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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GEOquery_2.78.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GEOquery.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GEOquery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEOquery’ version ‘2.78.0’
* 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 ... 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')
Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Failure when receiving data from the peer [ftp.ncbi.nlm.nih.gov]:
OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 0File stored at:
/home/biocbuild/tmp/RtmpPPC6UP/GDS10.soft.gz
Error in downloadFile(myurl, destfile, mode) : 
  Failed to download /home/biocbuild/tmp/RtmpPPC6UP/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:
    3.     └─GEOquery:::parseGSEMatrix(...)
    4.       └─GEOquery::getGEO(GPL, AnnotGPL = AnnotGPL, destdir = destdir)
    5.         └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
    6.           └─GEOquery:::downloadFile(myurl, destfile, mode = mode, quiet = TRUE)
    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.                 └─rlang::cnd_signal(resp)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 237 ]
  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: 2 ERRORs, 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/R/R/bin/R CMD INSTALL GEOquery
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 1 | WARN 0 | SKIP 0 | PASS 237 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_GSE.R:15:5'): case-mismatched IDs in GSEs handled correctly ────
<httr2_failure/httr2_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Failure when receiving data from the peer [www.ncbi.nlm.nih.gov]:
Recv failure: Connection reset by peer
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE35683") at test_GSE.R:15:5
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::parseGSEMatrix(...)
  4.       └─GEOquery::getGEO(GPL, AnnotGPL = AnnotGPL, destdir = destdir)
  5.         └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
  6.           └─GEOquery:::downloadFile(myurl, destfile, mode = mode, quiet = TRUE)
  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.                 └─rlang::cnd_signal(resp)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 237 ]
Error: Test failures
Execution halted