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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GEOexplorer.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GEOexplorer_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GEOexplorer.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘1.10.0’
* 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-3.19-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 ... WARNING
Loading required package: shiny
Loading required package: limma
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object is masked from ‘package:limma’:

    plotMA

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, 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")'.

Loading required package: plotly
Loading required package: ggplot2

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

Loading required package: enrichR
Welcome to enrichR
Checking connection ... 
Error: package or namespace load failed for ‘enrichR’:
 .onAttach failed in attachNamespace() for 'enrichR', details:
  call: curl::curl_fetch_memory(url, handle = handle)
  error: Timeout was reached: [maayanlab.cloud] Connection timeout after 10000 ms
Error: package ‘enrichR’ could not be loaded
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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:
      fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
      multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
      flush = flush, encoding = encoding, skipNul = skipNul)`: line 9 did not have 2 elements
  Backtrace:
      ▆
   1. └─GEOexplorer:::enrichGenes(downregulatedGenesGeneSymbols, "GO_Biological_Process_2015") at test_microarrayGseWithBlankColumn.R:738:13
   2.   └─enrichR::enrichr(geneSymbols, databaseNames)
   3.     └─base::lapply(...)
   4.       └─enrichR (local) FUN(X[[i]], ...)
   5.         └─utils::read.table(...)
   6.           └─base::scan(...)
  
  [ FAIL 1 | WARN 45 | SKIP 1 | PASS 1949 ]
  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, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/GEOexplorer.Rcheck/00check.log’
for details.