row.names = c(NA, -21L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = NULL, error = structure(list(message = "HTTP response code said error [www.ncbi.nlm.nih.gov]:\nThe requested URL returned error: 500",      call = curl::curl_download(url, local_path, quiet = !show_progress)), class = c("curl_error_http_returned_error", "curl_error", "error", "condition")), body = c(x = "HTTP response code said error [www.ncbi.nlm.nih.gov]:\nThe requested URL returned error: 500"), rlang = list(inherit = TRUE), call = vroom::vroom(file, delim = "\t", col_names = col_names, col_types = col_types, col_select = {     {         col_select     } }, id = id, .name_repair = name_repair, skip = skip, n_max = n_max, na = na, quote = quote, comment = comment, skip_empty_rows = skip_empty_rows, trim_ws = trim_ws, escape_double = TRUE, escape_backslash = FALSE, locale = locale, guess_max = guess_max, show_col_types = show_col_types, progress = progress, altrep = lazy, num_threads = num_threads), use_cli_format = TRUE), class = c("rlang_error", "error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': Failed to download
<https://www.ncbi.nlm.nih.gov/geo/download/?format=file&type=rnaseq_counts&file=Human.GRCh38.p13.annot.tsv.gz>.
✖ HTTP response code said error [www.ncbi.nlm.nih.gov]: The requested URL
  returned error: 500
Backtrace:
     ▆
  1. ├─GEOquery:::readRNAQuantAnnotation(link) at test_geo_rnaseq.R:43:3
  2. │ ├─BiocGenerics::as.data.frame(readr::read_tsv(link, show_col_types = FALSE))
  3. │ └─readr::read_tsv(link, show_col_types = FALSE)
  4. │   └─vroom::vroom(...)
  5. │     └─vroom:::standardise_path(file)
  6. │       └─base::lapply(...)
  7. │         └─vroom (local) FUN(X[[i]], ...)
  8. │           └─vroom:::download_file(p, ext, call = call)
  9. │             ├─rlang::try_fetch(...)
 10. │             │ ├─base::tryCatch(...)
 11. │             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12. │             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13. │             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 14. │             │ └─base::withCallingHandlers(...)
 15. │             └─curl::curl_download(url, local_path, quiet = !show_progress)
 16. ├─curl:::raise_libcurl_error(...)
 17. │ └─base::stop(e)
 18. ├─rlang (local) `<fn>`(`<crl_r___>`)
 19. │ └─handlers[[1L]](cnd)
 20. │   └─cli::cli_abort(...)
 21. │     └─rlang::abort(...)
 22. │       └─rlang:::signal_abort(cnd, .file)
 23. │         └─base::signalCondition(cnd)
 24. └─base (local) `<fn>`(`<rlng_rrr>`)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 235 ]
Error:
! Test failures.
Execution halted