##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GEOquery.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings GEOquery_2.77.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/GEOquery.Rcheck'
* using R version 4.5.0 (2025-04-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GEOquery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOquery' version '2.77.0'
* 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 whether package 'GEOquery' can be installed ... OK
* checking installed package size ... INFO
  installed size is 13.2Mb
  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 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 ... OK
* 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
getGEO        6.19   2.77   13.86
getRNASeqData 6.74   0.40   16.91
* 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:
    9.     ├─rvest::html_attr(...)
   10.     │ └─xml2::xml_attr(x, name, default = default)
   11.     ├─rvest::html_nodes(...)
   12.     │ └─rvest::html_elements(...)
   13.     ├─rvest::read_html(...)
   14.     ├─httr2::resp_body_string(...)
   15.     │ └─httr2:::check_response(resp)
   16.     │   └─httr2:::is_response(resp)
   17.     └─httr2::req_perform(...)
   18.       └─httr2:::handle_resp(req, resp, error_call = error_call)
   19.         └─rlang::cnd_signal(resp)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 234 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/GEOquery.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL GEOquery
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'GEOquery' ...
** this is package 'GEOquery' version '2.77.0'
** 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 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl//GSE1000_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 35307520 bytes (33.7 MB)
==================================================
downloaded 33.7 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz?tool=geoquery'
Content type 'application/x-gzip' length 3507725 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz?tool=geoquery'
Content type 'application/x-gzip' length 3507725 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 234 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_geo_rnaseq.R:52:3'): getRNASeqQuantResults returns list ────────
<httr2_failure/httr2_error/rlang_error/error/condition>
Error in `httr2::req_perform(httr2::req_url_query(httr2::req_retry(httr2::req_timeout(httr2::request(url), 
    15), 3), acc = gse))`: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Could not connect to server [www.ncbi.nlm.nih.gov]: Failed to connect to www.ncbi.nlm.nih.gov port 443 after 9556 ms: Could not connect to server
Backtrace:
     ▆
  1. └─GEOquery:::getRNASeqQuantResults(gse) at test_geo_rnaseq.R:52:3
  2.   └─GEOquery:::getGSEDownloadPageURLs(gse)
  3.     ├─stringr::str_replace(...)
  4.     │ └─stringr:::check_lengths(string, pattern, replacement)
  5.     │   └─vctrs::vec_size_common(...)
  6.     ├─stringr::str_replace(...)
  7.     │ └─stringr:::check_lengths(string, pattern, replacement)
  8.     │   └─vctrs::vec_size_common(...)
  9.     ├─rvest::html_attr(...)
 10.     │ └─xml2::xml_attr(x, name, default = default)
 11.     ├─rvest::html_nodes(...)
 12.     │ └─rvest::html_elements(...)
 13.     ├─rvest::read_html(...)
 14.     ├─httr2::resp_body_string(...)
 15.     │ └─httr2:::check_response(resp)
 16.     │   └─httr2:::is_response(resp)
 17.     └─httr2::req_perform(...)
 18.       └─httr2:::handle_resp(req, resp, error_call = error_call)
 19.         └─rlang::cnd_signal(resp)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 234 ]
Error: Test failures
Execution halted