##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GEOexplorer.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GEOexplorer_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GEOexplorer.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GEOexplorer/DESCRIPTION’ ... OK
* this is package ‘GEOexplorer’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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-3.21-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:
            by all functions ──
  `fig` has type 'object', not 'list'.
  ── Failure ('test_microarrayGseWithSingleColumn.R:302:13'): Microarray GSE with a single column is handled correctly by all
            functions ──
  `fig` has type 'object', not 'list'.
  ── Failure ('test_microarrayGseWithTwoColumns.R:354:13'): Microarray GSE with two columns is handled correctly by
            all functions ──
  `fig` has type 'object', not 'list'.
  ── Failure ('test_microarrayGseWithoutMissingValues.R:352:13'): Microarray GSE without missing values is handled correctly by all
            functions ──
  `fig` has type 'object', not 'list'.
  
  [ FAIL 6 | WARN 71 | SKIP 1 | PASS 1995 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/GEOexplorer.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GEOexplorer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘GEOexplorer’ ...
** this is package ‘GEOexplorer’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘GEOexplorer’
Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘GEOexplorer’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘GEOexplorer’
Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘GEOexplorer’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘GEOexplorer’
Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘GEOexplorer’
** testing if installed package keeps a record of temporary installation path
* DONE (GEOexplorer)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(GEOexplorer)
Loading required package: shiny
Loading required package: limma
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 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, 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")'.

