##############################################################################
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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_2.77.6.tar.gz
###
##############################################################################
##############################################################################


* 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 ‘2.77.6’
* 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')
> gds
An object of class "GDS"
channel_count 
[1] "1"
dataset_id 
 [1] "GDS10" "GDS10" "GDS10" "GDS10" "GDS10" "GDS10" "GDS10" "GDS10" "GDS10"
[10] "GDS10" "GDS10" "GDS10"
description 
 [1] "Examination of spleen and thymus of type 1 diabetes nonobese diabetic (NOD) mouse, four NOD-derived diabetes-resistant congenic strains and two nondiabetic control strains."
 [2] "spleen"                                                                                                                                                                      
 [3] "thymus"                                                                                                                                                                      
 [4] "NOD"                                                                                                                                                                         
 [5] "Idd3"                                                                                                                                                                        
 [6] "Idd5"                                                                                                                                                                        
 [7] "Idd3+Idd5"                                                                                                                                                                   
 [8] "Idd9"                                                                                                                                                                        
 [9] "B10.H2g7"                                                                                                                                                                    
[10] "B10.H2g7 Idd3"                                                                                                                                                               
[11] "diabetic"                                                                                                                                                                    
[12] "diabetic-resistant"                                                                                                                                                          
[13] "nondiabetic"                                                                                                                                                                 
email 
[1] "geo@ncbi.nlm.nih.gov"
feature_count 
[1] "39114"
institute 
[1] "NCBI NLM NIH"
name 
[1] "Gene Expression Omnibus (GEO)"
order 
[1] "none"
platform 
[1] "GPL24"
platform_organism 
[1] "Mus musculus"
platform_technology_type 
[1] "in situ oligonucleotide"
pubmed_id 
[1] "11827943"
ref 
[1] "Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D562-6"
reference_series 
[1] "GSE11"
sample_count 
[1] "28"
sample_id 
 [1] "GSM582,GSM583,GSM584,GSM585,GSM586,GSM587,GSM588,GSM589,GSM590,GSM591,GSM592,GSM593,GSM594,GSM595"              
 [2] "GSM596,GSM597,GSM598,GSM599,GSM600,GSM601,GSM602,GSM603,GSM604,GSM605,GSM606,GSM607,GSM608,GSM609"              
 [3] "GSM582,GSM589,GSM596,GSM603"                                                                                    
 [4] "GSM583,GSM590,GSM597,GSM604"                                                                                    
 [5] "GSM584,GSM591,GSM598,GSM605"                                                                                    
 [6] "GSM585,GSM592,GSM599,GSM606"                                                                                    
 [7] "GSM586,GSM593,GSM600,GSM607"                                                                                    
 [8] "GSM587,GSM594,GSM601,GSM608"                                                                                    
 [9] "GSM588,GSM595,GSM602,GSM609"                                                                                    
[10] "GSM582,GSM589,GSM596,GSM603"                                                                                    
[11] "GSM583,GSM590,GSM597,GSM604,GSM584,GSM591,GSM598,GSM605,GSM585,GSM592,GSM599,GSM606,GSM586,GSM593,GSM600,GSM607"
[12] "GSM587,GSM594,GSM601,GSM608,GSM588,GSM595,GSM602,GSM609"                                                        
sample_organism 
[1] "Mus musculus"
sample_type 
[1] "RNA"
title 
[1] "Type 1 diabetes gene expression profiling"
type 
 [1] "Expression profiling by array" "tissue"                       
 [3] "tissue"                        "strain"                       
