##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GEOexplorer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GEOexplorer_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GEOexplorer.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘1.11.0’
* 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-3.20-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 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 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:
    7.             └─GEOquery:::getAndParseGSEMatrices(...)
    8.               └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO))
    9.                 ├─xml2::read_html(url)
   10.                 └─xml2:::read_html.default(url)
   11.                   ├─base::suppressWarnings(...)
   12.                   │ └─base::withCallingHandlers(...)
   13.                   ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
   14.                   └─xml2:::read_xml.character(...)
   15.                     └─xml2:::read_xml.connection(...)
   16.                       ├─base::open(x, "rb")
   17.                       └─base::open.connection(x, "rb")
  
  [ FAIL 1 | WARN 37 | SKIP 1 | PASS 1597 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/GEOexplorer.Rcheck/00check.log’
for details.