##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GEOexplorer.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GEOexplorer_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GEOexplorer.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
* using option ‘--no-vignettes’
* checking for file ‘GEOexplorer/DESCRIPTION’ ... OK
* this is package ‘GEOexplorer’ version ‘1.8.0’
* 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 ‘GEOexplorer’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘GEOexplorer’
  Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘GEOexplorer’
See ‘/home/biocbuild/bbs-3.18-bioc/meat/GEOexplorer.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
combineExpressionData: no visible binding for global variable ‘rowname’
removeLowlyExpressedGenes: no visible binding for global variable
  ‘rnaExpressionData’
removeLowlyExpressedGenes: no visible binding for global variable
  ‘group’
Undefined global functions or variables:
  group rnaExpressionData rowname
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testGeoSearch.R:9:13'): GEO search works ────────────────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [eutils.ncbi.nlm.nih.gov] Failed to connect to eutils.ncbi.nlm.nih.gov port 443 after 5561 ms: Connection timed out
  Backtrace:
      ▆
   1. └─GEOexplorer:::searchGeo(searchTerm, firstResultNumber, lastResultNumber) at testGeoSearch.R:9:12
   2.   └─httr::GET(eSearchUrl)
   3.     └─httr:::request_perform(req, hu$handle$handle)
   4.       ├─httr:::request_fetch(req$output, req$url, handle)
   5.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   6.         └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 50 | SKIP 0 | PASS 2001 ]
  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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GEOexplorer.Rcheck/00check.log’
for details.