 [5] "strain"                        "strain"                       
 [7] "strain"                        "strain"                       
 [9] "strain"                        "strain"                       
[11] "disease state"                 "disease state"                
[13] "disease state"                
update_date 
[1] "Jul 15 2003"
value_type 
[1] "count"
web_link 
[1] "http://www.ncbi.nlm.nih.gov/geo"
An object of class "GEODataTable"
****** Column Descriptions ******
   sample tissue        strain      disease.state
1  GSM582 spleen           NOD           diabetic
2  GSM589 spleen           NOD           diabetic
3  GSM583 spleen          Idd3 diabetic-resistant
4  GSM590 spleen          Idd3 diabetic-resistant
5  GSM584 spleen          Idd5 diabetic-resistant
6  GSM591 spleen          Idd5 diabetic-resistant
7  GSM585 spleen     Idd3+Idd5 diabetic-resistant
8  GSM592 spleen     Idd3+Idd5 diabetic-resistant
9  GSM586 spleen          Idd9 diabetic-resistant
10 GSM593 spleen          Idd9 diabetic-resistant
11 GSM587 spleen      B10.H2g7        nondiabetic
12 GSM594 spleen      B10.H2g7        nondiabetic
13 GSM588 spleen B10.H2g7 Idd3        nondiabetic
14 GSM595 spleen B10.H2g7 Idd3        nondiabetic
15 GSM596 thymus           NOD           diabetic
16 GSM603 thymus           NOD           diabetic
17 GSM597 thymus          Idd3 diabetic-resistant
18 GSM604 thymus          Idd3 diabetic-resistant
19 GSM598 thymus          Idd5 diabetic-resistant
20 GSM605 thymus          Idd5 diabetic-resistant
21 GSM599 thymus     Idd3+Idd5 diabetic-resistant
22 GSM606 thymus     Idd3+Idd5 diabetic-resistant
23 GSM600 thymus          Idd9 diabetic-resistant
24 GSM607 thymus          Idd9 diabetic-resistant
25 GSM601 thymus      B10.H2g7        nondiabetic
26 GSM608 thymus      B10.H2g7        nondiabetic
27 GSM602 thymus B10.H2g7 Idd3        nondiabetic
28 GSM609 thymus B10.H2g7 Idd3        nondiabetic
                                       description
1            Value for GSM582: NOD_S1; src: Spleen
2            Value for GSM589: NOD_S2; src: Spleen
3           Value for GSM583: Idd3_S1; src: Spleen
4           Value for GSM590: Idd3_S2; src: Spleen
5           Value for GSM584: Idd5_S1; src: Spleen
6           Value for GSM591: Idd5_S2; src: Spleen
7         Value for GSM585: Idd3+5_S1; src: Spleen
8         Value for GSM592: Idd3+5_S2; src: Spleen
9           Value for GSM586: Idd9_S1; src: Spleen
10          Value for GSM593: Idd9_S2; src: Spleen
11      Value for GSM587: B10.H2g7_S1; src: Spleen
12      Value for GSM594: B10.H2g7_S2; src: Spleen
13 Value for GSM588: B10.H2g7 Idd3_S1; src: Spleen
14 Value for GSM595: B10.H2g7 Idd3_S2; src: Spleen
15           Value for GSM596: NOD_T1; src: Thymus
16           Value for GSM603: NOD_T2; src: Thymus
17          Value for GSM597: Idd3_T1; src: Thymus
18          Value for GSM604: Idd3_T2; src: Thymus
19          Value for GSM598: Idd5_T1; src: Thymus
20          Value for GSM605: Idd5_T2; src: Thymus
21        Value for GSM599: Idd3+5_T1; src: Thymus
22        Value for GSM606: Idd3+5_T2; src: Thymus
23          Value for GSM600: Idd9_T1; src: Thymus
24          Value for GSM607: Idd9_T2; src: Thymus
25      Value for GSM601: B10.H2g7_T1; src: Thymus
26      Value for GSM608: B10.H2g7_T2; src: Thymus
27 Value for GSM602: B10.H2g7 Idd3_T1; src: Thymus
28 Value for GSM609: B10.H2g7 Idd3_T2; src: Thymus
****** Data Table ******
> 
> gse <- getGEO('GSE10')
Found 1 file(s)
GSE10_series_matrix.txt.gz
Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ncbi.nlm.nih.gov]:
Failed to connect to www.ncbi.nlm.nih.gov port 443 after 134163 ms: Could not connect to serverFile stored at:
/home/biocbuild/tmp/RtmpBhpZVo/GPL4.soft.gz
Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE) : 
  Failed to download /home/biocbuild/tmp/RtmpBhpZVo/GPL4.soft.gz!
Calls: getGEO ... parseGSEMatrix -> 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:
       ▆
    1. └─GEOquery::getGEO("GPL96") at test_GPL.R:5:5
    2.   └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
    3.     └─GEOquery:::downloadFile(myurl, destfile, mode = mode, quiet = TRUE)
    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.           └─rlang::cnd_signal(resp)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 231 ]
  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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GEOquery
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘GEOquery’ ...
** this is package ‘GEOquery’ version ‘2.77.6’
** 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 231 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_GPL.R:5:5'): generic GPL parsing works as expected ─────────────
<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("GPL96") at test_GPL.R:5:5
  2.   └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
  3.     └─GEOquery:::downloadFile(myurl, destfile, mode = mode, quiet = TRUE)
  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.           └─rlang::cnd_signal(resp)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 231 ]
Error: Test failures
Execution halted