##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GEOquery_2.74.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GEOquery.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘GEOquery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEOquery’ version ‘2.74.0’
* 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 ... NOTE
  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 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 ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GEOquery-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGEO
> ### Title: Get a GEO object from NCBI or file
> ### Aliases: getGEO
> ### Keywords: IO
> 
> ### ** Examples
> 
> 
> gds <- getGEO('GDS10')
HTTP 403 Forbidden.File stored at:
/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDk0btO/GDS10.soft.gz
Error in downloadFile(myurl, destfile, mode) : 
  Failed to download /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDk0btO/GDS10.soft.gz!
Calls: getGEO -> getGEOfile -> downloadFile
Execution halted
* 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:
  nrow(res) not equivalent to 12.
  target is NULL, current is numeric
  ── Failure ('test_supp_files.R:22:5'): GSE supplemental file no-download works ──
  ncol(res) not equivalent to 2.
  target is NULL, current is numeric
  ── Failure ('test_supp_files.R:27:5'): GSE Supplemental file filtering works ───
  ncol(res) not equivalent to 2.
  target is NULL, current is numeric
  ── Failure ('test_supp_files.R:28:5'): GSE Supplemental file filtering works ───
  nrow(res) not equivalent to 4.
  target is NULL, current is numeric
  
  [ FAIL 12 | WARN 0 | SKIP 0 | PASS 208 ]
  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.Rmd’ using rmarkdown

Quitting from GEOquery.Rmd:134-139 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GEOquery.Rmd' failed with diagnostics:
HTTP 404 Not Found.
--- failed re-building ‘GEOquery.Rmd’

SUMMARY: processing the following file failed:
  ‘GEOquery.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/GEOquery.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GEOquery
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘GEOquery’ ...
** 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 4.4.3 (2025-02-28) -- "Trophy Case"
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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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/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 12 | WARN 0 | SKIP 0 | PASS 208 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_GSE.R:21:5'): single-sample GSE handled correctly ──────────────
<httr2_http_404/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 404 Not Found.
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_404/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 404 Not Found.
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:69:3'): GSE populates experimentData as much as possible ──
Error in `open.connection(x, "rb")`: cannot open the connection
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE99709") at test_GSE.R:69:3
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO))
  4.       ├─xml2::read_html(url)
  5.       └─xml2:::read_html.default(url)
  6.         ├─base::suppressWarnings(...)
  7.         │ └─base::withCallingHandlers(...)
  8.         ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
  9.         └─xml2:::read_xml.character(...)
 10.           └─xml2:::read_xml.connection(...)
 11.             ├─base::open(x, "rb")
 12.             └─base::open.connection(x, "rb")
── Error ('test_GSE.R:102:3'): GSE/GPL with integer64 columns handled correctly ──
<httr2_http_404/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 404 Not Found.
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_fetch_GPL_false.R:5:5'): GSE without GPL works ─────────────────
Error in `open.connection(x, "rb")`: cannot open the connection
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE2553", getGPL = FALSE) at test_fetch_GPL_false.R:5:5
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO))
  4.       ├─xml2::read_html(url)
  5.       └─xml2:::read_html.default(url)
  6.         ├─base::suppressWarnings(...)
  7.         │ └─base::withCallingHandlers(...)
  8.         ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
  9.         └─xml2:::read_xml.character(...)
 10.           └─xml2:::read_xml.connection(...)
 11.             ├─base::open(x, "rb")
 12.             └─base::open.connection(x, "rb")
── Error ('test_geo_rnaseq.R:62:3'): getRNASeqData returns SummarizedExperiment ──
<httr2_http_404/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 404 Not Found.
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(...)
── Failure ('test_supp_files.R:6:5'): GSE Supplemental files downloading works ──
nrow(res) not equivalent to 1.
target is NULL, current is numeric
── Failure ('test_supp_files.R:16:5'): GSM Supplemental files downloading to baseDir works ──
nrow(res) not equivalent to 1.
target is NULL, current is numeric
── Failure ('test_supp_files.R:21:5'): GSE supplemental file no-download works ──
nrow(res) not equivalent to 12.
target is NULL, current is numeric
── Failure ('test_supp_files.R:22:5'): GSE supplemental file no-download works ──
ncol(res) not equivalent to 2.
target is NULL, current is numeric
── Failure ('test_supp_files.R:27:5'): GSE Supplemental file filtering works ───
ncol(res) not equivalent to 2.
target is NULL, current is numeric
── Failure ('test_supp_files.R:28:5'): GSE Supplemental file filtering works ───
nrow(res) not equivalent to 4.
target is NULL, current is numeric

[ FAIL 12 | WARN 0 | SKIP 0 | PASS 208 ]
Error: Test failures
Execution halted