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 connections ... 
Enrichr ... Connection is Live!
FlyEnrichr ... Connection is Live!
WormEnrichr ... Connection is Live!
YeastEnrichr ... Connection is Live!
FishEnrichr ... Connection is Live!
OxEnrichr ... Connection is Live!
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Warning messages:
1: replacing previous import 'shiny::dataTableOutput' by 'DT::dataTableOutput' when loading 'GEOexplorer' 
2: replacing previous import 'shiny::renderDataTable' by 'DT::renderDataTable' when loading 'GEOexplorer' 
> 
> test_check("GEOexplorer")
Found 1 file(s)
GSE178351_series_matrix.txt.gz
Annotation GPL not available, so will use submitter GPL instead
Cluster size 24351 broken into 8281 16070 
Cluster size 8281 broken into 6052 2229 
Cluster size 6052 broken into 3427 2625 
Cluster size 3427 broken into 1621 1806 
Cluster size 1621 broken into 830 791 
Done cluster 830 
Done cluster 791 
Done cluster 1621 
Cluster size 1806 broken into 850 956 
Done cluster 850 
Done cluster 956 
Done cluster 1806 
Done cluster 3427 
Cluster size 2625 broken into 1160 1465 
Done cluster 1160 
Done cluster 1465 
Done cluster 2625 
Done cluster 6052 
Cluster size 2229 broken into 749 1480 
Done cluster 749 
Done cluster 1480 
Done cluster 2229 
Done cluster 8281 
Cluster size 16070 broken into 7624 8446 
Cluster size 7624 broken into 3559 4065 
Cluster size 3559 broken into 1881 1678 
Cluster size 1881 broken into 908 973 
Done cluster 908 
Done cluster 973 
Done cluster 1881 
Cluster size 1678 broken into 789 889 
Done cluster 789 
Done cluster 889 
Done cluster 1678 
Done cluster 3559 
Cluster size 4065 broken into 1962 2103 
Cluster size 1962 broken into 1058 904 
Done cluster 1058 
Done cluster 904 
Done cluster 1962 
Cluster size 2103 broken into 972 1131 
Done cluster 972 
Done cluster 1131 
Done cluster 2103 
Done cluster 4065 
Done cluster 7624 
Cluster size 8446 broken into 4144 4302 
Cluster size 4144 broken into 2283 1861 
Cluster size 2283 broken into 1197 1086 
Done cluster 1197 
Done cluster 1086 
Done cluster 2283 
Cluster size 1861 broken into 1234 627 
Done cluster 1234 
Done cluster 627 
Done cluster 1861 
Done cluster 4144 
Cluster size 4302 broken into 2165 2137 
Cluster size 2165 broken into 1098 1067 
Done cluster 1098 
Done cluster 1067 
Done cluster 2165 
Cluster size 2137 broken into 990 1147 
Done cluster 990 
Done cluster 1147 
Done cluster 2137 
Done cluster 4302 
Done cluster 8446 
Done cluster 16070 
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Found 2 file(s)
GSE18380-GPL4694_series_matrix.txt.gz
Annotation GPL not available, so will use submitter GPL instead
GSE18380-GPL9270_series_matrix.txt.gz
Annotation GPL not available, so will use submitter GPL instead
Cluster size 3877 broken into 207 3670 
Done cluster 207 
Cluster size 3670 broken into 2511 1159 
Cluster size 2511 broken into 631 1880 
Done cluster 631 
Cluster size 1880 broken into 862 1018 
Done cluster 862 
Done cluster 1018 
Done cluster 1880 
Done cluster 2511 
Done cluster 1159 
Done cluster 3670 
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Found 1 file(s)
GSE2_series_matrix.txt.gz
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Found 1 file(s)
GSE25758_series_matrix.txt.gz
Annotation GPL not available, so will use submitter GPL instead
Found 1 file(s)
GSE25743_series_matrix.txt.gz
Coefficients not estimable: Group2 
Found 1 file(s)
GSE18388_series_matrix.txt.gz
Cluster size 35557 broken into 16183 19374 
Cluster size 16183 broken into 11259 4924 
Cluster size 11259 broken into 5209 6050 
Cluster size 5209 broken into 2416 2793 
Cluster size 2416 broken into 1584 832 
Cluster size 1584 broken into 1008 576 
Done cluster 1008 
Done cluster 576 
Done cluster 1584 
Done cluster 832 
Done cluster 2416 
Cluster size 2793 broken into 1244 1549 
Done cluster 1244 
Cluster size 1549 broken into 679 870 
Done cluster 679 
Done cluster 870 
Done cluster 1549 
Done cluster 2793 
Done cluster 5209 
Cluster size 6050 broken into 3104 2946 
Cluster size 3104 broken into 2426 678 
Cluster size 2426 broken into 1633 793 
Cluster size 1633 broken into 867 766 
Done cluster 867 
Done cluster 766 
Done cluster 1633 
Done cluster 793 
Done cluster 2426 
Done cluster 678 
Done cluster 3104 
Cluster size 2946 broken into 956 1990 
Done cluster 956 
Cluster size 1990 broken into 931 1059 
Done cluster 931 
Done cluster 1059 
Done cluster 1990 
Done cluster 2946 
Done cluster 6050 
Done cluster 11259 
Cluster size 4924 broken into 3516 1408 
Cluster size 3516 broken into 2071 1445 
Cluster size 2071 broken into 1035 1036 
Done cluster 1035 
Done cluster 1036 
Done cluster 2071 
Done cluster 1445 
Done cluster 3516 
Done cluster 1408 
Done cluster 4924 
Done cluster 16183 
Cluster size 19374 broken into 11322 8052 
Cluster size 11322 broken into 5302 6020 
Cluster size 5302 broken into 2454 2848 
Cluster size 2454 broken into 1303 1151 
Done cluster 1303 
Done cluster 1151 
Done cluster 2454 
Cluster size 2848 broken into 1028 1820 
Done cluster 1028 
Cluster size 1820 broken into 436 1384 
Done cluster 436 
Done cluster 1384 
Done cluster 1820 
Done cluster 2848 
Done cluster 5302 
Cluster size 6020 broken into 3023 2997 
Cluster size 3023 broken into 1295 1728 
Done cluster 1295 
Cluster size 1728 broken into 572 1156 
Done cluster 572 
Done cluster 1156 
Done cluster 1728 
Done cluster 3023 
Cluster size 2997 broken into 1614 1383 
Cluster size 1614 broken into 647 967 
Done cluster 647 
Done cluster 967 
Done cluster 1614 
Done cluster 1383 
Done cluster 2997 
Done cluster 6020 
Done cluster 11322 
Cluster size 8052 broken into 3117 4935 
Cluster size 3117 broken into 1804 1313 
Cluster size 1804 broken into 972 832 
Done cluster 972 
Done cluster 832 
Done cluster 1804 
Done cluster 1313 
Done cluster 3117 
Cluster size 4935 broken into 2290 2645 
Cluster size 2290 broken into 1648 642 
Cluster size 1648 broken into 912 736 
Done cluster 912 
Done cluster 736 
Done cluster 1648 
Done cluster 642 
Done cluster 2290 
Cluster size 2645 broken into 1263 1382 
Done cluster 1263 
Done cluster 1382 
Done cluster 2645 
Done cluster 4935 
Done cluster 8052 
Done cluster 19374 
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2015... Done.
Parsing results... Done.
[ FAIL 6 | WARN 71 | SKIP 1 | PASS 1995 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'testGeoSearch.R:3:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_microarrayGseWithBlankColumn.R:360:13'): Microarray GSE with a blank column is handled correctly by all
          functions ──
`fig` has type 'object', not 'list'.
── Failure ('test_microarrayGseWithMissingValues.R:362:13'): Microarray GSE with missing values is handled correctly by all
          functions ──
`fig` has type 'object', not 'list'.
── Failure ('test_microarrayGseWithNonLogValues.R:353:13'): Microarray GSE with non-log values is handled correctly
          by all functions ──
`fig` has type 'object', not 'list'.
── Failure ('test_microarrayGseWithSingleColumn.R:302:13'): Microarray GSE with a single column is handled correctly by all
          functions ──
`fig` has type 'object', not 'list'.
── Failure ('test_microarrayGseWithTwoColumns.R:354:13'): Microarray GSE with two columns is handled correctly by
          all functions ──
`fig` has type 'object', not 'list'.
── Failure ('test_microarrayGseWithoutMissingValues.R:352:13'): Microarray GSE without missing values is handled correctly by all
          functions ──
`fig` has type 'object', not 'list'.

[ FAIL 6 | WARN 71 | SKIP 1 | PASS 1995 ]
Error: Test failures
Execution halted