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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GEOexplorer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GEOexplorer_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GEOexplorer.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GEOexplorer/DESCRIPTION’ ... OK
* this is package ‘GEOexplorer’ version ‘1.5.0’
* 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 ... OK
* 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 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 ... OK
* 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
* 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:
    2.   └─base::tryCatch(...)
    3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    5.         └─value[[3L]](cond)
    6.           └─GEOquery::getGEO(geoAccessionCode, GSEMatrix = GSEMatrix, getGPL = FALSE)
    7.             └─GEOquery:::getAndParseGSEMatrices(...)
    8.               └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
    9.                 └─base::tryCatch(...)
   10.                   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   11.                     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   12.                       └─value[[3L]](cond)
  
  [ FAIL 4 | WARN 28 | SKIP 0 | PASS 1282 ]
  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 ...
  ‘GEOexplorer.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GEOexplorer.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GEOexplorer
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘GEOexplorer’ ...
** 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 (GEOexplorer)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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(GEOexplorer)
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, 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")'.

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: shinyBS
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("GEOexplorer")
Found 1 file(s)
GSE178351_series_matrix.txt.gz
Annotation GPL not available, so will use submitter GPL instead
Found 1 file(s)
GSE178351_series_matrix.txt.gz
Using locally cached version: /tmp/Rtmp6dum3O/GSE178351_series_matrix.txt.gz
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 
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 
Found 1 file(s)
GSE2_series_matrix.txt.gz
Annotation GPL not available, so will use submitter GPL instead
Found 1 file(s)
GSE25758_series_matrix.txt.gz
Annotation GPL not available, so will use submitter GPL instead
Found 1 file(s)
GSE25758_series_matrix.txt.gz
Using locally cached version: /tmp/Rtmp6dum3O/GSE25758_series_matrix.txt.gz
Found 1 file(s)
GSE25743_series_matrix.txt.gz
Found 1 file(s)
GSE25743_series_matrix.txt.gz
Coefficients not estimable: Group2 
Found 1 file(s)
GSE18388_series_matrix.txt.gz
Found 1 file(s)
GSE18388_series_matrix.txt.gz
[ FAIL 4 | WARN 28 | SKIP 0 | PASS 1282 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_microarrayGseWithNonLogValues.R:503'): Microarray GSE with non-log values is handled correctly
          by all functions ──
tT$Gene.symbol has type 'NULL', not 'character'.
── Failure ('test_microarrayGseWithNonLogValues.R:506'): Microarray GSE with non-log values is handled correctly
          by all functions ──
tT$Gene.title has type 'NULL', not 'character'.
── Failure ('test_microarrayGseWithNonLogValues.R:509'): Microarray GSE with non-log values is handled correctly
          by all functions ──
tT$Gene.ID has type 'NULL', not 'character'.
── Error ('test_microarrayGseWithoutMissingValues.R:19'): Microarray GSE without missing values is handled correctly by all
          functions ──
Error in `curl::curl_download(url, destfile, mode = mode, quiet = quiet, 
    handle = h)`: Timeout was reached: [] Operation timed out after 120000 milliseconds with 606208 out of 1677010 bytes received
Backtrace:
     ▆
  1. └─GEOexplorer:::getGeoObject(geoAccessionCode) at test_microarrayGseWithoutMissingValues.R:19:12
  2.   └─base::tryCatch(...)
  3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5.         └─value[[3L]](cond)
  6.           └─GEOquery::getGEO(geoAccessionCode, GSEMatrix = GSEMatrix, getGPL = FALSE)
  7.             └─GEOquery:::getAndParseGSEMatrices(...)
  8.               └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb")
  9.                 └─base::tryCatch(...)
 10.                   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.                     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                       └─value[[3L]](cond)

[ FAIL 4 | WARN 28 | SKIP 0 | PASS 1282 ]
Error: Test failures
Execution halted