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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ENCODExplorer.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ENCODExplorer_2.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ENCODExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ENCODExplorer’ version ‘2.20.0’
* 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 ‘ENCODExplorer’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'ENCODExplorer' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.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 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
createDesign: no visible binding for global variable ‘file_format’
createDesign: no visible binding for global variable ‘status’
createDesign: no visible binding for global variable ‘accession’
createDesign: no visible binding for global variable ‘controls’
createDesign : get_ctrl_design: no visible binding for global variable
  ‘accession’
createDesign : get_ctrl_design: no visible binding for global variable
  ‘href’
createDesign: no visible global function definition for ‘.’
createDesign: no visible binding for global variable ‘href’
createDesign: no visible binding for global variable ‘Experiment’
createDesign: no visible binding for global variable ‘Value’
downloadEncode: no visible binding for global variable ‘file_accession’
downloadEncode: no visible binding for global variable ‘file_format’
downloadEncode: no visible binding for global variable ‘accession’
shinyEncode: no visible binding for global variable ‘ui’
shinyEncode: no visible binding for global variable ‘server’
Undefined global functions or variables:
  . Experiment Value accession controls file_accession file_format href
  server status ui
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
get_encode_df_full            44.628  2.100  47.516
ENCODEBindingConsensus-class  29.671  1.489  43.338
buildExpressionSummary         4.998  0.358  49.632
queryTranscriptExpression      4.766  0.315  37.603
ENCODEExpressionSummary-class  3.794  0.685  27.343
buildConsensusPeaks            2.275  0.122  18.855
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  ENCODExplorer RUnit Tests - 28 test functions, 0 errors, 1 failure
  FAILURE in test.ret_content: Error in checkTrue(expr = !is.null(res$accession), msg = "res should be get an accession entry") : 
    Test not TRUE
  res should be get an accession entry
  
  Test files with failing tests
  
     test_search.R 
       test.ret_content 
  
  
  Error in BiocGenerics:::testPackage("ENCODExplorer") : 
    unit tests failed for package ENCODExplorer
  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-3.14-bioc/meat/ENCODExplorer.Rcheck/00check.log’
for details.