##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings GEOquery_2.69.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GEOquery.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘GEOquery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEOquery’ version ‘2.69.0’
* 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 ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘GEOquery’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘R.utils’
  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’
fastTabRead: no visible global function definition for ‘read.table’
fastTabRead: no visible global function definition for ‘read.delim’
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 characteristics k kvpair new read.delim read.table
  v
Consider adding
  importFrom("methods", "as", "new")
  importFrom("utils", "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 3.21  1.622   15.04
* 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:
  Error in `curl::curl_download(url, destfile, mode = mode, quiet = quiet, 
      handle = h)`: Timeout was reached: [] Operation timed out after 120000 milliseconds with 6373376 out of 8480960 bytes received
  Backtrace:
      ▆
   1. └─GEOquery::getGEO("GSE2553", getGPL = FALSE) at test_fetch_GPL_false.R:5:4
   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.             └─value[[3L]](cond)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 189 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GEOquery.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GEOquery.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL GEOquery
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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, setdiff, sort, 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/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 5 | WARN 0 | SKIP 0 | PASS 189 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_GSE.R:15:5'): case-mismatched IDs in GSEs handled correctly ────
Error in `curl::curl_download(url, destfile, mode = mode, quiet = quiet, 
    handle = h)`: Timeout was reached: [] Operation timed out after 120000 milliseconds with 7990671 bytes received
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE35683") at test_GSE.R:15:4
  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.                   └─value[[3L]](cond)
── Error ('test_GSE.R:47:3'): GSE with more than one value per characteristic handled ──
Error in `curl::curl_download(url, destfile, mode = mode, quiet = quiet, 
    handle = h)`: Timeout was reached: [] Operation timed out after 120000 milliseconds with 9350616 bytes received
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE71989") at test_GSE.R:47:2
  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.                   └─value[[3L]](cond)
── Error ('test_GSE.R:55:3'): GSE has populated experimentData ─────────────────
Error in `curl::curl_download(url, destfile, mode = mode, quiet = quiet, 
    handle = h)`: Timeout was reached: [] Operation timed out after 120000 milliseconds with 884736 out of 2848655 bytes received
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE53986") at test_GSE.R:55:2
 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.             └─value[[3L]](cond)
── Error ('test_GSE.R:81:3'): GSE populates experimentData as much as possible ──
Error in `curl::curl_download(url, destfile, mode = mode, quiet = quiet, 
    handle = h)`: Timeout was reached: [] Operation timed out after 120000 milliseconds with 2883584 out of 3312639 bytes received
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE27712") at test_GSE.R:81:2
 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.             └─value[[3L]](cond)
── Error ('test_fetch_GPL_false.R:5:5'): GSE without GPL works ─────────────────
Error in `curl::curl_download(url, destfile, mode = mode, quiet = quiet, 
    handle = h)`: Timeout was reached: [] Operation timed out after 120000 milliseconds with 6373376 out of 8480960 bytes received
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE2553", getGPL = FALSE) at test_fetch_GPL_false.R:5:4
 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.             └─value[[3L]](cond)

[ FAIL 5 | WARN 0 | SKIP 0 | PASS 189 ]
Error: Test failures
Execution halted